* Reference Sequence File: alu-2-repeats.uc * Library Sequence File: chrY.NT_087001.1.part1.fa.subset * * Output file format: * * LOCUS1 N1 N2 LOCUS2 M1 M2 F1 F2 F3 L S # * * ... aligned fragments ... * * ... statistics line from original file ... * * where N1,N2,M1,M2 - aligned fragments boundaries * F1 - (no. of Matches)/(no. of Matches + no. of Mismatches + no. of Gaps), * F2 - (Number of Gaps)/(Number of Mismatches), * which is set to 0 if (Number of Mismatches) == 0, * F3 - (Number of Mismatches)/(Number of Transitions), * which is set to 1 if (Number of Transitions) == 0 * and to 100 if both numbers == 0, * L - Length of the top sequence fragment, * S - Local Score. * * Local parameters: * Margin = 150 * Similarity threshold = 25.00 * Similarity threshold to always keep = 35.00 * Ratio threshold = 2.50 * Relative Similarity threshold = 0.23 * Gap Constant D1 = 1.0100 * Gap Constant D2 = 0.9100 * Mismatch Penalty D3 = -0.9000 * (Gap penalty = -(D1 + D2 * length)) ALUSX 21 282 NT_087001.1.PART1 7650 7918 0.81 0.25 1.90 269 160.47 # CCTGTAATCCCAGC-ACTTTGGGAGGCCGAGGCGGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGC- ******|******* ** *|*******|*****|** *|** |* ***| |*|**** | *** *| ** CCTGTAGTCCCAGCTAC-TCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAG-CTTGCA CTG-GCCAACATGGTG--A---AAC-CCCGTCTCTACTAAAAATACAAAAATTAG-CCGGGCGTGGTGGC ** ***|* ** *|* * ** ** *|** |* * *|* |*|*|* *| * *| *********** GTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGA-GCGAGACTCCGTCTCGGCGTGGTGGC GCATGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTT ********************************************************************** GCATGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTT GCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTC ************************************************************* GCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTC & Containing 218 matches, 10 gaps and 40 mismatches including 21 transitions ALUY 1 154 NT_087001.1.PART1 7496 7649 1.00 0.00 100.00 154 154.00 # GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTC ********************************************************************** GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTC AGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGG ********************************************************************** AGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGG GCGTGGTGGCGGGC ************** GCGTGGTGGCGGGC & Containing 154 matches, 0 gaps and 0 mismatches including 0 transitions ALUSX 1 282 NT_087001.1.PART1 911 1191 0.95 0.17 2.00 282 252.57 # GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACCTGAGG ********************************************************|******* **** GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCAC--GAGG TCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATAC-AAAAATTAGCC ******* ********* ******|****|**************************** *********** TCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCC GGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGG ************* ||*******|********************************* ** ********* GGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGG GAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGT ********* ************************************************************ GAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGT CTC *** CTC & Containing 268 matches, 2 gaps and 12 mismatches including 6 transitions ALUY 1 281 NT_087001.1.PART1 10439 10719 1.00 0.00 100.00 281 281.00 # GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTC ********************************************************************** GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTC AGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGG ********************************************************************** AGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGG GCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGA ********************************************************************** GCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGA GGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCT ********************************************************************** GGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCT C * C & Containing 281 matches, 0 gaps and 0 mismatches including 0 transitions ALUY 69 228 NT_087001.1.PART1 1192 1350 0.93 0.09 2.20 160 136.29 # TCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCC ******* ********* ******|****|**************************** *********** TCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATAC-AAAAATTAGCC GGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGG ************* ||*******|********************************* ** ********* GGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGG GAGGCGGAGCTTGCAGTGAG ********* ********** GAGGCGGAGGTTGCAGTGAG & Containing 148 matches, 1 gaps and 11 mismatches including 5 transitions ALUY 1 68 NT_087001.1.PART1 841 910 0.97 1.00 1.00 70 63.28 # GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCAC--GAGG ********************************************************|******* **** GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACCTGAGG & Containing 67 matches, 1 gaps and 1 mismatches including 1 transitions ALUSX 1 282 NT_087001.1.PART1 5674 5955 1.00 0.00 100.00 282 282.00 # GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACCTGAGG ********************************************************************** GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACCTGAGG TCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCG ********************************************************************** TCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCG GGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG ********************************************************************** GGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTC ********************************************************************** AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTC TC ** TC & Containing 282 matches, 0 gaps and 0 mismatches including 0 transitions ALUY 1 139 NT_087001.1.PART1 7356 7495 0.95 0.40 1.67 140 123.80 # GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCAC--GAGG ********************************************************|******* **** GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACCTGAGG TCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCC ******* ********* ******|****|**************************** *********** TCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATAC-AAAAATTAGCC G * G & Containing 133 matches, 2 gaps and 5 mismatches including 3 transitions ALUSX 230 282 NT_087001.1.PART1 1351 1403 1.00 0.00 100.00 53 53.00 # CCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTC ***************************************************** CCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTC & Containing 53 matches, 0 gaps and 0 mismatches including 0 transitions