Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 171 of 255
Found at i:56179797 original size:38 final size:38
Alignment explanation
Indices: 56179748--56179829 Score: 164
Period size: 38 Copynumber: 2.2 Consensus size: 38
56179738 AGAAACTATA
56179748 AAAGATTGATTAATCGGATGAATGATTGGTGTCTAGAT
1 AAAGATTGATTAATCGGATGAATGATTGGTGTCTAGAT
56179786 AAAGATTGATTAATCGGATGAATGATTGGTGTCTAGAT
1 AAAGATTGATTAATCGGATGAATGATTGGTGTCTAGAT
56179824 AAAGAT
1 AAAGAT
56179830 ATTACAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.33
Consensus pattern (38 bp):
AAAGATTGATTAATCGGATGAATGATTGGTGTCTAGAT
Found at i:56185861 original size:15 final size:15
Alignment explanation
Indices: 56185841--56185870 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56185831 CTATAGGTCA
*
56185841 TTTGTCATTGTGATG
1 TTTGTCATTATGATG
56185856 TTTGTCATTATGATG
1 TTTGTCATTATGATG
56185871 AATGACTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.23, T:0.53
Consensus pattern (15 bp):
TTTGTCATTATGATG
Found at i:56188641 original size:74 final size:75
Alignment explanation
Indices: 56188510--56188660 Score: 241
Period size: 74 Copynumber: 2.0 Consensus size: 75
56188500 CGAGTTCTAC
* *
56188510 AAGGTGACGATCTATAAGGAAAAGGGAACACAAACTAGGTAAGCATATAAGATGCTTAGTAAGTT
1 AAGGTGACGATCTACAAGGAAAAGGGAACAAAAACTAGGTAAGCATATAAGATGCTTAGTAAGTT
56188575 CATAGCCATT
66 CATAGCCATT
* *
56188585 AAGGTGATGATCTACAAGGAAAAGGGAA-AAAAACTAGGTAAGCGTATAAGATGCTTAGTAAGTT
1 AAGGTGACGATCTACAAGGAAAAGGGAACAAAAACTAGGTAAGCATATAAGATGCTTAGTAAGTT
* *
56188649 TATAGGCATT
66 CATAGCCATT
56188659 AA
1 AA
56188661 ACAAAACTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
74 44 0.63
75 26 0.37
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.23
Consensus pattern (75 bp):
AAGGTGACGATCTACAAGGAAAAGGGAACAAAAACTAGGTAAGCATATAAGATGCTTAGTAAGTT
CATAGCCATT
Found at i:56190048 original size:30 final size:30
Alignment explanation
Indices: 56189992--56190048 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
56189982 TTTTAGGCCC
* * **
56189992 AGGGGTAAAATGGTCATTTTGTCAAAGTCT
1 AGGGGCAAAATGATCATTTTACCAAAGTCT
56190022 AGGGGCAAAATGATCATTTTACCAAAG
1 AGGGGCAAAATGATCATTTTACCAAAG
56190049 ATATGAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (30 bp):
AGGGGCAAAATGATCATTTTACCAAAGTCT
Found at i:56193619 original size:46 final size:46
Alignment explanation
Indices: 56193552--56193727 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 46
56193542 TATTTGGGCA
56193552 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * * * * *
56193598 TCCGAACTCGTTGAGTTGAGTCGGAGTTC-GTGAAATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCGA-GCG
* * *
56193645 TCCGAACTTGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * *
56193691 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
56193728 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
45 1 0.01
46 67 0.65
47 35 0.34
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:56193707 original size:93 final size:93
Alignment explanation
Indices: 56193548--56193720 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
56193538 GGGATATTTG
* * *
56193548 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAG
*
56193613 TTGAGTCGGAGTTCGTGAAATGTAACTA
66 TTGAGTCCGAGTTCGTGAAATGTAACTA
* *
56193641 GGCATCCGAACTTGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAG
56193706 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
56193721 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAAATGTAACTA
Found at i:56196685 original size:15 final size:15
Alignment explanation
Indices: 56196646--56196725 Score: 76
Period size: 15 Copynumber: 5.4 Consensus size: 15
56196636 ACATCTTGGG
*
56196646 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
56196661 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
56196676 TTTCTTTATTCCAGG-
1 TTTCTTTATT-CTGGA
*
56196691 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
56196706 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
56196720 TTTCTT
1 TTTCTT
56196726 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
13 1 0.02
14 11 0.21
15 36 0.68
16 5 0.09
ACGTcount: A:0.11, C:0.19, G:0.12, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:56196715 original size:30 final size:31
Alignment explanation
Indices: 56196638--56196716 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 31
56196628 ATAGTATCAC
* * *
56196638 ATCTTGGGTTTCTTTA-TCCTGGATCTCTTT
1 ATCTTGGATTTCTTTATTCCAGGATCTCTCT
*
56196668 AT-TCTGGATTTCTTTATTCCAGG-TTTCTCT
1 ATCT-TGGATTTCTTTATTCCAGGATCTCTCT
56196698 ATCTTGGATTTCTTTATTC
1 ATCTTGGATTTCTTTATTC
56196717 GGTTTTCTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
29 1 0.02
30 35 0.83
31 6 0.14
ACGTcount: A:0.13, C:0.19, G:0.14, T:0.54
Consensus pattern (31 bp):
ATCTTGGATTTCTTTATTCCAGGATCTCTCT
Found at i:56202743 original size:3 final size:3
Alignment explanation
Indices: 56202711--56202775 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
56202701 AATATTCTTT
* * *
56202711 TTA TTT TTA -TA TTA TTA ATA TTA -TA CTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
56202757 TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA T-TA TTA
56202776 GTATATACTC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:56203190 original size:18 final size:19
Alignment explanation
Indices: 56203163--56203202 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
56203153 GTTATGTATG
* *
56203163 TATATGTTATGTGTATT-T
1 TATATATTATGTATATTAT
56203181 TATATATTATGTATATTAT
1 TATATATTATGTATATTAT
56203200 TAT
1 TAT
56203203 CTTTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (19 bp):
TATATATTATGTATATTAT
Found at i:56203212 original size:30 final size:29
Alignment explanation
Indices: 56203159--56203230 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
56203149 TTTTGTTATG
* * *
56203159 TATGTATATGTTATGTGTATTTTATATAT
1 TATGTATATATTATCTGTATTTTACATAT
*
56203188 TATGTATATTATTATCTTTATTTTACATAT
1 TATGTATA-TATTATCTGTATTTTACATAT
*
56203218 TACGTATATATTA
1 TATGTATATATTA
56203231 AATATCGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 13 0.35
30 24 0.65
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (29 bp):
TATGTATATATTATCTGTATTTTACATAT
Found at i:56204961 original size:24 final size:24
Alignment explanation
Indices: 56204880--56204961 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
56204870 TCTTCTTTCC
* *
56204880 TTCCTCTTTTCATTTTCTTTCTTTTT
1 TTCCTCTTTTC-TCTTCTTT-TCTTT
*
56204906 TTCCT-TTTCCTCTTCTTCGTTC-TT
1 TTCCTCTTTTCTCTTCTT--TTCTTT
*
56204930 ATCC-CTTTTCTCTTCTTTTCTTT
1 TTCCTCTTTTCTCTTCTTTTCTTT
56204953 TTCCTCTTT
1 TTCCTCTTT
56204962 GTTACCAGCT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
22 3 0.07
23 5 0.11
24 26 0.58
25 5 0.11
26 6 0.13
ACGTcount: A:0.02, C:0.29, G:0.01, T:0.67
Consensus pattern (24 bp):
TTCCTCTTTTCTCTTCTTTTCTTT
Found at i:56210543 original size:22 final size:23
Alignment explanation
Indices: 56210504--56210552 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 23
56210494 GTAATTAAAC
56210504 TTAGTTAATCATGATTAC-TTAT
1 TTAGTTAATCATGATTACATTAT
*
56210526 TTAGTTAATC-TTATTTACATTTAT
1 TTAGTTAATCATGA-TTACA-TTAT
56210550 TTA
1 TTA
56210553 ATTGTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 2 0.09
22 14 0.61
24 7 0.30
ACGTcount: A:0.31, C:0.08, G:0.06, T:0.55
Consensus pattern (23 bp):
TTAGTTAATCATGATTACATTAT
Found at i:56213292 original size:12 final size:14
Alignment explanation
Indices: 56213264--56213295 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
56213254 CACCATTATT
56213264 AATTTTACAAAATC
1 AATTTTACAAAATC
56213278 AATTTTA-AAAA-C
1 AATTTTACAAAATC
56213290 AATTTT
1 AATTTT
56213296 CTGTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 4 0.22
14 7 0.39
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTTTACAAAATC
Found at i:56213938 original size:18 final size:18
Alignment explanation
Indices: 56213915--56213949 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
56213905 TTTAATTAAT
56213915 AAATAATTATTATATTTG
1 AAATAATTATTATATTTG
*
56213933 AAATAATTATTTTATTT
1 AAATAATTATTATATTT
56213950 TATAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
AAATAATTATTATATTTG
Found at i:56214218 original size:22 final size:22
Alignment explanation
Indices: 56214192--56214237 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
56214182 TAAAATGATG
56214192 AATTA-AAATATAAAAATAAAAA
1 AATTATAAAT-TAAAAATAAAAA
*
56214214 AATTATTAATTAAAAATAAAAA
1 AATTATAAATTAAAAATAAAAA
56214236 AA
1 AA
56214238 CTTGAAACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (22 bp):
AATTATAAATTAAAAATAAAAA
Found at i:56215684 original size:27 final size:27
Alignment explanation
Indices: 56215654--56215831 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
56215644 ATATTGAGTC
* * * *
56215654 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
56215681 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
56215708 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
56215736 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
56215763 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
56215790 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
56215817 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
56215832 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:56215793 original size:82 final size:81
Alignment explanation
Indices: 56215675--56215830 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
56215665 TGCTATATAA
* *
56215675 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
56215740 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
56215757 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
56215821 CACTTAGTGC
65 CACTTAGTGC
56215831 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:56223738 original size:27 final size:27
Alignment explanation
Indices: 56223708--56223885 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
56223698 ATATTGAGTC
* * * *
56223708 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
56223735 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
56223762 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
56223790 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
56223817 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
56223844 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
56223871 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
56223886 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:56223847 original size:82 final size:81
Alignment explanation
Indices: 56223729--56223884 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
56223719 TGCTATATAA
* *
56223729 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
56223794 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
56223811 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
56223875 CACTTAGTGC
65 CACTTAGTGC
56223885 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:56227604 original size:63 final size:62
Alignment explanation
Indices: 56227505--56227680 Score: 235
Period size: 63 Copynumber: 2.8 Consensus size: 62
56227495 GCCGTGTGAT
* ** * * * * *
56227505 AGGCCGTGTAACCCGCTGTTTTGGAATTACAGTCACACGAGTTAGAGACACGGGCATGTTTCC
1 AGGCCGTGTAACTCATTGTTTTGGAATTA-AATCACACGGGCTAGAGACACGGCCATGTGTCC
* *
56227568 AGGCCGTGTAACTCATTGTTTTGGAATTAGAATCACACGGGCCAAAGACACGGCCATGTGTCC
1 AGGCCGTGTAACTCATTGTTTTGGAATTA-AATCACACGGGCTAGAGACACGGCCATGTGTCC
56227631 AGGCCGTGTAACTCATTGTTTTGGAATTAAAGTCACACGGGCTAGAGACA
1 AGGCCGTGTAACTCATTGTTTTGGAATTAAA-TCACACGGGCTAGAGACA
56227681 TGGGAGTGCG
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
62 2 0.02
63 97 0.98
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (62 bp):
AGGCCGTGTAACTCATTGTTTTGGAATTAAATCACACGGGCTAGAGACACGGCCATGTGTCC
Found at i:56234249 original size:15 final size:15
Alignment explanation
Indices: 56234229--56234277 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
56234219 TTATGTGGAG
56234229 TTTAAATTTAAATTT
1 TTTAAATTTAAATTT
56234244 TTTAAATTTAAATTAT
1 TTTAAATTTAAATT-T
* *
56234260 TATAAATCTAAATTT
1 TTTAAATTTAAATTT
56234275 TTT
1 TTT
56234278 TTAAGTACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAAATTTAAATTT
Found at i:56236780 original size:4 final size:4
Alignment explanation
Indices: 56236771--56236803 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
56236761 GGAGTCTGGT
56236771 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
56236804 AGGGGCATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:56237645 original size:6 final size:6
Alignment explanation
Indices: 56237634--56237665 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
56237624 TTAATAAATG
56237634 AAATTA AAATTA AAATTA AAATTA AAATTA AA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AA
56237666 TCATTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATTA
Found at i:56237872 original size:41 final size:41
Alignment explanation
Indices: 56237813--56237921 Score: 112
Period size: 41 Copynumber: 2.6 Consensus size: 41
56237803 TAAAAATTTC
* **
56237813 AAAACACAGAGCAATAGCGGC-ATTTTACCAAAAACGCTGCTA
1 AAAAC-CAGAGCATTAGCGGCGATTTT-CCAAAAACGCCACTA
* * ***
56237855 AAAACCAAAGCATTAGCGGCGCTTTTGGTAAAACGCCACTA
1 AAAACCAGAGCATTAGCGGCGATTTTCCAAAAACGCCACTA
*
56237896 AAAACCAGAGCATTAGCGGCGCTTTT
1 AAAACCAGAGCATTAGCGGCGATTTT
56237922 GATAAAACGT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 48 0.84
42 9 0.16
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (41 bp):
AAAACCAGAGCATTAGCGGCGATTTTCCAAAAACGCCACTA
Found at i:56237938 original size:41 final size:41
Alignment explanation
Indices: 56237843--56237939 Score: 149
Period size: 41 Copynumber: 2.4 Consensus size: 41
56237833 CATTTTACCA
*
56237843 AAAACGCTGCTAAAAACCAAAGCATTAGCGGCGCTTTTGGT
1 AAAACGCTGCTAAAAACCAAAGCATTAGCGGCGCTTTTGAT
** *
56237884 AAAACGCCACTAAAAACCAGAGCATTAGCGGCGCTTTTGAT
1 AAAACGCTGCTAAAAACCAAAGCATTAGCGGCGCTTTTGAT
*
56237925 AAAACGTTGCTAAAA
1 AAAACGCTGCTAAAA
56237940 GTCATATAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (41 bp):
AAAACGCTGCTAAAAACCAAAGCATTAGCGGCGCTTTTGAT
Found at i:56238119 original size:14 final size:14
Alignment explanation
Indices: 56238097--56238148 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
56238087 TTAATTATCA
*
56238097 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
56238111 TTATGGTTTAAGAT
1 TTATGGTTTAAGGT
*
56238125 ATATGGTTT-AGGAT
1 TTATGGTTTAAGG-T
*
56238139 TTAAGGTTTA
1 TTATGGTTTA
56238149 GGAGTTAACT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 2 0.07
14 28 0.93
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:56238215 original size:7 final size:7
Alignment explanation
Indices: 56238186--56238314 Score: 80
Period size: 7 Copynumber: 18.1 Consensus size: 7
56238176 GATGAATTAT
56238186 GGGTTTA
1 GGGTTTA
*
56238193 GGGATTA
1 GGGTTTA
* *
56238200 TGATTTA
1 GGGTTTA
56238207 GGGTTTA
1 GGGTTTA
*
56238214 GGGGTTA
1 GGGTTTA
*
56238221 GGGTTGA
1 GGGTTTA
*
56238228 -AGTTTA
1 GGGTTTA
* *
56238234 AGGTGTAA
1 GGGT-TTA
*
56238242 GGGTTTG
1 GGGTTTA
*
56238249 GGGTTAA
1 GGGTTTA
* *
56238256 AGGTTAA
1 GGGTTTA
56238263 GGGTTTA
1 GGGTTTA
56238270 GGGTTTA
1 GGGTTTA
*
56238277 GTGTTTA
1 GGGTTTA
*
56238284 TGGGATTA
1 -GGGTTTA
*
56238292 GGGTTAA
1 GGGTTTA
*
56238299 GAAGTTTA
1 G-GGTTTA
56238307 GGGTTTA
1 GGGTTTA
56238314 G
1 G
56238315 ATTAATTAGT
Statistics
Matches: 89, Mismatches: 29, Indels: 8
0.71 0.23 0.06
Matches are distributed among these distances:
6 4 0.04
7 70 0.79
8 15 0.17
ACGTcount: A:0.22, C:0.00, G:0.40, T:0.38
Consensus pattern (7 bp):
GGGTTTA
Found at i:56238314 original size:22 final size:22
Alignment explanation
Indices: 56238241--56238314 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
56238231 TTAAGGTGTA
* * *
56238241 AGGGTTTGGGGTTAA-AGGTTA
1 AGGGTTTAGGGTTAAGAAGTTT
* *
56238262 AGGGTTTAGGGTTTAG-TGTTT
1 AGGGTTTAGGGTTAAGAAGTTT
*
56238283 ATGGGATTAGGGTTAAGAAGTTT
1 A-GGGTTTAGGGTTAAGAAGTTT
56238306 AGGGTTTAG
1 AGGGTTTAG
56238315 ATTAATTAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
21 17 0.40
22 20 0.48
23 5 0.12
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.38
Consensus pattern (22 bp):
AGGGTTTAGGGTTAAGAAGTTT
Found at i:56238942 original size:3 final size:3
Alignment explanation
Indices: 56238934--56238965 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
56238924 CATTTTAGTA
56238934 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
56238966 AAGAGAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:56239315 original size:37 final size:37
Alignment explanation
Indices: 56239255--56239363 Score: 148
Period size: 37 Copynumber: 2.9 Consensus size: 37
56239245 TGATCAGAAA
*
56239255 AACCCATCTCCTCCGTCGCCTTCTCCCCGTGCATCGC
1 AACCCATCTCCTCCATCGCCTTCTCCCCGTGCATCGC
* *
56239292 AACTCAT-TCCCTCCATCGTCTTCTCCCCGTGCATCGC
1 AACCCATCT-CCTCCATCGCCTTCTCCCCGTGCATCGC
* * *
56239329 AACCCATCTCCTCTATCGCCTTCGCCCTGTGCATC
1 AACCCATCTCCTCCATCGCCTTCTCCCCGTGCATC
56239364 TGCTGCATAG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 1 0.02
37 60 0.97
38 1 0.02
ACGTcount: A:0.13, C:0.48, G:0.12, T:0.28
Consensus pattern (37 bp):
AACCCATCTCCTCCATCGCCTTCTCCCCGTGCATCGC
Found at i:56241347 original size:38 final size:38
Alignment explanation
Indices: 56241304--56241379 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
56241294 TTCATCCTTT
*
56241304 TTCATTTCTTTTGGCCGAAATTTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
56241342 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
56241380 GGAGTTCTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:56242657 original size:40 final size:40
Alignment explanation
Indices: 56242563--56242707 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
56242553 TACTCGAATG
*
56242563 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
56242604 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
56242644 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
56242684 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
56242708 CTTGTGCGAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.67
41 28 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:56255751 original size:85 final size:85
Alignment explanation
Indices: 56255608--56255786 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
56255598 GGCCGGCCAT
56255608 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
56255673 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
56255693 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
56255758 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
56255778 GGGCATGGG
1 GAGCATGGG
56255787 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:56258023 original size:47 final size:47
Alignment explanation
Indices: 56257969--56258502 Score: 726
Period size: 47 Copynumber: 11.1 Consensus size: 47
56257959 TTAGGATTTT
*
56257969 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
***
56258016 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCA
56258067 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* * *
56258114 CTGTGATGGATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
** *
56258161 ATGTGATGAATGTGAACCCGTCTATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATG-C---GTATGTGTGATAAGGCCGAATGGCCA
56258212 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*** *
56258259 ATGTGATGAATGTGAACCTGTATATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA-C-----ATGCGTATGTGTGATAAGGCCGAATGGCCA
*
56258312 ATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
*
56258359 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGGATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
* * *
56258406 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
** * * *
56258453 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
56258500 ATG
1 ATG
56258503 CGAAACGTGT
Statistics
Matches: 437, Mismatches: 36, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
47 304 0.70
48 1 0.00
49 2 0.00
50 1 0.00
51 86 0.20
52 1 0.00
53 42 0.10
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
Found at i:56258139 original size:145 final size:144
Alignment explanation
Indices: 56257969--56258502 Score: 792
Period size: 145 Copynumber: 3.7 Consensus size: 144
56257959 TTAGGATTTT
* *
56257969 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
56258034 CGTATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
66 CG-ATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
56258099 AAGGCCGAATGGCCA
130 AAGGCCGAATGGCCA
* * **
56258114 CTGTGATGGATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
*
56258179 CGTCTATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
66 CG-ATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
56258244 AAGGCCGAATGGCCA
130 AAGGCCGAATGGCCA
** *
56258259 ATGTGATGAATGTGAACCTGTATATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATG
1 ATGTGATGAATGTGAA-C-----ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATG
* *
56258324 TGAA--C-ATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGT
60 TGAACCCGATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGT
*
56258386 GTGATAAGGCCGGATGGCCA
125 GTGATAAGGCCGAATGGCCA
* * *
56258406 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
* *
56258471 TGA-ATATATGTG-G-TAAGGCCGAATGGCTAATG
66 CGATATATATGTGTGATAAGGCCGAATGGCCAATG
56258503 CGAAACGTGT
Statistics
Matches: 359, Mismatches: 21, Indels: 22
0.89 0.05 0.05
Matches are distributed among these distances:
141 59 0.16
142 1 0.00
143 7 0.02
144 1 0.00
145 156 0.43
146 2 0.01
147 89 0.25
149 1 0.00
151 43 0.12
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.27
Consensus pattern (144 bp):
ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
CGATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGATA
AGGCCGAATGGCCA
Found at i:56258216 original size:24 final size:24
Alignment explanation
Indices: 56258188--56258263 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
56258178 CCGTCTATAT
56258188 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
* * **
56258212 ATGTGATGA-ATGTG--AACAT-GCGT
1 ATGTG-TGATAAG-GCCGA-ATGGCCA
56258235 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
56258259 ATGTG
1 ATGTG
56258264 ATGAATGTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 17 0.46
25 4 0.11
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (24 bp):
ATGTGTGATAAGGCCGAATGGCCA
Found at i:56258565 original size:46 final size:46
Alignment explanation
Indices: 56258476--56258566 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
56258466 GAACATGAAT
* * * *
56258476 ATATGTGGTAAGGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
* * *
56258522 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTACGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATG
56258567 TGTATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.33, C:0.10, G:0.32, T:0.25
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
Found at i:56258821 original size:37 final size:37
Alignment explanation
Indices: 56258715--56258821 Score: 160
Period size: 37 Copynumber: 2.9 Consensus size: 37
56258705 AAATATATTT
* * *
56258715 CGGGTAAGACCCGATGACTACGTGTGGAGATTATGTC
1 CGGGTAAGACCTGATGACTACATGTGGAGATTTTGTC
*
56258752 CGGGTAAGACCTGATGAGTACATGTGGAGATTTTGTC
1 CGGGTAAGACCTGATGACTACATGTGGAGATTTTGTC
* *
56258789 CGGGTAAGACCTGATAACTTCATGTGGAGATTT
1 CGGGTAAGACCTGATGACTACATGTGGAGATTT
56258822 CGTCTGAGCT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (37 bp):
CGGGTAAGACCTGATGACTACATGTGGAGATTTTGTC
Found at i:56260518 original size:40 final size:40
Alignment explanation
Indices: 56260075--56260506 Score: 702
Period size: 40 Copynumber: 10.8 Consensus size: 40
56260065 GAGAATTGAG
* *
56260075 AGTGATATATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
*
56260115 AGTGATGTATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
56260155 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
56260195 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
*
56260235 AGTGGTATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
56260275 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
56260315 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* * *
56260355 AGTGATATATCTGGGCTAAGTCTCGAGGAGCATTCATGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* * *
56260395 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* ** *
56260435 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
* * * *
56260475 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCA
56260507 ATCATGCTGG
Statistics
Matches: 366, Mismatches: 26, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 366 1.00
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
Found at i:56260787 original size:58 final size:57
Alignment explanation
Indices: 56260718--56260826 Score: 146
Period size: 57 Copynumber: 1.9 Consensus size: 57
56260708 CGAATGATTA
* * *
56260718 GAGGCACTGTGTGCGCAAATTCTTTTAACCGAGCACTATGTGTGCGAAATCGGTAATT
1 GAGGCACTGTGTACGCAAATTC-TTCAACCAAGCACTATGTGTGCGAAATCGGTAATT
* * * *
56260776 GAGGCACTGTGTATGCGAGTTCTTCAACCAAGCACTATGTGTGCGAGATCG
1 GAGGCACTGTGTACGCAAATTCTTCAACCAAGCACTATGTGTGCGAAATCG
56260827 ATCAGTGGGC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 26 0.59
58 18 0.41
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (57 bp):
GAGGCACTGTGTACGCAAATTCTTCAACCAAGCACTATGTGTGCGAAATCGGTAATT
Found at i:56262421 original size:85 final size:85
Alignment explanation
Indices: 56262278--56262456 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
56262268 GGCCGGCCAT
56262278 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
56262343 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
56262363 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
56262428 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
56262448 GGGCATGGG
1 GAGCATGGG
56262457 CAATAAAATA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:56264757 original size:98 final size:96
Alignment explanation
Indices: 56264639--56265316 Score: 926
Period size: 98 Copynumber: 7.0 Consensus size: 96
56264629 TTAGGATTTT
56264639 ATGTGATG-ATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-C
*
56264703 CGTATATATATGTGTGATAAGGCCAAATGGCCA
65 CG-ATATATATGTGTGATAAGGCCGAATGGCCA
* * *
56264736 ATGTAATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCACTGTGATGGATGTGAA-C
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
***
56264800 -ATGCGTATGTGTGATAAGGCCGAATGGCCA
66 GATATATATGTGTGATAAGGCCGAATGGCCA
***
56264830 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
1 ATGTGATGAATGTGAA--C--ATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
***
56264895 AA-C-ATGCGTATGTGTGATAAGGCCGAATGGCCA
62 AACCGATATATATGTGTGATAAGGCCGAATGGCCA
* * *
56264928 CTGTGATGGATGTGAACATGCGTATGTGGGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-C
56264993 CGTATATATATGTGTGATAAGGCCGAATGGCCA
65 CG-ATATATATGTGTGATAAGGCCGAATGGCCA
56265026 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
*
56265091 TGTATATATATATGCGTGATAAGGCCGAATGGCCA
66 -G---ATATATATGTGTGATAAGGCCGAATGGCCA
*
56265126 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-C
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
*** *
56265190 -ATGCGTATGTGTGATAAGGCCGGATGGCCA
66 GATATATATGTGTGATAAGGCCGAATGGCCA
* * *
56265220 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAC-
* *
56265285 TGA-ATATATGTG-G-TAAGGCCGAATGGCTA
65 CGATATATATGTGTGATAAGGCCGAATGGCCA
56265314 ATG
1 ATG
56265317 CGAAACGTGT
Statistics
Matches: 526, Mismatches: 40, Indels: 33
0.88 0.07 0.06
Matches are distributed among these distances:
94 186 0.35
95 1 0.00
96 10 0.02
97 10 0.02
98 226 0.43
99 1 0.00
100 92 0.17
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (96 bp):
ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
GATATATATGTGTGATAAGGCCGAATGGCCA
Found at i:56264780 original size:47 final size:47
Alignment explanation
Indices: 56264639--56265316 Score: 917
Period size: 47 Copynumber: 14.1 Consensus size: 47
56264629 TTAGGATTTT
*
56264639 ATGTGATG-ATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
** *
56264685 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCAAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCATATGTGTGATAAGGCCGAATGGCCA
* *
56264736 ATGTAATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* * *
56264783 CTGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
**
56264830 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCATATGTGTGATAAGGCCGAATGGCCA
*
56264881 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* * * *
56264928 CTGTGATGGATGTGAACATGCGTATGTGGGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
**
56264975 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCATATGTGTGATAAGGCCGAATGGCCA
*
56265026 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
** *
56265073 ATGTGATGAATGTGAACCTGTATATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA-C-----ATGCATATGTGTGATAAGGCCGAATGGCCA
56265126 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* *
56265173 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGGATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* *
56265220 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* * * *
56265267 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
56265314 ATG
1 ATG
56265317 CGAAACGTGT
Statistics
Matches: 564, Mismatches: 49, Indels: 37
0.87 0.08 0.06
Matches are distributed among these distances:
46 8 0.01
47 380 0.67
48 1 0.00
49 6 0.01
51 126 0.22
52 1 0.00
53 42 0.07
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
Found at i:56264812 original size:145 final size:145
Alignment explanation
Indices: 56264639--56265316 Score: 1059
Period size: 145 Copynumber: 4.7 Consensus size: 145
56264629 TTAGGATTTT
56264639 ATGTGAT-GATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
* *
56264703 CGTATATATATGTGTGATAAGGCCAAATGGCCAATGTAATGAATGTGAACATGCGTATGTGTGAT
66 CGTATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
56264768 AAGGCCGAATGGCCA
131 AAGGCCGAATGGCCA
*
56264783 CTGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
56264848 CGTATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
66 CGTATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
56264913 AAGGCCGAATGGCCA
131 AAGGCCGAATGGCCA
* *
56264928 CTGTGATGGATGTGAACATGCGTATGTGGGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
1 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
56264993 CGTATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
66 CGTATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
56265058 AAGGCCGAATGGCCA
131 AAGGCCGAATGGCCA
* *** *
56265073 ATGTGATGAATGTGAACCTGTATATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATG
1 ATGTGATGGATGTGAA-C-----ATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATG
**
56265138 TGAA--C--ATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATG
60 TGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATG
*
56265199 TGTGATAAGGCCGGATGGCCA
125 TGTGATAAGGCCGAATGGCCA
* * * * *
56265220 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
* *
56265285 TG-A-ATATATGTG-G-TAAGGCCGAATGGCTAATG
66 CGTATATATATGTGTGATAAGGCCGAATGGCCAATG
56265317 CGAAACGTGT
Statistics
Matches: 501, Mismatches: 23, Indels: 23
0.92 0.04 0.04
Matches are distributed among these distances:
141 59 0.12
142 1 0.00
143 7 0.01
144 7 0.01
145 293 0.58
146 2 0.00
147 90 0.18
149 1 0.00
151 41 0.08
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.26
Consensus pattern (145 bp):
ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACC
CGTATATATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCGTATGTGTGAT
AAGGCCGAATGGCCA
Found at i:56265030 original size:24 final size:24
Alignment explanation
Indices: 56265002--56265077 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
56264992 CCGTATATAT
56265002 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
* * **
56265026 ATGTGATGA-ATGTG--AACAT-GCGT
1 ATGTG-TGATAAG-GCCGA-ATGGCCA
56265049 ATGTGTGATAAGGCCGAATGGCCA
1 ATGTGTGATAAGGCCGAATGGCCA
56265073 ATGTG
1 ATGTG
56265078 ATGAATGTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 17 0.46
25 4 0.11
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (24 bp):
ATGTGTGATAAGGCCGAATGGCCA
Found at i:56265379 original size:46 final size:46
Alignment explanation
Indices: 56265290--56265380 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
56265280 GAACATGAAT
* * * *
56265290 ATATGTGGTAAGGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
* * *
56265336 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTACGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATG
56265381 TGTATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.33, C:0.10, G:0.32, T:0.25
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
Found at i:56265672 original size:37 final size:37
Alignment explanation
Indices: 56265530--56265671 Score: 248
Period size: 37 Copynumber: 3.8 Consensus size: 37
56265520 AATATATTCT
56265530 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
56265567 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
*
56265604 GGGTAAGACCCGATGACTACGTGTGGAGATTTTGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
* * *
56265641 GGGTAAGACCCGATAACTTCATGTGGAGATT
1 GGGTAAGACCCGATGACTACGTGTGGAGATT
56265672 TCGTCTGAGC
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 101 1.00
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (37 bp):
GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
Found at i:56266620 original size:47 final size:45
Alignment explanation
Indices: 56266558--56266684 Score: 152
Period size: 47 Copynumber: 2.7 Consensus size: 45
56266548 TCTTGAGGCT
*
56266558 GATGCATGTCTCAGACATGTCTTACACTATCGCTCGTC-TCAA-T-GCC
1 GATGCATGTCCCAGACATGTCTTACACTA--GCTC-TCAT-AAGTGGCC
56266604 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATAA-GTGGCC
*
56266652 TATGCATGTCCCAGACATGTCTTACACTAGCTC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTC
56266685 ACACAAGAGA
Statistics
Matches: 73, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
45 4 0.05
46 24 0.33
47 28 0.38
48 17 0.23
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAAGTGGCC
Found at i:56290838 original size:93 final size:93
Alignment explanation
Indices: 56290730--56290899 Score: 277
Period size: 93 Copynumber: 1.8 Consensus size: 93
56290720 CCCCTAAGTA
* * * *
56290730 AACTCGGACTCAACTCAACGAGCTCGGGCGTCCGCATCCATAAGTAAACTCGAACTGAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCAGACATCCGCATCCATAAGTAAACTCGAACTCAACTCAAC
56290795 GAGTTCGGATGCCTAGTTACATTTCACG
66 GAGTTCGGATGCCTAGTTACATTTCACG
* * *
56290823 AACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTAAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCAGACATCCGCATCCATAAGTAAACTCGAACTCAACTCAAC
56290888 GAGTTCGGATGC
66 GAGTTCGGATGC
56290900 TCAACCATCA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCAGACATCCGCATCCATAAGTAAACTCGAACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATTTCACG
Found at i:56290882 original size:46 final size:44
Alignment explanation
Indices: 56290724--56290894 Score: 150
Period size: 46 Copynumber: 3.7 Consensus size: 44
56290714 AACCCGCCCC
* *
56290724 TAAGTAAACTCGGACTCAACTCAACGAGCTCGGGCGTCCGCATCCA
1 TAAGTAAACTCGGACTCAACTCAACGAGTTC--GCATCCGCATCCA
* * * * *
56290770 TAAGTAAACTCGAACTGAACTCAACGAGTTCGGATGCCTAG-TTACA
1 TAAGTAAACTCGGACTCAACTCAACGAGTTCGCAT-CC--GCATCCA
* *
56290816 T--TTCACGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA
1 TAAGT-A--AACTCGGACTCAACTCAACGAGTTC-G-CATCCGCATCCA
56290863 TAAGTAAACTCGGACTCAACTCAACGAGTTCG
1 TAAGTAAACTCGGACTCAACTCAACGAGTTCG
56290895 GATGCTCAAC
Statistics
Matches: 99, Mismatches: 15, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
44 3 0.03
45 4 0.04
46 58 0.59
47 28 0.28
48 3 0.03
49 3 0.03
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.22
Consensus pattern (44 bp):
TAAGTAAACTCGGACTCAACTCAACGAGTTCGCATCCGCATCCA
Found at i:56298353 original size:46 final size:46
Alignment explanation
Indices: 56298252--56298339 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 46
56298242 TGTAACCCGC
* * * *
56298252 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
* *
56298298 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTC
56298340 AACCATCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGCTCCCAT
Found at i:56307217 original size:30 final size:30
Alignment explanation
Indices: 56307178--56307244 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
56307168 GCGAAGACAT
*
56307178 GGGCGTGTGTCTCAGCCGTGTGTGACACAC
1 GGGCATGTGTCTCAGCCGTGTGTGACACAC
*
56307208 GGGCATGTGTCTCAGTCGTGTGTGACACAC
1 GGGCATGTGTCTCAGCCGTGTGTGACACAC
*
56307238 GGTCATG
1 GGGCATG
56307245 GTATATGGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.15, C:0.24, G:0.36, T:0.25
Consensus pattern (30 bp):
GGGCATGTGTCTCAGCCGTGTGTGACACAC
Found at i:56308244 original size:21 final size:20
Alignment explanation
Indices: 56308206--56308246 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
56308196 GGTAAAGAGT
56308206 GAAAATTAAAAATTTAAGGG
1 GAAAATTAAAAATTTAAGGG
56308226 GAAAA-TAAAAAGTTTTAAGGG
1 GAAAATTAAAAA--TTTAAGGG
56308247 TTGAGGGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 5 0.26
21 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (20 bp):
GAAAATTAAAAATTTAAGGG
Found at i:56319575 original size:29 final size:29
Alignment explanation
Indices: 56319542--56319615 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
56319532 GTTGTGAGAT
* *
56319542 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA
* *
56319571 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGACTTGAAAGTACA
56319600 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
56319616 TGGTTGATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGACTTGAAAGTACA
Found at i:56334333 original size:40 final size:40
Alignment explanation
Indices: 56334142--56334326 Score: 189
Period size: 40 Copynumber: 4.7 Consensus size: 40
56334132 TCGAATGATG
* * * * *
56334142 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCAAAGGCATTTGTGC-GAGTTACTAAA
* * * *
56334182 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCAAAGGCATTTGTGCGAGTTACTAAA
* *
56334222 TCTGGGCTAAG-CCCAAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTAAA
* *
56334261 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTA-AA
*
56334302 -CCGGGCTATGTCCCAAAGGCATTTG
1 TCCGGGCTAAGTCCCAAAGGCATTTG
56334327 AACGAGTAGC
Statistics
Matches: 120, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
39 32 0.27
40 78 0.65
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTAAA
Found at i:56334348 original size:79 final size:79
Alignment explanation
Indices: 56334195--56334359 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
56334185 GGACTAAGAT
* * **
56334195 CCGAAGGCATTTGTGCGAGATACTAATTCTGGGCTAAGCCCAAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAA
*
56334260 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
56334274 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCAAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCAAAGGCATTGGAACGAGTTA-C
* *
56334337 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
56334353 CCGAAGG
1 CCGAAGG
56334360 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:56342083 original size:39 final size:40
Alignment explanation
Indices: 56341983--56342167 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
56341973 TCGAATGATG
* * * *
56341983 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
56342023 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
56342063 TTCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
56342102 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
56342143 -CCGGGCTATGTCCCAAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
56342168 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 33 0.27
40 79 0.65
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:56342148 original size:79 final size:81
Alignment explanation
Indices: 56341984--56342165 Score: 203
Period size: 79 Copynumber: 2.3 Consensus size: 81
56341974 CGAATGATGT
* *
56341984 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
*
56342048 GTGCGAGATACTAATT
66 GTGCGAGATACTAATA
* * * * **
56342064 TCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATT
*
56342126 TGTGCGAGTTACT-ATAA
65 TGTGCGAGATACTAAT-A
* *
56342143 CCGGGCTATGTCCCAAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
56342166 TGAACGAGTA
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
78 3 0.04
79 56 0.66
80 26 0.31
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATA
Found at i:56342189 original size:79 final size:79
Alignment explanation
Indices: 56342036--56342190 Score: 181
Period size: 79 Copynumber: 2.0 Consensus size: 79
56342026 GGACTAAGAT
** * **
56342036 CCGAAGGCATTTGTGCGAGATACTAATTTCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAA
56342101 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * *
56342115 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCAAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCAAAGGCATTGGAACGAGTTA-C
*
56342178 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
56342191 ATTTCGAAGG
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
78 2 0.03
79 39 0.61
80 23 0.36
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:56344616 original size:11 final size:11
Alignment explanation
Indices: 56344586--56344617 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
56344576 TACAGAATGA
*
56344586 GGAAACAAAAG
1 GGAAACAATAG
56344597 GGAAACAATAG
1 GGAAACAATAG
56344608 GGAAACAATA
1 GGAAACAATA
56344618 CCTCACGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.59, C:0.09, G:0.25, T:0.06
Consensus pattern (11 bp):
GGAAACAATAG
Found at i:56351740 original size:46 final size:47
Alignment explanation
Indices: 56351636--56351896 Score: 227
Period size: 46 Copynumber: 5.6 Consensus size: 47
56351626 ACATTATGAG
* * *
56351636 AGCCAGTGTATGACCATGTTTAGGACATGGCTTCGGCATT-GAGACG-A
1 AGCCAGTGTAAGACCATGTCTGGGACAT-GCTTCGGC-TTCGAGACGTA
* * * * *
56351683 GTGCTAGTGTAAGA-CATGTTTGGGACATACTTTGGCTTCGAGACGTA
1 -AGCCAGTGTAAGACCATGTCTGGGACATGCTTCGGCTTCGAGACGTA
*
56351730 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATT-GAGACG--
1 AGCCAGTGTAAGACCATGTCTGGGACAT-GCTTCGGC-TTCGAGACGTA
* *
56351776 AGTACCAGTGTAAGA-CATGTCTGGGACATGCTTCGGCCTCAAGACGTA
1 AG--CCAGTGTAAGACCATGTCTGGGACATGCTTCGGCTTCGAGACGTA
* * * * *
56351824 AACCAGTGTAAGA-CATGTTTGGGACATGCATCGGCTACGAGATGT-
1 AGCCAGTGTAAGACCATGTCTGGGACATGCTTCGGCTTCGAGACGTA
* *
56351869 -GTCAGTGTAAGATCATGTCTGGGACATG
1 AGCCAGTGTAAGACCATGTCTGGGACATG
56351897 GCATCGTCAC
Statistics
Matches: 177, Mismatches: 25, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
44 10 0.06
45 17 0.10
46 74 0.42
47 41 0.23
48 33 0.19
49 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (47 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGCTTCGGCTTCGAGACGTA
Found at i:56351756 original size:94 final size:94
Alignment explanation
Indices: 56351636--56351895 Score: 332
Period size: 94 Copynumber: 2.8 Consensus size: 94
56351626 ACATTATGAG
* * * * *
56351636 AGCCAGTGTATGACCATGTTTAGGACATGGCTTCGGCATTGAGACGAGTGCTAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGACGAGTACCAGTGTAAGACATG
* * * *
56351701 TTTGGGACATACTTTGGCTTCGAGACGTA
66 TCTGGGACATACTTCGGCCTCAAGACGTA
*
56351730 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGTACCAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGACGAGTACCAGTGTAAGACATG
*
56351795 TCTGGGACATGCTTCGGCCTCAAGACGTA
66 TCTGGGACATACTTCGGCCTCAAGACGTA
* * * *
56351824 AACCAGTGTAAGA-CATGTTTGGGACAT-GCATCGGC-TACGAGATGTGT--CAGTGTAAGATCA
1 AGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCAT-TGAGACGAGTACCAGTGTAAGA-CA
56351884 TGTCTGGGACAT
64 TGTCTGGGACAT
56351896 GGCATCGTCA
Statistics
Matches: 148, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
90 10 0.07
91 15 0.10
92 15 0.10
93 13 0.09
94 95 0.64
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (94 bp):
AGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGACGAGTACCAGTGTAAGACATG
TCTGGGACATACTTCGGCCTCAAGACGTA
Found at i:56352196 original size:46 final size:46
Alignment explanation
Indices: 56352143--56352233 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
56352133 AATGGTAAAG
56352143 TTATGTTGAATATTTATTTATGTGCAACTTACTAAGCTTTATGCTA
1 TTATGTTGAATATTTATTTATGTGCAACTTACTAAGCTTTATGCTA
56352189 TTATGTTGAATATTTATTTATGTGCAACTTACTAAGCTTTATGCT
1 TTATGTTGAATATTTATTTATGTGCAACTTACTAAGCTTTATGCT
56352234 TACTCCCCTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.48
Consensus pattern (46 bp):
TTATGTTGAATATTTATTTATGTGCAACTTACTAAGCTTTATGCTA
Found at i:56356515 original size:149 final size:148
Alignment explanation
Indices: 56356275--56356572 Score: 526
Period size: 149 Copynumber: 2.0 Consensus size: 148
56356265 GTAAGGCTTG
*
56356275 TTGTAAAGGCTTTGTAAAGGTGGTGGTCCTCCCATATGATAAGGGCTCTCATGATCCATAAACTA
1 TTGTAAAGGCTTTGTAAAGGTGATGGTCCTCCCATATGATAAGGGCTCTCATGATCCATAAACTA
*
56356340 TCTACGCATAAGAAATACCGATGCATTAAGCATGATTGCTTAGTTAGTAAACAATG-AAGGTATT
66 TCTACGCATAAGAAATAACGATGCATTAAGCATGATTGCTTAGTTAGTAAACAA-GAAAGGTATT
56356404 CAACTTACCTTCTCTCATA
130 CAACTTACCTTCTCTCATA
* *
56356423 TTGTAAAGGCTTTGTTAAGGTGATGGTCCTCCCGTATGATAAAGGGCTCTCATGATCCATAAACT
1 TTGTAAAGGCTTTGTAAAGGTGATGGTCCTCCCATATGAT-AAGGGCTCTCATGATCCATAAACT
*
56356488 ATCTACGCATAAGAAATAATGATGCATTAAGCATGATTGCTTAGTTAGTAAACAAGAAAGGTATT
65 ATCTACGCATAAGAAATAACGATGCATTAAGCATGATTGCTTAGTTAGTAAACAAGAAAGGTATT
56356553 CAACTTACCTTCTCTCATA
130 CAACTTACCTTCTCTCATA
56356572 T
1 T
56356573 GAAGGGGTTA
Statistics
Matches: 143, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
148 38 0.27
149 105 0.73
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (148 bp):
TTGTAAAGGCTTTGTAAAGGTGATGGTCCTCCCATATGATAAGGGCTCTCATGATCCATAAACTA
TCTACGCATAAGAAATAACGATGCATTAAGCATGATTGCTTAGTTAGTAAACAAGAAAGGTATTC
AACTTACCTTCTCTCATA
Found at i:56359099 original size:27 final size:27
Alignment explanation
Indices: 56359055--56359128 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
56359045 TACAGAAATG
* * *
56359055 CCCTCGACTTGTAAAATTACCAAAGTA
1 CCCTCGATTTATAGAATTACCAAAGTA
* ***
56359082 CCCTCGATTTATAGAATTACTATTTTA
1 CCCTCGATTTATAGAATTACCAAAGTA
*
56359109 CCCTTGATTTATAGAATTAC
1 CCCTCGATTTATAGAATTAC
56359129 TGTTTTACCC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.36
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCAAAGTA
Found at i:56359129 original size:27 final size:27
Alignment explanation
Indices: 56359080--56359144 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
56359070 ATTACCAAAG
56359080 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTATAGAATTACTATTT
* *
56359107 TACCCTTGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTATTT
56359134 TACCCTCGATT
1 TACCCTCGATT
56359145 GTGAAATTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.45
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACTATTT
Found at i:56359187 original size:27 final size:27
Alignment explanation
Indices: 56359148--56359274 Score: 96
Period size: 27 Copynumber: 4.7 Consensus size: 27
56359138 CTCGATTGTG
* *
56359148 AAATTACTAAAATACGCCTA-TAGGGTA
1 AAATTACCAAAATACCCCTAGT-GGGTA
* **
56359175 GAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTGGGTA
* * ** *
56359202 AAATTACCAAAATACCACTGGTTTGTG
1 AAATTACCAAAATACCCCTAGTGGGTA
* * **
56359229 AAATTACTAAAATA-CCCTCAATTTGTA
1 AAATTACCAAAATACCCCT-AGTGGGTA
56359256 AAATTACCAAAATACCCCT
1 AAATTACCAAAATACCCCT
56359275 GATTTACAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
26 3 0.04
27 74 0.90
28 5 0.06
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.28
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTAGTGGGTA
Found at i:56359234 original size:54 final size:54
Alignment explanation
Indices: 56359176--56359412 Score: 208
Period size: 54 Copynumber: 4.4 Consensus size: 54
56359166 TATAGGGTAG
* ***
56359176 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGA
1 AATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCACTGGTTTACAA
* * *
56359230 AATTACTAAAATA-CCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAA
1 AATTACTAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCACTGGTTTACAA
* * * * ** *
56359284 AATTACAAAAATACCCTTGACTTTTTAAGAATTATAAAAATACCATTGGTTTACAA
1 AATTACTAAAATACCCCT-AGTTTGTAA-AATTACCAAAATACCACTGGTTTACAA
* * * * * * * **
56359340 AATTACTAAAATACCCTTGGTTTGTAGATTTACCAAAACACC-CTTGTAGTATGA
1 AATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCACTGGT-TTACAA
*
56359394 AATGACTAAAATACCCCTA
1 AATTACTAAAATACCCCTA
56359413 ATAGGTAAAA
Statistics
Matches: 145, Mismatches: 34, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
53 7 0.05
54 84 0.58
55 15 0.10
56 39 0.27
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.31
Consensus pattern (54 bp):
AATTACTAAAATACCCCTAGTTTGTAAAATTACCAAAATACCACTGGTTTACAA
Found at i:56359243 original size:81 final size:81
Alignment explanation
Indices: 56359143--56359298 Score: 210
Period size: 81 Copynumber: 1.9 Consensus size: 81
56359133 TTACCCTCGA
* **
56359143 TTGTGAAATTACTAAAATACGCCT--ATAGGGTAGAATTACCAAAATACCCCT-AGTTTGTAAAA
1 TTGTGAAATTACTAAAATAC-CCTCAAT-GGGTAAAATTACCAAAATACCCCTGA-TTTACAAAA
*
56359205 TTACCAAAATACCACTGGT
63 TTACAAAAATACCACTGGT
**
56359224 TTGTGAAATTACTAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTA
1 TTGTGAAATTACTAAAATACCCTCAATGGGTAAAATTACCAAAATACCCCTGATTTACAAAATTA
56359289 CAAAAATACC
66 CAAAAATACC
56359299 CTTGACTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
80 3 0.05
81 60 0.91
82 3 0.05
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (81 bp):
TTGTGAAATTACTAAAATACCCTCAATGGGTAAAATTACCAAAATACCCCTGATTTACAAAATTA
CAAAAATACCACTGGT
Found at i:56359279 original size:27 final size:27
Alignment explanation
Indices: 56359176--56359382 Score: 157
Period size: 27 Copynumber: 7.6 Consensus size: 27
56359166 TATAGGGTAG
56359176 AATTACCAAAATACCCCT-AGTTTGTAA
1 AATTACCAAAATACCCCTGA-TTTGTAA
* * *
56359203 AATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTGATTTGTAA
* *
56359230 AATTACTAAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-GATTTGTAA
**
56359257 AATTACCAAAATACCCCTGATTTACAA
1 AATTACCAAAATACCCCTGATTTGTAA
* * *
56359284 AATTACAAAAATACCCTTGACTTTTTAA
1 AATTACCAAAATACCCCTGA-TTTGTAA
** ** * **
56359312 GAATTATAAAAATACCATTGGTTTACAA
1 -AATTACCAAAATACCCCTGATTTGTAA
* * * *
56359340 AATTACTAAAATACCCTTGGTTTGTAG
1 AATTACCAAAATACCCCTGATTTGTAA
* *
56359367 ATTTACCAAAACACCC
1 AATTACCAAAATACCC
56359383 TTGTAGTATG
Statistics
Matches: 145, Mismatches: 30, Indels: 10
0.78 0.16 0.05
Matches are distributed among these distances:
26 3 0.02
27 111 0.77
28 14 0.10
29 17 0.12
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGATTTGTAA
Found at i:56359364 original size:110 final size:108
Alignment explanation
Indices: 56359176--56359382 Score: 252
Period size: 110 Copynumber: 1.9 Consensus size: 108
56359166 TATAGGGTAG
* * * ***
56359176 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACTAAAA
1 AATTACAAAAATACCCCTACTTTGTAAAATTACAAAAATACCACTGGTTTACAAAATTACTAAAA
*
56359241 TACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAA
66 TACCCTCAATTTGTAAAATTACCAAAACACCCCTGATTTACAA
* * * *
56359284 AATTACAAAAATACCCTTGACTTTTTAAGAATTATAAAAATACCATTGGTTTACAAAATTACTAA
1 AATTACAAAAATACCCCT-ACTTTGTAA-AATTACAAAAATACCACTGGTTTACAAAATTACTAA
*** * *
56359349 AATACCCTTGGTTTGTAGATTTACCAAAACACCC
64 AATACCCTCAATTTGTAAAATTACCAAAACACCC
56359383 TTGTAGTATG
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
108 16 0.20
109 7 0.09
110 58 0.72
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.31
Consensus pattern (108 bp):
AATTACAAAAATACCCCTACTTTGTAAAATTACAAAAATACCACTGGTTTACAAAATTACTAAAA
TACCCTCAATTTGTAAAATTACCAAAACACCCCTGATTTACAA
Found at i:56359405 original size:110 final size:110
Alignment explanation
Indices: 56359210--56359409 Score: 240
Period size: 110 Copynumber: 1.8 Consensus size: 110
56359200 TAAAATTACC
*** *
56359210 AAAATACCACTGGTTTGTGAAATTACTAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCT
1 AAAATACCACTGGTTTACAAAATTACTAAAATACCCTCAATTTGTAAAATTACCAAAACACCCCT
* *
56359275 GATTTACAAAATTACAAAAATACCCTTGACTTTTTAAGAATTATA
66 GATGTACAAAATGACAAAAATACCCTTGACTTTTTAAGAATTATA
* *** * * *
56359320 AAAATACCATTGGTTTACAAAATTACTAAAATACCCTTGGTTTGTAGATTTACCAAAACACCCTT
1 AAAATACCACTGGTTTACAAAATTACTAAAATACCCTCAATTTGTAAAATTACCAAAACACCCCT
** *
56359385 G-TAGTATGAAATGACTAAAATACCC
66 GAT-GTACAAAATGACAAAAATACCC
56359410 CTAATAGGTA
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
109 1 0.01
110 72 0.99
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.31
Consensus pattern (110 bp):
AAAATACCACTGGTTTACAAAATTACTAAAATACCCTCAATTTGTAAAATTACCAAAACACCCCT
GATGTACAAAATGACAAAAATACCCTTGACTTTTTAAGAATTATA
Found at i:56359480 original size:27 final size:27
Alignment explanation
Indices: 56359403--56359480 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
56359393 AAATGACTAA
* *
56359403 AATACCCCT-AATAGGTAAAAAGACCGT
1 AATACCCCTGTAT-GGTAAAATGACCGT
* * *
56359430 AGA-GCCCCTGTAAGGTAAAGTGACCGT
1 A-ATACCCCTGTATGGTAAAATGACCGT
56359457 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
56359481 GAATATGCCA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
26 1 0.03
27 37 0.93
28 2 0.05
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGT
Found at i:56360165 original size:16 final size:16
Alignment explanation
Indices: 56360144--56360174 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
56360134 GTGACTGACT
56360144 TGGACTGTGTGGTTGA
1 TGGACTGTGTGGTTGA
56360160 TGGACTGTGTGGTTG
1 TGGACTGTGTGGTTG
56360175 GTGATATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.06, G:0.45, T:0.39
Consensus pattern (16 bp):
TGGACTGTGTGGTTGA
Found at i:56360356 original size:24 final size:25
Alignment explanation
Indices: 56360280--56360349 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
56360270 AGGAAGTGCT
* *
56360280 AAAAGGGCTATGCCCCAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
56360305 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
56360330 AAAAGGGCTTTGCCCTAGTT
1 AAAAGGGCTTTGCCCCAGTT
56360350 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:56360362 original size:24 final size:24
Alignment explanation
Indices: 56360279--56360362 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
56360269 GAGGAAGTGC
*
56360279 TAAAAGGGCTATGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
56360303 CGAAAAGGGCTTTGCCCCAGTTTAT
1 -TAAAAGGGCTTTGCCCCAGTTTAT
* *
56360328 CAAAAAGGGCTTTGCCCTAG-TTAT
1 -TAAAAGGGCTTTGCCCCAGTTTAT
56360352 TAAAAGAGGCT
1 TAAAAG-GGCT
56360363 AGGCCTCCAG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
23 5 0.09
24 8 0.15
25 40 0.75
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:56360373 original size:50 final size:50
Alignment explanation
Indices: 56360280--56360374 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
56360270 AGGAAGTGCT
**
56360280 AAAAGGGCTATGCCCCAGTTTATCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTATGCCCCAGTTTATCGAAAAGGGCTAGGCCCCAGTTTATCA
* * *
56360330 AAAAGGGCTTTGCCCTAG-TTAT-TAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTATGCCCCAGTTTATCGAAAAG-GGCTAGGCC-CCAGTT
56360375 GTATGATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 5 0.13
49 11 0.29
50 22 0.58
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.26
Consensus pattern (50 bp):
AAAAGGGCTATGCCCCAGTTTATCGAAAAGGGCTAGGCCCCAGTTTATCA
Found at i:56360620 original size:31 final size:30
Alignment explanation
Indices: 56360569--56360650 Score: 130
Period size: 31 Copynumber: 2.7 Consensus size: 30
56360559 CGCTTACAGT
56360569 AAAGGCTTCGGCCAGTGATATGATGTATGA
1 AAAGGCTTCGGCCAGTGATATGATGTATGA
*
56360599 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCC-AGTGATATGATGTATGA
56360630 AAAGGCTTCGGCCCAGT-ATAT
1 AAAGGCTTCGG-CCAGTGATAT
56360651 ATCGAGACTG
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
30 17 0.35
31 30 0.61
32 2 0.04
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
AAAGGCTTCGGCCAGTGATATGATGTATGA
Found at i:56369176 original size:94 final size:94
Alignment explanation
Indices: 56369000--56369186 Score: 261
Period size: 94 Copynumber: 2.0 Consensus size: 94
56368990 GATTTTATGA
* * *
56369000 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAGTGTGATGAATGTGAACATGCA
1 GATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTGAACATGCA
*
56369065 TATATGTGATAAGGCCGAATGGCCAATGT
66 TATATGTGAGAAGGCCGAATGGCCAATGT
* * *
56369094 GATGAATGTGAACATGCATATATGTGATAAGGTAGAATGGCCAATGTGATGAACGTGGAA-GTGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGT-GAACATGC
* *
56369158 ATATATGTGGCGAA-GCCGAATGGCTAATG
65 ATATATGT-GAGAAGGCCGAATGGCCAATG
56369187 CGAAATGTGT
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
94 76 0.93
95 6 0.07
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (94 bp):
GATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTGAACATGCA
TATATGTGAGAAGGCCGAATGGCCAATGT
Found at i:56369181 original size:47 final size:47
Alignment explanation
Indices: 56369000--56369146 Score: 267
Period size: 47 Copynumber: 3.1 Consensus size: 47
56368990 GATTTTATGA
*
56369000 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAGTGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
56369047 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
**
56369094 GATGAATGTGAACATGCATATATGTGATAAGGTAGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
56369141 GATGAA
1 GATGAA
56369147 CGTGGAAGTG
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 97 1.00
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.26
Consensus pattern (47 bp):
GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
Found at i:56369220 original size:46 final size:46
Alignment explanation
Indices: 56369170--56369342 Score: 283
Period size: 46 Copynumber: 3.8 Consensus size: 46
56369160 ATATGTGGCG
*
56369170 AAGCCGAATGGCTAATGCGAAATGTGTATGAGATGGATATGAGGTA
1 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
56369216 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
1 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
**
56369262 AAGTTGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
1 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
* * **
56369308 AAGCCGAATGGCTAATGTGAGATATGTATGAGATG
1 AAGCCGAATGGCTAATGCGAAACGTGTATGAGATG
56369343 TGTATATATA
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 118 1.00
ACGTcount: A:0.35, C:0.09, G:0.32, T:0.24
Consensus pattern (46 bp):
AAGCCGAATGGCTAATGCGAAACGTGTATGAGATGGATATGAGGTA
Found at i:56372207 original size:35 final size:35
Alignment explanation
Indices: 56372116--56372287 Score: 155
Period size: 35 Copynumber: 4.9 Consensus size: 35
56372106 GTTTCGAAGA
* * ** **
56372116 GACTAGCTCGTATGAGCATTGACGTGTTTCAGTTG
1 GACTATCTCTTATGAGCATTGGTGTGTTTTGGTTG
* *
56372151 GACTAGCTCATATGAGCATTGGTGTGTTTTGGTTG
1 GACTATCTCTTATGAGCATTGGTGTGTTTTGGTTG
* * ****
56372186 GACAATCTCTTATGAGCATTGGTATGTACCAGTTG
1 GACTATCTCTTATGAGCATTGGTGTGTTTTGGTTG
* * *
56372221 GACTTTCTCTTATGAGTATTGGCGTGTTTTGGTTG
1 GACTATCTCTTATGAGCATTGGTGTGTTTTGGTTG
* * *
56372256 GACTTTCTCTTGTGAGCATCTGGTGTGATTTG
1 GACTATCTCTTATGAGCAT-TGGTGTGTTTTG
56372288 AAGGGATTGA
Statistics
Matches: 110, Mismatches: 26, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
35 100 0.91
36 10 0.09
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (35 bp):
GACTATCTCTTATGAGCATTGGTGTGTTTTGGTTG
Found at i:56372219 original size:70 final size:71
Alignment explanation
Indices: 56372145--56372279 Score: 191
Period size: 70 Copynumber: 1.9 Consensus size: 71
56372135 TGACGTGTTT
*
56372145 CAGTTGGACTAGCTCATATGAGCATTGGTGTGTTTTGGTTGGACAATCTCTTATGAGCAT-TGGT
1 CAGTTGGACTAGCTCATATGAGCATTGGCGTGTTTTGGTTGGACAATCTCTTATGAGCATCTGGT
56372209 ATGTAC
66 ATGTAC
** * * ** *
56372215 CAGTTGGACTTTCTCTTATGAGTATTGGCGTGTTTTGGTTGGACTTTCTCTTGTGAGCATCTGGT
1 CAGTTGGACTAGCTCATATGAGCATTGGCGTGTTTTGGTTGGACAATCTCTTATGAGCATCTGGT
56372280 GTGATTTGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
70 52 0.93
71 4 0.07
ACGTcount: A:0.17, C:0.15, G:0.27, T:0.41
Consensus pattern (71 bp):
CAGTTGGACTAGCTCATATGAGCATTGGCGTGTTTTGGTTGGACAATCTCTTATGAGCATCTGGT
ATGTAC
Found at i:56375030 original size:24 final size:24
Alignment explanation
Indices: 56374973--56375087 Score: 89
Period size: 23 Copynumber: 4.9 Consensus size: 24
56374963 AAGCTCCTCC
56374973 TGAGCTGATAAACAGTAAGCTCTAT
1 TGAGCTGA-AAACAGTAAGCTCTAT
**
56374998 TGATATGAAAA-ATGTAAGCTCTAT
1 TGAGCTGAAAACA-GTAAGCTCTAT
*
56375022 TGAGCTG--AACTGTAAGCTCT-T
1 TGAGCTGAAAACAGTAAGCTCTAT
* * * *
56375043 TCGACCTG-AATCGGTAAGCTCTAA
1 T-GAGCTGAAAACAGTAAGCTCTAT
*
56375067 TGAGATG-AAACAGTAAGCTCT
1 TGAGCTGAAAACAGTAAGCTCT
56375088 TACGAGCTGT
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
21 2 0.03
22 16 0.22
23 28 0.39
24 20 0.28
25 6 0.08
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (24 bp):
TGAGCTGAAAACAGTAAGCTCTAT
Found at i:56375063 original size:23 final size:22
Alignment explanation
Indices: 56375011--56375065 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
56375001 TATGAAAAAT
* *
56375011 GTAAGCTCTATTGAGCTGAACT
1 GTAAGCTCTATTGACCTGAACG
56375033 GTAAGCTCT-TTCGACCTGAATCG
1 GTAAGCTCTATT-GACCTGAA-CG
56375056 GTAAGCTCTA
1 GTAAGCTCTA
56375066 ATGAGATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.07
22 16 0.57
23 10 0.36
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (22 bp):
GTAAGCTCTATTGACCTGAACG
Found at i:56375706 original size:20 final size:21
Alignment explanation
Indices: 56375678--56375727 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
56375668 TCACTTTGTA
*
56375678 AAACTTTTAT-ATCTATCATT
1 AAACATTTATAATCTATCATT
*
56375698 AAACCTTTATAATCTATCATT
1 AAACATTTATAATCTATCATT
56375719 AAACATTTA
1 AAACATTTA
56375728 AATACTCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (21 bp):
AAACATTTATAATCTATCATT
Found at i:56380838 original size:24 final size:24
Alignment explanation
Indices: 56380794--56380839 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
56380784 TTACATGAAA
*
56380794 ATAGACTCATTAAGCTTTAATTTT
1 ATAGACTCATTAAGCTCTAATTTT
*
56380818 ATAG-CTCATTCAGCCTCTAATT
1 ATAGACTCATTAAG-CTCTAATT
56380840 GAATTTATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (24 bp):
ATAGACTCATTAAGCTCTAATTTT
Found at i:56383011 original size:27 final size:28
Alignment explanation
Indices: 56382965--56383018 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
56382955 TACTTAGACC
56382965 CCCTATATATGATAAAATGACTATTTTT
1 CCCTATATATGATAAAATGACTATTTTT
* * *
56382993 CCCT-TATATGGTAAGATGACTGTTTT
1 CCCTATATATGATAAAATGACTATTTT
56383019 GCCCCTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.43
Consensus pattern (28 bp):
CCCTATATATGATAAAATGACTATTTTT
Found at i:56383819 original size:18 final size:18
Alignment explanation
Indices: 56383796--56383832 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
56383786 TATAATTAAT
56383796 AATGTTTTAATATAACTA
1 AATGTTTTAATATAACTA
*
56383814 AATGTTTTAATATGACTA
1 AATGTTTTAATATAACTA
56383832 A
1 A
56383833 CTATTTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (18 bp):
AATGTTTTAATATAACTA
Found at i:56383839 original size:18 final size:18
Alignment explanation
Indices: 56383800--56383839 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
56383790 ATTAATAATG
*
56383800 TTTTAATATAACTAAATG
1 TTTTAATATAACTAAATA
* *
56383818 TTTTAATATGACTAACTA
1 TTTTAATATAACTAAATA
56383836 TTTT
1 TTTT
56383840 CTAAATGACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (18 bp):
TTTTAATATAACTAAATA
Found at i:56409162 original size:15 final size:17
Alignment explanation
Indices: 56409142--56409173 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
56409132 TATAACTTAA
56409142 CAATTC-AT-ACAATAT
1 CAATTCAATGACAATAT
56409157 CAATTCAATGACAATAT
1 CAATTCAATGACAATAT
56409174 GAATACAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (17 bp):
CAATTCAATGACAATAT
Found at i:56412784 original size:18 final size:18
Alignment explanation
Indices: 56412757--56412803 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
56412747 TTCAGAAAAT
* *
56412757 TGGGCTCACACGCCCATG
1 TGGGCCCACACGCCCATA
* *
56412775 TGGGCCCACAAGCCCGTA
1 TGGGCCCACACGCCCATA
56412793 T-GGCCCACACG
1 TGGGCCCACACG
56412804 GCCGAAATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.19, C:0.40, G:0.28, T:0.13
Consensus pattern (18 bp):
TGGGCCCACACGCCCATA
Found at i:56436550 original size:50 final size:48
Alignment explanation
Indices: 56436398--56436641 Score: 147
Period size: 50 Copynumber: 5.1 Consensus size: 48
56436388 TGGGTTGGAT
* * * * *
56436398 TGAAGCTACAATAGCAAATCTTATCTCCCTGAAGTTGTAATGGTGCAAGA
1 TGAAGCTACCATGGC-AATCTTATCTCCCTAAAGTTGTAGT-GAGCAAGA
* * * * *
56436448 TAAAGCTA-CA----AATCCTATAC-CCCTGAAGTTGCAGTTAGTC-AGA
1 TGAAGCTACCATGGCAATCTTAT-CTCCCTAAAGTTGTAGTGAG-CAAGA
56436491 TTGAAGCTACCATGGCTAATCTTATCTCCCTAAAGTTGTAGTAGAGCAAGA
1 -TGAAGCTACCATGGC-AATCTTATCTCCCTAAAGTTGTAGT-GAGCAAGA
* * *
56436542 TGAAGCTA-CA----AATCCTATAC-CCCTGAAGTTGTAGTGGGTC-AGA
1 TGAAGCTACCATGGCAATCTTAT-CTCCCTAAAGTTGTAGTGAG-CAAGA
* *
56436585 TTGAAGCTACCATGGCGAATCTTATCTCCCTAAAGATGCAGTGGAGCAAGA
1 -TGAAGCTACCATGGC-AATCTTATCTCCCTAAAGTTGTAGT-GAGCAAGA
56436636 TGAAGC
1 TGAAGC
56436642 CACAAATCCT
Statistics
Matches: 150, Mismatches: 20, Indels: 48
0.69 0.09 0.22
Matches are distributed among these distances:
43 9 0.06
44 58 0.39
45 6 0.04
49 5 0.03
50 62 0.41
51 10 0.07
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (48 bp):
TGAAGCTACCATGGCAATCTTATCTCCCTAAAGTTGTAGTGAGCAAGA
Found at i:56436590 original size:44 final size:44
Alignment explanation
Indices: 56436362--56436594 Score: 154
Period size: 44 Copynumber: 5.0 Consensus size: 44
56436352 TCAGTGTCCT
* **
56436362 CAAATCCTATACCTCTGAAGTTGTAGTGGGTTGGATTGAAGCTA
1 CAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAGCTA
* * *
56436406 CAATAGCAAATCT-TATCTCCCTGAAGTTGTAAT-GGTGCAAGA-TAAAGCTA
1 CAA-ATC----CTATA-C-CCCTGAAGTTGTAGTGGGT-C-AGATTGAAGCTA
* **
56436456 CAAATCCTATACCCCTGAAGTTGCAGTTAGTCAGATTGAAGCTA
1 CAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAGCTA
* * *
56436500 CCATGGCTAATCTTAT-CTCCCTAAAGTTGTAGTAGAG-CAAGA-TGAAGCTA
1 -CA-----AATCCTATAC-CCCTGAAGTTGTAGT-GGGTC-AGATTGAAGCTA
56436550 CAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAGCTA
1 CAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAGCTA
56436594 C
1 C
56436595 CATGGCGAAT
Statistics
Matches: 147, Mismatches: 18, Indels: 48
0.69 0.08 0.23
Matches are distributed among these distances:
43 8 0.05
44 55 0.37
45 10 0.07
46 2 0.01
48 2 0.01
49 11 0.07
50 52 0.35
51 7 0.05
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (44 bp):
CAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAGCTA
Found at i:56436666 original size:94 final size:94
Alignment explanation
Indices: 56436362--56436653 Score: 422
Period size: 94 Copynumber: 3.1 Consensus size: 94
56436352 TCAGTGTCCT
* ** * *
56436362 CAAATCCTATACCTCTGAAGTTGTAGTGGGTTGGATTGAAGCTACAATAGCAAATCTTATCTCCC
1 CAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAGCTACCATGGCAAATCTTATCTCCC
* * * *
56436427 TGAAGTTGTAATGGTGCAAGATAAAGCTA
66 TAAAGTTGTAGTGGAGCAAGATGAAGCTA
* ** *
56436456 CAAATCCTATACCCCTGAAGTTGCAGTTAGTCAGATTGAAGCTACCATGGCTAATCTTATCTCCC
1 CAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAGCTACCATGGCAAATCTTATCTCCC
*
56436521 TAAAGTTGTAGTAGAGCAAGATGAAGCTA
66 TAAAGTTGTAGTGGAGCAAGATGAAGCTA
*
56436550 CAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAGCTACCATGGCGAATCTTATCTCCC
1 CAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAGCTACCATGGCAAATCTTATCTCCC
* * *
56436615 TAAAGATGCAGTGGAGCAAGATGAAGCCA
66 TAAAGTTGTAGTGGAGCAAGATGAAGCTA
56436644 CAAATCCTAT
1 CAAATCCTAT
56436654 CTCCTTAAAG
Statistics
Matches: 176, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 176 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (94 bp):
CAAATCCTATACCCCTGAAGTTGTAGTGGGTCAGATTGAAGCTACCATGGCAAATCTTATCTCCC
TAAAGTTGTAGTGGAGCAAGATGAAGCTA
Found at i:56436909 original size:3 final size:3
Alignment explanation
Indices: 56436903--56436943 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
56436893 AAAAAACCAA
56436903 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
56436944 AGAATCCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:56439488 original size:10 final size:10
Alignment explanation
Indices: 56439475--56439567 Score: 73
Period size: 10 Copynumber: 9.1 Consensus size: 10
56439465 TTTTATAAAA
56439475 TTTTAAATTT
1 TTTTAAATTT
* *
56439485 TTTTATATAT
1 TTTTAAATTT
*
56439495 TTTTAGATTT
1 TTTTAAATTT
*
56439505 TTTTAAAATT
1 TTTTAAATTT
*
56439515 TTAT-AATTT
1 TTTTAAATTT
56439524 TTTTAAATATAAAT
1 TTTTAAAT-T---T
*
56439538 TTTGAAATTT
1 TTTTAAATTT
*
56439548 TTATAAATTT
1 TTTTAAATTT
56439558 TTTT-AATTT
1 TTTTAAATTT
56439567 T
1 T
56439568 AAAAATTGTT
Statistics
Matches: 65, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
9 13 0.20
10 42 0.65
11 1 0.02
13 1 0.02
14 8 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:56439490 original size:20 final size:20
Alignment explanation
Indices: 56439465--56439549 Score: 84
Period size: 20 Copynumber: 4.1 Consensus size: 20
56439455 AAAATTATTA
56439465 TTTTATAAAATTTTAAATTT
1 TTTTATAAAATTTTAAATTT
* * *
56439485 TTTTATATATTTTTAGA-TT
1 TTTTATAAAATTTTAAATTT
56439504 TTTT-TAAAATTTTATAATTT
1 TTTTATAAAATTTTA-AATTT
56439524 TTTTAAATATAAATTTTGAAATTT
1 TTTT--ATA-AAATTTT-AAATTT
56439548 TT
1 TT
56439550 ATAAATTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
18 8 0.15
19 7 0.13
20 20 0.38
23 2 0.04
24 14 0.27
25 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTATAAAATTTTAAATTT
Found at i:56439496 original size:19 final size:18
Alignment explanation
Indices: 56439474--56439564 Score: 71
Period size: 19 Copynumber: 5.0 Consensus size: 18
56439464 ATTTTATAAA
56439474 ATTTTAAATTTTTTTATAT
1 ATTTTAAATTTTTTTA-AT
* *
56439493 ATTTTTAGATTTTTTTAAA
1 A-TTTTAAATTTTTTTAAT
56439512 ATTTTATAATTTTTTTAA-
1 ATTTTA-AATTTTTTTAAT
* **
56439530 A-TATAAA-TTTTGAAAT
1 ATTTTAAATTTTTTTAAT
*
56439546 TTTTATAAATTTTTTTAAT
1 ATTT-TAAATTTTTTTAAT
56439565 TTTAAAAATT
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
15 6 0.11
16 2 0.04
17 4 0.07
18 10 0.18
19 20 0.36
20 14 0.25
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTTAAATTTTTTTAAT
Found at i:56439546 original size:24 final size:24
Alignment explanation
Indices: 56439510--56439555 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
56439500 GATTTTTTTA
*
56439510 AAATTTTATAATTTTTTTAAATAT
1 AAATTTTATAATTTTTATAAATAT
56439534 AAATTTTGA-AATTTTTATAAAT
1 AAATTTT-ATAATTTTTATAAAT
56439556 TTTTTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
AAATTTTATAATTTTTATAAATAT
Found at i:56439565 original size:19 final size:19
Alignment explanation
Indices: 56439478--56439608 Score: 80
Period size: 20 Copynumber: 6.9 Consensus size: 19
56439468 TATAAAATTT
56439478 TAAATTTTTTTATATATTTT-
1 TAAATTTTTTTA-AT-TTTTA
* *
56439498 TAGATTTTTTTAAAATTTTA
1 TAAATTTTTTT-AATTTTTA
*
56439518 T-AATTTTTTTAA---ATA
1 TAAATTTTTTTAATTTTTA
**
56439533 TAAA-TTTTGAAATTTTTA
1 TAAATTTTTTTAATTTTTA
56439551 TAAATTTTTTTAA-TTTTA
1 TAAATTTTTTTAATTTTTA
* *
56439569 AAAATTGTTTTGAATTTTTGA
1 TAAATT-TTTTTAATTTTT-A
56439590 -AAATTATTTTGTAATTTTT
1 TAAATT-TTTT-TAATTTTT
56439609 GTTTCGAGAG
Statistics
Matches: 87, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
15 9 0.10
16 2 0.02
18 18 0.21
19 24 0.28
20 25 0.29
21 9 0.10
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TAAATTTTTTTAATTTTTA
Found at i:56439691 original size:9 final size:9
Alignment explanation
Indices: 56439677--56439706 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
56439667 ACACTAATAT
56439677 ATTATTCGA
1 ATTATTCGA
56439686 ATTATTCGA
1 ATTATTCGA
*
56439695 GTTATTCGA
1 ATTATTCGA
56439704 ATT
1 ATT
56439707 GTAAAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (9 bp):
ATTATTCGA
Found at i:56442529 original size:29 final size:29
Alignment explanation
Indices: 56442479--56442574 Score: 151
Period size: 28 Copynumber: 3.4 Consensus size: 29
56442469 TAAGTCCGCG
56442479 CACTTAGTG-TTATATAATCAAACTCGCA
1 CACTTAGTGCTTATATAATCAAACTCGCA
*
56442507 CACTTAGTGCTTACATAATCAAACTCGCA
1 CACTTAGTGCTTATATAATCAAACTCGCA
* *
56442536 CAGTTAGTGC-TATATAATCAAACTTGCA
1 CACTTAGTGCTTATATAATCAAACTCGCA
56442564 CACTTAGTGCT
1 CACTTAGTGCT
56442575 ATGAAATTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
28 34 0.56
29 27 0.44
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.31
Consensus pattern (29 bp):
CACTTAGTGCTTATATAATCAAACTCGCA
Found at i:56442573 original size:28 final size:28
Alignment explanation
Indices: 56442479--56442602 Score: 153
Period size: 29 Copynumber: 4.4 Consensus size: 28
56442469 TAAGTCCGCG
*
56442479 CACTTAGTGTTATATAATCAAACTCGCA
1 CACTTAGTGCTATATAATCAAACTCGCA
*
56442507 CACTTAGTGCTTACATAATCAAACTCGCA
1 CACTTAGTGC-TATATAATCAAACTCGCA
* *
56442536 CAGTTAGTGCTATATAATCAAACTTGCA
1 CACTTAGTGCTATATAATCAAACTCGCA
*
56442564 CACTTAGTGCTATGA-AATTTAAAC-CTGCA
1 CACTTAGTGCTAT-ATAA-TCAAACTC-GCA
56442593 CACTTAGTGC
1 CACTTAGTGC
56442603 CAATCTCATG
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
28 39 0.46
29 45 0.54
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.31
Consensus pattern (28 bp):
CACTTAGTGCTATATAATCAAACTCGCA
Found at i:56457967 original size:55 final size:56
Alignment explanation
Indices: 56457902--56458081 Score: 290
Period size: 56 Copynumber: 3.2 Consensus size: 56
56457892 TTTTTACTTG
*
56457902 CACACATATATCGGAGTCACATATCGATGCCAATGTAT-AAACGTGGTCTTACTCA
1 CACACATATATCGGAGTCACATATCGATGCCAACGTATAAAACGTGGTCTTACTCA
56457957 CACACATATATCGGAGTCACATATCGATGCCAACGTATAAAACGTGGTCTTACTCA
1 CACACATATATCGGAGTCACATATCGATGCCAACGTATAAAACGTGGTCTTACTCA
* * * * *
56458013 CACACATATATCAGAGTTACATATCGATGCCAACGTATGAAACGTGATCTTACTCG
1 CACACATATATCGGAGTCACATATCGATGCCAACGTATAAAACGTGGTCTTACTCA
*
56458069 TACACATATATCG
1 CACACATATATCG
56458082 ATGCCATGGT
Statistics
Matches: 116, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
55 37 0.32
56 79 0.68
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (56 bp):
CACACATATATCGGAGTCACATATCGATGCCAACGTATAAAACGTGGTCTTACTCA
Found at i:56462076 original size:20 final size:20
Alignment explanation
Indices: 56462053--56462096 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
56462043 TAAAGAAAGT
* * *
56462053 AAATGCAATGGAAAGTAATA
1 AAATGCAAAGGAAAATAAGA
56462073 AAATGCAAAGGAAAATAAGA
1 AAATGCAAAGGAAAATAAGA
56462093 AAAT
1 AAAT
56462097 TTGAAATGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.61, C:0.05, G:0.18, T:0.16
Consensus pattern (20 bp):
AAATGCAAAGGAAAATAAGA
Found at i:56468983 original size:18 final size:18
Alignment explanation
Indices: 56468960--56469002 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
56468950 CATGGTCACG
56468960 TTATCATGAAAATTAGAA
1 TTATCATGAAAATTAGAA
56468978 TTATCATGAAAATTAGAA
1 TTATCATGAAAATTAGAA
56468996 TTATCAT
1 TTATCAT
56469003 ATTGTACCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (18 bp):
TTATCATGAAAATTAGAA
Found at i:56469646 original size:17 final size:18
Alignment explanation
Indices: 56469604--56469652 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
56469594 TTCGTTCAGC
*
56469604 CCAAAAAAATAATAATAAA
1 CCAAATAAATAA-AATAAA
*
56469623 TCAAATAAATAAAA-AAA
1 CCAAATAAATAAAATAAA
56469640 CCAAATAAATAAA
1 CCAAATAAATAAA
56469653 TCAAAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 15 0.56
18 2 0.07
19 10 0.37
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.16
Consensus pattern (18 bp):
CCAAATAAATAAAATAAA
Found at i:56469920 original size:17 final size:17
Alignment explanation
Indices: 56469884--56469921 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
56469874 TAGAGGGATA
*
56469884 AAAAAACAAAGATAAAG
1 AAAAAACAAAGAAAAAG
56469901 AAAAAACAAA-AAAAATG
1 AAAAAACAAAGAAAAA-G
56469918 AAAA
1 AAAA
56469922 GAAAAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.82, C:0.05, G:0.08, T:0.05
Consensus pattern (17 bp):
AAAAAACAAAGAAAAAG
Found at i:56486797 original size:94 final size:94
Alignment explanation
Indices: 56486631--56487285 Score: 583
Period size: 94 Copynumber: 7.0 Consensus size: 94
56486621 CTGTGAAACA
* ** * * *
56486631 ACAAA-TCATATACCCCTAAAGTT-CTAGTAGGTCAGATTGAAGCTACCATAACGAATCTTATCT
1 ACAAATTC-TATACCCCTAAAGTTGC-AGTGGGTTGGAATGAAGCTACCATAGCAAATCTTATCT
*
56486694 CCTTGAAGTTGCAGTGGAGCAAGATGAAGCT
64 CCTTAAAGTTGCAGTGGAGCAAGATGAAGCT
* *
56486725 ACAAATTCTATACCCCTGAAGTTCCAGTGGGTTGGAATGAAGCTACCATAGCAAATCTTATCTCC
1 ACAAATTCTATACCCCTAAAGTTGCAGTGGGTTGGAATGAAGCTACCATAGCAAATCTTATCTCC
* ** *
56486790 CTAAAGTTATAGTAGAGCAAGATGAAGCT
66 TTAAAGTTGCAGTGGAGCAAGATGAAGCT
* * * * * * *
56486819 ACAAA-TCATATACCCCTGAAGTTGTAGTAGGTCT-GATTGAAGCTACCATAACTAATTTTATCT
1 ACAAATTC-TATACCCCTAAAGTTGCAGTGGGT-TGGAATGAAGCTACCATAGCAAATCTTATCT
* * *
56486882 CCCTAAAGTTGCAGTGGAGTAAGATGAAACT
64 CCTTAAAGTTGCAGTGGAGCAAGATGAAGCT
* * *
56486913 ACAAATAT-TATGCCCTTCAAA-TTG-AGTGGGTCGGAATGAAGCTACCATAGCAAATCTTATCT
1 ACAAAT-TCTATACCCCT-AAAGTTGCAGTGGGTTGGAATGAAGCTACCATAGCAAATCTTATCT
* * * *
56486975 CCCTGAAGTT-CTAGTGAAGCAAGATGAAGTT
64 CCTTAAAGTTGC-AGTGGAGCAAGATGAAGCT
* * * * * ** * *
56487006 ACAAATCCTATGCCCTTAAAGATGAAGTGGGTCAGAATGAAGCTATCATAGCGAATCTTATCTCC
1 ACAAATTCTATACCCCTAAAGTTGCAGTGGGTTGGAATGAAGCTACCATAGCAAATCTTATCTCC
* *
56487071 TTAAAGTTGTAGTGGAGCAAGATGAAACT
66 TTAAAGTTGCAGTGGAGCAAGATGAAGCT
* * * * * * * *
56487100 ATAAATCCTATACTCATAAAGTTGCAGTGGATTGGAATGAAACTACAATAGCAAATCTTATCTTC
1 ACAAATTCTATACCCCTAAAGTTGCAGTGGGTTGGAATGAAGCTACCATAGCAAATCTTATCTCC
* *
56487165 TTAAAGTTGTAG-GGAAACAAGATGAAGCT
66 TTAAAGTTGCAGTGG-AGCAAGATGAAGCT
* ** * ** * * * * * * *
56487194 ACAAATCCTATACCATTGAAGTTGCAGTAAGTTGAAATGAAACTACAACAACAAATCTTATTTCT
1 ACAAATTCTATACCCCTAAAGTTGCAGTGGGTTGGAATGAAGCTACCATAGCAAATCTTATCTCC
*
56487259 TTAAA-TTGCAATGGAGCAAGATGAAGC
66 TTAAAGTTGCAGTGGAGCAAGATGAAGC
56487286 CATGATACTA
Statistics
Matches: 464, Mismatches: 82, Indels: 31
0.80 0.14 0.05
Matches are distributed among these distances:
92 4 0.01
93 92 0.20
94 361 0.78
95 6 0.01
96 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (94 bp):
ACAAATTCTATACCCCTAAAGTTGCAGTGGGTTGGAATGAAGCTACCATAGCAAATCTTATCTCC
TTAAAGTTGCAGTGGAGCAAGATGAAGCT
Found at i:56487096 original size:50 final size:50
Alignment explanation
Indices: 56486761--56487194 Score: 138
Period size: 50 Copynumber: 9.2 Consensus size: 50
56486751 GTGGGTTGGA
* * * *
56486761 ATGAAGCTACCATAGCAAATCTTATCTCCCTAAAGTTATAGTAGAGCAAG
1 ATGAAGCTATCATAGCAAATCTTATCTCCTTAAAGTTGTAGTGGAGCAAG
* * * * *
56486811 ATGAAG----C-TA-CAAATCATATAC-CCCTGAAGTTGTAGTAGG-TC-TG
1 ATGAAGCTATCATAGCAAATCTTAT-CTCCTTAAAGTTGTAGT-GGAGCAAG
* * * * * * *
56486854 ATTGAAGCTACCATAACTAATTTTATCTCCCTAAAGTTGCAGTGGAGTAAG
1 A-TGAAGCTATCATAGCAAATCTTATCTCCTTAAAGTTGTAGTGGAGCAAG
* *
56486905 ATGAA---A-C-TA-CAAATATTATGC-CCTTCAAA-TTG-AGTGG-GTC-GG
1 ATGAAGCTATCATAGCAAATCTTAT-CTCCTT-AAAGTTGTAGTGGAG-CAAG
* * * * *
56486947 AATGAAGCTACCATAGCAAATCTTATCTCCCTGAAGTTCTAGTGAAGCAAG
1 -ATGAAGCTATCATAGCAAATCTTATCTCCTTAAAGTTGTAGTGGAGCAAG
* * *
56486998 ATGAAG---T--TA-CAAATCCTATGC-CCTTAAAGATGAAGTGG-GTC-AG
1 ATGAAGCTATCATAGCAAATCTTAT-CTCCTTAAAGTTGTAGTGGAG-CAAG
*
56487041 AATGAAGCTATCATAGCGAATCTTATCTCCTTAAAGTTGTAGTGGAGCAAG
1 -ATGAAGCTATCATAGCAAATCTTATCTCCTTAAAGTTGTAGTGGAGCAAG
* * * * *
56487092 ATGAA---A-C-TA-TAAATCCTATACT-CATAAAGTTGCAGTGGATTG-GA-
1 ATGAAGCTATCATAGCAAATCTTAT-CTCCTTAAAGTTGTAGTGGA--GCAAG
* * *
56487136 ATGAAACTA-CAATAGCAAATCTTATCTTCTTAAAGTTGTAG-GGAAACAAG
1 ATGAAGCTATC-ATAGCAAATCTTATCTCCTTAAAGTTGTAGTGG-AGCAAG
56487186 ATGAAGCTA
1 ATGAAGCTA
56487195 CAAATCCTAT
Statistics
Matches: 282, Mismatches: 50, Indels: 104
0.65 0.11 0.24
Matches are distributed among these distances:
42 2 0.01
43 15 0.05
44 96 0.34
45 18 0.06
46 5 0.02
47 6 0.02
48 6 0.02
49 29 0.10
50 98 0.35
51 7 0.02
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (50 bp):
ATGAAGCTATCATAGCAAATCTTATCTCCTTAAAGTTGTAGTGGAGCAAG
Found at i:56487172 original size:281 final size:281
Alignment explanation
Indices: 56486668--56487199 Score: 658
Period size: 281 Copynumber: 1.9 Consensus size: 281
56486658 TAGGTCAGAT
* * * *
56486668 TGAAGCTACCATAACGAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATTC
1 TGAAGCTACCATAACAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAAGATGAAGCTACAAATCC
* * * **
56486733 TATACCCCTGAAGTTCCAGTGGGTTGGAATGAAGCTACCATAGCAAATCTTATCTCCCTAAAGTT
66 TATACCCCTAAAGATCAAGTGGGTCAGAATGAAGCTACCATAGCAAATCTTATCTCCCTAAAGTT
* * * * * *
56486798 ATAGTAGAGCAAGATGAAGCTACAAATCATATACCCCTGAAGTTGTAGTAGGTCTGATTGAAGCT
131 ATAGTAGAGCAAGATGAAACTACAAATCATATACCCATAAAGTTGCAGTAGGTCTGAATGAAACT
* * * **
56486863 ACCATAACTAATTTTATCTCCCTAAAGTTGCAGTGG-AGTAAGATGAAACTACAAATATTATGCC
196 ACAATAACAAATCTTATCTCCCTAAAGTTGCAG-GGAAACAAGATGAAACTACAAATATTATGCC
56486927 CTTCAAATTGAGTGGGTCGGAA
260 CTTCAAATTGAGTGGGTCGGAA
* *
56486949 TGAAGCTACCATAGCAAATCTTATCTCCCTGAAGTT-CTAGTGAAGCAAGATGAAGTTACAAATC
1 TGAAGCTACCATAACAAATCTTATCTCCCTGAAGTTGC-AGTGAAGCAAGATGAAGCTACAAATC
* * * * * *
56487013 CTATGCCCTTAAAGATGAAGTGGGTCAGAATGAAGCTATCATAGCGAATCTTATCTCCTTAAAGT
65 CTATACCCCTAAAGATCAAGTGGGTCAGAATGAAGCTACCATAGCAAATCTTATCTCCCTAAAGT
* * * * *
56487078 TGTAGTGGAGCAAGATGAAACTATAAATCCTATACTCATAAAGTTGCAGT-GGAT-TGGAATGAA
130 TATAGTAGAGCAAGATGAAACTACAAATCATATACCCATAAAGTTGCAGTAGG-TCT-GAATGAA
* * * * *
56487141 ACTACAATAGCAAATCTTATCTTCTTAAAGTTGTAGGGAAACAAGATGAAGCTACAAAT
193 ACTACAATAACAAATCTTATCTCCCTAAAGTTGCAGGGAAACAAGATGAAACTACAAAT
56487200 CCTATACCAT
Statistics
Matches: 209, Mismatches: 38, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
280 6 0.03
281 203 0.97
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28
Consensus pattern (281 bp):
TGAAGCTACCATAACAAATCTTATCTCCCTGAAGTTGCAGTGAAGCAAGATGAAGCTACAAATCC
TATACCCCTAAAGATCAAGTGGGTCAGAATGAAGCTACCATAGCAAATCTTATCTCCCTAAAGTT
ATAGTAGAGCAAGATGAAACTACAAATCATATACCCATAAAGTTGCAGTAGGTCTGAATGAAACT
ACAATAACAAATCTTATCTCCCTAAAGTTGCAGGGAAACAAGATGAAACTACAAATATTATGCCC
TTCAAATTGAGTGGGTCGGAA
Found at i:56487279 original size:281 final size:281
Alignment explanation
Indices: 56486684--56487285 Score: 638
Period size: 281 Copynumber: 2.1 Consensus size: 281
56486674 TACCATAACG
* * *
56486684 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATTCTATACCCCTGAAGTTC
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTAAAGATC
* **
56486749 CAGTGGGTTGGAATGAAGCTACCATAGCAAATCTTATCTCCCTAAAGTTATAGTAGAGCAAGATG
66 AAGTGGGTCAGAATGAAGCTACCATAGCAAATCTTATCTCCCTAAAGTTATAGTAGAGCAAGATG
* * * * * * * * *
56486814 AAGCTACAAATCATATACCCCTGAAGTTGTAGTAGGTCTGATTGAAGCTACCATAACTAATTTTA
131 AAACTACAAATCATATACCCATAAAGTTGCAGTAGGTCTGAATGAAACTACAATAACAAATCTTA
** * * * **
56486879 TCTCCCTAAAGTTGCAGTGGAGTAAGATGAAACTACAAATATTATGCCCTTCAAATTGAGTGGGT
196 TCTCCCTAAAGTTGCAGTGGAACAAGATGAAACTACAAATACTATACCATTCAAATTGAGTAAGT
* * * * *
56486944 CGGAATGAAGCTACCATAGCA
261 CGAAATGAAACTACAACAACA
* * * * *
56486965 AATCTTATCTCCCTGAAGTT-CTAGTGAAGCAAGATGAAGTTACAAATCCTATGCCCTTAAAGAT
1 AATCTTATCTCCTTGAAGTTGC-AGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTAAAGAT
* * * * * *
56487029 GAAGTGGGTCAGAATGAAGCTATCATAGCGAATCTTATCTCCTTAAAGTTGTAGTGGAGCAAGAT
65 CAAGTGGGTCAGAATGAAGCTACCATAGCAAATCTTATCTCCCTAAAGTTATAGTAGAGCAAGAT
* * * *
56487094 GAAACTATAAATCCTATACTCATAAAGTTGCAGT-GGAT-TGGAATGAAACTACAATAGCAAATC
130 GAAACTACAAATCATATACCCATAAAGTTGCAGTAGG-TCT-GAATGAAACTACAATAACAAATC
* * * * * * *
56487157 TTATCTTCTTAAAGTTGTAG-GGAAACAAGATGAAGCTACAAATCCTATACCATTGAAGTTGCAG
193 TTATCTCCCTAAAGTTGCAGTGG-AACAAGATGAAACTACAAATACTATACCATTCAAATTG-AG
*
56487221 TAAGTTGAAATGAAACTACAACAACA
256 TAAGTCGAAATGAAACTACAACAACA
* * * *
56487247 AATCTTAT-TTCTTTAAATTGCAATGGAGCAAGATGAAGC
1 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGATGAAGC
56487286 CATGATACTA
Statistics
Matches: 258, Mismatches: 57, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
280 6 0.02
281 223 0.86
282 29 0.11
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (281 bp):
AATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATACCCCTAAAGATC
AAGTGGGTCAGAATGAAGCTACCATAGCAAATCTTATCTCCCTAAAGTTATAGTAGAGCAAGATG
AAACTACAAATCATATACCCATAAAGTTGCAGTAGGTCTGAATGAAACTACAATAACAAATCTTA
TCTCCCTAAAGTTGCAGTGGAACAAGATGAAACTACAAATACTATACCATTCAAATTGAGTAAGT
CGAAATGAAACTACAACAACA
Found at i:56489122 original size:12 final size:12
Alignment explanation
Indices: 56489107--56489139 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
56489097 AAATATTTTT
56489107 ATTATTATTGTC
1 ATTATTATTGTC
56489119 ATTATTATT-TC
1 ATTATTATTGTC
56489130 -TTATTATTGT
1 ATTATTATTGT
56489140 ATTCACTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 3 0.15
12 9 0.45
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (12 bp):
ATTATTATTGTC
Found at i:56493328 original size:14 final size:13
Alignment explanation
Indices: 56493297--56493335 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
56493287 TATCCTGGAA
56493297 AATTAA-AACAAG
1 AATTAAGAACAAG
*
56493309 AATTAAGAACACAT
1 AATTAAGAACA-AG
56493323 AATTAAGAACAAG
1 AATTAAGAACAAG
56493336 TCAAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 6 0.26
13 5 0.22
14 12 0.52
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.18
Consensus pattern (13 bp):
AATTAAGAACAAG
Found at i:56504824 original size:2 final size:2
Alignment explanation
Indices: 56504819--56504843 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56504809 GGTGAATCAT
56504819 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
56504844 TTTGTTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:56507772 original size:27 final size:26
Alignment explanation
Indices: 56507731--56507821 Score: 119
Period size: 27 Copynumber: 3.4 Consensus size: 26
56507721 ACAAGGAATG
* *
56507731 GCCTTTGTGGTGAACTCTAAAAGAACA
1 GCCTTTGTGGCGAACTCTAAAA-AATA
* *
56507758 GCCTTTGTAGCGAACTATAAAATAATA
1 GCCTTTGTGGCGAACTCTAAAA-AATA
56507785 GCCTTTGTGGCGAACTCTGAAAAAATA
1 GCCTTTGTGGCGAACTCT-AAAAAATA
56507812 GCCTTTGTGG
1 GCCTTTGTGG
56507822 AAAATTCTAA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 52 0.93
28 4 0.07
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (26 bp):
GCCTTTGTGGCGAACTCTAAAAAATA
Found at i:56507843 original size:54 final size:54
Alignment explanation
Indices: 56507731--56507843 Score: 120
Period size: 54 Copynumber: 2.1 Consensus size: 54
56507721 ACAAGGAATG
* ** *
56507731 GCCTTTGTGGTGAACTCTAAAAGAACAGCCTTTGTAGCGAACTATAAAATAATA
1 GCCTTTGTGGCGAACTCTAAAAGAACAGCCTTTGTAGAAAACTATAAAACAATA
* * * * * *
56507785 GCCTTTGTGGCGAACTCTGAAAA-AATAGCCTTTGTGGAAAATTCTAAAACGATT
1 GCCTTTGTGGCGAACTCT-AAAAGAACAGCCTTTGTAGAAAACTATAAAACAATA
56507839 GCCTT
1 GCCTT
56507844 AGTAGTATGT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
54 44 0.92
55 4 0.08
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (54 bp):
GCCTTTGTGGCGAACTCTAAAAGAACAGCCTTTGTAGAAAACTATAAAACAATA
Found at i:56516188 original size:50 final size:50
Alignment explanation
Indices: 56516069--56516361 Score: 288
Period size: 50 Copynumber: 5.8 Consensus size: 50
56516059 GTTGTGAGAA
* * * *
56516069 CACATGCGTAGTACTATGTGCAGGCTACTATGTGTTTAAGACAG-TT-TTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTG--T-A-CCAGATTGTTAGGT
*
56516121 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* ** * * * * * *
56516171 TACATGTGTAGTACTAAGTGGGGGCTACTATGCGTACCCGATAGCTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG-TTAGGT
* * * *
56516222 CACGTGTGTAGTACTAAGTGCAGGCTATTACGTGTATCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* * *
56516272 CACGTGTGCAGTACTAAGTGCAGGCTACTACGTG-A-CTGAATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG-ATTGTTAGGT
* * *
56516321 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA
56516362 GAGCTTCGGT
Statistics
Matches: 198, Mismatches: 37, Indels: 14
0.80 0.15 0.06
Matches are distributed among these distances:
48 5 0.03
49 42 0.21
50 81 0.41
51 40 0.20
52 30 0.15
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
Done.