Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 174 of 187
Found at i:53255279 original size:80 final size:80
Alignment explanation
Indices: 53255194--53255423 Score: 354
Period size: 80 Copynumber: 2.9 Consensus size: 80
53255184 ATTACCACAA
* * * * * * *
53255194 GCACAATTGCCTTCGGGTCTTAACCCGG-GCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATC-ACTAGCACAAATGCCTTCGGGTCTTAGC
53255258 TCGGATATATCAACTC
65 TCGGATATATCAACTC
*
53255274 GCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACTAGCACAAATGCCTTCGGGTCTTAGCT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACTAGCACAAATGCCTTCGGGTCTTAGCT
53255339 CGGATATATCAACTC
66 CGGATATATCAACTC
* *
53255354 GCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACTAGCACAAATGCCTTCGGGACTTAGCC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACTAGCACAAATGCCTTCGGGTCTTAGCT
53255419 CGGAT
66 CGGAT
53255424 CTCATTCACA
Statistics
Matches: 138, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
80 134 0.97
81 4 0.03
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACTAGCACAAATGCCTTCGGGTCTTAGCT
CGGATATATCAACTC
Found at i:53255398 original size:120 final size:120
Alignment explanation
Indices: 53255193--53255424 Score: 358
Period size: 120 Copynumber: 1.9 Consensus size: 120
53255183 TATTACCACA
* * *
53255193 AGCACAATTGCCTTCGGGTCTTAACCCGGGCATAGCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 AGCACAAATGCCTTCGGGTCTTAACCCGGACATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
* * *
53255258 TCGGATATATCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
66 CCGGATAAATCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
* * * *
53255313 AGCACAAATGCCTTCGGGTCTTAGCTCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 AGCACAAATGCCTTCGGGTCTTAACCCGGACATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
53255378 CCGGATCAAATC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATC
66 CCGGAT-AAATCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATC
53255425 TCATTCACAT
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
120 97 0.96
121 4 0.04
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (120 bp):
AGCACAAATGCCTTCGGGTCTTAACCCGGACATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
CCGGATAAATCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
Found at i:53255423 original size:40 final size:41
Alignment explanation
Indices: 53255193--53255424 Score: 303
Period size: 40 Copynumber: 5.8 Consensus size: 41
53255183 TATTACCACA
* * * *
53255193 AGCACAATTGCCTTCGGGTCTTAACCCGG-GCATAGCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCATATCAACT
* * *
53255233 CGCACGAATGCCTTCGGGTCTTAGCTCGGAT-ATATCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCATATCAACT
* * *
53255273 CGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATC-ACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCATATCAACT
*
53255313 AGCACAAATGCCTTCGGGTCTTAGCTCGGAT-ATATCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCATATCAACT
* *
53255353 CGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATC-ACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCATATCAACT
*
53255393 AGCACAAATGCCTTCGGGACTTAGCCCGGATC
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATC
53255425 TCATTCACAT
Statistics
Matches: 168, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
39 4 0.02
40 156 0.93
41 8 0.05
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (41 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATCATATCAACT
Found at i:53259298 original size:18 final size:18
Alignment explanation
Indices: 53259275--53259310 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
53259265 CAAGTACTAA
*
53259275 TTAGTTTAGTTTTCCAGT
1 TTAGTTTAATTTTCCAGT
*
53259293 TTAGTTTAATTTTTCAGT
1 TTAGTTTAATTTTCCAGT
53259311 ACAACAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.14, T:0.58
Consensus pattern (18 bp):
TTAGTTTAATTTTCCAGT
Found at i:53261212 original size:15 final size:15
Alignment explanation
Indices: 53261192--53261220 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53261182 AAGCCTTACA
53261192 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
53261207 CACCGTGTTATCAA
1 CACCGTGTTATCAA
53261221 ACAACAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:53261409 original size:9 final size:9
Alignment explanation
Indices: 53261392--53261425 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
53261382 TGAGTTTTCG
53261392 AATTCGAAT
1 AATTCGAAT
*
53261401 AACTCGAAT
1 AATTCGAAT
53261410 AATTCGAAT
1 AATTCGAAT
53261419 AATTCGA
1 AATTCGA
53261426 GTATCAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (9 bp):
AATTCGAAT
Found at i:53262440 original size:5 final size:5
Alignment explanation
Indices: 53262430--53262455 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
53262420 CTCGAAAATT
53262430 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
53262456 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:53264727 original size:8 final size:8
Alignment explanation
Indices: 53264714--53264764 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
53264704 TTTTCACTAA
53264714 TAATTATT
1 TAATTATT
53264722 TAATTACTT
1 TAATTA-TT
*
53264731 TAA--AAT
1 TAATTATT
53264737 TAATTATT
1 TAATTATT
53264745 TAATTATT
1 TAATTATT
53264753 TAATTACTT
1 TAATTA-TT
53264762 TAA
1 TAA
53264765 AATTTAAGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
6 4 0.11
7 1 0.03
8 22 0.59
9 10 0.27
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (8 bp):
TAATTATT
Found at i:53264769 original size:16 final size:16
Alignment explanation
Indices: 53264719--53264771 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
53264709 ACTAATAATT
53264719 ATTTAATTACTTTAAA
1 ATTTAATTACTTTAAA
*
53264735 A-TTAATTA-TTTAATT
1 ATTTAATTACTTTAA-A
53264750 ATTTAATTACTTTAAA
1 ATTTAATTACTTTAAA
53264766 ATTTAA
1 ATTTAA
53264772 GGACTGTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
16 14 0.44
17 5 0.16
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTAATTACTTTAAA
Found at i:53272110 original size:40 final size:40
Alignment explanation
Indices: 53272020--53272128 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 40
53272010 ATCCATGTAC
**
53272020 TGAATATGTTACGGTAAGCATGTTAAGCACGAATTTTGAAA
1 TGAATATGTTACCATAAGCATGTTAAGCACGAA-TTTGAAA
* * * * *
53272061 TGATTATGTTACCATAATCATGTTAAGCATGCCA-TTGAAT
1 TGAATATGTTACCATAAGCATGTTAAGCACG-AATTTGAAA
53272101 TGAATATGTTACCATAAGCATGTTAAGC
1 TGAATATGTTACCATAAGCATGTTAAGC
53272129 TTGAGTTTGC
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
40 31 0.53
41 26 0.45
42 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (40 bp):
TGAATATGTTACCATAAGCATGTTAAGCACGAATTTGAAA
Found at i:53274241 original size:50 final size:50
Alignment explanation
Indices: 53274166--53274299 Score: 223
Period size: 50 Copynumber: 2.7 Consensus size: 50
53274156 CATTTGGGTA
*
53274166 AAGAGGTCCCATGTAAGATCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
53274216 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* * **
53274266 GAGAAGTCCCCCGTAAGACCATGTCTGGGACATG
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATG
53274300 ACATGGGCAC
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 79 1.00
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.20
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
Found at i:53275863 original size:39 final size:39
Alignment explanation
Indices: 53275746--53276124 Score: 563
Period size: 39 Copynumber: 9.6 Consensus size: 39
53275736 GCTCCTCGTT
* *
53275746 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
53275786 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
53275826 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53275865 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53275904 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53275943 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53275982 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
53276021 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * *
53276060 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCA
53276101 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
53276125 CATCATTCAA
Statistics
Matches: 321, Mismatches: 11, Indels: 15
0.93 0.03 0.04
Matches are distributed among these distances:
39 249 0.78
40 61 0.19
41 11 0.03
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:53277497 original size:58 final size:58
Alignment explanation
Indices: 53277402--53277518 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
53277392 TACATACCTC
*
53277402 ACTAGGCCAACATGTTCCCAACATGTTTCCACCCATAGCATGGCCAACCACTAGCTCA
1 ACTAAGCCAACATGTTCCCAACATGTTTCCACCCATAGCATGGCCAACCACTAGCTCA
53277460 ACTAAGCCAACATGTTCCCAACATGTTTCCACCCATAGCATGGCCAACCACTAGCTCA
1 ACTAAGCCAACATGTTCCCAACATGTTTCCACCCATAGCATGGCCAACCACTAGCTCA
53277518 A
1 A
53277519 ATTTTGGGTA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.31, C:0.36, G:0.13, T:0.21
Consensus pattern (58 bp):
ACTAAGCCAACATGTTCCCAACATGTTTCCACCCATAGCATGGCCAACCACTAGCTCA
Found at i:53283937 original size:40 final size:40
Alignment explanation
Indices: 53283893--53284610 Score: 1384
Period size: 40 Copynumber: 17.9 Consensus size: 40
53283883 GCTCCTCGTT
* * * *
53283893 CAAATGCCTTCGGGACATAGCCCTG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
53283933 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53283973 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284013 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284053 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284093 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284133 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284173 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284213 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284253 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284293 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284333 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284373 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284413 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284453 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284493 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284533 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
53284573 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCG
53284611 NNNNNNNNNN
Statistics
Matches: 673, Mismatches: 4, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
40 671 1.00
41 2 0.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:53290541 original size:15 final size:15
Alignment explanation
Indices: 53290521--53290551 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
53290511 ATCTCATTTT
53290521 ATAATTAATTTAGTA
1 ATAATTAATTTAGTA
53290536 ATAATTAATTTAGTA
1 ATAATTAATTTAGTA
53290551 A
1 A
53290552 CTGCTACGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAATTAATTTAGTA
Found at i:53297295 original size:16 final size:17
Alignment explanation
Indices: 53297274--53297316 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
53297264 TATCCTTATT
53297274 TTTAATTTTTAATTTC-
1 TTTAATTTTTAATTTCA
53297290 TTTAA-TTTTAATTTCA
1 TTTAATTTTTAATTTCA
*
53297306 TTTTATTTTTA
1 TTTAATTTTTA
53297317 GTTGTAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 10 0.42
16 9 0.38
17 5 0.21
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTAATTTTTAATTTCA
Found at i:53297300 original size:15 final size:16
Alignment explanation
Indices: 53297274--53297314 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
53297264 TATCCTTATT
53297274 TTTAATTTTTAATTTC-
1 TTTAA-TTTTAATTTCA
53297290 TTTAATTTTAATTTCA
1 TTTAATTTTAATTTCA
*
53297306 TTTTATTTT
1 TTTAATTTT
53297315 TAGTTGTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTAATTTTAATTTCA
Found at i:53300664 original size:20 final size:20
Alignment explanation
Indices: 53300639--53300677 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
53300629 AACATTCAAA
53300639 ATACCATAATCAC-AACCAAG
1 ATACCATAA-CACAAACCAAG
53300659 ATACCATAACACAAACCAA
1 ATACCATAACACAAACCAA
53300678 ACCATATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.54, C:0.31, G:0.03, T:0.13
Consensus pattern (20 bp):
ATACCATAACACAAACCAAG
Found at i:53301825 original size:25 final size:25
Alignment explanation
Indices: 53301784--53301941 Score: 110
Period size: 25 Copynumber: 6.3 Consensus size: 25
53301774 TATGATCATA
* *
53301784 CGAGCTGTGAACCGGTATGCTCACT
1 CGAGCTGTAAATCGGTATGCTCACT
*
53301809 CGAGCTGTAAATTGGTATGCTCACAT
1 CGAGCTGTAAATCGGTATGCTCAC-T
* * *
53301835 -GAGCTGTAGATTGATATGCT-A-T
1 CGAGCTGTAAATCGGTATGCTCACT
**
53301857 CGCAAGCTGTAAATCAATATGCTCACAT
1 CG--AGCTGTAAATCGGTATGCTCAC-T
* * *
53301885 -GAGTTGTAGATCGGTATGCTC-TT
1 CGAGCTGTAAATCGGTATGCTCACT
* * *
53301908 ACGAGCTATAAATCAGTATGCTCACA
1 -CGAGCTGTAAATCGGTATGCTCACT
53301934 CGAGCTGT
1 CGAGCTGT
53301942 GGGTCAAAAT
Statistics
Matches: 103, Mismatches: 20, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
22 1 0.01
23 2 0.02
24 1 0.01
25 95 0.92
26 2 0.02
27 1 0.01
28 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (25 bp):
CGAGCTGTAAATCGGTATGCTCACT
Found at i:53301839 original size:50 final size:49
Alignment explanation
Indices: 53301796--53301941 Score: 168
Period size: 50 Copynumber: 2.9 Consensus size: 49
53301786 AGCTGTGAAC
**
53301796 CGGTATGCTCACTCGAGCTGTAAATTGGTATGCTCACATGAGCTGTAGAT
1 CGGTATGCTCA-TCGAGCTGTAAATCAGTATGCTCACATGAGCTGTAGAT
* * * *
53301846 TGATATGCT-ATCGCAAGCTGTAAATCAATATGCTCACATGAGTTGTAGAT
1 CGGTATGCTCATCG--AGCTGTAAATCAGTATGCTCACATGAGCTGTAGAT
* * *
53301896 CGGTATGCTCTTACGAGCTATAAATCAGTATGCTCACACGAGCTGT
1 CGGTATGCTCAT-CGAGCTGTAAATCAGTATGCTCACATGAGCTGT
53301942 GGGTCAAAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
48 3 0.04
49 1 0.01
50 72 0.91
51 1 0.01
52 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (49 bp):
CGGTATGCTCATCGAGCTGTAAATCAGTATGCTCACATGAGCTGTAGAT
Found at i:53306645 original size:20 final size:20
Alignment explanation
Indices: 53306620--53306658 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
53306610 AACATTCAAA
53306620 ATACCATAATCACAA-CCAAG
1 ATACCATAA-CACAAGCCAAG
53306640 ATACCATAACACAAGCCAA
1 ATACCATAACACAAGCCAA
53306659 ACCATATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.51, C:0.31, G:0.05, T:0.13
Consensus pattern (20 bp):
ATACCATAACACAAGCCAAG
Found at i:53307790 original size:25 final size:25
Alignment explanation
Indices: 53307762--53307980 Score: 153
Period size: 25 Copynumber: 8.8 Consensus size: 25
53307752 TCCTGTACAT
*
53307762 GTATGCTCATACGAGCTGTGAATCG
1 GTATGCTCATACGAGCTGTAAATCG
* * * *
53307787 GTATGCTCATTCGAGTTTTAGATCG
1 GTATGCTCATACGAGCTGTAAATCG
*
53307812 ATATGATCTCA-A-GAGCTGTAAATCG
1 GTATG--CTCATACGAGCTGTAAATCG
* * * *
53307837 GTATGCTCACATGAGTTGTAGATCG
1 GTATGCTCATACGAGCTGTAAATCG
* *
53307862 GTATGCTC-TCACAAGCTGTAGATCG
1 GTATGCTCAT-ACGAGCTGTAAATCG
** * **
53307887 GTATAATC-TAATGAGCTGTAAATTA
1 GTATGCTCAT-ACGAGCTGTAAATCG
* *
53307912 GTATGCTCACACGAGCTGTAGA-CTG
1 GTATGCTCATACGAGCTGTAAATC-G
*
53307937 GTATGCTC-TCACGAGCTGTAAATCA
1 GTATGCTCAT-ACGAGCTGTAAATCG
*
53307962 GTATGCTCACACGAGCTGT
1 GTATGCTCATACGAGCTGT
53307981 GGGTCTGAAC
Statistics
Matches: 148, Mismatches: 36, Indels: 20
0.73 0.18 0.10
Matches are distributed among these distances:
23 4 0.03
24 1 0.01
25 138 0.93
26 1 0.01
27 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (25 bp):
GTATGCTCATACGAGCTGTAAATCG
Found at i:53307885 original size:75 final size:75
Alignment explanation
Indices: 53307762--53307956 Score: 209
Period size: 75 Copynumber: 2.6 Consensus size: 75
53307752 TCCTGTACAT
* * * * * * *
53307762 GTATGCTCATACGAGCTGT-GAATCGGTATGCTCAT-TCGAGTTTTAGATCGATATGATCTCAA-
1 GTATGCTCACACGAGCTGTAGACT-GGTATGCTC-TCACAAGCTGTAGATCGATATAATCT-AAT
*
53307824 GAGCTGTAAATCG
63 GAGCTGTAAATCA
* * *
53307837 GTATGCTCACATGAGTTGTAGA-TCGGTATGCTCTCACAAGCTGTAGATCGGTATAATCTAATGA
1 GTATGCTCACACGAGCTGTAGACT-GGTATGCTCTCACAAGCTGTAGATCGATATAATCTAATGA
*
53307901 GCTGTAAATTA
65 GCTGTAAATCA
*
53307912 GTATGCTCACACGAGCTGTAGACTGGTATGCTCTCACGAGCTGTA
1 GTATGCTCACACGAGCTGTAGACTGGTATGCTCTCACAAGCTGTA
53307957 AATCAGTATG
Statistics
Matches: 102, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
74 3 0.03
75 96 0.94
76 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (75 bp):
GTATGCTCACACGAGCTGTAGACTGGTATGCTCTCACAAGCTGTAGATCGATATAATCTAATGAG
CTGTAAATCA
Found at i:53310661 original size:35 final size:35
Alignment explanation
Indices: 53310615--53310685 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
53310605 CTTTTTAGAA
53310615 CTTAGTTAAATCTCTTGATGTTCTTCCCGAGTTTC
1 CTTAGTTAAATCTCTTGATGTTCTTCCCGAGTTTC
53310650 CTTAGTTAAATCTCTTGATGTTCTTCCCGAGTTTC
1 CTTAGTTAAATCTCTTGATGTTCTTCCCGAGTTTC
53310685 C
1 C
53310686 AGATTCTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.45
Consensus pattern (35 bp):
CTTAGTTAAATCTCTTGATGTTCTTCCCGAGTTTC
Found at i:53310902 original size:5 final size:5
Alignment explanation
Indices: 53310892--53310919 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
53310882 GACATTACCT
53310892 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
53310920 TGCAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:53313701 original size:12 final size:12
Alignment explanation
Indices: 53313684--53313709 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53313674 ATATCCGACT
53313684 TTTTAAAAAGAG
1 TTTTAAAAAGAG
53313696 TTTTAAAAAGAG
1 TTTTAAAAAGAG
53313708 TT
1 TT
53313710 GGGAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (12 bp):
TTTTAAAAAGAG
Found at i:53344418 original size:9 final size:9
Alignment explanation
Indices: 53344404--53344438 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
53344394 TCCAAAATAA
*
53344404 AATAGTACT
1 AATAGTATT
53344413 AATAGTATT
1 AATAGTATT
53344422 AATAGTATT
1 AATAGTATT
53344431 AATAGTAT
1 AATAGTAT
53344439 CAACATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (9 bp):
AATAGTATT
Found at i:53346193 original size:44 final size:44
Alignment explanation
Indices: 53346145--53346381 Score: 124
Period size: 44 Copynumber: 5.1 Consensus size: 44
53346135 CTATTGTACT
* *
53346145 TTCATTCCAACCCACTGCAACTTCAGGAGTATAGGATTTGTAGC
1 TTCATTCCAACCCACTACAACTTCAGGAGTATAAGATTTGTAGC
*** * *
53346189 TTCA-TCTTGCTCCACTGCAACTTCAAGGAG-ATAAGATTCGCCATTGTAGT
1 TTCATTCCAAC-CCACTACAACTTC-AGGAGTATAAGA-T-----TTGTAGC
* *
53346239 TTCATCCCAACCCACTACAA-TTCCAGGGGTATAAGATTTGTAGC
1 TTCATTCCAACCCACTACAACTT-CAGGAGTATAAGATTTGTAGC
*** *
53346283 TTCA-TCTTGCTCCATTACAACTTCA-GAGATATAAGATTCGCTATGGTAGC
1 TTCATTCCAAC-CCACTACAACTTCAGGAG-TATAAGA-T---T-T-GTAGC
* * * * *
53346333 TTCATTTCAACCTACTACAACTTTAGGGGTATAGGATTTGTAGC
1 TTCATTCCAACCCACTACAACTTCAGGAGTATAAGATTTGTAGC
53346377 TTCAT
1 TTCAT
53346382 ATTGCTCCAC
Statistics
Matches: 144, Mismatches: 27, Indels: 44
0.67 0.13 0.20
Matches are distributed among these distances:
43 7 0.05
44 59 0.41
45 10 0.07
46 1 0.01
48 1 0.01
49 9 0.06
50 51 0.35
51 6 0.04
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (44 bp):
TTCATTCCAACCCACTACAACTTCAGGAGTATAAGATTTGTAGC
Found at i:53346235 original size:94 final size:94
Alignment explanation
Indices: 53346097--53346730 Score: 616
Period size: 94 Copynumber: 6.8 Consensus size: 94
53346087 ATGTCATAGT
* * * * *
53346097 TTCATCTTGCT-C-TTGCAATTTCTAGGAGATAATATTTGCTATTGTACTTTCATTCCAACCCAC
1 TTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTATTGTACTTTCATTCCAACCCAC
*
53346160 TGCAACTTCAGGAGTATAGGATTTGTAGC
66 TGCAACTTCAGGGGTATAGGATTTGTAGC
* * *
53346189 TTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCCATTGTAGTTTCATCCCAACCCAC
1 TTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTATTGTACTTTCATTCCAACCCAC
* *
53346254 TACAA-TTCCAGGGGTATAAGATTTGTAGC
66 TGCAACTT-CAGGGGTATAGGATTTGTAGC
* * * * * *
53346283 TTCATCTTGCTCCATTACAACTTC-AGAGATATAAGATTCGCTATGGTAGC-TTCATTTCAACCT
1 TTCATCTTGCTCCACTGCAACTTCAAG-GAGATAAGATTCGCTATTGTA-CTTTCATTCCAACCC
* *
53346346 ACTACAACTTTAGGGGTATAGGATTTGTAGC
64 ACTGCAACTTCAGGGGTATAGGATTTGTAGC
* * * * * *
53346377 TTCATATTGCTCCACTACAACTTCTAGGAGAGAAGATTCGCTATGGTAGCTTT-ATTCCGACCCA
1 TTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTATTGTA-CTTTCATTCCAACCCA
* *
53346441 CTGTAACTTCA--GG---A-G-TTTGTAAC
65 CTGCAACTTCAGGGGTATAGGATTTGTAGC
* * * * ** * * * *
53346464 TTCATATTGCTCCACTGTATCTTCAGGGAGATAAGATT-TTTCGTTGTAGTTTTATTCCAACCTA
1 TTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCT-ATTGTACTTTCATTCCAACCCA
* *
53346528 TTGCAACTTCAAGGGTATAGGATTTGTAGC
65 CTGCAACTTCAGGGGTATAGGATTTGTAGC
* * * *
53346558 TTCATCTTGCTCCACTGCAACTT-AAGGGAGATAAGATTCACCAATGTAGTTTCATTCCAACCCA
1 TTCATCTTGCTCCACTGCAACTTCAA-GGAGATAAGATTCGCTATTGTACTTTCATTCCAACCCA
* *
53346622 CTGTAACTTCAGGGGTATAGGATTTGTAGT
65 CTGCAACTTCAGGGGTATAGGATTTGTAGC
* * * * **
53346652 TTTATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTT-ATTCTGACCCA
1 TTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTATTGTA-CTTTCATTCCAACCCA
* *
53346716 CTACAACTTTAGGGG
65 CTGCAACTTCAGGGG
53346731 GATTGGAATT
Statistics
Matches: 445, Mismatches: 76, Indels: 40
0.79 0.14 0.07
Matches are distributed among these distances:
86 4 0.01
87 61 0.14
88 1 0.00
89 3 0.01
92 14 0.03
93 7 0.02
94 345 0.78
95 10 0.02
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (94 bp):
TTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCTATTGTACTTTCATTCCAACCCAC
TGCAACTTCAGGGGTATAGGATTTGTAGC
Found at i:53346394 original size:44 final size:44
Alignment explanation
Indices: 53346250--53346400 Score: 130
Period size: 44 Copynumber: 3.3 Consensus size: 44
53346240 TCATCCCAAC
53346250 CCACTACAA-TTCCAGGGGTATAAGATTTGTAGCTTCATCTTGCT
1 CCACTACAACTTCCAGGGGTATAAGATTTGTAGCTTCAT-TTGCT
* * * *
53346294 CCATTACAACTT-CAGAGATATAAGATTCGCTATGGTAGCTTCATTT-CAA
1 CCACTACAACTTCCAGGGGTATAAGA-T---T-T-GTAGCTTCATTTGC-T
* *
53346343 CCTACTACAACTT-TAGGGGTATAGGATTTGTAGCTTCATATTGCT
1 CC-ACTACAACTTCCAGGGGTATAAGATTTGTAGCTTCAT-TTGCT
53346388 CCACTACAACTTC
1 CCACTACAACTTC
53346401 TAGGAGAGAA
Statistics
Matches: 85, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
44 39 0.46
45 8 0.09
46 2 0.02
48 2 0.02
49 6 0.07
50 28 0.33
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (44 bp):
CCACTACAACTTCCAGGGGTATAAGATTTGTAGCTTCATTTGCT
Found at i:53346570 original size:181 final size:180
Alignment explanation
Indices: 53346138--53346693 Score: 550
Period size: 181 Copynumber: 3.0 Consensus size: 180
53346128 ATATTTGCTA
* *
53346138 TTGTACTTTCATTCCAACCCACTGCAACTTC-AGGAGTATAGGATTTGTAGCTTCATCTTGCTCC
1 TTGTAGTTTCATTCCAACCTACTGCAACTTCAAGG-GTATAGGATTTGTAGCTTCATCTTGCTCC
* * **
53346202 ACTGCAACTTCAAGGAGATAAGATTCGCCATTGTAGTTTCATCCCAACCCACTACAA-TTCCAGG
65 ACTGCAACTTCAAGGAGATAAGATTCG-CAATGTAGTTTCATTCCAACCCACTGTAACTT-CA--
* * * *
53346266 GGTATAAGATTTGTAGCTTCATCTTGCTCCATTACAACTTCAGAGATATAAGATTCGC
126 GG---AAGATTTGTAACTTCATATTGCTCCACTACAACTTCAGAGAGATAAGATTCGC
* * * * * *
53346324 TATGGTAGCTTCATTTCAACCTACTACAACTTTAGGGGTATAGGATTTGTAGCTTCATATTGCTC
1 T-T-GTAGTTTCATTCCAACCTACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCATCTTGCTC
* * * * *
53346389 CACTACAACTTCTAGGAGAGAAGATTCGCTATGGTAGCTTT-ATTCCGACCCACTGTAACTTCAG
64 CACTGCAACTTCAAGGAGATAAGATTCGCAAT-GTAG-TTTCATTCCAACCCACTGTAACTTCAG
** * *
53346453 G-AG-TTTGTAACTTCATATTGCTCCACTGTATCTTCAGGGAGATAAGATTTTTCG-
127 GAAGATTTGTAACTTCATATTGCTCCACTACAACTTCAGAGAGATAAGA---TTCGC
* *
53346507 TTGTAGTTTTATTCCAACCTATTGCAACTTCAAGGGTATAGGATTTGTAGCTTCATCTTGCTCCA
1 TTGTAGTTTCATTCCAACCTACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCATCTTGCTCCA
*
53346572 CTGCAACTT-AAGGGAGATAAGATTCACCAATGTAGTTTCATTCCAACCCACTGTAACTTCAGGG
66 CTGCAACTTCAA-GGAGATAAGATTC-GCAATGTAGTTTCATTCCAACCCACTGTAACTTCA--G
** * * * * *
53346636 GTATAGGATTTGTAGTTTTATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGC
127 G-A-A-GATTTGTAACTTCATATTGCTCCACTACAACTTCAGAGAGATAAGATTCGC
53346693 T
1 T
53346694 ATGGTAGCTT
Statistics
Matches: 304, Mismatches: 46, Indels: 40
0.78 0.12 0.10
Matches are distributed among these distances:
180 4 0.01
181 136 0.45
182 6 0.02
183 3 0.01
184 4 0.01
185 4 0.01
186 5 0.02
187 4 0.01
188 131 0.43
189 7 0.02
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (180 bp):
TTGTAGTTTCATTCCAACCTACTGCAACTTCAAGGGTATAGGATTTGTAGCTTCATCTTGCTCCA
CTGCAACTTCAAGGAGATAAGATTCGCAATGTAGTTTCATTCCAACCCACTGTAACTTCAGGAAG
ATTTGTAACTTCATATTGCTCCACTACAACTTCAGAGAGATAAGATTCGC
Found at i:53346578 original size:44 final size:44
Alignment explanation
Indices: 53346529--53346674 Score: 125
Period size: 44 Copynumber: 3.2 Consensus size: 44
53346519 TCCAACCTAT
*
53346529 TGCAACTTCAAGGGTATAGGATTTGTAGCTTCATCTTGCTCCAC
1 TGCAACTTCAAGGGTATAGGATTTGTAGTTTCATCTTGCTCCAC
* * ***
53346573 TGCAACTT-AAGGGAGATAAGATTCACCAATGTAGTTTCATTCCAAC-CCAC
1 TGCAACTTCAAGGG-TATAGGATT------TGTAGTTTCA-TCTTGCTCCAC
* * *
53346623 TGTAACTTCAGGGGTATAGGATTTGTAGTTTTATCTTGCTCCAC
1 TGCAACTTCAAGGGTATAGGATTTGTAGTTTCATCTTGCTCCAC
53346667 TGCAACTT
1 TGCAACTT
53346675 TAGGGAGATA
Statistics
Matches: 77, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
43 8 0.10
44 35 0.45
50 27 0.35
51 7 0.09
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (44 bp):
TGCAACTTCAAGGGTATAGGATTTGTAGTTTCATCTTGCTCCAC
Found at i:53346638 original size:275 final size:274
Alignment explanation
Indices: 53346177--53346717 Score: 710
Period size: 275 Copynumber: 2.0 Consensus size: 274
53346167 TCAGGAGTAT
* *
53346177 AGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCCATTGTAGTTTC
1 AGGATTTGTAACTTCATATTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCCATTGTAGTTTC
* * *
53346242 ATCCCAACCCACTACAATTCCAGGGGTATAAGATTTGTAGCTTCATCTTGCTCCATTACAACTTC
66 ATCCCAACCCACTACAATTCCAAGGGTATAAGATTTGTAGCTTCATCTTGCTCCACTACAACTTA
* * * * * *
53346307 AGAGATATAAGATTCGCTATGGTAGCTTCATTTCAACCTACTACAACTTTAGGGGTATAGGATTT
131 AGAGAGATAAGATTCCCAATGGTAGCTTCATTCCAACCCACTACAACTTCAGGGGTATAGGATTT
53346372 GTAGCTTCATATTGCTCCACTACAACTTCTA-GGAGAGAAGATTCGCTATGGTAGCTTTATTCCG
196 GTAGCTTCATATTGCTCCACTACAACTT-TAGGGAGAGAAGATTCGCTATGGTAGCTTTATTCCG
53346436 ACCCACTGTAACTTC
260 ACCCACTGTAACTTC
* * * *** *
53346451 AGGAGTTTGTAACTTCATATTGCTCCACTGTATCTTCAGGGAGATAAGATTTTTCGTTGTAGTTT
1 AGGA-TTTGTAACTTCATATTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCCATTGTAGTTT
* * * * * * *
53346516 TATTCCAACCTATTGCAACTT-CAAGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACT
65 CATCCCAACCCACTACAA-TTCCAAGGGTATAAGATTTGTAGCTTCATCTTGCTCCACTACAACT
* * **
53346580 TAAGGGAGATAAGATTCACCAAT-GTAGTTTCATTCCAACCCACTGTAACTTCAGGGGTATAGGA
129 TAAGAGAGATAAGATTC-CCAATGGTAGCTTCATTCCAACCCACTACAACTTCAGGGGTATAGGA
* * * * *
53346644 TTTGTAGTTTTATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTCGCTATGGTAGCTTTATTC
193 TTTGTAGCTTCATATTGCTCCACTACAACTTTAGGGAGAGAAGATTCGCTATGGTAGCTTTATTC
*
53346709 TGACCCACT
258 CGACCCACT
53346718 ACAACTTTAG
Statistics
Matches: 228, Mismatches: 35, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
274 6 0.03
275 217 0.95
276 5 0.02
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (274 bp):
AGGATTTGTAACTTCATATTGCTCCACTGCAACTTCAAGGAGATAAGATTCGCCATTGTAGTTTC
ATCCCAACCCACTACAATTCCAAGGGTATAAGATTTGTAGCTTCATCTTGCTCCACTACAACTTA
AGAGAGATAAGATTCCCAATGGTAGCTTCATTCCAACCCACTACAACTTCAGGGGTATAGGATTT
GTAGCTTCATATTGCTCCACTACAACTTTAGGGAGAGAAGATTCGCTATGGTAGCTTTATTCCGA
CCCACTGTAACTTC
Found at i:53353815 original size:41 final size:41
Alignment explanation
Indices: 53353758--53353840 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
53353748 GGGAAAATGT
* *
53353758 TCAGCATGTTATAAAACATAAGAATAAGAGATGAAGTTTAA
1 TCAGCAGGTCATAAAACATAAGAATAAGAGATGAAGTTTAA
* *
53353799 TCAGCAGGTCATAAAACATAATAATATGAGATGAAGTTTAA
1 TCAGCAGGTCATAAAACATAAGAATAAGAGATGAAGTTTAA
53353840 T
1 T
53353841 TTCCGAGCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (41 bp):
TCAGCAGGTCATAAAACATAAGAATAAGAGATGAAGTTTAA
Found at i:53354291 original size:35 final size:35
Alignment explanation
Indices: 53354251--53354318 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
53354241 AAAGAGGTCC
* *
53354251 CATGTAAGACCATGTTTGGGACATAGCGTTGGCCA
1 CATGTAAGACCATGTCTGGGACATAGCATTGGCCA
*
53354286 CATGTAAGACCATGTCTGGGACATGGCATTGGC
1 CATGTAAGACCATGTCTGGGACATAGCATTGGC
53354319 ACCGAGATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (35 bp):
CATGTAAGACCATGTCTGGGACATAGCATTGGCCA
Found at i:53354363 original size:50 final size:51
Alignment explanation
Indices: 53354286--53354420 Score: 209
Period size: 50 Copynumber: 2.7 Consensus size: 51
53354276 GCGTTGGCCA
**
53354286 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG-AGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACATCC
* * *
53354336 CCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACATCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACATCC
*
53354387 CATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
53354421 TGTTATTATC
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
50 41 0.54
51 35 0.46
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (51 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACATCC
Found at i:53358040 original size:25 final size:24
Alignment explanation
Indices: 53357973--53358048 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 24
53357963 TGACATTAAC
53357973 AAAATAACAACATAAATAATGAAAT
1 AAAATAACAA-ATAAATAATGAAAT
*
53357998 AAAATAA-ATATAATATAATGAATAT
1 AAAATAACAAATAA-ATAATGAA-AT
53358023 AACAATAACAAAT-AATAATGATAAT
1 AA-AATAACAAATAAATAATGA-AAT
53358048 A
1 A
53358049 GTTATTCAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
23 4 0.09
24 9 0.20
25 21 0.48
26 7 0.16
27 3 0.07
ACGTcount: A:0.66, C:0.05, G:0.04, T:0.25
Consensus pattern (24 bp):
AAAATAACAAATAAATAATGAAAT
Found at i:53360010 original size:22 final size:23
Alignment explanation
Indices: 53359966--53360010 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
53359956 AATAAAAAAA
*
53359966 ATTTATATATAAAAATTATATTT
1 ATTTATATATAAAAATTAGATTT
53359989 ATTTA-AT-TAAAAACTTAGATTT
1 ATTTATATATAAAAA-TTAGATTT
53360011 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 9 0.45
23 5 0.25
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTTATATATAAAAATTAGATTT
Found at i:53370478 original size:18 final size:19
Alignment explanation
Indices: 53370455--53370509 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 19
53370445 TTTTATTGCT
53370455 AGTGGTTTATCCACAAC-A
1 AGTGGTTTATCCACAACAA
**
53370473 AGTGGTTCGTCCACAACGATA
1 AGTGGTTTATCCACAAC-A-A
53370494 AGTGGTTTATCCACAA
1 AGTGGTTTATCCACAA
53370510 AGTGGTGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 15 0.50
21 15 0.50
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (19 bp):
AGTGGTTTATCCACAACAA
Found at i:53371861 original size:6 final size:6
Alignment explanation
Indices: 53371850--53371979 Score: 260
Period size: 6 Copynumber: 21.7 Consensus size: 6
53371840 TAAATCAATA
53371850 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
53371898 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
53371946 TTAATT TTAATT TTAATT TTAATT TTAATT TTAA
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAA
53371980 AATATAAATA
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 124 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTAATT
Found at i:53382328 original size:37 final size:37
Alignment explanation
Indices: 53382287--53382360 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
53382277 CGCAATCCAC
53382287 AGCAATAGTGCAAAAAACTTGAACGCCAATAAATGTG
1 AGCAATAGTGCAAAAAACTTGAACGCCAATAAATGTG
* *
53382324 AGCAATAGTGCAAAAAACTTGACCGCCTATAAATGTG
1 AGCAATAGTGCAAAAAACTTGAACGCCAATAAATGTG
53382361 TAATCGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (37 bp):
AGCAATAGTGCAAAAAACTTGAACGCCAATAAATGTG
Found at i:53383661 original size:16 final size:16
Alignment explanation
Indices: 53383637--53383680 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
53383627 AATCACCATT
53383637 TGGCAAACTCTAAGGC
1 TGGCAAACTCTAAGGC
* *
53383653 TGGCGAACTCTAGGGC
1 TGGCAAACTCTAAGGC
*
53383669 TTGGCAGACTCT
1 -TGGCAAACTCT
53383681 TTTATGAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (16 bp):
TGGCAAACTCTAAGGC
Found at i:53388196 original size:36 final size:36
Alignment explanation
Indices: 53388143--53388214 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
53388133 CCCCTCTAGA
*
53388143 CTTGATAGACGGTATATTAGCCTTTCAATCAATTTG
1 CTTGATAGACGGCATATTAGCCTTTCAATCAATTTG
*
53388179 CTTGATAGATGGCATATTAGCCTTTCAATCAATTTG
1 CTTGATAGACGGCATATTAGCCTTTCAATCAATTTG
53388215 ATTACTTTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (36 bp):
CTTGATAGACGGCATATTAGCCTTTCAATCAATTTG
Found at i:53388751 original size:116 final size:116
Alignment explanation
Indices: 53388538--53388903 Score: 651
Period size: 116 Copynumber: 3.1 Consensus size: 116
53388528 TGTTGATGAA
*
53388538 GAGCCTTGAGGGCTTGAGGAGCCTACACTCGAAGTTACTTTGGAGGCTTACAGTTTTCCTTAACT
1 GAGCCTTG-GGGCTTGAGAAGCCTACACTCGAAGTTACTTTGGAGGCTTACAGTTTTCCTTAACT
53388603 ACTTGAACTCCCCTTAAATATGAAGTACTGGCTTTCAAGAATACACGACAAG
65 ACTTGAACTCCCCTTAAATATGAAGTACTGGCTTTCAAGAATACACGACAAG
53388655 GAGCCTTGGGGCTTGAGAAGCCTACACTCGAAGTTACTTTGGAGGCTTACAGTTTTCCTTAACTA
1 GAGCCTTGGGGCTTGAGAAGCCTACACTCGAAGTTACTTTGGAGGCTTACAGTTTTCCTTAACTA
53388720 CTTGAACTCCCCTTAAATATGAAGTACTGGCTTTCAAGAATACACGACAAG
66 CTTGAACTCCCCTTAAATATGAAGTACTGGCTTTCAAGAATACACGACAAG
*
53388771 GAGCCTTGGGGCTTGAGAAGCCTACACTCGAAGTTACTTTGGAGGCTTATAGTTTTCCTTAACTA
1 GAGCCTTGGGGCTTGAGAAGCCTACACTCGAAGTTACTTTGGAGGCTTACAGTTTTCCTTAACTA
* * * *
53388836 ATTGAACTCCCTTTAAATATGAAGTATTGCCTTTCAAGAATACACGACAAG
66 CTTGAACTCCCCTTAAATATGAAGTACTGGCTTTCAAGAATACACGACAAG
* *
53388887 AAGCCTTAGGGCTTGAG
1 GAGCCTTGGGGCTTGAG
53388904 GTGTTTAGGC
Statistics
Matches: 241, Mismatches: 8, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
116 233 0.97
117 8 0.03
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (116 bp):
GAGCCTTGGGGCTTGAGAAGCCTACACTCGAAGTTACTTTGGAGGCTTACAGTTTTCCTTAACTA
CTTGAACTCCCCTTAAATATGAAGTACTGGCTTTCAAGAATACACGACAAG
Found at i:53400112 original size:20 final size:20
Alignment explanation
Indices: 53400080--53400133 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
53400070 CTTGCTTAAC
* *
53400080 AAAAATTACAAAATAATTTTT
1 AAAAATTTCAAAAT-ATTTAT
53400101 AAAAATTT-AAAATATTTAT
1 AAAAATTTCAAAATATTTAT
*
53400120 AAATATTTCAAAAT
1 AAAAATTTCAAAAT
53400134 TTATATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 12 0.41
20 10 0.34
21 7 0.24
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATTTCAAAATATTTAT
Found at i:53401719 original size:26 final size:27
Alignment explanation
Indices: 53401683--53401738 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
53401673 TAAAAAACAT
* * *
53401683 AAAAATTAAAAA-AATATTTTTTTTAA
1 AAAAAATAAAAATAATAATTTGTTTAA
*
53401709 AAAAAATAAAAATTATAATTTGTTTAA
1 AAAAAATAAAAATAATAATTTGTTTAA
53401736 AAA
1 AAA
53401739 TAAAAATATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
AAAAAATAAAAATAATAATTTGTTTAA
Found at i:53404992 original size:125 final size:123
Alignment explanation
Indices: 53404752--53405031 Score: 384
Period size: 125 Copynumber: 2.3 Consensus size: 123
53404742 TTATTTCGAG
** *
53404752 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGTATGCTATCAAAGAAGAAATTAT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTGATACCAGGATGCTATCAAAGAAGAAATTAT
* ** *
53404816 GAAATCGTGCCCTCGTGGACGCGCTTTCGGTACAGTTGGTCATGTAAGAAATAATTTTTT
65 GAAATCGCGCCCTCGTGGACGCAATTTCGCTACAGTTGGTCATGTAAGAAATAA-TTTTT
* * * *
53404876 TTGACGTTTTTTGAGCAAATAGTATAAAATCGGTGATACCAGGATGCTAT-ATGAGAAGAAATTG
1 TTGACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCA-AAGAAGAAATTA
*
53404940 TGAAATCGCGCCCTCGTGGACGCAATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTT
64 TGAAATCGCGCCCTCGTGGACGCAATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTT
* *
53405000 TTGACGTTTCTGAGCAAATAGTGTCAAATCGC
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGC
53405032 GCCCTCGTGG
Statistics
Matches: 137, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
123 22 0.16
124 18 0.13
125 96 0.70
126 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATCAAAGAAGAAATTATG
AAATCGCGCCCTCGTGGACGCAATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTT
Found at i:53408251 original size:17 final size:18
Alignment explanation
Indices: 53408214--53408251 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
53408204 GCCCAAAAAC
*
53408214 TTTTGTTAATTAAAATGG
1 TTTTGTTAATTAAAATAG
*
53408232 TTTT-TTAATTAAATTAG
1 TTTTGTTAATTAAAATAG
53408249 TTT
1 TTT
53408252 AGGGTTAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (18 bp):
TTTTGTTAATTAAAATAG
Found at i:53408325 original size:58 final size:58
Alignment explanation
Indices: 53408234--53409375 Score: 1746
Period size: 58 Copynumber: 19.7 Consensus size: 58
53408224 TAAAATGGTT
*** * * *
53408234 TTTTAATTAAATTAGTTTAGGGTTAGGGTTTTTAATTAAAATGGGTTAGGG-TTAGGG
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
*** * * ***
53408291 TTTTTAATTAAATTAGGTTAGAGTTTAGGG-TTTTAATTAAATTAAACTAGGG-TTAGGG
1 -TTTTAATTAAATTAAACTAG-GGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
* *** *
53408349 TTTTTAATCAAATTAGGTTAGGGTTTAGGG-TTTTAATTAAATTAGGTTAGGGTTTAGGG
1 -TTTTAATTAAATTAAACTAGGG-TTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
53408408 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
53408466 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
53408524 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
53408582 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
53408640 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
53408698 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
53408756 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
53408814 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
53408872 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
53408930 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
53408988 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
53409046 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
* * * *
53409104 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATTAAAATGGGTTAGGG-TTAGAGT
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAG-GG
* * ****
53409162 TTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAAACCAGGG-TTAGGG
1 TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
* **** * ** *
53409219 TTTTTAATTAAAATGGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAAGG-TTAGGG
1 -TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
* * *
53409277 TTTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATTAAAAT-GGATTAGGG-TTGGGG
1 -TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGG-TTAGGGTTTAGGG
* *
53409335 TTTTTAATTAAATTAAATTA-GGTTAGGGTTTTGAATCAAAT
1 -TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAAT
53409376 AATATCAAAA
Statistics
Matches: 1027, Mismatches: 50, Indels: 15
0.94 0.05 0.01
Matches are distributed among these distances:
57 30 0.03
58 984 0.96
59 13 0.01
ACGTcount: A:0.31, C:0.03, G:0.24, T:0.42
Consensus pattern (58 bp):
TTTTAATTAAATTAAACTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTTAGGG
Found at i:53408386 original size:24 final size:27
Alignment explanation
Indices: 53408239--53409196 Score: 478
Period size: 29 Copynumber: 33.2 Consensus size: 27
53408229 TGGTTTTTTA
*
53408239 ATTAAATTAGTTTAGGG-TTAGGGTTTTT
1 ATTAAATTAGGTTAGGGTTTAGGG--TTT
* *
53408267 AATTAAAATGGGTTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
*
53408296 AATTAAATTAGGTTAGAGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
***
53408325 AATTAAATTAAACTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
*
53408354 AATCAAATTAGGTTAGGGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
53408383 AATTAAATTAGGTTAGGGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
***
53408412 AATTAAATTAAACTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
*
53408441 AATCAAATTAGGTTAGGGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
***
53408470 AATTAAATTAAACTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
*
53408499 AATCAAATTAGGTTAGGGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
***
53408528 AATTAAATTAAACTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
*
53408557 AATCAAATTAGGTTAGGGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
***
53408586 AATTAAATTAAACTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
*
53408615 AATCAAATTAGGTTAGGGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
***
53408644 AATTAAATTAAACTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
*
53408673 AATCAAATTAGGTTAGGGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
***
53408702 AATTAAATTAAACTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
*
53408731 AATCAAATTAGGTTAGGGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
***
53408760 AATTAAATTAAACTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
*
53408789 AATCAAATTAGGTTAGGGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
***
53408818 AATTAAATTAAACTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
*
53408847 AATCAAATTAGGTTAGGGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
***
53408876 AATTAAATTAAACTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
*
53408905 AATCAAATTAGGTTAGGGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
***
53408934 AATTAAATTAAACTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
*
53408963 AATCAAATTAGGTTAGGGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
***
53408992 AATTAAATTAAACTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
*
53409021 AATCAAATTAGGTTAGGGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
***
53409050 AATTAAATTAAACTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
*
53409079 AATCAAATTAGGTTAGGGTTTAGGGTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG-TTT
***
53409108 AATTAAATTAAACTAGGG-TTAGGGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAGGG--TTT
* * *
53409137 AATTAAAATGGGTTAGGG-TTAGAGTTTTT
1 -ATTAAATTAGGTTAGGGTTTAG-G-GTTT
**
53409166 AATTAAATTAAATTAGGG-TTAGGGTTT
1 -ATTAAATTAGGTTAGGGTTTAGGGTTT
53409193 -TTAA
1 ATTAA
53409197 TTAAATTAAA
Statistics
Matches: 774, Mismatches: 125, Indels: 64
0.80 0.13 0.07
Matches are distributed among these distances:
25 4 0.01
27 3 0.00
28 85 0.11
29 597 0.77
30 85 0.11
ACGTcount: A:0.31, C:0.03, G:0.24, T:0.42
Consensus pattern (27 bp):
ATTAAATTAGGTTAGGGTTTAGGGTTT
Found at i:53410548 original size:7 final size:7
Alignment explanation
Indices: 53410538--53410562 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53410528 TTATATACAT
53410538 AATACTA
1 AATACTA
53410545 AATACTA
1 AATACTA
53410552 AATACTA
1 AATACTA
53410559 AATA
1 AATA
53410563 TCAATCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:53411692 original size:29 final size:29
Alignment explanation
Indices: 53411651--53411709 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
53411641 TTGAAAGTAT
53411651 TAAAAATTTTAAAATTAT-TTTAAAAAAA
1 TAAAAATTTTAAAATTATCTTTAAAAAAA
*
53411679 TAAAAATATTTAAAATTTTCTTTAAAAAAA
1 TAAAAAT-TTTAAAATTATCTTTAAAAAAA
53411709 T
1 T
53411710 GAAATTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 7 0.25
29 10 0.36
30 11 0.39
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (29 bp):
TAAAAATTTTAAAATTATCTTTAAAAAAA
Found at i:53411771 original size:22 final size:21
Alignment explanation
Indices: 53411743--53411793 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
53411733 AAATATGGAT
53411743 TTGAGAGATTTTGTGAAGGAAA
1 TTGAGAGATTTTG-GAAGGAAA
*
53411765 TTGAGAGGATTTTGGAAGGAAT
1 TTGAGA-GATTTTGGAAGGAAA
53411787 TTGAGAG
1 TTGAGAG
53411794 TTTAAGAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.70
23 7 0.26
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.31
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:53412151 original size:29 final size:29
Alignment explanation
Indices: 53412095--53412150 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
53412085 TTCGCGGAAT
*
53412095 TGGCCCATTCCGGTAAATAATTAAAAAAG
1 TGGCCCATTCCGATAAATAATTAAAAAAG
* *
53412124 TGGCCCATTTCGATAAAT-TTTAAAAAA
1 TGGCCCATTCCGATAAATAATTAAAAAA
53412151 AATGGTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (29 bp):
TGGCCCATTCCGATAAATAATTAAAAAAG
Found at i:53412840 original size:20 final size:21
Alignment explanation
Indices: 53412789--53412841 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
53412779 AAAAAACTTT
* *
53412789 AAAATTCAAAAAATAAAACTA
1 AAAATTCAAAATATAAAACAA
*
53412810 AAAA-TAAAAATAT-AAACAA
1 AAAATTCAAAATATAAAACAA
53412829 AAAATTCAAAATA
1 AAAATTCAAAATA
53412842 AAATGTTATC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 9 0.33
20 14 0.52
21 4 0.15
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.19
Consensus pattern (21 bp):
AAAATTCAAAATATAAAACAA
Found at i:53415201 original size:12 final size:12
Alignment explanation
Indices: 53415184--53415217 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53415174 TTTATCAAGA
53415184 TAAATATTATAT
1 TAAATATTATAT
*
53415196 TAAATATAATAT
1 TAAATATTATAT
*
53415208 TAAATCTTAT
1 TAAATATTAT
53415218 TAAAATAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (12 bp):
TAAATATTATAT
Found at i:53415298 original size:20 final size:18
Alignment explanation
Indices: 53415251--53415299 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
53415241 CAAGATAAAC
53415251 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
53415268 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
53415288 ATTAAATTAATA
1 ATTAAATTAATA
53415300 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:53415359 original size:62 final size:64
Alignment explanation
Indices: 53415151--53415359 Score: 178
Period size: 62 Copynumber: 3.2 Consensus size: 64
53415141 ACTTAATTAC
* * * * * *
53415151 TTTAATATTATATTAATATAATATTTATCAAGATAAATATTATATTAAATATAATATTAAATCT
1 TTTAAAATAATATTAATAAAATATCTATCAAGATAAATATTAAATTAAATTTAATATTAAATCT
* *** *
53415215 TATTAAAATAATA-GAAT-GTTTATCTA-CAAGATAAACATTAAATTAAATTTAATATTAAGATA
1 T-TTAAAATAATATTAATAAAATATCTATCAAGATAAATATTAAATTAAATTTAATATT---A-A
*
53415277 ATCAC
61 ATC-T
* * *
53415282 TTTAATATTAA-ATTAATAAAATA-CTATTAAGATAAGTATTAAATTAAATTTAATATTAAA-CT
1 TTTAA-AATAATATTAATAAAATATCTATCAAGATAAATATTAAATTAAATTTAATATTAAATCT
53415344 TTTAAAATAATATTAA
1 TTTAAAATAATATTAA
53415360 ACTATCTAGT
Statistics
Matches: 113, Mismatches: 21, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
61 4 0.04
62 37 0.33
63 6 0.05
64 6 0.05
65 11 0.10
66 9 0.08
67 11 0.10
68 29 0.26
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (64 bp):
TTTAAAATAATATTAATAAAATATCTATCAAGATAAATATTAAATTAAATTTAATATTAAATCT
Found at i:53415998 original size:16 final size:16
Alignment explanation
Indices: 53415977--53416007 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
53415967 CTATGCATGC
53415977 AAAATATAAAAGACAG
1 AAAATATAAAAGACAG
53415993 AAAATATAAAAGACA
1 AAAATATAAAAGACA
53416008 TAATAGTGAA
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:0.71, C:0.06, G:0.10, T:0.13
Consensus pattern (16 bp):
AAAATATAAAAGACAG
Found at i:53416913 original size:11 final size:12
Alignment explanation
Indices: 53416893--53416917 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53416883 AAAATTATCA
53416893 TTTTGTTTTTTT
1 TTTTGTTTTTTT
53416905 TTTTGTTTTTTT
1 TTTTGTTTTTTT
53416917 T
1 T
53416918 CCATCATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:53419939 original size:31 final size:31
Alignment explanation
Indices: 53419904--53419976 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
53419894 AAATGGTAAT
53419904 ATAAGTGACTAAAATGTAACCTG-AGTCAAAC
1 ATAAGTGACTAAAATGTAACCTGAAG-CAAAC
**
53419935 ATAAGTGACTAAAATGTAATTTGAAGCAAAC
1 ATAAGTGACTAAAATGTAACCTGAAGCAAAC
*
53419966 AAAAGTGACTA
1 ATAAGTGACTA
53419977 TTTTTGTAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 36 0.95
32 2 0.05
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.23
Consensus pattern (31 bp):
ATAAGTGACTAAAATGTAACCTGAAGCAAAC
Found at i:53420421 original size:23 final size:23
Alignment explanation
Indices: 53420385--53420439 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
53420375 AATTTGGAAC
53420385 AAAAT-TAAATTTTAAATAATGTA
1 AAAATATAAATTTTAAATAATG-A
* *
53420408 AAAATATAAA-TTTAACTTATGA
1 AAAATATAAATTTTAAATAATGA
*
53420430 AAAACATAAA
1 AAAATATAAA
53420440 AAATAGTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.36
23 14 0.50
24 4 0.14
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (23 bp):
AAAATATAAATTTTAAATAATGA
Found at i:53420585 original size:16 final size:15
Alignment explanation
Indices: 53420559--53420590 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
53420549 CATTTATTTA
53420559 TTAAAAATATTACAT
1 TTAAAAATATTACAT
53420574 TTAAAGAATATTACAT
1 TTAAA-AATATTACAT
53420590 T
1 T
53420591 AACACACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (15 bp):
TTAAAAATATTACAT
Found at i:53420592 original size:15 final size:14
Alignment explanation
Indices: 53420558--53420592 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
53420548 ACATTTATTT
53420558 ATTAAAAATATTAC
1 ATTAAAAATATTAC
53420572 ATTTAAAGAATATTAC
1 A-TTAAA-AATATTAC
53420588 ATTAA
1 ATTAA
53420593 CACACTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 9 0.47
16 9 0.47
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (14 bp):
ATTAAAAATATTAC
Found at i:53422520 original size:9 final size:9
Alignment explanation
Indices: 53422506--53422530 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53422496 ACATAGATGT
53422506 GACTGACTG
1 GACTGACTG
53422515 GACTGACTG
1 GACTGACTG
53422524 GACTGAC
1 GACTGAC
53422531 AGTACATCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (9 bp):
GACTGACTG
Found at i:53432278 original size:23 final size:26
Alignment explanation
Indices: 53432250--53432310 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
53432240 ATCAGCTCTT
53432250 ATGAGCTTACCG-T-TTCAGCTC-G-
1 ATGAGCTTACCGTTCTTCAGCTCGGA
53432272 ATAGAGCTTACCGTTCTTCAGCTCGGA
1 AT-GAGCTTACCGTTCTTCAGCTCGGA
53432299 ATGAGCTTACCG
1 ATGAGCTTACCG
53432311 ATCATGGCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
22 2 0.06
23 10 0.29
24 1 0.03
25 8 0.24
26 11 0.32
27 2 0.06
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (26 bp):
ATGAGCTTACCGTTCTTCAGCTCGGA
Found at i:53432309 original size:26 final size:22
Alignment explanation
Indices: 53432241--53432310 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 22
53432231 TATCGATATA
*
53432241 TCAGCTCTTATGAGCTTACCGTT
1 TCAGCTC-GATGAGCTTACCGTT
53432264 TCAGCTCGATAGAGCTTACCGTTCT
1 TCAGCTCGAT-GAGCTTACCG-T-T
53432289 TCAGCTCGGAATGAGCTTACCG
1 TCAGCTC-G-ATGAGCTTACCG
53432311 ATCATGGCTC
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
22 2 0.05
23 17 0.41
24 1 0.02
25 8 0.20
26 11 0.27
27 2 0.05
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.31
Consensus pattern (22 bp):
TCAGCTCGATGAGCTTACCGTT
Found at i:53443887 original size:190 final size:191
Alignment explanation
Indices: 53443449--53444027 Score: 836
Period size: 190 Copynumber: 3.0 Consensus size: 191
53443439 GGCTTCTTGG
* * * *
53443449 TATATTTTATTAGTTAGTCGAATGATGTTGATTTCTTATACTTTTACATTTCTTTACTTAATTGT
1 TATATTTTATTAGTTAGCCAAATGATTTTGATTTCTTATACTTTTACATTTCTTTCCTTAATTGT
* * * *
53443514 TGCATTTTCTCCATGGATATATCCTCATTCAATTGTTAGCTTTGATTAATGTTGTCAGGATCAAT
66 TGCATTTTCTCCATGAATATATCCTCATTCAACTGCTAGCTTTGATTAATGTTGTCAGGATCAGT
* * * *
53443579 TGCAGTTTTGGTACTATGTTGTTGCTTGCCACTACAAGAAATTTTGTTTATAGTGGCATTTTT
131 TGCACTTCTGGTACCA--TTGTTGCTTGCCACTACAAGAAATTCTGTTTATAGTGGCATTTTT
* * *
53443642 TAAATATTTTATTAGTTAGCCAAATGATTTTGGTTTCTTATACTTTTATATTTCTTTCCTTAACT
1 T--ATATTTTATTAGTTAGCCAAATGATTTTGATTTCTTATACTTTTACATTTCTTTCCTTAATT
* * ** * ** *
53443707 ATTTCATTTTCTTTATGAATATATCCTTATTCAACAACTAGCTTTGATTAATGTTGTCAAGATCA
64 GTTGCATTTTCTCCATGAATATATCCTCATTCAACTGCTAGCTTTGATTAATGTTGTCAGGATCA
53443772 GTTGCACTTCTGGTACCA-TGTTGCTTGCCACTACAAGAAATTCTGTTTATAGTGGCATTTTT
129 GTTGCACTTCTGGTACCATTGTTGCTTGCCACTACAAGAAATTCTGTTTATAGTGGCATTTTT
* *
53443834 TATATTTTCTTAGTTAGCCAAATGATTTTGATTTCTTATACTTATACATTTCTTTCCTTAATTGT
1 TATATTTTATTAGTTAGCCAAATGATTTTGATTTCTTATACTTTTACATTTCTTTCCTTAATTGT
*
53443899 TGCATTTTCTCCATGAACATATCCTCATTCAACTGCTAGCTTTGATTAATGTTGTCAGGATCAGT
66 TGCATTTTCTCCATGAATATATCCTCATTCAACTGCTAGCTTTGATTAATGTTGTCAGGATCAGT
* * *
53443964 TGCACTTCTGGTACCATGTTGTTGCTTGCCACTATAAGAAATTCTATTTATAGAGGCATTTTT
131 TGCACTTCTGGTACCA--TTGTTGCTTGCCACTACAAGAAATTCTGTTTATAGTGGCATTTTT
53444027 T
1 T
53444028 TTCACCTTTA
Statistics
Matches: 341, Mismatches: 40, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
190 131 0.38
192 44 0.13
193 43 0.13
195 123 0.36
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (191 bp):
TATATTTTATTAGTTAGCCAAATGATTTTGATTTCTTATACTTTTACATTTCTTTCCTTAATTGT
TGCATTTTCTCCATGAATATATCCTCATTCAACTGCTAGCTTTGATTAATGTTGTCAGGATCAGT
TGCACTTCTGGTACCATTGTTGCTTGCCACTACAAGAAATTCTGTTTATAGTGGCATTTTT
Found at i:53448431 original size:191 final size:192
Alignment explanation
Indices: 53448100--53448486 Score: 749
Period size: 191 Copynumber: 2.0 Consensus size: 192
53448090 TCCAGGTCCA
53448100 TTTTCTAAATTCCTCAAAAGTTGTGGCATATGTGCACAGTATACCATACCAGACATACCTCAAAA
1 TTTTCTAAATTCCTCAAAAGTTGTGGCATATGTGCACAGTATACCATACCAGACATACCTCAAAA
53448165 AATGATATTGCAGAAAGGCGTAATCAGACTTTATTGGATATGGTTAGGAGGATGATAACTAGCTC
66 AATGATATTGCAGAAAGGCGTAATCAGACTTTATTGGATATGGTTAGGAGGATGATAACTAGCTC
53448230 CTTATTACCTATATCATTGTGGATGCATGCACTTAAAATAGTTGTATATTTATTAAATAAGG
131 CTTATTACCTATATCATTGTGGATGCATGCACTTAAAATAGTTGTATATTTATTAAATAAGG
53448292 TTTTCTAAATTCCTCAAAAGTTGTGGCATATGTGCACAGTATACCATACCAGACATACCTC-AAA
1 TTTTCTAAATTCCTCAAAAGTTGTGGCATATGTGCACAGTATACCATACCAGACATACCTCAAAA
*
53448356 AATGATATTGTAGAAAGGCGTAATCAGACTTTATTGGATATGGTTAGGAGGATGATAACTAGCTC
66 AATGATATTGCAGAAAGGCGTAATCAGACTTTATTGGATATGGTTAGGAGGATGATAACTAGCTC
*
53448421 CTTCTTACCTATATCATTGTGGATGCATGCACTTAAAATAGTTGTATATTTATTAAATAAGG
131 CTTATTACCTATATCATTGTGGATGCATGCACTTAAAATAGTTGTATATTTATTAAATAAGG
53448483 TTTT
1 TTTT
53448487 TAGTAAAACA
Statistics
Matches: 193, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
191 132 0.68
192 61 0.32
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (192 bp):
TTTTCTAAATTCCTCAAAAGTTGTGGCATATGTGCACAGTATACCATACCAGACATACCTCAAAA
AATGATATTGCAGAAAGGCGTAATCAGACTTTATTGGATATGGTTAGGAGGATGATAACTAGCTC
CTTATTACCTATATCATTGTGGATGCATGCACTTAAAATAGTTGTATATTTATTAAATAAGG
Found at i:53449959 original size:19 final size:19
Alignment explanation
Indices: 53449935--53449977 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
53449925 CTCAAGTGAA
53449935 CTTTTATCACTAAACGTCT
1 CTTTTATCACTAAACGTCT
*
53449954 CTTTTATCACTAAAGGTCT
1 CTTTTATCACTAAACGTCT
53449973 CTTTT
1 CTTTT
53449978 CTCTCAGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.47
Consensus pattern (19 bp):
CTTTTATCACTAAACGTCT
Found at i:53451579 original size:21 final size:21
Alignment explanation
Indices: 53451555--53451631 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
53451545 GGAAACCTAT
*
53451555 AAGAGTTAAACTGAAGCTCAA
1 AAGAGTTAAACTGAAACTCAA
* * *
53451576 AAGAGCTAAACGGAAACCCAA
1 AAGAGTTAAACTGAAACTCAA
* * * *
53451597 TAGGGTTAAACTAAAACTCAT
1 AAGAGTTAAACTGAAACTCAA
*
53451618 ATGAGTT-AACTGAA
1 AAGAGTTAAACTGAA
53451632 GCTTATGAGA
Statistics
Matches: 41, Mismatches: 15, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
20 6 0.15
21 35 0.85
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.19
Consensus pattern (21 bp):
AAGAGTTAAACTGAAACTCAA
Found at i:53451605 original size:42 final size:42
Alignment explanation
Indices: 53451529--53451608 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
53451519 TGAATAGAGA
* * *
53451529 CTCATAAGAGCTGAACGGAAACCTATAAGAGTTAAACTGAAG
1 CTCAAAAGAGCTAAACGGAAACCAATAAGAGTTAAACTGAAG
*
53451571 CTCAAAAGAGCTAAACGGAAACCCAAT-AGGGTTAAACT
1 CTCAAAAGAGCTAAACGGAAA-CCAATAAGAGTTAAACT
53451609 AAAACTCATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 29 0.88
43 4 0.12
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.17
Consensus pattern (42 bp):
CTCAAAAGAGCTAAACGGAAACCAATAAGAGTTAAACTGAAG
Found at i:53460070 original size:120 final size:120
Alignment explanation
Indices: 53459897--53460211 Score: 402
Period size: 120 Copynumber: 2.6 Consensus size: 120
53459887 TTATTGAATG
* * * * * *
53459897 AATGCACATACATTCCCATATTTGTACTTC-GATACACC-TAAATGCACATACGTGCCCTTGTTT
1 AATGCACATACGTGCCCCTAATTGTACTTCAG-TAC-CCTTGAATGCACATACGTGCCCTTGATT
* * * *
53459960 GTACTTCGGTACCCTTGGATGCACATACATGCCTCTGATTGTACTTCGATACCCCTA
64 GTACTTCGGTACCCTTGAATGCACATACATGCCCCTGATTATACTTCCATACCCCTA
* * *
53460017 AATGCACATACGTGCCTCTGATTGTACTTCAGTACCCTTGAATGCACACACGTGCTCC-TGATTG
1 AATGCACATACGTGCCCCTAATTGTACTTCAGTACCCTTGAATGCACATACGTGC-CCTTGATTG
* * *
53460081 TACTTCGGTATCCTTGAATGCACATACATGCCCCTGTTTATACTTCCATACCCCTG
65 TACTTCGGTACCCTTGAATGCACATACATGCCCCTGATTATACTTCCATACCCCTA
** *
53460137 AATGCACATACGTGCCCCTAATTGTACTTTGGTACCCTTGAATGCACATACGTGCTCTTGATTGT
1 AATGCACATACGTGCCCCTAATTGTACTTCAGTACCCTTGAATGCACATACGTGCCCTTGATTGT
*
53460202 ACTTTGGTAC
66 ACTTCGGTAC
53460212 ATACATGCCC
Statistics
Matches: 167, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
119 3 0.02
120 161 0.96
121 3 0.02
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (120 bp):
AATGCACATACGTGCCCCTAATTGTACTTCAGTACCCTTGAATGCACATACGTGCCCTTGATTGT
ACTTCGGTACCCTTGAATGCACATACATGCCCCTGATTATACTTCCATACCCCTA
Found at i:53460154 original size:20 final size:20
Alignment explanation
Indices: 53460131--53460191 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
53460121 TACTTCCATA
53460131 CCCCTGAATGCACATACGTG
1 CCCCTGAATGCACATACGTG
* * ** *
53460151 CCCCT-AATTGTACTTTGGTA
1 CCCCTGAA-TGCACATACGTG
*
53460171 CCCTTGAATGCACATACGTG
1 CCCCTGAATGCACATACGTG
53460191 C
1 C
53460192 TCTTGATTGT
Statistics
Matches: 28, Mismatches: 11, Indels: 4
0.65 0.26 0.09
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (20 bp):
CCCCTGAATGCACATACGTG
Found at i:53460206 original size:40 final size:40
Alignment explanation
Indices: 53459895--53460211 Score: 320
Period size: 40 Copynumber: 7.9 Consensus size: 40
53459885 AATTATTGAA
* * * *
53459895 TGAATGCACATACATTCCCAT-ATTTGTACTTCGATACACC-
1 TGAATGCACATACGTGCCCTTGA-TTGTACTTCGGTAC-CCT
* *
53459935 TAAATGCACATACGTGCCCTTGTTTGTACTTCGGTACCCT
1 TGAATGCACATACGTGCCCTTGATTGTACTTCGGTACCCT
* * * *
53459975 TGGATGCACATACATG-CCTCTGATTGTACTTCGATACCCC
1 TGAATGCACATACGTGCCCT-TGATTGTACTTCGGTACCCT
* *
53460015 TAAATGCACATACGTG-CCTCTGATTGTACTTCAGTACCCT
1 TGAATGCACATACGTGCCCT-TGATTGTACTTCGGTACCCT
* *
53460055 TGAATGCACACACGTGCTCC-TGATTGTACTTCGGTATCCT
1 TGAATGCACATACGTGC-CCTTGATTGTACTTCGGTACCCT
* * * * ** *
53460095 TGAATGCACATACATGCCCCTGTTTATACTTCCATACCCC
1 TGAATGCACATACGTGCCCTTGATTGTACTTCGGTACCCT
* * *
53460135 TGAATGCACATACGTGCCCCTAATTGTACTTTGGTACCCT
1 TGAATGCACATACGTGCCCTTGATTGTACTTCGGTACCCT
* *
53460175 TGAATGCACATACGTGCTCTTGATTGTACTTTGGTAC
1 TGAATGCACATACGTGCCCTTGATTGTACTTCGGTAC
53460212 ATACATGCCC
Statistics
Matches: 230, Mismatches: 41, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
39 7 0.03
40 221 0.96
42 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCTTGATTGTACTTCGGTACCCT
Found at i:53460256 original size:68 final size:67
Alignment explanation
Indices: 53460142--53460277 Score: 175
Period size: 68 Copynumber: 2.0 Consensus size: 67
53460132 CCCTGAATGC
* ** *
53460142 ACATACGTGCCCCTAATTGTACTTTGGTACCCTTGAATGCACATACGTGCTCTTGATTGTACTTT
1 ACATACATGCCCCTAATTGTACTTAAGTACCCTTGAATGCACATACGTGC-CCTGATTGTACTTT
53460207 GGT
65 GGT
* * * *
53460210 ACATACATGCCCTTATTTGTACTTAAGTATCCC-TGAATGCATATACGTGCCCTGTTTGTACTTT
1 ACATACATGCCCCTAATTGTACTTAAGTA-CCCTTGAATGCACATACGTGCCCTGATTGTACTTT
53460274 GGT
65 GGT
53460277 A
1 A
53460278 ATCCTGAATT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
67 16 0.27
68 40 0.68
69 3 0.05
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.38
Consensus pattern (67 bp):
ACATACATGCCCCTAATTGTACTTAAGTACCCTTGAATGCACATACGTGCCCTGATTGTACTTTG
GT
Found at i:53465666 original size:39 final size:40
Alignment explanation
Indices: 53465585--53465668 Score: 116
Period size: 39 Copynumber: 2.1 Consensus size: 40
53465575 AATTATTGAA
* *
53465585 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCAGTAACCC
* * *
53465625 TGAATGTACATACGTG-CCCTGTTTGTACTTTAGTAATCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCAGTAACCC
53465664 TGAAT
1 TGAAT
53465669 TATATAATAC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 24 0.62
40 15 0.38
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCCTGTTTGTACTTCAGTAACCC
Found at i:53475512 original size:10 final size:10
Alignment explanation
Indices: 53475464--53475509 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
53475454 AATATTTCAA
53475464 CACATATGAAT
1 CACATAT-AAT
*
53475475 CACATATAAG
1 CACATATAAT
53475485 CACATATAAT
1 CACATATAAT
* *
53475495 TACATTTAAT
1 CACATATAAT
53475505 CACAT
1 CACAT
53475510 TTAGTCACAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 23 0.77
11 7 0.23
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (10 bp):
CACATATAAT
Found at i:53482409 original size:43 final size:43
Alignment explanation
Indices: 53482349--53482438 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
53482339 CTTTGAGTTC
* ** *
53482349 ATTA-CAAGATTTCCTTGATTAAGTCAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
* *
53482391 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATGTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
53482434 ATTAC
1 ATTAC
53482439 ATTGCATATG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 4 0.10
43 37 0.90
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATCTTTT
Found at i:53482893 original size:43 final size:43
Alignment explanation
Indices: 53482699--53482893 Score: 205
Period size: 43 Copynumber: 4.5 Consensus size: 43
53482689 GATATGTTTT
* * *
53482699 TAGCGGCGTTTGTGTGAAAAGC-CTCGCTAAAGGTC-TGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGC-CGCTAAAAGTCATGATCTA
* *** * *
53482741 TAGCGGTGTTTGTACAAAAAAGCGTCGCTAAAAGTGATGATCTA
1 TAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAAGTCATGATCTA
* * ** *
53482785 TAGCGGCGTTAGTGGGAAAAACGCTACTAAAAGTCATGACCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
*
53482828 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAATCATGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
* *
53482871 TTGCGGCGTTTGTGGGATAAGCG
1 TAGCGGCGTTTGTGGGAAAAGCG
53482894 GCGTTTATTT
Statistics
Matches: 123, Mismatches: 27, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
42 12 0.10
43 94 0.76
44 17 0.14
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCTA
Found at i:53483343 original size:34 final size:35
Alignment explanation
Indices: 53483303--53483370 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
53483293 AACATCCCTA
*
53483303 ATTTAATCTGTATTTTA-TAATATTAGTATCCTTT
1 ATTTAATCTGTATTTTATTAAGATTAGTATCCTTT
* *
53483337 ATTTAATGTTTATTTTATTAAGATTAGTATCCTT
1 ATTTAATCTGTATTTTATTAAGATTAGTATCCTT
53483371 ATGTTTCGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 15 0.50
35 15 0.50
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.56
Consensus pattern (35 bp):
ATTTAATCTGTATTTTATTAAGATTAGTATCCTTT
Found at i:53484826 original size:14 final size:14
Alignment explanation
Indices: 53484807--53484855 Score: 82
Period size: 14 Copynumber: 3.6 Consensus size: 14
53484797 TCAAGTTGTG
53484807 AAAAAAAATTTTGA
1 AAAAAAAATTTTGA
*
53484821 AAAAAAAATTGTGA
1 AAAAAAAATTTTGA
53484835 AAAAAAAA-TTTGA
1 AAAAAAAATTTTGA
53484848 AAAAAAAA
1 AAAAAAAA
53484856 GAGAGCTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
13 12 0.36
14 21 0.64
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.20
Consensus pattern (14 bp):
AAAAAAAATTTTGA
Found at i:53484832 original size:27 final size:27
Alignment explanation
Indices: 53484802--53484855 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
53484792 GGATATCAAG
*
53484802 TTGTGAAAAAAAATTTTGAAAAAAAAA
1 TTGTGAAAAAAAAATTTGAAAAAAAAA
53484829 TTGTGAAAAAAAAATTTGAAAAAAAAA
1 TTGTGAAAAAAAAATTTGAAAAAAAAA
53484856 GAGAGCTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (27 bp):
TTGTGAAAAAAAAATTTGAAAAAAAAA
Found at i:53484855 original size:13 final size:13
Alignment explanation
Indices: 53484805--53484855 Score: 84
Period size: 13 Copynumber: 3.8 Consensus size: 13
53484795 TATCAAGTTG
*
53484805 TGAAAAAAAATTT
1 TGAAAAAAAAATT
53484818 TGAAAAAAAAATT
1 TGAAAAAAAAATT
53484831 GTGAAAAAAAAATT
1 -TGAAAAAAAAATT
53484845 TGAAAAAAAAA
1 TGAAAAAAAAA
53484856 GAGAGCTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
13 23 0.64
14 13 0.36
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.22
Consensus pattern (13 bp):
TGAAAAAAAAATT
Found at i:53485804 original size:18 final size:17
Alignment explanation
Indices: 53485783--53485827 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
53485773 GAGTGACGAG
53485783 AGAAAAAGAAACTGAAAA
1 AGAAAAA-AAACTGAAAA
*
53485801 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAACTGAAAA
53485819 AGAGAAAAA
1 AGA-AAAAA
53485828 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAACTGAAAA
Found at i:53485832 original size:18 final size:18
Alignment explanation
Indices: 53485781--53485832 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
53485771 AAGAGTGACG
*
53485781 AGAGAAAAAGAAACTGAAAA
1 AGAGAAAAAG--ATTGAAAA
*
53485801 AGA-AACAAAAATTGAAAA
1 AGAGAA-AAAGATTGAAAA
53485819 AGAGAAAAAGATTG
1 AGAGAAAAAGATTG
53485833 GAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.63
19 4 0.15
20 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10
Consensus pattern (18 bp):
AGAGAAAAAGATTGAAAA
Found at i:53491065 original size:80 final size:80
Alignment explanation
Indices: 53490972--53491133 Score: 315
Period size: 80 Copynumber: 2.0 Consensus size: 80
53490962 TCACGACTTT
53490972 AATAGAATTAGATTTGGATTAAGAGAATTATTTAATTAAAAAATTAATTAATTTAGTTAATTAAT
1 AATAGAATTAGATTTGGATTAAGAGAATTATTTAATTAAAAAATTAATTAATTTAGTTAATTAAT
53491037 TAATATTTATTTTGA
66 TAATATTTATTTTGA
*
53491052 AATAGAATTAGATTTTGATTAAGAGAATTATTTAATTAAAAAATTAATTAATTTAGTTAATTAAT
1 AATAGAATTAGATTTGGATTAAGAGAATTATTTAATTAAAAAATTAATTAATTTAGTTAATTAAT
53491117 TAATATTTATTTTGA
66 TAATATTTATTTTGA
53491132 AA
1 AA
53491134 AAAGTGAATA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (80 bp):
AATAGAATTAGATTTGGATTAAGAGAATTATTTAATTAAAAAATTAATTAATTTAGTTAATTAAT
TAATATTTATTTTGA
Found at i:53493669 original size:16 final size:18
Alignment explanation
Indices: 53493648--53493689 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
53493638 ATGAGTAGTG
53493648 TTTCAC-CA-CCTTCCTT
1 TTTCACACACCCTTCCTT
53493664 TTTCACAACACCCTTCCTT
1 TTTCAC-ACACCCTTCCTT
53493683 TTTCACA
1 TTTCACA
53493690 TACAGTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.26
18 3 0.13
19 14 0.61
ACGTcount: A:0.19, C:0.40, G:0.00, T:0.40
Consensus pattern (18 bp):
TTTCACACACCCTTCCTT
Found at i:53505832 original size:7 final size:7
Alignment explanation
Indices: 53505817--53505853 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
53505807 ATTTATATCT
53505817 TTCTCCA
1 TTCTCCA
*
53505824 TTCTACA
1 TTCTCCA
53505831 TTCTCCA
1 TTCTCCA
53505838 TTCTCCA
1 TTCTCCA
*
53505845 TTATCCA
1 TTCTCCA
53505852 TT
1 TT
53505854 AAGCTTAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.46
Consensus pattern (7 bp):
TTCTCCA
Found at i:53508009 original size:50 final size:52
Alignment explanation
Indices: 53507955--53508095 Score: 207
Period size: 52 Copynumber: 2.8 Consensus size: 52
53507945 TAATAAAGTT
* * *
53507955 ATGCATTATGTAACTTCCATGCTAG-TTAAGTATGCATCA-TAAA-TAATGAC
1 ATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCATCATTAAATTAA-GAC
*
53508005 ATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCATCATTAAATTAAGTC
1 ATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCATCATTAAATTAAGAC
*
53508057 TTGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCATC
1 ATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCATC
53508096 TCATTTGTTC
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
50 23 0.28
51 13 0.16
52 44 0.53
53 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (52 bp):
ATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCATCATTAAATTAAGAC
Found at i:53511370 original size:130 final size:130
Alignment explanation
Indices: 53511169--53511492 Score: 479
Period size: 130 Copynumber: 2.5 Consensus size: 130
53511159 TAGAAGCCTG
* * * * * *
53511169 GACTCAATCAATCATTTTAAATTAAAGT-TGGTCAACCTAATCTAAGACATCAACAAACAACTAC
1 GACTCAATCAATCACTTTAAATCAAA-TACGATCAACCCAATCTAATACATCAACAAACAACTAC
** * *
53511233 ATGTATAAATGATATGTTATTTCAATATTATATTTTAATGTTGTCACATTTAGTTGTGGAAATAT
65 ATGTATAAATGATATGTTATTTCAATATTATATTTTAATGTCATCAAATTTAGTTGTGAAAATAT
*
53511298 T
130 A
* *
53511299 GACTCAATCAATCACTTTAAATCAAATACCATCAACCCAATCTAATACATCAACAACCAACTACA
1 GACTCAATCAATCACTTTAAATCAAATACGATCAACCCAATCTAATACATCAACAAACAACTACA
* *
53511364 TTTATAAATGATATGTTATTTTAATATTATATTTTAATGTCATCAAATTTAGTTGTGAAAATATA
66 TGTATAAATGATATGTTATTTCAATATTATATTTTAATGTCATCAAATTTAGTTGTGAAAATATA
* *
53511429 GATTCAATCAATCACTTTAAATCAAGTACGATCAACCCAATCTAATACATCAACAAACAACTAC
1 GACTCAATCAATCACTTTAAATCAAATACGATCAACCCAATCTAATACATCAACAAACAACTAC
53511493 CTTCAAGCAT
Statistics
Matches: 174, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
129 1 0.01
130 173 0.99
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (130 bp):
GACTCAATCAATCACTTTAAATCAAATACGATCAACCCAATCTAATACATCAACAAACAACTACA
TGTATAAATGATATGTTATTTCAATATTATATTTTAATGTCATCAAATTTAGTTGTGAAAATATA
Found at i:53511788 original size:7 final size:8
Alignment explanation
Indices: 53511734--53511815 Score: 85
Period size: 8 Copynumber: 10.0 Consensus size: 8
53511724 AAAAATACAA
53511734 AAAATTATT
1 AAAATT-TT
53511743 AAAATTATT
1 AAAATT-TT
**
53511752 AAAATTAG
1 AAAATTTT
53511760 AAAATTTAT
1 AAAATTT-T
**
53511769 AAAATTAA
1 AAAATTTT
53511777 AAAATTTT
1 AAAATTTT
53511785 -AAATTTT
1 AAAATTTT
*
53511792 AAATTTTT
1 AAAATTTT
53511800 AAAATTTT
1 AAAATTTT
53511808 AAAATTTT
1 AAAATTTT
53511816 TTAAATCGCA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
7 7 0.11
8 33 0.54
9 21 0.34
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (8 bp):
AAAATTTT
Found at i:53511816 original size:9 final size:9
Alignment explanation
Indices: 53511734--53511821 Score: 55
Period size: 9 Copynumber: 10.6 Consensus size: 9
53511724 AAAAATACAA
*
53511734 AAAATTATT
1 AAAATTTTT
*
53511743 AAAATTATT
1 AAAATTTTT
**
53511752 AAAA-TTAG
1 AAAATTTTT
*
53511760 AAAATTTAT
1 AAAATTTTT
*
53511769 AAAA--TTA
1 AAAATTTTT
*
53511776 AAAAATTTT
1 AAAATTTTT
53511785 -AAA-TTTT
1 AAAATTTTT
53511792 -AAATTTTT
1 AAAATTTTT
53511800 AAAA-TTTT
1 AAAATTTTT
53511808 AAAATTTTT
1 AAAATTTTT
*
53511817 TAAAT
1 AAAAT
53511822 CGCATTTACT
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
7 12 0.18
8 20 0.31
9 33 0.51
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (9 bp):
AAAATTTTT
Found at i:53511816 original size:17 final size:17
Alignment explanation
Indices: 53511734--53511821 Score: 83
Period size: 17 Copynumber: 5.3 Consensus size: 17
53511724 AAAAATACAA
*
53511734 AAAATTATTAAAATTATT
1 AAAATT-TTAAAATTTTT
** *
53511752 AAAATTAGAAAATTTAT
1 AAAATTTTAAAATTTTT
* *
53511769 AAAA-TTAAAAAATTTT
1 AAAATTTTAAAATTTTT
53511785 -AAATTTT-AAATTTTT
1 AAAATTTTAAAATTTTT
53511800 AAAATTTTAAAATTTTT
1 AAAATTTTAAAATTTTT
*
53511817 TAAAT
1 AAAAT
53511822 CGCATTTACT
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
15 10 0.18
16 17 0.30
17 23 0.41
18 6 0.11
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (17 bp):
AAAATTTTAAAATTTTT
Found at i:53519945 original size:27 final size:27
Alignment explanation
Indices: 53519898--53519956 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
53519888 AGCAGGAGAA
* *
53519898 CACCACTAGGATTGGTGAGCTAGAGTT
1 CACCACTAGGATTGATAAGCTAGAGTT
* *
53519925 CACCACTAGGATT-ATCAAGCTGGTGTT
1 CACCACTAGGATTGAT-AAGCTAGAGTT
53519952 CACCA
1 CACCA
53519957 GAAGACTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (27 bp):
CACCACTAGGATTGATAAGCTAGAGTT
Found at i:53519972 original size:27 final size:27
Alignment explanation
Indices: 53519942--53519999 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
53519932 AGGATTATCA
*
53519942 AGCTGGTGTTCACCAGAA-GACTTGGCG
1 AGCTGGTGTTCACCAAAATG-CTTGGCG
*
53519969 AGCTGGTGTTTACCAAAATGCTTGGCG
1 AGCTGGTGTTCACCAAAATGCTTGGCG
53519996 AGCT
1 AGCT
53520000 AGTATACACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (27 bp):
AGCTGGTGTTCACCAAAATGCTTGGCG
Found at i:53522616 original size:39 final size:39
Alignment explanation
Indices: 53522550--53522633 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 39
53522540 AATTACACCT
* * **
53522550 CTGATCGCACTTACGTGCCCCTATTGTACTTTGGTACCC
1 CTGATCACACTTACATGCCCCTATTGTACTTCAGTACCC
* * *
53522589 CTGATCACACTTACATGTCCTTGTTGTACTTCAGTACCC
1 CTGATCACACTTACATGCCCCTATTGTACTTCAGTACCC
53522628 CTGATC
1 CTGATC
53522634 GTACTTTTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.18, C:0.32, G:0.15, T:0.35
Consensus pattern (39 bp):
CTGATCACACTTACATGCCCCTATTGTACTTCAGTACCC
Found at i:53525157 original size:16 final size:17
Alignment explanation
Indices: 53525136--53525167 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53525126 ACTGGAATGA
53525136 GAAAA-TTATTTAATTG
1 GAAAATTTATTTAATTG
53525152 GAAAATTTATTTAATT
1 GAAAATTTATTTAATT
53525168 TTGAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (17 bp):
GAAAATTTATTTAATTG
Found at i:53528392 original size:6 final size:7
Alignment explanation
Indices: 53528376--53528401 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53528366 AATTGGACCA
53528376 TTTTAAT
1 TTTTAAT
53528383 TTTTAAT
1 TTTTAAT
53528390 TTTTAAT
1 TTTTAAT
53528397 TTTTA
1 TTTTA
53528402 CTCCAAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTAAT
Found at i:53528436 original size:18 final size:18
Alignment explanation
Indices: 53528413--53528447 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53528403 TCCAAACTTG
*
53528413 TGATTTTTATTTTTTGGA
1 TGATTTCTATTTTTTGGA
53528431 TGATTTCTATTTTTTGG
1 TGATTTCTATTTTTTGG
53528448 TTTTCTTAGA
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:0.14, C:0.03, G:0.17, T:0.66
Consensus pattern (18 bp):
TGATTTCTATTTTTTGGA
Found at i:53530103 original size:13 final size:13
Alignment explanation
Indices: 53530085--53530109 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53530075 TTAGCAATGC
53530085 TTTTAAAAAGTGA
1 TTTTAAAAAGTGA
53530098 TTTTAAAAAGTG
1 TTTTAAAAAGTG
53530110 TTGTAGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
TTTTAAAAAGTGA
Found at i:53534083 original size:19 final size:19
Alignment explanation
Indices: 53534059--53534100 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53534049 AAGAAACAAA
*
53534059 AAAATAAAGGGAAAAGAAG
1 AAAATAAAGAGAAAAGAAG
* *
53534078 AAAATAAAGAGAAGAGAGG
1 AAAATAAAGAGAAAAGAAG
53534097 AAAA
1 AAAA
53534101 ACCCTATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (19 bp):
AAAATAAAGAGAAAAGAAG
Found at i:53535293 original size:154 final size:154
Alignment explanation
Indices: 53535013--53535319 Score: 551
Period size: 154 Copynumber: 2.0 Consensus size: 154
53535003 ACACTTTAAG
*
53535013 CAAGCACTCAATTTCTTCCAACACTTACCTATGTGGTATTTTTCTCAATACGCATAACTAGGAGT
1 CAAGCACTCAATTTCTTCCAACACTTACCTATGTGGTATTTTTCACAATACGCATAACTAGGAGT
* *
53535078 CTAACGCCTTGAATTAGTTACAACAACCTCTTATTGCGGTCTACCCTTTCTAGTTTGTTTTATAG
66 CTAACCCCTCGAATTAGTTACAACAACCTCTTATTGCGGTCTACCCTTTCTAGTTTGTTTTATAG
53535143 GATGAGAATTTGAGTCAGTAGAAA
131 GATGAGAATTTGAGTCAGTAGAAA
*
53535167 CAAGCACTCAATTTCTTCCAACACTTACTTATGTGGTATTTTTCACAATACGCATAACTAGGAGT
1 CAAGCACTCAATTTCTTCCAACACTTACCTATGTGGTATTTTTCACAATACGCATAACTAGGAGT
* * *
53535232 CTAACCCCTCGAATTAGTTACAACAACCTCTTGTTGTGGTCTACCCTTTGTAGTTTGTTTTATAG
66 CTAACCCCTCGAATTAGTTACAACAACCTCTTATTGCGGTCTACCCTTTCTAGTTTGTTTTATAG
53535297 GATGAGAATTTGAGTCAGTAGAA
131 GATGAGAATTTGAGTCAGTAGAA
53535320 CCAGAATCTC
Statistics
Matches: 146, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
154 146 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (154 bp):
CAAGCACTCAATTTCTTCCAACACTTACCTATGTGGTATTTTTCACAATACGCATAACTAGGAGT
CTAACCCCTCGAATTAGTTACAACAACCTCTTATTGCGGTCTACCCTTTCTAGTTTGTTTTATAG
GATGAGAATTTGAGTCAGTAGAAA
Found at i:53538122 original size:28 final size:28
Alignment explanation
Indices: 53538081--53538196 Score: 126
Period size: 28 Copynumber: 4.1 Consensus size: 28
53538071 TGTGAAGCAA
*
53538081 GGGAGAAAATTATAAAATCTGAAAAATAG
1 GGGA-AAAACTATAAAATCTGAAAAATAG
*
53538110 GGGAAAAACTATAAAATCTAAAAAATAG
1 GGGAAAAACTATAAAATCTGAAAAATAG
* * *
53538138 AGG-TAAACTATAAAATTTGAAAAATAG
1 GGGAAAAACTATAAAATCTGAAAAATAG
* * * * *
53538165 GGGCAAAATTGTAAAATTTGAAAAATAA
1 GGGAAAAACTATAAAATCTGAAAAATAG
53538193 GGGA
1 GGGA
53538197 CACACTGTCG
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
27 23 0.31
28 47 0.64
29 4 0.05
ACGTcount: A:0.55, C:0.04, G:0.19, T:0.22
Consensus pattern (28 bp):
GGGAAAAACTATAAAATCTGAAAAATAG
Found at i:53538476 original size:46 final size:46
Alignment explanation
Indices: 53538404--53538497 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
53538394 AGAATGAAGA
* * *
53538404 TTAATACCTTACAATAGTTTACCCTATGAATTTAGATATAAATCCT
1 TTAATACCTTAAAATAGTTCAACCTATGAATTTAGATATAAATCCT
*
53538450 TTAATACCTTAAAATAGTTCAACCTATGAATTTAGATATAAATTCT
1 TTAATACCTTAAAATAGTTCAACCTATGAATTTAGATATAAATCCT
53538496 TT
1 TT
53538498 CCATAAAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.40
Consensus pattern (46 bp):
TTAATACCTTAAAATAGTTCAACCTATGAATTTAGATATAAATCCT
Found at i:53539599 original size:27 final size:27
Alignment explanation
Indices: 53539569--53539718 Score: 103
Period size: 27 Copynumber: 5.5 Consensus size: 27
53539559 GTATACCGTC
*
53539569 AAGGAATTCCTTTTAGAGTTTTCCACA
1 AAGGCATTCCTTTTAGAGTTTTCCACA
* * *
53539596 AAGGCATTCCTTTCAGAGTCTGT-GACA
1 AAGGCATTCCTTTTAGAGT-TTTCCACA
** *
53539623 AACTCATTCCTTTTAGAGTTTGCCACA
1 AAGGCATTCCTTTTAGAGTTTTCCACA
* *
53539650 AAGGCATT--TTTTCCACA-TATTGCCACA
1 AAGGCATTCCTTTT--AGAGT-TTTCCACA
* * *
53539677 AAGGCATTTCTTTTCATA-TATTGCCACA
1 AAGGCATTCCTTTT-AGAGT-TTTCCACA
53539705 AAGGCATTCCTTTT
1 AAGGCATTCCTTTT
53539719 CATATGTGTT
Statistics
Matches: 101, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
25 4 0.04
26 2 0.02
27 63 0.62
28 28 0.28
29 4 0.04
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (27 bp):
AAGGCATTCCTTTTAGAGTTTTCCACA
Found at i:53539678 original size:54 final size:54
Alignment explanation
Indices: 53539574--53539717 Score: 143
Period size: 54 Copynumber: 2.6 Consensus size: 54
53539564 CCGTCAAGGA
* * * *
53539574 ATTCCTTTTAGAGTTTTCCACAAAGGCATTCCTTTCAGAGTCTGTGACAAACTC
1 ATTCCTTTTAGAGTTTGCCACAAAGGCATTCCTTTCACAGTATGTGACAAACGC
* *
53539628 ATTCCTTTTAGAGTTTGCCACAAAGGCATT-TTTTCCACA-TAT-TGCCACAAAGGC
1 ATTCCTTTTAGAGTTTGCCACAAAGGCATTCCTTT-CACAGTATGTG--ACAAACGC
* *
53539682 ATTTCTTTTCATA-TATTGCCACAAAGGCATTCCTTT
1 ATTCCTTTT-AGAGT-TTGCCACAAAGGCATTCCTTT
53539718 TCATATGTGT
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
52 2 0.03
53 5 0.07
54 47 0.63
55 18 0.24
56 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (54 bp):
ATTCCTTTTAGAGTTTGCCACAAAGGCATTCCTTTCACAGTATGTGACAAACGC
Found at i:53539706 original size:28 final size:28
Alignment explanation
Indices: 53539642--53539723 Score: 130
Period size: 28 Copynumber: 3.0 Consensus size: 28
53539632 CTTTTAGAGT
* *
53539642 TTGCCACAAAGGCATTT-TTTCCACATA
1 TTGCCACAAAGGCATTTCTTTTCATATA
53539669 TTGCCACAAAGGCATTTCTTTTCATATA
1 TTGCCACAAAGGCATTTCTTTTCATATA
*
53539697 TTGCCACAAAGGCATTCCTTTTCATAT
1 TTGCCACAAAGGCATTTCTTTTCATAT
53539724 GTGTTTATGA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 17 0.33
28 34 0.67
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (28 bp):
TTGCCACAAAGGCATTTCTTTTCATATA
Found at i:53543180 original size:21 final size:21
Alignment explanation
Indices: 53543154--53543226 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
53543144 AATAATTAAC
53543154 TAAATTAAATAGTATTTTTTA
1 TAAATTAAATAGTATTTTTTA
* * *
53543175 TAAATTAATTATACTAATTTTAA
1 TAAATTAA--ATAGTATTTTTTA
* *
53543198 CTAAATTACATAGTATTTATTA
1 -TAAATTAAATAGTATTTTTTA
*
53543220 TTAATTA
1 TAAATTA
53543227 TGTATACTTA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
21 14 0.35
22 9 0.22
23 10 0.25
24 7 0.17
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (21 bp):
TAAATTAAATAGTATTTTTTA
Found at i:53543198 original size:45 final size:45
Alignment explanation
Indices: 53543149--53543234 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
53543139 TACCAAATAA
*
53543149 TTAACTAAATTAAATAGTATTTTTTATAAATTAAT-TATACTAATT
1 TTAACTAAATTAAATAGTATTTATTATAAATT-ATGTATACTAATT
* *
53543194 TTAACTAAATTACATAGTATTTATTATTAATTATGTATACT
1 TTAACTAAATTAAATAGTATTTATTATAAATTATGTATACT
53543235 TAGCCAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 2 0.05
45 35 0.95
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (45 bp):
TTAACTAAATTAAATAGTATTTATTATAAATTATGTATACTAATT
Found at i:53543496 original size:16 final size:17
Alignment explanation
Indices: 53543465--53543497 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53543455 ATTATTGATA
*
53543465 ATTTTTATAATATTAAT
1 ATTTTTAAAATATTAAT
53543482 ATTTTTAAAAT-TTAAT
1 ATTTTTAAAATATTAAT
53543498 TTTATTTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTTAAAATATTAAT
Found at i:53544254 original size:16 final size:16
Alignment explanation
Indices: 53544235--53544265 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53544225 TATAGTCAAG
53544235 ACTCCCTATAACAACC
1 ACTCCCTATAACAACC
*
53544251 ACTCTCTATAACAAC
1 ACTCCCTATAACAAC
53544266 ATTTCGTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.23
Consensus pattern (16 bp):
ACTCCCTATAACAACC
Found at i:53545669 original size:29 final size:30
Alignment explanation
Indices: 53545627--53545701 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
53545617 ACAATACGAT
* **
53545627 AACATAAGTGACTATAACGTAACAT-TTCA
1 AACAAAAGTGACTATAACGTAACATAGACA
* * *
53545656 AACAAAAGTGACTAAAATGTAACCTGAGACA
1 AACAAAAGTGACTATAACGTAACAT-AGACA
53545687 AACAAAAGTGACTAT
1 AACAAAAGTGACTAT
53545702 TTTGGTAGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
29 21 0.57
31 16 0.43
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.21
Consensus pattern (30 bp):
AACAAAAGTGACTATAACGTAACATAGACA
Found at i:53546473 original size:23 final size:26
Alignment explanation
Indices: 53546447--53546511 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
53546437 TTAATAGCTT
*
53546447 AAAAACTAAAAA-A-TTGTTAAAAGA
1 AAAAACAAAAAATATTTGTTAAAAGA
*
53546471 AAAAACAAAAAATATTTTTTTAAAAGA
1 AAAAACAAAAAATA-TTTGTTAAAAGA
53546498 AAAACAGCAAAAAA
1 AAAA-A-CAAAAAA
53546512 AATTATTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 11 0.32
25 1 0.03
27 14 0.41
28 1 0.03
29 7 0.21
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.20
Consensus pattern (26 bp):
AAAAACAAAAAATATTTGTTAAAAGA
Found at i:53546524 original size:29 final size:27
Alignment explanation
Indices: 53546465--53546528 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
53546455 AAAAATTGTT
* * **
53546465 AAAAGAAAAAACAAAAAATATTTTTTT
1 AAAAGAAAAAACAAAAAAAATTATTCA
53546492 AAAAGAAAAACAGCAAAAAAAATTATTCA
1 AAAAGAAAAA-A-CAAAAAAAATTATTCA
53546521 AAAAGAAA
1 AAAAGAAA
53546529 CAAGCATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 10 0.32
28 1 0.03
29 20 0.65
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (27 bp):
AAAAGAAAAAACAAAAAAAATTATTCA
Found at i:53547716 original size:40 final size:40
Alignment explanation
Indices: 53547553--53547717 Score: 134
Period size: 40 Copynumber: 4.1 Consensus size: 40
53547543 TGTTTATGAC
* * * *
53547553 AAAAATGCCGCAAAAGGTCAAGCATTAGCGGCGCTTTTTG
1 AAAAATGCCACTATAGGTCGAGCATTAGCGGCGCTTTTTG
* * *
53547593 AAAAACG-TAGCTATAGGTCGAGCATTAGCGACGCTTTTTG
1 AAAAATGCCA-CTATAGGTCGAGCATTAGCGGCGCTTTTTG
* * * ** * * ** *
53547633 AAAAGTACCGCTATAGGTTAAGCATTAGCAGCACTCCTAG
1 AAAAATGCCACTATAGGTCGAGCATTAGCGGCGCTTTTTG
* * *
53547673 AAAAATGCCACTATAGATCGAGCATTAGTGGCGCTTTTCG
1 AAAAATGCCACTATAGGTCGAGCATTAGCGGCGCTTTTTG
53547713 AAAAA
1 AAAAA
53547718 CACGACATAA
Statistics
Matches: 91, Mismatches: 32, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
40 91 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (40 bp):
AAAAATGCCACTATAGGTCGAGCATTAGCGGCGCTTTTTG
Found at i:53547841 original size:40 final size:40
Alignment explanation
Indices: 53547797--53547886 Score: 121
Period size: 40 Copynumber: 2.2 Consensus size: 40
53547787 CAAAAGGTCA
*
53547797 AGCATTAGCGATGC-TTTTTAAAAAACGCTGCTATAGATTG
1 AGCATTAGCGA-GCGTTTTTAAAAAACGCTGCTATAGATCG
* *
53547837 AGCATTAGC-AGCGTTTTTTGAAAAACGTTGCTATAGATCG
1 AGCATTAGCGAGCG-TTTTTAAAAAACGCTGCTATAGATCG
53547877 AGCATTAGCG
1 AGCATTAGCG
53547887 GCACTTTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
38 2 0.05
39 1 0.02
40 41 0.93
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (40 bp):
AGCATTAGCGAGCGTTTTTAAAAAACGCTGCTATAGATCG
Found at i:53547895 original size:40 final size:40
Alignment explanation
Indices: 53547810--53547904 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 40
53547800 ATTAGCGATG
* * *
53547810 CTTTTTAAAAAACGCTGCTATAGATTGAGCATTAGCAGCG
1 CTTTTTGAAAAACGCTGCTATAGATCGAGCATTAGCAGCA
* * *
53547850 TTTTTTGAAAAACGTTGCTATAGATCGAGCATTAGCGGCA
1 CTTTTTGAAAAACGCTGCTATAGATCGAGCATTAGCAGCA
*
53547890 CTTTTTGGAAAACGC
1 CTTTTTGAAAAACGC
53547905 CACAATAAAG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.32
Consensus pattern (40 bp):
CTTTTTGAAAAACGCTGCTATAGATCGAGCATTAGCAGCA
Found at i:53548029 original size:40 final size:40
Alignment explanation
Indices: 53547985--53548119 Score: 159
Period size: 40 Copynumber: 3.4 Consensus size: 40
53547975 AACGTCGCAG
*
53547985 TAGATCAAGCATTAGCGGCGCTATTTGAAAAATGCCACTA
1 TAGATCAAGCATTAGCAGCGCTATTTGAAAAATGCCACTA
* * * *
53548025 TAGATCAAGCATTAGCAGTGCTTTTTGCAAAA--CCCCGTAA
1 TAGATCAAGCATTAGCAGCGCTATTTGAAAAATGCCAC-T-A
* * *
53548065 TAGATCGAGCATTAGCAGTGCTATTTGAAAAATGCCGCTA
1 TAGATCAAGCATTAGCAGCGCTATTTGAAAAATGCCACTA
53548105 TAGATCAA-CATTAGC
1 TAGATCAAGCATTAGC
53548120 GGCACTTTTC
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
38 3 0.04
39 8 0.10
40 66 0.81
41 1 0.01
42 3 0.04
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (40 bp):
TAGATCAAGCATTAGCAGCGCTATTTGAAAAATGCCACTA
Found at i:53548471 original size:30 final size:30
Alignment explanation
Indices: 53548437--53548522 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
53548427 GGTTTTAGAA
* *
53548437 TTTAGAGTTTTAAGGTTTTAGTATTTAAGG
1 TTTAGAGTTTTAGGGTTTTAGGATTTAAGG
*
53548467 TTTAGAGTTTT-GGAGTTTTAGGGTTTAAGG
1 TTTAGAGTTTTAGG-GTTTTAGGATTTAAGG
*
53548497 TTTAGAGTTTTAGGG-TTTAGGGTTTA
1 TTTAGAGTTTTAGGGTTTTAGGATTTA
53548523 TTTCCATATA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
29 12 0.24
30 37 0.73
31 2 0.04
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (30 bp):
TTTAGAGTTTTAGGGTTTTAGGATTTAAGG
Done.