Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 15 of 335
Found at i:5347129 original size:27 final size:27
Alignment explanation
Indices: 5347099--5347202 Score: 72
Period size: 27 Copynumber: 3.9 Consensus size: 27
5347089 ATTTATAGTA
5347099 TATTAGTTTTGTTATATAAATTTAATT
1 TATTAGTTTTGTTATATAAATTTAATT
* * * *
5347126 TATTTA-TTTAGTTATATCAACTCAATT
1 TA-TTAGTTTTGTTATATAAATTTAATT
* * *
5347153 AATT-GTTTTATT-TAT-AATATTAATA
1 TATTAGTTTTGTTATATAAAT-TTAATT
* * *
5347178 TATTAATTATGTTACATAAATTTAA
1 TATTAGTTTTGTTATATAAATTTAA
5347203 AAAAAAAATT
Statistics
Matches: 56, Mismatches: 15, Indels: 12
0.67 0.18 0.14
Matches are distributed among these distances:
24 2 0.04
25 10 0.18
26 12 0.21
27 26 0.46
28 6 0.11
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.54
Consensus pattern (27 bp):
TATTAGTTTTGTTATATAAATTTAATT
Found at i:5351567 original size:46 final size:45
Alignment explanation
Indices: 5351514--5351686 Score: 197
Period size: 46 Copynumber: 3.8 Consensus size: 45
5351504 TTGGGCATCT
5351514 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCC
*** * *
5351560 GAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-TCC
1 GAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAGTCC
* *
5351607 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCC
* *
5351653 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5351687 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 65 0.61
47 32 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (45 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGTCC
Found at i:5351666 original size:93 final size:93
Alignment explanation
Indices: 5351507--5351679 Score: 301
Period size: 93 Copynumber: 1.9 Consensus size: 93
5351497 AGGATATTTG
* * *
5351507 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
5351572 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
5351600 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
5351665 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
5351680 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:5353733 original size:18 final size:18
Alignment explanation
Indices: 5353710--5353745 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5353700 TAAGATTGTA
5353710 TTTTGTTTCTTAGAAATT
1 TTTTGTTTCTTAGAAATT
5353728 TTTTGTTTCTTAGAAATT
1 TTTTGTTTCTTAGAAATT
5353746 CTTACCTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.11, T:0.61
Consensus pattern (18 bp):
TTTTGTTTCTTAGAAATT
Found at i:5354450 original size:5 final size:5
Alignment explanation
Indices: 5354429--5354481 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
5354419 TGTTAAAATA
* *
5354429 TATAT TAAAT TATTAT TATAT TATAG TATAT TATATT ATATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T -TATAT TATAT
5354477 TATAT
1 TATAT
5354482 AAATAAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 31 0.76
6 6 0.15
7 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:5354460 original size:10 final size:9
Alignment explanation
Indices: 5354426--5354482 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
5354416 ATGTGTTAAA
5354426 ATATATATT
1 ATATATATT
*
5354435 AAAT-TATT
1 ATATATATT
5354443 AT-TATATT
1 ATATATATT
5354451 ATAGTATATT
1 ATA-TATATT
5354461 ATAT-TA-T
1 ATATATATT
5354468 ATATTATATT
1 ATA-TATATT
5354478 ATATA
1 ATATA
5354483 AATAAGTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.35
9 8 0.20
10 13 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:5354472 original size:12 final size:12
Alignment explanation
Indices: 5354427--5354482 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
5354417 TGTGTTAAAA
*
5354427 TATATATTAAAT
1 TATATATTATAT
5354439 TAT-TATTATATT
1 TATATATTATA-T
5354451 ATAGTATATTATAT
1 -TA-TATATTATAT
5354465 TATATATTATAT
1 TATATATTATAT
5354477 TATATA
1 TATATA
5354483 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:5355807 original size:18 final size:19
Alignment explanation
Indices: 5355786--5355824 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5355776 ATATATAGAT
5355786 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
5355804 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
5355823 AT
1 AT
5355825 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:5356173 original size:39 final size:39
Alignment explanation
Indices: 5356063--5356197 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
5356053 GACCTCGAGT
* * * *
5356063 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
5356104 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
5356142 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
5356181 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
5356198 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:5356341 original size:18 final size:19
Alignment explanation
Indices: 5356320--5356360 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5356310 AATGAAATGA
5356320 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
5356338 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
5356357 GAAA
1 GAAA
5356361 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:5357202 original size:3 final size:3
Alignment explanation
Indices: 5357194--5357243 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
5357184 AAATAGCCTC
* * * * *
5357194 AAT AAT AAT AAT AAT AAT AAT GAT GAT GAT AAT ATT AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5357242 AA
1 AA
5357244 GTAGTCTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5357598 original size:8 final size:8
Alignment explanation
Indices: 5357556--5357604 Score: 53
Period size: 8 Copynumber: 5.6 Consensus size: 8
5357546 AAAATGGTTT
5357556 TAAAATAA
1 TAAAATAA
5357564 TAATAATAA
1 TAA-AATAA
5357573 TAATAAGGTAA
1 TAA-AA--TAA
*
5357584 AAAAATAA
1 TAAAATAA
5357592 TAAAATAA
1 TAAAATAA
5357600 TAAAA
1 TAAAA
5357605 GCACTATTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 18 0.50
9 11 0.31
10 2 0.06
11 5 0.14
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.24
Consensus pattern (8 bp):
TAAAATAA
Found at i:5357629 original size:3 final size:3
Alignment explanation
Indices: 5357623--5357743 Score: 64
Period size: 3 Copynumber: 42.7 Consensus size: 3
5357613 ACGTCACTAC
* * * * *
5357623 TAA TAA TAA TAA TAA -AA GAA -AA CAG TAA T-A TTA TATA GAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
* *
5357666 TAG TAA -AA GTAA TAA -AA -AA TAA TAA TAA TAA TAG TAA TAA -AA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
5357708 AAA TAA TAA TAC TAA T-A TAA T-A TCAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA
5357744 GCACTCTCCC
Statistics
Matches: 93, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
2 20 0.22
3 67 0.72
4 6 0.06
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:5357728 original size:25 final size:26
Alignment explanation
Indices: 5357661--5357729 Score: 97
Period size: 25 Copynumber: 2.7 Consensus size: 26
5357651 TATTATATAG
* *
5357661 AATAATAGTAAAAGTAAT-AAAAAAT
1 AATAATAATAATAGTAATAAAAAAAT
5357686 AATAATAATAATAGTAATAAAAAAAT
1 AATAATAATAATAGTAATAAAAAAAT
*
5357712 AATAATACTAATA-TAATA
1 AATAATAATAATAGTAATA
5357730 TCAATAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 21 0.52
26 19 0.47
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (26 bp):
AATAATAATAATAGTAATAAAAAAAT
Found at i:5359297 original size:21 final size:21
Alignment explanation
Indices: 5359271--5359454 Score: 115
Period size: 21 Copynumber: 9.0 Consensus size: 21
5359261 TTATGTTAAG
*
5359271 CTCTTATGAGCTTCTATTCAA
1 CTCTTATGAGCTTCTGTTCAA
* * * *
5359292 CTCTTATGAGTTTCTATTTAG
1 CTCTTATGAGCTTCTGTTCAA
* * * *
5359313 CTCTTACGAGCTTCTATTTAG
1 CTCTTATGAGCTTCTGTTCAA
* *
5359334 CT-TT-CGAGCTTTTGTTCAA
1 CTCTTATGAGCTTCTGTTCAA
* * * *
5359353 CTCTTATGAGTTTTTGTTTAG
1 CTCTTATGAGCTTCTGTTCAA
* *
5359374 CTCTTACGAGCTTATGTTC-A
1 CTCTTATGAGCTTCTGTTCAA
* *
5359394 -GCTTCTGAGCTTCTGTTCAA
1 CTCTTATGAGCTTCTGTTCAA
* * * *
5359414 CTCTTATGAGTTTTTGTTTAG
1 CTCTTATGAGCTTCTGTTCAA
* *
5359435 CTATTATGAGCTTCTATTCA
1 CTCTTATGAGCTTCTGTTCA
5359455 GTTTTCAAGT
Statistics
Matches: 126, Mismatches: 33, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
19 27 0.21
20 5 0.04
21 94 0.75
ACGTcount: A:0.18, C:0.19, G:0.15, T:0.47
Consensus pattern (21 bp):
CTCTTATGAGCTTCTGTTCAA
Found at i:5359343 original size:19 final size:21
Alignment explanation
Indices: 5359269--5359492 Score: 111
Period size: 21 Copynumber: 11.0 Consensus size: 21
5359259 CTTTATGTTA
* *
5359269 AGCTCTTATGAGCTTCTATTC
1 AGCTCTTACGAGCTTCTATTT
* * *
5359290 AACTCTTATGAGTTTCTATTT
1 AGCTCTTACGAGCTTCTATTT
5359311 AGCTCTTACGAGCTTCTATTT
1 AGCTCTTACGAGCTTCTATTT
* * *
5359332 AGCT-TT-CGAGCTTTTGTTC
1 AGCTCTTACGAGCTTCTATTT
* * * * *
5359351 AACTCTTATGAGTTTTTGTTT
1 AGCTCTTACGAGCTTCTATTT
* * *
5359372 AGCTCTTACGAGCTTATGTTC
1 AGCTCTTACGAGCTTCTATTT
* *
5359393 AG--CTT-CTGAGCTTCTGTTC
1 AGCTCTTAC-GAGCTTCTATTT
* * * * *
5359412 AACTCTTATGAGTTTTTGTTT
1 AGCTCTTACGAGCTTCTATTT
* * *
5359433 AGCTATTATGAGCTTCTATTC
1 AGCTCTTACGAGCTTCTATTT
* * * * *
5359454 AG-T-TTTCAAGTTTCTGTTC
1 AGCTCTTACGAGCTTCTATTT
5359473 AGCTCTTACGAGCTTCTATT
1 AGCTCTTACGAGCTTCTATT
5359493 GGTGTATTTA
Statistics
Matches: 156, Mismatches: 39, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
18 1 0.01
19 41 0.26
20 6 0.04
21 108 0.69
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.47
Consensus pattern (21 bp):
AGCTCTTACGAGCTTCTATTT
Found at i:5359373 original size:61 final size:61
Alignment explanation
Indices: 5359278--5359480 Score: 273
Period size: 61 Copynumber: 3.3 Consensus size: 61
5359268 AAGCTCTTAT
* * * *
5359278 GAGCTTCTATTCAACTCTTATGAGTTTCTATTTAGCTCTTACGAGCTTCTATTTAGCTTTC
1 GAGCTTCTGTTCAACTCTTATGAGTTTTTGTTTAGCTCTTACGAGCTTCTATTCAGCTTTC
* * *
5359339 GAGCTTTTGTTCAACTCTTATGAGTTTTTGTTTAGCTCTTACGAGCTTATGTTCAGC-TTC
1 GAGCTTCTGTTCAACTCTTATGAGTTTTTGTTTAGCTCTTACGAGCTTCTATTCAGCTTTC
* * *
5359399 TGAGCTTCTGTTCAACTCTTATGAGTTTTTGTTTAGCTATTATGAGCTTCTATTCAGTTTTC
1 -GAGCTTCTGTTCAACTCTTATGAGTTTTTGTTTAGCTCTTACGAGCTTCTATTCAGCTTTC
* * *
5359461 AAGTTTCTGTTCAGCTCTTA
1 GAGCTTCTGTTCAACTCTTA
5359481 CGAGCTTCTA
Statistics
Matches: 124, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
60 3 0.02
61 118 0.95
62 3 0.02
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.47
Consensus pattern (61 bp):
GAGCTTCTGTTCAACTCTTATGAGTTTTTGTTTAGCTCTTACGAGCTTCTATTCAGCTTTC
Found at i:5362617 original size:8 final size:9
Alignment explanation
Indices: 5362613--5362649 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
5362603 TTTAATAATA
5362613 AAAT-AAAT
1 AAATAAAAT
5362621 AAATAAAAT
1 AAATAAAAT
5362630 AAAT-AAAT
1 AAATAAAAT
*
5362638 AAATGAAAT
1 AAATAAAAT
5362647 AAA
1 AAA
5362650 AGAAATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 12 0.44
9 15 0.56
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (9 bp):
AAATAAAAT
Found at i:5362622 original size:4 final size:4
Alignment explanation
Indices: 5362613--5362649 Score: 56
Period size: 4 Copynumber: 8.8 Consensus size: 4
5362603 TTTAATAATA
5362613 AAAT AAAT AAAT AAAAT AAAT AAAT AAAT GAAAT AAA
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT -AAAT AAA
5362650 AGAAATGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 23 0.74
5 8 0.26
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5362627 original size:13 final size:13
Alignment explanation
Indices: 5362609--5362649 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
5362599 ATAGTTTAAT
5362609 AATAAAATAAATA
1 AATAAAATAAATA
5362622 AATAAAATAAATA
1 AATAAAATAAATA
5362635 AAT-AAATGAAATA
1 AATAAAAT-AAATA
5362648 AA
1 AA
5362650 AGAAATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 4 0.15
13 23 0.85
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (13 bp):
AATAAAATAAATA
Found at i:5362635 original size:17 final size:17
Alignment explanation
Indices: 5362613--5362649 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
5362603 TTTAATAATA
5362613 AAATAAATAAATAAAAT
1 AAATAAATAAATAAAAT
*
5362630 AAATAAATAAATGAAAT
1 AAATAAATAAATAAAAT
5362647 AAA
1 AAA
5362650 AGAAATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
AAATAAATAAATAAAAT
Found at i:5363936 original size:15 final size:15
Alignment explanation
Indices: 5363913--5363960 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
5363903 TATCAAATTT
5363913 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
5363928 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
5363943 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
5363957 ATAT
1 ATAT
5363961 ATTATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:5364616 original size:18 final size:19
Alignment explanation
Indices: 5364595--5364635 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5364585 AATGAAATGA
5364595 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
5364613 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
5364632 GAAA
1 GAAA
5364636 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:5366555 original size:44 final size:45
Alignment explanation
Indices: 5366467--5366555 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 45
5366457 CAGAACGAAA
*
5366467 TGAGCCATGTAAGTCCATATTAGAAATATGACTTTGGAGACAGGAT
1 TGAGCCATGTAAGTCCATATTA-AAATATGACATTGGAGACAGGAT
* *
5366513 TGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGGA
1 TGAGCCATGTAAGTCCATATTAAAATATGACATTGGAGACAGGA
5366556 ATAATTCATA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 19 0.47
46 21 0.52
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (45 bp):
TGAGCCATGTAAGTCCATATTAAAATATGACATTGGAGACAGGAT
Found at i:5366570 original size:44 final size:45
Alignment explanation
Indices: 5366469--5366574 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 45
5366459 GAACGAAATG
* * * *
5366469 AGCCATGTAAGTCCATATTAGAAATATGACTTTGGAGACAGGATTG
1 AGCCATATAAGTCCATATTA-AAATATGACATTGGAGACAGGAATA
* * *
5366515 AGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGGAATA
1 AGCCATATAAGTCCATATTAAAATATGACATTGGAGACAGGAATA
**
5366559 ATTCATATAAGTCCAT
1 AGCCATATAAGTCCAT
5366575 GTCAAAGACA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 33 0.63
46 19 0.37
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (45 bp):
AGCCATATAAGTCCATATTAAAATATGACATTGGAGACAGGAATA
Found at i:5373178 original size:20 final size:20
Alignment explanation
Indices: 5373153--5373192 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5373143 CTCACTACTT
5373153 TGACAAAAGGGACGGGGCTA
1 TGACAAAAGGGACGGGGCTA
5373173 TGACAAAAGGGACGGGGCTA
1 TGACAAAAGGGACGGGGCTA
5373193 GTAAAAGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.40, T:0.10
Consensus pattern (20 bp):
TGACAAAAGGGACGGGGCTA
Found at i:5377897 original size:13 final size:13
Alignment explanation
Indices: 5377879--5377903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5377869 TATACTTCTT
5377879 TAAAAAAGTCCTA
1 TAAAAAAGTCCTA
5377892 TAAAAAAGTCCT
1 TAAAAAAGTCCT
5377904 GTCTATTTAA
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:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (13 bp):
TAAAAAAGTCCTA
Found at i:5391256 original size:2 final size:2
Alignment explanation
Indices: 5391251--5391282 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5391241 GTGTGTGTGT
5391251 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5391283 CTATAAGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5392758 original size:24 final size:24
Alignment explanation
Indices: 5392723--5392768 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
5392713 ACCAAAAAAA
*
5392723 TAAATTTGTATTTAGTAAATTAAT
1 TAAATTTATATTTAGTAAATTAAT
5392747 TAAATTTATATTTAGTAAATTA
1 TAAATTTATATTTAGTAAATTA
5392769 GTGATGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (24 bp):
TAAATTTATATTTAGTAAATTAAT
Found at i:5399714 original size:29 final size:29
Alignment explanation
Indices: 5399669--5399724 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
5399659 CTACAAATGA
*
5399669 TGTTTTAACTCTATAGTTATTCAGGATTG
1 TGTTTAAACTCTATAGTTATTCAGGATTG
*
5399698 TGTTTAAACTCTGTAGTTATTCAGGAT
1 TGTTTAAACTCTATAGTTATTCAGGAT
5399725 AACCAATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (29 bp):
TGTTTAAACTCTATAGTTATTCAGGATTG
Found at i:5404649 original size:9 final size:9
Alignment explanation
Indices: 5404625--5404671 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
5404615 TGGCTGAAGC
5404625 TCTTCCTCT
1 TCTTCCTCT
* *
5404634 TCATCCTCG
1 TCTTCCTCT
5404643 TCTTCCTCT
1 TCTTCCTCT
*
5404652 TCTTCTTCT
1 TCTTCCTCT
*
5404661 TCCTCCTCT
1 TCTTCCTCT
5404670 TC
1 TC
5404672 CTCACCATCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.02, C:0.45, G:0.02, T:0.51
Consensus pattern (9 bp):
TCTTCCTCT
Found at i:5404658 original size:24 final size:24
Alignment explanation
Indices: 5404624--5404674 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
5404614 GTGGCTGAAG
*
5404624 CTCTTCCTCTTCATCCTCGTCTTC
1 CTCTTCCTCTTCATCCTCCTCTTC
* *
5404648 CTCTTCTTCTTCTTCCTCCTCTTC
1 CTCTTCCTCTTCATCCTCCTCTTC
5404672 CTC
1 CTC
5404675 ACCATCATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.02, C:0.47, G:0.02, T:0.49
Consensus pattern (24 bp):
CTCTTCCTCTTCATCCTCCTCTTC
Found at i:5404717 original size:15 final size:15
Alignment explanation
Indices: 5404697--5404725 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5404687 GTCGTCATCG
5404697 TCATCATCCTCGTCC
1 TCATCATCCTCGTCC
5404712 TCATCATCCTCGTC
1 TCATCATCCTCGTC
5404726 TCCACTGGCA
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:0.14, C:0.45, G:0.07, T:0.34
Consensus pattern (15 bp):
TCATCATCCTCGTCC
Found at i:5404844 original size:21 final size:21
Alignment explanation
Indices: 5404791--5404845 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
5404781 TCACCAGATG
*
5404791 CATCCTCCTCATCTGCATCTT
1 CATCTTCCTCATCTGCATCTT
** *
5404812 CATCTTGATCATCT-CCTGCTT
1 CATCTTCCTCATCTGCAT-CTT
5404833 CATCTTCCTCATC
1 CATCTTCCTCATC
5404846 CTCATCATCC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.15, C:0.40, G:0.05, T:0.40
Consensus pattern (21 bp):
CATCTTCCTCATCTGCATCTT
Found at i:5414599 original size:14 final size:14
Alignment explanation
Indices: 5414580--5414607 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5414570 CAATGCGGAA
5414580 AATAACGCATTAGT
1 AATAACGCATTAGT
5414594 AATAACGCATTAGT
1 AATAACGCATTAGT
5414608 TCTAAAGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
AATAACGCATTAGT
Found at i:5414860 original size:18 final size:17
Alignment explanation
Indices: 5414818--5414866 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 17
5414808 AAAAAGTTCA
5414818 TAAATATTTTTAAAAATT
1 TAAAT-TTTTTAAAAATT
*
5414836 AATAATTTTTTAAAAATTT
1 TA-AATTTTTTAAAAA-TT
5414855 TAAATTATTTTA
1 TAAATT-TTTTA
5414867 CCATTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATTTTTTAAAAATT
Found at i:5421393 original size:17 final size:17
Alignment explanation
Indices: 5421373--5421405 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5421363 TTTTTTTTAA
5421373 TAAATAATTA-TTAAATT
1 TAAAT-ATTAGTTAAATT
5421390 TAAATATTAGTTAAAT
1 TAAATATTAGTTAAAT
5421406 CAGATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TAAATATTAGTTAAATT
Found at i:5439098 original size:14 final size:14
Alignment explanation
Indices: 5439079--5439105 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5439069 ATACAAATTA
5439079 AATATTTTTTTATT
1 AATATTTTTTTATT
5439093 AATATTTTTTTAT
1 AATATTTTTTTAT
5439106 AAAAAGAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
AATATTTTTTTATT
Found at i:5441778 original size:19 final size:20
Alignment explanation
Indices: 5441742--5441781 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5441732 AAATTAATAT
*
5441742 AAAATTTTAAAGTATTTATA
1 AAAATTTCAAAGTATTTATA
*
5441762 AAAATTTCAAA-TTTTTATA
1 AAAATTTCAAAGTATTTATA
5441781 A
1 A
5441782 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
AAAATTTCAAAGTATTTATA
Found at i:5441820 original size:22 final size:22
Alignment explanation
Indices: 5441789--5441830 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5441779 TAATTTTTTA
*
5441789 AAAATTATAAATTAAAAAATCT
1 AAAATAATAAATTAAAAAATCT
* *
5441811 AAAATAATAATTTTAAAAAT
1 AAAATAATAAATTAAAAAAT
5441831 TGAAATTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAATAATAAATTAAAAAATCT
Found at i:5444371 original size:16 final size:16
Alignment explanation
Indices: 5444352--5444402 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
5444342 AGAGTGAAAT
5444352 AAAATTAGAAAAATAA
1 AAAATTAGAAAAATAA
** *
5444368 AAAATT-GAAAGGTTA
1 AAAATTAGAAAAATAA
*
5444383 AAAACTAGAAAAATAA
1 AAAATTAGAAAAATAA
5444399 AAAA
1 AAAA
5444403 ATTTCATCTA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.18
Consensus pattern (16 bp):
AAAATTAGAAAAATAA
Found at i:5454610 original size:14 final size:16
Alignment explanation
Indices: 5454584--5454617 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5454574 CGAGGGTGCC
5454584 TTTTTCTCTTCTTTT-
1 TTTTTCTCTTCTTTTA
5454599 TTTTTCTC-TCTTTTA
1 TTTTTCTCTTCTTTTA
5454614 TTTT
1 TTTT
5454618 GATTTTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTCTCTTCTTTTA
Found at i:5464610 original size:51 final size:50
Alignment explanation
Indices: 5464451--5464607 Score: 251
Period size: 51 Copynumber: 3.1 Consensus size: 50
5464441 ACTTCTGATC
* *
5464451 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAGTGACA
* *
5464502 AGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
*
5464552 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
5464603 AGTGA
1 AGTGA
5464608 TAAATGTGAT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
50 46 0.47
51 52 0.53
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
Found at i:5469208 original size:75 final size:75
Alignment explanation
Indices: 5469089--5469259 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
5469079 CATGGCAAAG
** *
5469089 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
5469148 CCATACTGAGC
65 CCATACCGAGC
5469159 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
5469224 CATACCGAGT
66 CATACCGAGC
***
5469234 TAAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
5469260 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:5469227 original size:35 final size:35
Alignment explanation
Indices: 5469092--5469257 Score: 174
Period size: 35 Copynumber: 4.6 Consensus size: 35
5469082 GGCAAAGTGT
* **
5469092 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
5469127 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
5469162 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
5469202 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
*
5469237 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
5469258 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
35 85 0.73
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:5476708 original size:75 final size:74
Alignment explanation
Indices: 5476587--5476758 Score: 216
Period size: 75 Copynumber: 2.4 Consensus size: 74
5476577 TCCATGGCAA
** *
5476587 AGTGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTA
1 AGTGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-
*
5476647 T-CCATACTG
65 TCCCATACCG
5476656 AGCTGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT
1 AG-TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT
5476721 TCCCATACCG
65 TCCCATACCG
*
5476731 AGT-TAAAAATGTAGGTATGGTATT-TCAA
1 AGTGT-GAAATGTAGGTATGGTATTATCAA
5476759 TGAGGAAAAC
Statistics
Matches: 90, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
69 2 0.02
70 18 0.20
73 9 0.10
74 20 0.22
75 41 0.46
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (74 bp):
AGTGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTT
CCCATACCG
Found at i:5476727 original size:35 final size:35
Alignment explanation
Indices: 5476592--5476756 Score: 174
Period size: 35 Copynumber: 4.6 Consensus size: 35
5476582 GGCAAAGTGT
* **
5476592 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
5476627 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
5476662 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
5476702 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
5476737 -AAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
5476757 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
34 19 0.16
35 66 0.57
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:5480635 original size:19 final size:20
Alignment explanation
Indices: 5480606--5480646 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
5480596 TGAATAAATC
5480606 TTTTAACAAAAAAAAATTAA
1 TTTTAACAAAAAAAAATTAA
**
5480626 TTTT-ACAAAAATTAATTAA
1 TTTTAACAAAAAAAAATTAA
5480645 TT
1 TT
5480647 AATTTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTTAACAAAAAAAAATTAA
Found at i:5484385 original size:75 final size:75
Alignment explanation
Indices: 5484266--5484436 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
5484256 CATGGCAAAG
** *
5484266 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
5484325 CCATACTGAGC
65 CCATACCGAGC
5484336 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
5484401 CATACCGAGT
66 CATACCGAGC
***
5484411 TAAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
5484437 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:5484404 original size:35 final size:35
Alignment explanation
Indices: 5484269--5484434 Score: 174
Period size: 35 Copynumber: 4.6 Consensus size: 35
5484259 GGCAAAGTGT
* **
5484269 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
5484304 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
5484339 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
5484379 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
*
5484414 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
5484435 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
35 85 0.73
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:5492065 original size:75 final size:75
Alignment explanation
Indices: 5491946--5492116 Score: 212
Period size: 75 Copynumber: 2.4 Consensus size: 75
5491936 CATGGCAAAG
** *
5491946 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
5492005 CCATACTGAGC
65 CCATACCGAGC
5492016 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
5492081 CATACCGAGT
66 CATACCGAGC
***
5492091 TAAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
5492117 TGAGGAAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 60 0.69
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:5492084 original size:35 final size:35
Alignment explanation
Indices: 5491949--5492114 Score: 174
Period size: 35 Copynumber: 4.6 Consensus size: 35
5491939 GGCAAAGTGT
* **
5491949 GAAATGTAGGTATGGTATCAT-CCATACTGAGTTGT
1 GAAATGTAGGTATGGTAT-TTCCCATACTGAGTTAA
* **
5491984 GAAATGTAGGTATGGTATTAT-CCATACTGAGCTGT
1 GAAATGTAGGTATGGTATT-TCCCATACTGAGTTAA
5492019 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATT-TC----CCATACTGAGTTAA
* *
5492059 GAAATGTAGGTATGGCATTTCCCATACCGAGTTAA
1 GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
*
5492094 AAAATGTAGGTATGGTATTTC
1 GAAATGTAGGTATGGTATTTC
5492115 AATGAGGAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
35 85 0.73
39 2 0.02
40 29 0.25
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTTCCCATACTGAGTTAA
Found at i:5514009 original size:36 final size:36
Alignment explanation
Indices: 5513969--5514042 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
5513959 TCATTACAGT
5513969 AGTAATCAACGTATATATGGTAGCTAAAAGGGTCAG
1 AGTAATCAACGTATATATGGTAGCTAAAAGGGTCAG
5514005 AGTAATCAACGTATATATGGTAGCTAAAAGGGTCAG
1 AGTAATCAACGTATATATGGTAGCTAAAAGGGTCAG
5514041 AG
1 AG
5514043 AAACAAAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (36 bp):
AGTAATCAACGTATATATGGTAGCTAAAAGGGTCAG
Found at i:5538539 original size:15 final size:17
Alignment explanation
Indices: 5538518--5538558 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
5538508 TAATCATTTA
5538518 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
5538534 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
5538550 AAAATTATA
1 AAAATTATA
5538559 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:5539001 original size:2 final size:2
Alignment explanation
Indices: 5538994--5539025 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5538984 TATTAATGAC
5538994 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5539026 GAGAACTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5542945 original size:96 final size:96
Alignment explanation
Indices: 5542781--5542973 Score: 305
Period size: 96 Copynumber: 2.0 Consensus size: 96
5542771 TCAAGTGTAG
* * * *
5542781 TGAAGGTGAAAACTTAGCTATGGAACCATCAGTTATTGAAAAGGAAGGGTATCTTATGGTCCAAC
1 TGAAGATGAAAACTTAGCAATGGAACCATCAGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
*
5542846 CTAGTCGACAGGGAAGTTACATTCCTGATAA
66 CTAGGCGACAGGGAAGTTACATTCCTGATAA
* *
5542877 TGAAGATGAAAACTTTGCAATGGAACCATCGGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
1 TGAAGATGAAAACTTAGCAATGGAACCATCAGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
* *
5542942 CTAGGCGACAGGGAAGTTATATTCCTGGTAA
66 CTAGGCGACAGGGAAGTTACATTCCTGATAA
5542973 T
1 T
5542974 CTTGGCTCAT
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 88 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (96 bp):
TGAAGATGAAAACTTAGCAATGGAACCATCAGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
CTAGGCGACAGGGAAGTTACATTCCTGATAA
Found at i:5547589 original size:2 final size:2
Alignment explanation
Indices: 5547582--5547614 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5547572 TTTCTTTGCA
5547582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5547615 CTTTAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5562562 original size:4 final size:4
Alignment explanation
Indices: 5562553--5562598 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
5562543 TTGTCAATTG
5562553 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
5562599 ATCAAAGCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:5569667 original size:20 final size:21
Alignment explanation
Indices: 5569642--5569681 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5569632 CGTTGAGTTT
*
5569642 GTGGCA-GGGTCTCAAGGATA
1 GTGGCATGGATCTCAAGGATA
5569662 GTGGCATTGGATCTCAAGGA
1 GTGGCA-TGGATCTCAAGGA
5569682 ATCACCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.25, C:0.15, G:0.38, T:0.23
Consensus pattern (21 bp):
GTGGCATGGATCTCAAGGATA
Found at i:5572083 original size:21 final size:19
Alignment explanation
Indices: 5572058--5572096 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
5572048 AAATTATATG
5572058 AATAAAAAATGATCTTTTAAT
1 AATAAAAAATG-T-TTTTAAT
*
5572079 AATAAATAATGTTTTTAA
1 AATAAAAAATGTTTTTAA
5572097 CTATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
AATAAAAAATGTTTTTAAT
Found at i:5596556 original size:6 final size:6
Alignment explanation
Indices: 5596545--5596571 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5596535 GGTGCTGCTG
5596545 ATGCAA ATGCAA ATGCAA ATGCAA ATG
1 ATGCAA ATGCAA ATGCAA ATGCAA ATG
5596572 GGTGCTGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
ATGCAA
Found at i:5599782 original size:14 final size:14
Alignment explanation
Indices: 5599763--5599790 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5599753 TCTATTTCCT
5599763 TAAATAAAATAAAA
1 TAAATAAAATAAAA
5599777 TAAATAAAATAAAA
1 TAAATAAAATAAAA
5599791 ATGACTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAATAAAATAAAA
Found at i:5610671 original size:5 final size:5
Alignment explanation
Indices: 5610655--5610687 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
5610645 ATAAACCACT
*
5610655 GCATA GCTTA GCATA GCATA GCATA GCA-A GCAT
1 GCATA GCATA GCATA GCATA GCATA GCATA GCAT
5610688 TATAGCTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (5 bp):
GCATA
Found at i:5611400 original size:44 final size:44
Alignment explanation
Indices: 5611351--5611439 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
5611341 AAGTATACAC
5611351 ATGTATATTCAGTGGACTAAAACAATAAAAGTAGGAATCAACAG
1 ATGTATATTCAGTGGACTAAAACAATAAAAGTAGGAATCAACAG
*
5611395 ATGTATATTCAGTGGACTAAAATAATAAAAGTAGGAATCAACAG
1 ATGTATATTCAGTGGACTAAAACAATAAAAGTAGGAATCAACAG
5611439 A
1 A
5611440 GCTGATGGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (44 bp):
ATGTATATTCAGTGGACTAAAACAATAAAAGTAGGAATCAACAG
Found at i:5614838 original size:2 final size:2
Alignment explanation
Indices: 5614831--5614865 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5614821 AACTAATCCT
5614831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5614866 TAAATTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5615435 original size:2 final size:2
Alignment explanation
Indices: 5615422--5615451 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5615412 TTTTATTCAA
*
5615422 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5615452 CTTTTATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5621244 original size:21 final size:21
Alignment explanation
Indices: 5621218--5621261 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5621208 ATAAGAACAA
5621218 AAACTAGTATTTAATTCAAAC
1 AAACTAGTATTTAATTCAAAC
5621239 AAACTAGTATTTAATTCAAAC
1 AAACTAGTATTTAATTCAAAC
5621260 AA
1 AA
5621262 CTGATTGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.32
Consensus pattern (21 bp):
AAACTAGTATTTAATTCAAAC
Found at i:5631157 original size:2 final size:2
Alignment explanation
Indices: 5631144--5631176 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5631134 GAAAAGGTTA
*
5631144 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5631177 GCTTCTTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5635579 original size:17 final size:18
Alignment explanation
Indices: 5635543--5635580 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5635533 TATCATTCTT
*
5635543 TTATTTTGATTGAGGGTA
1 TTATTTTGATTCAGGGTA
*
5635561 TTATTTTG-TTCATGGTA
1 TTATTTTGATTCAGGGTA
5635578 TTA
1 TTA
5635581 CCTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.21, C:0.03, G:0.21, T:0.55
Consensus pattern (18 bp):
TTATTTTGATTCAGGGTA
Found at i:5638292 original size:75 final size:75
Alignment explanation
Indices: 5638119--5638294 Score: 253
Period size: 75 Copynumber: 2.3 Consensus size: 75
5638109 AAGCCACGTT
* * * * * *
5638119 AGGGAGTGGTGGAGGAGGAGGGGAAGCTGAAGATGAATTATTTACGGTAGAAGATGGAGATATAG
1 AGGGAGTGGTGGAGGGGGAGGGGGAGCTGAAAACGAATTATTTACAGAAGAAGATGGAGATATAG
5638184 CTGAGAATGG
66 CTGAGAATGG
* * *
5638194 AGGGAGTGGGGGAGGGGGAGGGGGAGCTGAAAACGAATTCTTTACAGAAGAAGATGGAGATGTAG
1 AGGGAGTGGTGGAGGGGGAGGGGGAGCTGAAAACGAATTATTTACAGAAGAAGATGGAGATATAG
*
5638259 CTGAGGATGG
66 CTGAGAATGG
*
5638269 AGGGAGTGGTGGTGGGGGAGGGGGAG
1 AGGGAGTGGTGGAGGGGGAGGGGGAG
5638295 ACTGGCACAA
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 89 1.00
ACGTcount: A:0.30, C:0.05, G:0.49, T:0.17
Consensus pattern (75 bp):
AGGGAGTGGTGGAGGGGGAGGGGGAGCTGAAAACGAATTATTTACAGAAGAAGATGGAGATATAG
CTGAGAATGG
Found at i:5643042 original size:22 final size:21
Alignment explanation
Indices: 5642991--5643043 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 21
5642981 TAAGAATAAA
5642991 TTAAAATTATAATGATTAAAAT
1 TTAAAA-TATAATGATTAAAAT
*
5643013 TCAAAATATAATTGATTAAAAT
1 TTAAAATATAA-TGATTAAAAT
5643035 TTAAAATAT
1 TTAAAATAT
5643044 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (21 bp):
TTAAAATATAATGATTAAAAT
Found at i:5648002 original size:47 final size:47
Alignment explanation
Indices: 5647893--5648003 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
5647883 CCGGGATAAG
*
5647893 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
5647940 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
5647987 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
5648004 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:5648775 original size:4 final size:4
Alignment explanation
Indices: 5648766--5648790 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5648756 CCCTTTTCTA
5648766 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
5648791 CAAGTTTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:5649338 original size:25 final size:27
Alignment explanation
Indices: 5649304--5649357 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
5649294 AACCTTGAAA
* *
5649304 TCCCTAATTTCCCTT-TCTTTTTC-TT
1 TCCCCAATTTCCCTTCTCTGTTTCGTT
*
5649329 TCCCCAATTTTCCTTCTCTGTTTCGTT
1 TCCCCAATTTCCCTTCTCTGTTTCGTT
5649356 TC
1 TC
5649358 ATATTCTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 13 0.54
26 7 0.29
27 4 0.17
ACGTcount: A:0.07, C:0.33, G:0.04, T:0.56
Consensus pattern (27 bp):
TCCCCAATTTCCCTTCTCTGTTTCGTT
Found at i:5649593 original size:29 final size:29
Alignment explanation
Indices: 5649560--5649616 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
5649550 AATTAATATA
* *
5649560 AAATAAT-ATTAATACAATAATATTTACTT
1 AAATAATAAGTAA-ACAATAATAATTACTT
5649589 AAATAATAAGTAAACAATAATAATTACT
1 AAATAATAAGTAAACAATAATAATTACT
5649617 AATATATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (29 bp):
AAATAATAAGTAAACAATAATAATTACTT
Found at i:5657666 original size:5 final size:5
Alignment explanation
Indices: 5657656--5657680 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5657646 TTGCTAGCTG
5657656 GCCTC GCCTC GCCTC GCCTC GCCTC
1 GCCTC GCCTC GCCTC GCCTC GCCTC
5657681 CCACACAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.20, T:0.20
Consensus pattern (5 bp):
GCCTC
Found at i:5663795 original size:29 final size:30
Alignment explanation
Indices: 5663739--5663795 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
5663729 TTCTATACAT
* * *
5663739 AAATTTTGATTTTATATAGTTTTATATATA
1 AAATTTTAATTTGATATAATTTTATATATA
*
5663769 AAATTTTAATTTGATCTAATTTT-TATA
1 AAATTTTAATTTGATATAATTTTATATA
5663796 AATTATTAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 4 0.17
30 19 0.83
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (30 bp):
AAATTTTAATTTGATATAATTTTATATATA
Found at i:5666521 original size:23 final size:24
Alignment explanation
Indices: 5666485--5666532 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
5666475 AAACATATAT
5666485 TTTTATACATTAAAAATTATTTAAA
1 TTTTATACATTAAAAATT-TTTAAA
*
5666510 TTTTAT-CA-TAAATATTTTTAAA
1 TTTTATACATTAAAAATTTTTAAA
5666532 T
1 T
5666533 GATTATCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 7 0.32
24 2 0.09
25 6 0.27
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTTATACATTAAAAATTTTTAAA
Found at i:5666538 original size:23 final size:23
Alignment explanation
Indices: 5666495--5666539 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5666485 TTTTATACAT
*
5666495 TAAAAATTATTTAAATTTTATCA
1 TAAAAATTATTTAAATATTATCA
*
5666518 TAAATATT-TTTAAATGATTATC
1 TAAAAATTATTTAAAT-ATTATC
5666540 CTTCAAAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAAATTATTTAAATATTATCA
Found at i:5671427 original size:15 final size:17
Alignment explanation
Indices: 5671397--5671428 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5671387 ATTAACATCT
5671397 AAATATAAATATAATTA
1 AAATATAAATATAATTA
5671414 AAAT-TAAA-ATAATTA
1 AAATATAAATATAATTA
5671429 GTTAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATAAATATAATTA
Found at i:5672462 original size:12 final size:11
Alignment explanation
Indices: 5672443--5672473 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
5672433 TATATAAAAC
5672443 TTATTTTATTA
1 TTATTTTATTA
5672454 TTAATTTTATTA
1 TT-ATTTTATTA
5672466 TTATTTTA
1 TTATTTTA
5672474 AAGGTATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:5672489 original size:30 final size:30
Alignment explanation
Indices: 5672454--5672513 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
5672444 TATTTTATTA
*
5672454 TTAATTTTATTATTATTTTAAAGGTATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
* *
5672484 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTATTATTATTTTAAAGGCATTTG
5672514 CTTATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.58
Consensus pattern (30 bp):
TTAATTTTATTATTATTTTAAAGGCATTTG
Found at i:5672610 original size:25 final size:23
Alignment explanation
Indices: 5672553--5672610 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 23
5672543 TTTAAGTCTA
5672553 CATATTTTTA-AAAATTTATTTT
1 CATATTTTTAGAAAATTTATTTT
5672575 CA-ATTTGTTAGGAAATATTTATTTT
1 CATATTT-TTA-GAAA-ATTTATTTT
*
5672600 GATATTTTTAG
1 CATATTTTTAG
5672611 TATTTTTGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
21 4 0.13
22 5 0.17
24 4 0.13
25 13 0.43
26 4 0.13
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (23 bp):
CATATTTTTAGAAAATTTATTTT
Found at i:5674594 original size:28 final size:28
Alignment explanation
Indices: 5674562--5674624 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
5674552 TCCCATATTA
5674562 ATGGGGTATAGGAAAAGTTTCATAACTT
1 ATGGGGTATAGGAAAAGTTTCATAACTT
* *
5674590 ATGGGGTATAGGAAGAGTTTTATAACTT
1 ATGGGGTATAGGAAAAGTTTCATAACTT
5674618 ATGGGGT
1 ATGGGGT
5674625 TGATAATGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (28 bp):
ATGGGGTATAGGAAAAGTTTCATAACTT
Found at i:5677526 original size:21 final size:21
Alignment explanation
Indices: 5677493--5677565 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
5677483 GCACTTTATT
5677493 TGTCGTATTTCAGGCACCTCTTG
1 TGTCGTA--TCAGGCACCTCTTG
*
5677516 TGTCGTATCAGGCACCTCGTG
1 TGTCGTATCAGGCACCTCTTG
* * *
5677537 TGTCGTTTTAGGCA-CTTTATG
1 TGTCGTATCAGGCACCTCT-TG
5677558 TGTCGTAT
1 TGTCGTAT
5677566 ACTGATCAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.05
21 34 0.79
23 7 0.16
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.40
Consensus pattern (21 bp):
TGTCGTATCAGGCACCTCTTG
Found at i:5680174 original size:62 final size:62
Alignment explanation
Indices: 5680077--5680201 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
5680067 AAGACGATGA
*
5680077 CCACGATGTGGTAATAGGTATATTTTTACTGTATTCTGAGCCTGTTTATGCTTTAATTGATC
1 CCACGATGTGGTAACAGGTATATTTTTACTGTATTCTGAGCCTGTTTATGCTTTAATTGATC
5680139 CCACGATGTGGTAACAGGTATATTTTTACTGTATTCTGAGCCTGTTTATGCTTTAATTGATC
1 CCACGATGTGGTAACAGGTATATTTTTACTGTATTCTGAGCCTGTTTATGCTTTAATTGATC
5680201 C
1 C
5680202 TGGATCTTCA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.42
Consensus pattern (62 bp):
CCACGATGTGGTAACAGGTATATTTTTACTGTATTCTGAGCCTGTTTATGCTTTAATTGATC
Found at i:5681390 original size:11 final size:11
Alignment explanation
Indices: 5681374--5681398 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5681364 AATTCGGGTT
5681374 GATCCAAAGAA
1 GATCCAAAGAA
5681385 GATCCAAAGAA
1 GATCCAAAGAA
5681396 GAT
1 GAT
5681399 TGAAGCGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.20, T:0.12
Consensus pattern (11 bp):
GATCCAAAGAA
Found at i:5683959 original size:26 final size:29
Alignment explanation
Indices: 5683916--5683969 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 29
5683906 TAAAGTGAAT
*
5683916 AAAAGAAACAGAGTAAAGA-AA-AGAAAC
1 AAAAGAAACAGAGAAAAGAGAACAGAAAC
*
5683943 AAAA-AAATAGAGAAAAGAGAACAGAAA
1 AAAAGAAACAGAGAAAAGAGAACAGAAA
5683970 GCATTCGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 12 0.52
27 6 0.26
28 5 0.22
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.04
Consensus pattern (29 bp):
AAAAGAAACAGAGAAAAGAGAACAGAAAC
Found at i:5684460 original size:23 final size:23
Alignment explanation
Indices: 5684430--5684516 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
5684420 GTTTTACTGA
* *
5684430 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
5684453 TCAGGCACCTCATGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
5684474 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* * *
5684496 T-AGGCACTTTATGTGCCGTAT
1 TCAGGCACCTCATGTGTCGTAT
5684517 ACTGATCAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
21 33 0.61
22 2 0.04
23 19 0.35
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:5688998 original size:28 final size:28
Alignment explanation
Indices: 5688937--5688999 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
5688927 TCTTATATTA
*
5688937 ATGGGATACAGGAAGAGTTTTATAACTT
1 ATGGGGTACAGGAAGAGTTTTATAACTT
*
5688965 ATGGGGTATAGGAAGAGTTTTATAACTT
1 ATGGGGTACAGGAAGAGTTTTATAACTT
5688993 ATGGGGT
1 ATGGGGT
5689000 TGATAATGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (28 bp):
ATGGGGTACAGGAAGAGTTTTATAACTT
Found at i:5693498 original size:12 final size:12
Alignment explanation
Indices: 5693481--5693505 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5693471 TAGAACCAAC
5693481 AGTTCATTATCT
1 AGTTCATTATCT
5693493 AGTTCATTATCT
1 AGTTCATTATCT
5693505 A
1 A
5693506 ATGGATTTTT
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:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (12 bp):
AGTTCATTATCT
Found at i:5693623 original size:33 final size:33
Alignment explanation
Indices: 5693584--5693649 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
5693574 AGAAGACTAT
5693584 TGGATCAAATGACAAAGACATTGTTGAGAAAAA
1 TGGATCAAATGACAAAGACATTGTTGAGAAAAA
*
5693617 TGGATCAAATGGCAAAGACATTGTTGAGAAAAA
1 TGGATCAAATGACAAAGACATTGTTGAGAAAAA
5693650 GATGGTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.47, C:0.09, G:0.23, T:0.21
Consensus pattern (33 bp):
TGGATCAAATGACAAAGACATTGTTGAGAAAAA
Found at i:5693725 original size:12 final size:12
Alignment explanation
Indices: 5693708--5693732 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5693698 AAGATATATG
5693708 GTCATGAAATAA
1 GTCATGAAATAA
5693720 GTCATGAAATAA
1 GTCATGAAATAA
5693732 G
1 G
5693733 AATTAAGTAA
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:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (12 bp):
GTCATGAAATAA
Found at i:5712111 original size:15 final size:16
Alignment explanation
Indices: 5712093--5712125 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5712083 ATTTTTGTAT
*
5712093 TATTTT-AATATTAAA
1 TATTTTAAAGATTAAA
5712108 TATTTTAAAGATTAAA
1 TATTTTAAAGATTAAA
5712124 TA
1 TA
5712126 AATTCTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TATTTTAAAGATTAAA
Found at i:5720119 original size:29 final size:29
Alignment explanation
Indices: 5720077--5720132 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
5720067 GTGAAAGCAT
*
5720077 ATATCTGACATTAGAATATAAATCCATCC
1 ATATCTGACATTAGAATATAAAACCATCC
* * *
5720106 ATATCTTACGTTAGCATATAAAACCAT
1 ATATCTGACATTAGAATATAAAACCAT
5720133 TAATATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (29 bp):
ATATCTGACATTAGAATATAAAACCATCC
Found at i:5745538 original size:22 final size:22
Alignment explanation
Indices: 5745510--5745553 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5745500 GACATTTCTT
5745510 ATGACTTTGTCTAGAGCTGCTG
1 ATGACTTTGTCTAGAGCTGCTG
5745532 ATGACTTTGTCTAGAGCTGCTG
1 ATGACTTTGTCTAGAGCTGCTG
5745554 TAACACCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.36
Consensus pattern (22 bp):
ATGACTTTGTCTAGAGCTGCTG
Found at i:5746901 original size:28 final size:27
Alignment explanation
Indices: 5746870--5746926 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 27
5746860 AAAAAAACCT
*
5746870 AACCCAAAAAAAAAATGAAAAAATGAAA
1 AACCCAAAAAAAAAAT-AAAAAATAAAA
* *
5746898 AACCTAACAAAAAAATAAAAAATAAAA
1 AACCCAAAAAAAAAATAAAAAATAAAA
5746925 AA
1 AA
5746927 AAACCTAGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.77, C:0.11, G:0.04, T:0.09
Consensus pattern (27 bp):
AACCCAAAAAAAAAATAAAAAATAAAA
Found at i:5746925 original size:33 final size:32
Alignment explanation
Indices: 5746862--5746926 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
5746852 GCCCCCCAAA
**
5746862 AAAAACCTAACCCAAAAAAAAAATGAAAAAATG
1 AAAAACCTAACAAAAAAAAAAAAT-AAAAAATG
5746895 AAAAACCTAACAAAAAAATAAAAAATAAAAAA
1 AAAAACCTAAC-AAAAAA-AAAAAATAAAAAA
5746927 AAACCTAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 11 0.39
34 10 0.36
35 7 0.25
ACGTcount: A:0.75, C:0.12, G:0.03, T:0.09
Consensus pattern (32 bp):
AAAAACCTAACAAAAAAAAAAAATAAAAAATG
Found at i:5747164 original size:18 final size:17
Alignment explanation
Indices: 5747125--5747163 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5747115 CCTAAAGGTG
*
5747125 ATTTTATCTTCTTTATT
1 ATTTTATCTTATTTATT
5747142 ATTTTACTCTTATTT-TT
1 ATTTTA-TCTTATTTATT
5747159 ATTTT
1 ATTTT
5747164 TTTTCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTATCTTATTTATT
Found at i:5747673 original size:11 final size:11
Alignment explanation
Indices: 5747655--5747684 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5747645 GTGTATATTG
5747655 TATATATTATA
1 TATATATTATA
*
5747666 TTTATATTATA
1 TATATATTATA
5747677 TATATATT
1 TATATATT
5747685 CTTAATGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATATTATA
Found at i:5750459 original size:21 final size:21
Alignment explanation
Indices: 5750435--5750506 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 21
5750425 CTTTCTGAAA
5750435 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* * * *
5750456 TGAAA-GATACTATGGCAACATGAT
1 TGAAATG-T-GTA-AG-ACCATGGT
5750480 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
5750502 TGAAA
1 TGAAA
5750507 GATACCATGG
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
20 1 0.03
21 11 0.30
22 8 0.22
23 2 0.05
24 8 0.22
25 6 0.16
26 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.26
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:5750485 original size:25 final size:25
Alignment explanation
Indices: 5750456--5750531 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
5750446 AGACCATGGT
5750456 TGAAAGATACTATGGCAACATGATA
1 TGAAAGATACTATGGCAACATGATA
* * * *
5750481 TGAAATG-T-GTA-AG-ACCATGGT-
1 TGAAA-GATACTATGGCAACATGATA
*
5750502 TGAAAGATACCATGGCAACATGATA
1 TGAAAGATACTATGGCAACATGATA
5750527 TGAAA
1 TGAAA
5750532 TGTGTAAGAC
Statistics
Matches: 36, Mismatches: 9, Indels: 12
0.63 0.16 0.21
Matches are distributed among these distances:
20 1 0.03
21 6 0.17
22 7 0.19
23 2 0.06
24 8 0.22
25 11 0.31
26 1 0.03
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (25 bp):
TGAAAGATACTATGGCAACATGATA
Found at i:5750793 original size:46 final size:46
Alignment explanation
Indices: 5750434--5750781 Score: 459
Period size: 46 Copynumber: 7.6 Consensus size: 46
5750424 GCTTTCTGAA
*
5750434 ATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
5750480 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
5750526 ATGAAATGTGTAAGACCATGGTTGAAAAATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
5750572 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATTGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
5750618 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG--
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* ** * * ** * *
5750662 ACGAGAATGAATAAGACCGTCGTTGAAAGATACCATGGCAATGTAAC
1 ATGA-AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*** * * *
5750709 ATGAAATGAACAAGACAATGGTTGAAAGATACCATGGCAACCTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
5750755 A-GAAAATGAGTAAGACCATAGTTGAAA
1 ATG-AAATGTGTAAGACCATGGTTGAAA
5750782 AACACTATGG
Statistics
Matches: 269, Mismatches: 29, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
44 3 0.01
45 34 0.13
46 229 0.85
47 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:5751100 original size:16 final size:17
Alignment explanation
Indices: 5751079--5751111 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5751069 ATGATGGAGC
5751079 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
5751095 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
5751112 TATTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:5751546 original size:17 final size:17
Alignment explanation
Indices: 5751526--5751559 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5751516 TAAATGACTC
5751526 AGAATTATCTGAAAATG
1 AGAATTATCTGAAAATG
5751543 AGAATTATCTGAAAATG
1 AGAATTATCTGAAAATG
5751560 TTCAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (17 bp):
AGAATTATCTGAAAATG
Found at i:5752464 original size:46 final size:47
Alignment explanation
Indices: 5752401--5752721 Score: 438
Period size: 46 Copynumber: 7.0 Consensus size: 47
5752391 TTCGACATGA
* * * * *
5752401 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
* ** * *** *
5752447 TGCCATGGTATCATTCAACCATGGTCTTATTCATTTCCCCGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
* * *
5752494 TGCCATAGTATCTTTCAACCATGGTCTTACACA-TTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
*
5752540 TGCCATGGTATCTTTCAACCATGGTCTTACAC-GTTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
*
5752586 TGCCATGGTATCTTTCAACCATGGTCTTACAC-GTTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
5752632 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
5752678 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC-TATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAG
5752722 AGAGCACACT
Statistics
Matches: 252, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
46 214 0.85
47 38 0.15
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCATATCAGGT
Found at i:5756077 original size:33 final size:37
Alignment explanation
Indices: 5755997--5756077 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 37
5755987 ACTAATTACA
5755997 AATATTTAATTGTTATATTTAAATATTTAAAATATATT
1 AATATTT-ATTGTTATATTTAAATATTTAAAATATATT
* *
5756035 -TTATATATTG-TA-A-TTAAAT-TTTATAAATA-ATT
1 AATATTTATTGTTATATTTAAATATTTA-AAATATATT
5756067 AATATTTATTG
1 AATATTTATTG
5756078 CTTGAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
32 7 0.19
33 19 0.51
34 1 0.03
35 2 0.05
36 4 0.11
37 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (37 bp):
AATATTTATTGTTATATTTAAATATTTAAAATATATT
Found at i:5757221 original size:8 final size:8
Alignment explanation
Indices: 5757208--5757240 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
5757198 GAAAGCTTTC
5757208 AAATACAT
1 AAATACAT
5757216 AAATACAT
1 AAATACAT
5757224 AAATACAT
1 AAATACAT
5757232 AAA-ACAT
1 AAATACAT
5757239 AA
1 AA
5757241 TATCATGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (8 bp):
AAATACAT
Found at i:5757505 original size:9 final size:10
Alignment explanation
Indices: 5757477--5757516 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
5757467 GCATGAGAAA
*
5757477 TTTTCTTTTT
1 TTTTGTTTTT
* *
5757487 CTTTCTTTTT
1 TTTTGTTTTT
5757497 TTTTGTTTTT
1 TTTTGTTTTT
5757507 TTTTGTTTTT
1 TTTTGTTTTT
5757517 GTAACACTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (10 bp):
TTTTGTTTTT
Found at i:5758875 original size:46 final size:44
Alignment explanation
Indices: 5758771--5758878 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
5758761 TGTCTTTGAC
** * * *
5758771 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
5758815 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
5758861 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
5758879 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:5766255 original size:46 final size:44
Alignment explanation
Indices: 5766151--5766258 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
5766141 TGTCTTTGAC
** * * *
5766151 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
5766195 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
5766241 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
5766259 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:5769453 original size:13 final size:14
Alignment explanation
Indices: 5769421--5769458 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
5769411 ATTTGAAATG
*
5769421 TTTTATAATATATAT
1 TTTTAAAAT-TATAT
5769436 TTTTAAAATTAT-T
1 TTTTAAAATTATAT
5769449 TTTTAAAATT
1 TTTTAAAATT
5769459 TTAAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.50
14 3 0.14
15 8 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTAAAATTATAT
Found at i:5769460 original size:21 final size:21
Alignment explanation
Indices: 5769436--5769497 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
5769426 TAATATATAT
5769436 TTTTAAAATTATTTTTTAAAA
1 TTTTAAAATTATTTTTTAAAA
*
5769457 TTTTAAATATTATTTTTTTAAA
1 TTTTAAA-ATTATTTTTTAAAA
*
5769479 TATT-AAATATATTTTTTAA
1 TTTTAAAAT-TATTTTTTAA
5769498 TAATATAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 2 0.06
21 18 0.50
22 16 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTAAAATTATTTTTTAAAA
Found at i:5769468 original size:22 final size:22
Alignment explanation
Indices: 5769436--5769497 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
5769426 TAATATATAT
5769436 TTTTAAA-ATTATTTTTTAAAA
1 TTTTAAATATTATTTTTTAAAA
*
5769457 TTTTAAATATTATTTTTTTAAA
1 TTTTAAATATTATTTTTTAAAA
*
5769479 TATTAAATA-TATTTTTTAA
1 TTTTAAATATTATTTTTTAA
5769498 TAATATAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 16 0.43
22 21 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAAATATTATTTTTTAAAA
Found at i:5785697 original size:27 final size:27
Alignment explanation
Indices: 5785624--5785698 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 27
5785614 AAAGGTATAG
5785624 ATATTTAATTAAGA-AAAAAAATCTCAA
1 ATATTTAATTAA-ATAAAAAAATCTCAA
*
5785651 ATA-CTAATTAAATATTAAAAAA-CTCAA
1 ATATTTAATTAAATA--AAAAAATCTCAA
5785678 ATATTTAATTACAATAAAAAA
1 ATATTTAATTA-AATAAAAAA
5785699 TTAATATCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
25 1 0.02
26 8 0.20
27 16 0.39
28 12 0.29
29 4 0.10
ACGTcount: A:0.60, C:0.08, G:0.01, T:0.31
Consensus pattern (27 bp):
ATATTTAATTAAATAAAAAAATCTCAA
Found at i:5785727 original size:23 final size:24
Alignment explanation
Indices: 5785667--5785731 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
5785657 ATTAAATATT
**
5785667 AAAAAACTCAAATATTTAATTACA
1 AAAAAACTCAAATATCAAATTACA
* *
5785691 ATAAAAAAT-TAATATCAAATTA-A
1 A-AAAAACTCAAATATCAAATTACA
5785714 AAAAAACTCAAATATCAA
1 AAAAAACTCAAATATCAA
5785732 TTTCAATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
22 6 0.18
23 10 0.30
24 11 0.33
25 6 0.18
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAAAACTCAAATATCAAATTACA
Found at i:5795301 original size:21 final size:19
Alignment explanation
Indices: 5795257--5795296 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
5795247 AGCTACCTTG
*
5795257 ATTTTAA-AAAGAAATATT
1 ATTTTAATAAAGAAACATT
5795275 ATTTTAATAAAGAAACATT
1 ATTTTAATAAAGAAACATT
5795294 ATT
1 ATT
5795297 CTTTATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (19 bp):
ATTTTAATAAAGAAACATT
Found at i:5801781 original size:2 final size:2
Alignment explanation
Indices: 5801774--5801799 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5801764 TCTTGAATGA
5801774 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5801800 CTGGCGCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5815553 original size:32 final size:32
Alignment explanation
Indices: 5815515--5815579 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
5815505 AAATCTTTTG
5815515 TATTTAGGATAAGTATCCTCATTTCAAACATT
1 TATTTAGGATAAGTATCCTCATTTCAAACATT
*
5815547 TATTTAGGATAAGTATCCTTATTTCAAACATT
1 TATTTAGGATAAGTATCCTCATTTCAAACATT
5815579 T
1 T
5815580 GTAAGTTTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (32 bp):
TATTTAGGATAAGTATCCTCATTTCAAACATT
Found at i:5822315 original size:46 final size:44
Alignment explanation
Indices: 5822211--5822318 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
5822201 TGTCTTTGAC
** * * *
5822211 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
5822255 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
5822301 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
5822319 TTTTGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Done.