Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 139 of 143
Found at i:41259106 original size:41 final size:41
Alignment explanation
Indices: 41259009--41259099 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 41
41258999 GGCAAACCTG
* ** *
41259009 AAAATCAACAATTCTGAAATTTATATGCAAGAAATTAGTAA
1 AAAATTAACAATTCAAAAATTTATATGCAAGAAATTAGCAA
* * * * *
41259050 AAATTTAGCAATTCAAAAATTTATATGCGATAAGTTAGCAA
1 AAAATTAACAATTCAAAAATTTATATGCAAGAAATTAGCAA
41259091 AAAATTAAC
1 AAAATTAAC
41259100 CCTTCAACTT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30
Consensus pattern (41 bp):
AAAATTAACAATTCAAAAATTTATATGCAAGAAATTAGCAA
Found at i:41266403 original size:41 final size:41
Alignment explanation
Indices: 41266346--41266433 Score: 158
Period size: 41 Copynumber: 2.1 Consensus size: 41
41266336 TTTTTATTTT
**
41266346 AAATTTCAAATAAGGCAAAGTTAATACTGTGGGCCAAAATA
1 AAATTTCAAATAAGGCAAAGCCAATACTGTGGGCCAAAATA
41266387 AAATTTCAAATAAGGCAAAGCCAATACTGTGGGCCAAAATA
1 AAATTTCAAATAAGGCAAAGCCAATACTGTGGGCCAAAATA
41266428 AAATTT
1 AAATTT
41266434 TAAAGTTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.24
Consensus pattern (41 bp):
AAATTTCAAATAAGGCAAAGCCAATACTGTGGGCCAAAATA
Found at i:41272903 original size:29 final size:28
Alignment explanation
Indices: 41272860--41272917 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 28
41272850 AAAGAAGGAG
*
41272860 AAAAAAAAGTTTGGGGGACTGGTATGTA
1 AAAAAAAAGTCTGGGGGACTGGTATGTA
41272888 AAAAGAAAAGTCTGGGGGACTGGTATGTA
1 AAAA-AAAAGTCTGGGGGACTGGTATGTA
41272917 A
1 A
41272918 GGGGTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.22
Consensus pattern (28 bp):
AAAAAAAAGTCTGGGGGACTGGTATGTA
Found at i:41274107 original size:31 final size:31
Alignment explanation
Indices: 41274083--41274150 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
41274073 TAAAATTTTA
41274083 AAATTCGAAAAGTACAAGAACTAAAAATGAC
1 AAATTCGAAAAGTACAAGAACTAAAAATGAC
* *
41274114 CAATTCGAAAAGTACAA-AGACTAAAAGTGATC
1 AAATTCGAAAAGTACAAGA-ACTAAAAATGA-C
41274146 AAATT
1 AAATT
41274151 AAAGTATAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 26 0.81
32 5 0.16
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.19
Consensus pattern (31 bp):
AAATTCGAAAAGTACAAGAACTAAAAATGAC
Found at i:41276760 original size:31 final size:31
Alignment explanation
Indices: 41276717--41276781 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
41276707 TAATCTACTG
*
41276717 TGACTTAAATAAAAACTTTCAAATAGTTCAA
1 TGACTTAAATAAAAACTTTCAAATAATTCAA
* * *
41276748 TGACTTAGATAAAAATTTTCAAGTAATTCAA
1 TGACTTAAATAAAAACTTTCAAATAATTCAA
41276779 TGA
1 TGA
41276782 TCATTTTGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAATTCAA
Found at i:41284236 original size:31 final size:31
Alignment explanation
Indices: 41284181--41284243 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
41284171 TAATCCACTG
*
41284181 TGACTTAAATAAAACCTTTAAAATACTTCAA
1 TGACTTAAATAAAACCTTTAAAATAATTCAA
* *
41284212 TGACTTAGATGAAAA-CTTTCAAATAATTCAA
1 TGACTTAAAT-AAAACCTTTAAAATAATTCAA
41284243 T
1 T
41284244 AACCATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAACCTTTAAAATAATTCAA
Found at i:41291621 original size:36 final size:35
Alignment explanation
Indices: 41291556--41291624 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
41291546 AAAACAGTAA
* *
41291556 CAAATTTAATAATATAATAAGAATTATATAATATT
1 CAAATTTAATAATAAAATAAGAATAATATAATATT
* *
41291591 CAAATATTAATAATAAAATAATAGTAATATAATA
1 CAAAT-TTAATAATAAAATAAGAATAATATAATA
41291625 ACAAAAAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 5 0.17
36 24 0.83
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (35 bp):
CAAATTTAATAATAAAATAAGAATAATATAATATT
Found at i:41298989 original size:20 final size:21
Alignment explanation
Indices: 41298951--41299005 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
41298941 AAGTCCCAAA
41298951 ATTATTATTTTAAATTATTATT
1 ATTATT-TTTTAAATTATTATT
* *
41298973 ATTATTTTTTACA-TATTTTT
1 ATTATTTTTTAAATTATTATT
**
41298993 AGAATTTTTTAAA
1 ATTATTTTTTAAA
41299006 AAATAAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 16 0.57
21 6 0.21
22 6 0.21
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTATTTTTTAAATTATTATT
Found at i:41299029 original size:21 final size:20
Alignment explanation
Indices: 41298976--41299044 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
41298966 TATTATTATT
* *
41298976 ATTTTTT-ACATATTTTTAGA
1 ATTTTTTAAAATAATTTTA-A
41298996 ATTTTTTAAAAAATAAATTTTAA
1 ATTTTTT--AAAAT-AATTTTAA
* *
41299019 CTTTTTTAAAATTATTTTAA
1 ATTTTTTAAAATAATTTTAA
41299039 ATTTTT
1 ATTTTT
41299045 ATTGTAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
20 19 0.47
21 5 0.12
23 10 0.25
24 6 0.15
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (20 bp):
ATTTTTTAAAATAATTTTAA
Found at i:41301717 original size:25 final size:26
Alignment explanation
Indices: 41301670--41301718 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
41301660 AAGTAAAAAA
*
41301670 AATTTTATTTAAATGTTTATCAATAT
1 AATTTTATTTAAATGTTAATCAATAT
41301696 AATTTT-TTTAAAT-TTAATTCAAT
1 AATTTTATTTAAATGTTAA-TCAAT
41301719 TATGAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 12 0.57
26 6 0.29
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (26 bp):
AATTTTATTTAAATGTTAATCAATAT
Found at i:41302389 original size:20 final size:21
Alignment explanation
Indices: 41302364--41302409 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
41302354 TATAATAAAA
41302364 TTATTTTAA-AAAA-TAATTAT
1 TTATTTTAATAAAATTAATT-T
41302384 TTATTTTTAATAAAATTAATTT
1 TTA-TTTTAATAAAATTAATTT
41302406 TTAT
1 TTAT
41302410 AATTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 3 0.13
21 7 0.30
22 8 0.35
23 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATTTTAATAAAATTAATTT
Found at i:41302408 original size:22 final size:21
Alignment explanation
Indices: 41302367--41302419 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 21
41302357 AATAAAATTA
41302367 TTTTAAAAAATAATTATTTAT
1 TTTTAAAAAATAATTATTTAT
*
41302388 TTTTAATAAAATTAATTTTTATAAT
1 TTTTAA-AAAA-TAATTATT-T-AT
41302413 TTTTAAA
1 TTTTAAA
41302420 TTTCAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 6 0.22
22 4 0.15
23 7 0.26
24 2 0.07
25 8 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTAAAAAATAATTATTTAT
Found at i:41309058 original size:13 final size:14
Alignment explanation
Indices: 41309029--41309061 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41309019 ATGTATAAAT
*
41309029 AAATAAAAATGATG
1 AAATAAAAAAGATG
41309043 AAATAAAAAAGA-G
1 AAATAAAAAAGATG
41309056 AAATAA
1 AAATAA
41309062 TGTGAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (14 bp):
AAATAAAAAAGATG
Found at i:41309562 original size:23 final size:24
Alignment explanation
Indices: 41309518--41309577 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
41309508 ATAACATCCA
* *
41309518 AACAACCAAAATAACAATCAAAAC
1 AACAACAAAAATAACAAGCAAAAC
* * *
41309542 AGCAGCAAAAATAAC-AGCAAAAT
1 AACAACAAAAATAACAAGCAAAAC
41309565 AACAACAAAAATA
1 AACAACAAAAATA
41309578 GAAACAAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.67, C:0.20, G:0.05, T:0.08
Consensus pattern (24 bp):
AACAACAAAAATAACAAGCAAAAC
Found at i:41309586 original size:35 final size:35
Alignment explanation
Indices: 41309524--41309592 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
41309514 TCCAAACAAC
* *
41309524 CAAAATAACAATCAAAACAGCAGCAAAAATAACAG
1 CAAAATAACAATCAAAACAGAAACAAAAATAACAG
*
41309559 CAAAATAACAA-CAAAAATAGAAACAAAAATAACA
1 CAAAATAACAATC-AAAACAGAAACAAAAATAACA
41309593 ATAAAAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 1 0.03
35 29 0.97
ACGTcount: A:0.68, C:0.17, G:0.06, T:0.09
Consensus pattern (35 bp):
CAAAATAACAATCAAAACAGAAACAAAAATAACAG
Found at i:41309599 original size:12 final size:12
Alignment explanation
Indices: 41309518--41309610 Score: 75
Period size: 12 Copynumber: 7.8 Consensus size: 12
41309508 ATAACATCCA
*
41309518 AACAACCAAAAT
1 AACAACAAAAAT
*
41309530 AACAATC-AAAAC
1 AACAA-CAAAAAT
* *
41309542 AGCAGCAAAAAT
1 AACAACAAAAAT
*
41309554 AACAGC-AAAAT
1 AACAACAAAAAT
41309565 AACAACAAAAAT
1 AACAACAAAAAT
41309577 AGA-AACAAAAAT
1 A-ACAACAAAAAT
* *
41309589 AACAATAAAAAC
1 AACAACAAAAAT
*
41309601 AACACCAAAA
1 AACAACAAAA
41309611 CAATAAAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
11 12 0.18
12 52 0.79
13 2 0.03
ACGTcount: A:0.69, C:0.19, G:0.04, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:41309620 original size:21 final size:21
Alignment explanation
Indices: 41309589--41309637 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
41309579 AAACAAAAAT
41309589 AACAAT-AAAAACAACACCAA
1 AACAATAAAAAACAACACCAA
* *
41309609 AACAATAAAAAACAGCACTAA
1 AACAATAAAAAACAACACCAA
41309630 AACAATAA
1 AACAATAA
41309638 CCAAAACAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 6 0.23
21 20 0.77
ACGTcount: A:0.69, C:0.20, G:0.02, T:0.08
Consensus pattern (21 bp):
AACAATAAAAAACAACACCAA
Found at i:41309620 original size:33 final size:33
Alignment explanation
Indices: 41309583--41309654 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
41309573 AAATAGAAAC
*
41309583 AAAAATAACAATAAAAACAA-CACCAAAACAATA
1 AAAAATAACAAT-AAAACAATAACCAAAACAATA
* * * *
41309616 AAAAACAGCACTAAAACAATAACCAAAACAGTA
1 AAAAATAACAATAAAACAATAACCAAAACAATA
41309649 AAAAAT
1 AAAAAT
41309655 CATCAAAACA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
32 7 0.22
33 25 0.78
ACGTcount: A:0.69, C:0.18, G:0.03, T:0.10
Consensus pattern (33 bp):
AAAAATAACAATAAAACAATAACCAAAACAATA
Found at i:41309652 original size:21 final size:19
Alignment explanation
Indices: 41309627--41309693 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 19
41309617 AAAACAGCAC
41309627 TAAAACAATAACCAAAACAG
1 TAAAA-AATAACCAAAACAG
* * *
41309647 TAAAAAATCATCAAAACAA
1 TAAAAAATAACCAAAACAG
41309666 TAAAAAATAACATCAAAACAG
1 TAAAAAATAAC--CAAAACAG
41309687 TAAAAAA
1 TAAAAAA
41309694 AATGGTACCA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
19 20 0.51
20 5 0.13
21 14 0.36
ACGTcount: A:0.69, C:0.15, G:0.03, T:0.13
Consensus pattern (19 bp):
TAAAAAATAACCAAAACAG
Found at i:41309663 original size:19 final size:20
Alignment explanation
Indices: 41309639--41309693 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 20
41309629 AAACAATAAC
41309639 CAAAACAGTAAAAAAT-CAT
1 CAAAACAGTAAAAAATACAT
*
41309658 CAAAACAATAAAAAATAACAT
1 CAAAACAGTAAAAAAT-ACAT
41309679 CAAAACAGTAAAAAA
1 CAAAACAGTAAAAAA
41309694 AATGGTACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 15 0.47
21 17 0.53
ACGTcount: A:0.69, C:0.15, G:0.04, T:0.13
Consensus pattern (20 bp):
CAAAACAGTAAAAAATACAT
Found at i:41310439 original size:2 final size:2
Alignment explanation
Indices: 41310434--41310459 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41310424 TAAAAAAAAA
41310434 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
41310460 TTGTAATTGG
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:41311524 original size:2 final size:2
Alignment explanation
Indices: 41311517--41311565 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
41311507 TAATGGGTTT
41311517 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
41311559 AG AG AG A
1 AG AG AG A
41311566 CGTATGCAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41324844 original size:12 final size:13
Alignment explanation
Indices: 41324779--41324855 Score: 50
Period size: 13 Copynumber: 5.5 Consensus size: 13
41324769 AATTAAAAAT
*
41324779 ATAAAAAATTTAA
1 ATAAAAAATATAA
*
41324792 TATATATAAAATCTAGA
1 -ATA-A-AAAATATA-A
41324809 A-AAAAACATATAA
1 ATAAAAA-ATATAA
41324822 ATTATAAAAATA-AA
1 A-TA-AAAAATATAA
41324836 ATAAAAAATATAA
1 ATAAAAAATATAA
*
41324849 TTAAAAA
1 ATAAAAA
41324856 GGAATTAGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
12 7 0.13
13 15 0.29
14 11 0.21
15 6 0.12
16 12 0.23
17 1 0.02
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (13 bp):
ATAAAAAATATAA
Found at i:41324928 original size:12 final size:11
Alignment explanation
Indices: 41324902--41324941 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
41324892 GTGAAAAGTA
*
41324902 TAAAAAAATTG
1 TAAAAAAATTT
41324913 TAAAAGAAATTT
1 TAAAA-AAATTT
*
41324925 TAAAAAAAGTT
1 TAAAAAAATTT
41324936 TAAAAA
1 TAAAAA
41324942 TATATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (11 bp):
TAAAAAAATTT
Found at i:41328411 original size:65 final size:65
Alignment explanation
Indices: 41328304--41328430 Score: 227
Period size: 65 Copynumber: 2.0 Consensus size: 65
41328294 GACAAGAAAG
41328304 TAAGTTTCTCTACACATCATATTTCCTTGTTTATAAGAAACTTCTGTGATACTATGCAATAGAGA
1 TAAGTTTCTCTACACATCATATTTCCTTGTTTATAAGAAACTTCTGTGATACTATGCAATAGAGA
* * *
41328369 TAAGTTTCTCTACTCATCATATTTCCTTGTTTATAAGGAACTTCTGTGATACTATGCTATAG
1 TAAGTTTCTCTACACATCATATTTCCTTGTTTATAAGAAACTTCTGTGATACTATGCAATAG
41328431 TGATTATCAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (65 bp):
TAAGTTTCTCTACACATCATATTTCCTTGTTTATAAGAAACTTCTGTGATACTATGCAATAGAGA
Found at i:41329192 original size:15 final size:15
Alignment explanation
Indices: 41329169--41329208 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
41329159 TAGACACTGG
41329169 AAAAGATGATAATGA
1 AAAAGATGATAATGA
* *
41329184 AAAATATGATTATGA
1 AAAAGATGATAATGA
*
41329199 AATAGATGAT
1 AAAAGATGAT
41329209 GAGCAGAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (15 bp):
AAAAGATGATAATGA
Found at i:41331974 original size:22 final size:22
Alignment explanation
Indices: 41331950--41331991 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
41331940 GTCTTTATAT
41331950 TTTTTCTA-TATTT-GAATTTAG
1 TTTTTCTACT-TTTCGAATTTAG
41331971 TTTTTCTACTTTTCGAATTTA
1 TTTTTCTACTTTTCGAATTTA
41331992 AAATTAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (22 bp):
TTTTTCTACTTTTCGAATTTAG
Found at i:41333218 original size:20 final size:20
Alignment explanation
Indices: 41333193--41333232 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
41333183 CGATTCGATT
41333193 ATAATGTTATACATGAAATA
1 ATAATGTTATACATGAAATA
*
41333213 ATAATGTTATACATTAAATA
1 ATAATGTTATACATGAAATA
41333233 TTAAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (20 bp):
ATAATGTTATACATGAAATA
Found at i:41333242 original size:20 final size:20
Alignment explanation
Indices: 41333199--41333243 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
41333189 GATTATAATG
**
41333199 TTATACATGAAATAATAATG
1 TTATACATGAAATAATAAAA
* *
41333219 TTATACATTAAATATTAAAA
1 TTATACATGAAATAATAAAA
41333239 TTATA
1 TTATA
41333244 TATTGACAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (20 bp):
TTATACATGAAATAATAAAA
Found at i:41333845 original size:10 final size:9
Alignment explanation
Indices: 41333818--41333851 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 9
41333808 TACGTACCTA
41333818 CATGCATG-
1 CATGCATGC
41333826 CATGCATGC
1 CATGCATGC
41333835 CATGCCATGC
1 CATG-CATGC
41333845 CATGCAT
1 CATGCAT
41333852 AAATATATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.33
9 7 0.29
10 9 0.38
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (9 bp):
CATGCATGC
Found at i:41334389 original size:15 final size:15
Alignment explanation
Indices: 41334339--41334391 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
41334329 TAAAAATAAG
41334339 TTTATATTATTTTTAA
1 TTTATA-TATTTTTAA
*
41334355 TTTA-ATATTTAATAA
1 TTTATATATTT-TTAA
*
41334370 TTTTATATATTTTTTA
1 -TTTATATATTTTTAA
41334386 TTTATA
1 TTTATA
41334392 AAAAATTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.16
15 10 0.32
16 10 0.32
17 6 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATATATTTTTAA
Found at i:41337103 original size:2 final size:2
Alignment explanation
Indices: 41337092--41337127 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
41337082 AAAAAAACAT
* *
41337092 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
41337128 CCAACGTCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
TC
Found at i:41341650 original size:26 final size:26
Alignment explanation
Indices: 41341621--41341673 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
41341611 ATATTCCTTG
** *
41341621 AACCAAATTTCAATACCATTATTTAT
1 AACCAAACATCAAAACCATTATTTAT
41341647 AACCAAACATCAAAACCATTATTTAT
1 AACCAAACATCAAAACCATTATTTAT
41341673 A
1 A
41341674 GTAACCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (26 bp):
AACCAAACATCAAAACCATTATTTAT
Found at i:41348017 original size:13 final size:12
Alignment explanation
Indices: 41347962--41348028 Score: 57
Period size: 13 Copynumber: 5.5 Consensus size: 12
41347952 ATAGTAGTTA
*
41347962 ATAATAATAA-T
1 ATAATATTAATT
*
41347973 ATAATACTAATT
1 ATAATATTAATT
*
41347985 A-AATAATAATTT
1 ATAATATTAA-TT
*
41347997 ATATTATTATATT
1 ATAATATTA-ATT
41348010 ATAATATTAATT
1 ATAATATTAATT
41348022 AATAATA
1 -ATAATA
41348029 AATTAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
11 16 0.35
12 8 0.17
13 21 0.46
14 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (12 bp):
ATAATATTAATT
Found at i:41350607 original size:31 final size:31
Alignment explanation
Indices: 41350537--41350650 Score: 107
Period size: 30 Copynumber: 3.8 Consensus size: 31
41350527 AACTTGACAC
41350537 TTTTTCTTAATTTGGTA-TCTAAATTT--T-T
1 TTTTTCTTAATTTGGTACTC-AAATTTGATAT
* *
41350565 TTTGTC-CAATTTGGTACTCAAATTTGATAT
1 TTTTTCTTAATTTGGTACTCAAATTTGATAT
* *
41350595 TTTTTCTTAATTTGGTAC-CTAACTTGATACT
1 TTTTTCTTAATTTGGTACTCAAATTTGATA-T
* *
41350626 TTTTT-TTAAATTGGTACTTAAATTT
1 TTTTTCTTAATTTGGTACTCAAATTT
41350651 TTTGGGGTCC
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
27 15 0.22
28 7 0.10
29 1 0.01
30 26 0.38
31 20 0.29
ACGTcount: A:0.25, C:0.11, G:0.10, T:0.55
Consensus pattern (31 bp):
TTTTTCTTAATTTGGTACTCAAATTTGATAT
Found at i:41350688 original size:89 final size:89
Alignment explanation
Indices: 41350515--41350701 Score: 213
Period size: 89 Copynumber: 2.1 Consensus size: 89
41350505 ATAATATAAC
* * **
41350515 ATTTGGTACTTGAACTTGACACTTTTTCTTAATTTGGTATCTAAATTTTTTTTGTCCAATTTGGT
1 ATTTGGTACCTGAACTTGACACTTTTTCTTAAATTGGTATCTAAATTTTTTGGGTCCAATTTGGT
* *
41350580 ACTCAAATTTGATATTTTTTCTTA
66 ACTCAAACTTGATATTTTTTCCTA
* *
41350604 ATTTGGTACCT-AACTTGATACTTTTTTTTAAATTGGTA-CTTAAATTTTTTGGGGTCCAATTTG
1 ATTTGGTACCTGAACTTGACACTTTTTCTTAAATTGGTATC-TAAATTTTTT-GGGTCCAATTTG
*
41350667 GTAC-CTGAACTT-A-ACTCTTTTTCCTA
64 GTACTC-AAACTTGATA-T-TTTTTCCTA
41350693 ATTTGGTAC
1 ATTTGGTAC
41350702 ATAATTTTCT
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
87 2 0.02
88 37 0.44
89 45 0.54
ACGTcount: A:0.24, C:0.14, G:0.13, T:0.50
Consensus pattern (89 bp):
ATTTGGTACCTGAACTTGACACTTTTTCTTAAATTGGTATCTAAATTTTTTGGGTCCAATTTGGT
ACTCAAACTTGATATTTTTTCCTA
Found at i:41350974 original size:26 final size:25
Alignment explanation
Indices: 41350938--41350993 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 25
41350928 GAGTCATTTT
41350938 AAAAAAAAATTAAGTACCAAATTAA
1 AAAAAAAAATTAAGTACCAAATTAA
*
41350963 ATAAAAAAAATTAAGTATCAAATTAA
1 A-AAAAAAAATTAAGTACCAAATTAA
41350989 AAAAA
1 AAAAA
41350994 GTATCAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.70, C:0.05, G:0.04, T:0.21
Consensus pattern (25 bp):
AAAAAAAAATTAAGTACCAAATTAA
Found at i:41371185 original size:31 final size:31
Alignment explanation
Indices: 41371150--41371210 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
41371140 AAATTTCAAA
*
41371150 AAAAGTTTAGAAACTAAAATTGACCAAATCG
1 AAAAGTATAGAAACTAAAATTGACCAAATCG
* * * *
41371181 AAAAGTATCGAAATTAGAATTGACGAAATC
1 AAAAGTATAGAAACTAAAATTGACCAAATC
41371211 TTCAGGTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23
Consensus pattern (31 bp):
AAAAGTATAGAAACTAAAATTGACCAAATCG
Found at i:41374911 original size:17 final size:18
Alignment explanation
Indices: 41374891--41374933 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 18
41374881 AATTAATTGT
41374891 TTTAAAAAAAT-AATTTA
1 TTTAAAAAAATAAATTTA
41374908 TTTATTCAAAAAATAAATTTA
1 TTTA---AAAAAATAAATTTA
41374929 TTTAA
1 TTTAA
41374934 TGCAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
17 4 0.18
18 1 0.05
20 7 0.32
21 10 0.45
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTAAAAAAATAAATTTA
Found at i:41376162 original size:13 final size:13
Alignment explanation
Indices: 41376144--41376171 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41376134 TCTAAGATGC
41376144 GGATCCAACTTAT
1 GGATCCAACTTAT
41376157 GGATCCAACTTAT
1 GGATCCAACTTAT
41376170 GG
1 GG
41376172 GTCTAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (13 bp):
GGATCCAACTTAT
Found at i:41397272 original size:15 final size:15
Alignment explanation
Indices: 41397245--41397279 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
41397235 AAGTGATTTG
41397245 ATAAAAAACATAAAA
1 ATAAAAAACATAAAA
41397260 ACTAAAAAA-ATAAAA
1 A-TAAAAAACATAAAA
41397275 ATAAA
1 ATAAA
41397280 TTAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 8 0.42
16 7 0.37
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (15 bp):
ATAAAAAACATAAAA
Found at i:41401041 original size:2 final size:2
Alignment explanation
Indices: 41401030--41401066 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
41401020 ACATATGCAC
41401030 AT AT -T 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 AT AT AT
41401067 GATTGTTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:41405683 original size:46 final size:47
Alignment explanation
Indices: 41405603--41405700 Score: 148
Period size: 46 Copynumber: 2.1 Consensus size: 47
41405593 AATTTTGTGT
41405603 ATATCATATCATATCCTTCCTTCTATCTAATTTATTAGTA-CAATATC
1 ATATCATATCATATCCTTCCTTCTATCTAATTTATTAGTATC-ATATC
*
41405650 ATATCATATCAT-TCCTT-CTTTTGATCTAATTTATTAGTATCATATC
1 ATATCATATCATATCCTTCCTTCT-ATCTAATTTATTAGTATCATATC
41405696 ATATC
1 ATATC
41405701 TTTTTCTTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
45 4 0.08
46 31 0.65
47 13 0.27
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (47 bp):
ATATCATATCATATCCTTCCTTCTATCTAATTTATTAGTATCATATC
Found at i:41415992 original size:20 final size:20
Alignment explanation
Indices: 41415967--41416004 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41415957 CAATATTAAT
41415967 ATTTTTC-TATTTTTCATCAC
1 ATTTTTCATA-TTTTCATCAC
41415987 ATTTTTCATATTTTCATC
1 ATTTTTCATATTTTCATC
41416005 TGTATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.21, C:0.18, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTTCATATTTTCATCAC
Found at i:41416420 original size:3 final size:3
Alignment explanation
Indices: 41416406--41416436 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
41416396 AGTGGTCGGA
*
41416406 GAC GAT GAC GAC GAC GAC GAC GAC GAC GAC G
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC G
41416437 GCGGCAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.29, G:0.35, T:0.03
Consensus pattern (3 bp):
GAC
Found at i:41428048 original size:129 final size:127
Alignment explanation
Indices: 41427897--41428157 Score: 468
Period size: 129 Copynumber: 2.0 Consensus size: 127
41427887 CCAAGTAGCC
*
41427897 ATATATATATAAACATGTGTATGTATGCATACATATAGATGAAAGCTGCACATGAACCAACAAAT
1 ATATATATATAAACATGTGTATGTATGCATACATATACATGAAAGCTGCACATGAACCAACAAAT
41427962 ATAACCAGGTTACCTCCCAAGTAGCCAAATTGGGCCTTAAGCTTAATAAACTATAGAAACCAT
66 ATAACCAGGTTACCTCCCAAG-AGCCAAATTGGGCCTTAAGCTTAATAAACTATAGAAACCAT
* *
41428025 ATATATAATATATACATGTGTATGTATGCATATATATACATGAAAGCTGCACATGAACCAACAAA
1 ATATAT-ATATAAACATGTGTATGTATGCATACATATACATGAAAGCTGCACATGAACCAACAAA
*
41428090 TATAACCAGGTTACCTCCCAAGAGCCAAATTGGGCCTTAAGCTTAATAAACTTTAGAAACCAT
65 TATAACCAGGTTACCTCCCAAGAGCCAAATTGGGCCTTAAGCTTAATAAACTATAGAAACCAT
41428153 ATATA
1 ATATA
41428158 GCAAGATTCT
Statistics
Matches: 128, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
128 51 0.40
129 77 0.60
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.27
Consensus pattern (127 bp):
ATATATATATAAACATGTGTATGTATGCATACATATACATGAAAGCTGCACATGAACCAACAAAT
ATAACCAGGTTACCTCCCAAGAGCCAAATTGGGCCTTAAGCTTAATAAACTATAGAAACCAT
Found at i:41429856 original size:8 final size:8
Alignment explanation
Indices: 41429843--41429869 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
41429833 GAAGATCAAG
41429843 CATCATCA
1 CATCATCA
41429851 CATCATCA
1 CATCATCA
41429859 CATCATCA
1 CATCATCA
41429867 CAT
1 CAT
41429870 GAAATAGACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.26
Consensus pattern (8 bp):
CATCATCA
Found at i:41433606 original size:21 final size:21
Alignment explanation
Indices: 41433582--41433634 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
41433572 AAATGACAAC
* *
41433582 AAAACAATAGTAAAA-AGTGAA
1 AAAACAATAATAAAACA-TAAA
*
41433603 AAAACAACAATAAAACATAAA
1 AAAACAATAATAAAACATAAA
41433624 AAAACAATAAT
1 AAAACAATAAT
41433635 TTTTTATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.72, C:0.09, G:0.06, T:0.13
Consensus pattern (21 bp):
AAAACAATAATAAAACATAAA
Found at i:41434874 original size:23 final size:23
Alignment explanation
Indices: 41434844--41434892 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
41434834 TTTTAATTTT
41434844 AAAAAAACTCG-TA-AAAAATTAAA
1 AAAAAAACT-GATAGAAAAA-TAAA
41434867 AAAAAAACTGATAGAAAAATAAA
1 AAAAAAACTGATAGAAAAATAAA
41434890 AAA
1 AAA
41434893 GGGGAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 1 0.04
23 18 0.75
24 5 0.21
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.14
Consensus pattern (23 bp):
AAAAAAACTGATAGAAAAATAAA
Found at i:41444590 original size:17 final size:18
Alignment explanation
Indices: 41444551--41444591 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41444541 ATCCTTCAAT
*
41444551 GTTACAAAGAAAATAAAA
1 GTTACAAAAAAAATAAAA
*
41444569 GTTACAAAAAAAATCAAA
1 GTTACAAAAAAAATAAAA
41444587 -TTACA
1 GTTACA
41444592 CAATGTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.63, C:0.10, G:0.07, T:0.20
Consensus pattern (18 bp):
GTTACAAAAAAAATAAAA
Found at i:41449876 original size:21 final size:23
Alignment explanation
Indices: 41449851--41449899 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
41449841 AGTTTAATTT
*
41449851 TATATAAAAA-AAACTA-TATAA
1 TATATAAAAATAAAATATTATAA
*
41449872 TATATAAAAATAAAATATTTTAA
1 TATATAAAAATAAAATATTATAA
41449895 TATAT
1 TATAT
41449900 TACATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.42
22 5 0.21
23 9 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TATATAAAAATAAAATATTATAA
Found at i:41449886 original size:23 final size:21
Alignment explanation
Indices: 41449851--41449899 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
41449841 AGTTTAATTT
41449851 TATATAAAAAAAACTA-TATAA
1 TATATAAAAAAAA-TATTATAA
*
41449872 TATATAAAAATAAAATATTTTAA
1 TATAT-AAAA-AAAATATTATAA
41449895 TATAT
1 TATAT
41449900 TACATAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 6 0.25
23 13 0.54
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TATATAAAAAAAATATTATAA
Found at i:41458042 original size:16 final size:16
Alignment explanation
Indices: 41458021--41458051 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41458011 TTAAATTTTA
41458021 TTTTAATTATTTTGAT
1 TTTTAATTATTTTGAT
*
41458037 TTTTAATTTTTTTGA
1 TTTTAATTATTTTGA
41458052 AATTTTAAAA
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:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTAATTATTTTGAT
Found at i:41463421 original size:46 final size:46
Alignment explanation
Indices: 41463354--41463442 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
41463344 GGTATGTAGG
41463354 TGTTCCCGCTCTGTGAACCCCACCTCAGGTCAGGTTTGGATTCGAT
1 TGTTCCCGCTCTGTGAACCCCACCTCAGGTCAGGTTTGGATTCGAT
41463400 TGTTCCCGCTCTGTGAACCCCACCTCAGGTCAGGTTTGGATTC
1 TGTTCCCGCTCTGTGAACCCCACCTCAGGTCAGGTTTGGATTC
41463443 TCAATCGAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.15, C:0.31, G:0.24, T:0.30
Consensus pattern (46 bp):
TGTTCCCGCTCTGTGAACCCCACCTCAGGTCAGGTTTGGATTCGAT
Found at i:41474665 original size:18 final size:18
Alignment explanation
Indices: 41474644--41474690 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
41474634 AGAACATTTT
*
41474644 TATATTTTTAACTTTATA
1 TATATTTTTAAATTTATA
41474662 TATATTTTTAAAATTTATA
1 TATATTTTT-AAATTTATA
41474681 -AT-TTTTTAAA
1 TATATTTTTAAA
41474691 AAATATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 11 0.41
19 8 0.30
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATTTTTAAATTTATA
Found at i:41474670 original size:19 final size:18
Alignment explanation
Indices: 41474644--41474691 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
41474634 AGAACATTTT
* *
41474644 TATATTTTTAACTTTATA
1 TATATTTTAAAATTTATA
41474662 TATATTTTTAAAATTTATA
1 TATA-TTTTAAAATTTATA
*
41474681 -ATTTTTTAAAA
1 TATATTTTAAAA
41474692 AATATAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 8 0.31
18 6 0.23
19 12 0.46
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATTTTAAAATTTATA
Found at i:41474697 original size:17 final size:18
Alignment explanation
Indices: 41474666--41474703 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
41474656 TTTATATATA
**
41474666 TTTTTAAAATTTAT-AAT
1 TTTTTAAAAAATATAAAT
41474683 TTTTTAAAAAATATAAAT
1 TTTTTAAAAAATATAAAT
41474701 TTT
1 TTT
41474704 GGAATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTTAAAAAATATAAAT
Found at i:41475463 original size:116 final size:120
Alignment explanation
Indices: 41475257--41475608 Score: 518
Period size: 116 Copynumber: 2.9 Consensus size: 120
41475247 TCCGTATTTA
41475257 TATAGGGAAGTTGGCTTGGCATGGGTCTTGGTCTCCAAGCATTTTACTTCATAGGTGCAAATGGT
1 TATAGGGAAGTTGGCTTGGCATGGGTCTTGGTCTCCAAGCATTTTACTTCATAGGTGCAAATGGT
*
41475322 AGAA-TAGCGGGTTGTCAATTAAAAACATTGTTAGAGGTGATATTTTT-TAG-T-G-
66 A-AAGTAGCGGGTTGTCAATTAAAAACATTGTTAGAGGCGATATTTTTGT-GTTCGT
41475374 T-TAGGGAAGTTGGCTTGGCATGGGTCTTGGTCTCCAAGCATTTTACTTCATAGGTGCAAATGGT
1 TATAGGGAAGTTGGCTTGGCATGGGTCTTGGTCTCCAAGCATTTTACTTCATAGGTGCAAATGGT
41475438 AAAGTAGCGGGTTGTCAATTAAAAACATTGTTAGAGGCGATAATTTTTGGTGTTCCGTATTT
66 AAAGTAGCGGGTTGTCAATTAAAAACATTGTTAGAGGCGAT-ATTTTT-GTGTT-CG----T
* *
41475500 ATATAGAGAAGTTGGCTTGGCATGGGTCTTGATCTCCAAGCATTTTACTTCATAGGTGCAAATGG
1 -TATAGGGAAGTTGGCTTGGCATGGGTCTTGGTCTCCAAGCATTTTACTTCATAGGTGCAAATGG
* * *
41475565 TAGAGTAGCGGATTGTCAATTAAAAATATTGTTAGAGGCGATAT
65 TAAAGTAGCGGGTTGTCAATTAAAAACATTGTTAGAGGCGATAT
41475609 GTAGTGATTG
Statistics
Matches: 215, Mismatches: 6, Indels: 18
0.90 0.03 0.08
Matches are distributed among these distances:
115 2 0.01
116 100 0.47
117 7 0.03
118 1 0.00
119 2 0.01
121 1 0.00
127 3 0.01
128 99 0.46
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (120 bp):
TATAGGGAAGTTGGCTTGGCATGGGTCTTGGTCTCCAAGCATTTTACTTCATAGGTGCAAATGGT
AAAGTAGCGGGTTGTCAATTAAAAACATTGTTAGAGGCGATATTTTTGTGTTCGT
Found at i:41494050 original size:4 final size:4
Alignment explanation
Indices: 41494041--41494071 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
41494031 TCATTATGCA
41494041 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
41494072 TTGCCAACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:41495058 original size:44 final size:44
Alignment explanation
Indices: 41494986--41495072 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
41494976 ATTTTAAAAT
* * *
41494986 ATTTTAAGGCAATAAATTGTTGCTTTTCTTGAATCAATCAATAG
1 ATTTAAAGGCAATAAATTCTTGCATTTCTTGAATCAATCAATAG
* *
41495030 ATTTAAAGGCAATAAATTCTTGCATTTCTTGGATCTATCAATA
1 ATTTAAAGGCAATAAATTCTTGCATTTCTTGAATCAATCAATA
41495073 TATTACAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (44 bp):
ATTTAAAGGCAATAAATTCTTGCATTTCTTGAATCAATCAATAG
Found at i:41496771 original size:18 final size:19
Alignment explanation
Indices: 41496736--41496773 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41496726 GATTTTTGAG
* *
41496736 TTAATTTTATGTTCAATTT
1 TTAATTTAATGTTAAATTT
41496755 TTAATTTAAT-TTAAATTT
1 TTAATTTAATGTTAAATTT
41496773 T
1 T
41496774 CGATTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (19 bp):
TTAATTTAATGTTAAATTT
Found at i:41505461 original size:4 final size:4
Alignment explanation
Indices: 41505452--41505482 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
41505442 TCATTATGCA
41505452 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
41505483 TTGCCAACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:41506469 original size:44 final size:44
Alignment explanation
Indices: 41506397--41506483 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
41506387 ATTTTAAAAT
* * *
41506397 ATTTTAAGGCAATAAATTGTTGCTTTTCTTGAATCAATCAATAG
1 ATTTAAAGGCAATAAATTCTTGCATTTCTTGAATCAATCAATAG
* *
41506441 ATTTAAAGGCAATAAATTCTTGCATTTCTTGGATCTATCAATA
1 ATTTAAAGGCAATAAATTCTTGCATTTCTTGAATCAATCAATA
41506484 TATTACAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (44 bp):
ATTTAAAGGCAATAAATTCTTGCATTTCTTGAATCAATCAATAG
Found at i:41508182 original size:18 final size:19
Alignment explanation
Indices: 41508147--41508184 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
41508137 GATTTTTGAG
* *
41508147 TTAATTTTATGTTCAATTT
1 TTAATTTAATGTTAAATTT
41508166 TTAATTTAAT-TTAAATTT
1 TTAATTTAATGTTAAATTT
41508184 T
1 T
41508185 CGATTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (19 bp):
TTAATTTAATGTTAAATTT
Found at i:41514948 original size:4 final size:4
Alignment explanation
Indices: 41514939--41514969 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
41514929 TCATTATGCA
41514939 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
41514970 TTGCCAACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:41522729 original size:59 final size:59
Alignment explanation
Indices: 41522666--41522817 Score: 220
Period size: 59 Copynumber: 2.6 Consensus size: 59
41522656 ATTTTTAACT
*
41522666 TTCGGGGGTAAAAAT-GTAATTTTTGGTGAAATCAGAGTCAAAAATGGGATTTTAGGAAA-
1 TTCGGGGGT-AAAATGGTAATTTTTGGTGAAATCAGAGTCAAAAATGGAATTTT-GGAAAG
* * *
41522725 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCAGAGTCAAAAATGGAATTTTGGAAAG
*
41522784 TTCGAGGGTAAAATGGTAA-TTTTGGTGAAATCAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCAG
41522818 GGGAAAATGT
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
58 24 0.28
59 61 0.72
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.32
Consensus pattern (59 bp):
TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCAGAGTCAAAAATGGAATTTTGGAAAG
Found at i:41522746 original size:29 final size:29
Alignment explanation
Indices: 41522667--41522835 Score: 113
Period size: 29 Copynumber: 5.8 Consensus size: 29
41522657 TTTTTAACTT
*
41522667 TCGGGGGTAAAAAT-GTAATTTTTGGTGAAA
1 TCGGGGGT-AAAATGGTAA-TTTTAGTGAAA
* * *
41522697 TC-AGAGTCAAAAATGG-GATTTTAG-GAAA
1 TCGGGGGT--AAAATGGTAATTTTAGTGAAA
*
41522725 TTCGGGGGTAAAATGGTAATTTTTGGTGAAA
1 -TCGGGGGTAAAATGGTAA-TTTTAGTGAAA
*
41522756 TCGGGGTTAAAAATGG-AATTTT-G-GAAA
1 TCGGGGGT-AAAATGGTAATTTTAGTGAAA
* *
41522783 GTTCGAGGGTAAAATGGTAATTTTGGTGAAA
1 --TCGGGGGTAAAATGGTAATTTTAGTGAAA
*
41522814 TCAGGGG-AAAAT-GTAATTTTAG
1 TCGGGGGTAAAATGGTAATTTTAG
41522836 AAAAGTTGTA
Statistics
Matches: 112, Mismatches: 14, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
27 13 0.12
28 24 0.21
29 32 0.29
30 27 0.24
31 16 0.14
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.31
Consensus pattern (29 bp):
TCGGGGGTAAAATGGTAATTTTAGTGAAA
Found at i:41522815 original size:58 final size:58
Alignment explanation
Indices: 41522666--41522863 Score: 210
Period size: 59 Copynumber: 3.4 Consensus size: 58
41522656 ATTTTTAACT
* * * *
41522666 TTCGGGGGTAAAAATGTAATTTTTGGTGAAATCAGAGTCAAAAATGGGATTTTAGGAAA-
1 TTCGAGGGT-AAAATGTAATTTTTGGTGAAATCGGGGT-AAAAATGGAATTTTAGGAAAG
*
41522725 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-GGAAAG
1 TTCGAGGGTAAAAT-GTAATTTTTGGTGAAATCGGGG-TAAAAATGGAATTTTAGGAAAG
* *
41522784 TTCGAGGGTAAAATGGTAA-TTTTGGTGAAATCAGGGG--AAAATGTAATTTTAGAAAAG
1 TTCGAGGGTAAAAT-GTAATTTTTGGTGAAATC-GGGGTAAAAATGGAATTTTAGGAAAG
*
41522841 TT-GTAAGGTTAAAATGTAATTTT
1 TTCG--AGGGTAAAATGTAATTTT
41522864 GGAAAAGTTT
Statistics
Matches: 124, Mismatches: 7, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
56 13 0.10
57 11 0.09
58 35 0.28
59 64 0.52
60 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.33
Consensus pattern (58 bp):
TTCGAGGGTAAAATGTAATTTTTGGTGAAATCGGGGTAAAAATGGAATTTTAGGAAAG
Found at i:41522857 original size:30 final size:30
Alignment explanation
Indices: 41522821--41522923 Score: 154
Period size: 30 Copynumber: 3.4 Consensus size: 30
41522811 AAATCAGGGG
* *
41522821 AAAATGTAATTTTAGAAAAGTTGTAAGGTT
1 AAAATGTAATTTTAGAAAAGTTTTAGGGTT
*
41522851 AAAATGTAATTTTGGAAAAGTTTTAGGGTT
1 AAAATGTAATTTTAGAAAAGTTTTAGGGTT
*
41522881 AAAATGTAATTTTCA-AAAAGTTTTAGGGTC
1 AAAATGTAATTTT-AGAAAAGTTTTAGGGTT
41522911 AAAATGTAATTTT
1 AAAATGTAATTTT
41522924 GGGGCAGTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.41, C:0.02, G:0.18, T:0.39
Consensus pattern (30 bp):
AAAATGTAATTTTAGAAAAGTTTTAGGGTT
Found at i:41524763 original size:6 final size:6
Alignment explanation
Indices: 41524752--41524810 Score: 59
Period size: 6 Copynumber: 9.8 Consensus size: 6
41524742 TGAAATTTGA
* *
41524752 TTAAAT TTAAAT TTAAA- GTAAAT TTAAAT AGGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
41524800 ATAAAT TTAAA
1 TTAAAT TTAAA
41524811 ATCAATTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 8 0.19
6 30 0.70
8 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:41524773 original size:17 final size:17
Alignment explanation
Indices: 41524753--41524810 Score: 77
Period size: 17 Copynumber: 3.6 Consensus size: 17
41524743 GAAATTTGAT
41524753 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAG
*
41524770 TAAATTTAAA--T-AGG
1 TAAATTTAAATTTAAAG
*
41524784 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAG
41524801 TAAATTTAAA
1 TAAATTTAAA
41524811 ATCAATTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
14 12 0.34
15 1 0.03
16 1 0.03
17 21 0.60
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:41526964 original size:24 final size:24
Alignment explanation
Indices: 41526937--41526982 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41526927 AAATAAAATG
41526937 TAAAATCAA-ATTTAAATTTATTGA
1 TAAAATCAACA-TTAAATTTATTGA
*
41526961 TAAAATTAACATTAAATTTATT
1 TAAAATCAACATTAAATTTATT
41526983 TTATTGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
TAAAATCAACATTAAATTTATTGA
Found at i:41527014 original size:29 final size:29
Alignment explanation
Indices: 41526944--41527020 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
41526934 ATGTAAAATC
41526944 AAATTTAAATTTATTGATAAAATTAACATT
1 AAATTTAAATTTATTGATAAAATT-ACATT
*
41526974 AAATTT-ATTTTATTGATAAAA-T-CATT
1 AAATTTAAATTTATTGATAAAATTACATT
*
41527000 AAAATTTTAAATTTAATGATA
1 -AAA-TTTAAATTTATTGATA
41527021 TTAGTAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 4 0.10
27 3 0.07
28 4 0.10
29 24 0.59
30 6 0.15
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (29 bp):
AAATTTAAATTTATTGATAAAATTACATT
Found at i:41533051 original size:22 final size:22
Alignment explanation
Indices: 41533004--41533065 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
41532994 TTGATAATCT
* *
41533004 AAAT-TTAAAAAAT-AATTTTA
1 AAATGTTAAAAATTAAATTTGA
41533024 ACAATGTTAAAAATTAAATTTGA
1 A-AATGTTAAAAATTAAATTTGA
* *
41533047 AAATGTGAGAAATTAAATT
1 AAATGTTAAAAATTAAATT
41533066 CTAAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 3 0.09
22 24 0.69
23 7 0.20
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (22 bp):
AAATGTTAAAAATTAAATTTGA
Found at i:41535011 original size:13 final size:14
Alignment explanation
Indices: 41534993--41535022 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
41534983 AATTTAGTCC
41534993 TTTTCCTCTCTT-T
1 TTTTCCTCTCTTCT
41535006 TTTTCCTCTCTTCT
1 TTTTCCTCTCTTCT
41535020 TTT
1 TTT
41535023 GAAGTTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTCCTCTCTTCT
Found at i:41538477 original size:12 final size:12
Alignment explanation
Indices: 41538462--41538497 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
41538452 AATAATAACC
41538462 AAAATAGCAGCA
1 AAAATAGCAGCA
*
41538474 AAAATAGCAACA
1 AAAATAGCAGCA
*
41538486 AAAATAACAGCA
1 AAAATAGCAGCA
41538498 TAAACAACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.64, C:0.17, G:0.11, T:0.08
Consensus pattern (12 bp):
AAAATAGCAGCA
Found at i:41538489 original size:24 final size:24
Alignment explanation
Indices: 41538443--41538506 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
41538433 ATAATATCCA
* * *
41538443 AACAACAAAAATAATAACCAAAAT
1 AACAGCAAAAATAACAACAAAAAT
* *
41538467 AGCAGCAAAAATAGCAACAAAAAT
1 AACAGCAAAAATAACAACAAAAAT
* *
41538491 AACAGCATAAACAACA
1 AACAGCAAAAATAACA
41538507 CTAAAACAGT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.66, C:0.19, G:0.06, T:0.09
Consensus pattern (24 bp):
AACAGCAAAAATAACAACAAAAAT
Found at i:41538528 original size:20 final size:20
Alignment explanation
Indices: 41538509--41538619 Score: 96
Period size: 22 Copynumber: 5.2 Consensus size: 20
41538499 AAACAACACT
*
41538509 AAAACAGTAAAAAAATCACT
1 AAAACAGTAAAAAAATCACC
* * * *
41538529 AAAACAACCTCAAAATAGCAACC
1 AAAAC-A-GTAAAAAAATC-ACC
*
41538552 AAAACAGTAAAAAAAGCACC
1 AAAACAGTAAAAAAATCACC
*
41538572 AAAACAGTAAAAAACAATAACC
1 AAAACAGT-AAAAA-AATCACC
41538594 AAAACAGTAAAAAAATAACACC
1 AAAACAGTAAAAAAAT--CACC
41538616 AAAA
1 AAAA
41538620 TAACAATATA
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
20 19 0.26
21 19 0.26
22 28 0.38
23 7 0.10
ACGTcount: A:0.66, C:0.20, G:0.05, T:0.09
Consensus pattern (20 bp):
AAAACAGTAAAAAAATCACC
Found at i:41538943 original size:28 final size:28
Alignment explanation
Indices: 41538912--41538968 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
41538902 TTTTATATCT
*
41538912 TATATAATTTATAATACT-AAAAATTAAA
1 TATATAATATA-AATACTAAAAAATTAAA
*
41538940 TATATAATATAAATATTAAAAAATTAAA
1 TATATAATATAAATACTAAAAAATTAAA
41538968 T
1 T
41538969 TGGTTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (28 bp):
TATATAATATAAATACTAAAAAATTAAA
Found at i:41538945 original size:21 final size:20
Alignment explanation
Indices: 41538921--41538959 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41538911 TTATATAATT
41538921 TATAATACTAAAAATTAAATA
1 TATAATA-TAAAAATTAAATA
*
41538942 TATAATATAAATATTAAA
1 TATAATATAAAAATTAAA
41538960 AAATTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
TATAATATAAAAATTAAATA
Found at i:41543302 original size:18 final size:20
Alignment explanation
Indices: 41543281--41543324 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
41543271 TAAATATTAT
41543281 TTTTTTAA-TTTTA-AAATA
1 TTTTTTAATTTTTATAAATA
* *
41543299 TTTTATAATTTTTATGAATA
1 TTTTTTAATTTTTATAAATA
41543319 TTTTTT
1 TTTTTT
41543325 TCGAATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 7 0.33
19 5 0.24
20 9 0.43
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTTTAATTTTTATAAATA
Found at i:41547898 original size:26 final size:26
Alignment explanation
Indices: 41547859--41547908 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
41547849 CTTTTTAAAG
*
41547859 TCAAAAAAACATTTGAACATAATTCT
1 TCAAAAAAACATTTAAACATAATTCT
* *
41547885 TCAAGAAAATATTTAAACATAATT
1 TCAAAAAAACATTTAAACATAATT
41547909 ACATTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.32
Consensus pattern (26 bp):
TCAAAAAAACATTTAAACATAATTCT
Found at i:41548288 original size:17 final size:17
Alignment explanation
Indices: 41548249--41548281 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41548239 TTATTGGGTT
*
41548249 AAATAGAAAATAAAAAA
1 AAATAAAAAATAAAAAA
41548266 AAATAAAAAATAAAAA
1 AAATAAAAAATAAAAA
41548282 CTAATAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (17 bp):
AAATAAAAAATAAAAAA
Found at i:41555257 original size:20 final size:20
Alignment explanation
Indices: 41555223--41555263 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
41555213 TCTAATTGAG
41555223 TTATTTTTTAAAATTT-TAT
1 TTATTTTTTAAAATTTGTAT
*
41555242 TTATTTATTTACAATTTGTAT
1 TTATTT-TTTAAAATTTGTAT
41555263 T
1 T
41555264 ACACCAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TTATTTTTTAAAATTTGTAT
Found at i:41558705 original size:17 final size:18
Alignment explanation
Indices: 41558673--41558706 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41558663 TATTACCGGA
41558673 TTAAAAAATATATATTTC
1 TTAAAAAATATATATTTC
*
41558691 TTAAATAAT-TATATTT
1 TTAAAAAATATATATTT
41558707 ATCAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAAAAAATATATATTTC
Found at i:41564945 original size:131 final size:131
Alignment explanation
Indices: 41564477--41564947 Score: 685
Period size: 131 Copynumber: 3.6 Consensus size: 131
41564467 GCTTGAGTTA
* ** * * *
41564477 TAAAAAGATGGTATTTTTATTTTAGGCTTATCAATGATTTCAGGTTGCTTCTTGATAAAATCTTT
1 TAAAAAAATGGTAACTTTATTTTAGTCTTATCAATGATTTCAGGTTGCTTGTTAATAAAATCTTT
* * * * *
41564542 TGCTTT-CCTTGT-TTTAGAAAAAAGGAAATTCCAGTGATGAATTCAAGTGCTAATCATGTAATT
66 TACTTTCCCTT-TCTTT--ATAAGATGAAATTCTAGTGATGAATTCAAGTGCTAATCATGTAATT
41564605 TGAT
128 TGAT
* ** *
41564609 TAAACAAATGGCGACTTTATTTTAGTCTTATCAATGATTTCAGGTTCCTTGTTAATAAAATCTTT
1 TAAAAAAATGGTAACTTTATTTTAGTCTTATCAATGATTTCAGGTTGCTTGTTAATAAAATCTTT
* * * *
41564674 TTCTTTCCCCTTCTTTATAAGATGAAATTCTAATGATGAATTCAAATGCTAATCATGTAATTTGA
66 TACTTTCCCTTTCTTTATAAGATGAAATTCTAGTGATGAATTCAAGTGCTAATCATGTAATTTGA
41564739 T
131 T
*
41564740 TAAAAAAATGGTAACTTTATTTTAGTCTTATCAATGATTTCAGGTTGCTTGCTAATAAAATCTTT
1 TAAAAAAATGGTAACTTTATTTTAGTCTTATCAATGATTTCAGGTTGCTTGTTAATAAAATCTTT
* *
41564805 TACTTTCCCTTTCTTTATAAGATGAAATTCTAGTTATGAATTCAAGTGCTACTCATGTAATTTGA
66 TACTTTCCCTTTCTTTATAAGATGAAATTCTAGTGATGAATTCAAGTGCTAATCATGTAATTTGA
41564870 T
131 T
* *
41564871 TAAAAAAATGGTAACTTTATTTTAGTCTTATCAATGATTTCAGGTTGCTTGTTGATAAAATCTTG
1 TAAAAAAATGGTAACTTTATTTTAGTCTTATCAATGATTTCAGGTTGCTTGTTAATAAAATCTTT
41564936 TACTTTCCCTTT
66 TACTTTCCCTTT
41564948 TTTGTAGAAA
Statistics
Matches: 305, Mismatches: 32, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
131 238 0.78
132 61 0.20
133 6 0.02
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (131 bp):
TAAAAAAATGGTAACTTTATTTTAGTCTTATCAATGATTTCAGGTTGCTTGTTAATAAAATCTTT
TACTTTCCCTTTCTTTATAAGATGAAATTCTAGTGATGAATTCAAGTGCTAATCATGTAATTTGA
T
Found at i:41571857 original size:30 final size:31
Alignment explanation
Indices: 41571788--41571857 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
41571778 AAATTATATA
*
41571788 ATTTTGGTGCCAGAATTTAGTAGCTGGATTC
1 ATTTTGGTCCCAGAATTTAGTAGCTGGATTC
* * *
41571819 ATTTTGGTCCCTGAATTTAGTAGTTGGATTT
1 ATTTTGGTCCCAGAATTTAGTAGCTGGATTC
41571850 A-TTTGGTC
1 ATTTTGGTC
41571858 TTGGAACTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 7 0.20
31 28 0.80
ACGTcount: A:0.20, C:0.11, G:0.24, T:0.44
Consensus pattern (31 bp):
ATTTTGGTCCCAGAATTTAGTAGCTGGATTC
Found at i:41584655 original size:15 final size:15
Alignment explanation
Indices: 41584635--41584668 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
41584625 GAATGCTTAA
41584635 TTTATCTCTTTTCAT
1 TTTATCTCTTTTCAT
41584650 TTTATCTCTTTTCAT
1 TTTATCTCTTTTCAT
41584665 TTTA
1 TTTA
41584669 ATTTAGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATCTCTTTTCAT
Found at i:41586906 original size:159 final size:159
Alignment explanation
Indices: 41586617--41586933 Score: 634
Period size: 159 Copynumber: 2.0 Consensus size: 159
41586607 TATTAGTCTG
41586617 TCGAAGGTTGAATATAGAATGCTGGAAGTCGTGTGTAAGAGTAACAGCAACTCTCATTCAACTTA
1 TCGAAGGTTGAATATAGAATGCTGGAAGTCGTGTGTAAGAGTAACAGCAACTCTCATTCAACTTA
41586682 AATATTAATCAGTAGAAAAGTGAGAGATATGGATCAGTTGCCTATGTCTACTTTCGTATAAATGA
66 AATATTAATCAGTAGAAAAGTGAGAGATATGGATCAGTTGCCTATGTCTACTTTCGTATAAATGA
41586747 AGCAGTATCTTCACTTCTCTATACTGGTT
131 AGCAGTATCTTCACTTCTCTATACTGGTT
41586776 TCGAAGGTTGAATATAGAATGCTGGAAGTCGTGTGTAAGAGTAACAGCAACTCTCATTCAACTTA
1 TCGAAGGTTGAATATAGAATGCTGGAAGTCGTGTGTAAGAGTAACAGCAACTCTCATTCAACTTA
41586841 AATATTAATCAGTAGAAAAGTGAGAGATATGGATCAGTTGCCTATGTCTACTTTCGTATAAATGA
66 AATATTAATCAGTAGAAAAGTGAGAGATATGGATCAGTTGCCTATGTCTACTTTCGTATAAATGA
41586906 AGCAGTATCTTCACTTCTCTATACTGGT
131 AGCAGTATCTTCACTTCTCTATACTGGT
41586934 ATAATTTTCC
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 158 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (159 bp):
TCGAAGGTTGAATATAGAATGCTGGAAGTCGTGTGTAAGAGTAACAGCAACTCTCATTCAACTTA
AATATTAATCAGTAGAAAAGTGAGAGATATGGATCAGTTGCCTATGTCTACTTTCGTATAAATGA
AGCAGTATCTTCACTTCTCTATACTGGTT
Found at i:41602531 original size:12 final size:12
Alignment explanation
Indices: 41602504--41602532 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
41602494 TATAATTGAA
41602504 TAAAAAAAAAAG
1 TAAAAAAAAAAG
41602516 -AAAAAAAAAAG
1 TAAAAAAAAAAG
41602527 TAAAAA
1 TAAAAA
41602533 CCTACCAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (12 bp):
TAAAAAAAAAAG
Found at i:41604141 original size:11 final size:11
Alignment explanation
Indices: 41604127--41604188 Score: 56
Period size: 11 Copynumber: 5.8 Consensus size: 11
41604117 ATATTCAAAC
41604127 AATAATAATAA
1 AATAATAATAA
41604138 AATAATAATAA
1 AATAATAATAA
* * *
41604149 TATGATAATGA
1 AATAATAATAA
* *
41604160 AATGATAACAA
1 AATAATAATAA
*
41604171 AACAATAA-AA
1 AATAATAATAA
41604181 AA-AATAAT
1 AATAATAAT
41604189 GACAAAACAG
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
9 5 0.12
10 4 0.10
11 33 0.79
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATAATAA
Found at i:41604193 original size:23 final size:23
Alignment explanation
Indices: 41604167--41604210 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
41604157 TGAAATGATA
41604167 ACAAAACAATAAAAAAAATAATG
1 ACAAAACAATAAAAAAAATAATG
*
41604190 ACAAAACAGTAAAAAAAATAA
1 ACAAAACAATAAAAAAAATAA
41604211 CAGCAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.75, C:0.09, G:0.05, T:0.11
Consensus pattern (23 bp):
ACAAAACAATAAAAAAAATAATG
Found at i:41605198 original size:23 final size:20
Alignment explanation
Indices: 41605144--41605199 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 20
41605134 TACAAATATT
41605144 AATAAATTTTAAATTGGAAA
1 AATAAATTTTAAATTGGAAA
*
41605164 AAT-AATTATTAAGTGGTCGGAAA
1 AATAAATT-TTAAAT--T-GGAAA
41605187 AATAAATTTTAAA
1 AATAAATTTTAAA
41605200 CTTAAAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 4 0.14
20 8 0.28
22 1 0.03
23 12 0.41
24 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.34
Consensus pattern (20 bp):
AATAAATTTTAAATTGGAAA
Found at i:41615870 original size:253 final size:247
Alignment explanation
Indices: 41615428--41615921 Score: 808
Period size: 253 Copynumber: 2.0 Consensus size: 247
41615418 TACCCTGATT
*
41615428 TTTTTATTCATTTATTTGAAACGGTTTTTTTCTCTTCTACCATCGTCATCATTCTAGCATGTCTA
1 TTTTTATTCATTTATTTGAAACGGTTTTTTTCTCTTCTACCATCGTCATCATTCTACCATGTCTA
* *
41615493 TCTCTTCTTTGTCATATTTGCAAATCAAAGTGTTTCTTTATTTTTTTTTCTCTCTTATCAGTTCT
66 TCTCTTCTCTCTCATATTTGCAAATCAAAGTGTTTCTTTATTTTTTTTTCTCTCTTATCAGTTCT
* *
41615558 AACCCACCGCCATGTCCACCGCTTTTCACCAGATCTGATCCATATCCCACGTTGGATCATGTTAA
131 AACCCACCGCCATGTCCACCGCTTTTCACCAGATCTGATCCATATCCCACGTAGGATCATGTCAA
*
41615623 TACGGGTACGGCACCCCAAACTGCCAAATCCGGCTAAGGAAGTTTCAAACGG
196 CACGGGTACGGCACCCCAAACTGCCAAATCCGGCTAAGGAAGTTTCAAACGG
*
41615675 TTTTTATTCATTTATTTGAAACGGTTTTTTTTCTCTTCTATCATCGTCATCATTCTACCATGTCT
1 TTTTTATTCATTTATTTGAAACGG-TTTTTTTCTCTTCTACCATCGTCATCATTCTACCATGTCT
* *
41615740 ATCTCTTCTCTCTCATCTTTGCAAATCAAAGTGTTTTTTTCGTATTCTTTTTTCTCTCTCTTATC
65 ATCTCTTCTCTCTCATATTTGCAAATCAAAGTG-TTTCTT--TATT-TTTTTT-TCTCTCTTATC
* *
41615805 AGTTCTTACCCACCGCCATGTCCACCGCTTTTCACCAGATCTGATCCTTATCCCACGTAGGATCA
125 AGTTCTAACCCACCGCCATGTCCACCGCTTTTCACCAGATCTGATCCATATCCCACGTAGGATCA
* * *
41615870 TGTCAACACGGGTATGGCACCCCAAACTGCCAAATCTGGCTAATGAAGTTTC
190 TGTCAACACGGGTACGGCACCCCAAACTGCCAAATCCGGCTAAGGAAGTTTC
41615922 TCACTAGTCA
Statistics
Matches: 227, Mismatches: 14, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
247 24 0.11
248 68 0.30
249 5 0.02
251 4 0.02
252 6 0.03
253 120 0.53
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (247 bp):
TTTTTATTCATTTATTTGAAACGGTTTTTTTCTCTTCTACCATCGTCATCATTCTACCATGTCTA
TCTCTTCTCTCTCATATTTGCAAATCAAAGTGTTTCTTTATTTTTTTTTCTCTCTTATCAGTTCT
AACCCACCGCCATGTCCACCGCTTTTCACCAGATCTGATCCATATCCCACGTAGGATCATGTCAA
CACGGGTACGGCACCCCAAACTGCCAAATCCGGCTAAGGAAGTTTCAAACGG
Found at i:41616858 original size:109 final size:110
Alignment explanation
Indices: 41616667--41616867 Score: 311
Period size: 109 Copynumber: 1.8 Consensus size: 110
41616657 GCTATAAATA
*
41616667 GCATACCTGTAAAAGTGCAGCAATAGTACCAAAAGAATTCCACAACAATGGAGCCAAATCTTGAA
1 GCATACCTGTAAAAGTGCAGCAATAGTACCAAAAGAATTCCACAACAAAGGAGCCAAATCTTGAA
41616732 ATAATTCTCTCTTCT-AAAAATAAAAACAAAAACAAGTTTATTAG
66 ATAATTCTCTCTTCTAAAAAATAAAAACAAAAACAAGTTTATTAG
* *
41616776 GCATACCTG-AATGAGTGCAGCTATAGTACCAAAAGAATTCCAC-ACGAAAGGAGCCAAATCTTG
1 GCATACCTGTAA-AAGTGCAGCAATAGTACCAAAAGAATTCCACAAC-AAAGGAGCCAAATCTTG
*
41616839 AAATAATTC-CTTGTTCTAAAAAATAAAAA
64 AAATAATTCTC-TCTTCTAAAAAATAAAAA
41616868 GGTAGACGCT
Statistics
Matches: 84, Mismatches: 4, Indels: 7
0.88 0.04 0.07
Matches are distributed among these distances:
108 5 0.06
109 68 0.81
110 11 0.13
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.23
Consensus pattern (110 bp):
GCATACCTGTAAAAGTGCAGCAATAGTACCAAAAGAATTCCACAACAAAGGAGCCAAATCTTGAA
ATAATTCTCTCTTCTAAAAAATAAAAACAAAAACAAGTTTATTAG
Found at i:41619191 original size:14 final size:15
Alignment explanation
Indices: 41619161--41619194 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
41619151 GTAATTTATA
41619161 TTCAATACTTAATTT
1 TTCAATACTTAATTT
* *
41619176 TTCAATATTTATTTT
1 TTCAATACTTAATTT
41619191 TTCA
1 TTCA
41619195 GTTTGTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (15 bp):
TTCAATACTTAATTT
Found at i:41621445 original size:20 final size:20
Alignment explanation
Indices: 41621395--41621461 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 20
41621385 TATAAAAAAA
*
41621395 AAAATTCAAAA-TAA-TGTT
1 AAAATTCAAAATTAATTTTT
41621413 AAGAACTTC-AAATTAATTTTT
1 AA-AA-TTCAAAATTAATTTTT
41621434 AAAATTCAAAATTTATATTTTAT
1 AAAATTCAAAA-TTA-ATTTT-T
41621457 AAAAT
1 AAAAT
41621462 AATTCAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
18 2 0.05
19 8 0.20
20 11 0.28
21 8 0.20
22 5 0.12
23 6 0.15
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (20 bp):
AAAATTCAAAATTAATTTTT
Found at i:41632639 original size:31 final size:29
Alignment explanation
Indices: 41632614--41632674 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
41632604 AAAATTTGAT
41632614 CAAATAAAAAAATTCATATATAAAATTGCA
1 CAAA-AAAAAAATTCATATATAAAATTGCA
** * *
41632644 CAAAATCAAAATTCATATATACAATGGCA
1 CAAAAAAAAAATTCATATATAAAATTGCA
41632673 CA
1 CA
41632675 TTAAATCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.25
Consensus pattern (29 bp):
CAAAAAAAAAATTCATATATAAAATTGCA
Found at i:41632656 original size:29 final size:30
Alignment explanation
Indices: 41632622--41632695 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
41632612 ATCAAATAAA
*
41632622 AAAATTCATATATAAAATTGCACA-AAATC
1 AAAATTCATATATAAAATGGCACATAAATC
*
41632651 AAAATTCATATATACAATGGCACATTAAATC
1 AAAATTCATATATAAAATGGCACA-TAAATC
* *
41632682 ATAATTCATGTATA
1 AAAATTCATATATA
41632696 GTTTTGAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 22 0.56
31 17 0.44
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (30 bp):
AAAATTCATATATAAAATGGCACATAAATC
Found at i:41638216 original size:15 final size:17
Alignment explanation
Indices: 41638195--41638234 Score: 66
Period size: 15 Copynumber: 2.5 Consensus size: 17
41638185 TAATTATTTA
41638195 AAAATTATTAAAAT-AT
1 AAAATTATTAAAATAAT
41638211 -AAATTATTAAAATAAT
1 AAAATTATTAAAATAAT
41638227 AAAATTAT
1 AAAATTAT
41638235 AATTTTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.59
16 2 0.09
17 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATTATTAAAATAAT
Found at i:41638238 original size:23 final size:26
Alignment explanation
Indices: 41638181--41638238 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 26
41638171 ATAAAATTTT
*
41638181 AATT-TAATTATTTAAAAATTATTAA
1 AATTATAATTATTTAAAAATTAATAA
41638206 AA-TATAAATTA-TT-AAAA-TAATAA
1 AATTAT-AATTATTTAAAAATTAATAA
41638229 AATTATAATT
1 AATTATAATT
41638239 TTACTATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
23 11 0.38
24 8 0.28
25 5 0.17
26 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AATTATAATTATTTAAAAATTAATAA
Found at i:41640266 original size:25 final size:23
Alignment explanation
Indices: 41640214--41640266 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
41640204 ACTTGATTTG
**
41640214 ATAATTTATTTATTCAAAACCTT
1 ATAATTTATTTATTCAAAAAATT
*
41640237 A-AATTTATTACTATTTAAAAAATT
1 ATAATTTATT--TATTCAAAAAATT
41640261 ATAATT
1 ATAATT
41640267 AGAATTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 8 0.33
23 1 0.04
24 11 0.46
25 4 0.17
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAATTTATTTATTCAAAAAATT
Found at i:41642195 original size:27 final size:25
Alignment explanation
Indices: 41642135--41642199 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 25
41642125 AATGACATAG
41642135 TTATAATAAAAAATATCAAAATTAAA
1 TTATAA-AAAAAATATCAAAATTAAA
*
41642161 ATATTAAAAGAAAATAT-AATAATTATAA
1 TTA-TAAAA-AAAATATCAA-AATTA-AA
41642189 TTATAAAAAAA
1 TTATAAAAAAA
41642200 TCTACAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
26 9 0.27
27 20 0.61
28 4 0.12
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
TTATAAAAAAAATATCAAAATTAAA
Found at i:41642261 original size:15 final size:15
Alignment explanation
Indices: 41642209--41642261 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
41642199 ATCTACAATT
*
41642209 AAATAACTATA-ACCA
1 AAATAA-TATATATCA
41642224 AAATAATATATAT-A
1 AAATAATATATATCA
41642238 AAAT--T-TATATCA
1 AAATAATATATATCA
41642250 AAATAATATATA
1 AAATAATATATA
41642262 AAACCTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
11 5 0.16
12 6 0.19
14 10 0.31
15 11 0.34
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAATATATATCA
Found at i:41643573 original size:10 final size:10
Alignment explanation
Indices: 41643558--41643587 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
41643548 GAAATATTTT
41643558 ATTATTGTTA
1 ATTATTGTTA
41643568 ATTATTGTTA
1 ATTATTGTTA
41643578 ATTATT-TTA
1 ATTATTGTTA
41643587 A
1 A
41643588 AAAAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.20
10 16 0.80
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (10 bp):
ATTATTGTTA
Found at i:41644267 original size:29 final size:29
Alignment explanation
Indices: 41644232--41644287 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
41644222 TTGTTTGCCT
41644232 AATGTTATATTTTAGTCACGTATATTTGA
1 AATGTTATATTTTAGTCACGTATATTTGA
* *
41644261 AATGTTATGTTTTAGTCACTTATATTT
1 AATGTTATATTTTAGTCACGTATATTT
41644288 TTGTTTTGTT
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:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (29 bp):
AATGTTATATTTTAGTCACGTATATTTGA
Found at i:41649541 original size:41 final size:41
Alignment explanation
Indices: 41649496--41649578 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
41649486 TATAAAGGTT
*
41649496 ATTAAAGGGCTAAATTGAAAATTTGATAGATATTATGTTTA
1 ATTAAAGGGCTAAATTGAAAATTTGATAGAAATTATGTTTA
* * *
41649537 ATTAATGGGTTAAATTGAAAATTTGATAGAAATTCTGTTTA
1 ATTAAAGGGCTAAATTGAAAATTTGATAGAAATTATGTTTA
41649578 A
1 A
41649579 CGATAAAATT
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:0.41, C:0.02, G:0.17, T:0.40
Consensus pattern (41 bp):
ATTAAAGGGCTAAATTGAAAATTTGATAGAAATTATGTTTA
Found at i:41651002 original size:18 final size:17
Alignment explanation
Indices: 41650979--41651017 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
41650969 GTGTATTCAT
*
41650979 TTTTTTTCACTAAGAAAA
1 TTTTTTCCA-TAAGAAAA
*
41650997 TTTTTTCCATAGGAAAA
1 TTTTTTCCATAAGAAAA
41651014 TTTT
1 TTTT
41651018 AACGAGACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (17 bp):
TTTTTTCCATAAGAAAA
Found at i:41658502 original size:168 final size:163
Alignment explanation
Indices: 41658168--41658525 Score: 393
Period size: 168 Copynumber: 2.2 Consensus size: 163
41658158 CGTAAAAACC
* * * * * * *
41658168 AGAACAATTAA-TCAAGACGTTTCAATTACATTCAATTCAATAAAATTCATTGATTATAATTATT
1 AGAACAATTAATTGAAG-TGTTCCAATTACACTCAATTAAATAAAATTCATTGATTATAATGATC
* * * * *
41658232 ATTCAAATATATCATACGTAATTACATCCGAATCCACTTATAATTTTATTTCAATTCTCCTTAAA
65 ATTCAAATACATCATACGTAATTACATCCGAACCCACTTATAATTTCATTTC-ATGCCCCTTAAA
* *
41658297 CAAAATTTTTAACATTGCCCCTACTTGTAAGAATT
129 CAAAACTTTTAACATTGCCCCTACTCGTAAGAATT
*
41658332 AGAACAATTAATTGAGGTGTTCCAATTACACTCAATTAAATAAAATTCATTGATTATAATGATCA
1 AGAACAATTAATTGAAGTGTTCCAATTACACTCAATTAAATAAAATTCATTGATTATAATGATCA
*
41658397 GTT-AAATACGCCA-CATATACGTAATTACATTCGAACCCACTTATAATTTCATTTC-TGCACCC
66 -TTCAAATA---CATC--ATACGTAATTACATCCGAACCCACTTATAATTTCATTTCATGC-CCC
* * * *
41658459 TTAAAACAAAACTTTTGAC-TATGTCCTTACTCGTAATAATT
124 TT-AAACAAAACTTTTAACAT-TGCCCCTACTCGTAAGAATT
*
41658500 AGAACAATTAATTGAAGTGTTTCAAT
1 AGAACAATTAATTGAAGTGTTCCAAT
41658526 AATACTCGAT
Statistics
Matches: 162, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
164 58 0.36
165 5 0.03
166 3 0.02
167 6 0.04
168 90 0.56
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (163 bp):
AGAACAATTAATTGAAGTGTTCCAATTACACTCAATTAAATAAAATTCATTGATTATAATGATCA
TTCAAATACATCATACGTAATTACATCCGAACCCACTTATAATTTCATTTCATGCCCCTTAAACA
AAACTTTTAACATTGCCCCTACTCGTAAGAATT
Found at i:41658581 original size:19 final size:20
Alignment explanation
Indices: 41658546--41658587 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
41658536 TTGTTATAAT
*
41658546 AAACGTCGATAATGGCAGTA
1 AAACGTCGATAATGGCAATA
41658566 AAACGATCG-TAA-GGCAATA
1 AAACG-TCGATAATGGCAATA
41658585 AAA
1 AAA
41658588 AAATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 8 0.40
21 3 0.15
ACGTcount: A:0.48, C:0.14, G:0.21, T:0.17
Consensus pattern (20 bp):
AAACGTCGATAATGGCAATA
Found at i:41660829 original size:31 final size:30
Alignment explanation
Indices: 41660782--41660841 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
41660772 ATTTTTTGGA
41660782 TTTAATGAAAAATTTCAAAAGATTTAAAGGG
1 TTTAATGAAAAATTTCAAAA-ATTTAAAGGG
* * *
41660813 TTTAATTAAAATTTTCAAAACTTTAAAGG
1 TTTAATGAAAAATTTCAAAAATTTAAAGG
41660842 ATTTGTGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (30 bp):
TTTAATGAAAAATTTCAAAAATTTAAAGGG
Found at i:41661891 original size:14 final size:14
Alignment explanation
Indices: 41661872--41661902 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41661862 TATCAAACAG
41661872 TAACAACAAAATAA
1 TAACAACAAAATAA
*
41661886 TAACAACATAATAA
1 TAACAACAAAATAA
41661900 TAA
1 TAA
41661903 AATGACAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19
Consensus pattern (14 bp):
TAACAACAAAATAA
Found at i:41661946 original size:11 final size:11
Alignment explanation
Indices: 41661872--41661943 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 11
41661862 TATCAAACAG
41661872 TAACAACAAAA
1 TAACAACAAAA
* *
41661883 TAATAACAACA
1 TAACAACAAAA
* *
41661894 TAATAATAAAA
1 TAACAACAAAA
* *
41661905 TGACAGCAAAA
1 TAACAACAAAA
*
41661916 TGACAACAAAA
1 TAACAACAAAA
** *
41661927 TAATGAGAAAA
1 TAACAACAAAA
41661938 TAACAA
1 TAACAA
41661944 GAATAATTAG
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 46 1.00
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (11 bp):
TAACAACAAAA
Found at i:41664042 original size:27 final size:27
Alignment explanation
Indices: 41664012--41664340 Score: 106
Period size: 27 Copynumber: 13.2 Consensus size: 27
41664002 AGGAGGAGGA
41664012 GGAGGTGGAGACTTGTAGACATATGGT
1 GGAGGTGGAGACTTGTAGACATATGGT
* ** *
41664039 GGAGGTGGGGACTTGTAGATGTAAT-GA
1 GGAGGTGGAGACTTGTAGACAT-ATGGT
* *
41664066 GGAGGT-G-G---TG-AGAGAGATGGT
1 GGAGGTGGAGACTTGTAGACATATGGT
*
41664087 GGAGGTGGAGACTTGTAGATATATGGT
1 GGAGGTGGAGACTTGTAGACATATGGT
** ** *
41664114 GGA-----AGAGGTG-AGGGAGATGGT
1 GGAGGTGGAGACTTGTAGACATATGGT
* * *
41664135 GGAGGTGGTGACTTGTAAACATAAGGT
1 GGAGGTGGAGACTTGTAGACATATGGT
** *
41664162 GGAGGT-G-G---TG-AGGGAGATGGT
1 GGAGGTGGAGACTTGTAGACATATGGT
* * * * *
41664183 GGTGATGGGGACTTGTACACATAAGGT
1 GGAGGTGGAGACTTGTAGACATATGGT
** *
41664210 GGAGGT-G-G---TG-AGGGAGATGGT
1 GGAGGTGGAGACTTGTAGACATATGGT
* *
41664231 GGTGGT-GAGGACTTGTAGACATAAGGT
1 GGAGGTGGA-GACTTGTAGACATATGGT
* * ** *
41664258 GAAGGAGGAGA--TG-AGGGAGATGGT
1 GGAGGTGGAGACTTGTAGACATATGGT
*
41664282 GGAGG-CGATGACTTGTAGACATATGGT
1 GGAGGTGGA-GACTTGTAGACATATGGT
*
41664309 GGAGGTGGTGACTTGTAGACATATGGT
1 GGAGGTGGAGACTTGTAGACATATGGT
41664336 GGAGG
1 GGAGG
41664341 AAGTGAGGGA
Statistics
Matches: 209, Mismatches: 61, Indels: 64
0.63 0.18 0.19
Matches are distributed among these distances:
20 2 0.01
21 43 0.21
22 13 0.06
23 5 0.02
24 13 0.06
25 5 0.02
26 15 0.07
27 108 0.52
28 5 0.02
ACGTcount: A:0.26, C:0.05, G:0.47, T:0.23
Consensus pattern (27 bp):
GGAGGTGGAGACTTGTAGACATATGGT
Found at i:41664090 original size:21 final size:21
Alignment explanation
Indices: 41664066--41664145 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 21
41664056 GATGTAATGA
41664066 GGAGGTGGTGAGAGAGATGGT
1 GGAGGTGGTGAGAGAGATGGT
* *
41664087 GGAGGTGGAGACTTGTAGATATATGGT
1 GGAGGT-G-G---TG-AGAGAGATGGT
* * *
41664114 GGAAGAGGTGAGGGAGATGGT
1 GGAGGTGGTGAGAGAGATGGT
41664135 GGAGGTGGTGA
1 GGAGGTGGTGA
41664146 CTTGTAAACA
Statistics
Matches: 44, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
21 23 0.52
22 3 0.07
23 1 0.02
25 1 0.02
26 3 0.07
27 13 0.30
ACGTcount: A:0.25, C:0.01, G:0.53, T:0.21
Consensus pattern (21 bp):
GGAGGTGGTGAGAGAGATGGT
Found at i:41664105 original size:48 final size:48
Alignment explanation
Indices: 41664034--41664319 Score: 292
Period size: 48 Copynumber: 5.9 Consensus size: 48
41664024 TTGTAGACAT
* ** * *
41664034 ATGGTGGAGGTGGGGACTTGTAGATGTAATGAGGAGGTGGTGAGAGAG
1 ATGGTGGAGGTGGAGACTTGTAGACATAATGTGGAGGTGGTGAGGGAG
* * *
41664082 ATGGTGGAGGTGGAGACTTGTAGATAT-ATGGTGGAAGAGGTGAGGGAG
1 ATGGTGGAGGTGGAGACTTGTAGACATAAT-GTGGAGGTGGTGAGGGAG
* * *
41664130 ATGGTGGAGGTGGTGACTTGTAAACATAAGGTGGAGGTGGTGAGGGAG
1 ATGGTGGAGGTGGAGACTTGTAGACATAATGTGGAGGTGGTGAGGGAG
* * * * *
41664178 ATGGTGGTGATGGGGACTTGTACACATAAGGTGGAGGTGGTGAGGGAG
1 ATGGTGGAGGTGGAGACTTGTAGACATAATGTGGAGGTGGTGAGGGAG
* * * *
41664226 ATGGTGGTGGT-GAGGACTTGTAGACATAAGGTGAAGGAGGAGATGAGGGAG
1 ATGGTGGAGGTGGA-GACTTGTAGACATAA--TG-TGGAGGTGGTGAGGGAG
*
41664277 ATGGTGGAGG-CGATGACTTGTAGACAT-ATGGTGGAGGTGGTGA
1 ATGGTGGAGGTGGA-GACTTGTAGACATAAT-GTGGAGGTGGTGA
41664320 CTTGTAGACA
Statistics
Matches: 202, Mismatches: 28, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
47 3 0.01
48 157 0.78
49 2 0.01
50 2 0.01
51 38 0.19
ACGTcount: A:0.26, C:0.04, G:0.48, T:0.23
Consensus pattern (48 bp):
ATGGTGGAGGTGGAGACTTGTAGACATAATGTGGAGGTGGTGAGGGAG
Found at i:41664148 original size:96 final size:95
Alignment explanation
Indices: 41664034--41664311 Score: 324
Period size: 96 Copynumber: 2.9 Consensus size: 95
41664024 TTGTAGACAT
** *
41664034 ATGGTGGAGGTGGGGACTTGTAGATGTAATGAGGAGGTGGTGAGAGAGATGGTGGAGGTGGAGAC
1 ATGGTGGAGGT-GGGACTTGTAGACATAATGAGGAGGTGGTGAGGGAGATGGTGGAGGTGGAGAC
*
41664099 TTGTAGATATATGGTGGAAGAGGTGAGGGAG
65 TTGTAGACATATGGTGGAAGAGGTGAGGGAG
* * * * * *
41664130 ATGGTGGAGGTGGTGACTTGTAAACATAAGGTGGAGGTGGTGAGGGAGATGGTGGTGATGGGGAC
1 ATGGTGGAGGTGG-GACTTGTAGACATAATGAGGAGGTGGTGAGGGAGATGGTGGAGGTGGAGAC
* * * *
41664195 TTGTACACATAAGGTGGAGGTGGTGAGGGAG
65 TTGTAGACATATGGTGGAAGAGGTGAGGGAG
* * * *
41664226 ATGGTGGTGGTGAGGACTTGTAGACATAAGGTGAAGGAGGAGATGAGGGAGATGGTGGAGG-CGA
1 ATGGTGGAGGTG-GGACTTGTAGACATAA--TG-AGGAGGTGGTGAGGGAGATGGTGGAGGTGGA
41664290 TGACTTGTAGACATATGGTGGA
62 -GACTTGTAGACATATGGTGGA
41664312 GGTGGTGACT
Statistics
Matches: 150, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
95 2 0.01
96 104 0.69
97 1 0.01
98 2 0.01
99 41 0.27
ACGTcount: A:0.26, C:0.04, G:0.47, T:0.23
Consensus pattern (95 bp):
ATGGTGGAGGTGGGACTTGTAGACATAATGAGGAGGTGGTGAGGGAGATGGTGGAGGTGGAGACT
TGTAGACATATGGTGGAAGAGGTGAGGGAG
Found at i:41664163 original size:75 final size:75
Alignment explanation
Indices: 41664082--41664388 Score: 201
Period size: 75 Copynumber: 4.1 Consensus size: 75
41664072 GGTGAGAGAG
* *
41664082 ATGGTGGAGGTGGAGACTTGTAGATATATGGTGGAAGAGG-TGAGGGAGATGGTGGAGGTGGTGA
1 ATGGTGGAGGTGGAGACTTGTAGACATATGGT-GAAGAGGATGAGGGAGATGGTGGAGGCGGTGA
41664146 CTTGTAAACAT
65 CTTGTAAACAT
* * * * * * * *** * * *
41664157 AAGGTGGAGGTGGTGA---G-GGAGATGGTGGTGATGGGGACTTGTACACATAAGGTGGAGGTGG
1 ATGGTGGAGGTGGAGACTTGTAGACAT-ATGGTGAAGAGGA--TG-AGGGAGATGGTGGAGGCGG
** *
41664218 TGA---G---GGAG
62 TGACTTGTAAACAT
* * *
41664226 ATGGTGGTGGT-GAGGACTTGTAGACATAAGGTGAAGGAGGAGATGAGGGAGATGGTGGAGGCGA
1 ATGGTGGAGGTGGA-GACTTGTAGACATATGGTGAA-GA-G-GATGAGGGAGATGGTGGAGGCGG
*
41664290 TGACTTGTAGACAT
62 TGACTTGTAAACAT
* *
41664304 ATGGTGGAGGTGGTGACTTGTAGACATATGGTG--GAGGAAGTGAGGGAGATGGTGGAGGCAGTG
1 ATGGTGGAGGTGGAGACTTGTAGACATATGGTGAAGAGG-A-TGAGGGAGATGGTGGAGGCGGTG
41664367 ACTTGTAAACAT
64 ACTTGTAAACAT
41664379 ATGGTGGAGG
1 ATGGTGGAGG
41664389 AGGTGAAGGA
Statistics
Matches: 170, Mismatches: 40, Indels: 44
0.67 0.16 0.17
Matches are distributed among these distances:
68 1 0.01
69 12 0.07
71 9 0.05
72 27 0.16
73 8 0.05
74 5 0.03
75 78 0.46
78 29 0.17
79 1 0.01
ACGTcount: A:0.26, C:0.05, G:0.46, T:0.23
Consensus pattern (75 bp):
ATGGTGGAGGTGGAGACTTGTAGACATATGGTGAAGAGGATGAGGGAGATGGTGGAGGCGGTGAC
TTGTAAACAT
Found at i:41664199 original size:144 final size:147
Alignment explanation
Indices: 41664034--41664319 Score: 384
Period size: 144 Copynumber: 2.0 Consensus size: 147
41664024 TTGTAGACAT
* * ** *
41664034 ATGGTGGAGGTGGGGACTTGTAGATGTAATGAGGAGGTGGTGAGAGAGATGGTGGAGGTG-GAGA
1 ATGGTGGAGATGGGGACTTGTACACATAAGGAGGAGGTGGTGAGAGAGATGGTGGAGGTGAG-GA
* * * *
41664098 CTTGTAGATATATGGTGGAA-GA-G-G-TGAGGGAGATGGTGGAGGTGGTGACTTGTAAACATAA
65 CTTGTAGACATAAGGT-GAAGGAGGAGATGAGGGAGATGGTGGAGGCGATGACTTGTAAACATAA
41664159 GGTGGAGGTGGTGAGGGAG
129 GGTGGAGGTGGTGAGGGAG
* * * *
41664178 ATGGTGGTGATGGGGACTTGTACACATAAGGTGGAGGTGGTGAGGGAGATGGTGGTGGTGAGGAC
1 ATGGTGGAGATGGGGACTTGTACACATAAGGAGGAGGTGGTGAGAGAGATGGTGGAGGTGAGGAC
* *
41664243 TTGTAGACATAAGGTGAAGGAGGAGATGAGGGAGATGGTGGAGGCGATGACTTGTAGACATATGG
66 TTGTAGACATAAGGTGAAGGAGGAGATGAGGGAGATGGTGGAGGCGATGACTTGTAAACATAAGG
41664308 TGGAGGTGGTGA
131 TGGAGGTGGTGA
41664320 CTTGTAGACA
Statistics
Matches: 122, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
143 3 0.02
144 69 0.57
145 2 0.02
146 1 0.01
147 47 0.39
ACGTcount: A:0.26, C:0.04, G:0.48, T:0.23
Consensus pattern (147 bp):
ATGGTGGAGATGGGGACTTGTACACATAAGGAGGAGGTGGTGAGAGAGATGGTGGAGGTGAGGAC
TTGTAGACATAAGGTGAAGGAGGAGATGAGGGAGATGGTGGAGGCGATGACTTGTAAACATAAGG
TGGAGGTGGTGAGGGAG
Found at i:41664331 original size:126 final size:123
Alignment explanation
Indices: 41664178--41664439 Score: 319
Period size: 126 Copynumber: 2.1 Consensus size: 123
41664168 GGTGAGGGAG
* * ** * *
41664178 ATGGTGGTGATGGGGACTTGTACACATAAGGTGGAGGTGGTGAGGGAGATGGTGGTGGTGAG-GA
1 ATGGTGGAGGTGGGGACTTGTACACATAAGGTGGAGGAAGTGAGGGAGATGGTGGAGG-CAGTGA
* * * *
41664242 CTTGTAGACATAAGGTGAAGGAGGAGATGAGGGAGATGGTGGAGGCGATGACTTGTAGACAT
65 CTTGTAAACATAAGGT---GGAGGAGATGAAGGAGATGGTGGAGGCGATGACTTATAAACAT
* * *
41664304 ATGGTGGAGGTGGTGACTTGTAGACATATGGTGGAGGAAGTGAGGGAGATGGTGGAGGCAGTGAC
1 ATGGTGGAGGTGGGGACTTGTACACATAAGGTGGAGGAAGTGAGGGAGATGGTGGAGGCAGTGAC
* * * *
41664369 TTGTAAACATATGGTGGAGGAGGTGAAGGAGATGGTGGAGGTGGTGACTTATAAACAT
66 TTGTAAACATAAGGTGGAGGAGATGAAGGAGATGGTGGAGGCGATGACTTATAAACAT
*
41664427 AAGGTGGAGGTGG
1 ATGGTGGAGGTGG
41664440 CGAGGGAGAT
Statistics
Matches: 117, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
123 49 0.42
125 2 0.02
126 66 0.56
ACGTcount: A:0.27, C:0.06, G:0.45, T:0.23
Consensus pattern (123 bp):
ATGGTGGAGGTGGGGACTTGTACACATAAGGTGGAGGAAGTGAGGGAGATGGTGGAGGCAGTGAC
TTGTAAACATAAGGTGGAGGAGATGAAGGAGATGGTGGAGGCGATGACTTATAAACAT
Done.