Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_51.0, whole genome shotgun sequence
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: 10072460
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 70252 characters in sequence are not A, C, G, or T
File 3 of 20
Found at i:799509 original size:31 final size:29
Alignment explanation
Indices: 799466--799550 Score: 98
Period size: 31 Copynumber: 2.8 Consensus size: 29
799456 ACCTTATGGA
799466 AGAAGGACTAAATTGAAAAGAAAGTAAACAT
1 AGAAGGACTAAATTGAAAAGAAAG-AAA-AT
* *
799497 AGAAAGACTAAATTAAAAAGAAAGAAAAT
1 AGAAGGACTAAATTGAAAAGAAAGAAAAT
* *
799526 ATTAATGGACCAAATTGAAAAGAAA
1 A-GAA-GGACTAAATTGAAAAGAAA
799551 AATAAGGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 3 0.07
30 5 0.11
31 38 0.83
ACGTcount: A:0.61, C:0.06, G:0.16, T:0.16
Consensus pattern (29 bp):
AGAAGGACTAAATTGAAAAGAAAGAAAAT
Found at i:802648 original size:2 final size:2
Alignment explanation
Indices: 802641--802697 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
802631 ATGCACATCC
** * * **
802641 AT AT AT AT AT AT AT AT AT AT GC AT AT GT AC AT CC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
802683 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
802698 CACATATGCT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:802660 original size:34 final size:34
Alignment explanation
Indices: 802617--802694 Score: 147
Period size: 34 Copynumber: 2.3 Consensus size: 34
802607 ATAGTGAACA
802617 ATATATATATGCATATGCACATCCATATATATAT
1 ATATATATATGCATATGCACATCCATATATATAT
*
802651 ATATATATATGCATATGTACATCCATATATATAT
1 ATATATATATGCATATGCACATCCATATATATAT
802685 ATATATATAT
1 ATATATATAT
802695 ATACACATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (34 bp):
ATATATATATGCATATGCACATCCATATATATAT
Found at i:803330 original size:24 final size:26
Alignment explanation
Indices: 803279--803332 Score: 76
Period size: 24 Copynumber: 2.1 Consensus size: 26
803269 TGACTCCCTC
803279 TCTTCTAACCATTTTAGCTGCCCATGGA
1 TCTTCTAACCATTTTA-C-GCCCATGGA
803307 TCTT-TAACCATTTTA-GCCCATGGA
1 TCTTCTAACCATTTTACGCCCATGGA
803331 TC
1 TC
803333 ACAACCTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 11 0.42
27 11 0.42
28 4 0.15
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37
Consensus pattern (26 bp):
TCTTCTAACCATTTTACGCCCATGGA
Found at i:803749 original size:2 final size:2
Alignment explanation
Indices: 803742--803774 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
803732 TTTGCAATAG
803742 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 T
803775 TAGGCCCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:803907 original size:73 final size:73
Alignment explanation
Indices: 803785--803927 Score: 232
Period size: 73 Copynumber: 2.0 Consensus size: 73
803775 TAGGCCCTTA
* * *
803785 TTGTAATGGTCATCTTGCGAAGACAAAGAAAAAGACGTTTTAATTGTAAATCTTGTCTTTTCTAT
1 TTGTAATGGTCATCTTCCCAAGACAAAGAAAAAGACGTTTTAATCGTAAATCTTGTCTTTTCTAT
803850 TCAATTTT
66 TCAATTTT
* * *
803858 TTGTAATGGTTATCTTCCCAAGTCAAAGAAAAAGACGTTTTACTCGTAAATCTTGTCTTTTCTAT
1 TTGTAATGGTCATCTTCCCAAGACAAAGAAAAAGACGTTTTAATCGTAAATCTTGTCTTTTCTAT
803923 TCAAT
66 TCAAT
803928 ATAAAGTATT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (73 bp):
TTGTAATGGTCATCTTCCCAAGACAAAGAAAAAGACGTTTTAATCGTAAATCTTGTCTTTTCTAT
TCAATTTT
Found at i:812360 original size:12 final size:12
Alignment explanation
Indices: 812343--812380 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
812333 TTTTAATATA
812343 TATATATGTATG
1 TATATATGTATG
812355 TATATATGTATG
1 TATATATGTATG
*
812367 TATGTATGTATG
1 TATATATGTATG
812379 TA
1 TA
812381 AATGTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (12 bp):
TATATATGTATG
Found at i:812362 original size:8 final size:8
Alignment explanation
Indices: 812339--812390 Score: 54
Period size: 8 Copynumber: 6.8 Consensus size: 8
812329 AAATTTTTAA
*
812339 TATATATA
1 TATATATG
*
812347 TATGTATG
1 TATATATG
812355 TATATATG
1 TATATATG
*
812363 TATGTATG
1 TATATATG
*
812371 TATGTATG
1 TATATATG
812379 TA-A-ATG
1 TATATATG
812385 TATATA
1 TATATA
812391 GATGGGATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
6 5 0.14
7 1 0.03
8 31 0.84
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (8 bp):
TATATATG
Found at i:812366 original size:4 final size:4
Alignment explanation
Indices: 812347--812380 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
812337 AATATATATA
*
812347 TATG TATG TATA TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TA
812381 AATGTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:814432 original size:23 final size:24
Alignment explanation
Indices: 814377--814436 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 24
814367 AATAGAGAAA
*
814377 AATAAAAAATTATACAACTAATTT
1 AATAAAAAATTATTCAACTAATTT
* *
814401 AAT-ATAAATTATTTAA-TAATTT
1 AATAAAAAATTATTCAACTAATTT
*
814423 AATAACAAATTATT
1 AATAAAAAATTATT
814437 GATGTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 9 0.29
23 19 0.61
24 3 0.10
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (24 bp):
AATAAAAAATTATTCAACTAATTT
Found at i:814806 original size:21 final size:21
Alignment explanation
Indices: 814776--814827 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
814766 TACATAATAA
* *
814776 TAATTTTATTTTATTCCTTCT
1 TAATTCTATTCTATTCCTTCT
*
814797 TAATTCTATTCTATTCTTTCT
1 TAATTCTATTCTATTCCTTCT
*
814818 TTATTCTATT
1 TAATTCTATT
814828 ATCACATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.65
Consensus pattern (21 bp):
TAATTCTATTCTATTCCTTCT
Found at i:820316 original size:39 final size:38
Alignment explanation
Indices: 820230--820316 Score: 93
Period size: 39 Copynumber: 2.2 Consensus size: 38
820220 TCCAATAGCA
* * * **
820230 CCTAAAAATGATATTCAATCATCAAGATTCTCAAAGTC
1 CCTAAAAATGATATTCAATCAGCAAAATTCTAAAAAAC
* *
820268 CCAATAAAATGATATTTAATCAGCAAAATTCTAAAAAAC
1 CCTA-AAAATGATATTCAATCAGCAAAATTCTAAAAAAC
820307 CCTTAAAAAT
1 CC-TAAAAAT
820317 TTCATATCAC
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
38 3 0.08
39 35 0.90
40 1 0.03
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.28
Consensus pattern (38 bp):
CCTAAAAATGATATTCAATCAGCAAAATTCTAAAAAAC
Found at i:825008 original size:31 final size:32
Alignment explanation
Indices: 824930--825020 Score: 121
Period size: 31 Copynumber: 2.8 Consensus size: 32
824920 GAACCATGAT
* **
824930 CAAATTTAGAAAGTTTCCTAATTTGATTAAGAC
1 CAAATTTGGAAAGTTTCCTAAAATG-TTAAGAC
*
824963 CAAATATGGAAAGTTTCCTAAAATGTTAAGA-
1 CAAATTTGGAAAGTTTCCTAAAATGTTAAGAC
*
824994 CAAATTTGGTAAGTTTCCTAAAATGTT
1 CAAATTTGGAAAGTTTCCTAAAATGTT
825021 TAAGGTGTCT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 25 0.48
32 6 0.12
33 21 0.40
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (32 bp):
CAAATTTGGAAAGTTTCCTAAAATGTTAAGAC
Found at i:825781 original size:18 final size:19
Alignment explanation
Indices: 825758--825796 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
825748 GTAGAACAAC
825758 ATGTGATAGA-TTAAAT-TT
1 ATGTGATA-ATTTAAATGTT
825776 ATGTGATAATTTAAATGTT
1 ATGTGATAATTTAAATGTT
825795 AT
1 AT
825797 ACATGCTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.05
18 14 0.74
19 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (19 bp):
ATGTGATAATTTAAATGTT
Found at i:828710 original size:3 final size:3
Alignment explanation
Indices: 828702--828730 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
828692 TCATGCATGT
828702 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
828731 AAATGAGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:836879 original size:21 final size:21
Alignment explanation
Indices: 836853--836935 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
836843 GTTCATGCAG
*
836853 TTCATGAAAAAGATTGATACA
1 TTCATGAAAAAGACTGATACA
* *
836874 TTCATGACAAAGACTGATGCA
1 TTCATGAAAAAGACTGATACA
* **
836895 TTCAT-AACAAAGACCGATGTA
1 TTCATGAA-AAAGACTGATACA
* * *
836916 TTTATGATAAGGACTGATAC
1 TTCATGAAAAAGACTGATAC
836936 CTCTATTCAA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.02
21 46 0.96
22 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (21 bp):
TTCATGAAAAAGACTGATACA
Found at i:837557 original size:24 final size:24
Alignment explanation
Indices: 837537--837591 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
837527 ATTCCTTGCA
*
837537 CTATTGTTTCAATAATGCCTTCAT
1 CTATTGCTTCAATAATGCCTTCAT
837561 CTATTGCTTCAATAATGCCTTCAT
1 CTATTGCTTCAATAATGCCTTCAT
837585 CTATTGC
1 CTATTGC
837592 CAGAAAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.44
Consensus pattern (24 bp):
CTATTGCTTCAATAATGCCTTCAT
Found at i:838269 original size:18 final size:18
Alignment explanation
Indices: 838246--838280 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
838236 TTACTTTCTT
* *
838246 TTTATTTTTTTATTTATA
1 TTTATTTATTTAATTATA
838264 TTTATTTATTTAATTAT
1 TTTATTTATTTAATTAT
838281 TAAATCATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTATTTAATTATA
Found at i:842778 original size:26 final size:28
Alignment explanation
Indices: 842715--842795 Score: 105
Period size: 26 Copynumber: 2.9 Consensus size: 28
842705 TGTGTTCTTG
*
842715 TATTT-GATAGAAAAAACCATCCTAATATA
1 TATTTGGATAGCAAAAACCATCC--ATATA
842744 TATTTGGATAGCAAAAACCATCC-TA-A
1 TATTTGGATAGCAAAAACCATCCATATA
842770 TATTTGGATAGCAAAAACCATGCCAT
1 TATTTGGATAGCAAAAACCAT-CCAT
842796 TTCTTTCCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
26 22 0.46
27 4 0.08
28 1 0.02
29 5 0.10
30 16 0.33
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.28
Consensus pattern (28 bp):
TATTTGGATAGCAAAAACCATCCATATA
Found at i:847356 original size:30 final size:30
Alignment explanation
Indices: 847320--847379 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
847310 ATTGATTGAG
* *
847320 GATGAAGAAGATGATATGCAAAAAGATGAA
1 GATGAAGAAAATGACATGCAAAAAGATGAA
* *
847350 GATGAAGAAAATGACATGGAAGAAGATGAA
1 GATGAAGAAAATGACATGCAAAAAGATGAA
847380 AAGGAAGATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.53, C:0.03, G:0.28, T:0.15
Consensus pattern (30 bp):
GATGAAGAAAATGACATGCAAAAAGATGAA
Found at i:847371 original size:21 final size:21
Alignment explanation
Indices: 847345--847398 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
847335 ATGCAAAAAG
*
847345 ATGAAGATGAAGAAAATG-AC
1 ATGAAGATGAAGAAAAGGAAC
* * *
847365 ATGGAAGAAGATGAAAAGGAAG
1 AT-GAAGATGAAGAAAAGGAAC
847387 ATGAAGATGAAG
1 ATGAAGATGAAG
847399 TTGAAGCCGA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 2 0.08
21 21 0.81
22 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.31, T:0.13
Consensus pattern (21 bp):
ATGAAGATGAAGAAAAGGAAC
Found at i:847387 original size:30 final size:30
Alignment explanation
Indices: 847323--847387 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
847313 GATTGAGGAT
* * * *
847323 GAAGAAGATGATATGCAAAAAGATGAAGAT
1 GAAGAAAATGACATGCAAAAAGATGAAAAG
* *
847353 GAAGAAAATGACATGGAAGAAGATGAAAAG
1 GAAGAAAATGACATGCAAAAAGATGAAAAG
847383 GAAGA
1 GAAGA
847388 TGAAGATGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.55, C:0.03, G:0.29, T:0.12
Consensus pattern (30 bp):
GAAGAAAATGACATGCAAAAAGATGAAAAG
Found at i:849441 original size:12 final size:12
Alignment explanation
Indices: 849424--849461 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
849414 CTTGGATAAG
849424 ATACGTGAGGAA
1 ATACGTGAGGAA
849436 ATACGTG-GAGAA
1 ATACGTGAG-GAA
*
849448 ATACGTGAAGAA
1 ATACGTGAGGAA
849460 AT
1 AT
849462 TAAGAATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 1 0.04
12 22 0.96
ACGTcount: A:0.45, C:0.08, G:0.29, T:0.18
Consensus pattern (12 bp):
ATACGTGAGGAA
Found at i:850025 original size:30 final size:30
Alignment explanation
Indices: 849991--850052 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
849981 ATTTCCAACT
*
849991 GAATTCTCTGTTGGGAATCATTTTCTGACG
1 GAATTCTCCGTTGGGAATCATTTTCTGACG
**
850021 GAATTCTCCGTTGGGAATGGTTTTCTGACG
1 GAATTCTCCGTTGGGAATCATTTTCTGACG
850051 GA
1 GA
850053 TTTTTTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.37
Consensus pattern (30 bp):
GAATTCTCCGTTGGGAATCATTTTCTGACG
Found at i:850271 original size:75 final size:74
Alignment explanation
Indices: 850099--850272 Score: 185
Period size: 75 Copynumber: 2.4 Consensus size: 74
850089 GTTGAAAATT
* *
850099 TCCAACG-A-AATTCCGTTAGAAATTAATTTCCTATAGAATTTTTTCCACGGAATTTTCCATTGG
1 TCCAACGAACAATTCCGTTAGAAATTAATTTCCTATAGAATTATTTCCACGGAATTTTCCATGGG
850162 AAATGCTTG
66 AAATGCTTG
* ** * * ***
850171 TCCAAC-AACGGAATTTCGTTAGAAATTCCTTTCCTATGGAATTATTTCCAATGGAATTTTTTGT
1 TCCAACGAAC--AATTCCGTTAGAAATTAATTTCCTATAGAATTATTTCC-ACGGAATTTTCCAT
850235 GGGAAATGCTT-
63 GGGAAATGCTTG
*
850246 TACCAACGAACAATTCCGTTGGAAATT
1 T-CCAACGAACAATTCCGTTAGAAATT
850273 TTCAACAGAA
Statistics
Matches: 83, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
72 7 0.08
75 48 0.58
76 25 0.30
77 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (74 bp):
TCCAACGAACAATTCCGTTAGAAATTAATTTCCTATAGAATTATTTCCACGGAATTTTCCATGGG
AAATGCTTG
Found at i:850812 original size:3 final size:3
Alignment explanation
Indices: 850804--850835 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
850794 ACTTTATCTC
*
850804 TAG TAG TAG TAA TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TA
850836 ATTATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:856046 original size:16 final size:15
Alignment explanation
Indices: 856025--856054 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
856015 ACAAAATTTA
856025 GATTTTGATTCTTTTG
1 GATTTTGATT-TTTTG
856041 GATTTTGATTTTTT
1 GATTTTGATTTTTT
856055 AAAATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.03, G:0.17, T:0.67
Consensus pattern (15 bp):
GATTTTGATTTTTTG
Found at i:856256 original size:21 final size:20
Alignment explanation
Indices: 856232--856307 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 20
856222 TTTTATTTCG
*
856232 AATGTATTGATACATGTTCAT
1 AATGTATCGATACAT-TTCAT
* **
856253 AATGTATCGATACATATGGT
1 AATGTATCGATACATTTCAT
* *
856273 CATGTATTGATACATTTTCAT
1 AATGTATCGATACA-TTTCAT
856294 AATGTATCGATACA
1 AATGTATCGATACA
856308 ATTTTTCCAG
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTTCAT
Found at i:865443 original size:68 final size:67
Alignment explanation
Indices: 865364--865492 Score: 195
Period size: 68 Copynumber: 1.9 Consensus size: 67
865354 GATATGTTAT
* * *
865364 GTATATGATGTATATACCATATACTACATGAGATGATTGAGAAAGCATGATGAATGCCATGAAAT
1 GTATATGATGTACATACCATATACTACATAAAATGATTGAGAAAGCATGATGAATG-CATGAAAT
865429 TAA
65 TAA
* * *
865432 GTATATGATGTACATTCCATATACTACTTAAAATGATTGAGAAGGCATGATGAATGCATGA
1 GTATATGATGTACATACCATATACTACATAAAATGATTGAGAAAGCATGATGAATGCATGA
865493 GCTTATTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
67 5 0.09
68 50 0.91
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (67 bp):
GTATATGATGTACATACCATATACTACATAAAATGATTGAGAAAGCATGATGAATGCATGAAATT
AA
Found at i:866141 original size:16 final size:17
Alignment explanation
Indices: 866120--866152 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
866110 TGAATTTGAT
866120 AAGAATTT-CAAAGGTA
1 AAGAATTTCCAAAGGTA
866136 AAGAATTTCCAAAGGTA
1 AAGAATTTCCAAAGGTA
866153 CAAACCTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.24
Consensus pattern (17 bp):
AAGAATTTCCAAAGGTA
Found at i:883358 original size:11 final size:13
Alignment explanation
Indices: 883328--883367 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
883318 AACTTTTGAA
883328 ATAAAATAATATT
1 ATAAAATAATATT
883341 ATAAAATAATATT
1 ATAAAATAATATT
883354 A-AAATATTAATATT
1 ATAAA-A-TAATATT
883368 TTACTTGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 3 0.12
13 15 0.60
14 7 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAAAATAATATT
Found at i:891027 original size:2 final size:2
Alignment explanation
Indices: 891020--891050 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
891010 TAATTCTCAA
891020 AT AT 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 A
891051 CATAACTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:894738 original size:32 final size:32
Alignment explanation
Indices: 894697--894775 Score: 158
Period size: 32 Copynumber: 2.5 Consensus size: 32
894687 ATACTCATTA
894697 TCTTCCAGTAAAGCAAAAACCCAAGTAAGATT
1 TCTTCCAGTAAAGCAAAAACCCAAGTAAGATT
894729 TCTTCCAGTAAAGCAAAAACCCAAGTAAGATT
1 TCTTCCAGTAAAGCAAAAACCCAAGTAAGATT
894761 TCTTCCAGTAAAGCA
1 TCTTCCAGTAAAGCA
894776 TCTAACTTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.23
Consensus pattern (32 bp):
TCTTCCAGTAAAGCAAAAACCCAAGTAAGATT
Found at i:895945 original size:19 final size:19
Alignment explanation
Indices: 895914--895952 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
895904 ACAATTGATA
895914 ATTTAAATATTAATATTTT
1 ATTTAAATATTAATATTTT
895933 ATTTATAAT-TTAATATTTT
1 ATTTA-AATATTAATATTTT
895952 A
1 A
895953 ATCAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTAAATATTAATATTTT
Found at i:896012 original size:151 final size:148
Alignment explanation
Indices: 895705--896003 Score: 340
Period size: 151 Copynumber: 2.0 Consensus size: 148
895695 TTTATTTTTG
* * * *
895705 ATTTATATTTTTTAAATATTAATAATTTAAAATCTATTCAAAATATTAATAATTGATCATTTAAA
1 ATTTTTATTTTTTAAATATCAATAATTTAAAATCTATTCAAAATATTAACAATTGATAATTTAAA
* * ** *
895770 TATTAATATTTTATTTTTATTTTAATCATTAATATTTTAAATTTTTAATATACTATTTATAATTT
66 TATTAATATTTTATTTATAATTTAATCATTAATATTTTAAATAGTTAAAATACTATTTATAA--T
**
895835 AAAATATTATTATGATTATTT
129 AAAATATTATTA-GAAAATTT
* * *
895856 ATTTTTATTTTTTAAATATCAATAGTTTATAAT-TAATTTAAAATATTAACAATTGATAATTTAA
1 ATTTTTATTTTTTAAATATCAATAATTTAAAATCT-ATTCAAAATATTAACAATTGATAATTTAA
*
895920 ATATTAATATTTTATTTATAATTTAAT-ATTTTAATCAATTTTAAA-AGTTAAAATA-TATTTCT
65 ATATTAATATTTTATTTATAATTTAATCA--TTAAT--ATTTTAAATAGTTAAAATACTATTTAT
*
895982 AA-AACATATTATTA-AAAATTT
126 AATAAAATATTATTAGAAAATTT
896003 A
1 A
896004 AACTTTTTTT
Statistics
Matches: 127, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
147 6 0.05
149 11 0.09
150 2 0.02
151 80 0.63
152 13 0.10
153 7 0.06
154 8 0.06
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (148 bp):
ATTTTTATTTTTTAAATATCAATAATTTAAAATCTATTCAAAATATTAACAATTGATAATTTAAA
TATTAATATTTTATTTATAATTTAATCATTAATATTTTAAATAGTTAAAATACTATTTATAATAA
AATATTATTAGAAAATTT
Found at i:896196 original size:21 final size:21
Alignment explanation
Indices: 896142--896196 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
896132 TAATATTTTA
*
896142 ATTAA-TTTTAAAATTTAAAT
1 ATTAATTTTTAAAATATAAAT
*
896162 ATTATTTTTATAAAATAT-AAT
1 ATTAATTTT-TAAAATATAAAT
896183 ATGTAATTTTTAAA
1 AT-TAATTTTTAAA
896197 CTTATAAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.14
21 12 0.41
22 13 0.45
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTAATTTTTAAAATATAAAT
Found at i:896202 original size:22 final size:21
Alignment explanation
Indices: 896142--896203 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
896132 TAATATTTTA
896142 ATTAA-TTTTAAAATT-TAAAT
1 ATTAATTTTTAAAATTAT-AAT
*
896162 ATT-ATTTTTATAAAATATAAT
1 ATTAATTTTTA-AAATTATAAT
*
896183 ATGTAATTTTTAAACTTATAA
1 AT-TAATTTTTAAAATTATAA
896204 AGGACATTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
19 1 0.03
20 8 0.24
21 9 0.26
22 9 0.26
23 7 0.21
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTAATTTTTAAAATTATAAT
Found at i:899641 original size:2 final size:2
Alignment explanation
Indices: 899598--899631 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
899588 GTGTTTGACG
899598 AT 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
899632 GAGTTATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:901297 original size:24 final size:23
Alignment explanation
Indices: 901270--901324 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
901260 TTTTTTATTT
901270 AGAAT-TTCTAATGATTTTTTTAAA
1 AGAATATT-TAAT-ATTTTTTTAAA
*
901294 AGAATATTTTATATTTTTTTAATGA
1 AGAATATTTAATATTTTTTTAA--A
901319 AGAATA
1 AGAATA
901325 AAGTGTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 10 0.37
24 8 0.30
25 9 0.33
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (23 bp):
AGAATATTTAATATTTTTTTAAA
Found at i:905079 original size:18 final size:19
Alignment explanation
Indices: 905048--905083 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
905038 TGGTGGAAGA
905048 GAATAAAAAGAGAATTAGG
1 GAATAAAAAGAGAATTAGG
905067 GAATAAAAA-AGAATTAG
1 GAATAAAAAGAGAATTAG
905084 AAAGAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (19 bp):
GAATAAAAAGAGAATTAGG
Found at i:905724 original size:20 final size:20
Alignment explanation
Indices: 905699--905736 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
905689 TGCTCTATTT
905699 ATTCTAGTTATTCTGCATGA
1 ATTCTAGTTATTCTGCATGA
*
905719 ATTCTAGTTGTTCTGCAT
1 ATTCTAGTTATTCTGCAT
905737 AAAGAAGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTAGTTATTCTGCATGA
Found at i:905783 original size:35 final size:35
Alignment explanation
Indices: 905742--905825 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 35
905732 TGCATAAAGA
* *
905742 AGTACTTCACTTATTTTAATTATTCCGCTTGAAGT
1 AGTACTTCACTTATTTTAATTATTCCGCATGAAAT
* * * * *
905777 AGTACTTCATTTGTTTTAGTTGTTCTGCATGAAAT
1 AGTACTTCACTTATTTTAATTATTCCGCATGAAAT
*
905812 AGTGCTTCACTTAT
1 AGTACTTCACTTAT
905826 AATGGTTGTT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.46
Consensus pattern (35 bp):
AGTACTTCACTTATTTTAATTATTCCGCATGAAAT
Found at i:924660 original size:15 final size:16
Alignment explanation
Indices: 924630--924690 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 16
924620 GATTAGCTTA
*
924630 GAAGCAAAGTGAGAAAG
1 GAAG-AAAGAGAGAAAG
*
924647 GAAGAAA-AGAGAAAA
1 GAAGAAAGAGAGAAAG
* *
924662 AAAGAAAGAAAGAAAG
1 GAAGAAAGAGAGAAAG
924678 G-AGAAAGA-AGAAA
1 GAAGAAAGAGAGAAA
924691 AATAGAGAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
14 5 0.14
15 19 0.51
16 9 0.24
17 4 0.11
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.02
Consensus pattern (16 bp):
GAAGAAAGAGAGAAAG
Found at i:937438 original size:40 final size:40
Alignment explanation
Indices: 937362--937440 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
937352 TTGGCTATTT
* **
937362 TTCATCTTAATGGGGTTTTCAACCTTGTCAAGATTGGTGA
1 TTCACCTTAATGGGGTTTTCAACCTTACCAAGATTGGTGA
*
937402 TTCACCTTAGTGGGGTTTTCAACCTTACCACA-ATTGGTG
1 TTCACCTTAATGGGGTTTTCAACCTTACCA-AGATTGGTG
937441 TCTTTCCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 33 0.97
41 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (40 bp):
TTCACCTTAATGGGGTTTTCAACCTTACCAAGATTGGTGA
Found at i:943208 original size:67 final size:67
Alignment explanation
Indices: 943080--943209 Score: 172
Period size: 67 Copynumber: 1.9 Consensus size: 67
943070 GAAATGTTAG
*
943080 TTTTGGATTTTGGTTGATCCCAAGAAAAACCATTGTTAAAAGTTGTAGCTGAGCCTATGAAAAGC
1 TTTTGGATTTTGGTTGATCCCAAGAAAAACCATTGTTAAAAGTTGTAGCTAAGCCTATGAAAAGC
943145 CA
66 CA
* * * * * * *
943147 TTTTGGGTTTTGGTTGATCCTATGAAAAATCATTGTTAAAGGTTG-AGACTAAGCTTGTGAAAA
1 TTTTGGATTTTGGTTGATCCCAAGAAAAACCATTGTTAAAAGTTGTAG-CTAAGCCTATGAAAA
943210 CACATTGTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
66 2 0.04
67 52 0.96
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.35
Consensus pattern (67 bp):
TTTTGGATTTTGGTTGATCCCAAGAAAAACCATTGTTAAAAGTTGTAGCTAAGCCTATGAAAAGC
CA
Found at i:952792 original size:2 final size:2
Alignment explanation
Indices: 952785--952811 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
952775 ACTCAGTCCG
952785 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 A
952812 AGTACCAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:960878 original size:22 final size:22
Alignment explanation
Indices: 960853--960898 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
960843 TATGCATGCA
960853 TATCAAATG-ACTCTCAACAACT
1 TATCAAA-GAACTCTCAACAACT
* *
960875 TATCTAAGAACTCTCAACAGCT
1 TATCAAAGAACTCTCAACAACT
960897 TA
1 TA
960899 CAATTGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (22 bp):
TATCAAAGAACTCTCAACAACT
Found at i:967241 original size:27 final size:27
Alignment explanation
Indices: 967211--967263 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
967201 ATAATATATA
967211 TACAATGCAATATTTTGATGAAAGTAT
1 TACAATGCAATATTTTGATGAAAGTAT
* *
967238 TACAATGTATTATTTTGATGAAAGTA
1 TACAATGCAATATTTTGATGAAAGTA
967264 ATAGTGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.40
Consensus pattern (27 bp):
TACAATGCAATATTTTGATGAAAGTAT
Found at i:967304 original size:27 final size:27
Alignment explanation
Indices: 967243--967480 Score: 214
Period size: 27 Copynumber: 8.9 Consensus size: 27
967233 AGTATTACAA
*
967243 TGTATTATTTTGAT-GAAAGT--AATAG
1 TGTAGTATTTTGATGGAAA-TAAAATAG
* *
967268 TGTATTATTTTGATGGAAATCAAATAG
1 TGTAGTATTTTGATGGAAATAAAATAG
* **
967295 TGTAGCATTTTGATGGAAATAAAACGG
1 TGTAGTATTTTGATGGAAATAAAATAG
* *
967322 TGTAGTATTTTCATGGAGAAAAAAATAG
1 TGTAGTATTTTGATGGA-AATAAAATAG
* *
967350 TGTATTATTTTGATGGAAAT-AAACAG
1 TGTAGTATTTTGATGGAAATAAAATAG
* * *
967376 TGTAGAATTCTAATGGAAATAAAATAG
1 TGTAGTATTTTGATGGAAATAAAATAG
*
967403 TGTAGTATTTTGATGGAGATAAAATAG
1 TGTAGTATTTTGATGGAAATAAAATAG
* * * *** *
967430 GGCATTATTTTGACAAAAATAATATAG
1 TGTAGTATTTTGATGGAAATAAAATAG
* * *
967457 TATACTATTTTGATAGAAATAAAA
1 TGTAGTATTTTGATGGAAATAAAA
967481 CTTAAACCTC
Statistics
Matches: 170, Mismatches: 38, Indels: 8
0.79 0.18 0.04
Matches are distributed among these distances:
25 15 0.09
26 25 0.15
27 108 0.64
28 22 0.13
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (27 bp):
TGTAGTATTTTGATGGAAATAAAATAG
Found at i:967412 original size:81 final size:81
Alignment explanation
Indices: 967263--967442 Score: 254
Period size: 81 Copynumber: 2.2 Consensus size: 81
967253 TGATGAAAGT
* * * * *
967263 AATAGTGTATTATTTTGATGGAAATCAAATAGTGTAGCATTTTGATGGAAATAAAACGGTGTAGT
1 AATAGTGTATTATTTTGATGGAAATCAAACAGTGTAGAATTCTAATGGAAATAAAACAGTGTAGT
967328 ATTTTCATGGAGAAAAA
66 ATTTTCATGGAG-AAAA
*
967345 AATAGTGTATTATTTTGATGGAAAT-AAACAGTGTAGAATTCTAATGGAAATAAAATAGTGTAGT
1 AATAGTGTATTATTTTGATGGAAATCAAACAGTGTAGAATTCTAATGGAAATAAAACAGTGTAGT
* *
967409 ATTTTGATGGAGATAA
66 ATTTTCATGGAGAAAA
* *
967425 AATAGGGCATTATTTTGA
1 AATAGTGTATTATTTTGA
967443 CAAAAATAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 19 0.22
81 44 0.50
82 25 0.28
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (81 bp):
AATAGTGTATTATTTTGATGGAAATCAAACAGTGTAGAATTCTAATGGAAATAAAACAGTGTAGT
ATTTTCATGGAGAAAA
Found at i:967439 original size:108 final size:107
Alignment explanation
Indices: 967243--967440 Score: 256
Period size: 108 Copynumber: 1.8 Consensus size: 107
967233 AGTATTACAA
* ** * * *
967243 TGTATTATTTTGATGAAAGTAATAGTGTATTATTTTGATGGAAATCAAATAGTGTAGCATTTTGA
1 TGTATTATTTTGATGAAAGTAACAGTGTAGAATTCTAATGGAAATAAAATAGTGTAGCATTTTGA
* *
967308 TGGAAATAAAACGGTGTAGTATTTTCATGGAGAAAAAAATAG
66 TGGAAATAAAAAGGTGCAGTATTTTCATGGAGAAAAAAATAG
*
967350 TGTATTATTTTGATGGAAA-TAAACAGTGTAGAATTCTAATGGAAATAAAATAGTGTAGTATTTT
1 TGTATTATTTTGAT-GAAAGT-AACAGTGTAGAATTCTAATGGAAATAAAATAGTGTAGCATTTT
* *
967414 GATGGAGATAAAATAGG-GCATTATTTT
64 GATGGAAATAAAA-AGGTGCAGTATTTT
967441 GACAAAAATA
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
107 15 0.19
108 60 0.78
109 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.37
Consensus pattern (107 bp):
TGTATTATTTTGATGAAAGTAACAGTGTAGAATTCTAATGGAAATAAAATAGTGTAGCATTTTGA
TGGAAATAAAAAGGTGCAGTATTTTCATGGAGAAAAAAATAG
Found at i:968073 original size:20 final size:20
Alignment explanation
Indices: 968045--968090 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
968035 ATAAATTCTA
* *
968045 AATTTTTATGATATATTTGG
1 AATTATTATGATATATTTGC
* *
968065 AATTATTATTATTTATTTGC
1 AATTATTATGATATATTTGC
968085 AATTAT
1 AATTAT
968091 AGGTTCAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.57
Consensus pattern (20 bp):
AATTATTATGATATATTTGC
Found at i:968461 original size:21 final size:19
Alignment explanation
Indices: 968423--968466 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
968413 AATAATATTT
968423 TATTAATAAAATTTTTAAC
1 TATTAATAAAATTTTTAAC
*
968442 TATTAATATTAATATTTTAAC
1 TATTAATA-AAAT-TTTTAAC
968463 TATT
1 TATT
968467 GTCGAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 3 0.14
21 11 0.50
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTAATAAAATTTTTAAC
Found at i:979815 original size:14 final size:14
Alignment explanation
Indices: 979796--979822 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
979786 AACTCTATTT
979796 AATTAAATTAATAA
1 AATTAAATTAATAA
979810 AATTAAATTAATA
1 AATTAAATTAATA
979823 TTTGTCACTT
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTAAATTAATAA
Found at i:981297 original size:18 final size:19
Alignment explanation
Indices: 981274--981313 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
981264 TAAGTGAAGA
*
981274 ATTTTA-GAATGAAATAAT
1 ATTTTATGAATAAAATAAT
*
981292 ATTTTATTAATAAAATAAT
1 ATTTTATGAATAAAATAAT
981311 ATT
1 ATT
981314 AAAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:988265 original size:8 final size:9
Alignment explanation
Indices: 988244--988275 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
988234 ACTACTTTTC
988244 TAGTTTATT
1 TAGTTTATT
988253 TAGTTTA-T
1 TAGTTTATT
988261 TAGTTTATT
1 TAGTTTATT
988270 TAGTTT
1 TAGTTT
988276 TGATTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.66
Consensus pattern (9 bp):
TAGTTTATT
Found at i:991491 original size:74 final size:75
Alignment explanation
Indices: 991366--991549 Score: 264
Period size: 74 Copynumber: 2.5 Consensus size: 75
991356 AGGCAAAGCA
* * * ** *
991366 AACTTAGTTGACTAAGAAGTATGGTTAGTGAACTAAGAGCTCACTGTTAGAGACTTCAATTACAA
1 AACTTAATTGACTAAGAAGTATGGTTAGTCAACTAAAAGCTCACTACTAGAGAATTCAATTACAA
*
991431 GA-TAGAAAG
66 GACAAGAAAG
* *
991440 AACTTAATTGACTAACAAGCATGGTTAGTCAACTAAAAGCTCACTACTAGAGAATTCAATTACAA
1 AACTTAATTGACTAAGAAGTATGGTTAGTCAACTAAAAGCTCACTACTAGAGAATTCAATTACAA
991505 GACAAGAAAG
66 GACAAGAAAG
*
991515 -ACTTAATCGACTAAGAAGTATGGTTAGTCAACTAA
1 AACTTAATTGACTAAGAAGTATGGTTAGTCAACTAA
991550 GAGAACTCTA
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
74 91 0.94
75 6 0.06
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.26
Consensus pattern (75 bp):
AACTTAATTGACTAAGAAGTATGGTTAGTCAACTAAAAGCTCACTACTAGAGAATTCAATTACAA
GACAAGAAAG
Found at i:1004220 original size:13 final size:12
Alignment explanation
Indices: 1004202--1004245 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
1004192 TAAAAAAGAT
1004202 AAAAAAGAAAAAG
1 AAAAAAG-AAAAG
1004215 AAAAAAGAAAAG
1 AAAAAAGAAAAG
*
1004227 -CAAAAGAAAAG
1 AAAAAAGAAAAG
1004238 AAGAAAAG
1 AA-AAAAG
1004246 CATTGCTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 10 0.37
12 5 0.19
13 12 0.44
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:1004231 original size:19 final size:20
Alignment explanation
Indices: 1004204--1004247 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
1004194 AAAAAGATAA
1004204 AAAAG-AAAAAGAAAA-AAG
1 AAAAGCAAAAAGAAAAGAAG
1004222 AAAAGC-AAAAGAAAAGAAG
1 AAAAGCAAAAAGAAAAGAAG
1004241 AAAAGCA
1 AAAAGCA
1004248 TTGCTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAGCAAAAAGAAAAGAAG
Found at i:1007168 original size:23 final size:23
Alignment explanation
Indices: 1007138--1007186 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1007128 TTTTTAAATG
1007138 GTTTTAGTTAAGAAGAAGTCTAT
1 GTTTTAGTTAAGAAGAAGTCTAT
*
1007161 GTTTTAGTTAAGAAGAATTCTAT
1 GTTTTAGTTAAGAAGAAGTCTAT
1007184 GTT
1 GTT
1007187 AATCAACCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (23 bp):
GTTTTAGTTAAGAAGAAGTCTAT
Found at i:1011515 original size:20 final size:20
Alignment explanation
Indices: 1011492--1011534 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1011482 AGTATAACAT
1011492 AGAA-AAGACTTAGTCAACTA
1 AGAAGAAGA-TTAGTCAACTA
* *
1011512 AGAAGTATATTAGTCAACTA
1 AGAAGAAGATTAGTCAACTA
1011532 AGA
1 AGA
1011535 GCGCACTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (20 bp):
AGAAGAAGATTAGTCAACTA
Found at i:1014225 original size:50 final size:50
Alignment explanation
Indices: 1014169--1014266 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 50
1014159 CCAATATTCT
* * *
1014169 TATTTTATTTCTATTTGAACTTAAAATATTAAATATAAAACTATAATGCA
1 TATTTTATTTCTATTTAAACTTAAAATACTAAATACAAAACTATAATGCA
* *
1014219 TATTTTATTTCTATTTAAACTTAAATTACTAATTACAAAACTATAATG
1 TATTTTATTTCTATTTAAACTTAAAATACTAAATACAAAACTATAATG
1014267 AATAAAACAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (50 bp):
TATTTTATTTCTATTTAAACTTAAAATACTAAATACAAAACTATAATGCA
Found at i:1014668 original size:28 final size:28
Alignment explanation
Indices: 1014636--1014694 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
1014626 AGTGCCATGA
1014636 AAAATATATATAATAAATAATA-ATTTTT
1 AAAATATATATAATAAATAA-ACATTTTT
1014664 AAAATATATATAATAAATAAACATTTTT
1 AAAATATATATAATAAATAAACATTTTT
1014692 AAA
1 AAA
1014695 TATTTTGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (28 bp):
AAAATATATATAATAAATAAACATTTTT
Found at i:1014852 original size:21 final size:20
Alignment explanation
Indices: 1014802--1014852 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1014792 ATAGTAAGCT
*
1014802 AATGTGTTTTTGCCGTGAGG
1 AATGTATTTTTGCCGTGAGG
*
1014822 AATGTATTTTTGCCTTGAGG
1 AATGTATTTTTGCCGTGAGG
1014842 AATGTATTTTT
1 AATGTATTTTT
1014853 CTCATGATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.08, G:0.25, T:0.47
Consensus pattern (20 bp):
AATGTATTTTTGCCGTGAGG
Found at i:1014864 original size:20 final size:20
Alignment explanation
Indices: 1014821--1014892 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
1014811 TTGCCGTGAG
* *
1014821 GAATGTATTTTTGC-CTTGAG
1 GAATGTATTTTT-CTCATGAT
1014841 GAATGTATTTTTCTCATGAT
1 GAATGTATTTTTCTCATGAT
* * *
1014861 GAATGTGTTCTTCTCATAAT
1 GAATGTATTTTTCTCATGAT
* *
1014881 AAATGTGTTTTT
1 GAATGTATTTTT
1014893 TCAAACATGT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 1 0.02
20 43 0.98
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.49
Consensus pattern (20 bp):
GAATGTATTTTTCTCATGAT
Found at i:1015280 original size:21 final size:19
Alignment explanation
Indices: 1015252--1015298 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
1015242 ATGCTTTGTG
1015252 ATAT-TAAATGTTATGAATAT
1 ATATATAAATGTTAT--ATAT
*
1015272 ATATATAAATTTTATATAT
1 ATATATAAATGTTATATAT
*
1015291 ACATATAA
1 ATATATAA
1015299 TTTATACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.46
20 4 0.17
21 9 0.38
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (19 bp):
ATATATAAATGTTATATAT
Found at i:1015290 original size:17 final size:18
Alignment explanation
Indices: 1015268--1015301 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1015258 AATGTTATGA
*
1015268 ATATATATATA-AATTTT
1 ATATATACATATAATTTT
1015285 ATATATACATATAATTT
1 ATATATACATATAATTT
1015302 ATACATAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATACATATAATTTT
Found at i:1015343 original size:23 final size:23
Alignment explanation
Indices: 1015294--1015339 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1015284 TATATATACA
* *
1015294 TATAATTTATACATAAGCATTAT
1 TATAACTTATACATAAACATTAT
*
1015317 TATAACTTATA-ATAAACTTTAT
1 TATAACTTATACATAAACATTAT
1015339 T
1 T
1015340 TATATAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (23 bp):
TATAACTTATACATAAACATTAT
Found at i:1025747 original size:24 final size:23
Alignment explanation
Indices: 1025688--1025754 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 23
1025678 TGATAATGTT
1025688 ATTATATTATATAAAT-ATATTATA
1 ATTA-ATTA-ATAAATAATATTATA
*
1025712 ATATGAAATAATAAATAATATTTATA
1 AT-T-AATTAATAAATAATA-TTATA
*
1025738 ATTAATTAATAATTAAT
1 ATTAATTAATAAATAAT
1025755 TATAAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 20 0.56
25 8 0.22
26 8 0.22
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (23 bp):
ATTAATTAATAAATAATATTATA
Found at i:1025772 original size:17 final size:17
Alignment explanation
Indices: 1025750--1025789 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1025740 TAATTAATAA
*
1025750 TTAATTATAAAA-TATAT
1 TTAATTAAAAAATTA-AT
1025767 TTAATTAAAAAATTAAT
1 TTAATTAAAAAATTAAT
1025784 TTAATT
1 TTAATT
1025790 TTTAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATTAAAAAATTAAT
Found at i:1026631 original size:4 final size:4
Alignment explanation
Indices: 1026617--1026662 Score: 56
Period size: 4 Copynumber: 10.8 Consensus size: 4
1026607 AGGTAAAGTT
*
1026617 TTTA TTTTA TTTA TTTA TTTA TATTA TTATT TTTA TTTA TTTA TTT
1 TTTA -TTTA TTTA TTTA TTTA T-TTA TT-TA TTTA TTTA TTTA TTT
1026663 TTTCAATTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
4 26 0.70
5 11 0.30
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1026643 original size:22 final size:22
Alignment explanation
Indices: 1026618--1026660 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1026608 GGTAAAGTTT
1026618 TTATT-TTATTTATTTATTTATA
1 TTATTATT-TTTATTTATTTATA
1026640 TTATTATTTTTATTTATTTAT
1 TTATTATTTTTATTTATTTAT
1026661 TTTTTCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
TTATTATTTTTATTTATTTATA
Found at i:1026646 original size:12 final size:13
Alignment explanation
Indices: 1026617--1026662 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1026607 AGGTAAAGTT
1026617 TTTATTT-TATTTA
1 TTTATTTATA-TTA
1026630 TTTATTTATATTA
1 TTTATTTATATTA
*
1026643 -TTATTTTTATTTA
1 TTTATTTATA-TTA
1026656 TTTATTT
1 TTTATTT
1026663 TTTCAATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTATATTA
Found at i:1026675 original size:22 final size:22
Alignment explanation
Indices: 1026628--1026681 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
1026618 TTATTTTATT
* *
1026628 TATTTATTTATATTATTATTTT
1 TATTTATTTATATTATTAATTC
*
1026650 TATTTATTTAT-TTTTTCAATTC
1 TATTTATTTATATTATT-AATTC
1026672 TATTCTATTT
1 TATT-TATTT
1026682 GCTCATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 18 0.67
23 5 0.19
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTTATTTATATTATTAATTC
Found at i:1032504 original size:37 final size:37
Alignment explanation
Indices: 1032449--1032524 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
1032439 AAGTGTTGGT
*
1032449 TTGACATAGAAAAGGGTATTAAGGTAAACCTCTTTTG
1 TTGACATAGAAAAAGGTATTAAGGTAAACCTCTTTTG
1032486 TTGACATAGAAAAAGGTATTAAGGTAAACCTCTTTTG
1 TTGACATAGAAAAAGGTATTAAGGTAAACCTCTTTTG
1032523 TT
1 TT
1032525 AGATTAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (37 bp):
TTGACATAGAAAAAGGTATTAAGGTAAACCTCTTTTG
Found at i:1034158 original size:30 final size:30
Alignment explanation
Indices: 1034122--1034184 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
1034112 CTTGATTGAG
* *
1034122 GATGAAGAAGATGACATGTAAAGCGATGAA
1 GATGAAGAAGATGACATGCAAAGAGATGAA
*
1034152 GATGAAGAAGATGACATGCAAGGAGATGAA
1 GATGAAGAAGATGACATGCAAAGAGATGAA
1034182 GAT
1 GAT
1034185 TGTTAAGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.46, C:0.06, G:0.32, T:0.16
Consensus pattern (30 bp):
GATGAAGAAGATGACATGCAAAGAGATGAA
Found at i:1037832 original size:20 final size:21
Alignment explanation
Indices: 1037788--1037843 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1037778 TAACAATAAG
* *
1037788 ATGTATCGATACATGTTCTTC
1 ATGTATCGATACATGTGCGTC
*
1037809 ATGTATCGATACAT-TGGGTC
1 ATGTATCGATACATGTGCGTC
*
1037829 ATGTGTCGATACATG
1 ATGTATCGATACATG
1037844 AACCTCTGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (21 bp):
ATGTATCGATACATGTGCGTC
Found at i:1046731 original size:20 final size:20
Alignment explanation
Indices: 1046702--1046741 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1046692 CTACATCCAC
1046702 TACCTAGATTGTTCAACCAA
1 TACCTAGATTGTTCAACCAA
*
1046722 TACCTGGATTGTTCAACCAA
1 TACCTAGATTGTTCAACCAA
1046742 GGATTTTTCA
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:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (20 bp):
TACCTAGATTGTTCAACCAA
Found at i:1052756 original size:22 final size:22
Alignment explanation
Indices: 1052722--1052763 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1052712 ATTTTCATAT
1052722 ATTAATATAAAAACTAAGCTAA
1 ATTAATATAAAAACTAAGCTAA
* * *
1052744 ATTACTATCAAAATTAAGCT
1 ATTAATATAAAAACTAAGCT
1052764 CAAACAACTC
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:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (22 bp):
ATTAATATAAAAACTAAGCTAA
Found at i:1053126 original size:17 final size:19
Alignment explanation
Indices: 1053104--1053142 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1053094 TAAGTGAAGG
1053104 ATTTTA-GAATAAAAT-AT
1 ATTTTATGAATAAAATAAT
*
1053121 ATTTTATTAATAAAATAAT
1 ATTTTATGAATAAAATAAT
1053140 ATT
1 ATT
1053143 AAAATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 8 0.42
19 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:1063049 original size:19 final size:18
Alignment explanation
Indices: 1063015--1063056 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
1063005 CATTTTAGTT
1063015 ATTTTTATAATTA-TTTA
1 ATTTTTATAATTATTTTA
1063032 ATTTTTAGTAAGTTATTTTA
1 ATTTTTA-TAA-TTATTTTA
1063052 ATTTT
1 ATTTT
1063057 ATGTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 3 0.14
19 3 0.14
20 9 0.41
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (18 bp):
ATTTTTATAATTATTTTA
Found at i:1064694 original size:10 final size:10
Alignment explanation
Indices: 1064666--1064696 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1064656 ACTTAATTTC
*
1064666 TTTAGTTACT
1 TTTAGTTATT
1064676 TTTAGTTATT
1 TTTAGTTATT
1064686 TTTAGTTATT
1 TTTAGTTATT
1064696 T
1 T
1064697 ACATATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.19, C:0.03, G:0.10, T:0.68
Consensus pattern (10 bp):
TTTAGTTATT
Found at i:1068291 original size:44 final size:44
Alignment explanation
Indices: 1068228--1068330 Score: 206
Period size: 44 Copynumber: 2.3 Consensus size: 44
1068218 GCAGTTTAAC
1068228 CAAACATCCACAATCATATTGGGTCTATAGTCCATAACCATCAA
1 CAAACATCCACAATCATATTGGGTCTATAGTCCATAACCATCAA
1068272 CAAACATCCACAATCATATTGGGTCTATAGTCCATAACCATCAA
1 CAAACATCCACAATCATATTGGGTCTATAGTCCATAACCATCAA
1068316 CAAACATCCACAATC
1 CAAACATCCACAATC
1068331 TAGTTATAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.40, C:0.29, G:0.08, T:0.23
Consensus pattern (44 bp):
CAAACATCCACAATCATATTGGGTCTATAGTCCATAACCATCAA
Found at i:1070969 original size:36 final size:36
Alignment explanation
Indices: 1070863--1071074 Score: 202
Period size: 35 Copynumber: 6.1 Consensus size: 36
1070853 AATTATTTAA
* * *
1070863 TTTAATCAATTAGACCCAATAATTTAATTAAACAA-
1 TTTAATCAATTAGGCCCAATGACTTAATTAAACAAT
* * * * * * * *
1070898 TTCAATTAGTTAAGCCTAATAATTTAGTTAAACAAT
1 TTTAATCAATTAGGCCCAATGACTTAATTAAACAAT
* *
1070934 TTTAATCAATTTGGCCGAATGACTTAATTAAACAAT
1 TTTAATCAATTAGGCCCAATGACTTAATTAAACAAT
* * *
1070970 TTTAATCAATGAGGCCCAATGAATTAATTCAACAA-
1 TTTAATCAATTAGGCCCAATGACTTAATTAAACAAT
* *
1071005 TTTAATTAATTAGGCCCAATGACTTAATTAAATAA-
1 TTTAATCAATTAGGCCCAATGACTTAATTAAACAAT
* *
1071040 TTTAATTAATTAGGCAC-A--ACTTAATTAAACAAT
1 TTTAATCAATTAGGCCCAATGACTTAATTAAACAAT
1071073 TT
1 TT
1071075 NNNNNNNNNN
Statistics
Matches: 147, Mismatches: 28, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
32 13 0.09
33 2 0.01
34 1 0.01
35 74 0.50
36 57 0.39
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (36 bp):
TTTAATCAATTAGGCCCAATGACTTAATTAAACAAT
Found at i:1071066 original size:71 final size:69
Alignment explanation
Indices: 1070861--1071067 Score: 209
Period size: 71 Copynumber: 2.9 Consensus size: 69
1070851 TTAATTATTT
* * * * * * *
1070861 AATTTAATCAATTAGACCCAATAATTTAATTAAACAATTCAATTAGTTAAGCCTAA-TAATTTAG
1 AATTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAGGCC-AATTAA-TTAA
1070925 TTAAAC
64 TTAAAC
* * * * *
1070931 AATTTTAATCAATTTGGCCGAATGACTTAATTAAACAATTTTAATCAATGAGGCCCAATGAATTA
1 AA-TTTAATCAATTAGGCCCAATGACTTAATTAAACAA-TTTAATTAATTAGG-CCAATTAATTA
*
1070996 ATTCAAC
63 ATTAAAC
* *
1071003 AATTTAATTAATTAGGCCCAATGACTTAATTAAATAATTTAATTAATTAGGCACAACTTAATTAA
1 AATTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAGGC-CAA-TTAATTAA
1071068 ACAATTTNNN
Statistics
Matches: 111, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
69 1 0.01
70 17 0.15
71 68 0.61
72 21 0.19
73 4 0.04
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.35
Consensus pattern (69 bp):
AATTTAATCAATTAGGCCCAATGACTTAATTAAACAATTTAATTAATTAGGCCAATTAATTAATT
AAAC
Found at i:1072469 original size:14 final size:14
Alignment explanation
Indices: 1072450--1072476 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1072440 TTAGTTTAAA
1072450 TTTTAGTTAATTAG
1 TTTTAGTTAATTAG
1072464 TTTTAGTTAATTA
1 TTTTAGTTAATTA
1072477 ATTCATTTTG
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:0.11, T:0.59
Consensus pattern (14 bp):
TTTTAGTTAATTAG
Found at i:1075789 original size:14 final size:14
Alignment explanation
Indices: 1075770--1075802 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1075760 ATAAATAGTA
1075770 GACATGACCTCATT-
1 GACATGACC-CATTC
1075784 GACATGACCCATTC
1 GACATGACCCATTC
1075798 GACAT
1 GACAT
1075803 AGTTTAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.24
Consensus pattern (14 bp):
GACATGACCCATTC
Found at i:1076841 original size:22 final size:21
Alignment explanation
Indices: 1076791--1076847 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
1076781 TAGTGGACAA
1076791 AATGTATCGATACAATTTAGG
1 AATGTATCGATACAATTTAGG
* *
1076812 GATGTATCGATACAAGTTCT-TG
1 AATGTATCGATACAA-TT-TAGG
1076834 AATGTATCGATACA
1 AATGTATCGATACA
1076848 TGGGTTAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.45
22 16 0.52
23 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (21 bp):
AATGTATCGATACAATTTAGG
Found at i:1085176 original size:3 final size:3
Alignment explanation
Indices: 1085168--1085197 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1085158 ATTAGGTTCA
1085168 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1085198 TTGTTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1097872 original size:35 final size:35
Alignment explanation
Indices: 1097798--1097901 Score: 111
Period size: 35 Copynumber: 3.0 Consensus size: 35
1097788 TATGAAGTAG
* * * * * *
1097798 TTGTTCCGCATGAAGTAATGCTTCATTTGCTT-TAG
1 TTGTTCTGCGTGAAGTAATGCCTAACTTG-TTCTAA
*
1097833 TTGTTCTGCGTGAAGTAGTGCCTAACTTGTTCTAA
1 TTGTTCTGCGTGAAGTAATGCCTAACTTGTTCTAA
* *
1097868 TTGTTCTGTGTGAAGTAATGCCTCACTTGTTCTA
1 TTGTTCTGCGTGAAGTAATGCCTAACTTGTTCTA
1097902 GTTATTCTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
34 2 0.03
35 56 0.97
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.42
Consensus pattern (35 bp):
TTGTTCTGCGTGAAGTAATGCCTAACTTGTTCTAA
Found at i:1111857 original size:29 final size:29
Alignment explanation
Indices: 1111824--1111934 Score: 123
Period size: 29 Copynumber: 3.8 Consensus size: 29
1111814 CTTATTCTTG
* * *
1111824 TGTACCTGTTCACATACAGCTTCTTCTCA
1 TGTACCTGTTAACATACAGCTTCTTTTCT
* *
1111853 TGTACTTGTTAACATATAGCTTCTTTTCT
1 TGTACCTGTTAACATACAGCTTCTTTTCT
* * * *
1111882 TGTATCTATTCACGTACAGCTTCTTTTCT
1 TGTACCTGTTAACATACAGCTTCTTTTCT
* *
1111911 TGTACTTGTTAACATATAGCTTCT
1 TGTACCTGTTAACATACAGCTTCT
1111935 GTAATGATTG
Statistics
Matches: 65, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.46
Consensus pattern (29 bp):
TGTACCTGTTAACATACAGCTTCTTTTCT
Found at i:1112992 original size:27 final size:25
Alignment explanation
Indices: 1112937--1113000 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 25
1112927 ATATCAATTG
*
1112937 TGGCCTAGCCACATATAACAACTTG
1 TGGCCTAGCCACATATAACAACTTA
*
1112962 TGGCCTTGCCACATATATCACAAAC-TA
1 TGGCCTAGCCACATATA--AC-AACTTA
1112989 TGGCCCTAGCCA
1 TGG-CCTAGCCA
1113001 TGTCTAACAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 16 0.50
27 6 0.19
28 10 0.31
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (25 bp):
TGGCCTAGCCACATATAACAACTTA
Found at i:1114308 original size:4 final size:4
Alignment explanation
Indices: 1114299--1114331 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
1114289 NNNNNNNATC
*
1114299 CTTT CTTT CTTT CTTT CTTC CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
1114332 CTCTCATTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:1115818 original size:28 final size:29
Alignment explanation
Indices: 1115744--1115818 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
1115734 TGTTGCAACT
* *
1115744 TCTTCTCTTGTACCTTTTCACGTACAGCT
1 TCTTCTCTTGTACCTTTTCACATACAGCC
* * * *
1115773 TATTCTCTTGTGCTTTTTTACATACA-CC
1 TCTTCTCTTGTACCTTTTCACATACAGCC
*
1115801 TCTTCTCTTTTACCTTTT
1 TCTTCTCTTGTACCTTTT
1115819 ACTTGAGAAC
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
28 15 0.42
29 21 0.58
ACGTcount: A:0.13, C:0.28, G:0.07, T:0.52
Consensus pattern (29 bp):
TCTTCTCTTGTACCTTTTCACATACAGCC
Found at i:1121961 original size:3 final size:3
Alignment explanation
Indices: 1121947--1121978 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1121937 CGTTGCTTTT
*
1121947 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1121979 TCAACAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:1129355 original size:20 final size:20
Alignment explanation
Indices: 1129313--1129357 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1129303 ACCACGATTA
*
1129313 GTGTCTTTCACAATGCCTAG
1 GTGTCTTTCACAACGCCTAG
* * *
1129333 GTGTCTTTTACAACGTCTCG
1 GTGTCTTTCACAACGCCTAG
1129353 GTGTC
1 GTGTC
1129358 AGTTCGGTAT
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:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (20 bp):
GTGTCTTTCACAACGCCTAG
Found at i:1130020 original size:14 final size:14
Alignment explanation
Indices: 1130001--1130027 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1129991 TGGCTGAAAA
1130001 AAGGAAATGAAGTT
1 AAGGAAATGAAGTT
1130015 AAGGAAATGAAGT
1 AAGGAAATGAAGT
1130028 GCTGTTATGT
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:0.52, C:0.00, G:0.30, T:0.19
Consensus pattern (14 bp):
AAGGAAATGAAGTT
Found at i:1141598 original size:23 final size:23
Alignment explanation
Indices: 1141549--1141598 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1141539 TATGTGAGAT
* *
1141549 GGCATGTCGGGAATGAGTGGCAG
1 GGCATGTCGGGAATGAGTGACAC
*
1141572 GGCATGGT-GGGAATGTGTGACAC
1 GGCAT-GTCGGGAATGAGTGACAC
1141595 GGCA
1 GGCA
1141599 ATGACACGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.22, C:0.14, G:0.46, T:0.18
Consensus pattern (23 bp):
GGCATGTCGGGAATGAGTGACAC
Found at i:1141666 original size:23 final size:23
Alignment explanation
Indices: 1141640--1141720 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
1141630 ACCATGGAGG
*
1141640 GAATATGTGACATGACAGGGTGA
1 GAATATGTGACATGACATGGTGA
* *
1141663 GAATATGTGACATGAC-TTGTAGG
1 GAATATGTGACATGACATGGT-GA
*
1141686 GAATATGTGATATGACATGGTGA
1 GAATATGTGACATGACATGGTGA
1141709 GAGA-ATGTGACA
1 GA-ATATGTGACA
1141721 CGTCAGCATC
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
22 2 0.04
23 42 0.88
24 4 0.08
ACGTcount: A:0.35, C:0.07, G:0.32, T:0.26
Consensus pattern (23 bp):
GAATATGTGACATGACATGGTGA
Found at i:1142547 original size:30 final size:31
Alignment explanation
Indices: 1142501--1142558 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
1142491 TGTTAGCATG
*
1142501 TAACAACAGTTTTCTTGAGATGCATGGCGGT
1 TAACAACAGGTTTCTTGAGATGCATGGCGGT
*
1142532 TAACAAC-GGTTTCTTGATATGCATGGC
1 TAACAACAGGTTTCTTGAGATGCATGGC
1142559 ATGTAACAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (31 bp):
TAACAACAGGTTTCTTGAGATGCATGGCGGT
Found at i:1142587 original size:31 final size:30
Alignment explanation
Indices: 1142496--1142634 Score: 163
Period size: 31 Copynumber: 4.5 Consensus size: 30
1142486 GTCAGTGTTA
*
1142496 GCATGTAACAACAGTTTTCTTGAGATGCATG
1 GCATGTAACAACA-TTTTCTTGATATGCATG
* **
1142527 GC-GGTTAACAACGGTTTCTTGATATGCATG
1 GCATG-TAACAACATTTTCTTGATATGCATG
*
1142557 GCATGTAACAACATTTTACTTGATACGCATG
1 GCATGTAACAACATTTT-CTTGATATGCATG
** *
1142588 GTGTGTAACAACATTTTACTTGATTTGCATG
1 GCATGTAACAACATTTT-CTTGATATGCATG
1142619 GCATGTAACAACATTT
1 GCATGTAACAACATTT
1142635 ATTTCTTTCT
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
30 28 0.31
31 63 0.69
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (30 bp):
GCATGTAACAACATTTTCTTGATATGCATG
Found at i:1142597 original size:61 final size:61
Alignment explanation
Indices: 1142496--1142634 Score: 183
Period size: 61 Copynumber: 2.3 Consensus size: 61
1142486 GTCAGTGTTA
* *
1142496 GCATGTAACAACAGTTTTCTTGAGATGCATGGCGGTTAACAACGGTTT-CTTGATATGCATG
1 GCATGTAACAACA-TTTTCTTGAGACGCATGGCGGTTAACAACAGTTTACTTGATATGCATG
* * * *
1142557 GCATGTAACAACATTTTACTTGATACGCATGG-TGTGTAACAACATTTTACTTGATTTGCATG
1 GCATGTAACAACATTTT-CTTGAGACGCATGGCGGT-TAACAACAGTTTACTTGATATGCATG
1142619 GCATGTAACAACATTT
1 GCATGTAACAACATTT
1142635 ATTTCTTTCT
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
60 6 0.09
61 35 0.51
62 28 0.41
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (61 bp):
GCATGTAACAACATTTTCTTGAGACGCATGGCGGTTAACAACAGTTTACTTGATATGCATG
Found at i:1146568 original size:31 final size:31
Alignment explanation
Indices: 1146399--1146588 Score: 136
Period size: 31 Copynumber: 6.2 Consensus size: 31
1146389 AATCTGTTTT
*
1146399 CACTCAACATGTCACGCCCTAAATCTGGTAC
1 CACTCAACATGTCATGCCCTAAATCTGGTAC
* * * * ** *
1146430 CACTCACCACGTCATGCCATATATCTCTTAG
1 CACTCAACATGTCATGCCCTAAATCTGGTAC
* *
1146461 TACTCAACATGTCATGCCATAAATCT-GTCAC
1 CACTCAACATGTCATGCCCTAAATCTGGT-AC
* * * **
1146492 CACTCAACGTGTCA-CCCCATAAATCTGCTTT
1 CACTCAACATGTCATGCCC-TAAATCTGGTAC
* ***
1146523 CATTCAGTGTGTCATGCCCTAAATCTGGTAC
1 CACTCAACATGTCATGCCCTAAATCTGGTAC
* * *
1146554 CACTCAACTTGTCATG-CC-ATATCTAGTAC
1 CACTCAACATGTCATGCCCTAAATCTGGTAC
1146583 CACTCA
1 CACTCA
1146589 GCCTGTCACC
Statistics
Matches: 121, Mismatches: 34, Indels: 10
0.73 0.21 0.06
Matches are distributed among these distances:
29 15 0.12
30 5 0.04
31 97 0.80
32 4 0.03
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.28
Consensus pattern (31 bp):
CACTCAACATGTCATGCCCTAAATCTGGTAC
Found at i:1146574 original size:62 final size:61
Alignment explanation
Indices: 1146366--1146574 Score: 188
Period size: 62 Copynumber: 3.4 Consensus size: 61
1146356 TAAATCTACC
* ** * * * *
1146366 ACCACTCAGCATGTCACCCCATCAATCTGTTTTCACTCAACATGTCACGCCCTAAATCTGGT
1 ACCACTCAACATGTCATGCCATAAATCTCTTAT-ACTCAACATGTCATGCCCTAAATCTGGT
* * * *
1146428 ACCACTCACCACGTCATGCCATATATCTCTTAGTACTCAACATGTCATGCCATAAATCT-GT
1 ACCACTCAACATGTCATGCCATAAATCTCTTA-TACTCAACATGTCATGCCCTAAATCTGGT
* ** * ***
1146489 CACCACTCAACGTGTCACCCCATAAATCTGCTT-TCATTCAGTGTGTCATGCCCTAAATCTGGT
1 -ACCACTCAACATGTCATGCCATAAATCT-CTTAT-ACTCAACATGTCATGCCCTAAATCTGGT
*
1146552 ACCACTCAACTTGTCATGCCATA
1 ACCACTCAACATGTCATGCCATA
1146575 TCTAGTACCA
Statistics
Matches: 118, Mismatches: 24, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
61 3 0.03
62 109 0.92
63 6 0.05
ACGTcount: A:0.27, C:0.33, G:0.11, T:0.29
Consensus pattern (61 bp):
ACCACTCAACATGTCATGCCATAAATCTCTTATACTCAACATGTCATGCCCTAAATCTGGT
Found at i:1146697 original size:122 final size:122
Alignment explanation
Indices: 1146354--1146781 Score: 315
Period size: 122 Copynumber: 3.5 Consensus size: 122
1146344 CGTGTGATGC
* * * * * * * ** * * *
1146354 CATAAATCTACCACCACTCAGCATGTCACCCCATCAATCTGTTTTCACTCAACATGTCACGCCCT
1 CATAAATCTGCTACTACTCAACGTGTCACACCATAAATCTACTTTCACCCAGCGTGTCACGCCCT
* ** ** ** * * ***
1146419 AAATCTGGTACCACTCACCACGTCATGCCATATATCTCTTAGTACTCAACATGTCATGC
66 AAATCTGGTACCACTCAACTTGTCATGCC--ATATCTAGTACCACTCAGCCTGTCACAT
* * * ** * *
1146478 CATAAATCTG-TCACCACTCAACGTGTCACCCCATAAATCTGCTTTCATTCAGTGTGTCATGCCC
1 CATAAATCTGCT-ACTACTCAACGTGTCACACCATAAATCTACTTTCACCCAGCGTGTCACGCCC
*
1146542 TAAATCTGGTACCACTCAACTTGTCATGCCATATCTAGTACCACTCAGCCTGTCACCT
65 TAAATCTGGTACCACTCAACTTGTCATGCCATATCTAGTACCACTCAGCCTGTCACAT
* *
1146600 CATAAATCTGCTACTACTCAAC-TG-CGACACCATATATCTACTTTCACCCAGCGTGTCACGTCC
1 CATAAATCTGCTACTACTCAACGTGTC-ACACCATAAATCTACTTTCACCCAGCGTGTCACGCCC
* * * * * * * *
1146663 TCAATCTGGTACCACT-TAGTGTGTCAATGTCATATCTTGTACGACTCATCTTGTCACAT
65 TAAATCTGGTACCACTCAACT-TGTC-ATGCCATATCTAGTACCACTCAGCCTGTCACAT
* * * * ** * * *
1146722 CATAAATCTACTACTACTTAGCATGTCACGTCATAAATCTGCTTCCACTCAGCGTGTCAC
1 CATAAATCTGCTACTACTCAACGTGTCACACCATAAATCTACTTTCACCCAGCGTGTCAC
1146782 AACAAGATGT
Statistics
Matches: 247, Mismatches: 50, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
120 3 0.01
121 50 0.20
122 84 0.34
123 30 0.12
124 80 0.32
ACGTcount: A:0.27, C:0.32, G:0.12, T:0.30
Consensus pattern (122 bp):
CATAAATCTGCTACTACTCAACGTGTCACACCATAAATCTACTTTCACCCAGCGTGTCACGCCCT
AAATCTGGTACCACTCAACTTGTCATGCCATATCTAGTACCACTCAGCCTGTCACAT
Found at i:1146780 original size:31 final size:31
Alignment explanation
Indices: 1146338--1146781 Score: 134
Period size: 31 Copynumber: 14.5 Consensus size: 31
1146328 ATATGCTATT
* * * * *
1146338 ACTCAGCGTGTGATGCCATAAATCTACCACC
1 ACTCAGCGTGTCACGTCATAAATCTGCTACC
* ** * * **
1146369 ACTCAGCATGTCACCCCATCAATCTGTTTTC
1 ACTCAGCGTGTCACGTCATAAATCTGCTACC
* * * * *
1146400 ACTCAACATGTCACGCCCTAAATCTGGTACC
1 ACTCAGCGTGTCACGTCATAAATCTGCTACC
* ** * * * **
1146431 ACTCACCACGTCATGCCATATATCT-CTTAGT
1 ACTCAGCGTGTCACGTCATAAATCTGC-TACC
* * * *
1146462 ACTCAACATGTCATGCCATAAATCTG-TCACC
1 ACTCAGCGTGTCACGTCATAAATCTGCT-ACC
* ** **
1146493 ACTCAACGTGTCACCCCATAAATCTGCTTTC
1 ACTCAGCGTGTCACGTCATAAATCTGCTACC
* * * * * *
1146524 ATTCAGTGTGTCATGCCCTAAATCTGGTACC
1 ACTCAGCGTGTCACGTCATAAATCTGCTACC
* * * *
1146555 ACTCAACTTGTCATGCCAT--ATCTAG-TACC
1 ACTCAGCGTGTCACGTCATAAATCT-GCTACC
* * *
1146584 ACTCAGCCTGTCACCTCATAAATCTGCTACT
1 ACTCAGCGTGTCACGTCATAAATCTGCTACC
* ** * * **
1146615 ACTCAAC-TG-CGACACCATATATCTACTTTC
1 ACTCAGCGTGTC-ACGTCATAAATCTGCTACC
* * * *
1146645 ACCCAGCGTGTCACGTCCTCAATCTGGTACC
1 ACTCAGCGTGTCACGTCATAAATCTGCTACC
* * * *
1146676 ACTTAGTGTGTCAATGTCAT--ATCTTG-TACG
1 ACTCAGCGTGTC-ACGTCATAAATC-TGCTACC
* * * * *
1146706 ACTCATCTTGTCACATCATAAATCTACTACT
1 ACTCAGCGTGTCACGTCATAAATCTGCTACC
* * *
1146737 ACTTAGCATGTCACGTCATAAATCTGCTTCC
1 ACTCAGCGTGTCACGTCATAAATCTGCTACC
1146768 ACTCAGCGTGTCAC
1 ACTCAGCGTGTCAC
1146782 AACAAGATGT
Statistics
Matches: 300, Mismatches: 97, Indels: 32
0.70 0.23 0.07
Matches are distributed among these distances:
29 28 0.09
30 37 0.12
31 228 0.76
32 7 0.02
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.30
Consensus pattern (31 bp):
ACTCAGCGTGTCACGTCATAAATCTGCTACC
Found at i:1147582 original size:21 final size:21
Alignment explanation
Indices: 1147558--1147598 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1147548 CTTACACCAC
*
1147558 CAGCAGCTTCACTTGGTGCAG
1 CAGCAGCTTCACTTGATGCAG
1147579 CAGCAGCTTCACTTGATGCA
1 CAGCAGCTTCACTTGATGCA
1147599 CCAGTAGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.24
Consensus pattern (21 bp):
CAGCAGCTTCACTTGATGCAG
Found at i:1155870 original size:23 final size:23
Alignment explanation
Indices: 1155812--1155953 Score: 98
Period size: 23 Copynumber: 6.3 Consensus size: 23
1155802 TCAGTCATGT
*
1155812 TGTTACACACCATTTTTCAAATA
1 TGTTACACACCATTTTTCAAAAA
**
1155835 TGTTGTA-AGCCATTTTTCAAAAA
1 TGTTACACA-CCATTTTTCAAAAA
*
1155858 TGTTACACACCATGTTT-AAAAA
1 TGTTACACACCATTTTTCAAAAA
* * ** *
1155880 GTGATATATGCCA-TGTTCAAAAA
1 -TGTTACACACCATTTTTCAAAAA
**
1155903 TGTTACACA-CA-AGTTCAAAAA
1 TGTTACACACCATTTTTCAAAAA
* *
1155924 TTGTTACACGCC-TTATTCAAAAA
1 -TGTTACACACCATTTTTCAAAAA
1155947 TGTTACA
1 TGTTACA
1155954 TGCAAGTTCA
Statistics
Matches: 92, Mismatches: 20, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
21 11 0.12
22 28 0.30
23 52 0.57
24 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (23 bp):
TGTTACACACCATTTTTCAAAAA
Found at i:1155893 original size:46 final size:45
Alignment explanation
Indices: 1155812--1155953 Score: 137
Period size: 44 Copynumber: 3.2 Consensus size: 45
1155802 TCAGTCATGT
* * * *
1155812 TGTTACACACCATTTTTCAAATATGTTGTAAGCCATTTTTCAAAAA
1 TGTTACACACCATGTTT-AAAAATGTTATAAGCCATTATTCAAAAA
* * *
1155858 TGTTACACACCATGTTTAAAAAGTGATATATGCCA-TGTTCAAAAA
1 TGTTACACACCATGTTTAAAAA-TGTTATAAGCCATTATTCAAAAA
* * * *
1155903 TGTTACACA-CAAGTTCAAAAATTGTTACACGCC-TTATTCAAAAA
1 TGTTACACACCATGTTTAAAAA-TGTTATAAGCCATTATTCAAAAA
1155947 TGTTACA
1 TGTTACA
1155954 TGCAAGTTCA
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
44 34 0.42
45 22 0.27
46 25 0.31
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (45 bp):
TGTTACACACCATGTTTAAAAATGTTATAAGCCATTATTCAAAAA
Found at i:1155928 original size:22 final size:22
Alignment explanation
Indices: 1155894--1155999 Score: 139
Period size: 22 Copynumber: 4.9 Consensus size: 22
1155884 TATATGCCAT
*
1155894 GTTCAAAAA-TGTTACACACAA
1 GTTCAAAAATTGTTACACGCAA
*
1155915 GTTCAAAAATTGTTACACGCCTTA
1 GTTCAAAAATTGTTACACG-C-AA
*
1155939 -TTCAAAAA-TGTTACATGCAA
1 GTTCAAAAATTGTTACACGCAA
1155959 GTTC-AAAATTGTTACACGCAA
1 GTTCAAAAATTGTTACACGCAA
1155980 GTTCAAAAATTGTTACACGC
1 GTTCAAAAATTGTTACACGC
1156000 CATCTTCACA
Statistics
Matches: 74, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.07
21 28 0.38
22 31 0.42
23 9 0.12
24 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (22 bp):
GTTCAAAAATTGTTACACGCAA
Found at i:1155945 original size:44 final size:44
Alignment explanation
Indices: 1155850--1155997 Score: 158
Period size: 44 Copynumber: 3.4 Consensus size: 44
1155840 TAAGCCATTT
* * * * * * *
1155850 TTCAAAAATGTTACACACCATGTTTAAAAAGTGATATATGCCATG
1 TTCAAAAATGTTACACA-CAAGTTCAAAAATTGTTACACGCCATA
*
1155895 TTCAAAAATGTTACACACAAGTTCAAAAATTGTTACACGCCTTA
1 TTCAAAAATGTTACACACAAGTTCAAAAATTGTTACACGCCATA
**
1155939 TTCAAAAATGTTACATGCAAGTTC-AAAATTGTTACACG-CA-A
1 TTCAAAAATGTTACACACAAGTTCAAAAATTGTTACACGCCATA
1155980 GTTCAAAAATTGTTACAC
1 -TTCAAAAA-TGTTACAC
1155998 GCCATCTTCA
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
41 1 0.01
42 9 0.10
43 21 0.24
44 41 0.46
45 17 0.19
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (44 bp):
TTCAAAAATGTTACACACAAGTTCAAAAATTGTTACACGCCATA
Found at i:1155972 original size:65 final size:67
Alignment explanation
Indices: 1155850--1156007 Score: 205
Period size: 65 Copynumber: 2.4 Consensus size: 67
1155840 TAAGCCATTT
* * * * *
1155850 TTCAAAAA-TGTTACACACCATGTTTAAAAAGTGATATATGCCATGTTCAAAAATGTTACACACA
1 TTCAAAAATTGTTACACGCCATATTCAAAAAGTGATACATGCCAAGTTCAAAAATGTTACACACA
1155914 AG
66 AG
* * * *
1155916 TTCAAAAATTGTTACACGCCTTATTCAAAAA-TGTTACATG-CAAGTTCAAAATTGTTACACGCA
1 TTCAAAAATTGTTACACGCCATATTCAAAAAGTGATACATGCCAAGTTCAAAAATGTTACACACA
1155979 AG
66 AG
*
1155981 TTCAAAAATTGTTACACGCCATCTTCA
1 TTCAAAAATTGTTACACGCCATATTCA
1156008 CAACATTTTA
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
65 47 0.59
66 15 0.19
67 18 0.22
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.30
Consensus pattern (67 bp):
TTCAAAAATTGTTACACGCCATATTCAAAAAGTGATACATGCCAAGTTCAAAAATGTTACACACA
AG
Found at i:1156380 original size:63 final size:63
Alignment explanation
Indices: 1156259--1156381 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 63
1156249 CCACAGCACA
* * **
1156259 ATGATGATGGTGCTCAATAGAGAGTTGACAAAGCTTATACAGTTCAAAGAGTTAAGAGAGCTG
1 ATGATGATGGTGCTCAACAGAGAGTTGACAAAGCTTATACAATTCAAAGAACTAAGAGAGCTG
* * * * *
1156322 ATGATGATGGTGCTTAACAGAGAGTTGACAGAG-TTGATACAATTCACATAACTGAGAGAG
1 ATGATGATGGTGCTCAACAGAGAGTTGACAAAGCTT-ATACAATTCAAAGAACTAAGAGAG
1156382 AAAGATGAGC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
62 2 0.04
63 48 0.96
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (63 bp):
ATGATGATGGTGCTCAACAGAGAGTTGACAAAGCTTATACAATTCAAAGAACTAAGAGAGCTG
Found at i:1158001 original size:15 final size:15
Alignment explanation
Indices: 1157971--1158034 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 15
1157961 ACTACCAAGA
*
1157971 AGAAAAGAGAAA-GG
1 AGAAAAAAGAAAGGG
1157985 AGAAAAAAGAAAGGG
1 AGAAAAAAGAAAGGG
*
1158000 AGAAAGGAGGAAGAAAGAG
1 AGAAA--A--AAGAAAGGG
*
1158019 AAAAAAAAGAAAGGG
1 AGAAAAAAGAAAGGG
1158034 A
1 A
1158035 AGGCTTAGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
14 11 0.27
15 16 0.39
17 2 0.05
19 12 0.29
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
AGAAAAAAGAAAGGG
Found at i:1159629 original size:27 final size:25
Alignment explanation
Indices: 1159573--1159632 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
1159563 GAATATCACT
*
1159573 TATGGCCTAGCCACATATAACAACC
1 TATGGCCTAGCCACATATAACAAAC
* * *
1159598 CATGGCCTTGCCACATATATCATAAAC
1 TATGGCCTAGCCACATATA--ACAAAC
1159625 TATGGCCT
1 TATGGCCT
1159633 CAACCAAGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 17 0.61
27 11 0.39
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.25
Consensus pattern (25 bp):
TATGGCCTAGCCACATATAACAAAC
Found at i:1165603 original size:68 final size:68
Alignment explanation
Indices: 1165366--1165606 Score: 250
Period size: 68 Copynumber: 3.5 Consensus size: 68
1165356 TATATGCAAA
* * * * * * * * *
1165366 ATACATCATATACAAAATCTCATGGCATTCATCATACTTTCTCAATAATCC-CATGTAGTATATG
1 ATACATCATATACATAATCTTATGGCATTCATTATACATACTTAATCA-CCTCATATAGTATATA
1165430 GAAT
65 GAAT
* * * * *
1165434 ATACATCATATACATAATCTTATGGCATTTATCACATATACTTAATCACCTCATATGGTATATAG
1 ATACATCATATACATAATCTTATGGCATTCATTATACATACTTAATCACCTCATATAGTATATAG
1165499 AAT
66 AAT
* * * * * *
1165502 TTACATCATATACACAATCTTATAGTATACATTATGCATACTTAATCACCTCATATAGTATATAG
1 ATACATCATATACATAATCTTATGGCATTCATTATACATACTTAATCACCTCATATAGTATATAG
1165567 AAT
66 AAT
* * * *
1165570 ATGCATCATATATATTATCTCATGGCATTCATTATAC
1 ATACATCATATACATAATCTTATGGCATTCATTATAC
1165607 CAAACATGCA
Statistics
Matches: 139, Mismatches: 33, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
67 2 0.01
68 137 0.99
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (68 bp):
ATACATCATATACATAATCTTATGGCATTCATTATACATACTTAATCACCTCATATAGTATATAG
AAT
Found at i:1176614 original size:43 final size:43
Alignment explanation
Indices: 1176548--1176633 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
1176538 AAGATGGTGC
* * *
1176548 CAAAATCATGTGAAGATTGAGATCAACATTTTGTTGATTAAAA
1 CAAAATCATGTGAAGAATAAGATCAACATTTTGTTGATCAAAA
1176591 CAAAATCATGTGAAGAATAAGATCAACATTTTGTTGATCAAAA
1 CAAAATCATGTGAAGAATAAGATCAACATTTTGTTGATCAAAA
1176634 GCTTCCCAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.30
Consensus pattern (43 bp):
CAAAATCATGTGAAGAATAAGATCAACATTTTGTTGATCAAAA
Found at i:1179273 original size:171 final size:167
Alignment explanation
Indices: 1178986--1179437 Score: 590
Period size: 169 Copynumber: 2.7 Consensus size: 167
1178976 CTAAGTCACA
* *
1178986 GTTTTTGAATTTTTTGAATAGTCTAATCACCGTT-TAAAATCTTG-AAAGTTAAATTTTGGAATT
1 GTTTTTGAATTTTTTGAATAGTCAAATCACC-TTCTAAAATCTTGAAAAATT--ATTTTGGAATT
* *
1179049 GTTT-CATGAGTTAGTTATCAGGATAAATTTTATTGGAATTTAATTCCTAATTTTAGGCCACCAA
63 -TTTCCATGAGTTAGCTATCA-G-TAAATTTTATTGGAATTTAATTCTTAATTTTAGGCCACCAA
1179113 AGAATTTAAAAAAATCGATTTTGCAACCTACAGATATAGG-TTATG
125 AGAATTT--AAAAATCGATTTTGCAACCTACAGATAT-GGTTTATG
* *
1179158 GTTTTTGAATTTTTTGAATAGCCAAATCACCTTCAAAAATCTTGAAAAATTATTTTGGAATTTTT
1 GTTTTTGAATTTTTTGAATAGTCAAATCACCTTCTAAAATCTTGAAAAATTATTTTGGAATTTTT
1179223 CCATGAGTTAGCTATCAGTTTAAATTTTATTGGAATTTAATTCTTAATTTTAGGCCACCAAAGAA
66 CCATGAGTTAGCTATCAG--TAAATTTTATTGGAATTTAATTCTTAATTTTAGGCCACCAAAGAA
** * * **
1179288 TTTAAAAATTTATTTTTCCACCTATTGATATGGTTTATG
129 TTTAAAAATCGATTTTGCAACCTACAGATATGGTTTATG
* * * **
1179327 GTTTTTGAATTTTTTGAATAGTCAAATCACCTCCTAAAAT-TTCAAAAAAGTATTTTGGAATTGC
1 GTTTTTGAATTTTTTGAATAGTCAAATCACCTTCTAAAATCTT-GAAAAATTATTTTGGAATTTT
*
1179391 TCCATGAGTTAGCTATCAAGTAAATTTTATTGGAATTAAATTCTTAA
65 TCCATGAGTTAGCTATC-AGTAAATTTTATTGGAATTTAATTCTTAA
1179438 AAATAGGCCA
Statistics
Matches: 252, Mismatches: 21, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
168 30 0.12
169 98 0.39
170 6 0.02
171 75 0.30
172 38 0.15
173 5 0.02
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (167 bp):
GTTTTTGAATTTTTTGAATAGTCAAATCACCTTCTAAAATCTTGAAAAATTATTTTGGAATTTTT
CCATGAGTTAGCTATCAGTAAATTTTATTGGAATTTAATTCTTAATTTTAGGCCACCAAAGAATT
TAAAAATCGATTTTGCAACCTACAGATATGGTTTATG
Found at i:1192447 original size:21 final size:22
Alignment explanation
Indices: 1192422--1192465 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1192412 AAGTGATTAA
1192422 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
1192443 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
1192465 T
1 T
1192466 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:1193016 original size:22 final size:22
Alignment explanation
Indices: 1192991--1193037 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1192981 GAGAGCTCCC
*
1192991 CGCTGCAGCGCTGGAGAAGTAG
1 CGCTACAGCGCTGGAGAAGTAG
1193013 CGCTACAGCGCTGGAGAAGTAG
1 CGCTACAGCGCTGGAGAAGTAG
1193035 CGC
1 CGC
1193038 CGTAGCTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.26, G:0.38, T:0.13
Consensus pattern (22 bp):
CGCTACAGCGCTGGAGAAGTAG
Done.