Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 148 of 163
Found at i:40339843 original size:32 final size:32
Alignment explanation
Indices: 40339802--40339870 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
40339792 TTGCAGGATA
** *
40339802 TTGTCTATTTTGAATTATCATGTC-TAATGATG
1 TTGTCTATTTCAAATTATCAAG-CGTAATGATG
*
40339834 TTGTCTATTTCAAATTATCAAGCGTAGTGATG
1 TTGTCTATTTCAAATTATCAAGCGTAATGATG
40339866 TTGTC
1 TTGTC
40339871 CACAAATGGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 1 0.03
32 31 0.97
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (32 bp):
TTGTCTATTTCAAATTATCAAGCGTAATGATG
Found at i:40349354 original size:7 final size:7
Alignment explanation
Indices: 40349342--40349366 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40349332 ATTCGAAAAA
40349342 AATTTCG
1 AATTTCG
40349349 AATTTCG
1 AATTTCG
40349356 AATTTCG
1 AATTTCG
40349363 AATT
1 AATT
40349367 ATTCGAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (7 bp):
AATTTCG
Found at i:40360145 original size:27 final size:29
Alignment explanation
Indices: 40360115--40360173 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 29
40360105 AATTTGATTA
* *
40360115 TTTTAATAGATTATAT-ATATTTATA-AT
1 TTTTAAAAGATTAAATCATATTTATATAT
*
40360142 TTTTAAAAGATTAAATCATATTTTTATAT
1 TTTTAAAAGATTAAATCATATTTATATAT
40360171 TTT
1 TTT
40360174 AGGGGTCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 14 0.52
28 8 0.30
29 5 0.19
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (29 bp):
TTTTAAAAGATTAAATCATATTTATATAT
Found at i:40370684 original size:9 final size:9
Alignment explanation
Indices: 40370670--40370694 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40370660 AACTCTGATC
40370670 CAAGAAAAT
1 CAAGAAAAT
40370679 CAAGAAAAT
1 CAAGAAAAT
40370688 CAAGAAA
1 CAAGAAA
40370695 TCTTACTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.12, G:0.12, T:0.08
Consensus pattern (9 bp):
CAAGAAAAT
Found at i:40377120 original size:2 final size:2
Alignment explanation
Indices: 40377115--40377166 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
40377105 CATTGTCATA
40377115 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
40377157 TC AC TC TC TC
1 TC TC TC TC TC
40377167 GGGAAAAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:40383772 original size:15 final size:15
Alignment explanation
Indices: 40383716--40383766 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
40383706 AACCTTTAAG
40383716 CCAAACC-AATTGAAAA
1 CCAAACCTAATTG--AA
* *
40383732 CCAAACCCAAAGTGAA
1 CCAAA-CCTAATTGAA
40383748 CCAAACCTAATTGAA
1 CCAAACCTAATTGAA
40383763 CCAA
1 CCAA
40383767 GTCTAAACCC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 12 0.40
16 12 0.40
17 2 0.07
18 4 0.13
ACGTcount: A:0.51, C:0.29, G:0.08, T:0.12
Consensus pattern (15 bp):
CCAAACCTAATTGAA
Found at i:40393069 original size:14 final size:14
Alignment explanation
Indices: 40393050--40393080 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
40393040 GTTTTGAGCT
40393050 AATGAACTAAACTG
1 AATGAACTAAACTG
40393064 AATGAACTAAACTG
1 AATGAACTAAACTG
40393078 AAT
1 AAT
40393081 AAAATTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.23
Consensus pattern (14 bp):
AATGAACTAAACTG
Found at i:40394020 original size:52 final size:52
Alignment explanation
Indices: 40393942--40394128 Score: 277
Period size: 52 Copynumber: 3.6 Consensus size: 52
40393932 TAATGGAAAA
*
40393942 AGGTCCGGTGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
40393994 AGGTCCGATGACTATGTGTCATCGTGAGTGTATGAATCCTCTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
40394046 AGGTCCGATGACTATGTGTCATCGTGAGTATATGGATCCTTTTACGGATT-TA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTTACGGATTATG
* * *
40394098 AGGTCTGATGACTTTGTGTTATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
40394129 TAAATGGGAA
Statistics
Matches: 122, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
52 114 0.93
53 8 0.07
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:40394021 original size:26 final size:26
Alignment explanation
Indices: 40393992--40394073 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
40393982 TTACGGATTA
40393992 TGAGGTCCGATGACTATGTGTCATCG
1 TGAGGTCCGATGACTATGTGTCATCG
** ** **
40394018 TGAGTGTATGAATCCTCTATG-G--ATTA
1 TGAG-GTCCG-AT-GACTATGTGTCATCG
40394044 TGAGGTCCGATGACTATGTGTCATCG
1 TGAGGTCCGATGACTATGTGTCATCG
40394070 TGAG
1 TGAG
40394074 TATATGGATC
Statistics
Matches: 38, Mismatches: 12, Indels: 12
0.61 0.19 0.19
Matches are distributed among these distances:
23 5 0.13
24 3 0.08
25 3 0.08
26 16 0.42
27 3 0.08
28 3 0.08
29 5 0.13
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (26 bp):
TGAGGTCCGATGACTATGTGTCATCG
Found at i:40398643 original size:24 final size:23
Alignment explanation
Indices: 40398585--40398653 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
40398575 CTAGTAAATG
**
40398585 AAATATTTAAATAATTTTTTAAT
1 AAATATTTAAATAATTTAATAAT
40398608 AAATTATTTAAATAATTTAATATAT
1 AAA-TATTTAAATAATTTAATA-AT
* *
40398633 AAATATATAAATTAATCTAAT
1 AAATATTTAAA-TAATTTAAT
40398654 TTTTATATAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.08
24 23 0.59
25 13 0.33
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATATTTAAATAATTTAATAAT
Found at i:40400898 original size:82 final size:82
Alignment explanation
Indices: 40400761--40400927 Score: 300
Period size: 82 Copynumber: 2.0 Consensus size: 82
40400751 CTTGCTACTC
* *
40400761 CTTTGGAATTTTTTGTTGTTTATGTGTTAAGAGTGCTTGGATCCCAATGATGAGAGAACTTTTTC
1 CTTTGGAATTTTTCGTTGTTTATGTGTTAAGAGTGATTGGATCCCAATGATGAGAGAACTTTTTC
40400826 AAGGATGAGTAGTGAAT
66 AAGGATGAGTAGTGAAT
40400843 CTTTGGAATTTTTCGTTGTTTATGTGTTAAGAGTGATTGGATCCCACA-GATGAGAGAACTTTTT
1 CTTTGGAATTTTTCGTTGTTTATGTGTTAAGAGTGATTGGATCCCA-ATGATGAGAGAACTTTTT
40400907 CAAGGATGAGTAGTGAAT
65 CAAGGATGAGTAGTGAAT
40400925 CTT
1 CTT
40400928 AGAGTAGGTT
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
82 81 0.99
83 1 0.01
ACGTcount: A:0.26, C:0.10, G:0.25, T:0.40
Consensus pattern (82 bp):
CTTTGGAATTTTTCGTTGTTTATGTGTTAAGAGTGATTGGATCCCAATGATGAGAGAACTTTTTC
AAGGATGAGTAGTGAAT
Found at i:40403954 original size:23 final size:26
Alignment explanation
Indices: 40403910--40403959 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
40403900 GGTTTATGGA
* *
40403910 AAAAATAATATTATTATTATTTTAAT
1 AAAAATAATATTATTATCATTTAAAT
40403936 AAAAATAATA-T-TT-TCATTTAAAT
1 AAAAATAATATTATTATCATTTAAAT
40403959 A
1 A
40403960 TAATAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 9 0.41
24 2 0.09
25 1 0.05
26 10 0.45
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
AAAAATAATATTATTATCATTTAAAT
Found at i:40428795 original size:22 final size:22
Alignment explanation
Indices: 40428769--40428817 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
40428759 TCCGGATAAC
* *
40428769 ATTAAATTAAAATAATAAATTT
1 ATTAAAATAAAAAAATAAATTT
*
40428791 ATTAAAAATAAAAAAATAATTTT
1 ATT-AAAATAAAAAAATAAATTT
40428814 ATTA
1 ATTA
40428818 TATAAATGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTAAAATAAAAAAATAAATTT
Found at i:40434420 original size:21 final size:21
Alignment explanation
Indices: 40434396--40434435 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40434386 TGGGGTTATG
40434396 GGGTATGA-GTTTAAGGTTTAA
1 GGGT-TGAGGTTTAAGGTTTAA
*
40434417 GGGTTGAGGTTTAGGGTTT
1 GGGTTGAGGTTTAAGGTTT
40434436 TATATTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (21 bp):
GGGTTGAGGTTTAAGGTTTAA
Found at i:40450437 original size:50 final size:50
Alignment explanation
Indices: 40450379--40450480 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
40450369 GCATAAATTT
40450379 TTCGAGTTTGAGCTAGTAGATTGGCTCTTATTAAATTTAGAGGGTCAAGA
1 TTCGAGTTTGAGCTAGTAGATTGGCTCTTATTAAATTTAGAGGGTCAAGA
*
40450429 TTCGAGTTTGAGCTAGTGGATTGGCTCTTATTAAATTTAGAGGGTCAAGA
1 TTCGAGTTTGAGCTAGTAGATTGGCTCTTATTAAATTTAGAGGGTCAAGA
40450479 TT
1 TT
40450481 GGATGGGAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.37
Consensus pattern (50 bp):
TTCGAGTTTGAGCTAGTAGATTGGCTCTTATTAAATTTAGAGGGTCAAGA
Found at i:40457297 original size:13 final size:13
Alignment explanation
Indices: 40457271--40457334 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
40457261 TCGACTAGAC
40457271 CCGTTGACTGTTGA
1 CCGTTGACT-TTGA
*
40457285 TCGTTGACTTTGA
1 CCGTTGACTTTGA
** *
40457298 TTGTTGACTTTTA
1 CCGTTGACTTTGA
*
40457311 CCATTGACTTTGA
1 CCGTTGACTTTGA
*
40457324 CCGTTAACTTT
1 CCGTTGACTTT
40457335 TTTCGAGAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
13 33 0.80
14 8 0.20
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (13 bp):
CCGTTGACTTTGA
Found at i:40459757 original size:2 final size:2
Alignment explanation
Indices: 40459752--40459819 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
40459742 AAAGAAAGTA
40459752 AT AT AT AT 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 AT AT AT AT
*
40459794 AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
40459820 CAAACTTCAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40464575 original size:22 final size:22
Alignment explanation
Indices: 40464550--40464648 Score: 79
Period size: 19 Copynumber: 4.8 Consensus size: 22
40464540 ATTATATTAT
40464550 TGTTTTGG-TGCTATTTTTTTAC
1 TGTTTTGGTTGCTA-TTTTTTAC
*
40464572 TGTTTTGGTTGCTATTTTTTGC
1 TGTTTTGGTTGCTATTTTTTAC
* *
40464594 TG-TTT--TTG-TGTTTTTTAT
1 TGTTTTGGTTGCTATTTTTTAC
* *
40464612 TGCTTTGG-TGC--TTTTTTAT
1 TGTTTTGGTTGCTATTTTTTAC
*
40464631 TGTTTTGGTTGTTATTTT
1 TGTTTTGGTTGCTATTTT
40464649 CGTGTTGTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
18 9 0.14
19 21 0.33
20 4 0.06
21 3 0.05
22 21 0.33
23 5 0.08
ACGTcount: A:0.06, C:0.06, G:0.20, T:0.68
Consensus pattern (22 bp):
TGTTTTGGTTGCTATTTTTTAC
Found at i:40464588 original size:23 final size:21
Alignment explanation
Indices: 40464550--40464648 Score: 82
Period size: 22 Copynumber: 4.8 Consensus size: 21
40464540 ATTATATTAT
40464550 TGTTTTGGTGCTATTTTTTTAC
1 TGTTTTGGTGCTA-TTTTTTAC
*
40464572 TGTTTTGGTTGCTATTTTTTGC
1 TGTTTTGG-TGCTATTTTTTAC
* *
40464594 TGTTTT--TG-TGTTTTTTAT
1 TGTTTTGGTGCTATTTTTTAC
* *
40464612 TGCTTTGGTGC--TTTTTTAT
1 TGTTTTGGTGCTATTTTTTAC
*
40464631 TGTTTTGGTTGTTATTTT
1 TGTTTTGG-TGCTATTTT
40464649 CGTGTTGTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
18 12 0.19
19 17 0.27
20 4 0.06
22 25 0.40
23 5 0.08
ACGTcount: A:0.06, C:0.06, G:0.20, T:0.68
Consensus pattern (21 bp):
TGTTTTGGTGCTATTTTTTAC
Found at i:40464647 original size:59 final size:63
Alignment explanation
Indices: 40464541--40464671 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 63
40464531 AATAAAAAAA
* * *
40464541 TTATATTATTGTTTTGGTGCTATTTTTTTACTGTTTTGGTTGCTATTTT-TTGCTGTTTTTG-TG
1 TTATTTTATTGCTTTGGTGC--TTTTTTTACTGTTTTGGTTGCTATTTTCGTGCTGTTTTTGCTG
* * *
40464604 TT-TTTTATTGCTTTGGTGC-TTTTTTATTGTTTTGGTTGTTATTTTCGTGTTGTTTTTGCTG
1 TTATTTTATTGCTTTGGTGCTTTTTTTACTGTTTTGGTTGCTATTTTCGTGCTGTTTTTGCTG
40464665 TTATTTT
1 TTATTTT
40464672 TGTTATTGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
59 24 0.41
60 10 0.17
61 4 0.07
62 19 0.32
63 2 0.03
ACGTcount: A:0.08, C:0.06, G:0.19, T:0.67
Consensus pattern (63 bp):
TTATTTTATTGCTTTGGTGCTTTTTTTACTGTTTTGGTTGCTATTTTCGTGCTGTTTTTGCTG
Found at i:40464683 original size:23 final size:23
Alignment explanation
Indices: 40464623--40464698 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
40464613 GCTTTGGTGC
40464623 TTTT-TTATTGTTTTGGTTGTTAT
1 TTTTGTTATTGTTTT-GTTGTTAT
* * *
40464646 TTTCG-TGTTGTTTTTGCTGTTAT
1 TTTTGTTATTG-TTTTGTTGTTAT
*
40464669 TTTTGTTATTGTTTTGTTGCTAT
1 TTTTGTTATTGTTTTGTTGTTAT
40464692 TTTTGTT
1 TTTTGTT
40464699 GTTTTAATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
23 35 0.81
24 8 0.19
ACGTcount: A:0.07, C:0.04, G:0.18, T:0.71
Consensus pattern (23 bp):
TTTTGTTATTGTTTTGTTGTTAT
Found at i:40466612 original size:28 final size:28
Alignment explanation
Indices: 40466558--40466617 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
40466548 ACAAATACAT
40466558 ATTTTGTAATTAATCTATATTTCATATA
1 ATTTTGTAATTAATCTATATTTCATATA
* * *
40466586 ATTTTCGTAATTAAT-TATTTTTTATATT
1 ATTTT-GTAATTAATCTATATTTCATATA
40466614 ATTT
1 ATTT
40466618 GAATAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (28 bp):
ATTTTGTAATTAATCTATATTTCATATA
Found at i:40482331 original size:17 final size:18
Alignment explanation
Indices: 40482311--40482360 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
40482301 TTTTAAAAAA
40482311 TATAAAA-TTTGAAAATT
1 TATAAAATTTTGAAAATT
40482328 TATAAATATTTTG--AATT
1 TATAAA-ATTTTGAAAATT
40482345 T-TAAAATTTTGAAAAT
1 TATAAAATTTTGAAAAT
40482361 ATTTAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 6 0.21
16 4 0.14
17 14 0.48
18 1 0.03
19 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
TATAAAATTTTGAAAATT
Found at i:40482352 original size:8 final size:8
Alignment explanation
Indices: 40482313--40482371 Score: 50
Period size: 8 Copynumber: 7.1 Consensus size: 8
40482303 TTAAAAAATA
40482313 TAAAATTT
1 TAAAATTT
*
40482321 GAAAATTT
1 TAAAATTT
40482329 ATAAATATTT
1 -TAAA-ATTT
*
40482339 T-GAATTT
1 TAAAATTT
40482346 TAAAATTT
1 TAAAATTT
40482354 TGAAAATATT
1 T-AAAAT-TT
40482364 T-AAATTT
1 TAAAATTT
40482371 T
1 T
40482372 CTTTTGTAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
7 8 0.19
8 18 0.43
9 9 0.21
10 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (8 bp):
TAAAATTT
Found at i:40482355 original size:15 final size:17
Alignment explanation
Indices: 40482324--40482357 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
40482314 AAAATTTGAA
40482324 AATTTATAAATATTTTG
1 AATTTATAAATATTTTG
40482341 AATTT-TAAA-ATTTTG
1 AATTTATAAATATTTTG
40482356 AA
1 AA
40482358 AATATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
AATTTATAAATATTTTG
Found at i:40504515 original size:60 final size:59
Alignment explanation
Indices: 40504414--40504569 Score: 136
Period size: 60 Copynumber: 2.6 Consensus size: 59
40504404 TTTGATCATA
* * * * * ** **
40504414 CAATATTTACACATTTTATCAATTTGATTTTAAATTTAAAAATTCAAC-AAATTTAGTCCT
1 CAATATTTACAAAATTTATC-ATTTAATTCT-AATTTAAAAAATCAACTAAAGCTAACCCT
*
40504474 CAATATTTACAAAATTTATCATTTAATTCTAATTCTAAAAAAATCCACTAAAGCTAACCCT
1 CAATATTTACAAAATTTATCATTTAATTCTAATT-T-AAAAAATCAACTAAAGCTAACCCT
* * *
40504535 -AGTATTTACAAAATTTGTGGATTTAATTCTAATTT
1 CAATATTTACAAAATTTAT-CATTTAATTCTAATTT
40504570 GTTGGGCAAG
Statistics
Matches: 79, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
58 4 0.05
59 9 0.11
60 44 0.56
61 22 0.28
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.41
Consensus pattern (59 bp):
CAATATTTACAAAATTTATCATTTAATTCTAATTTAAAAAATCAACTAAAGCTAACCCT
Found at i:40511978 original size:2 final size:2
Alignment explanation
Indices: 40511971--40512004 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40511961 GCTTCTTTTA
40511971 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
40512005 CAGCGTGTGC
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:40521066 original size:3 final size:3
Alignment explanation
Indices: 40521058--40521085 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40521048 ATTAAAAATT
40521058 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
40521086 TAAAGACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:40524694 original size:23 final size:22
Alignment explanation
Indices: 40524618--40524744 Score: 123
Period size: 23 Copynumber: 5.5 Consensus size: 22
40524608 AAGTGATGGG
40524618 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAAGCACACA-AGTGC
* * **
40524641 -AATCCAGTAGGCACACATAGCAC
1 GAA-ACAGTAAGCACACA-AGTGC
*
40524664 -AAATCAGTAGGCACACAATGTGC
1 GAAA-CAGTAAGCACACAA-GTGC
40524687 GAAACAGTAAGCACACGAAGTGC
1 GAAACAGTAAGCACAC-AAGTGC
*
40524710 GAAATAGTAAGCACACAAAGTGC
1 GAAACAGTAAGCACAC-AAGTGC
40524733 GAAACAGTAAGC
1 GAAACAGTAAGC
40524745 GCGCTAGCGT
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
22 3 0.03
23 79 0.91
24 5 0.06
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (22 bp):
GAAACAGTAAGCACACAAGTGC
Found at i:40527216 original size:31 final size:31
Alignment explanation
Indices: 40527181--40527239 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
40527171 GGTCACTTAG
* *
40527181 TTATTTGAAAGTTTTCATTAAAATCACTAAA
1 TTATTCGAAAATTTTCATTAAAATCACTAAA
* *
40527212 TTATTCGAAAATTTTTATTTAAATCACT
1 TTATTCGAAAATTTTCATTAAAATCACT
40527240 GGACTATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (31 bp):
TTATTCGAAAATTTTCATTAAAATCACTAAA
Found at i:40549106 original size:52 final size:53
Alignment explanation
Indices: 40549026--40549131 Score: 135
Period size: 52 Copynumber: 2.0 Consensus size: 53
40549016 TACGAATAAA
** *
40549026 AAATTATTTTTTTTAGTATTTGCCAAGCCATGACCTACACCCCTTTATCAGAT
1 AAATTATTTTTTTTAGTATTTGCCAAGCCACAACCGACACCCCTTTATCAGAT
* * *
40549079 AAATTTTTTTTTTTA-TGA-TTGTCAAGCCACAACCGACACCCCTTTTTCAGAT
1 AAATTATTTTTTTTAGT-ATTTGCCAAGCCACAACCGACACCCCTTTATCAGAT
40549131 A
1 A
40549132 CAAAGTACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
52 31 0.67
53 15 0.33
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (53 bp):
AAATTATTTTTTTTAGTATTTGCCAAGCCACAACCGACACCCCTTTATCAGAT
Found at i:40549222 original size:18 final size:19
Alignment explanation
Indices: 40549170--40549223 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
40549160 ATTCAAAATA
*
40549170 AAATACTAATTTGAAATTT
1 AAATACTAGTTTGAAATTT
40549189 AAATACTAGTTTGAAATTT
1 AAATACTAGTTTGAAATTT
40549208 AAATTA-TAG-TTGAAAT
1 AAA-TACTAGTTTGAAAT
40549224 GAAAATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 7 0.21
19 24 0.73
20 2 0.06
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (19 bp):
AAATACTAGTTTGAAATTT
Found at i:40549498 original size:13 final size:13
Alignment explanation
Indices: 40549433--40549507 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
40549423 AATTTCAAAT
* *
40549433 TTAAAAAATAAAA
1 TTAAAAATTATAA
40549446 TTAAAACAATTATAA
1 TT-AAA-AATTATAA
* *
40549461 TTAAAATAATATTTA
1 TTAAAA-ATTA-TAA
**
40549476 TTTCAAATTATAA
1 TTAAAAATTATAA
40549489 TTAAAAATTATAA
1 TTAAAAATTATAA
*
40549502 CTAAAA
1 TTAAAA
40549508 TTAATATTAA
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
13 21 0.45
14 12 0.26
15 14 0.30
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAAATTATAA
Found at i:40549501 original size:41 final size:44
Alignment explanation
Indices: 40549444--40549528 Score: 131
Period size: 42 Copynumber: 2.0 Consensus size: 44
40549434 TAAAAAATAA
* *
40549444 AATTAAAACAATTATAATTAAAA-TAATATTTATTTCAAATTAT
1 AATTAAAACAATTATAACTAAAATTAATATTAATTTCAAATTAT
40549487 AATT-AAA-AATTATAACTAAAATTAATATTAATTTCAAATTAT
1 AATTAAAACAATTATAACTAAAATTAATATTAATTTCAAATTAT
40549529 TTTTGAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
41 13 0.33
42 22 0.56
43 4 0.10
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (44 bp):
AATTAAAACAATTATAACTAAAATTAATATTAATTTCAAATTAT
Found at i:40555419 original size:56 final size:59
Alignment explanation
Indices: 40555358--40555481 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 59
40555348 TTAAAGTTTC
* * *
40555358 AATGATCACTCAATTATTAGT-AAGTTTTTTAATCATT-T-AACGATCAAAAGTTATAA
1 AATGATCAATCAATTATTAGTAAAATTTTTTAATCATTATCAACGATAAAAAGTTATAA
* ** * *
40555414 AATGATCAATTAATTATTAGTAAAATTTTTTCTTCGTTATCCAACTATAAAAAGTTATAA
1 AATGATCAATCAATTATTAGTAAAATTTTTTAATCATTAT-CAACGATAAAAAGTTATAA
40555474 AATGATCA
1 AATGATCA
40555482 TTAAACTATT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
56 19 0.34
57 12 0.21
58 1 0.02
60 24 0.43
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (59 bp):
AATGATCAATCAATTATTAGTAAAATTTTTTAATCATTATCAACGATAAAAAGTTATAA
Found at i:40557045 original size:52 final size:52
Alignment explanation
Indices: 40556936--40557046 Score: 125
Period size: 52 Copynumber: 2.1 Consensus size: 52
40556926 TAAAAAAATA
* ** *
40556936 TAATTTTGTAAATATTGAAGGTTCAATTTTTTTAAATTTGAATAAAAATGAT
1 TAATTTTGTAAACATTGAAGACTCAATTTTTTTAAATTTGAATAAAAAGGAT
* * ** *
40556988 AAATTTTGTAAACATTGAAGACT-AATTTTTTTTGAATTTTTATAAATAGGAT
1 TAATTTTGTAAACATTGAAGACTCAA-TTTTTTTAAATTTGAATAAAAAGGAT
40557040 TAATTTT
1 TAATTTT
40557047 ATATAGTGTG
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
51 2 0.04
52 46 0.96
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.48
Consensus pattern (52 bp):
TAATTTTGTAAACATTGAAGACTCAATTTTTTTAAATTTGAATAAAAAGGAT
Found at i:40559005 original size:18 final size:19
Alignment explanation
Indices: 40558971--40559012 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
40558961 TTACAAAAAA
*
40558971 AAAAATCAAAATAATTTTT
1 AAAAATCAAAATAATTTAT
*
40558990 AAAATTCAAAAT-ATTTAT
1 AAAAATCAAAATAATTTAT
40559008 AAAAA
1 AAAAA
40559013 ATTTCAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATCAAAATAATTTAT
Found at i:40561304 original size:5 final size:6
Alignment explanation
Indices: 40561288--40561312 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40561278 ATTGATTCTT
40561288 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
40561313 CATTAAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:40564411 original size:12 final size:12
Alignment explanation
Indices: 40564394--40564419 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40564384 TTGAAAAAAG
40564394 AACTAAAATAAT
1 AACTAAAATAAT
40564406 AACTAAAATAAT
1 AACTAAAATAAT
40564418 AA
1 AA
40564420 TAATAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AACTAAAATAAT
Found at i:40568362 original size:16 final size:15
Alignment explanation
Indices: 40568342--40568370 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40568332 CATGCGTTTT
40568342 TTTTTTTAATATTTA
1 TTTTTTTAATATTTA
40568357 TTTTTTTAATATTT
1 TTTTTTTAATATTT
40568371 TACTAGACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTTAATATTTA
Found at i:40568372 original size:16 final size:16
Alignment explanation
Indices: 40568338--40568372 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
40568328 TTATCATGCG
40568338 TTTT-TTTTTTTAATA
1 TTTTATTTTTTTAATA
40568353 -TTTATTTTTTTAATA
1 TTTTATTTTTTTAATA
40568368 TTTTA
1 TTTTA
40568373 CTAGACAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.17
15 11 0.61
16 4 0.22
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTTTTTTAATA
Found at i:40580285 original size:37 final size:38
Alignment explanation
Indices: 40580237--40580310 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
40580227 AATGGTAACT
* *
40580237 TTTGGTTAAATCGGGG-TTAAAATGAAATTTTGGAAAC
1 TTTGGTGAAATCGGGGCTAAAAATGAAATTTTGGAAAC
*
40580274 TTTGGTGAAATCGGGGCTAAAAATGGAATTTTGGAAA
1 TTTGGTGAAATCGGGGCTAAAAATGAAATTTTGGAAA
40580311 GTTCGGGGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.32
Consensus pattern (38 bp):
TTTGGTGAAATCGGGGCTAAAAATGAAATTTTGGAAAC
Found at i:40580400 original size:59 final size:58
Alignment explanation
Indices: 40580274--40580454 Score: 222
Period size: 59 Copynumber: 3.0 Consensus size: 58
40580264 TTTTGGAAAC
* * *
40580274 TTTGGTGAAATCGGGGCTAAAAATGGAATTTTGGAAAGTTCGGGGGGGTAAAATGGTGATT
1 TTTGGTGAAATC-GGGTTAAAAATGGAATTTTGGAAAGTTC--AGGGGTAAAATGGTAATT
* *
40580335 TTTGGTGAAACCAGGGTT-AAAATAGG-ATTTTGGAAAGTTTAGGGGTAAAAATGGTAATT
1 TTTGGTGAAATC-GGGTTAAAAAT-GGAATTTTGGAAAGTTCAGGGGT-AAAATGGTAATT
* *
40580394 TTTGGTGAGATCGAGGTTAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAATGGTAATT
1 TTTGGTGAAATCG-GGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATT
40580453 TT
1 TT
40580455 CGGATAGTCC
Statistics
Matches: 105, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
58 6 0.06
59 41 0.39
60 41 0.39
61 17 0.16
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (58 bp):
TTTGGTGAAATCGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATT
Found at i:40580443 original size:29 final size:30
Alignment explanation
Indices: 40580361--40580454 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 30
40580351 TTAAAATAGG
* *
40580361 ATTTTGGAAAGTTTAGGGGTAAAAATGGTA
1 ATTTTGGAAAGTTCAAGGGTAAAAATGGTA
** * * *
40580391 ATTTTTGGTGAGATCGAGGTTAAAAATGG-A
1 A-TTTTGGAAAGTTCAAGGGTAAAAATGGTA
40580421 ATTTTGGAAAGTTCAAGGGT-AAAATGGTA
1 ATTTTGGAAAGTTCAAGGGTAAAAATGGTA
40580450 ATTTT
1 ATTTT
40580455 CGGATAGTCC
Statistics
Matches: 50, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
28 7 0.14
29 20 0.40
30 3 0.06
31 20 0.40
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (30 bp):
ATTTTGGAAAGTTCAAGGGTAAAAATGGTA
Found at i:40582422 original size:6 final size:6
Alignment explanation
Indices: 40582411--40582447 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
40582401 TCATAATTTG
*
40582411 ATTTAA ATTTAA ATTTAA A-ATAA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
40582448 AAATCAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATTTAA
Found at i:40582434 original size:17 final size:16
Alignment explanation
Indices: 40582414--40582451 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
40582404 TAATTTGATT
40582414 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
40582431 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
40582447 TAAAT
1 TAAAT
40582452 CAAAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:40582450 original size:27 final size:28
Alignment explanation
Indices: 40582411--40582479 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 28
40582401 TCATAATTTG
**
40582411 ATTTAAATTTAAATTTAAAATAAATTTAA
1 ATTTAAA-TTAAATCAAAAATAAATTTAA
*
40582440 ATTTAAA-TAAATCAAAAATTAATTTAA
1 ATTTAAATTAAATCAAAAATAAATTTAA
*
40582467 ATTCAAAATTAAA
1 ATT-TAAATTAAA
40582480 ACATAAAGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 20 0.59
28 3 0.09
29 11 0.32
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (28 bp):
ATTTAAATTAAATCAAAAATAAATTTAA
Found at i:40586846 original size:23 final size:23
Alignment explanation
Indices: 40586819--40586872 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
40586809 TTATTAATGC
*
40586819 AATGTTTTATGACCATTAAACAA
1 AATGTTTCATGACCATTAAACAA
*
40586842 AATGTTTCATGCCCATTAAACAA
1 AATGTTTCATGACCATTAAACAA
40586865 AATGTTTC
1 AATGTTTC
40586873 TTTTTATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (23 bp):
AATGTTTCATGACCATTAAACAA
Found at i:40595070 original size:20 final size:20
Alignment explanation
Indices: 40595045--40595085 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40595035 TCTTAAATTG
*
40595045 TTTTATTCATAAGATTATTA
1 TTTTATTCATAAAATTATTA
*
40595065 TTTTATTTATAAAATTATTA
1 TTTTATTCATAAAATTATTA
40595085 T
1 T
40595086 GTTAATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTATTCATAAAATTATTA
Found at i:40595183 original size:19 final size:19
Alignment explanation
Indices: 40595142--40595184 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
40595132 ATATATTTTC
40595142 TTAT-ATTATTTATTTTAA
1 TTATAATTATTTATTTTAA
*
40595160 ATATAATTATTT-TTTTAA
1 TTATAATTATTTATTTTAA
40595178 TTTATAA
1 -TTATAA
40595185 AATTCCAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATAATTATTTATTTTAA
Found at i:40597574 original size:46 final size:47
Alignment explanation
Indices: 40597491--40597584 Score: 172
Period size: 46 Copynumber: 2.0 Consensus size: 47
40597481 AGTTGAATTT
40597491 GCTTAATTGAGAGCATATATATATATAATGCGCTTCAACGCACTCGAA
1 GCTTAATTGAGAGCA-ATATATATATAATGCGCTTCAACGCACTCGAA
40597539 GCTTAATTGAGAGC-ATATATATATAATGCGCTTCAACGCACTCGAA
1 GCTTAATTGAGAGCAATATATATATAATGCGCTTCAACGCACTCGAA
40597585 CCCATGTCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 32 0.70
48 14 0.30
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (47 bp):
GCTTAATTGAGAGCAATATATATATAATGCGCTTCAACGCACTCGAA
Found at i:40600717 original size:41 final size:40
Alignment explanation
Indices: 40600669--40600769 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
40600659 TCGACCTCGA
** *
40600669 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
40600709 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
40600747 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
40600770 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:40602507 original size:21 final size:22
Alignment explanation
Indices: 40602482--40602528 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
40602472 AAGCCTTCAG
40602482 CTTTTAAC-GAATTTGATCCTT
1 CTTTTAACTGAATTTGATCCTT
**
40602503 CTTTTGGCTGAATTTGATCCTT
1 CTTTTAACTGAATTTGATCCTT
40602525 CTTT
1 CTTT
40602529 GGCTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.17, C:0.19, G:0.13, T:0.51
Consensus pattern (22 bp):
CTTTTAACTGAATTTGATCCTT
Found at i:40602531 original size:21 final size:22
Alignment explanation
Indices: 40602490--40602541 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
40602480 AGCTTTTAAC
40602490 GAATTTGATCCTTCTTTTGGCT
1 GAATTTGATCCTTCTTTTGGCT
40602512 GAATTTGATCCTTC-TTTGGCT
1 GAATTTGATCCTTCTTTTGGCT
*
40602533 AAATTTGAT
1 GAATTTGAT
40602542 TAAAATCGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.48
Consensus pattern (22 bp):
GAATTTGATCCTTCTTTTGGCT
Found at i:40602801 original size:45 final size:45
Alignment explanation
Indices: 40602746--40602841 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 45
40602736 TTGATTTAAC
* * *
40602746 TTAAAAGTATTGAAGAAGCT-TATTTCTTAGCGTTAAATTATGTAA
1 TTAAATGTATTGAAGAAGCTCTAGTT-TTAGCGTTAAATTAAGTAA
* **
40602791 TTAAATGTATTGAGGAAGCTCTAGTTTTATTGTTAAATTAAGTAA
1 TTAAATGTATTGAAGAAGCTCTAGTTTTAGCGTTAAATTAAGTAA
40602836 TTAAAT
1 TTAAAT
40602842 TGAATCTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
45 40 0.91
46 4 0.09
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.42
Consensus pattern (45 bp):
TTAAATGTATTGAAGAAGCTCTAGTTTTAGCGTTAAATTAAGTAA
Found at i:40611304 original size:21 final size:22
Alignment explanation
Indices: 40611278--40611328 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
40611268 AAATGTTTTT
*
40611278 TTAAAAATATATAA-AATAAA-A
1 TTAAAAA-ATATAATAACAAATA
40611299 TTAAAAAATATAATAACAAATA
1 TTAAAAAATATAATAACAAATA
40611321 TTAAAAAA
1 TTAAAAAA
40611329 AAAAGTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 6 0.22
21 12 0.44
22 9 0.33
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
TTAAAAAATATAATAACAAATA
Found at i:40611305 original size:22 final size:22
Alignment explanation
Indices: 40611280--40611328 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
40611270 ATGTTTTTTT
40611280 AAAAATAT-ATAAAATAAAATTA
1 AAAAATATAATAAAA-AAAATTA
* *
40611302 AAAAATATAATAACAAATATTA
1 AAAAATATAATAAAAAAAATTA
40611324 AAAAA
1 AAAAA
40611329 AAAAGTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAAATATAATAAAAAAAATTA
Found at i:40621678 original size:3 final size:3
Alignment explanation
Indices: 40621670--40621730 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
40621660 TTAGCCCCTC
*
40621670 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
40621718 TGT TAT TAT TAT T
1 TAT TAT TAT TAT T
40621731 TTCTCAGATT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40632091 original size:2 final size:2
Alignment explanation
Indices: 40632084--40632114 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40632074 GAGTAAGGCA
40632084 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
40632115 TATTACATTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:40641606 original size:14 final size:14
Alignment explanation
Indices: 40641587--40641618 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
40641577 TTCAGGATGC
40641587 ATATATATATACAT
1 ATATATATATACAT
40641601 ATATATATATACAT
1 ATATATATATACAT
40641615 ATAT
1 ATAT
40641619 CAATCTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATATATACAT
Found at i:40654506 original size:3 final size:3
Alignment explanation
Indices: 40654498--40654544 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
40654488 TGATTTACAA
40654498 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40654545 AGATTCATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40656351 original size:10 final size:10
Alignment explanation
Indices: 40656294--40656356 Score: 58
Period size: 10 Copynumber: 6.5 Consensus size: 10
40656284 GATATAAACT
*
40656294 TAAAAAAGTA
1 TAAAAAATTA
*
40656304 TAAAATATTA
1 TAAAAAATTA
* *
40656314 T-GAATATTA
1 TAAAAAATTA
*
40656323 TAAAAAA-TC
1 TAAAAAATTA
*
40656332 TAATAAATTA
1 TAAAAAATTA
40656342 TAAAAAATTA
1 TAAAAAATTA
40656352 TAAAA
1 TAAAA
40656357 GTAATAAAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
9 15 0.36
10 27 0.64
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:40656356 original size:9 final size:9
Alignment explanation
Indices: 40656202--40656396 Score: 82
Period size: 9 Copynumber: 21.1 Consensus size: 9
40656192 TTTAATATTT
40656202 TTATAAAAA
1 TTATAAAAA
*
40656211 ATATTAAAAA
1 TTA-TAAAAA
*
40656221 TTATATAAA
1 TTATAAAAA
40656230 -TA-AAAGAA
1 TTATAAA-AA
*
40656238 CTATCAAAACA
1 TTAT-AAAA-A
40656249 -TATAAAAA
1 TTATAAAAA
*
40656257 TTAT-TAAA
1 TTATAAAAA
40656265 -TATTAAAAA
1 TTA-TAAAAA
40656274 -TATAAAAA
1 TTATAAAAA
*
40656282 TTGATATAAAC
1 TT-ATA-AAAA
40656293 TTA-AAAAA
1 TTATAAAAA
*
40656301 GTATAAAATA
1 TTATAAAA-A
* *
40656311 TTATGAATA
1 TTATAAAAA
40656320 TTATAAAAA
1 TTATAAAAA
* *
40656329 ATCTAATAAA
1 TTATAA-AAA
40656339 TTATAAAAAA
1 TTAT-AAAAA
*
40656349 TTATAAAAG
1 TTATAAAAA
*
40656358 TAATAAAACA
1 TTATAAAA-A
* *
40656368 -TATTAAGAT
1 TTA-TAAAAA
*
40656377 TCTATAGAAA
1 T-TATAAAAA
40656387 TTATAAAAA
1 TTATAAAAA
40656396 T
1 T
40656397 ATTTTTAAAA
Statistics
Matches: 138, Mismatches: 28, Indels: 40
0.67 0.14 0.19
Matches are distributed among these distances:
7 4 0.03
8 20 0.14
9 59 0.43
10 42 0.30
11 13 0.09
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:40656413 original size:41 final size:41
Alignment explanation
Indices: 40656361--40656450 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
40656351 ATAAAAGTAA
* * *
40656361 TAAAACATATTAAGATTCTATAGAAA-TTATAAAAA-TATTTT
1 TAAAAAATATTAAAATT-TATAGAAATTTATAAAAATTA-TGT
**
40656402 TAAAAAATATTAAAATTTATTTAAATTTATAAAAATTATGT
1 TAAAAAATATTAAAATTTATAGAAATTTATAAAAATTATGT
40656443 TAAAAAAT
1 TAAAAAAT
40656451 CATAAAAACT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 6 0.14
41 34 0.81
42 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.40
Consensus pattern (41 bp):
TAAAAAATATTAAAATTTATAGAAATTTATAAAAATTATGT
Found at i:40657476 original size:12 final size:10
Alignment explanation
Indices: 40657450--40657499 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
40657440 TATATATTTG
40657450 AATTATAAAA
1 AATTATAAAA
40657460 AATTATAAAA
1 AATTATAAAA
* *
40657470 AA-TATTAAT
1 AATTATAAAA
*
40657479 AATTATAAGA
1 AATTATAAAA
40657489 AATTAATAAAA
1 AATT-ATAAAA
40657500 TATGACTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
9 7 0.22
10 20 0.62
11 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (10 bp):
AATTATAAAA
Found at i:40666137 original size:4 final size:4
Alignment explanation
Indices: 40666128--40666155 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
40666118 CGCTGACTGG
40666128 CAGA CAGA CAGA CAGA CAGA CAGA CAGA
1 CAGA CAGA CAGA CAGA CAGA CAGA CAGA
40666156 GAGGCTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.25, T:0.00
Consensus pattern (4 bp):
CAGA
Found at i:40668718 original size:16 final size:17
Alignment explanation
Indices: 40668686--40668718 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40668676 TTTAGATCAT
*
40668686 AATTTTATAATTTATAA
1 AATTTTATAATTAATAA
40668703 AATTTTA-AATTAATAA
1 AATTTTATAATTAATAA
40668719 TGATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTTATAATTAATAA
Found at i:40668843 original size:30 final size:27
Alignment explanation
Indices: 40668793--40668847 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 27
40668783 AAAAATATAA
*
40668793 ACTATTAAAATAATAAAATTACATTTTT
1 ACTATTAAAAAAATAAAATTA-ATTTTT
*
40668821 ACTATTATAAAAACATACAATTAATTT
1 ACTATTA-AAAAA-ATAAAATTAATTT
40668848 CGACCCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 7 0.30
29 8 0.35
30 8 0.35
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (27 bp):
ACTATTAAAAAAATAAAATTAATTTTT
Found at i:40669941 original size:29 final size:29
Alignment explanation
Indices: 40669898--40669978 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
40669888 GAATTGGATC
40669898 AAATCAAAATTTCATGTATAAAATTGCACA-
1 AAATC-AAA-TTCATGTATAAAATTGCACAT
* *
40669928 AAATCAAAGTTCATGCATACAATTGCACATT
1 AAATCAAA-TTCATGTATAAAATTGCACA-T
40669959 AAATCATAATTCATGTATAA
1 AAATCA-AATTCATGTATAA
40669979 TTTTGATATT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 21 0.49
30 5 0.12
31 15 0.35
32 2 0.05
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (29 bp):
AAATCAAATTCATGTATAAAATTGCACAT
Found at i:40671536 original size:18 final size:19
Alignment explanation
Indices: 40671504--40671544 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
40671494 ATGCCTCTAA
40671504 AATAATAACAAAATTA-AC
1 AATAATAACAAAATTATAC
40671522 AATAA-AACAAGAATTATAC
1 AATAATAACAA-AATTATAC
40671541 AATA
1 AATA
40671545 TTCAAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 10 0.48
19 6 0.29
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (19 bp):
AATAATAACAAAATTATAC
Found at i:40671578 original size:22 final size:22
Alignment explanation
Indices: 40671553--40671595 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40671543 TATTCAAACA
40671553 ATAACAATGAAATAGTAGCAAT
1 ATAACAATGAAATAGTAGCAAT
* *
40671575 ATAATAATGAAATGGTAGCAA
1 ATAACAATGAAATAGTAGCAA
40671596 AACAACAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.23
Consensus pattern (22 bp):
ATAACAATGAAATAGTAGCAAT
Found at i:40673563 original size:25 final size:25
Alignment explanation
Indices: 40673526--40673595 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
40673516 GACTATATAC
40673526 AAAATT-TTGATAAATTAAAAATGTAT
1 AAAATTATT-ATAAATTAAAAAT-TAT
*
40673552 -AAATTATTAT-AATAAAAAAATTAT
1 AAAATTATTATAAAT-TAAAAATTAT
40673576 AAAATTATTA-AATATTAAAA
1 AAAATTATTATAA-ATTAAAA
40673596 TAATACAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
24 6 0.16
25 27 0.73
26 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (25 bp):
AAAATTATTATAAATTAAAAATTAT
Found at i:40673592 original size:32 final size:32
Alignment explanation
Indices: 40673537--40673598 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
40673527 AAATTTTGAT
*
40673537 AAATTAAAAATGTATAAATTATTATAATAAAA
1 AAATTAAAAATGTATAAATTATTAAAATAAAA
40673569 AAATTATAAAAT-TATTAAA-TATTAAAATAA
1 AAATTA-AAAATGTA-TAAATTATTAAAATAA
40673599 TACAATACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 18 0.67
33 9 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (32 bp):
AAATTAAAAATGTATAAATTATTAAAATAAAA
Found at i:40673596 original size:24 final size:25
Alignment explanation
Indices: 40673542--40673589 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
40673532 TTGATAAATT
40673542 AAAAATGTATAAATTATTATAATAA
1 AAAAATGTATAAATTATTATAATAA
40673567 AAAAAT-TATAAAATTATTA-AATA
1 AAAAATGTAT-AAATTATTATAATA
40673590 TTAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
AAAAATGTATAAATTATTATAATAA
Found at i:40682190 original size:31 final size:32
Alignment explanation
Indices: 40682154--40682234 Score: 101
Period size: 32 Copynumber: 2.6 Consensus size: 32
40682144 GATCCCTGAA
* *
40682154 AAGTTTAAGTATTAACTTAAG-AAAAAGTGTC
1 AAGTTTAAGTACTAAATTAAGAAAAAAGTGTC
* *
40682185 AAGTTTAGGTACTAAATTAGGAAAAAAGTGTC
1 AAGTTTAAGTACTAAATTAAGAAAAAAGTGTC
* *
40682217 AAGTTTGAGTACCAAATT
1 AAGTTTAAGTACTAAATT
40682235 GGATAAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 17 0.40
32 25 0.60
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (32 bp):
AAGTTTAAGTACTAAATTAAGAAAAAAGTGTC
Found at i:40682216 original size:32 final size:32
Alignment explanation
Indices: 40682175--40682243 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
40682165 TTAACTTAAG
*
40682175 AAAAAGTGTCAAGTTT-AGGTACTAAATTAGGA-
1 AAAAAGTGTCAAGTTTGA-GTACCAAATT-GGAT
40682207 AAAAAGTGTCAAGTTTGAGTACCAAATTGGAT
1 AAAAAGTGTCAAGTTTGAGTACCAAATTGGAT
40682239 AAAAA
1 AAAAA
40682244 AAATTAGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
31 3 0.09
32 30 0.88
33 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.26
Consensus pattern (32 bp):
AAAAAGTGTCAAGTTTGAGTACCAAATTGGAT
Found at i:40684063 original size:21 final size:20
Alignment explanation
Indices: 40684039--40684228 Score: 123
Period size: 21 Copynumber: 9.7 Consensus size: 20
40684029 CATCTTGAAG
40684039 GAGAAGGAGGAGGAGAAGATA
1 GAGAAGGAGGAGGAGAAGA-A
* *
40684060 GAGAAGGAGAAGAAGAAGAA
1 GAGAAGGAGGAGGAGAAGAA
*
40684080 G-GAA-GAGGAGGAGGAGAA
1 GAGAAGGAGGAGGAGAAGAA
*
40684098 G-G-A-GAGGA--AGAGGAA
1 GAGAAGGAGGAGGAGAAGAA
40684113 -AG-AGGAGGAGGAGAAGAA
1 GAGAAGGAGGAGGAGAAGAA
*
40684131 GAAGGAGGAGGAGGAGAAGAAA
1 G-AGAAGGAGGAGGAGAAG-AA
* * *
40684153 GAGGAGGAGGAGGGGAAGGAG
1 GAGAAGGAGGAGGAGAA-GAA
40684174 GAGGAAGGAAAGGAGGAGAAGAA
1 GA-GAAGG--AGGAGGAGAAGAA
** * *
40684197 -AG-AGGAGGAAAAGGAGGAG
1 GAGAAGGAGGAGGA-GAAGAA
40684216 GAGAAGGAGGAGG
1 GAGAAGGAGGAGG
40684229 TTGAAGATGA
Statistics
Matches: 135, Mismatches: 19, Indels: 30
0.73 0.10 0.16
Matches are distributed among these distances:
15 7 0.05
16 5 0.04
17 6 0.04
18 24 0.18
19 7 0.05
20 9 0.07
21 57 0.42
22 9 0.07
23 2 0.01
24 9 0.07
ACGTcount: A:0.47, C:0.00, G:0.52, T:0.01
Consensus pattern (20 bp):
GAGAAGGAGGAGGAGAAGAA
Found at i:40684090 original size:3 final size:3
Alignment explanation
Indices: 40684079--40684228 Score: 99
Period size: 3 Copynumber: 50.0 Consensus size: 3
40684069 AAGAAGAAGA
* * * *
40684079 AGG AAG AGG AGG AGG AGA AGG A-G AGG AAG AGG AAAG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG -AGG AGG AGG AGG
* * * * * *
40684124 AGA AGA AGA AGG AGG AGG AGG AGA AGA AAG AGG AGG AGG AGG -GG AAGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG -AGG
* * * * **
40684172 AGG AGG AAGG A-A AGG AGG AGA AGA AAG AGG AGG AAA AGG AGG AGG
1 AGG AGG -AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
*
40684217 AGA AGG AGG AGG
1 AGG AGG AGG AGG
40684229 TTGAAGATGA
Statistics
Matches: 115, Mismatches: 26, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
2 5 0.04
3 103 0.90
4 7 0.06
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:40684156 original size:15 final size:15
Alignment explanation
Indices: 40684040--40684221 Score: 85
Period size: 15 Copynumber: 12.1 Consensus size: 15
40684030 ATCTTGAAGG
*
40684040 AGAAGGAGGAGGAGA
1 AGAAAGAGGAGGAGA
* *
40684055 AGATAGAGAAGGAGA
1 AGAAAGAGGAGGAGA
* *
40684070 AG-AAGAAGAAG-GA
1 AGAAAGAGGAGGAGA
*
40684083 AG-AGGAGGAGGAGA
1 AGAAAGAGGAGGAGA
* *
40684097 AG-GAGAGGAAGAGGAA
1 AGAAAGAGGAGGA-G-A
* *
40684113 AGAGGAGGAGGAGAAGA
1 AGA--AAGAGGAGGAGA
40684130 AGAAGGAGGAGGAGGAGA
1 AGAA--A-GAGGAGGAGA
*
40684148 AGAAAGAGGAGGAGG
1 AGAAAGAGGAGGAGA
**
40684163 AG-GGGAAGGAGGAGGA
1 AGAAAG-AGGAGGA-GA
*
40684179 AGGAA-AGGAGGAGA
1 AGAAAGAGGAGGAGA
40684193 AGAAAGAGGA-G-GA
1 AGAAAGAGGAGGAGA
*
40684206 A-AAGGAGGAGGAGA
1 AGAAAGAGGAGGAGA
40684220 AG
1 AG
40684222 GAGGAGGTTG
Statistics
Matches: 124, Mismatches: 27, Indels: 32
0.68 0.15 0.17
Matches are distributed among these distances:
12 7 0.06
13 14 0.11
14 27 0.22
15 45 0.36
16 7 0.06
17 4 0.03
18 14 0.11
19 6 0.05
ACGTcount: A:0.48, C:0.00, G:0.51, T:0.01
Consensus pattern (15 bp):
AGAAAGAGGAGGAGA
Found at i:40684160 original size:24 final size:24
Alignment explanation
Indices: 40684037--40684228 Score: 157
Period size: 24 Copynumber: 8.2 Consensus size: 24
40684027 ACCATCTTGA
* *
40684037 AGGAGAAGGAGGAGGAGAAGATAG
1 AGGAGGAGGAGGAGGAGAAGAAAG
* * * * *
40684061 AGAAGGAGAAGAAGAAGAAGGAAG
1 AGGAGGAGGAGGAGGAGAAGAAAG
* *
40684085 AGGAGGAGGAGAAGGAG-AGGAAG
1 AGGAGGAGGAGGAGGAGAAGAAAG
*
40684108 AGGAAAGAGGAGGAGGAGAAG-AAG
1 AGG-AGGAGGAGGAGGAGAAGAAAG
40684132 A--AGGAGGAGGAGGAGAAGAAAG
1 AGGAGGAGGAGGAGGAGAAGAAAG
* *
40684154 AGGAGGAGGA-G-GG-GAAGGAGG
1 AGGAGGAGGAGGAGGAGAAGAAAG
*
40684175 AGGAAGGA-AAGGAGGAGAAGAAAG
1 AGG-AGGAGGAGGAGGAGAAGAAAG
** * *
40684199 AGGAGGAAAAGGAGGAGGAGAAGG
1 AGGAGGAGGAGGAGGAGAAGAAAG
40684223 AGGAGG
1 AGGAGG
40684229 TTGAAGATGA
Statistics
Matches: 138, Mismatches: 20, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
21 26 0.19
22 11 0.08
23 16 0.12
24 83 0.60
25 2 0.01
ACGTcount: A:0.47, C:0.00, G:0.52, T:0.01
Consensus pattern (24 bp):
AGGAGGAGGAGGAGGAGAAGAAAG
Found at i:40684174 original size:18 final size:18
Alignment explanation
Indices: 40684037--40684228 Score: 151
Period size: 18 Copynumber: 10.8 Consensus size: 18
40684027 ACCATCTTGA
40684037 AGGAGAAGGAGGAGGA-G
1 AGGAGAAGGAGGAGGAGG
* * * * *
40684054 AAGATAGAGAAGGAGAAGA
1 AGGAGA-AGGAGGAGGAGG
* *
40684073 AGAAGAAGGAAGAGGAGG
1 AGGAGAAGGAGGAGGAGG
*
40684091 AGGAGAAGGA-GAGGAAG
1 AGGAGAAGGAGGAGGAGG
* *
40684108 AGGAAAGAGGAGGAGGAGA
1 AGGAGA-AGGAGGAGGAGG
*
40684127 AGAAGAAGGAGGAGGAGG
1 AGGAGAAGGAGGAGGAGG
* *
40684145 AGAAGAAAGAGGAGGAGG
1 AGGAGAAGGAGGAGGAGG
*
40684163 AGGGGAAGGAGGAGGA--
1 AGGAGAAGGAGGAGGAGG
* *
40684179 AGGA-AAGGAGGAGAAGA
1 AGGAGAAGGAGGAGGAGG
* * **
40684196 AAGAGGAGGAAAAGGAGG
1 AGGAGAAGGAGGAGGAGG
40684214 AGGAGAAGGAGGAGG
1 AGGAGAAGGAGGAGG
40684229 TTGAAGATGA
Statistics
Matches: 132, Mismatches: 36, Indels: 13
0.73 0.20 0.07
Matches are distributed among these distances:
15 10 0.08
16 3 0.02
17 18 0.14
18 89 0.67
19 12 0.09
ACGTcount: A:0.47, C:0.00, G:0.52, T:0.01
Consensus pattern (18 bp):
AGGAGAAGGAGGAGGAGG
Found at i:40687061 original size:34 final size:33
Alignment explanation
Indices: 40686996--40687063 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 33
40686986 TAGGGGTAAA
*
40686996 AATATAATTTTATTTTTATTAATTTAAAATTTTT
1 AATAAAATTTTATTTTTATT-ATTTAAAATTTTT
*
40687030 AATAAAATTTTATTTTGATATT-TTTATAATTTTT
1 AATAAAATTTTATTTT--TATTATTTAAAATTTTT
40687064 TAACATGTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 26 0.87
36 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (33 bp):
AATAAAATTTTATTTTTATTATTTAAAATTTTT
Found at i:40693488 original size:24 final size:24
Alignment explanation
Indices: 40693460--40693505 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
40693450 ATAATTAATG
*
40693460 AAAAT-AATAATATTATTCATTTAA
1 AAAATAAATAA-ATTAATCATTTAA
40693484 AAAATAAATAAATTAATCATTT
1 AAAATAAATAAATTAATCATTT
40693506 CTTAACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAATAAATAAATTAATCATTTAA
Found at i:40693756 original size:38 final size:37
Alignment explanation
Indices: 40693691--40693766 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 37
40693681 TTAATCTTAA
* *
40693691 TTTTAAAAATTAAAAATTATATGAAAATA-AAATTAT
1 TTTTAAAAATTAAAAATTATATAAAAATATAAAATAT
40693727 TTTTAAAAATTATTAAAATGT-TATAAAAATATAAAATAT
1 TTTTAAAAATTA--AAAAT-TATATAAAAATATAAAATAT
40693766 T
1 T
40693767 AATATTTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 12 0.35
38 14 0.41
39 8 0.24
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (37 bp):
TTTTAAAAATTAAAAATTATATAAAAATATAAAATAT
Found at i:40711211 original size:21 final size:21
Alignment explanation
Indices: 40711187--40711244 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
40711177 TAGTGCAGAT
*
40711187 TTCTACCGATACAAGTGA-TAA
1 TTCTACCAATACAAGTGACT-A
*
40711208 TTCTACCAATACAAGTGACTC
1 TTCTACCAATACAAGTGACTA
40711229 TTCTACCAATACAAGT
1 TTCTACCAATACAAGT
40711245 TTCACCTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.29
Consensus pattern (21 bp):
TTCTACCAATACAAGTGACTA
Found at i:40711254 original size:21 final size:21
Alignment explanation
Indices: 40711188--40711256 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
40711178 AGTGCAGATT
* * **
40711188 TCTACCGATACAAGTGATAAT
1 TCTACCAATACAAGTGACACC
* *
40711209 TCTACCAATACAAGTGACTCT
1 TCTACCAATACAAGTGACACC
**
40711230 TCTACCAATACAAGTTTCACC
1 TCTACCAATACAAGTGACACC
40711251 TCTACC
1 TCTACC
40711257 GACACTAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.33, C:0.29, G:0.09, T:0.29
Consensus pattern (21 bp):
TCTACCAATACAAGTGACACC
Found at i:40716107 original size:23 final size:23
Alignment explanation
Indices: 40716077--40716200 Score: 101
Period size: 23 Copynumber: 5.4 Consensus size: 23
40716067 TACTAGTGTA
40716077 CTCTCTGTTTAGCAC-GTCTCGTG
1 CTCTCTGTTTAGCACTGTCT-GTG
*
40716100 CTCTCTGTTATTAGCACTGTGTGTG
1 CTCTCTG-T-TTAGCACTGTCTGTG
* * * *
40716125 CTCTTTGATTAGCACTTTGTGTG
1 CTCTCTGTTTAGCACTGTCTGTG
* * * * *
40716148 CTCTCTGATTAGTACTTTGTGTA
1 CTCTCTGTTTAGCACTGTCTGTG
40716171 CTCTCTGTTTAGCACTG--TGTG
1 CTCTCTGTTTAGCACTGTCTGTG
*
40716192 CTCTATGTT
1 CTCTCTGTT
40716201 GCCCAGCACT
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
21 11 0.13
23 55 0.64
24 1 0.01
25 16 0.19
26 3 0.03
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (23 bp):
CTCTCTGTTTAGCACTGTCTGTG
Found at i:40716183 original size:46 final size:46
Alignment explanation
Indices: 40716072--40716195 Score: 144
Period size: 48 Copynumber: 2.7 Consensus size: 46
40716062 AGGAATACTA
* *
40716072 GTGTACTCTCTGTTTAGCACGTCTCGTGCTCTCTGTTATTAGCACTGT
1 GTGTACTCTCTGTTTAGCACTTGT-GTGCTCTCTG-TATTAGCACTGT
* * * * *
40716120 GTGTGCTCTTTGATTAGCACTTTGTGTGCTCTCTG-ATTAGTACTTT
1 GTGTACTCTCTGTTTAGCAC-TTGTGTGCTCTCTGTATTAGCACTGT
40716166 GTGTACTCTCTGTTTAGCAC-TGTGTGCTCT
1 GTGTACTCTCTGTTTAGCACTTGTGTGCTCT
40716196 ATGTTGCCCA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
44 10 0.15
46 26 0.40
48 27 0.42
49 2 0.03
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (46 bp):
GTGTACTCTCTGTTTAGCACTTGTGTGCTCTCTGTATTAGCACTGT
Found at i:40723316 original size:23 final size:23
Alignment explanation
Indices: 40723286--40723408 Score: 113
Period size: 23 Copynumber: 5.3 Consensus size: 23
40723276 CACTAGCGCA
40723286 CTCTCTGTTTAGCAC-GTCTCGTG
1 CTCTCTGTTTAGCACTGTCT-GTG
*
40723309 CTCTCTGTTATTAGCACTGTGTGTG
1 CTCTCTG-T-TTAGCACTGTCTGTG
* * *
40723334 CTCTCTGATTAGCACTTTGTGTG
1 CTCTCTGTTTAGCACTGTCTGTG
* * * * *
40723357 CTCTCTGATTAGTACTTTGTGTA
1 CTCTCTGTTTAGCACTGTCTGTG
* *
40723380 CCCTCTGTTTAGCACTGTGTGTG
1 CTCTCTGTTTAGCACTGTCTGTG
40723403 CTCTCT
1 CTCTCT
40723409 ATTGCCCAGC
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 65 0.76
24 1 0.01
25 17 0.20
26 3 0.03
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.43
Consensus pattern (23 bp):
CTCTCTGTTTAGCACTGTCTGTG
Found at i:40723386 original size:46 final size:47
Alignment explanation
Indices: 40723288--40723408 Score: 138
Period size: 46 Copynumber: 2.6 Consensus size: 47
40723278 CTAGCGCACT
* * * *
40723288 CTCTGTTTAGCAC-GTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCT
1 CTCTGATTAGCACTGTGT-GTGCTCTCTG-TATTAGCACTGTGTGTACC
* * *
40723336 CTCTGATTAGCACTTTGTGTGCTCTCTG-ATTAGTACTTTGTGTACC
1 CTCTGATTAGCACTGTGTGTGCTCTCTGTATTAGCACTGTGTGTACC
*
40723382 CTCTGTTTAGCACTGTGTGTGCTCTCT
1 CTCTGATTAGCACTGTGTGTGCTCTCT
40723409 ATTGCCCAGC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 39 0.62
48 22 0.35
49 2 0.03
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (47 bp):
CTCTGATTAGCACTGTGTGTGCTCTCTGTATTAGCACTGTGTGTACC
Found at i:40723401 original size:69 final size:66
Alignment explanation
Indices: 40723319--40723458 Score: 174
Period size: 69 Copynumber: 2.0 Consensus size: 66
40723309 CTCTCTGTTA
* *
40723319 TTAGCACTGTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACCC
1 TTAGCACTGTGTGTGCTCTCT-ATTCAGCAC-TTATGTGCTATCT-ATTAGTACTTTG-GTACCC
40723383 TCTGT
62 TCTGT
* *
40723388 TTAGCACTGTGTGTGCTCTCTATTGCCCAGCACTTATGTGCTATCTATTCGTACTTTGGTACTCT
1 TTAGCACTGTGTGTGCTCTCTATT---CAGCACTTATGTGCTATCTATTAGTACTTTGGTACCCT
40723453 CTGT
63 CTGT
40723457 TT
1 TT
40723459 GTTTCGTATA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
68 3 0.05
69 33 0.52
70 11 0.17
71 11 0.17
72 5 0.08
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (66 bp):
TTAGCACTGTGTGTGCTCTCTATTCAGCACTTATGTGCTATCTATTAGTACTTTGGTACCCTCTG
T
Found at i:40750375 original size:15 final size:16
Alignment explanation
Indices: 40750355--40750394 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
40750345 GGTTCAAAGC
40750355 AAATAAATTATTA-AA
1 AAATAAATTATTATAA
**
40750370 AAATAAAAAATTATAA
1 AAATAAATTATTATAA
40750386 AAATAAATT
1 AAATAAATT
40750395 CAACTGCCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAATTATTATAA
Found at i:40753199 original size:5 final size:5
Alignment explanation
Indices: 40753160--40753198 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
40753150 TTGTCTATGT
* * *
40753160 GTTGT GTTGT GTTGA GTTGA GTTGA GTTGA GTTGG GTTG
1 GTTGA GTTGA GTTGA GTTGA GTTGA GTTGA GTTGA GTTG
40753199 GATTGAAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (5 bp):
GTTGA
Found at i:40761706 original size:20 final size:20
Alignment explanation
Indices: 40761677--40761718 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
40761667 TGACTTTAGA
40761677 GAAAAAAGAGAAAAAAATTG
1 GAAAAAAGAGAAAAAAATTG
* *
40761697 GAAAAGAGAGAAAGAAATTG
1 GAAAAAAGAGAAAAAAATTG
40761717 GA
1 GA
40761719 TATGGTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.26, T:0.10
Consensus pattern (20 bp):
GAAAAAAGAGAAAAAAATTG
Found at i:40762152 original size:25 final size:25
Alignment explanation
Indices: 40762124--40762179 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
40762114 ATTTATTTAC
*
40762124 TATTTCATTAT-TTTCAATTTTTATT
1 TATTTCATTATATTT-AATTTTCATT
*
40762149 TATTTCTTTATACTTTAATTTTCATT
1 TATTTCATTATA-TTTAATTTTCATT
40762175 TATTT
1 TATTT
40762180 ATTTTACACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 10 0.37
26 14 0.52
27 3 0.11
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (25 bp):
TATTTCATTATATTTAATTTTCATT
Found at i:40768938 original size:10 final size:9
Alignment explanation
Indices: 40768886--40768952 Score: 59
Period size: 9 Copynumber: 7.2 Consensus size: 9
40768876 TCATGCAATT
40768886 TTTTTA-AA
1 TTTTTATAA
40768894 TTTTTTGATAA
1 -TTTTT-ATAA
40768905 TTTTATATATA
1 TTTT-TATA-A
*
40768916 TTTTTAAAA
1 TTTTTATAA
40768925 TTTTT-TAA
1 TTTTTATAA
40768933 TCTTTTATAA
1 T-TTTTATAA
40768943 TTTTTA-AA
1 TTTTTATAA
40768951 TT
1 TT
40768953 ATTTGTTAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
8 7 0.14
9 20 0.40
10 15 0.30
11 8 0.16
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:40770114 original size:16 final size:16
Alignment explanation
Indices: 40770084--40770123 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
40770074 TTTTGTTTCA
*
40770084 TCTTCTTTCTTCTTCCC
1 TCTT-TTTCTCCTTCCC
40770101 TCTTTTTCTCCTTCCC
1 TCTTTTTCTCCTTCCC
*
40770117 TATTTTT
1 TCTTTTT
40770124 TTTTCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (16 bp):
TCTTTTTCTCCTTCCC
Found at i:40799936 original size:20 final size:21
Alignment explanation
Indices: 40799911--40799950 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40799901 ATGGTTCGGT
*
40799911 TAAATAAAT-TATTAAAAATA
1 TAAATAAATATAATAAAAATA
*
40799931 TAAATATATATAATAAAAAT
1 TAAATAAATATAATAAAAAT
40799951 TAGATCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAATAAATATAATAAAAATA
Found at i:40813656 original size:20 final size:18
Alignment explanation
Indices: 40813615--40813653 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
40813605 TATTGATTTT
*
40813615 AATATTTTATAAATTATA
1 AATATTTTATAAAATATA
*
40813633 AATACTTTTTTAAAATATA
1 AATA-TTTTATAAAATATA
40813652 AA
1 AA
40813654 ATATAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATTTTATAAAATATA
Found at i:40814169 original size:8 final size:8
Alignment explanation
Indices: 40814156--40814182 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
40814146 TATATAATTT
40814156 TTAAAAAC
1 TTAAAAAC
40814164 TTAAAAAC
1 TTAAAAAC
40814172 TTAAAAAC
1 TTAAAAAC
40814180 TTA
1 TTA
40814183 GTGAGTTAAA
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:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (8 bp):
TTAAAAAC
Found at i:40816817 original size:29 final size:32
Alignment explanation
Indices: 40816765--40816824 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 32
40816755 TAGGCCCGAA
40816765 TATATTATGTTATAAAAATTAATTATATTAAT
1 TATATTATGTTATAAAAATTAATTATATTAAT
* *
40816797 TATA-TATGTTA-AATAA-TAATTATGTTAA
1 TATATTATGTTATAAAAATTAATTATATTAA
40816825 ATAAAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.42
30 4 0.15
31 7 0.27
32 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (32 bp):
TATATTATGTTATAAAAATTAATTATATTAAT
Found at i:40816822 original size:16 final size:16
Alignment explanation
Indices: 40816763--40816832 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
40816753 GCTAGGCCCG
*
40816763 AATATATTATGTTATAAA
1 AATA-ATTATGTTA-AAT
*
40816781 AATTAATTATATT-AAT
1 AA-TAATTATGTTAAAT
*
40816797 TAT-A-TATGTTAAAT
1 AATAATTATGTTAAAT
40816811 AATAATTATGTTAAAT
1 AATAATTATGTTAAAT
40816827 AA-AATT
1 AATAATT
40816833 TGGCTGAGCT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
13 5 0.12
14 6 0.14
15 6 0.14
16 15 0.35
18 9 0.21
19 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (16 bp):
AATAATTATGTTAAAT
Found at i:40818520 original size:31 final size:31
Alignment explanation
Indices: 40818482--40818540 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
40818472 TAAACTTTAT
40818482 GCATTAGGGGATAGT-TCCAGTTATGCATTCA
1 GCATTAGGGGATAGTAT-CAGTTATGCATTCA
40818513 GCATTAGGGGATAGTATCAGTTATGCAT
1 GCATTAGGGGATAGTATCAGTTATGCAT
40818541 CTAGATTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (31 bp):
GCATTAGGGGATAGTATCAGTTATGCATTCA
Found at i:40822914 original size:61 final size:61
Alignment explanation
Indices: 40822823--40822978 Score: 137
Period size: 61 Copynumber: 2.6 Consensus size: 61
40822813 AGAGCTTAAT
* *
40822823 TAAAATTTTC-AATAAAATTAAAAGGCAAAATGTCAAA-TTTC-AAAAATT-AGGGGAAG-CTAA
1 TAAAATTTTCTAA-AAAATTAAAAGG-AAAA-ATAAAATTTTCTAAAAATTCAGGGG--GCCTAA
40822883 C
61 C
* * *
40822884 TAAAATTTTCTAAAAACTT-AAAGAGAAAAATAAAATTTTCTAAAAATTCTGGGGGCCTAAT
1 TAAAATTTTCTAAAAAATTAAAAG-GAAAAATAAAATTTTCTAAAAATTCAGGGGGCCTAAC
** *
40822945 TAAAATTTTCT-AAAAATTTCAAGGAAAAGTAAAA
1 TAAAATTTTCTAAAAAATTAAAAGGAAAAATAAAA
40822979 ATTCCCAAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 15
0.78 0.08 0.15
Matches are distributed among these distances:
59 4 0.05
60 29 0.36
61 41 0.51
62 6 0.08
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.29
Consensus pattern (61 bp):
TAAAATTTTCTAAAAAATTAAAAGGAAAAATAAAATTTTCTAAAAATTCAGGGGGCCTAAC
Found at i:40828614 original size:2 final size:2
Alignment explanation
Indices: 40828609--40828644 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40828599 ATTTTTTTGA
40828609 AT 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 AT
40828645 GGACTTTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40833949 original size:21 final size:20
Alignment explanation
Indices: 40833917--40833959 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
40833907 TTTAAATTTT
*
40833917 AATTAAGTTTAATTAAG-AA
1 AATTAAGTTTAATGAAGTAA
40833936 AATTAAGTGATTAATGAAGTAA
1 AATTAAGT--TTAATGAAGTAA
40833958 AA
1 AA
40833960 ATCTAAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
21 8 0.40
22 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (20 bp):
AATTAAGTTTAATGAAGTAA
Found at i:40834935 original size:17 final size:17
Alignment explanation
Indices: 40834913--40834959 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
40834903 CTTAATAAAG
40834913 GATTAGGTATAAAATGC
1 GATTAGGTATAAAATGC
*
40834930 GATTAGGTATAACATGC
1 GATTAGGTATAAAATGC
*
40834947 CATTAGGGTATAA
1 GATTA-GGTATAA
40834960 TATGAAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (17 bp):
GATTAGGTATAAAATGC
Found at i:40835111 original size:29 final size:29
Alignment explanation
Indices: 40835069--40835142 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
40835059 CGATACAATG
*
40835069 TCAGTTTGTGTGAGCAACCCTAATCACTA
1 TCAGCTTGTGTGAGCAACCCTAATCACTA
* *
40835098 TCAGCTTGTGTGAGCAACCCTAGTCACTG
1 TCAGCTTGTGTGAGCAACCCTAATCACTA
*
40835127 TCAACTTGTGTGAGCA
1 TCAGCTTGTGTGAGCA
40835143 CTATAGTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (29 bp):
TCAGCTTGTGTGAGCAACCCTAATCACTA
Found at i:40837831 original size:5 final size:5
Alignment explanation
Indices: 40837821--40837845 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40837811 TATAAAATTT
40837821 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
40837846 CTGAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:40838702 original size:18 final size:17
Alignment explanation
Indices: 40838674--40838710 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
40838664 GATCTTAGAA
40838674 TTAATAAACAATAAAAT
1 TTAATAAACAATAAAAT
40838691 TTAATCAAACAATAAAAT
1 TTAAT-AAACAATAAAAT
40838709 TT
1 TT
40838711 TTAATTTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAATAAACAATAAAAT
Found at i:40838957 original size:58 final size:59
Alignment explanation
Indices: 40838877--40839047 Score: 197
Period size: 58 Copynumber: 2.9 Consensus size: 59
40838867 TTAATATAAC
* * *
40838877 ATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGGTATTTAAA-TTTCTTTT-A-CTT
1 ATTTGATACCTGAACTTGACACTTTTTCTTAATTTGGTATCTAAACTTT-TTTTAACCTA
* * *
40838934 ATTTAGATACTTGAACTTGACACTTTTTTTTAATTTGGTACCTAAACTTTTTTTGAACCTA
1 ATTT-GATACCTGAACTTGACACTTTTTCTTAATTTGGTATCTAAACTTTTTTT-AACCTA
* * * *
40838995 ATTTGGTACCTGAACTTGATA-TTTTTCCTAATTTGGTATCTAATCTTTTTTTA
1 ATTTGATACCTGAACTTGACACTTTTTCTTAATTTGGTATCTAAACTTTTTTTA
40839048 GATTCAATTT
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
57 4 0.04
58 41 0.43
59 30 0.31
60 15 0.16
61 6 0.06
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.51
Consensus pattern (59 bp):
ATTTGATACCTGAACTTGACACTTTTTCTTAATTTGGTATCTAAACTTTTTTTAACCTA
Found at i:40838997 original size:29 final size:29
Alignment explanation
Indices: 40838964--40839067 Score: 106
Period size: 29 Copynumber: 3.6 Consensus size: 29
40838954 CACTTTTTTT
*
40838964 TAATTTGGTACCTAAACTTTTTTTGAACC
1 TAATTTGGTACCTAAACTTTTTTTGATCC
*
40838993 TAATTTGGTACCTGAACTTGATATTTT--TCC
1 TAATTTGGTACCTAAACTT--T-TTTTGATCC
* * *
40839023 TAATTTGGTATCTAATCTTTTTTTAGATTC
1 TAATTTGGTACCTAAACTTTTTTT-GATCC
40839053 -AATTTGGTACCTAAA
1 TAATTTGGTACCTAAA
40839068 TTTATTAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
27 4 0.07
28 1 0.02
29 31 0.51
30 20 0.33
31 1 0.02
32 4 0.07
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (29 bp):
TAATTTGGTACCTAAACTTTTTTTGATCC
Found at i:40839031 original size:59 final size:59
Alignment explanation
Indices: 40838877--40839064 Score: 206
Period size: 59 Copynumber: 3.2 Consensus size: 59
40838867 TTAATATAAC
* *
40838877 ATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGGTATTTAAA-TTTCTTTT--ACTT
1 ATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGGTATCTAAACTTT-TTTTGAACTA
* * * *
40838934 ATTTAGATACTTGAACTTGACACTTTTTTTTAATTTGGTACCTAAACTTTTTTTGAACCTA
1 ATTT-GGTACCTGAACTTGACACTTTTTCTTAATTTGGTATCTAAACTTTTTTTGAA-CTA
* * * *
40838995 ATTTGGTACCTGAACTTGATA-TTTTTCCTAATTTGGTATCTAATCTTTTTTT-AGATTCA
1 ATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGGTATCTAAACTTTTTTTGA-ACT-A
40839054 ATTTGGTACCT
1 ATTTGGTACCT
40839065 AAATTTATTA
Statistics
Matches: 110, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
57 4 0.04
58 42 0.38
59 43 0.39
60 15 0.14
61 6 0.05
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.50
Consensus pattern (59 bp):
ATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGGTATCTAAACTTTTTTTGAACTA
Found at i:40844419 original size:8 final size:8
Alignment explanation
Indices: 40844408--40844433 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
40844398 TTTCTTCCTT
40844408 TCTTTTAA
1 TCTTTTAA
40844416 TCTTTTAA
1 TCTTTTAA
40844424 TCTTTTAA
1 TCTTTTAA
40844432 TC
1 TC
40844434 AACCTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (8 bp):
TCTTTTAA
Found at i:40844529 original size:12 final size:12
Alignment explanation
Indices: 40844502--40844535 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
40844492 AACTAACAAA
40844502 TTAAAAA-AAA-
1 TTAAAAATAAAT
40844512 TTAAAAATAAAT
1 TTAAAAATAAAT
40844524 TTAAAAATAAAT
1 TTAAAAATAAAT
40844536 ACATTACCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.32
11 3 0.14
12 12 0.55
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
TTAAAAATAAAT
Found at i:40846914 original size:16 final size:17
Alignment explanation
Indices: 40846884--40846916 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40846874 ATGGATAAGT
40846884 CAAAAGCAAGTGAGAAA
1 CAAAAGCAAGTGAGAAA
*
40846901 CAAAGGCAAG-GAGAAA
1 CAAAAGCAAGTGAGAAA
40846917 TTTTCTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.12, G:0.27, T:0.03
Consensus pattern (17 bp):
CAAAAGCAAGTGAGAAA
Found at i:40848599 original size:17 final size:17
Alignment explanation
Indices: 40848577--40848613 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
40848567 AATTAATTTT
* *
40848577 AATTAATTAATTTTTCC
1 AATTAAATAATTTTTAC
40848594 AATTAAATAATTTTTAC
1 AATTAAATAATTTTTAC
40848611 AAT
1 AAT
40848614 CCGATTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTAAATAATTTTTAC
Found at i:40850406 original size:59 final size:59
Alignment explanation
Indices: 40850326--40850516 Score: 256
Period size: 59 Copynumber: 3.2 Consensus size: 59
40850316 TCGCGGGGGC
* * * *
40850326 AAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAAGGGAATTTTGGAAAATTCGAGGGT
1 AAAATAGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
** * * * *
40850385 AAGGTAGTAATTTTTAGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATAGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
* **
40850444 AAAATGGTAATTTTTGGCAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
1 AAAATAGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
*
40850503 AAAATGGTAATTTT
1 AAAATAGTAATTTT
40850517 GGACTCGCGG
Statistics
Matches: 113, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 113 1.00
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.32
Consensus pattern (59 bp):
AAAATAGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT
Found at i:40850515 original size:88 final size:86
Alignment explanation
Indices: 40850403--40850726 Score: 271
Period size: 88 Copynumber: 3.7 Consensus size: 86
40850393 AATTTTTAGT
* *
40850403 GAAA-TCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGCAAAAT
1 GAAATTCGAGGGTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG-AAAAT
40850467 CGGGGTTAAAAATGGAATTTTG
65 CGGGGTTAAAAATGGAATTTTG
* * * *
40850489 GAAAGTTCGAGGGT-AAAATGGTAATTTTGG--ACTCGCGGGGGCAAAAATGGTAATTTTTGGTG
1 GAAA-TTCGAGGGTAAAAATGG-AATTTTGGAAAGT-TCGGGGG-TAAAATGGTAATTTTTGG-A
* *
40850551 AAATCGAGGTTAAAAAGGGAATTTTG
61 AAATCGGGGTTAAAAATGGAATTTTG
* *
40850577 GAAAATTCGAGGGT-AAAATAGTAATTTTTGGTGAAA--TC-GTGGTCAAAAATGG-AA-TTTTG
1 G-AAATTCGAGGGTAAAAAT-GGAA-TTTT-G-GAAAGTTCGGGGGT--AAAATGGTAATTTTTG
*
40850636 GAAAGTTCGAGGG-T-AAAATGGTAATTTTTGG
59 GAAA-ATCG-GGGTTAAAAATGG-AA-TTTT-G
40850667 TGAAATT-G-GGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGA
1 -GAAATTCGAGGG-TAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGA
40850727 CAGTCCAAGG
Statistics
Matches: 192, Mismatches: 19, Indels: 51
0.73 0.07 0.19
Matches are distributed among these distances:
86 10 0.05
87 28 0.15
88 96 0.50
89 35 0.18
90 20 0.10
91 2 0.01
93 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.31
Consensus pattern (86 bp):
GAAATTCGAGGGTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGAAAATC
GGGGTTAAAAATGGAATTTTG
Found at i:40850542 original size:147 final size:147
Alignment explanation
Indices: 40850391--40850663 Score: 456
Period size: 147 Copynumber: 1.9 Consensus size: 147
40850381 GGGTAAGGTA
* * * * *
40850391 GTAATTTTTAGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATT
1 GTAATTTTTAGTGAAATCGAGGTTAAAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAGTAATT
*
40850456 TTTGGCAAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGGAC
66 TTTGGCAAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGGAC
40850521 TCGCGGGGGCAAAAATG
131 TCGCGGGGGCAAAAATG
*
40850538 GTAATTTTTGGTGAAATCGAGGTTAAAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAGTAATT
1 GTAATTTTTAGTGAAATCGAGGTTAAAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAGTAATT
** *
40850603 TTTGGTGAAATCGTGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTT
66 TTTGGCAAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTT
40850664 TGGTGAAATT
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
147 116 1.00
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.32
Consensus pattern (147 bp):
GTAATTTTTAGTGAAATCGAGGTTAAAAAGGGAATTTTGGAAAATTCGAGGGTAAAATAGTAATT
TTTGGCAAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGGAC
TCGCGGGGGCAAAAATG
Done.