Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 54 of 187
Found at i:16070118 original size:51 final size:51
Alignment explanation
Indices: 16070008--16070107 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
16069998 CTCAATTTCT
*
16070008 TCTCAAATTGCTCTCAATTTCCTTCTAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAATTTCCTTCTAAATTTCTCTCAAATCCATATTTAA
* *
16070059 TCTCAATTTGCTCTCAATTTCC-TCTTAAATTTCTCTTAAATCCTTATTT
1 TCTCAATTTGCTCTCAATTTCCTTC-TAAATTTCTCTCAAATCCATATTT
16070108 TTAGTTAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 2 0.04
51 43 0.96
ACGTcount: A:0.26, C:0.25, G:0.02, T:0.47
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAATTTCCTTCTAAATTTCTCTCAAATCCATATTTAA
Found at i:16074021 original size:18 final size:18
Alignment explanation
Indices: 16073998--16074040 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
16073988 TGCCAGGTGC
* *
16073998 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
16074016 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
16074034 GTTTCCT
1 GTATCCT
16074041 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:16074320 original size:21 final size:21
Alignment explanation
Indices: 16074281--16074342 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
16074271 CCAACACTGA
*
16074281 CAACCAG-ATCCCCTACCGGATG
1 CAACCAGAATCCCC-GCCGGA-G
16074303 -AACCAGAATCCCCGCCGGAG
1 CAACCAGAATCCCCGCCGGAG
* *
16074323 CAACCACAAGCCCCGCCGGA
1 CAACCAGAATCCCCGCCGGA
16074343 AGCTGGACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 1 0.03
21 28 0.80
22 6 0.17
ACGTcount: A:0.29, C:0.44, G:0.21, T:0.06
Consensus pattern (21 bp):
CAACCAGAATCCCCGCCGGAG
Found at i:16075369 original size:25 final size:23
Alignment explanation
Indices: 16075312--16075369 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 23
16075302 AATTATTGAT
*
16075312 ATATTTTTGTCTGAATGTCTTAA
1 ATATTTTTGTATGAATGTCTTAA
16075335 ATATTATTTTGTATGAATGTCTTAA
1 ATA-T-TTTTGTATGAATGTCTTAA
16075360 CACTATTTTT
1 -A-TATTTTT
16075370 AACCTTACAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 3 0.10
24 1 0.03
25 22 0.73
26 2 0.07
27 2 0.07
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.53
Consensus pattern (23 bp):
ATATTTTTGTATGAATGTCTTAA
Found at i:16081661 original size:110 final size:110
Alignment explanation
Indices: 16081468--16081669 Score: 325
Period size: 110 Copynumber: 1.8 Consensus size: 110
16081458 TTTTCTTAAG
* * **
16081468 TAAGCCTCTTCAAATCCTCAAGCCAACCCAGTCGGCATTCACAACACAAACTGGTATGACACAAA
1 TAAGCCTCTTCAAACCCTCAAGCCAACCCAGTCGGCATTCACAAAACAAACTGCCATGACACAAA
16081533 AAGGTAAATTTACCTATCTTCCTGTAACTCAAGTCGCAGCTAAAA
66 AAGGTAAATTTACCTATCTTCCTGTAACTCAAGTCGCAGCTAAAA
* * *
16081578 TAAGCCTC-TCAAAACCCTCAAGCCAGCCCAGTTGGCATTCACAAAACAAACTGCCATGACACCA
1 TAAGCCTCTTC-AAACCCTCAAGCCAACCCAGTCGGCATTCACAAAACAAACTGCCATGACACAA
16081642 AAAGGTAAATTTACCTATCTTCCTGTAA
65 AAAGGTAAATTTACCTATCTTCCTGTAA
16081670 TAACTTAATT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
109 2 0.02
110 82 0.98
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.22
Consensus pattern (110 bp):
TAAGCCTCTTCAAACCCTCAAGCCAACCCAGTCGGCATTCACAAAACAAACTGCCATGACACAAA
AAGGTAAATTTACCTATCTTCCTGTAACTCAAGTCGCAGCTAAAA
Found at i:16089424 original size:20 final size:20
Alignment explanation
Indices: 16089399--16089441 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
16089389 AATCACACTT
16089399 ATTCAAATTTTCTCATTTCA
1 ATTCAAATTTTCTCATTTCA
16089419 ATTCAAATTTTCTCATTTCA
1 ATTCAAATTTTCTCATTTCA
16089439 ATT
1 ATT
16089442 ATTTACCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTCAAATTTTCTCATTTCA
Found at i:16090677 original size:26 final size:26
Alignment explanation
Indices: 16090633--16090688 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
16090623 AAATCCCAAA
*
16090633 TTTTCTTTCTTTCCTCCCT-TTTTCT
1 TTTTCTTTCTTTCCTCCCTGTTTTCG
16090658 TTTTCTTTCCTTT-CTCCCCTGTTTTCG
1 TTTTCTTT-CTTTCCT-CCCTGTTTTCG
16090685 TTTT
1 TTTT
16090689 GCTATTCTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 10 0.37
26 8 0.30
27 9 0.33
ACGTcount: A:0.00, C:0.30, G:0.04, T:0.66
Consensus pattern (26 bp):
TTTTCTTTCTTTCCTCCCTGTTTTCG
Found at i:16090808 original size:23 final size:23
Alignment explanation
Indices: 16090778--16090824 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
16090768 AATAAGTATG
16090778 TACATATATTAATTACAAATGTA
1 TACATATATTAATTACAAATGTA
* *
16090801 TACATATATTTATTACACATGTA
1 TACATATATTAATTACAAATGTA
16090824 T
1 T
16090825 TTATAATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (23 bp):
TACATATATTAATTACAAATGTA
Found at i:16095071 original size:8 final size:8
Alignment explanation
Indices: 16095058--16095088 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
16095048 AAAGCATAAA
16095058 AAAAAAAG
1 AAAAAAAG
*
16095066 AAAAAAAC
1 AAAAAAAG
16095074 AAAAAAAG
1 AAAAAAAG
16095082 AAAAAAA
1 AAAAAAA
16095089 ATAATTTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.03, G:0.06, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:16095079 original size:16 final size:16
Alignment explanation
Indices: 16095058--16095088 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16095048 AAAGCATAAA
16095058 AAAAAAAGAAAAAAAC
1 AAAAAAAGAAAAAAAC
16095074 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
16095089 ATAATTTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.90, C:0.03, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAAAAC
Found at i:16100504 original size:30 final size:31
Alignment explanation
Indices: 16100465--16100524 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
16100455 AGAGGTGGGA
*
16100465 TGGGAAGGGAATAAAATTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
16100496 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
16100525 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.22
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:16100825 original size:9 final size:9
Alignment explanation
Indices: 16100808--16100839 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
16100798 TCGAGTTGAT
16100808 TCGAATAAC
1 TCGAATAAC
*
16100817 TCGATTAAC
1 TCGAATAAC
16100826 TCGAATAAC
1 TCGAATAAC
16100835 TCGAA
1 TCGAA
16100840 ATTTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (9 bp):
TCGAATAAC
Found at i:16101338 original size:82 final size:80
Alignment explanation
Indices: 16101176--16101339 Score: 197
Period size: 82 Copynumber: 2.0 Consensus size: 80
16101166 AAATTTTCAA
* * **
16101176 GTGATAAAAGTGATCGAATGGTTGAGAGAGATGAAAAAAAGAAGTTTTGTTTTTGTGACATGGGT
1 GTGATAAAAGTGATCGAATGGTTAAGAGAGATG--AAAAAGAAGTTCTGGCTTTGTGACATGGGT
16101241 TTGAACTTTGGGTGTGT
64 TTGAACTTTGGGTGTGT
* * ** *
16101258 GTGATAAAAGTGA-CAGAATGGTTAAGGGAGATG-AAAAGAAGTTCTGGCTTTGTTATGTTGGTT
1 GTGATAAAAGTGATC-GAATGGTTAAGAGAGATGAAAAAGAAGTTCTGGCTTTGTGACATGGGTT
16101321 TGAAACTTTGGGTGTGT
65 TG-AACTTTGGGTGTGT
16101338 GT
1 GT
16101340 CAGAATTTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
79 25 0.35
80 16 0.23
81 1 0.01
82 29 0.41
ACGTcount: A:0.29, C:0.04, G:0.32, T:0.34
Consensus pattern (80 bp):
GTGATAAAAGTGATCGAATGGTTAAGAGAGATGAAAAAGAAGTTCTGGCTTTGTGACATGGGTTT
GAACTTTGGGTGTGT
Found at i:16105692 original size:114 final size:111
Alignment explanation
Indices: 16105478--16105806 Score: 344
Period size: 113 Copynumber: 2.9 Consensus size: 111
16105468 CAAATAAGCA
* * * * * * *
16105478 TTAGCGGCGTTTTCGAGAAAGCGCCGCAAAACACCTAATCCCAACGACGCCATTTTCTGAGCTTT
1 TTAGCGGCGTTTTAGATAAAGCGCCACAAAAAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTT
* * *
16105543 CGGGGAATTAGCGGCGTTTTTTTAG-AAGCGACGCTAATACCCAG-GCT
66 C-GGGATTTAGCGGCG--TTTTTAGTAAGCGCCGCTAATACCCAGAGAT
* * * *
16105590 TTCGCGGCGTTTTCA-ACT-AAGTGCCACAAAAAAAAACTGAGCCCAACGATGCCGTTTTC-GAG
1 TTAGCGGCGTTTT-AGA-TAAAGCGCCAC--AAAAAAACTAAGCCCAACGACGCCGTTTTCTGAG
*
16105652 CTTTCGTGGATTTAGCGGCGTTTTTCAAGTAAGCGCCGCTAATATCCAGAGAT
62 CTTTCG-GGATTTAGCGGCGTTTTT--AGTAAGCGCCGCTAATACCCAGAGAT
* * *
16105705 TTAGCGGCGTTTTAGATAAAGCGCCACAAATAACCTAAGCACAACGACGCCGTTTTCTGAGCTTT
1 TTAGCGGCGTTTTAGATAAAGCGCCACAAAAAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTT
* *
16105770 CGGGATTTAGTGGCGTTTTTTGTAAAGCGCCGCTAAT
66 CGGGATTTAGCGGCGTTTTTAGT-AAGCGCCGCTAAT
16105807 GCTCAGTAAT
Statistics
Matches: 180, Mismatches: 24, Indels: 26
0.78 0.10 0.11
Matches are distributed among these distances:
111 7 0.04
112 34 0.19
113 64 0.36
114 52 0.29
115 23 0.13
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (111 bp):
TTAGCGGCGTTTTAGATAAAGCGCCACAAAAAAACTAAGCCCAACGACGCCGTTTTCTGAGCTTT
CGGGATTTAGCGGCGTTTTTAGTAAGCGCCGCTAATACCCAGAGAT
Found at i:16106432 original size:14 final size:14
Alignment explanation
Indices: 16106413--16106494 Score: 60
Period size: 14 Copynumber: 5.9 Consensus size: 14
16106403 TTAATGTGAT
* *
16106413 TTAAGGTTTATGGG
1 TTAAGGGTTAGGGG
16106427 TTAAGGGTTAGGGG
1 TTAAGGGTTAGGGG
*
16106441 TTAGGGGTTA--GG
1 TTAAGGGTTAGGGG
* **
16106453 TTAGGGGTTAGATG
1 TTAAGGGTTAGGGG
* *
16106467 TTAAGAGTTAGGGA
1 TTAAGGGTTAGGGG
*
16106481 TTTAGGGTTTAGGG
1 TTAAGGG-TTAGGG
16106495 ATTTAGTGTT
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
12 12 0.22
14 36 0.67
15 6 0.11
ACGTcount: A:0.22, C:0.00, G:0.43, T:0.35
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:16106456 original size:12 final size:12
Alignment explanation
Indices: 16106425--16106463 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
16106415 AAGGTTTATG
*
16106425 GGTTAAGGGTTA
1 GGTTAGGGGTTA
16106437 GGGGTTAGGGGTTA
1 --GGTTAGGGGTTA
16106451 GGTTAGGGGTTA
1 GGTTAGGGGTTA
16106463 G
1 G
16106464 ATGTTAAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.54
14 11 0.46
ACGTcount: A:0.18, C:0.00, G:0.51, T:0.31
Consensus pattern (12 bp):
GGTTAGGGGTTA
Found at i:16106463 original size:7 final size:7
Alignment explanation
Indices: 16106424--16106463 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
16106414 TAAGGTTTAT
*
16106424 GGGTTAA
1 GGGTTAG
16106431 GGGTTAG
1 GGGTTAG
16106438 GGGTTAG
1 GGGTTAG
16106445 GGGTTA-
1 GGGTTAG
16106451 -GGTTAG
1 GGGTTAG
16106457 GGGTTAG
1 GGGTTAG
16106464 ATGTTAAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 5 0.17
7 25 0.83
ACGTcount: A:0.17, C:0.00, G:0.53, T:0.30
Consensus pattern (7 bp):
GGGTTAG
Found at i:16106469 original size:19 final size:20
Alignment explanation
Indices: 16106425--16106479 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 20
16106415 AAGGTTTATG
*
16106425 GGTTAAGGGTTAGGGGTTAGG
1 GGTTAA-GGTTAGGGGTTAGA
16106446 GGTT-AGGTTAGGGGTTAGA
1 GGTTAAGGTTAGGGGTTAGA
*
16106465 TGTTAAGAGTTAGGG
1 GGTTAAG-GTTAGGG
16106480 ATTTAGGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 16 0.53
20 3 0.10
21 11 0.37
ACGTcount: A:0.22, C:0.00, G:0.47, T:0.31
Consensus pattern (20 bp):
GGTTAAGGTTAGGGGTTAGA
Found at i:16106469 original size:26 final size:26
Alignment explanation
Indices: 16106425--16106478 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
16106415 AAGGTTTATG
* * *
16106425 GGTTAAGGGTTAGGGGTTAGGGGTTA
1 GGTTAAGGGTTAGAGGTTAAGAGTTA
* *
16106451 GGTTAGGGGTTAGATGTTAAGAGTTA
1 GGTTAAGGGTTAGAGGTTAAGAGTTA
16106477 GG
1 GG
16106479 GATTTAGGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.46, T:0.31
Consensus pattern (26 bp):
GGTTAAGGGTTAGAGGTTAAGAGTTA
Found at i:16106631 original size:29 final size:29
Alignment explanation
Indices: 16106594--16106656 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
16106584 TTCAAGATCG
16106594 GGTTTAGGGGTAATGGATTTGGGGTTTAA
1 GGTTTAGGGGTAATGGATTTGGGGTTTAA
*
16106623 GGTTTAGGGGTAATGGATTTGGGGTTTAG
1 GGTTTAGGGGTAATGGATTTGGGGTTTAA
16106652 GGTTT
1 GGTTT
16106657 CAACGGTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (29 bp):
GGTTTAGGGGTAATGGATTTGGGGTTTAA
Found at i:16109466 original size:9 final size:9
Alignment explanation
Indices: 16109452--16110003 Score: 578
Period size: 9 Copynumber: 60.4 Consensus size: 9
16109442 TAAGACTAGC
16109452 TACATAACT
1 TACATAACT
*
16109461 TACATAAAT
1 TACATAACT
16109470 TA-AGTAACT
1 TACA-TAACT
16109479 TACATAACT
1 TACATAACT
16109488 TACATAAACT
1 TACAT-AACT
* *
16109498 TGCATAAAT
1 TACATAACT
*
16109507 TAAATAACT
1 TACATAACT
16109516 TACATAACT
1 TACATAACT
16109525 TACATAACT
1 TACATAACT
16109534 TACATAACT
1 TACATAACT
*
16109543 TACATAACC
1 TACATAACT
16109552 TACATAACT
1 TACATAACT
*
16109561 TACATAAAT
1 TACATAACT
16109570 TA-AGTAACT
1 TACA-TAACT
16109579 TACATAACT
1 TACATAACT
16109588 TACATAAACT
1 TACAT-AACT
* *
16109598 TGCATAAAT
1 TACATAACT
*
16109607 TAAATAACT
1 TACATAACT
16109616 TACATAACT
1 TACATAACT
*
16109625 TACATAACC
1 TACATAACT
* *
16109634 AACATAA-A
1 TACATAACT
*
16109642 TAAAGTAACT
1 TACA-TAACT
16109652 TACATAACT
1 TACATAACT
*
16109661 TACATAAAT
1 TACATAACT
16109670 TA-AGTAACT
1 TACA-TAACT
16109679 TACATAAACT
1 TACAT-AACT
* *
16109689 TGCATAAAT
1 TACATAACT
*
16109698 TAAATAACT
1 TACATAACT
*
16109707 TACATAACC
1 TACATAACT
*
16109716 TACATAAAT
1 TACATAACT
*
16109725 TAAATAACT
1 TACATAACT
16109734 TACATAACT
1 TACATAACT
*
16109743 TACATAAAAT
1 TACAT-AACT
16109753 TA-AGTAACT
1 TACA-TAACT
16109762 TACATAACT
1 TACATAACT
16109771 TACATAAACT
1 TACAT-AACT
* *
16109781 TGCATAAAT
1 TACATAACT
*
16109790 TAAATAACT
1 TACATAACT
16109799 TACATAACT
1 TACATAACT
*
16109808 TACATAACC
1 TACATAACT
*
16109817 TACATAAAT
1 TACATAACT
*
16109826 TAAATAACT
1 TACATAACT
16109835 TACATAACT
1 TACATAACT
*
16109844 TACATAAAT
1 TACATAACT
16109853 TA-AGTAACT
1 TACA-TAACT
16109862 TACATAACT
1 TACATAACT
16109871 TACATAAACT
1 TACAT-AACT
* *
16109881 TGCATAAAT
1 TACATAACT
*
16109890 TAAATAACT
1 TACATAACT
16109899 TACATAAACT
1 TACAT-AACT
*
16109909 TACATAACC
1 TACATAACT
*
16109918 TACATAAAT
1 TACATAACT
*
16109927 TAAATAACT
1 TACATAACT
16109936 TACATAACT
1 TACATAACT
*
16109945 TACATAAAT
1 TACATAACT
16109954 TA-AGTAACT
1 TACA-TAACT
16109963 TACATAACT
1 TACATAACT
16109972 TACATAAACT
1 TACAT-AACT
* *
16109982 TGCATAAAT
1 TACATAACT
*
16109991 TAAATAACT
1 TACATAACT
16110000 TACA
1 TACA
16110004 NNNNNNNNNN
Statistics
Matches: 446, Mismatches: 75, Indels: 44
0.79 0.13 0.08
Matches are distributed among these distances:
8 7 0.02
9 367 0.82
10 72 0.16
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:16112845 original size:21 final size:21
Alignment explanation
Indices: 16112819--16112868 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
16112809 CTACAACTTA
*
16112819 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGGG
16112840 AAGCAGAGGCCGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGGG
16112861 AAGCAGAG
1 AAGCAGAG
16112869 CAGGCCAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.20, G:0.48, T:0.00
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGGG
Found at i:16113243 original size:42 final size:42
Alignment explanation
Indices: 16113188--16113437 Score: 437
Period size: 42 Copynumber: 5.9 Consensus size: 42
16113178 TTTTGTATAA
*
16113188 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
* *
16113230 AAGCACCGCTAAAGAACATGATCTTTAGTGGCGTTTTTCTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT-TTCT
*
16113273 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
16113315 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
16113357 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTTCT
*
16113400 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
16113438 GTTTGTAAAC
Statistics
Matches: 198, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
42 118 0.60
43 80 0.40
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.33
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCT
Found at i:16113313 original size:85 final size:84
Alignment explanation
Indices: 16113188--16113437 Score: 446
Period size: 85 Copynumber: 3.0 Consensus size: 84
16113178 TTTTGTATAA
*
16113188 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCACCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
*
16113253 TTTAGTGGCGTTTTTCTTCT
66 TTTAGCGGCGTTTTT-TTCT
16113273 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
16113338 TTTAGCGGCGTTTTTTTCT
66 TTTAGCGGCGTTTTTTTCT
* *
16113357 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTCTAAGCGCCGCTAAAGAACATGGT
1 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCG-TTTTTTTCTAAGCGCCGCTAAAGAACATGAT
16113422 CTTTAGCGGCGTTTTT
65 CTTTAGCGGCGTTTTT
16113438 GTTTGTAAAC
Statistics
Matches: 160, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
84 36 0.22
85 124 0.77
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.33
Consensus pattern (84 bp):
AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
TTTAGCGGCGTTTTTTTCT
Found at i:16113401 original size:127 final size:127
Alignment explanation
Indices: 16113188--16113437 Score: 464
Period size: 127 Copynumber: 2.0 Consensus size: 127
16113178 TTTTGTATAA
*
16113188 AAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCACCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCACCGCTAAAGAACATGATC
*
16113253 TTTAGTGGCGTTTTTCTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCT
66 TTTAGCGGCGTTTTTCTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCT
*
16113315 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCACCGCTAAAGAACATGATC
*
16113380 TTTAGCGGCGTTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
66 TTTAGCGGCGTTTTTCTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
16113438 GTTTGTAAAC
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 119 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.33
Consensus pattern (127 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCACCGCTAAAGAACATGATC
TTTAGCGGCGTTTTTCTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCT
Found at i:16113508 original size:48 final size:48
Alignment explanation
Indices: 16113449--16113544 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
16113439 TTTGTAAACG
* *
16113449 CTGCAAAAGTTTGCGACGTTTTTGTTAGCGGTATTTTTTGCGGCGCTT
1 CTGCAAAAGTTTGCGACGTTTTCGTTAGCGGCATTTTTTGCGGCGCTT
16113497 CTGCAAAAGTTTGCGACGTTTTCGTTAGCGGCATTTTTTGCGGCGCTT
1 CTGCAAAAGTTTGCGACGTTTTCGTTAGCGGCATTTTTTGCGGCGCTT
16113545 ATGGAAGCGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.40
Consensus pattern (48 bp):
CTGCAAAAGTTTGCGACGTTTTCGTTAGCGGCATTTTTTGCGGCGCTT
Found at i:16116484 original size:3 final size:3
Alignment explanation
Indices: 16116469--16116508 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
16116459 TACTATGACT
* *
16116469 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16116509 CCTTACATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:16129709 original size:21 final size:20
Alignment explanation
Indices: 16129681--16129720 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16129671 ATATTTGTTG
16129681 ATGGTTGTAAAAGGACTTTA
1 ATGGTTGTAAAAGGACTTTA
**
16129701 ATGGATTGTTTAAGGACTTT
1 ATGG-TTGTAAAAGGACTTT
16129721 TATAACTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.40
Consensus pattern (20 bp):
ATGGTTGTAAAAGGACTTTA
Found at i:16139984 original size:18 final size:18
Alignment explanation
Indices: 16139953--16139996 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
16139943 TTGAAAAATG
* * *
16139953 CATAAAAATTAAAATAAA
1 CATAAACATAAAAACAAA
16139971 CATAAACATAAAAACAAA
1 CATAAACATAAAAACAAA
*
16139989 AATAAACA
1 CATAAACA
16139997 CACATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.73, C:0.11, G:0.00, T:0.16
Consensus pattern (18 bp):
CATAAACATAAAAACAAA
Found at i:16145788 original size:8 final size:8
Alignment explanation
Indices: 16145775--16145799 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
16145765 CCTATAACCA
16145775 AAACCCAT
1 AAACCCAT
16145783 AAACCCAT
1 AAACCCAT
16145791 AAACCCAT
1 AAACCCAT
16145799 A
1 A
16145800 CTATGCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.36, G:0.00, T:0.12
Consensus pattern (8 bp):
AAACCCAT
Found at i:16146917 original size:18 final size:19
Alignment explanation
Indices: 16146896--16146935 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
16146886 ATTTTGGAGT
*
16146896 TTTTATAAA-TATTTTAAA
1 TTTTAAAAATTATTTTAAA
16146914 TTTTAAAAATTATTTTAAA
1 TTTTAAAAATTATTTTAAA
16146933 TTT
1 TTT
16146936 CATTTTTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:16150427 original size:21 final size:21
Alignment explanation
Indices: 16150381--16150424 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
16150371 TCCAACATTT
*
16150381 ATTATTATTTAAATATTATTA
1 ATTATTATTTAAATATTAATA
16150402 ATTATTATATTAAA-A-TAATA
1 ATTATTAT-TTAAATATTAATA
16150422 ATT
1 ATT
16150425 TATCATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTATTATTTAAATATTAATA
Found at i:16154074 original size:14 final size:14
Alignment explanation
Indices: 16154055--16154085 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
16154045 CCTGTTGTTG
16154055 TCTCTGGAAATTCT
1 TCTCTGGAAATTCT
16154069 TCTCTGGAAATTCT
1 TCTCTGGAAATTCT
16154083 TCT
1 TCT
16154086 GGCAGTGTGG
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:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (14 bp):
TCTCTGGAAATTCT
Found at i:16157757 original size:3 final size:3
Alignment explanation
Indices: 16157749--16157829 Score: 153
Period size: 3 Copynumber: 26.7 Consensus size: 3
16157739 GTTCAACCTT
16157749 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16157797 TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
16157830 TTCATATATT
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 74 0.96
4 3 0.04
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16158412 original size:131 final size:131
Alignment explanation
Indices: 16158178--16158439 Score: 506
Period size: 131 Copynumber: 2.0 Consensus size: 131
16158168 TAGCAGCAAG
16158178 GGTTCCCAGCACCGCAGTAGTGACGTCCCCTCGCTCTCCCTCTGCGCGTGACGAGCCCTCGTACG
1 GGTTCCCAGCACCGCAGTAGTGACGTCCCCTCGCTCTCCCTCTGCGCGTGACGAGCCCTCGTACG
16158243 CGTGCGCCTTCACCTCCGTACGTGCCACGTCCGCACCTCTGCACACCGTACCTGTAAGAGACGAA
66 CGTGCGCCTTCACCTCCGTACGTGCCACGTCCGCACCTCTGCACACCGTACCTGTAAGAGACGAA
16158308 C
131 C
*
16158309 GGTTCCCAGCACCGCAGTAGTGATGTCCCCTCGCTCTCCCTCTGCGCGTGACGAGCCCTCGTACG
1 GGTTCCCAGCACCGCAGTAGTGACGTCCCCTCGCTCTCCCTCTGCGCGTGACGAGCCCTCGTACG
*
16158374 CGTGCGCCTTCACCTCCGTACGTGCCACGTCCGTACCTCTGCACACCGTACCTGTAAGAGACGAA
66 CGTGCGCCTTCACCTCCGTACGTGCCACGTCCGCACCTCTGCACACCGTACCTGTAAGAGACGAA
16158439 C
131 C
16158440 AAATGAGTAG
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 129 1.00
ACGTcount: A:0.16, C:0.40, G:0.24, T:0.20
Consensus pattern (131 bp):
GGTTCCCAGCACCGCAGTAGTGACGTCCCCTCGCTCTCCCTCTGCGCGTGACGAGCCCTCGTACG
CGTGCGCCTTCACCTCCGTACGTGCCACGTCCGCACCTCTGCACACCGTACCTGTAAGAGACGAA
C
Found at i:16159559 original size:24 final size:23
Alignment explanation
Indices: 16159515--16159559 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
16159505 TATTTTTGGT
*
16159515 ATTTTTATATGTATATATATAGC
1 ATTTTTATATATATATATATAGC
* *
16159538 ATTTTTAGTATATGTATGTATA
1 ATTTTTA-TATATATATATATA
16159560 TATATAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.53
Consensus pattern (23 bp):
ATTTTTATATATATATATATAGC
Found at i:16160968 original size:16 final size:16
Alignment explanation
Indices: 16160947--16161003 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
16160937 TTTGGTTCGC
*
16160947 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
16160963 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
16160979 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
16160995 TGTAATGGA
1 TGTAATGGA
16161004 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:16161272 original size:18 final size:17
Alignment explanation
Indices: 16161250--16161284 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
16161240 TTATTATTAA
*
16161250 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
16161268 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
16161285 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:16161280 original size:28 final size:28
Alignment explanation
Indices: 16161209--16161280 Score: 65
Period size: 28 Copynumber: 2.6 Consensus size: 28
16161199 TATTATCAAT
* *
16161209 AATAAATAATTTAATCATATTTAAAACAT
1 AATATATAATTTAAT-ATATTTAAAACAA
* * * **
16161238 AAT-TATTATTAAATATATTTTAATTAA
1 AATATATAATTTAATATATTTAAAACAA
16161265 AATATATAATTTAATA
1 AATATATAATTTAATA
16161281 AAATTCTTAT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
27 12 0.36
28 18 0.55
29 3 0.09
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (28 bp):
AATATATAATTTAATATATTTAAAACAA
Found at i:16174401 original size:24 final size:23
Alignment explanation
Indices: 16174364--16174411 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
16174354 TGCTCGCCCT
*
16174364 ATTTAAATCCATTAA-ATTATAAA
1 ATTTAAACCCATTAATATT-TAAA
16174387 ATTTAATACCCATTAATATTTAAA
1 ATTTAA-ACCCATTAATATTTAAA
16174411 A
1 A
16174412 CCCTGATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 13 0.59
25 3 0.14
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTTAAACCCATTAATATTTAAA
Found at i:16175774 original size:16 final size:16
Alignment explanation
Indices: 16175753--16175783 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16175743 TTTAAGAAAA
*
16175753 ATTTAATAAACAAATG
1 ATTTAATAAAAAAATG
16175769 ATTTAATAAAAAAAT
1 ATTTAATAAAAAAAT
16175784 TCGAATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (16 bp):
ATTTAATAAAAAAATG
Found at i:16177904 original size:25 final size:24
Alignment explanation
Indices: 16177876--16177940 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
16177866 ATAAGTAAAC
*
16177876 AATTTAATATTATAATTAGAAATAT
1 AATTTAATAATATAATTA-AAATAT
* *
16177901 AATTTAGTAATATATATTATAATAT
1 AATTTAATAATATA-ATTAAAATAT
*
16177926 -ATTTAATAGTATAAT
1 AATTTAATAATATAAT
16177941 ATATTATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.06
24 11 0.32
25 17 0.50
26 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (24 bp):
AATTTAATAATATAATTAAAATAT
Found at i:16180436 original size:2 final size:2
Alignment explanation
Indices: 16180429--16180465 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
16180419 ACAATTATCT
16180429 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16180466 TGCTCCATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16199408 original size:29 final size:30
Alignment explanation
Indices: 16199376--16199434 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
16199366 TAAAATAATC
16199376 ATTTAATATT-ATC-ACTTAATTAAATTAAA
1 ATTTAATATTAATCTA-TTAATTAAATTAAA
* *
16199405 ATTTATTATTAATCTATTAATTAATTTAAA
1 ATTTAATATTAATCTATTAATTAAATTAAA
16199435 TTAATGTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 9 0.35
30 16 0.62
31 1 0.04
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTTAATATTAATCTATTAATTAAATTAAA
Found at i:16202788 original size:47 final size:47
Alignment explanation
Indices: 16202715--16202854 Score: 217
Period size: 47 Copynumber: 2.9 Consensus size: 47
16202705 AACTTTCTGA
* *
16202715 TCCCCTTCACATTTTATAGAACAAAAACTTATCACCACGTCAAGTAATC
1 TCCCCTTGACA-TTT-TACAACAAAAACTTATCACCACGTCAAGTAATC
* * *
16202764 TCCCTTTGACATTTTACAACAAAAACTCATCACCACTTCAAGTAATC
1 TCCCCTTGACATTTTACAACAAAAACTTATCACCACGTCAAGTAATC
16202811 TCCCCTTGACATTTTACAACAAAAACTTATCACCACGTCAAGTA
1 TCCCCTTGACATTTTACAACAAAAACTTATCACCACGTCAAGTA
16202855 GGAGTAAGCA
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
47 71 0.86
48 3 0.04
49 9 0.11
ACGTcount: A:0.36, C:0.29, G:0.06, T:0.29
Consensus pattern (47 bp):
TCCCCTTGACATTTTACAACAAAAACTTATCACCACGTCAAGTAATC
Found at i:16208789 original size:27 final size:27
Alignment explanation
Indices: 16208751--16208802 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
16208741 AGGAAAAATG
16208751 GTTCTTTGGAACTAGAATTAGAAGCCT
1 GTTCTTTGGAACTAGAATTAGAAGCCT
16208778 GTTCTTTGGAACTAGAATTAGAAGC
1 GTTCTTTGGAACTAGAATTAGAAGC
16208803 TAACATAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (27 bp):
GTTCTTTGGAACTAGAATTAGAAGCCT
Found at i:16212401 original size:16 final size:16
Alignment explanation
Indices: 16212382--16212413 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16212372 TCGGTCGGTC
16212382 GGGTAATTCGGTTAAT
1 GGGTAATTCGGTTAAT
16212398 GGGTAATTCGGTTAAT
1 GGGTAATTCGGTTAAT
16212414 TCGATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (16 bp):
GGGTAATTCGGTTAAT
Found at i:16212408 original size:25 final size:25
Alignment explanation
Indices: 16212361--16212422 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
16212351 TAACCGACCG
**
16212361 AATTCGGTTAATCGGTCGGTCGGGT
1 AATTCGGTTAATCGGTAAGTCGGGT
* * *
16212386 AATTCGGTTAATGGGTAATTCGGTT
1 AATTCGGTTAATCGGTAAGTCGGGT
*
16212411 AATTCGATTAAT
1 AATTCGGTTAAT
16212423 TTTTAACCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.37
Consensus pattern (25 bp):
AATTCGGTTAATCGGTAAGTCGGGT
Found at i:16216762 original size:30 final size:31
Alignment explanation
Indices: 16216728--16216787 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
16216718 AAACCTTTTA
*
16216728 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
16216758 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
16216788 TCTCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:16217057 original size:9 final size:9
Alignment explanation
Indices: 16217043--16217080 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
16217033 AATTTCACAT
16217043 TTTATATTA
1 TTTATATTA
16217052 TTTATATTA
1 TTTATATTA
*
16217061 TTTATTTTA
1 TTTATATTA
16217070 TTTATATTA
1 TTTATATTA
16217079 TT
1 TT
16217081 GAATTGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTATATTA
Found at i:16217786 original size:21 final size:20
Alignment explanation
Indices: 16217758--16217796 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
16217748 TTAAAACAAA
16217758 AAATATATATTTTAATTTTT
1 AAATATATATTTTAATTTTT
*
16217778 AAATGATATTTTTTAATTT
1 AAAT-ATATATTTTAATTT
16217797 GTATGACATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
AAATATATATTTTAATTTTT
Found at i:16220565 original size:4 final size:4
Alignment explanation
Indices: 16220556--16220591 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
16220546 TGTCATTATT
*
16220556 TTTA TTTA TTTA TTTA TTTA TTTA TTCA TATTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTT
16220592 CTATGCAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 26 0.90
5 3 0.10
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:16222817 original size:3 final size:3
Alignment explanation
Indices: 16222803--16222887 Score: 152
Period size: 3 Copynumber: 28.0 Consensus size: 3
16222793 TTGCTATTTT
16222803 TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
16222849 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16222888 CATTTCCATT
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
3 76 0.96
4 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:16223087 original size:43 final size:43
Alignment explanation
Indices: 16223018--16223100 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
16223008 CATTTTGATA
16223018 ATATATATACATATGCACGTACATATTTT-TATAATTTATTTAT
1 ATATATATACATATGCAC-TACATATTTTATATAATTTATTTAT
* *
16223061 ATATATGTACATATGCA-TACTTATATTTTATATATTTTAT
1 ATATATATACATATGCACTAC--ATATTTTATATAATTTAT
16223101 AATTTGTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 3 0.09
43 23 0.66
44 9 0.26
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (43 bp):
ATATATATACATATGCACTACATATTTTATATAATTTATTTAT
Found at i:16223168 original size:16 final size:16
Alignment explanation
Indices: 16223149--16223235 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
16223139 TTTATAAACA
16223149 TATATATATACATACT
1 TATATATATACATACT
* **
16223165 TATATATTTTTATACT
1 TATATATATACATACT
* *
16223181 T-TATAATTTTAATATACT
1 TATAT-A-TAT-ACATACT
* *
16223199 TATATACAT--ATACA
1 TATATATATACATACT
*
16223213 TATACATATACATACT
1 TATATATATACATACT
16223229 TATATAT
1 TATATAT
16223236 CTTTTTATAT
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
14 11 0.20
15 3 0.06
16 25 0.46
17 4 0.07
18 8 0.15
19 3 0.06
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATATATACATACT
Found at i:16223202 original size:6 final size:6
Alignment explanation
Indices: 16223200--16223226 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16223190 TAATATACTT
16223200 ATATAC ATATAC ATATAC ATATAC ATA
1 ATATAC ATATAC ATATAC ATATAC ATA
16223227 CTTATATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:16223273 original size:4 final size:4
Alignment explanation
Indices: 16223264--16223288 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
16223254 ATTTTATAAT
16223264 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
16223289 GCTTTCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:16228585 original size:35 final size:36
Alignment explanation
Indices: 16228546--16228620 Score: 89
Period size: 38 Copynumber: 2.1 Consensus size: 36
16228536 AATATTTGAA
*
16228546 CTCTTGTAT-TAGGATCCATTTTGGTAAAGTAGTTG
1 CTCTTGTATCTAGGATCCATTTTGGTAAAGTAATTG
* * *
16228581 CTCTTTTTTCCCTTGGATCCATTTTGGTAAAGTAATTG
1 CTCTTGTAT--CTAGGATCCATTTTGGTAAAGTAATTG
16228619 CT
1 CT
16228621 TTTTTTTCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 7 0.21
38 26 0.79
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (36 bp):
CTCTTGTATCTAGGATCCATTTTGGTAAAGTAATTG
Found at i:16228599 original size:38 final size:38
Alignment explanation
Indices: 16228557--16228632 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
16228547 TCTTGTATTA
*
16228557 GGATCCATTTTGGTAAAGTAGTTGCTCTTTTTTCCCTT
1 GGATCCATTTTGGTAAAGTAATTGCTCTTTTTTCCCTT
*
16228595 GGATCCATTTTGGTAAAGTAATTGCTTTTTTTTCCCTT
1 GGATCCATTTTGGTAAAGTAATTGCTCTTTTTTCCCTT
16228633 TCCTCAACCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (38 bp):
GGATCCATTTTGGTAAAGTAATTGCTCTTTTTTCCCTT
Found at i:16230018 original size:27 final size:27
Alignment explanation
Indices: 16229983--16230060 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 27
16229973 TTATATTAAG
*
16229983 AATTTTATTAAATTATATATATTATTA
1 AATTATATTAAATTATATATATTATTA
*
16230010 AATTATATTTAA-TA-ATA-ATTATGTTA
1 AATTATATTAAATTATATATATTA--TTA
*
16230036 AAATATGATTAAATTAT-T-TATTATT
1 AATTAT-ATTAAATTATATATATTATT
16230061 TATATTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
24 4 0.10
25 3 0.07
26 12 0.29
27 15 0.37
28 7 0.17
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (27 bp):
AATTATATTAAATTATATATATTATTA
Found at i:16230081 original size:44 final size:43
Alignment explanation
Indices: 16229972--16230083 Score: 104
Period size: 44 Copynumber: 2.6 Consensus size: 43
16229962 TATAAGAATA
* * *
16229972 ATTATATTAAGAATTTTATTAAATTATATATATTATTAAATTAT
1 ATTATATTAATAA-TTTATTAAAATATATAAATTATTAAATTAT
* * *
16230016 ATT-TAATAATAATTATGTTAAAATATGATTAAATTATT-TATTAT
1 ATTATATTAATAATT-TATTAAAATAT-A-TAAATTATTAAATTAT
16230060 -TTATATTAATAATCTTATTAAAAT
1 ATTATATTAATAAT-TTATTAAAAT
16230084 TTAATAACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.04
43 18 0.33
44 26 0.47
45 9 0.16
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.51
Consensus pattern (43 bp):
ATTATATTAATAATTTATTAAAATATATAAATTATTAAATTAT
Found at i:16230262 original size:45 final size:44
Alignment explanation
Indices: 16230176--16230268 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
16230166 ATTACAACAT
16230176 CATTCCATCTAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATCTAACCAAACACAAGAATACTATTACAGTTCTATTC
*
16230220 CATTCCAT-TCAACCAAACA-ATTGAATTACTATTACAGTTCTATTC
1 CATTCCATCT-AACCAAACACA-AGAA-TACTATTACAGTTCTATTC
16230265 CATT
1 CATT
16230269 ACAGCTCTAC
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
43 2 0.04
44 20 0.44
45 23 0.51
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (44 bp):
CATTCCATCTAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:16230271 original size:16 final size:16
Alignment explanation
Indices: 16230250--16230305 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
16230240 TTGAATTACT
* *
16230250 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCA
*
16230266 ATTACAGCTCTACTCA
1 ATTACAGCTCTATTCA
16230282 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
16230298 ATTACAGC
1 ATTACAGC
16230306 GAACCAAACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:16230634 original size:28 final size:28
Alignment explanation
Indices: 16230581--16230720 Score: 90
Period size: 29 Copynumber: 5.0 Consensus size: 28
16230571 TAATATTAAA
**
16230581 AAGTTTAAAATAAATAATATGTAAAAAG
1 AAGTTTAAAATAAATAATATACAAAAAG
*
16230609 AAGTTTCAAATAAATAATATAC-AAAA-
1 AAGTTTAAAATAAATAATATACAAAAAG
** * * *
16230635 CTGTTTAAAAATAAATGATATGTATAAAAAC
1 AAGTTT-AAAATAAAT-A-ATATACAAAAAG
* * *
16230666 AA-TTCAAAATAAATAATATATATATAA-
1 AAGTTTAAAATAAATAATATACA-AAAAG
* *
16230693 CAGTTTAAAAATAAATAATATATAAAAA
1 AAGTTT-AAAATAAATAATATACAAAAA
16230721 TGAAAAATAG
Statistics
Matches: 88, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
26 4 0.05
27 19 0.22
28 29 0.33
29 30 0.34
30 6 0.07
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (28 bp):
AAGTTTAAAATAAATAATATACAAAAAG
Found at i:16230650 original size:55 final size:53
Alignment explanation
Indices: 16230493--16230720 Score: 174
Period size: 58 Copynumber: 4.3 Consensus size: 53
16230483 CAATTTAAAG
* * * *
16230493 TAAATAATATGTAAAACA-AATT-AAAATAAACAACATACAAAACAATTT-AAAA
1 TAAATAATATGTAAAAAACAATTCAAAATAAATAATATA-AAAAC-GTTTAAAAA
* * * *
16230545 TAAATAACA--TATAAGACAATTTAAAAT-AAT-AT-TAAAAA-GTTT-AAAA
1 TAAATAATATGTAAAAAACAATTCAAAATAAATAATATAAAAACGTTTAAAAA
*
16230591 TAAATAATATGTAAAAAGA-AGTTTC-AAATAAATAATATACAAAACTGTTTAAAAA
1 TAAATAATATGTAAAAA-ACA-ATTCAAAATAAATAATATA-AAAAC-GTTTAAAAA
*
16230646 TAAATGATATGTATAAAAACAATTCAAAATAAATAATATATATATAACAGTTTAAAAA
1 TAAATAATATGTA-AAAAACAATTCAAAATAAATAATATA-A-A-AAC-GTTTAAAAA
*
16230704 TAAATAATATATAAAAA
1 TAAATAATATGTAAAAA
16230721 TGAAAAATAG
Statistics
Matches: 141, Mismatches: 17, Indels: 31
0.75 0.09 0.16
Matches are distributed among these distances:
46 15 0.11
48 13 0.09
49 8 0.06
50 8 0.06
51 8 0.06
52 17 0.12
54 4 0.03
55 20 0.14
56 20 0.14
57 5 0.04
58 23 0.16
ACGTcount: A:0.61, C:0.06, G:0.04, T:0.29
Consensus pattern (53 bp):
TAAATAATATGTAAAAAACAATTCAAAATAAATAATATAAAAACGTTTAAAAA
Found at i:16230703 original size:29 final size:26
Alignment explanation
Indices: 16230444--16230833 Score: 199
Period size: 26 Copynumber: 15.2 Consensus size: 26
16230434 AAGCGAACCA
* * * *
16230444 AAATAATATATAGAACAATTTGAAGT
1 AAATAATATATAAAACAGTTTAAAAT
* * *
16230470 AAAT-A-GTATAAAACAATTTAAAGT
1 AAATAATATATAAAACAGTTTAAAAT
* **
16230494 AAATAATATGTAAAACAAATTAAAAT
1 AAATAATATATAAAACAGTTTAAAAT
* * * *
16230520 AAACAACATACAAAACAATTTAAAAT
1 AAATAATATATAAAACAGTTTAAAAT
* * *
16230546 AAATAACATATAAGACAATTT---A-
1 AAATAATATATAAAACAGTTTAAAAT
16230568 AAATAATAT-TAAAA-AGTTTAAAAT
1 AAATAATATATAAAACAGTTTAAAAT
* * *
16230592 AAATAATATGTAAAAAGAAGTTTCAAAT
1 AAATAATATAT-AAAA-CAGTTTAAAAT
* *
16230620 AAATAATATACAAAACTGTTTAAAAAT
1 AAATAATATATAAAACAGTTT-AAAAT
* * *
16230647 AAATGATATGTATAAAAACAATTCAAAAT
1 AAAT-A-ATATAT-AAAACAGTTTAAAAT
16230676 AAATAATATATATATAACAGTTTAAAAAT
1 AAATAATATATA-A-AACAGTTT-AAAAT
*
16230705 AAATAATATATAAAA-A---T-GAA-
1 AAATAATATATAAAACAGTTTAAAAT
* * *
16230725 AAATAGT-T-TGAAATAGTTTAAAAT
1 AAATAATATATAAAACAGTTTAAAAT
* * * *
16230749 ACATTATATGTGGAAAAC---TTGAAAT
1 AAATAATATAT--AAAACAGTTTAAAAT
*
16230774 AAATAATA-ATAAAACAATTTAAAAT
1 AAATAATATATAAAACAGTTTAAAAT
*
16230799 AAATAATATATGAGAAAAAGGTTTAAAAT
1 AAATAATATAT-A-AAACA-GTTTAAAAT
16230828 AAATAA
1 AAATAA
16230834 ATGAATAACA
Statistics
Matches: 282, Mismatches: 48, Indels: 65
0.71 0.12 0.16
Matches are distributed among these distances:
18 4 0.01
19 2 0.01
20 10 0.04
21 6 0.02
22 14 0.05
23 5 0.02
24 34 0.12
25 30 0.11
26 71 0.25
27 21 0.07
28 34 0.12
29 44 0.16
30 7 0.02
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (26 bp):
AAATAATATATAAAACAGTTTAAAAT
Found at i:16230788 original size:22 final size:23
Alignment explanation
Indices: 16230762--16230806 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
16230752 TTATATGTGG
*
16230762 AAAAC-TTGAAATAAATAATAAT
1 AAAACATTAAAATAAATAATAAT
16230784 AAAACAATTTAAAATAAATAATA
1 AAAAC-A-TTAAAATAAATAATA
16230807 TATGAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
25 14 0.74
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAACATTAAAATAAATAATAAT
Found at i:16231894 original size:16 final size:16
Alignment explanation
Indices: 16231870--16231907 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
16231860 TTTGGTTCGC
*
16231870 CGTATTGGAATAGAGG
1 CGTAATGGAATAGAGG
16231886 CGTAATGGAATAGAGG
1 CGTAATGGAATAGAGG
16231902 CGTAAT
1 CGTAAT
16231908 AGCAAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.08, G:0.34, T:0.24
Consensus pattern (16 bp):
CGTAATGGAATAGAGG
Found at i:16231951 original size:45 final size:44
Alignment explanation
Indices: 16231887--16231983 Score: 142
Period size: 44 Copynumber: 2.2 Consensus size: 44
16231877 GAATAGAGGC
16231887 GTAATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAAT
* *
16231932 GTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
*
16231976 GGAATGGA
1 GTAATGGA
16231984 GGTGTAATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.50
45 23 0.48
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
Found at i:16232186 original size:18 final size:17
Alignment explanation
Indices: 16232143--16232198 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
16232133 TTATTAAATA
* *
16232143 TAATTTAATAAAAATAT
1 TAATTTAATAAAATTCT
16232160 ATAATTTAATAAAATTCT
1 -TAATTTAATAAAATTCT
16232178 TAATATTAA-AAATATTCT
1 TAAT-TTAATAAA-ATTCT
16232196 TAA
1 TAA
16232199 ATGAATTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.21
18 27 0.79
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATTTAATAAAATTCT
Found at i:16232308 original size:18 final size:18
Alignment explanation
Indices: 16232263--16232308 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
16232253 TATTATTAAA
*
16232263 TATAATTTAATAAAAATG
1 TATAATTTAATAAAAATC
*
16232281 TATAATTTAATAAAATTC
1 TATAATTTAATAAAAATC
16232299 T-TAATATTAA
1 TATAAT-TTAA
16232309 ATATTCTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
TATAATTTAATAAAAATC
Found at i:16232372 original size:120 final size:120
Alignment explanation
Indices: 16232120--16232612 Score: 839
Period size: 120 Copynumber: 4.1 Consensus size: 120
16232110 GTAATCATAT
*
16232120 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
16232185 AAAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 --AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
16232242 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATGTATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
16232307 AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
16232362 TTTAAAATAATAATTATTAAAAATATAATTTAGTAAAAATATATAATTTAATAAAATTCTTTAAT
1 TTTAAAATAATTATTATT--AAATATAATTTAATAAAAATATATAATTTAATAAAATTC-TTAAT
16232427 ATTAAATATTCTT--A-GAATTTACTAAAATCATAATATATAATACTATAAAATATAA
63 ATTAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * * *
16232482 TTTAAATTAATTATTTTTAAATATAATTTAATAAAATTATATAATTTAATAAAATTATTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
16232547 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
16232602 TTTAAAATAAT
1 TTTAAAATAAT
16232613 AAAATTTGAA
Statistics
Matches: 353, Mismatches: 12, Indels: 14
0.93 0.03 0.04
Matches are distributed among these distances:
117 18 0.05
118 36 0.10
119 1 0.00
120 179 0.51
121 1 0.00
122 100 0.28
123 18 0.05
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:16232386 original size:16 final size:16
Alignment explanation
Indices: 16232365--16232409 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
16232355 AATATAATTT
*
16232365 AAAATAATAATTATTA
1 AAAATAATAATTAGTA
16232381 AAAAT-ATAATTTAGTA
1 AAAATAATAA-TTAGTA
16232397 AAAATATATAATT
1 AAAATA-ATAATT
16232410 TAATAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.16
16 15 0.60
17 2 0.08
18 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAATAATAATTAGTA
Found at i:16232405 original size:18 final size:17
Alignment explanation
Indices: 16232380--16232417 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
16232370 AATAATTATT
*
16232380 AAAAATATAATTTAGTA
1 AAAAATATAATTTAATA
16232397 AAAATATATAATTTAATA
1 AAAA-ATATAATTTAATA
16232415 AAA
1 AAA
16232418 TTCTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAAATATAATTTAATA
Found at i:16232525 original size:18 final size:18
Alignment explanation
Indices: 16232502--16232548 Score: 78
Period size: 18 Copynumber: 2.6 Consensus size: 18
16232492 TTATTTTTAA
16232502 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAATT
16232520 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAATT
16232538 AT-TAATATTAA
1 ATATAAT-TTAA
16232549 ATATTCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATAATTTAATAAAATT
Found at i:16232583 original size:59 final size:60
Alignment explanation
Indices: 16232158--16232583 Score: 268
Period size: 57 Copynumber: 7.1 Consensus size: 60
16232148 TAATAAAAAT
* *
16232158 ATATAATTTAATAAAATT-CTTAATATTAAAAATATTCTTAAATGAATTTACTAAAATCATA
1 ATATAATTTAATAAAATTAATTAATATT--AAATATTCTTATATGAATTTACTAAAATCATA
* * * * *
16232219 ATAT-ATAATACTATAAAATATAATTTAA-AATAATTATTATTAAATAT-AATTTAATAAAA--A
1 ATATAAT-TTA--ATAAAAT-TAA-TTAATATTAAATATTCTT--ATATGAATTTACTAAAATCA
16232279 T-
59 TA
* * *
16232280 GTATAATTTAATAAAATT-CTTAATATTAAATATTCTTAAATGAATTTACTAAAATCATA
1 ATATAATTTAATAAAATTAATTAATATTAAATATTCTTATATGAATTTACTAAAATCATA
* * * *** *
16232339 ATAT-ATAATACTATAAAATATAATTTAAAATAATAATTATTAAAAATAT-AATTTAGTAAAA--
1 ATATAAT-TTA--ATAAAAT-TAA-TT--AATATTAAATATT-CTTATATGAATTTACTAAAATC
16232400 AT-
58 ATA
**
16232402 ATATAATTTAATAAAATTCTTTAATATTAAATATTC-T-TA-GAATTTACTAAAATCATA
1 ATATAATTTAATAAAATTAATTAATATTAAATATTCTTATATGAATTTACTAAAATCATA
* * * *
16232459 ATAT-ATAATACTATAAAATATAATTTAA-ATTAATTATTTTTAAATAT-AATTTAATAAAAT--
1 ATATAAT-TTA--ATAAAAT-TAA-TTAATATTAAATATTCTT--ATATGAATTTACTAAAATCA
16232519 T-
59 TA
16232520 ATATAATTTAATAAAATT-ATTAATATTAAATATTCTTATATGAATTTACTAAAATCATA
1 ATATAATTTAATAAAATTAATTAATATTAAATATTCTTATATGAATTTACTAAAATCATA
16232579 ATATA
1 ATATA
16232584 TAATACTATA
Statistics
Matches: 278, Mismatches: 43, Indels: 90
0.68 0.10 0.22
Matches are distributed among these distances:
54 13 0.05
55 7 0.03
56 35 0.13
57 39 0.14
58 7 0.03
59 33 0.12
60 13 0.05
61 36 0.13
62 8 0.03
63 21 0.08
64 32 0.12
65 5 0.02
66 26 0.09
67 3 0.01
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (60 bp):
ATATAATTTAATAAAATTAATTAATATTAAATATTCTTATATGAATTTACTAAAATCATA
Found at i:16232623 original size:59 final size:59
Alignment explanation
Indices: 16232200--16232623 Score: 238
Period size: 59 Copynumber: 7.1 Consensus size: 59
16232190 TATTCTTAAA
*
16232200 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTAT-TAT
1 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATAATAT-T
* * * ** * * * * * * ** **
16232259 TAAATATAATTTAATAAAAATGTATAAT-TTAATAAAATTCTTAATATT-AAATATTCTTAAA
1 TGAATTTACTAAAATCATAATATATAATACT-ATAAAA-T-ATAAT-TTAAAATAATAATATT
16232320 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATAATTATT
1 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATAA-TATT
** * * ** * * * * * * *
16232380 AAAAATATAATTTAGTAAAAATATATAAT-TTAATAAAAT-T-CTTTAATATTA-AATATTCT
1 -TGAATTTACTAAAATCATAATATATAATACT-ATAAAATATAATTTAAAATAATAATA-T-T
* * *
16232439 TAGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAATTAATTATTTT
1 T-GAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATAATATT
* * * ** * * * ** *
16232499 TAAATATAATTTAAT-AAAATTATATAAT-TTAATAAAATTATTAATATT-AAATATTCTTATA
1 TGAATTTACTAAAATCATAA-TATATAATACT-ATAAAA-TA-TAAT-TTAAAATAATAATATT
*
16232560 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATAAAATT
1 TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATAATATT
16232619 TGAAT
1 TGAAT
16232624 CGATTAAATG
Statistics
Matches: 256, Mismatches: 84, Indels: 50
0.66 0.22 0.13
Matches are distributed among these distances:
57 2 0.01
58 12 0.05
59 111 0.43
60 14 0.05
61 106 0.41
62 11 0.04
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (59 bp):
TGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATAATATT
Found at i:16232657 original size:20 final size:20
Alignment explanation
Indices: 16232610--16232648 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16232600 AATTTAAAAT
*
16232610 AATAAAATTTGAATCGATTA
1 AATAATATTTGAATCGATTA
* *
16232630 AATGATATTTGAATTGATT
1 AATAATATTTGAATCGATT
16232649 TGATAATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (20 bp):
AATAATATTTGAATCGATTA
Found at i:16235714 original size:14 final size:14
Alignment explanation
Indices: 16235695--16235724 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
16235685 AGGGCAAATC
16235695 GGCAGAAGGTAGAA
1 GGCAGAAGGTAGAA
16235709 GGCAGAAGGTAGAA
1 GGCAGAAGGTAGAA
16235723 GG
1 GG
16235725 AAGGGAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.47, T:0.07
Consensus pattern (14 bp):
GGCAGAAGGTAGAA
Found at i:16237695 original size:15 final size:17
Alignment explanation
Indices: 16237667--16237701 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
16237657 AAAATAGTAG
16237667 ATAAAATAATATTTTAA
1 ATAAAATAATATTTTAA
16237684 ATAAAAT-A-ATTTTAA
1 ATAAAATAATATTTTAA
16237699 ATA
1 ATA
16237702 TAGTTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 1 0.06
17 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAAATAATATTTTAA
Found at i:16239258 original size:2 final size:2
Alignment explanation
Indices: 16239251--16239276 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16239241 CATTACTAGC
16239251 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
16239277 TCTTAAGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16246788 original size:27 final size:27
Alignment explanation
Indices: 16246758--16246824 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
16246748 CCTATCAGGT
16246758 AGGCGCCAATGAAGGTGCCTCACAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
*
16246785 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
16246812 AGGCGCCAATGAA
1 AGGCGCCAATGAA
16246825 TATTGTAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.31, C:0.24, G:0.33, T:0.12
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCACAGAG
Found at i:16246923 original size:21 final size:22
Alignment explanation
Indices: 16246892--16246943 Score: 88
Period size: 21 Copynumber: 2.4 Consensus size: 22
16246882 TTTGGATTAG
*
16246892 TATTTTGTATGAATATTGTAAT
1 TATTTTATATGAATATTGTAAT
16246914 T-TTTTATATGAATATTGTAAT
1 TATTTTATATGAATATTGTAAT
16246935 TATTTTATA
1 TATTTTATA
16246944 ATTAAATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 20 0.71
22 8 0.29
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.58
Consensus pattern (22 bp):
TATTTTATATGAATATTGTAAT
Found at i:16246954 original size:23 final size:22
Alignment explanation
Indices: 16246892--16246960 Score: 70
Period size: 21 Copynumber: 3.1 Consensus size: 22
16246882 TTTGGATTAG
* *
16246892 TATTTTGTATGAATATTGTAAT
1 TATTTTATATAAATATTGTAAT
*
16246914 T-TTTTATATGAATATTGTAAT
1 TATTTTATATAAATATTGTAAT
*
16246935 TATTTTATAATTAAAT-TTGTATT
1 TATTTTAT-A-TAAATATTGTAAT
16246958 TAT
1 TAT
16246961 AGTTTTGGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 20 0.49
22 7 0.17
23 10 0.24
24 4 0.10
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (22 bp):
TATTTTATATAAATATTGTAAT
Found at i:16246955 original size:82 final size:82
Alignment explanation
Indices: 16246820--16247017 Score: 364
Period size: 82 Copynumber: 2.4 Consensus size: 82
16246810 AGAGGCGCCA
*
16246820 ATGAATATTGTAATTTTGTAT-T-AATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTT
1 ATGAATATTGTAATTTTTTATATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTT
*
16246883 TTGGATTAGTATTTTGT
66 TTGGATTAATATTTTGT
16246900 ATGAATATTGTAATTTTTTATATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTT
1 ATGAATATTGTAATTTTTTATATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTT
16246965 TTGGATTAATATTTTGT
66 TTGGATTAATATTTTGT
16246982 ATGAATATTGTAATTTTTTATATGAATATTGTAATT
1 ATGAATATTGTAATTTTTTATATGAATATTGTAATT
16247018 TTGTGTTTGT
Statistics
Matches: 114, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
80 20 0.18
81 1 0.01
82 93 0.82
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (82 bp):
ATGAATATTGTAATTTTTTATATGAATATTGTAATTATTTTATAATTAAATTTGTATTTATAGTT
TTGGATTAATATTTTGT
Found at i:16247000 original size:21 final size:21
Alignment explanation
Indices: 16246971--16247038 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
16246961 AGTTTTGGAT
*
16246971 TAATATTTTGTATGAATATTG
1 TAATTTTTTGTATGAATATTG
*
16246992 TAATTTTTTATATGAATATTG
1 TAATTTTTTGTATGAATATTG
* * *
16247013 TAATTTTGTGTTTGTAATTTTG
1 TAATTTTTTGTATG-AATATTG
16247035 TAAT
1 TAAT
16247039 CAAAAAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
21 30 0.75
22 10 0.25
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.57
Consensus pattern (21 bp):
TAATTTTTTGTATGAATATTG
Found at i:16247153 original size:16 final size:16
Alignment explanation
Indices: 16247110--16247153 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
16247100 AAAATCAAAT
*
16247110 AAAATTTAATTATATA
1 AAAATTAAATTATATA
* *
16247126 AAAGTTACATTATATA
1 AAAATTAAATTATATA
16247142 AAAATTAAATTA
1 AAAATTAAATTA
16247154 GTTAACAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAATTAAATTATATA
Found at i:16247229 original size:38 final size:38
Alignment explanation
Indices: 16247186--16247267 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
16247176 AAAAAGTCAG
16247186 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
*
16247224 TTATAATTAAACTTTTAATAAGATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
16247262 TTATAA
1 TTATAA
16247268 ACTTTATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:16247520 original size:19 final size:19
Alignment explanation
Indices: 16247496--16247630 Score: 98
Period size: 19 Copynumber: 6.8 Consensus size: 19
16247486 NNNNNNNNNN
16247496 AATTACAATATTCATAAAA
1 AATTACAATATTCATAAAA
16247515 AATTACAATATTCATATAAAA
1 AATTACAATATTC--ATAAAA
*
16247536 AATTACAATATTCATACAA
1 AATTACAATATTCATAAAA
* *
16247555 AA-TACTA-ATCCA-AAACTA
1 AATTACAATATTCATAAA--A
*
16247573 TAAATACAAATTTAATT-ATAAAA
1 -AATTAC-AA--T-ATTCATAAAA
* *
16247596 TAATTACAATATTAATACAA
1 -AATTACAATATTCATAAAA
16247616 AATTACAATATTCAT
1 AATTACAATATTCAT
16247631 TGGCGCCTCT
Statistics
Matches: 94, Mismatches: 9, Indels: 26
0.73 0.07 0.20
Matches are distributed among these distances:
16 2 0.02
17 4 0.04
18 5 0.05
19 39 0.41
20 9 0.10
21 20 0.21
22 2 0.02
23 7 0.07
24 1 0.01
25 5 0.05
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTACAATATTCATAAAA
Found at i:16247535 original size:21 final size:21
Alignment explanation
Indices: 16247496--16247556 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
16247486 NNNNNNNNNN
16247496 AATTACAATATTC--ATAAAA
1 AATTACAATATTCATATAAAA
16247515 AATTACAATATTCATATAAAA
1 AATTACAATATTCATATAAAA
*
16247536 AATTACAATATTCATACAAAA
1 AATTACAATATTCATATAAAA
16247557 TACTAATCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 13 0.33
21 26 0.67
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (21 bp):
AATTACAATATTCATATAAAA
Found at i:16247664 original size:27 final size:27
Alignment explanation
Indices: 16247626--16247692 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
16247616 AATTACAATA
16247626 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
*
16247653 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
16247680 TTCATTGGCGCCT
1 TTCATTGGCGCCT
16247693 ACCTGATAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.12, C:0.33, G:0.24, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:16247759 original size:11 final size:11
Alignment explanation
Indices: 16247743--16247785 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
16247733 TCGTATTTTT
16247743 TTAAAAAATTA
1 TTAAAAAATTA
*
16247754 TTAAAAAAATA
1 TTAAAAAATTA
*
16247765 TAAAAAAATTTA
1 TTAAAAAA-TTA
16247777 TTCAAAAAA
1 TT-AAAAAA
16247786 AAATATTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 17 0.65
12 3 0.12
13 6 0.23
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (11 bp):
TTAAAAAATTA
Found at i:16247760 original size:12 final size:12
Alignment explanation
Indices: 16247745--16247786 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 12
16247735 GTATTTTTTT
16247745 AAAAAATTATTA
1 AAAAAATTATTA
16247757 AAAAAA-TA-TA
1 AAAAAATTATTA
16247767 AAAAAATTTATTCA
1 AAAAAA-TTATT-A
16247781 AAAAAA
1 AAAAAA
16247787 AATATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 8 0.31
11 2 0.08
12 8 0.31
13 1 0.04
14 7 0.27
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAAATTATTA
Found at i:16250234 original size:5 final size:5
Alignment explanation
Indices: 16250224--16250249 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16250214 GAACAAATAT
16250224 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
16250250 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:16250349 original size:5 final size:5
Alignment explanation
Indices: 16250339--16250384 Score: 92
Period size: 5 Copynumber: 9.2 Consensus size: 5
16250329 CTCGAAAATT
16250339 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
16250385 CGAATGCTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (5 bp):
TTCGA
Found at i:16257925 original size:33 final size:29
Alignment explanation
Indices: 16257883--16257946 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
16257873 TGAATTTTCA
16257883 AATAATTATAAAAATATATATTTAAAAATAATT
1 AATAATTATAAAAA-AT-TA--TAAAAATAATT
*
16257916 AATAATTATAATAAATTATAAAAATAATT
1 AATAATTATAAAAAATTATAAAAATAATT
16257945 AA
1 AA
16257947 AAACAACTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 13 0.43
31 2 0.07
32 2 0.07
33 13 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AATAATTATAAAAAATTATAAAAATAATT
Found at i:16257936 original size:16 final size:15
Alignment explanation
Indices: 16257884--16257936 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 15
16257874 GAATTTTCAA
16257884 ATAATTATAAAAATAT
1 ATAATTATAAAAAT-T
* *
16257900 ATATTTAAAAATAATT
1 ATAATTATAAA-AATT
16257916 AATAATTATAATAAATT
1 -ATAATTATAA-AAATT
16257933 ATAA
1 ATAA
16257937 AAATAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 14 0.47
17 15 0.50
18 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATTATAAAAATT
Found at i:16258034 original size:24 final size:23
Alignment explanation
Indices: 16257992--16258036 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
16257982 TAATAATTAT
16257992 AAATATAATAATAAAATTTTTAA
1 AAATATAATAATAAAATTTTTAA
* *
16258015 AAATATTAATAATTATATTTTT
1 AAATA-TAATAATAAAATTTTT
16258037 TTAATTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AAATATAATAATAAAATTTTTAA
Found at i:16259143 original size:22 final size:22
Alignment explanation
Indices: 16259115--16259242 Score: 184
Period size: 22 Copynumber: 5.8 Consensus size: 22
16259105 ATAGCATCAT
16259115 TACTAAGCTCTCATGTTTAACG
1 TACTAAGCTCTCATGTTTAACG
16259137 TACTAAGCTCTCATGTTTAACG
1 TACTAAGCTCTCATGTTTAACG
* * * **
16259159 AACTAAACCCTCATGGCTAACG
1 TACTAAGCTCTCATGTTTAACG
**
16259181 TACTAAGCTCTCATGGCTAACG
1 TACTAAGCTCTCATGTTTAACG
*
16259203 TACTAAGCTCTCATGTTTCACG
1 TACTAAGCTCTCATGTTTAACG
16259225 TACTAAGCTCTCATGTTT
1 TACTAAGCTCTCATGTTT
16259243 GAACAATAAA
Statistics
Matches: 95, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 95 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
TACTAAGCTCTCATGTTTAACG
Found at i:16275932 original size:3 final size:3
Alignment explanation
Indices: 16275924--16275949 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16275914 TTCTATTTCA
16275924 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
16275950 AGGTACATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16277025 original size:24 final size:23
Alignment explanation
Indices: 16276981--16277025 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
16276971 GTTTTATGGC
*
16276981 TTTTAGGGTTTAGGGTGCAGGCT
1 TTTTAGGGTTTAGGGTCCAGGCT
16277004 TTTTAGGAG-TTAGGGGTCCAGG
1 TTTTAGG-GTTTA-GGGTCCAGG
16277026 AAAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.16, C:0.09, G:0.40, T:0.36
Consensus pattern (23 bp):
TTTTAGGGTTTAGGGTCCAGGCT
Found at i:16277194 original size:123 final size:124
Alignment explanation
Indices: 16277067--16277321 Score: 363
Period size: 123 Copynumber: 2.1 Consensus size: 124
16277057 AAATAGTGGG
** * * * *
16277067 AAATCGCTTCTACTAGGATGCTATTTAAGAAGAAATTGTGAAATAGTGGCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
*
16277132 TCGCTACAG-TGGTCATGT-GAGAAATAA-TTTTTTTGACGTTTTCTGAGGAAATAGTATA
66 TCGCTACAGTTGGTCATGTAG-GAAATAATTTTTTTTGACG-TTTCTGAGCAAATAGTATA
* *
16277190 AAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGTGAAATCGCGCCCTCGTGGACGCGATT
1 AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
* *
16277255 TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTGTC
66 TCGCTACAGTTGGTCATGTAGGAAATAA-TTTTTTTTGACGTTTCTGAGCAAATAGTATA
16277315 AAATCGC
1 AAATCGC
16277322 GCCCTCGTGG
Statistics
Matches: 117, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
123 66 0.56
124 16 0.14
125 24 0.21
126 11 0.09
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (124 bp):
AAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTGAAATAGCGCCCTCGTGGACGCGATT
TCGCTACAGTTGGTCATGTAGGAAATAATTTTTTTTGACGTTTCTGAGCAAATAGTATA
Found at i:16279785 original size:22 final size:22
Alignment explanation
Indices: 16279757--16279857 Score: 116
Period size: 22 Copynumber: 4.5 Consensus size: 22
16279747 NNNNNNNNNN
16279757 GGAAGGAATTTGAGAG-AATTTT
1 GGAAGGAA-TTGAGAGAAATTTT
*
16279779 GGAAGGAAATTGATAGAAATTTT
1 GGAAGG-AATTGAGAGAAATTTT
16279802 -GAAGGGAATTGAGAGAAATTTT
1 GGAA-GGAATTGAGAGAAATTTT
* *
16279824 GAAAGGAATTGAGAGAATTTTT
1 GGAAGGAATTGAGAGAAATTTT
* *
16279846 GAAAGAAATTGA
1 GGAAGGAATTGA
16279858 TATTGAATTT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
22 58 0.83
23 12 0.17
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (22 bp):
GGAAGGAATTGAGAGAAATTTT
Found at i:16279834 original size:44 final size:44
Alignment explanation
Indices: 16279759--16279857 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
16279749 NNNNNNNNGG
* *
16279759 AAGGAATTTGAGAGAATTTTGGAAGGAAATTGATAGAAATTTTGA
1 AAGGAA-TTGAGAGAATTTTGAAAGGAAATTGAGAGAAATTTTGA
* *
16279804 AGGGAATTGAGAGAAATTTTGAAAGG-AATTGAGAGAATTTTTGA
1 AAGGAATTGAGAG-AATTTTGAAAGGAAATTGAGAGAAATTTTGA
*
16279848 AAGAAATTGA
1 AAGGAATTGA
16279858 TATTGAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 31 0.66
45 16 0.34
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.29
Consensus pattern (44 bp):
AAGGAATTGAGAGAATTTTGAAAGGAAATTGAGAGAAATTTTGA
Found at i:16289225 original size:20 final size:20
Alignment explanation
Indices: 16289202--16289241 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16289192 GAATTCAACA
*
16289202 AAAAAATATAAAACTATTTT
1 AAAAAATATAAAAATATTTT
*
16289222 AAAAACTATAAAAATATTTT
1 AAAAAATATAAAAATATTTT
16289242 TTTAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAATATAAAAATATTTT
Found at i:16289851 original size:17 final size:18
Alignment explanation
Indices: 16289829--16289862 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16289819 ACTAAATACT
*
16289829 AATTAA-ATTTTACATAA
1 AATTAATATTTAACATAA
16289846 AATTAATATTTAACATA
1 AATTAATATTTAACATA
16289863 TAAAATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTAATATTTAACATAA
Found at i:16290547 original size:15 final size:15
Alignment explanation
Indices: 16290527--16290561 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16290517 TGTAAACCCA
*
16290527 AACTACACCTAGCCC
1 AACTACACCAAGCCC
16290542 AACTACACCAAGCCC
1 AACTACACCAAGCCC
*
16290557 GACTA
1 AACTA
16290562 GCCTAAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.43, G:0.09, T:0.11
Consensus pattern (15 bp):
AACTACACCAAGCCC
Found at i:16303282 original size:45 final size:46
Alignment explanation
Indices: 16303196--16303290 Score: 140
Period size: 45 Copynumber: 2.1 Consensus size: 46
16303186 TGTAGATTTA
16303196 AAATTTTAAAAACTCTTCATGAAGATTAAAATTTTTAAGGCACAAC
1 AAATTTTAAAAACTCTTCATGAAGATTAAAATTTTTAAGGCACAAC
* * *
16303242 AAATTTTGAAAACTCTTGATG-AGATT-AAATTTTATAAGGCACAGC
1 AAATTTTAAAAACTCTTCATGAAGATTAAAATTTT-TAAGGCACAAC
16303287 AAAT
1 AAAT
16303291 GTAAATGTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 7 0.16
45 19 0.42
46 19 0.42
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (46 bp):
AAATTTTAAAAACTCTTCATGAAGATTAAAATTTTTAAGGCACAAC
Found at i:16305371 original size:7 final size:7
Alignment explanation
Indices: 16305359--16305390 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
16305349 TACTATCTAA
16305359 CTAAAAT
1 CTAAAAT
16305366 CTAAAAT
1 CTAAAAT
16305373 CTAAAAT
1 CTAAAAT
16305380 CTAAAAT
1 CTAAAAT
16305387 CTAA
1 CTAA
16305391 TTACTAAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
CTAAAAT
Found at i:16308200 original size:30 final size:29
Alignment explanation
Indices: 16308143--16308200 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
16308133 CTCCAATTTC
16308143 ACCAGCAGAGGGGAAAGAAAATTTGGGGA
1 ACCAGCAGAGGGGAAAGAAAATTTGGGGA
16308172 ACCAGCAGAGGGGAAA-AAAACGTTTGGGG
1 ACCAGCAGAGGGGAAAGAAAA--TTTGGGG
16308201 TAGAATTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 16 0.59
30 7 0.26
ACGTcount: A:0.40, C:0.12, G:0.38, T:0.10
Consensus pattern (29 bp):
ACCAGCAGAGGGGAAAGAAAATTTGGGGA
Found at i:16309941 original size:16 final size:16
Alignment explanation
Indices: 16309920--16309955 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
16309910 CGAATTTTCT
16309920 TTTTG-AAACACGAAAA
1 TTTTGAAAACAC-AAAA
16309936 TTTTGAAAACACAAAA
1 TTTTGAAAACACAAAA
16309952 TTTT
1 TTTT
16309956 ATTTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.33
Consensus pattern (16 bp):
TTTTGAAAACACAAAA
Found at i:16310045 original size:18 final size:17
Alignment explanation
Indices: 16310003--16310116 Score: 84
Period size: 17 Copynumber: 6.3 Consensus size: 17
16309993 ATAAGATTTT
16310003 TTTTTGAAACACGGAAA
1 TTTTTGAAACACGGAAA
* *
16310020 TTTATGAAACACGGTCAA
1 TTTTTGAAACACGG-AAA
*
16310038 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGGAAA
* **
16310056 TTTTTGAAAGACGGGATTTTT
1 TTTTTGAAACAC-GGA---AA
*
16310077 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGGAAA
* *
16310095 TTTATAAAACACGGAAA
1 TTTTTGAAACACGGAAA
16310112 TTTTT
1 TTTTT
16310117 TTCTGAAAAC
Statistics
Matches: 73, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
17 32 0.44
18 21 0.29
19 7 0.10
21 8 0.11
22 5 0.07
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (17 bp):
TTTTTGAAACACGGAAA
Found at i:16310092 original size:39 final size:39
Alignment explanation
Indices: 16309998--16310142 Score: 138
Period size: 39 Copynumber: 3.8 Consensus size: 39
16309988 GAAACATAAG
* * * *
16309998 ATTTTTTTTTG-AAACACGGAAATTTATGAAACACGGTCA
1 ATTTTTTTTTGAAAACACGAAAATTTTTAAAACACGG-AA
* * *
16310037 A----TTTTTGAAAACACGAAAATTTTTGAAAGACGGGA
1 ATTTTTTTTTGAAAACACGAAAATTTTTAAAACACGGAA
* *
16310072 TTTTTTTTTTGAAAACACGAAAATTTATAAAACACGGAA
1 ATTTTTTTTTGAAAACACGAAAATTTTTAAAACACGGAA
* * *
16310111 ATTTTTTTCTGAAAACAAGAAAATTTTCAAAA
1 ATTTTTTTTTGAAAACACGAAAATTTTTAAAA
16310143 AACGAGAATG
Statistics
Matches: 87, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
35 7 0.08
36 22 0.25
39 58 0.67
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (39 bp):
ATTTTTTTTTGAAAACACGAAAATTTTTAAAACACGGAA
Found at i:16310190 original size:18 final size:18
Alignment explanation
Indices: 16310003--16310292 Score: 137
Period size: 18 Copynumber: 16.0 Consensus size: 18
16309993 ATAAGATTTT
*
16310003 TTTTTG-AAACACGGAAA
1 TTTTTGAAAACACGAAAA
* **
16310020 TTTATG-AAACACGGTCAA
1 TTTTTGAAAACAC-GAAAA
16310038 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
** ***
16310056 TTTTTGAAAGACGGGATTTTT
1 TTTTTGAAA-ACACGA--AAA
16310077 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
16310095 TTTAT-AAAACACGGAAATTT
1 TTTTTGAAAACAC-GAAA--A
*
16310115 TTTTCTGAAAACAAGAAAA
1 TTTT-TGAAAACACGAAAA
* * *
16310134 -TTTTCAAAAAACGAGAA
1 TTTTTGAAAACACGAAAA
* * *
16310151 TGTTTGAAAATACGGGAAA
1 TTTTTGAAAACAC-GAAAA
*
16310170 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
** * *
16310188 TTTTTG-TTACACTAGAA
1 TTTTTGAAAACACGAAAA
*
16310205 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
* **
16310222 TTTTTG-AAACATGAGGA
1 TTTTTGAAAACACGAAAA
**
16310239 TTTTTGAAAACACGAAGC
1 TTTTTGAAAACACGAAAA
* *
16310257 TTTTTG-AAACATGAGAAT
1 TTTTTGAAAACACGA-AAA
* *
16310275 TTTTTGAGAACATGAAAA
1 TTTTTGAAAACACGAAAA
16310293 CACGAAAATT
Statistics
Matches: 202, Mismatches: 54, Indels: 33
0.70 0.19 0.11
Matches are distributed among these distances:
16 5 0.02
17 62 0.31
18 78 0.39
19 30 0.15
20 7 0.03
21 14 0.07
22 6 0.03
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:16310207 original size:35 final size:35
Alignment explanation
Indices: 16310168--16310292 Score: 137
Period size: 35 Copynumber: 3.6 Consensus size: 35
16310158 AAATACGGGA
* **
16310168 AATTTTTGAAAACATGAAAATTTTTGTTACACT-AG
1 AATTTTTGAAAACACGAAAATTTTTGAAACA-TGAG
*
16310203 AA-TTTTGAAAACACGAAGATTTTTGAAACATGAG
1 AATTTTTGAAAACACGAAAATTTTTGAAACATGAG
* **
16310237 GATTTTTGAAAACACGAAGCTTTTTGAAACATGAG
1 AATTTTTGAAAACACGAAAATTTTTGAAACATGAG
* *
16310272 AATTTTTTGAGAACATGAAAA
1 AA-TTTTTGAAAACACGAAAA
16310293 CACGAAAATT
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
33 1 0.01
34 27 0.36
35 34 0.45
36 14 0.18
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.34
Consensus pattern (35 bp):
AATTTTTGAAAACACGAAAATTTTTGAAACATGAG
Found at i:16310311 original size:44 final size:44
Alignment explanation
Indices: 16310243--16310330 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
16310233 TGAGGATTTT
** * * * *
16310243 TGAAAACACGAAGCTTTTTGAAACATGAGAATTTTTTGAGAACA
1 TGAAAACACGAAAATTTGTCAAACACGAGAATTTTTTGAAAACA
16310287 TGAAAACACGAAAATTTGTCAAACACGAGAATTTTTTGAAAACA
1 TGAAAACACGAAAATTTGTCAAACACGAGAATTTTTTGAAAACA
16310331 CGATAACATC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.27
Consensus pattern (44 bp):
TGAAAACACGAAAATTTGTCAAACACGAGAATTTTTTGAAAACA
Found at i:16310429 original size:18 final size:17
Alignment explanation
Indices: 16310406--16310455 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
16310396 AAGTGAAGAT
16310406 TTTTTGAAATACGAGAAA
1 TTTTTGAAATACGA-AAA
*
16310424 TTTTTGAAGATATGAAAA
1 TTTTTGAA-ATACGAAAA
*
16310442 TTTTTGAAACACGA
1 TTTTTGAAATACGA
16310456 TTTTTCTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 19 0.68
19 5 0.18
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (17 bp):
TTTTTGAAATACGAAAA
Found at i:16311255 original size:7 final size:6
Alignment explanation
Indices: 16311246--16311324 Score: 77
Period size: 6 Copynumber: 12.3 Consensus size: 6
16311236 CTTTTAATTT
* **
16311246 TTTTTC TTTTTC TTTCTC TTTTTC TTTTTTC TTTTTC TTCTCCC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TT-TTTC TTTTTC
*
16311296 TTCTTC TTTTTTC TTTCTTC TTTCTTC TT
1 TTTTTC -TTTTTC TTT-TTC TTT-TTC TT
16311325 CTTCGGGCCG
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
6 34 0.56
7 27 0.44
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:16311278 original size:13 final size:13
Alignment explanation
Indices: 16311245--16311324 Score: 74
Period size: 13 Copynumber: 6.2 Consensus size: 13
16311235 ACTTTTAATT
16311245 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
*
16311258 -TTTCTCTTTTTC
1 TTTTTTCTTTTTC
16311270 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
* **
16311283 TTCTCCCTTTTTC
1 TTTTTTCTTTTTC
*
16311296 -TTCTTCTTTTTTC
1 TTTTTTC-TTTTTC
*
16311309 TTTCTTCTTTCTTC
1 TTTTTTCTTT-TTC
16311323 TT
1 TT
16311325 CTTCGGGCCG
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
12 13 0.24
13 30 0.56
14 11 0.20
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:16311487 original size:19 final size:17
Alignment explanation
Indices: 16311465--16311503 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
16311455 TTTTCTTGTT
16311465 TTTTGCTGCTGCGTTTTTG
1 TTTTGCTGCT-C-TTTTTG
*
16311484 TTTTGCTTCTCTTTTTG
1 TTTTGCTGCTCTTTTTG
16311501 TTT
1 TTT
16311504 CAATTTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 1 0.05
19 9 0.47
ACGTcount: A:0.00, C:0.15, G:0.18, T:0.67
Consensus pattern (17 bp):
TTTTGCTGCTCTTTTTG
Done.