Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 75 of 144
Found at i:16501569 original size:801 final size:800
Alignment explanation
Indices: 16500029--16501633 Score: 3102
Period size: 801 Copynumber: 2.0 Consensus size: 800
16500019 ACTATACAAG
16500029 GGGTGATTAGTTTCATTTTAGCTTATCAATCAGAAATCACACTCTTATATTTGAATCTAAAGTGT
1 GGGTGATTAGTTTCATTTTAGCTTATCAATCAGAAATCACACTCTTATATTTGAATCTAAAGTGT
16500094 AGATCTGAGGTAGAGAAAGCCCGATGGAAGGCTCCTGAACCAAAGACATTCAAAGCAAACTTTGA
66 AGATCTGAGGTAGAGAAAGCCCGATGGAAGGCTCCTGAACCAAAGACATTCAAAGCAAACTTTGA
16500159 TGCCTCTTTTCTTCTACAGTTACAAACAACAATAGCGGGGGCTATAATACGTAATAGTTCAGGCA
131 TGCCTCTTTTCTTCTACAGTTACAAACAACAATAGCGGGGGCTATAATACGTAATAGTTCAGGCA
16500224 TGATGATGGGTTCAAGTGTGTACCCGTTTACTAGAGTGAAAGACCCAACCACTCTGAGGCTCTTG
196 TGATGATGGGTTCAAGTGTGTACCCGTTTACTAGAGTGAAAGACCCAACCACTCTGAGGCTCTTG
16500289 CTTGTCTGGAAACGGTACGATTTGCGACGGATCTGGGCTTTAGAGACGTCTACATAGAGGGAGAT
261 CTTGTCTGGAAACGGTACGATTTGCGACGGATCTGGGCTTTAGAGACGTCTACATAGAGGGAGAT
16500354 GCGTTAATAGTCATTAAGAACTCAAGTCGGAAGAGTTGGACATATCGTCAATCAGTAAAATCATT
326 GCGTTAATAGTCATTAAGAACTCAAGTCGGAAGAGTTGGACATATCGTCAATCAGTAAAATCATT
16500419 GATGAAATATGCATTCATAAGCAAAGGTTTAGAAACTTATCTTTTCACTTTCTCCGTAGATCTGC
391 GATGAAATATGCATTCATAAGCAAAGGTTTAGAAACTTATCTTTTCACTTTCTCCGTAGATCTGC
16500484 GAACAAAGCTGCCCACCAACTTGCTATCTAGGTCGACGGGTCGATGCTCCAAGGTTCTGGGTCGA
456 GAACAAAGCTGCCCACCAACTTGCTATCTAGGTCGACGGGTCGATGCTCCAAGGTTCTGGGTCGA
*
16500549 AGAGGCCCCGTCGGTTCTCGATCACGTCTTAGTCGTTGATAGGCAAGAAATAATAGGGTAGAAAG
521 AGAGGCCCCGTCGATTCTCGATCACGTCTTAGTCGTTGATAGGCAAGAAATAATAGGGTAGAAAG
16500614 TGTGTTTTTAGTTGTTGAGACAGGAGGAATATCTATGAAGGAAATCCTCCGATGGATCTCAGTCA
586 TGTGTTTTTAGTTGTTGAGACAGGAGGAATATCTATGAAGGAAATCCTCCGATGGATCTCAGTCA
*
16500679 GGCGTGGAACTGGCTTCGAACATGGTACCTAGAAAACGATCGGAAGTAATGGTGCCCAGAGGCAC
651 GGCGTGGAACTGGCTTCGAACATGGTACCTAGAAAACGATCGGAAGTAATGGTACCCAGAGGCAC
16500744 ACGAATTTGTTATCTGATGAAGGAAGGGCGTTTGGGCATCTGGAAGGGTGAAAGTTTTTCTTTTC
716 ACGAATTTGTTATCTGATGAAGGAAGGGCGTTTGGGCATCTGGAAGGGTGAAAGTTTTTCTTTTC
16500809 TTTACTTTTCTTAAGAAGAT
781 TTTACTTTTCTTAAGAAGAT
16500829 GGGTGATTAGTTTCATTTTAGCTTATCAATCAGAAATCACACTCTTATATTTGAATCTAAAGTGT
1 GGGTGATTAGTTTCATTTTAGCTTATCAATCAGAAATCACACTCTTATATTTGAATCTAAAGTGT
* *
16500894 AGATTTGAGGTAGAGGAAGCCCGATGGAAGGCTCCTGAACCAAAGACATTCAAAGCAAACTTTGA
66 AGATCTGAGGTAGAGAAAGCCCGATGGAAGGCTCCTGAACCAAAGACATTCAAAGCAAACTTTGA
* *
16500959 TGCCTCTTTTCTTCTACAGTTACAAATAACAATAGCGGGGGCTATAGTACGTAATAGTTCAGGCA
131 TGCCTCTTTTCTTCTACAGTTACAAACAACAATAGCGGGGGCTATAATACGTAATAGTTCAGGCA
16501024 TGATGATGGGTTCAAGTGTGTACCCGTTTACTAGAGTGAAAGACCCAACCACTGCTGAGGCTCTT
196 TGATGATGGGTTCAAGTGTGTACCCGTTTACTAGAGTGAAAGACCCAACCACT-CTGAGGCTCTT
16501089 GCTTGTCTGGAAACGGTACGATTTGCGACGGATCTGGGCTTTAGAGACGTCTACATAGAGGGAGA
260 GCTTGTCTGGAAACGGTACGATTTGCGACGGATCTGGGCTTTAGAGACGTCTACATAGAGGGAGA
16501154 TGCGTTAATAGTCATTAAGAACTCAAGTCGGAAGAGTTGGACATATCGTCAATCAGTAAAATCAT
325 TGCGTTAATAGTCATTAAGAACTCAAGTCGGAAGAGTTGGACATATCGTCAATCAGTAAAATCAT
*
16501219 TGATGAAATATGCATTCATAGGCAAAGGTTTAGAAACTTATCTTTTCACTTTCTCCGTAGATCTG
390 TGATGAAATATGCATTCATAAGCAAAGGTTTAGAAACTTATCTTTTCACTTTCTCCGTAGATCTG
16501284 CGAACAAAGCTGCCCACCAACTTGCTATCTAGGTCGACGGGTCGATGCTCCAAGGTTCTGGGTCG
455 CGAACAAAGCTGCCCACCAACTTGCTATCTAGGTCGACGGGTCGATGCTCCAAGGTTCTGGGTCG
16501349 AAGAGGCCCCGTCGATTCTCGATCACGTCTTAGTCGTTGATAGGCAAGAAATAATAGGGTAGAAA
520 AAGAGGCCCCGTCGATTCTCGATCACGTCTTAGTCGTTGATAGGCAAGAAATAATAGGGTAGAAA
16501414 GTGTGTTTTTAGTTGTTGAGACAGGAGGAATATCTATGAAGGAAATCCTCCGATGGATCTCAGTC
585 GTGTGTTTTTAGTTGTTGAGACAGGAGGAATATCTATGAAGGAAATCCTCCGATGGATCTCAGTC
* *
16501479 AGGCGTGGAACTGGCTTCGAACATGGTACCTAGAAAACGATCGGAAGTAGTGGTACCCAGAGGCG
650 AGGCGTGGAACTGGCTTCGAACATGGTACCTAGAAAACGATCGGAAGTAATGGTACCCAGAGGCA
*
16501544 CACGAATTTGTTATCTGATGAAGGAAGGGCGTTTGGGTATCTGGAAGGGTGAAAGTTTTTCTTTT
715 CACGAATTTGTTATCTGATGAAGGAAGGGCGTTTGGGCATCTGGAAGGGTGAAAGTTTTTCTTTT
*
16501609 CTTTATTTTTCTTAAGAAGAT
780 CTTTACTTTTCTTAAGAAGAT
16501630 GGGT
1 GGGT
16501634 TTTGTTTTCT
Statistics
Matches: 793, Mismatches: 11, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
800 244 0.31
801 549 0.69
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (800 bp):
GGGTGATTAGTTTCATTTTAGCTTATCAATCAGAAATCACACTCTTATATTTGAATCTAAAGTGT
AGATCTGAGGTAGAGAAAGCCCGATGGAAGGCTCCTGAACCAAAGACATTCAAAGCAAACTTTGA
TGCCTCTTTTCTTCTACAGTTACAAACAACAATAGCGGGGGCTATAATACGTAATAGTTCAGGCA
TGATGATGGGTTCAAGTGTGTACCCGTTTACTAGAGTGAAAGACCCAACCACTCTGAGGCTCTTG
CTTGTCTGGAAACGGTACGATTTGCGACGGATCTGGGCTTTAGAGACGTCTACATAGAGGGAGAT
GCGTTAATAGTCATTAAGAACTCAAGTCGGAAGAGTTGGACATATCGTCAATCAGTAAAATCATT
GATGAAATATGCATTCATAAGCAAAGGTTTAGAAACTTATCTTTTCACTTTCTCCGTAGATCTGC
GAACAAAGCTGCCCACCAACTTGCTATCTAGGTCGACGGGTCGATGCTCCAAGGTTCTGGGTCGA
AGAGGCCCCGTCGATTCTCGATCACGTCTTAGTCGTTGATAGGCAAGAAATAATAGGGTAGAAAG
TGTGTTTTTAGTTGTTGAGACAGGAGGAATATCTATGAAGGAAATCCTCCGATGGATCTCAGTCA
GGCGTGGAACTGGCTTCGAACATGGTACCTAGAAAACGATCGGAAGTAATGGTACCCAGAGGCAC
ACGAATTTGTTATCTGATGAAGGAAGGGCGTTTGGGCATCTGGAAGGGTGAAAGTTTTTCTTTTC
TTTACTTTTCTTAAGAAGAT
Found at i:16526535 original size:22 final size:22
Alignment explanation
Indices: 16526510--16526581 Score: 90
Period size: 22 Copynumber: 3.3 Consensus size: 22
16526500 TGTGAGTCAT
16526510 GTTATGTGAGCCCTGTACATAA
1 GTTATGTGAGCCCTGTACATAA
* * *
16526532 GTTATGTGAGCCCTGTATACAT
1 GTTATGTGAGCCCTGTACATAA
** *
16526554 GTTATACGAGCCTTGTACATAA
1 GTTATGTGAGCCCTGTACATAA
16526576 GTTATG
1 GTTATG
16526582 CGGTCATATT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (22 bp):
GTTATGTGAGCCCTGTACATAA
Found at i:16526661 original size:34 final size:33
Alignment explanation
Indices: 16526622--16526685 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
16526612 TATACGACCT
16526622 TGTATGCATGCGAAC-CTTAGGAATTATGTGATGA
1 TGTATGCATGCGAACTC-TAGGAA-TATGTGATGA
*
16526656 TGTATGTATGCGAACTCTAGGAATATGTGA
1 TGTATGCATGCGAACTCTAGGAATATGTGA
16526686 GCCTATATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 7 0.25
34 20 0.71
35 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.33
Consensus pattern (33 bp):
TGTATGCATGCGAACTCTAGGAATATGTGATGA
Found at i:16526704 original size:29 final size:29
Alignment explanation
Indices: 16526662--16526752 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
16526652 ATGATGTATG
* * ** *
16526662 TATGCGAACTCTAGGAATATGTGAGCCTA
1 TATGCGAACCCTAGGAACATGCAAACCTA
16526691 TATGCGAACCCTAGGAACATGCAAACCTA
1 TATGCGAACCCTAGGAACATGCAAACCTA
* * * *
16526720 CATGCGAACCCTAGGTACATGCAAGCCCA
1 TATGCGAACCCTAGGAACATGCAAACCTA
16526749 TATG
1 TATG
16526753 ACTATACGAA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (29 bp):
TATGCGAACCCTAGGAACATGCAAACCTA
Found at i:16531510 original size:37 final size:37
Alignment explanation
Indices: 16531443--16531629 Score: 205
Period size: 37 Copynumber: 5.1 Consensus size: 37
16531433 ATTCTAATGA
* *
16531443 ACACCGGCACGAAGCCTACTAGGCATATAGCCCGAAT
1 ACACCGGCACGAAGCCTGCTAGGCACATAGCCCGAAT
* * * *
16531480 ACATCGGCACGAAACCTGCTTGGCACATAGCCTGAAT
1 ACACCGGCACGAAGCCTGCTAGGCACATAGCCCGAAT
* *
16531517 ACACCGACACGAAGCTTGCTAGGCACATAGTCCC-AAT
1 ACACCGGCACGAAGCCTGCTAGGCACATAG-CCCGAAT
** * * *
16531554 GTACCGACACGAAACCTGCTAGGAACATAGCCCGAAT
1 ACACCGGCACGAAGCCTGCTAGGCACATAGCCCGAAT
* * * *
16531591 ACACCAGCACGAAGCCTGTTAGGCACATAACCAGAAT
1 ACACCGGCACGAAGCCTGCTAGGCACATAGCCCGAAT
16531628 AC
1 AC
16531630 TCAAATACAA
Statistics
Matches: 122, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
36 3 0.02
37 117 0.96
38 2 0.02
ACGTcount: A:0.34, C:0.31, G:0.20, T:0.15
Consensus pattern (37 bp):
ACACCGGCACGAAGCCTGCTAGGCACATAGCCCGAAT
Found at i:16532416 original size:12 final size:11
Alignment explanation
Indices: 16532396--16532429 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
16532386 TTTTTAGAGC
16532396 ATAAAAATAAA
1 ATAAAAATAAA
*
16532407 AGTGAAAATAAA
1 A-TAAAAATAAA
16532419 ATAAAAATAAA
1 ATAAAAATAAA
16532430 GGAAAGACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (11 bp):
ATAAAAATAAA
Found at i:16555311 original size:23 final size:23
Alignment explanation
Indices: 16555285--16555468 Score: 253
Period size: 23 Copynumber: 8.0 Consensus size: 23
16555275 ATTTACACAA
16555285 AAATCACATTAATATTTAAGCAC
1 AAATCACATTAATATTTAAGCAC
* * *
16555308 AAATCACAATAATATTCAAGCAT
1 AAATCACATTAATATTTAAGCAC
16555331 AAATCACATTAATATTTAAGCAC
1 AAATCACATTAATATTTAAGCAC
* *
16555354 AAATCACATTAATATTTAAGAAT
1 AAATCACATTAATATTTAAGCAC
* * **
16555377 AAATCATATTAACATTTAAGCTT
1 AAATCACATTAATATTTAAGCAC
* *
16555400 AAATCACATTAATACTTAAGAAC
1 AAATCACATTAATATTTAAGCAC
16555423 AAATCACATTAATATTTAAGCAC
1 AAATCACATTAATATTTAAGCAC
*
16555446 AAATCATATTAATATTTAA-CAC
1 AAATCACATTAATATTTAAGCAC
16555468 A
1 A
16555469 TTTAATGATA
Statistics
Matches: 140, Mismatches: 21, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
22 4 0.03
23 136 0.97
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (23 bp):
AAATCACATTAATATTTAAGCAC
Found at i:16555463 original size:69 final size:69
Alignment explanation
Indices: 16555285--16555464 Score: 279
Period size: 69 Copynumber: 2.6 Consensus size: 69
16555275 ATTTACACAA
* * * *
16555285 AAATCACATTAATATTTAAGCACAAATCACAATAATATTCAAGCATAAATCACATTAATATTTAA
1 AAATCACATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATACTTAA
*
16555350 GCAC
66 GAAC
* * * *
16555354 AAATCACATTAATATTTAAGAATAAATCATATTAACATTTAAGCTTAAATCACATTAATACTTAA
1 AAATCACATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATACTTAA
16555419 GAAC
66 GAAC
16555423 AAATCACATTAATATTTAAGCACAAATCATATTAATATTTAA
1 AAATCACATTAATATTTAAGCACAAATCATATTAATATTTAA
16555465 CACATTTAAT
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 99 1.00
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.32
Consensus pattern (69 bp):
AAATCACATTAATATTTAAGCACAAATCATATTAATATTTAAGCATAAATCACATTAATACTTAA
GAAC
Found at i:16555655 original size:66 final size:66
Alignment explanation
Indices: 16555541--16555671 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
16555531 AATACATGGA
* * * * * *
16555541 TCTCCAAACACACCAAATTGCTCATAGAGTCAAACATTTCTCATAAGTGAAGCATATAGCTAACA
1 TCTCCAAACACACCAAATAGCTCATAGAGTCAAACATGTCCCAAAAGTGAACCATAAAGCTAACA
16555606 C
66 C
*
16555607 TCTCCAAACACAGCAAA-AGACTCATAGAGTCAAACATGTCCCAAAAGTGAACCATAAAGCTAAC
1 TCTCCAAACACACCAAATAG-CTCATAGAGTCAAACATGTCCCAAAAGTGAACCATAAAGCTAAC
16555671 A
65 A
16555672 TGCTCCTTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 1 0.02
66 56 0.98
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.20
Consensus pattern (66 bp):
TCTCCAAACACACCAAATAGCTCATAGAGTCAAACATGTCCCAAAAGTGAACCATAAAGCTAACA
C
Found at i:16555971 original size:36 final size:36
Alignment explanation
Indices: 16555926--16556106 Score: 238
Period size: 36 Copynumber: 5.0 Consensus size: 36
16555916 ATATATTCAT
* **
16555926 TGTCACATGGCATGAATAACATAGTCACATATTTAC
1 TGTCTCATGGCATGAATAACATACCCACATATTTAC
* *
16555962 TGTCTCATGGCATGAATAACTTACCCACATATTTAT
1 TGTCTCATGGCATGAATAACATACCCACATATTTAC
* *
16555998 TGTCAT-ATGGCGTGAATAACATACCCGCATATTTAC
1 TGTC-TCATGGCATGAATAACATACCCACATATTTAC
* * *
16556034 TGTCACTTAGCATGAATAACATACCCACATATTTAC
1 TGTCTCATGGCATGAATAACATACCCACATATTTAC
* *
16556070 TATCTCATGGCATGAATAATATACCCACATATTTAC
1 TGTCTCATGGCATGAATAACATACCCACATATTTAC
16556106 T
1 T
16556107 TTCACAACAT
Statistics
Matches: 124, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
36 123 0.99
37 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.33
Consensus pattern (36 bp):
TGTCTCATGGCATGAATAACATACCCACATATTTAC
Found at i:16558766 original size:23 final size:23
Alignment explanation
Indices: 16558747--16559021 Score: 365
Period size: 23 Copynumber: 12.0 Consensus size: 23
16558737 TCCATTTACA
*
16558747 CATAAATTACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
16558770 CATAAATAACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
16558793 CATAAATCACATTAAAATTTAAG
1 CATAAATCACATTAATATTTAAG
*
16558816 CACAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* * *
16558839 CACAAATCACATCAATATTTAAA
1 CATAAATCACATTAATATTTAAG
*
16558862 CATAAATGACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* * *
16558885 AATAAATCATATTAACATTTATA-
1 CATAAATCACATTAATATTTA-AG
* *
16558908 CTTAAATTACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
*
16558931 CACAAATCACATTAATA-TTATAG
1 CATAAATCACATTAATATTTA-AG
*
16558954 CTTAAATCACATTAATATTTAAG
1 CATAAATCACATTAATATTTAAG
* *
16558977 CACAAATCACATTAATATTTACG
1 CATAAATCACATTAATATTTAAG
16559000 CATAAATCACATTAATATTTAA
1 CATAAATCACATTAATATTTAA
16559022 CACATTTAAT
Statistics
Matches: 218, Mismatches: 30, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
22 4 0.02
23 210 0.96
24 4 0.02
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (23 bp):
CATAAATCACATTAATATTTAAG
Found at i:16559228 original size:66 final size:65
Alignment explanation
Indices: 16559098--16559234 Score: 168
Period size: 66 Copynumber: 2.1 Consensus size: 65
16559088 GATACACGGA
* * * * * *
16559098 TCTCTAAACACACCAAATGACTCATAAAGTCGACCATGTCCCATAAGTGAAGCATATTGCTAACA
1 TCTCCAAACACACCAAAAGACTCATAAAGTCAAACATGTCCCAAAAGTGAAGCAAATT-CTAACA
16559163 C
65 C
* *
16559164 TCTCCAAACACACCAAAAGACTCATAGAGTCAAACATGTCCCAAAAGTGAAGTGTAAATT-TAAC
1 TCTCCAAACACACCAAAAGACTCATAAAGTCAAACATGTCCCAAAAGTGAA--GCAAATTCTAAC
16559228 AC
64 AC
16559230 TCTCC
1 TCTCC
16559235 TTATTTCCCC
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
66 56 0.92
68 5 0.08
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (65 bp):
TCTCCAAACACACCAAAAGACTCATAAAGTCAAACATGTCCCAAAAGTGAAGCAAATTCTAACAC
Found at i:16559538 original size:36 final size:36
Alignment explanation
Indices: 16559486--16559703 Score: 244
Period size: 36 Copynumber: 6.1 Consensus size: 36
16559476 TAATATGTTC
* * * *
16559486 ACTGTCACATGGCATGAATAACATACTCACATATTA
1 ACTGTCTCATGGCATGAAAAACATACCCACATATTT
* * *
16559522 ACTGTCTCATGACATGAAAAACATACTCATATATTT
1 ACTGTCTCATGGCATGAAAAACATACCCACATATTT
*
16559558 ACTGT-TACATGACATGAAAAACATACCCACATATTT
1 ACTGTCT-CATGGCATGAAAAACATACCCACATATTT
* *
16559594 ACTGACCCATGGCATGAAAAACATACCCACATATTT
1 ACTGTCTCATGGCATGAAAAACATACCCACATATTT
* * * *
16559630 ACCGTCACTTGGCATGAATAACATACCCACAT-TTT
1 ACTGTCTCATGGCATGAAAAACATACCCACATATTT
* * *
16559665 ACTGTCTCATGGCAT-AAATAACATAACAATATATTT
1 ACTGTCTCATGGCATGAAA-AACATACCCACATATTT
16559701 ACT
1 ACT
16559704 TTCACAACAG
Statistics
Matches: 156, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
34 2 0.01
35 26 0.17
36 128 0.82
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (36 bp):
ACTGTCTCATGGCATGAAAAACATACCCACATATTT
Found at i:16559574 original size:72 final size:71
Alignment explanation
Indices: 16559486--16559709 Score: 281
Period size: 72 Copynumber: 3.1 Consensus size: 71
16559476 TAATATGTTC
* * *
16559486 ACTGTCACATGGCATGAATAACATACTCACATATTAACTGTCTCATGACATGAAAAACATACTCA
1 ACTGTCACATGGCATGAATAACATACCCACATATTTACTGTCTCATGGCATGAAAAACATAC-CA
16559551 TATATTT
65 TATATTT
* * * * *
16559558 ACTGTTACATGACATGAAAAACATACCCACATATTTACTGACCCATGGCATGAAAAACATACCCA
1 ACTGTCACATGGCATGAATAACATACCCACATATTTACTGTCTCATGGCATGAAAAACATA-CCA
*
16559623 CATATTT
65 TATATTT
* * *
16559630 ACCGTCACTTGGCATGAATAACATACCCACAT-TTTACTGTCTCATGGCAT-AAATAACATAACA
1 ACTGTCACATGGCATGAATAACATACCCACATATTTACTGTCTCATGGCATGAAA-AACAT-ACC
16559693 ATATATTT
64 ATATATTT
*
16559701 ACTTTCACA
1 ACTGTCACA
16559710 ACAGTCATCA
Statistics
Matches: 128, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
70 3 0.02
71 35 0.27
72 89 0.70
73 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.29
Consensus pattern (71 bp):
ACTGTCACATGGCATGAATAACATACCCACATATTTACTGTCTCATGGCATGAAAAACATACCAT
ATATTT
Found at i:16562693 original size:16 final size:16
Alignment explanation
Indices: 16562672--16562704 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16562662 AAAAAAAATA
*
16562672 CTATTACAGTTTTATT
1 CTATTACAGTCTTATT
16562688 CTATTACAGTCTTATT
1 CTATTACAGTCTTATT
16562704 C
1 C
16562705 AATTTCAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (16 bp):
CTATTACAGTCTTATT
Found at i:16566650 original size:25 final size:24
Alignment explanation
Indices: 16566593--16566650 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
16566583 TTAAAAATAA
16566593 TAAAAACATTAAAATAAATATTTCC
1 TAAAAA-ATTAAAATAAATATTTCC
* * **
16566618 TAACAAATTGAAAATAAATTTTTTT
1 TAAAAAATT-AAAATAAATATTTCC
16566643 TAAAAAAT
1 TAAAAAAT
16566651 AATTAATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 3 0.11
25 24 0.89
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (24 bp):
TAAAAAATTAAAATAAATATTTCC
Found at i:16566725 original size:30 final size:30
Alignment explanation
Indices: 16566689--16566753 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
16566679 CAACTTAACA
* *
16566689 AACAAATGT-CTCTAAAATAGTAGCAAAATT
1 AACAAAT-TCCTCTAAAATAATAACAAAATT
16566719 AACAAATTCCTCTAAAATAATAACAAAATT
1 AACAAATTCCTCTAAAATAATAACAAAATT
16566749 AACAA
1 AACAA
16566754 TAATATAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.25
Consensus pattern (30 bp):
AACAAATTCCTCTAAAATAATAACAAAATT
Found at i:16573707 original size:25 final size:25
Alignment explanation
Indices: 16573655--16573784 Score: 96
Period size: 23 Copynumber: 5.4 Consensus size: 25
16573645 ACACTAGCAC
*
16573655 GCTCTCTG-T-TTAGCAC-GTCTTGT
1 GCTCTCTGTTATTAGCACTGT-ATGT
* *
16573678 ACTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTGTTATTAGCACTGTATGT
* * *
16573703 GCTCT-T-TGATTAGCACTTTGTGT
1 GCTCTCTGTTATTAGCACTGTATGT
* *
16573726 GCTCTCTG--ATTAGTACTTTATGT
1 GCTCTCTGTTATTAGCACTGTATGT
**
16573749 GCTCTCTGTTGACCAGCACT-TATGT
1 GCTCTCTGTT-ATTAGCACTGTATGT
16573774 GCTCTCTGTTA
1 GCTCTCTGTTA
16573785 GTACTTTGGT
Statistics
Matches: 89, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
23 48 0.54
24 4 0.04
25 29 0.33
26 8 0.09
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (25 bp):
GCTCTCTGTTATTAGCACTGTATGT
Found at i:16573731 original size:48 final size:49
Alignment explanation
Indices: 16573679--16573784 Score: 112
Period size: 48 Copynumber: 2.2 Consensus size: 49
16573669 ACGTCTTGTA
* ** *
16573679 CTCTCTGTTATTAGCACTGTGTGTG-CTCT-TTGATTAGCACTTTGTGTG
1 CTCTCTGTTATTAGCACTGTATGTGCCTCTGTTGACCAGCAC-TTATGTG
* *
16573727 CTCTCTG--ATTAGTACTTTATGTGCTCTCTGTTGACCAGCACTTATGTG
1 CTCTCTGTTATTAGCACTGTATGTGC-CTCTGTTGACCAGCACTTATGTG
16573775 CTCTCTGTTA
1 CTCTCTGTTA
16573785 GTACTTTGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
46 13 0.28
48 24 0.51
49 9 0.19
50 1 0.02
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (49 bp):
CTCTCTGTTATTAGCACTGTATGTGCCTCTGTTGACCAGCACTTATGTG
Found at i:16577056 original size:52 final size:52
Alignment explanation
Indices: 16576960--16577193 Score: 315
Period size: 52 Copynumber: 4.5 Consensus size: 52
16576950 ATTTCATTTA
* * * * * ** *
16576960 ATACTCACGATGACACGTAGTCATCAGATCTCTTATTCTGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCAGACCACATAATCCATAAAGGATTCAT
* * * * *
16577012 ACACTCACGATGACACATAGTCATCGGACCTCATAATCCCTAAAGGATTCTT
1 ATACTCACGATGACACATAGTCATCAGACCACATAATCCATAAAGGATTCAT
* *
16577064 ATACTCACGATGACACATAGTCATCGGACCACATAATCCATAAAGGATTCAA
1 ATACTCACGATGACACATAGTCATCAGACCACATAATCCATAAAGGATTCAT
*
16577116 ATACTCACGATGACACATAATCATCAGACCACATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCACATAATCCATAAAGGATTCAT
*
16577168 ATACTCACGATGACACTTAGTCATCA
1 ATACTCACGATGACACATAGTCATCA
16577194 AACCCTTTTG
Statistics
Matches: 162, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 162 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCACATAATCCATAAAGGATTCAT
Found at i:16583063 original size:23 final size:23
Alignment explanation
Indices: 16583030--16583091 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
16583020 AGTAGCCCTT
* *
16583030 AAGAAATAACGTCAAAAATCGTC
1 AAGAAAAAACGTCAAAAATCATC
16583053 AAGAAAAAACGTCAAAAATCATC
1 AAGAAAAAACGTCAAAAATCATC
16583076 AAGAAAAAA-GTCAAAA
1 AAGAAAAAACGTCAAAA
16583092 GTCACCATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 7 0.19
23 30 0.81
ACGTcount: A:0.61, C:0.15, G:0.11, T:0.13
Consensus pattern (23 bp):
AAGAAAAAACGTCAAAAATCATC
Found at i:16589911 original size:13 final size:13
Alignment explanation
Indices: 16589893--16589918 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16589883 CCCTCCTTAT
16589893 CTTATCTTACCTC
1 CTTATCTTACCTC
16589906 CTTATCTTACCTC
1 CTTATCTTACCTC
16589919 TCTCTTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.46
Consensus pattern (13 bp):
CTTATCTTACCTC
Found at i:16599222 original size:9 final size:10
Alignment explanation
Indices: 16599186--16599234 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
16599176 CTTATACACG
16599186 TACAACTAAC
1 TACAACTAAC
*
16599196 TGCAACTAAC
1 TACAACTAAC
*
16599206 TTCAACTAAC
1 TACAACTAAC
16599216 -ACAACTAAC
1 TACAACTAAC
*
16599225 -ATAACTAAC
1 TACAACTAAC
16599234 T
1 T
16599235 CAGCTGCAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
9 16 0.47
10 18 0.53
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.22
Consensus pattern (10 bp):
TACAACTAAC
Found at i:16601236 original size:61 final size:60
Alignment explanation
Indices: 16601105--16601236 Score: 167
Period size: 61 Copynumber: 2.2 Consensus size: 60
16601095 TTTTATAGAT
* * * * *
16601105 TTTCCATAAAGGCATTCCTTAACATTCAGTACTCTCCACAAAGGCTCTCTTATTTAGAGTA
1 TTTCCACAAAGGCATTCCTTAACATTCAATACTCACCACAAAGGCTCTCTCATTCAGAG-A
* *
16601166 TTTCCACAAAGGCATTCCTTTAACATTCAATACTCACCACAAAGGCTTTC-CCTTCAGAGA
1 TTTCCACAAAGGCATTCC-TTAACATTCAATACTCACCACAAAGGCTCTCTCATTCAGAGA
16601226 TTTGCCACAAA
1 TTT-CCACAAA
16601237 AGAGTTTTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
60 4 0.06
61 30 0.48
62 28 0.45
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (60 bp):
TTTCCACAAAGGCATTCCTTAACATTCAATACTCACCACAAAGGCTCTCTCATTCAGAGA
Found at i:16601347 original size:29 final size:29
Alignment explanation
Indices: 16601315--16601410 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 29
16601305 AAGAGGTTCA
*
16601315 CCACAAAGGCTTACCTTTAACAGAAACTG
1 CCACAAAGGCTTACCTTTAACAGAGACTG
* * **
16601344 CCACAAAGGCGTTA-C-TTATCATAGGTTG
1 CCACAAAGGC-TTACCTTTAACAGAGACTG
* * * *
16601372 CCATAGAGGCTTTCCTTTGACAGAGACTG
1 CCACAAAGGCTTACCTTTAACAGAGACTG
16601401 CCACAAAGGC
1 CCACAAAGGC
16601411 ATTTTGTTTC
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
27 2 0.04
28 17 0.35
29 27 0.55
30 3 0.06
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (29 bp):
CCACAAAGGCTTACCTTTAACAGAGACTG
Found at i:16604650 original size:15 final size:15
Alignment explanation
Indices: 16604632--16604660 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16604622 CAATTTAAGT
16604632 CATAAAGATTTGAAG
1 CATAAAGATTTGAAG
16604647 CATAAAGATTTGAA
1 CATAAAGATTTGAA
16604661 ATAAGCTCAA
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:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (15 bp):
CATAAAGATTTGAAG
Found at i:16608693 original size:39 final size:39
Alignment explanation
Indices: 16608639--16608718 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
16608629 AAATTCATAG
16608639 CTAGATTTGATTCAATTTGAATCCAACAAACTTGAATGC
1 CTAGATTTGATTCAATTTGAATCCAACAAACTTGAATGC
*
16608678 CTAGATTTGATTCAATTTGAATCCACCAAACTTGAATGC
1 CTAGATTTGATTCAATTTGAATCCAACAAACTTGAATGC
16608717 CT
1 CT
16608719 TGTTTAGGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (39 bp):
CTAGATTTGATTCAATTTGAATCCAACAAACTTGAATGC
Found at i:16608906 original size:43 final size:43
Alignment explanation
Indices: 16608853--16608956 Score: 163
Period size: 43 Copynumber: 2.4 Consensus size: 43
16608843 TAGTGGATGC
*
16608853 TTTCCACGTAGCTTCCTTCTTTGTCCTTTCATGAAAGTGGTTT
1 TTTCCACGTAGCTTCCTCCTTTGTCCTTTCATGAAAGTGGTTT
* * *
16608896 TTTCCACGTAGCTTCCTCCTTTGTCGTTTCTTGAATGTGGTTT
1 TTTCCACGTAGCTTCCTCCTTTGTCCTTTCATGAAAGTGGTTT
*
16608939 TTTCCACTTAGCTTCCTC
1 TTTCCACGTAGCTTCCTC
16608957 TGTCTTTTGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.12, C:0.26, G:0.15, T:0.47
Consensus pattern (43 bp):
TTTCCACGTAGCTTCCTCCTTTGTCCTTTCATGAAAGTGGTTT
Found at i:16614475 original size:1 final size:1
Alignment explanation
Indices: 16614471--16614495 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
16614461 CCCCGCCCCC
16614471 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
16614496 TTGTAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:16617160 original size:5 final size:5
Alignment explanation
Indices: 16617152--16617176 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
16617142 AATAAAATAA
16617152 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
16617177 ACATGTTTTC
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:16620429 original size:30 final size:30
Alignment explanation
Indices: 16620395--16620471 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 30
16620385 TCACACGGGT
*
16620395 AGTCACACGGTCGTGTGTCAGGCCGCGTGG
1 AGTCACACGGTCGTGTGTCAAGCCGCGTGG
* ** * * *
16620425 AGTCACATGACCATGTGTCAAGTCGTGTGG
1 AGTCACACGGTCGTGTGTCAAGCCGCGTGG
*
16620455 AGCCACACGGTCGTGTG
1 AGTCACACGGTCGTGTG
16620472 AGCCTAAACA
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.22
Consensus pattern (30 bp):
AGTCACACGGTCGTGTGTCAAGCCGCGTGG
Found at i:16625053 original size:34 final size:34
Alignment explanation
Indices: 16624996--16625077 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
16624986 GTTCACAAGT
* * * *
16624996 TATGGTGTGTTGGATGGATTAGCTCTTATGAGCA
1 TATGGTGTGATGGACGAAGTAGCTCTTATGAGCA
* *
16625030 TATGGTGTGGTGGACGAAGTAGCTCTTATGAGTA
1 TATGGTGTGATGGACGAAGTAGCTCTTATGAGCA
*
16625064 TATGGCGTGATGGA
1 TATGGTGTGATGGA
16625078 TGGAATGACT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.22, C:0.09, G:0.35, T:0.34
Consensus pattern (34 bp):
TATGGTGTGATGGACGAAGTAGCTCTTATGAGCA
Found at i:16635782 original size:18 final size:18
Alignment explanation
Indices: 16635752--16635801 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
16635742 AAACTTAATT
16635752 TATATGCAA-TTTTTAAA
1 TATATGCAATTTTTTAAA
16635769 TATATGCAATTTTTTAAA
1 TATATGCAATTTTTTAAA
16635787 TATATGCAATTTTTT
1 TATATGCAATTTTTT
16635802 TCTCTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 9 0.28
18 23 0.72
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (18 bp):
TATATGCAATTTTTTAAA
Found at i:16636740 original size:17 final size:17
Alignment explanation
Indices: 16636700--16636746 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
16636690 AAAATTTAAA
16636700 AATTTTT-ATAAATTTT
1 AATTTTTAATAAATTTT
* *
16636716 ATACTTTTAATAATTTTT
1 A-ATTTTTAATAAATTTT
16636734 AATTTTTAA-AAAT
1 AATTTTTAATAAAT
16636747 AATTTTTTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.16
17 12 0.48
18 9 0.36
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTTTAATAAATTTT
Found at i:16636749 original size:20 final size:21
Alignment explanation
Indices: 16636724--16636767 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
16636714 TTATACTTTT
16636724 AATAA-TTTTT-AATTTTTAAA
1 AATAATTTTTTGAA-TTTTAAA
16636744 AATAATTTTTTGAATTTTAAA
1 AATAATTTTTTGAATTTTAAA
16636765 AAT
1 AAT
16636768 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.23
21 15 0.68
22 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
AATAATTTTTTGAATTTTAAA
Found at i:16637684 original size:18 final size:17
Alignment explanation
Indices: 16637658--16637709 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
16637648 ATAGTGTACC
*
16637658 AAATATTATTTTTTTAT
1 AAATTTTATTTTTTTAT
*
16637675 AAAATTTTATATTTCTTAT
1 -AAATTTTAT-TTTTTTAT
* *
16637694 AATTTTTATATTTTTA
1 AAATTTTATTTTTTTA
16637710 CGATTTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 5 0.18
18 16 0.57
19 7 0.25
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
AAATTTTATTTTTTTAT
Found at i:16637715 original size:17 final size:18
Alignment explanation
Indices: 16637679--16637717 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16637669 TTTTATAAAA
*
16637679 TTTTATATTTCTTATAAT
1 TTTTATATTTCTTACAAT
*
16637697 TTTTATATTT-TTACGAT
1 TTTTATATTTCTTACAAT
16637714 TTTT
1 TTTT
16637718 TATAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTATATTTCTTACAAT
Found at i:16637727 original size:10 final size:9
Alignment explanation
Indices: 16637668--16637787 Score: 64
Period size: 10 Copynumber: 12.3 Consensus size: 9
16637658 AAATATTATT
16637668 TTTTTATAAA
1 TTTTTAT-AA
*
16637678 ATTTTAT-A
1 TTTTTATAA
16637686 TTTCTTATAA
1 TTT-TTATAA
16637696 TTTTTAT-A
1 TTTTTATAA
* *
16637704 TTTTTACGAT
1 TTTTTA-TAA
16637714 TTTTTATAAA
1 TTTTTAT-AA
*
16637724 TTTTTACAA
1 TTTTTATAA
**
16637733 CGTTTATAA
1 TTTTTATAA
*
16637742 TTCTTTTATGA
1 -T-TTTTATAA
16637753 TTTTTATAA
1 TTTTTATAA
16637762 TTTATTTCTATAA
1 --T-TTT-TATAA
16637775 TTTTCTATAA
1 TTTT-TATAA
16637785 TTT
1 TTT
16637788 ATTTTATAAT
Statistics
Matches: 85, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
8 10 0.12
9 23 0.27
10 36 0.42
11 8 0.09
12 3 0.04
13 5 0.06
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:16637773 original size:13 final size:13
Alignment explanation
Indices: 16637752--16637797 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
16637742 TTCTTTTATG
*
16637752 ATTTTTATAATTT
1 ATTTCTATAATTT
16637765 ATTTCTATAA--T
1 ATTTCTATAATTT
16637776 -TTTCTATAATTT
1 ATTTCTATAATTT
16637788 ATTT-TATAAT
1 ATTTCTATAAT
16637798 GATCTTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 9 0.31
11 1 0.03
12 7 0.24
13 12 0.41
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTTCTATAATTT
Found at i:16637795 original size:22 final size:21
Alignment explanation
Indices: 16637735--16637797 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 21
16637725 TTTTACAACG
* *
16637735 TTTATAA-TTCTTTTATGATT
1 TTTATAATTTATTTTATAATT
16637755 TTTATAATTTATTTCTATAATT
1 TTTATAATTTATTT-TATAATT
16637777 TTCTATAATTTATTTTATAAT
1 TT-TATAATTTATTTTATAAT
16637798 GATCTTTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.18
21 5 0.13
22 14 0.37
23 12 0.32
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTATAATTTATTTTATAATT
Found at i:16637810 original size:23 final size:24
Alignment explanation
Indices: 16637749--16637810 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
16637739 TAATTCTTTT
*
16637749 ATGATTTTTATAATTTATTTCTATA
1 ATGATCTTTAT-ATTTATTTCTATA
** *
16637774 ATTTTCTATA-ATTTATTT-TATA
1 ATGATCTTTATATTTATTTCTATA
16637796 ATGATCTTTATATTT
1 ATGATCTTTATATTT
16637811 TTTAAGAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
22 11 0.38
23 12 0.41
25 6 0.21
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (24 bp):
ATGATCTTTATATTTATTTCTATA
Found at i:16637840 original size:31 final size:30
Alignment explanation
Indices: 16637804--16637863 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
16637794 TAATGATCTT
*
16637804 TATATTTTTTAAGAAATTTAAAATATTTTTC
1 TATA-TTTTAAAGAAATTTAAAATATTTTTC
* *
16637835 TATATTTTAAATAAATTTTAAATATTTTT
1 TATATTTTAAAGAAATTTAAAATATTTTT
16637864 ATTTTTTAAT
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:0.02, G:0.02, T:0.57
Consensus pattern (30 bp):
TATATTTTAAAGAAATTTAAAATATTTTTC
Found at i:16637866 original size:26 final size:26
Alignment explanation
Indices: 16637810--16637895 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
16637800 TCTTTATATT
*
16637810 TTTTAAGA-AATTTAAAATATTTTTCTATA
1 TTTTAA-ATAATTTTAAATA-TTTT-T-TA
16637839 TTTTAAATAAATTTTAAATA-TTTTTA
1 TTTTAAAT-AATTTTAAATATTTTTTA
* * *
16637865 TTTTTTAATATTTTTTAATATTTTTTA
1 -TTTTAAATAATTTTAAATATTTTTTA
16637892 TTTT
1 TTTT
16637896 TTAATTTTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
26 15 0.31
27 14 0.29
28 4 0.08
29 6 0.12
30 10 0.20
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (26 bp):
TTTTAAATAATTTTAAATATTTTTTA
Found at i:16637876 original size:10 final size:10
Alignment explanation
Indices: 16637863--16637891 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
16637853 TAAATATTTT
16637863 TATTTTTTAA
1 TATTTTTTAA
16637873 TATTTTTTAA
1 TATTTTTTAA
16637883 TATTTTTTA
1 TATTTTTTA
16637892 TTTTTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:16637896 original size:26 final size:27
Alignment explanation
Indices: 16637806--16637896 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
16637796 ATGATCTTTA
* * *
16637806 TATTTTTTAAGAAATTTAAAATATTTTT
1 TATTTTTAAATAAATTT-TAATATTTTT
16637834 CTATATTTTAAATAAATTTTAA-ATATTTT
1 -TAT-TTTTAAATAAATTTTAATAT-TTTT
* **
16637863 TATTTTTTAATATTTTTTAATATTTTT
1 TATTTTTAAATAAATTTTAATATTTTT
16637890 TATTTTT
1 TATTTTT
16637897 TAATTTTCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
27 25 0.47
28 7 0.13
29 9 0.17
30 12 0.23
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (27 bp):
TATTTTTAAATAAATTTTAATATTTTT
Found at i:16638752 original size:14 final size:14
Alignment explanation
Indices: 16638727--16638769 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
16638717 AATAATTTGA
*
16638727 AAATTATTAAAATT
1 AAATTTTTAAAATT
**
16638741 ATTTTTTTAAAATAT
1 AAATTTTTAAAAT-T
16638756 AAATTTTTAAAATT
1 AAATTTTTAAAATT
16638770 TTTAAAATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AAATTTTTAAAATT
Found at i:16638768 original size:38 final size:40
Alignment explanation
Indices: 16638726--16638807 Score: 123
Period size: 38 Copynumber: 2.1 Consensus size: 40
16638716 AAATAATTTG
*
16638726 AAAATTATTAAAATTATTTTTTTAAAAT-AT-AAATTTTT
1 AAAATTATTAAAATTATTTTTTTAAAATAATAAAATTATT
* *
16638764 AAAATTTTTAAAATTATTTTTTTGAAATAATAAAATTATT
1 AAAATTATTAAAATTATTTTTTTAAAATAATAAAATTATT
16638804 AAAA
1 AAAA
16638808 AATATTAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
38 26 0.67
39 2 0.05
40 11 0.28
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (40 bp):
AAAATTATTAAAATTATTTTTTTAAAATAATAAAATTATT
Found at i:16639456 original size:21 final size:21
Alignment explanation
Indices: 16639432--16639473 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
16639422 ATCCTCAGGG
16639432 ATTTACTTGAAAACCATGGAT
1 ATTTACTTGAAAACCATGGAT
16639453 ATTTACTTGAAAACCATGGAT
1 ATTTACTTGAAAACCATGGAT
16639474 CAAACATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (21 bp):
ATTTACTTGAAAACCATGGAT
Found at i:16639634 original size:11 final size:11
Alignment explanation
Indices: 16639615--16639655 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
16639605 GAAAATTAAA
*
16639615 ATGATGAAGAG
1 ATGAAGAAGAG
16639626 ATGAAGAAGAG
1 ATGAAGAAGAG
16639637 ATGAAGAAGA-
1 ATGAAGAAGAG
16639647 A-GAAGAAGA
1 ATGAAGAAGA
16639656 AATTGGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 8 0.28
10 1 0.03
11 20 0.69
ACGTcount: A:0.56, C:0.00, G:0.34, T:0.10
Consensus pattern (11 bp):
ATGAAGAAGAG
Found at i:16639701 original size:30 final size:30
Alignment explanation
Indices: 16639667--16639729 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
16639657 ATTGGAAATT
* * *
16639667 AAAATTATTT-AATAATTTTATTATTTCAAA
1 AAAATAATTTCAATAATTTCATAATTT-AAA
16639697 AAAATAATTTCAATAATTTCATAATTTAAA
1 AAAATAATTTCAATAATTTCATAATTTAAA
16639727 AAA
1 AAA
16639730 TTGTATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (30 bp):
AAAATAATTTCAATAATTTCATAATTTAAA
Found at i:16648490 original size:22 final size:22
Alignment explanation
Indices: 16648448--16648490 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
16648438 AAATTATTTT
*
16648448 ATAATTTTATTATTTAAAAAAA
1 ATAATTTTATAATTTAAAAAAA
*
16648470 ATAATTTTAATAATTTTAAAA
1 ATAATTTT-ATAATTTAAAAA
16648491 TTATTTGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAATTTTATAATTTAAAAAAA
Found at i:16651123 original size:29 final size:30
Alignment explanation
Indices: 16651069--16651126 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
16651059 TCCAATTATA
*
16651069 TTTTAGATTTATCTATATTATTTTTTAATT
1 TTTTAAATTTATCTATATTATTTTTTAATT
*
16651099 TTTTAAATTTAT-TTTATT-TTATTTTAAT
1 TTTTAAATTTATCTATATTATT-TTTTAAT
16651127 ATTAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 12 0.48
30 11 0.44
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (30 bp):
TTTTAAATTTATCTATATTATTTTTTAATT
Found at i:16651301 original size:16 final size:15
Alignment explanation
Indices: 16651258--16651304 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 15
16651248 TTTAAATTAT
16651258 ATAATAT-ATA-AAA
1 ATAATATAATATAAA
16651271 ATAATATAATATAAA
1 ATAATATAATATAAA
* *
16651286 ATATTATAAATTTAAA
1 ATAATAT-AATATAAA
16651302 ATA
1 ATA
16651305 GATCGGGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 7 0.24
14 3 0.10
15 9 0.31
16 10 0.34
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAATATAATATAAA
Found at i:16651302 original size:32 final size:32
Alignment explanation
Indices: 16651240--16651302 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
16651230 GTTTATTTTT
* * *
16651240 TAATATACTTTAAATTATATAATATATAAAAA
1 TAATATAATATAAAATATATAATATATAAAAA
*
16651272 TAATATAATATAAAATATTATAA-ATTTAAAA
1 TAATATAATATAAAATA-TATAATATATAAAA
16651303 TAGATCGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 21 0.81
33 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (32 bp):
TAATATAATATAAAATATATAATATATAAAAA
Found at i:16656516 original size:21 final size:22
Alignment explanation
Indices: 16656491--16656546 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
16656481 CTAGAACTCA
16656491 TTGTATCGGTAGAAGGGT-AG-G
1 TTGTATCGGTAGAA-GGTCAGAG
*
16656512 TTGTATCGATAG-AGGTCAGAG
1 TTGTATCGGTAGAAGGTCAGAG
16656533 TTGTATCGGTAGAA
1 TTGTATCGGTAGAA
16656547 CTCTCACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.10
20 3 0.10
21 23 0.77
22 1 0.03
ACGTcount: A:0.27, C:0.07, G:0.36, T:0.30
Consensus pattern (22 bp):
TTGTATCGGTAGAAGGTCAGAG
Found at i:16656708 original size:3 final size:3
Alignment explanation
Indices: 16656700--16656746 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
16656690 TATCCGATGT
* *
16656700 TAA TAA TAA TAA GGT-A TGA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA --TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16656746 T
1 T
16656747 TTGGTGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
2 1 0.03
3 35 0.92
4 1 0.03
5 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:16664365 original size:4 final size:4
Alignment explanation
Indices: 16664356--16664385 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
16664346 ATCCGTCTAT
*
16664356 AATA AATA AATA AATA AATA AATA TATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
16664386 AGCATGAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:16671759 original size:25 final size:25
Alignment explanation
Indices: 16671713--16671760 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
16671703 AGGGTGGTAT
* *
16671713 TTTTGGTTAATTTAATGGAATTTCC
1 TTTTGGTGAATTTAATCGAATTTCC
* *
16671738 TTTTGGTGAGTTTAATCTAATTT
1 TTTTGGTGAATTTAATCGAATTT
16671761 TGGGAATAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (25 bp):
TTTTGGTGAATTTAATCGAATTTCC
Found at i:16672346 original size:196 final size:196
Alignment explanation
Indices: 16672012--16672404 Score: 705
Period size: 196 Copynumber: 2.0 Consensus size: 196
16672002 GGACTTCCCG
*
16672012 AATGTTTTTCCTGAGGAATGGTCAAGTGTTACTCCGAACAGGGAGGTTGAGTTTACAACTCACTA
1 AATGTTTTTCCCGAGGAATGGTCAAGTGTTACTCCGAACAGGGAGGTTGAGTTTACAACTCACTA
*
16672077 AATTTATTGATTGAATTTCAGGTAATTCACAGACTTGATCAGGTCGATGGATCGGGAGCTCGATC
66 AATTTATTGATTGAATTTCAGGTAATTCACAGACTTGATCAGGTCGACGGATCGGGAGCTCGATC
*
16672142 ACTATGCTTATCGGTTAACCTTTAATATTAGTTTATTTCAGTGTTTTCTTGTAATTCGACTTTTC
131 ACTATGCTTATCGGTTAACCTTTAATATTAGTTTATTTCAGTGTTTTCTCGTAATTCGACTTTTC
16672207 A
196 A
* *
16672208 AATGTTTTTCCCGAGGGATGGTCAAGTGTTACTCCGAACAGGGAGGTTGAGTTTACAACTCACTT
1 AATGTTTTTCCCGAGGAATGGTCAAGTGTTACTCCGAACAGGGAGGTTGAGTTTACAACTCACTA
* * * *
16672273 AATTTATTGATTGAATTTTAGGTAATTCACAGACTTGATCCGGTGGACGGATCGGGAGCTCGGTC
66 AATTTATTGATTGAATTTCAGGTAATTCACAGACTTGATCAGGTCGACGGATCGGGAGCTCGATC
16672338 ACTATGCTTATCGGTTAACCTTTAATATTAGTTTATTTCAGTGTTTTCTCGTAATTCGACTTTTC
131 ACTATGCTTATCGGTTAACCTTTAATATTAGTTTATTTCAGTGTTTTCTCGTAATTCGACTTTTC
16672403 A
196 A
16672404 A
1 A
16672405 GATTTTAAAC
Statistics
Matches: 188, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
196 188 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (196 bp):
AATGTTTTTCCCGAGGAATGGTCAAGTGTTACTCCGAACAGGGAGGTTGAGTTTACAACTCACTA
AATTTATTGATTGAATTTCAGGTAATTCACAGACTTGATCAGGTCGACGGATCGGGAGCTCGATC
ACTATGCTTATCGGTTAACCTTTAATATTAGTTTATTTCAGTGTTTTCTCGTAATTCGACTTTTC
A
Found at i:16674613 original size:18 final size:19
Alignment explanation
Indices: 16674582--16674618 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
16674572 GAGTACTTGT
*
16674582 AAAAAAATATAAAAATATA
1 AAAAAAACATAAAAATATA
16674601 AAAAAAACA-AAAAATATA
1 AAAAAAACATAAAAATATA
16674619 TTTTAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAAAACATAAAAATATA
Found at i:16675522 original size:30 final size:30
Alignment explanation
Indices: 16675486--16675642 Score: 142
Period size: 29 Copynumber: 5.3 Consensus size: 30
16675476 AAAAATCATG
*
16675486 TTTTGACCCCTAAACTTTTTAAAAATTACA
1 TTTTGACCCCTAAACTTTTCAAAAATTACA
* *
16675516 TATTGA-CCTTAAACTTTTCCAAAAATTACA
1 TTTTGACCCCTAAACTTTT-CAAAAATTACA
* * * *
16675546 TTTT-AGCCCTTAAAC-TTCCAAAAATCATA
1 TTTTGA-CCCCTAAACTTTTCAAAAATTACA
* * *
16675575 TTTTTACCCCTAAACTTTCCAAAAATCACA
1 TTTTGACCCCTAAACTTTTCAAAAATTACA
** *
16675605 TTTTG-CCCCCGAACTTCTCAAAAATTACA
1 TTTTGACCCCTAAACTTTTCAAAAATTACA
*
16675634 TTTTTACCC
1 TTTTGACCC
16675643 TCAAGCATTC
Statistics
Matches: 105, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
29 56 0.53
30 41 0.39
31 8 0.08
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.36
Consensus pattern (30 bp):
TTTTGACCCCTAAACTTTTCAAAAATTACA
Found at i:16675565 original size:29 final size:29
Alignment explanation
Indices: 16675463--16675637 Score: 138
Period size: 30 Copynumber: 5.9 Consensus size: 29
16675453 CTTATAAGGT
* * * **
16675463 CCCTGAACTATCCAAAAATCATGTTTTGAC
1 CCCTAAACTTTCCAAAAATTACATTTTG-C
** * *
16675493 CCCTAAACTTTTTAAAAATTACATATTGA
1 CCCTAAACTTTCCAAAAATTACATTTTGC
*
16675522 CCTTAAACTTTTCCAAAAATTACATTTTAGC
1 CCCTAAAC-TTTCCAAAAATTACATTTT-GC
* * * *
16675553 CCTTAAAC-TTCCAAAAATCATATTTTTAC
1 CCCTAAACTTTCCAAAAATTACA-TTTTGC
*
16675582 CCCTAAACTTTCCAAAAATCACATTTTGC
1 CCCTAAACTTTCCAAAAATTACATTTTGC
**
16675611 CCCCGAAC-TTCTCAAAAATTACATTTT
1 CCCTAAACTTTC-CAAAAATTACATTTT
16675638 TACCCTCAAG
Statistics
Matches: 117, Mismatches: 23, Indels: 11
0.77 0.15 0.07
Matches are distributed among these distances:
28 3 0.03
29 52 0.44
30 53 0.45
31 9 0.08
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAAATTACATTTTGC
Found at i:16675606 original size:59 final size:60
Alignment explanation
Indices: 16675473--16675642 Score: 166
Period size: 59 Copynumber: 2.9 Consensus size: 60
16675463 CCCTGAACTA
** * * * * * * *
16675473 TCCAAAAATCATGTTTTGACCCCTAAACTTTTTAAAAATTACATATTGA-CCTTAAACTTT
1 TCCAAAAATCACATTTTG-CCCCCAAACTTCTCAAAAATCACATTTTTACCCCTAAACTTT
* ** *
16675533 TCCAAAAATTACATTTTAGCCCTTAAACTTC-CAAAAATCATATTTTTACCCCTAAAC-TT
1 TCCAAAAATCACATTTT-GCCCCCAAACTTCTCAAAAATCACATTTTTACCCCTAAACTTT
* *
16675592 TCCAAAAATCACATTTTGCCCCCGAACTTCTCAAAAATTACATTTTTACCC
1 TCCAAAAATCACATTTTGCCCCCAAACTTCTCAAAAATCACATTTTTACCC
16675643 TCAAGCATTC
Statistics
Matches: 90, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
58 10 0.11
59 48 0.53
60 31 0.34
61 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (60 bp):
TCCAAAAATCACATTTTGCCCCCAAACTTCTCAAAAATCACATTTTTACCCCTAAACTTT
Found at i:16675753 original size:29 final size:29
Alignment explanation
Indices: 16675475--16675754 Score: 88
Period size: 29 Copynumber: 9.5 Consensus size: 29
16675465 CTGAACTATC
** *
16675475 CAAAAATCATGTTTTGACCCCTAAACTTTTT
1 CAAAAATCACATTTTAACCCC-AAA-TTTTT
* * * ** *
16675506 -AAAAATTACATATTGACCTTAAACTTTTC
1 CAAAAATCACATTTTAACCCCAAA-TTTTT
* * * * *
16675535 CAAAAATTACATTTTAGCCCTTAAA-CTTC
1 CAAAAATCACATTTTAACCC-CAAATTTTT
* * * *
16675564 CAAAAATCATATTTTTACCCCTAAACTTTC
1 CAAAAATCACATTTTAACCCC-AAATTTTT
** * * *
16675594 CAAAAATCACATTTTGCCCCCGAACTTCT
1 CAAAAATCACATTTTAACCCCAAATTTTT
* * ***
16675623 CAAAAATTACATTTTTACCCTC-AAGCATT
1 CAAAAATCACATTTTAACCC-CAAATTTTT
*
16675652 CAAAAAAT-ACCATTTT-ACCCTC-AATTTTC
1 C-AAAAATCA-CATTTTAACCC-CAAATTTTT
* *** * * *
16675681 CAAAAGTTTGACTTCAATCCCAAATTTTT
1 CAAAAATCACATTTTAACCCCAAATTTTT
16675710 CAAAAATTTCA-ATTTTAACCCCAAATTTTT
1 CAAAAA--TCACATTTTAACCCCAAATTTTT
16675740 CAAAAATCACATTTT
1 CAAAAATCACATTTT
16675755 CATCTCGGAT
Statistics
Matches: 188, Mismatches: 48, Indels: 28
0.71 0.18 0.11
Matches are distributed among these distances:
28 12 0.06
29 86 0.46
30 85 0.45
31 5 0.03
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (29 bp):
CAAAAATCACATTTTAACCCCAAATTTTT
Found at i:16676114 original size:97 final size:96
Alignment explanation
Indices: 16676008--16676200 Score: 314
Period size: 97 Copynumber: 2.0 Consensus size: 96
16675998 AAAACCTTTA
* *
16676008 AAATCGAGGTAATATTCTTTTATTTCGGGTTTTGAAAATTCATGCCTTAACTTACTAGACGCGAT
1 AAATCGAGGTAATATTCCTTTATTTCGGGTTTTGAAAATTCATGCCTTAACTTACTAGACGCGAC
16676073 TTTTCTTCAAACTGGGATAATCGAATACCCTT
66 TTTTCTTCAAACT-GGATAATCGAATACCCTT
* ** * *
16676105 AAATCGAGGTAATATTCCTTTATTTTGGGTTTTGAAAATTTGTGCCTTAACTTACTGGGCGCGAC
1 AAATCGAGGTAATATTCCTTTATTTCGGGTTTTGAAAATTCATGCCTTAACTTACTAGACGCGAC
16676170 TTTTCTTCAAACTGGATAATCGAATACCCTT
66 TTTTCTTCAAACTGGATAATCGAATACCCTT
16676201 TTTCAAGGTT
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
96 18 0.20
97 71 0.80
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (96 bp):
AAATCGAGGTAATATTCCTTTATTTCGGGTTTTGAAAATTCATGCCTTAACTTACTAGACGCGAC
TTTTCTTCAAACTGGATAATCGAATACCCTT
Found at i:16687599 original size:39 final size:39
Alignment explanation
Indices: 16687545--16688234 Score: 418
Period size: 39 Copynumber: 17.7 Consensus size: 39
16687535 AGAATATTCG
* * *
16687545 ATCTCTTACCCCGAGCTTGGGGTAAATCATCACCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGCCA
* * **
16687584 ATCTCTTACCCCGAGCCTGGGGCATATTA-CAACCATTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATC-ACCAGCCA
* * * ** *
16687623 ATCTCTTACCCTGATCTTAAGGCAGATCATTACCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGCCA
* * ****
16687662 ATCTCTTACCCCGAGCCTAGGGTAGAT--TGCAGCCATTTT
1 ATCTCTTACCCCGAGCCTGGGGCAGATCAT-CA-CCAGCCA
* * * *
16687701 ATCTCTTACCCCGAGCTTGGGGTAGATCATCATCAGCAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGCCA
* * * *
16687740 ATCTCTTACCCCAAGCCTAGGGCAGAT--TGCAACC-GTTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCAT-C-ACCAG-CCA
* * * *
16687779 ATCTCTTACACTGAGCCTGGGGAAGATCATCACTAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGCCA
* * * ** *
16687818 ATCTCTCACCCCTAGCCTGGGACAGAT--TGCAACCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCAT-C-ACCAGCCA
* * *
16687857 ATCTCTTACCCCGAGCTTGAGGCAGATCATCACTAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGCCA
* * ** *
16687896 ATCTCTTACCCCGAG-CTCGGGGAAGATTA-CAGCCATTCT
1 ATCTCTTACCCCGAGCCT-GGGGCAGATCATCA-CCAGCCA
* *
16687935 ATCTCTTACCTCGAGCCTGGGGCAGATCATCACCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGCCA
* ** * ** *
16687974 ATCTCTTACCTCGAGATTGGGGTAGAT--TGCAGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCAT-CA-CCAGCCA
* * **
16688013 ATCTCTTACCCCGAGCCTGGGACAGATCATCATCAGTAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGCCA
* * ** *
16688052 ATCTCTTACCCCGAGCCTGAGGCAGATTAAAACCA-CTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGC-CA
* * * **
16688091 ATCTCTTACCCTGAGCATGGGGCATATCATCAATAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGCCA
* * * ** *
16688130 ATCTCTTACCCCGAACCTTGGGCAGATTA-CAGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCA-CCAGCCA
* * * * ** *
16688169 ATCTCTTACCCCAAGCCTGAGGCAAATCACCTTCAGCAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGCCA
*
16688208 ATCTCTTACCCCGAGCCTAGGGCAGAT
1 ATCTCTTACCCCGAGCCTGGGGCAGAT
16688235 TGCAACCATT
Statistics
Matches: 480, Mismatches: 143, Indels: 56
0.71 0.21 0.08
Matches are distributed among these distances:
37 4 0.01
38 12 0.03
39 447 0.93
40 13 0.03
41 4 0.01
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCATCACCAGCCA
Found at i:16687674 original size:78 final size:78
Alignment explanation
Indices: 16687540--16688296 Score: 786
Period size: 78 Copynumber: 9.7 Consensus size: 78
16687530 AAGATAGAAT
* * * *
16687540 ATTCGATCTCTTACCCCGAGCTTGGGGTAAATCATCACCAGCCAATCTCTTACCCCGAGCCTGGG
1 ATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCTGGG
* *
16687605 GCATATTACAACC
66 GCAGATTGCAACC
* * * ** * *
16687618 ATTCAATCTCTTACCCTGATCTTAAGGCAGATCATTACCAGCCAATCTCTTACCCCGAGCCTAGG
1 ATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCTGGG
* *
16687683 GTAGATTGCAGCC
66 GCAGATTGCAACC
** * * * * * * *
16687696 ATTTTATCTCTTACCCCGAGCTTGGGGTAGATCATCATCAGCAAATCTCTTACCCCAAGCCTAGG
1 ATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCTGGG
16687761 GCAGATTGCAACC
66 GCAGATTGCAACC
* * * * * *
16687774 GTTCGATCTCTTACACTGAGCCTGGGGAAGATCATCACTAGCCAATCTCTCACCCCTAGCCTGGG
1 ATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCTGGG
*
16687839 ACAGATTGCAACC
66 GCAGATTGCAACC
* * * *
16687852 ATTCGATCTCTTACCCCGAGCTTGAGGCAGATCATCACTAGCCAATCTCTTACCCCGAG-CTCGG
1 ATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCT-GG
* * *
16687916 GGAAGATTACAGCC
65 GGCAGATTGCAACC
* * * **
16687930 ATTCTATCTCTTA-CCTCGAGCCTGGGGCAGATCATCACCAACCAATCTCTTACCTCGAGATTGG
1 ATTCGATCTCTTACCCT-GAGCCTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCTGG
* *
16687994 GGTAGATTGCAGCC
65 GGCAGATTGCAACC
* * * ** *
16688008 ATTCGATCTCTTACCCCGAGCCTGGGACAGATCATCATCAGTAAATCTCTTACCCCGAGCCTGAG
1 ATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCTGGG
**
16688073 GCAGATTAAAACC
66 GCAGATTGCAACC
* * * ** * *
16688086 ACTCGATCTCTTACCCTGAGCATGGGGCATATCATCAATAGCCAATCTCTTACCCCGAACCTTGG
1 ATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCTGGG
* *
16688151 GCAGATTACAGCC
66 GCAGATTGCAACC
** * * * ** * *
16688164 ATTCGATCTCTTACCCCAAGCCTGAGGCAAATCACCTTCAGCAAATCTCTTACCCCGAGCCTAGG
1 ATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCTGGG
16688229 GCAGATTGCAACC
66 GCAGATTGCAACC
* * * *
16688242 ATTCGATCTTTTACCCTGAG-CTTGGGCAAATCATCATCAGCCAATCTC--ACCCCGA
1 ATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGA
16688297 TCATGGGGTA
Statistics
Matches: 561, Mismatches: 114, Indels: 11
0.82 0.17 0.02
Matches are distributed among these distances:
75 7 0.01
77 27 0.05
78 524 0.93
79 3 0.01
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (78 bp):
ATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACCAGCCAATCTCTTACCCCGAGCCTGGG
GCAGATTGCAACC
Found at i:16687829 original size:156 final size:156
Alignment explanation
Indices: 16687540--16688322 Score: 889
Period size: 156 Copynumber: 5.0 Consensus size: 156
16687530 AAGATAGAAT
* * * * *
16687540 ATTCGATCTCTTACCCCGAGCTTGGGGTAAATCATCACCAGCCAATCTCTTACCCCGAGCCTGGG
1 ATTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTAGG
* * * * ** * *
16687605 GCATATTACAACCATTCAATCTCTTACCCTGATCTTAAGGCAGATCATTACCAGCCAATCTCTTA
66 GCAGATTACAACCATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACTAGCCAATCTCTTA
*
16687670 CCCCGAGCCTAGGGTAGATTGCAGCC
131 CCCCGAGCCTGGGGTAGATTGCAGCC
** * *
16687696 ATTTTATCTCTTACCCCGAGCTTGGGGTAGATCATCATCAGCAAATCTCTTACCCCAAGCCTAGG
1 ATTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTAGG
* * * * *
16687761 GCAGATTGCAACCGTTCGATCTCTTACACTGAGCCTGGGGAAGATCATCACTAGCCAATCTCTCA
66 GCAGATTACAACCATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACTAGCCAATCTCTTA
* ** *
16687826 CCCCTAGCCTGGGACAGATTGCAACC
131 CCCCGAGCCTGGGGTAGATTGCAGCC
* * *
16687852 ATTCGATCTCTTACCCCGAGCTTGAGGCAGATCATCA-CTAGCCAATCTCTTACCCCGAG-CTCG
1 ATTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCATC-AGCAAATCTCTTACCCCGAGCCT-A
* * * * *
16687915 GGGAAGATTACAGCCATTCTATCTCTTA-CCTCGAGCCTGGGGCAGATCATCACCAACCAATCTC
64 GGGCAGATTACAACCATTCGATCTCTTACCCT-GAGCCTGGGGCAGATCATCACTAGCCAATCTC
* **
16687979 TTACCTCGAGATTGGGGTAGATTGCAGCC
128 TTACCCCGAGCCTGGGGTAGATTGCAGCC
* * *
16688008 ATTCGATCTCTTACCCCGAGCCTGGGACAGATCATCATCAGTAAATCTCTTACCCCGAGCCT-GA
1 ATTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTAG-
* * * * *
16688072 GGCAGATTAAAACCACTCGATCTCTTACCCTGAGCATGGGGCATATCATCAATAGCCAATCTCTT
65 GGCAGATTACAACCATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACTAGCCAATCTCTT
* * * *
16688137 ACCCCGAACCTTGGGCAGATTACAGCC
130 ACCCCGAGCCTGGGGTAGATTGCAGCC
* * * * * *
16688164 ATTCGATCTCTTACCCCAAGCCTGAGGCAAATCACCTTCAGCAAATCTCTTACCCCGAGCCTAGG
1 ATTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTAGG
* * * *
16688229 GCAGATTGCAACCATTCGATCTTTTACCCTGAG-CTTGGGCAAATCATCA-TCAGCCAATCTC--
66 GCAGATTACAACCATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACT-AGCCAATCTCTT
* * * *
16688290 ACCCCGATCATGGGGTAGATGGCAGTC
130 ACCCCGAGCCTGGGGTAGATTGCAGCC
16688317 ATTCGA
1 ATTCGA
16688323 AGGAATAAAG
Statistics
Matches: 526, Mismatches: 92, Indels: 21
0.82 0.14 0.03
Matches are distributed among these distances:
153 26 0.05
154 1 0.00
155 29 0.06
156 463 0.88
157 7 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (156 bp):
ATTCGATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAGCAAATCTCTTACCCCGAGCCTAGG
GCAGATTACAACCATTCGATCTCTTACCCTGAGCCTGGGGCAGATCATCACTAGCCAATCTCTTA
CCCCGAGCCTGGGGTAGATTGCAGCC
Found at i:16687964 original size:234 final size:232
Alignment explanation
Indices: 16687540--16688296 Score: 921
Period size: 234 Copynumber: 3.2 Consensus size: 232
16687530 AAGATAGAAT
* *
16687540 ATTCGATCTCTTACCCCGAGCTTGGGGTAAATCATCACCAGCCAATCTCTTACCCCGAGCCTGGG
1 ATTCGATCTCTTACCCCGAGCCTGGGG-AAATCATCATCAGCCAATCTCTTACCCCGAGCCT-GG
* * * * * *
16687605 GCATATTACAACCATTCAATCTCTTACCCTGATCTTAAGGCAGATCATTACCAGCCAATCTCTTA
64 GCAGATTACAACCATTCGATCTCTTACCCTGAGCTTGAGGCAGATCATCACTAGCCAATCTCTTA
* * * * *
16687670 CCCCGAGCCTAGGGTAGATTGCAGCCATTTTATCTCTTACCCCGAGCTTGGGGTAGATCATCATC
129 CCCCGAGCCTAGGGAAGATTACAGCCATTCTATCTCTTACCCCGAGCCTGGGGCAGATCATCATC
*
16687735 AGCAAATCTCTTACCCCAAGCCTAGGGCAGATTGCAACC
194 AGCAAATCTCTTACCCCGAGCCTAGGGCAGATTGCAACC
* * * * *
16687774 GTTCGATCTCTTACACTGAGCCTGGGGAAGATCATCA-CTAGCCAATCTCTCACCCCTAGCCTGG
1 ATTCGATCTCTTACCCCGAGCCTGGGGAA-ATCATCATC-AGCCAATCTCTTACCCCGAGCCTGG
* *
16687838 GACAGATTGCAACCATTCGATCTCTTACCCCGAGCTTGAGGCAGATCATCACTAGCCAATCTCTT
64 G-CAGATTACAACCATTCGATCTCTTACCCTGAGCTTGAGGCAGATCATCACTAGCCAATCTCTT
* *
16687903 ACCCCGAG-CTCGGGGAAGATTACAGCCATTCTATCTCTTACCTCGAGCCTGGGGCAGATCATCA
128 ACCCCGAGCCT-AGGGAAGATTACAGCCATTCTATCTCTTACCCCGAGCCTGGGGCAGATCATCA
* * * * ** * * *
16687967 CCAACCAATCTCTTACCTCGAGATTGGGGTAGATTGCAGCC
192 TCAGCAAATCTCTTACCCCGAGCCTAGGGCAGATTGCAACC
**
16688008 ATTCGATCTCTTACCCCGAGCCT-GGGACAGATCATCATCAGTAAATCTCTTACCCCGAGCCTGA
1 ATTCGATCTCTTACCCCGAGCCTGGGGA-A-ATCATCATCAGCCAATCTCTTACCCCGAGCCTG-
* * * * * *
16688072 GGCAGATTAAAACCACTCGATCTCTTACCCTGAGCATGGGGCATATCATCAATAGCCAATCTCTT
63 GGCAGATTACAACCATTCGATCTCTTACCCTGAGCTTGAGGCAGATCATCACTAGCCAATCTCTT
* * * * * * * * *
16688137 ACCCCGAACCTTGGGCAGATTACAGCCATTCGATCTCTTACCCCAAGCCTGAGGCAAATCACCTT
128 ACCCCGAGCCTAGGGAAGATTACAGCCATTCTATCTCTTACCCCGAGCCTGGGGCAGATCATCAT
16688202 CAGCAAATCTCTTACCCCGAGCCTAGGGCAGATTGCAACC
193 CAGCAAATCTCTTACCCCGAGCCTAGGGCAGATTGCAACC
* * * *
16688242 ATTCGATCTTTTACCCTGAGCTTGGGCAAATCATCATCAGCCAATCTC--ACCCCGA
1 ATTCGATCTCTTACCCCGAGCCTGGGGAAATCATCATCAGCCAATCTCTTACCCCGA
16688297 TCATGGGGTA
Statistics
Matches: 443, Mismatches: 71, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
231 7 0.02
233 29 0.07
234 399 0.90
235 8 0.02
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (232 bp):
ATTCGATCTCTTACCCCGAGCCTGGGGAAATCATCATCAGCCAATCTCTTACCCCGAGCCTGGGC
AGATTACAACCATTCGATCTCTTACCCTGAGCTTGAGGCAGATCATCACTAGCCAATCTCTTACC
CCGAGCCTAGGGAAGATTACAGCCATTCTATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAG
CAAATCTCTTACCCCGAGCCTAGGGCAGATTGCAACC
Found at i:16688743 original size:17 final size:17
Alignment explanation
Indices: 16688721--16688816 Score: 104
Period size: 17 Copynumber: 5.7 Consensus size: 17
16688711 AAACTCATTT
* **
16688721 TTTAAATTTGTTTTAGG
1 TTTAAATTTATTTTAAA
16688738 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
16688755 TTTAAATTAATTTTGAG
1 TTTAAATTTATTTTAAA
*
16688772 TTTAAATTAATTTTAAA
1 TTTAAATTTATTTTAAA
* *
16688789 TTCAAAATTA-TTTAAA
1 TTTAAATTTATTTTAAA
16688805 TTTAAATTTATT
1 TTTAAATTTATT
16688817 CAAATCTAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
16 14 0.22
17 51 0.78
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:16688752 original size:11 final size:11
Alignment explanation
Indices: 16688738--16688790 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
16688728 TTGTTTTAGG
16688738 TTTAAATTTAT
1 TTTAAATTTAT
*
16688749 TTTAAATTTAA
1 TTTAAATTTAT
* * *
16688760 ATTAATTTTGAG
1 TTTAAATTT-AT
*
16688772 TTTAAATTAAT
1 TTTAAATTTAT
16688783 TTTAAATT
1 TTTAAATT
16688791 CAAAATTATT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
11 26 0.79
12 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:16688764 original size:5 final size:6
Alignment explanation
Indices: 16688738--16688814 Score: 56
Period size: 6 Copynumber: 13.7 Consensus size: 6
16688728 TTGTTTTAGG
* * * * *
16688738 TTTAAA TTT-AT TTTAAA TTTAAA -TTAAT TTTGAG TTTAAA -TTAAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
16688783 TTTAAA TTCAAA ATT--A TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
16688815 TTCAAATCTA
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
4 3 0.06
5 12 0.23
6 38 0.72
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:16688804 original size:16 final size:16
Alignment explanation
Indices: 16688783--16688821 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
16688773 TTAAATTAAT
16688783 TTTAAATTCAAAATTA
1 TTTAAATTCAAAATTA
* *
16688799 TTTAAATTTAAATTTA
1 TTTAAATTCAAAATTA
*
16688815 TTCAAAT
1 TTTAAAT
16688822 CTAAAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTAAATTCAAAATTA
Found at i:16690681 original size:59 final size:59
Alignment explanation
Indices: 16690618--16690758 Score: 162
Period size: 59 Copynumber: 2.4 Consensus size: 59
16690608 AAACTTTTTT
* * *
16690618 AAAAATTACATTTTAG-CCTCCGAACTTC-CAAAAATCACATTTTTACCCTTGAACTTTCC
1 AAAAATTACATTTTAGCCCT-CAAACTTCTCAAAAATCACATTTTTACCCCTGAAC-ATCC
* * * *
16690677 AAAAATCACATTTTTGCCCTCAAACTTCTCAAAAATTACATTTTTACCCCTGAGCATCC
1 AAAAATTACATTTTAGCCCTCAAACTTCTCAAAAATCACATTTTTACCCCTGAACATCC
*
16690736 AAAAATTACCATTCTA-CCCTCAA
1 AAAAATTA-CATTTTAGCCCTCAA
16690759 TTTTCCAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
59 38 0.55
60 31 0.45
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.32
Consensus pattern (59 bp):
AAAAATTACATTTTAGCCCTCAAACTTCTCAAAAATCACATTTTTACCCCTGAACATCC
Found at i:16690738 original size:29 final size:29
Alignment explanation
Indices: 16690543--16690744 Score: 133
Period size: 30 Copynumber: 6.7 Consensus size: 29
16690533 TCCAGAAGGT
* *
16690543 CCCTGAACTATCCAAAAAATCACATTTTGAC
1 CCCTGAACT-TCC-AAAAATTACATTTTTAC
* * * *
16690574 TCCCTAAACTTTCTAAAAAATACATTTTGAC
1 -CCCTGAAC-TTCCAAAAATTACATTTTTAC
* **
16690605 CCC-AAACTTTTTTAAAAATTACA-TTTTAGC
1 CCCTGAAC--TTCCAAAAATTACATTTTTA-C
*
16690635 CTCC-GAACTTCCAAAAATCACATTTTTAC
1 C-CCTGAACTTCCAAAAATTACATTTTTAC
* * *
16690664 CCTTGAACTTTCCAAAAATCACATTTTT-G
1 CCCTGAAC-TTCCAAAAATTACATTTTTAC
*
16690693 CCCTCAAACTTCTCAAAAATTACATTTTTAC
1 CCCT-GAACTTC-CAAAAATTACATTTTTAC
* *
16690724 CCCTGAGCATCCAAAAATTAC
1 CCCTGAACTTCCAAAAATTAC
16690745 CATTCTACCC
Statistics
Matches: 140, Mismatches: 20, Indels: 23
0.77 0.11 0.13
Matches are distributed among these distances:
28 1 0.01
29 41 0.29
30 64 0.46
31 24 0.17
32 9 0.06
33 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (29 bp):
CCCTGAACTTCCAAAAATTACATTTTTAC
Found at i:16691196 original size:97 final size:97
Alignment explanation
Indices: 16691078--16691280 Score: 255
Period size: 97 Copynumber: 2.1 Consensus size: 97
16691068 TCATACAAAT
* * * *
16691078 AAACCTTTAAAATCGAGGCAATATTCCTTTATTTTGGGTTTTGAAAATTCATGTCTTAACTT-AC
1 AAACCCTT-AAATCGAAGCAATATTCCTTTATTTCGGGTTTTGAAAATTCATGCCTTAA-TTAAC
* * * *
16691142 TATGCGTAATTTTTCTTCAAACTGGGATAATCGA
64 TAGGCGCAACTTTTCTTCAAACCGGGATAATCGA
* * ** *
16691176 ATACCCTTAAATCGAAGCAATATTCTTTTATTTCGGGTTTTGAAAATTTGTGCCTTAATTAATTA
1 AAACCCTTAAATCGAAGCAATATTCCTTTATTTCGGGTTTTGAAAATTCATGCCTTAATTAACTA
*
16691241 GGCGCGACTTTTCTTCAAACCGGGATAATCGA
66 GGCGCAACTTTTCTTCAAACCGGGATAATCGA
16691273 AAACCCTT
1 AAACCCTT
16691281 TTTCAAGATT
Statistics
Matches: 89, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
96 2 0.02
97 81 0.91
98 6 0.07
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (97 bp):
AAACCCTTAAATCGAAGCAATATTCCTTTATTTCGGGTTTTGAAAATTCATGCCTTAATTAACTA
GGCGCAACTTTTCTTCAAACCGGGATAATCGA
Found at i:16699559 original size:42 final size:42
Alignment explanation
Indices: 16699503--16699698 Score: 153
Period size: 43 Copynumber: 4.6 Consensus size: 42
16699493 TATGCTCTAA
* * **
16699503 CGAGACAT-AGGTCTTTCTTTAAACAAAATATCATGCTTTTTC
1 CGAGACATGA-GTCTTCCTTTAAACATAATATCATGCTCATTC
* * *
16699545 CGAGACATGAGTCTTCCTTT-AATATAATCTCATGCTCTTTTC
1 CGAGACATGAGTCTTCCTTTAAACATAATATCATGCTC-ATTC
* * * *
16699587 TGAGACATGAGGCTTCCTTTAAATATAATCTCATGCTCATTC
1 CGAGACATGAGTCTTCCTTTAAACATAATATCATGCTCATTC
* * * * * * * *
16699629 CAAGTCACGAGTATTTCATTTATACATAATATCACGCTCATCC
1 CGAGACATGAGT-CTTCCTTTAAACATAATATCATGCTCATTC
* *
16699672 CAAGACATGAGTCTTCCATTTATACAT
1 CGAGACATGAGTCTTCC-TTTAAACAT
16699699 CAAGTGATTC
Statistics
Matches: 125, Mismatches: 24, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
41 13 0.10
42 52 0.42
43 60 0.48
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (42 bp):
CGAGACATGAGTCTTCCTTTAAACATAATATCATGCTCATTC
Found at i:16699613 original size:43 final size:43
Alignment explanation
Indices: 16699503--16699624 Score: 160
Period size: 42 Copynumber: 2.9 Consensus size: 43
16699493 TATGCTCTAA
* * * *
16699503 CGAGACAT-AGGTCTTTCTTTAAACAAAATATCATGCT-TTTTC
1 CGAGACATGAGG-CTTCCTTTAAATATAATCTCATGCTCTTTTC
*
16699545 CGAGACATGAGTCTTCCTTT-AATATAATCTCATGCTCTTTTC
1 CGAGACATGAGGCTTCCTTTAAATATAATCTCATGCTCTTTTC
*
16699587 TGAGACATGAGGCTTCCTTTAAATATAATCTCATGCTC
1 CGAGACATGAGGCTTCCTTTAAATATAATCTCATGCTC
16699625 ATTCCAAGTC
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 13 0.19
42 38 0.54
43 19 0.27
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (43 bp):
CGAGACATGAGGCTTCCTTTAAATATAATCTCATGCTCTTTTC
Found at i:16701750 original size:20 final size:20
Alignment explanation
Indices: 16701727--16701771 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
16701717 TGCATTACGA
16701727 TGCCTCTATTTACATTTCGG
1 TGCCTCTATTTACATTTCGG
* **
16701747 TGCCCCTATTTGTATTTCGG
1 TGCCTCTATTTACATTTCGG
*
16701767 CGCCT
1 TGCCT
16701772 TTGTATTGCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.11, C:0.29, G:0.18, T:0.42
Consensus pattern (20 bp):
TGCCTCTATTTACATTTCGG
Found at i:16702622 original size:27 final size:27
Alignment explanation
Indices: 16702577--16702648 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
16702567 GATTGGTTAG
* **
16702577 CTCTTACGAGCCCAGAATCAGAATAATG
1 CTCTTTCGAG-CCAGAATCAGAATAACA
*
16702605 CTTTTTCGAGCCAGAATCAGAATAACA
1 CTCTTTCGAGCCAGAATCAGAATAACA
16702632 CTCTTTCGAGCCAGAAT
1 CTCTTTCGAGCCAGAAT
16702649 TAGATTACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 31 0.79
28 8 0.21
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (27 bp):
CTCTTTCGAGCCAGAATCAGAATAACA
Found at i:16707401 original size:26 final size:27
Alignment explanation
Indices: 16707338--16707401 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
16707328 TCTTACAAGC
*
16707338 CCAGAATCAGAATAATGCTTTTTCGAG
1 CCAGAATCAGAATAACGCTTTTTCGAG
16707365 CCAGAATCAGAATAACG-TCTTTT-GAG
1 CCAGAATCAGAATAACGCT-TTTTCGAG
*
16707391 CCAGAAACAGA
1 CCAGAATCAGA
16707402 TTACTCCTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 14 0.41
27 20 0.59
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (27 bp):
CCAGAATCAGAATAACGCTTTTTCGAG
Found at i:16709670 original size:54 final size:54
Alignment explanation
Indices: 16709548--16709675 Score: 152
Period size: 54 Copynumber: 2.4 Consensus size: 54
16709538 CACGGTTTGA
* * *
16709548 GACACAATCGTGTGTCCCAAGTTAGTGAGTTACACGGTCTAGGACATGGGTTGT
1 GACACAGTCGTGTGTCCCAAGTCAGTGAGTTACACGGTCTAGGACATGGGTTGG
* * *
16709602 GACACAGCCATGTGTCCCAAGTCAGTGAGTTACACGGT-TGATGACACT-GGTTGG
1 GACACAGTCGTGTGTCCCAAGTCAGTGAGTTACACGGTCT-AGGACA-TGGGTTGG
**
16709656 GACATGGTCGTGTGTCCCAA
1 GACACAGTCGTGTGTCCCAA
16709676 CTTCGAAAGC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
53 1 0.02
54 60 0.97
55 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (54 bp):
GACACAGTCGTGTGTCCCAAGTCAGTGAGTTACACGGTCTAGGACATGGGTTGG
Found at i:16711916 original size:12 final size:12
Alignment explanation
Indices: 16711899--16711924 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16711889 AAAATTCAAT
16711899 AATATTTAATTA
1 AATATTTAATTA
16711911 AATATTTAATTA
1 AATATTTAATTA
16711923 AA
1 AA
16711925 CTCTTAACTA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AATATTTAATTA
Found at i:16713690 original size:18 final size:20
Alignment explanation
Indices: 16713667--16713705 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
16713657 TAATTTATCA
*
16713667 ACTTAA-ATATTATA-ATAT
1 ACTTAACATATAATACATAT
16713685 ACTTAACATATAATACATAT
1 ACTTAACATATAATACATAT
16713705 A
1 A
16713706 ATACTAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
ACTTAACATATAATACATAT
Found at i:16715915 original size:24 final size:24
Alignment explanation
Indices: 16715831--16715905 Score: 141
Period size: 24 Copynumber: 3.1 Consensus size: 24
16715821 AGAAATAATC
*
16715831 TTTCAGTTAAACTTTGTTTATTTG
1 TTTCAATTAAACTTTGTTTATTTG
16715855 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTTTGTTTATTTG
16715879 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAATTAAACTTTGTTTATTTG
16715903 TTT
1 TTT
16715906 GAGTCAAACT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.23, C:0.08, G:0.09, T:0.60
Consensus pattern (24 bp):
TTTCAATTAAACTTTGTTTATTTG
Found at i:16719641 original size:25 final size:25
Alignment explanation
Indices: 16719611--16719661 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
16719601 ATAACAAAAA
*
16719611 ATGATTGCTTAATATTAGTAATATG
1 ATGATTGCTTAATATTACTAATATG
16719636 ATGATTGCTTAATATTACTAATATG
1 ATGATTGCTTAATATTACTAATATG
16719661 A
1 A
16719662 GAGAGAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (25 bp):
ATGATTGCTTAATATTACTAATATG
Found at i:16723338 original size:21 final size:21
Alignment explanation
Indices: 16723300--16723340 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16723290 CATTTTACAT
*
16723300 ATATACATTGTATGCATGTTC
1 ATATACATGGTATGCATGTTC
16723321 ATATACATGGATAT-CATGTT
1 ATATACATGG-TATGCATGTT
16723341 ACGAGAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (21 bp):
ATATACATGGTATGCATGTTC
Found at i:16729333 original size:17 final size:17
Alignment explanation
Indices: 16729306--16729348 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
16729296 ACAGAATTAA
*
16729306 AATTGAATTGAAAAAATT
1 AATTTAATTG-AAAAATT
*
16729324 -ATTTAATTGAGAAATT
1 AATTTAATTGAAAAATT
16729340 AATTTAATT
1 AATTTAATT
16729349 AATTAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
AATTTAATTGAAAAATT
Found at i:16729354 original size:13 final size:14
Alignment explanation
Indices: 16729335--16729368 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
16729325 TTTAATTGAG
16729335 AAATTAATTTAATT
1 AAATTAATTTAATT
16729349 -AATTAA-TTAATT
1 AAATTAATTTAATT
16729361 AAATTAAT
1 AAATTAAT
16729369 GGAATAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATTAATTTAATT
Found at i:16729356 original size:17 final size:17
Alignment explanation
Indices: 16729336--16729368 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16729326 TTAATTGAGA
*
16729336 AATTAATTTAATTAATT
1 AATTAATTAAATTAATT
16729353 AATTAATTAAATTAAT
1 AATTAATTAAATTAAT
16729369 GGAATAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTAATTAAATTAATT
Found at i:16731232 original size:17 final size:17
Alignment explanation
Indices: 16731210--16731243 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16731200 AATGTTTTTA
16731210 TTTAATTTTAATATATT
1 TTTAATTTTAATATATT
*
16731227 TTTAATTTTAATTTATT
1 TTTAATTTTAATATATT
16731244 AAAAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTAATTTTAATATATT
Found at i:16731447 original size:17 final size:17
Alignment explanation
Indices: 16731420--16731465 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
16731410 AAAATAGTTG
* *
16731420 AATTCTAAAATTTTAAC
1 AATTTTAAAATTTTAAA
* *
16731437 ATTTTTAAAATCTTAAA
1 AATTTTAAAATTTTAAA
16731454 AATTTTAAAATT
1 AATTTTAAAATT
16731466 CTTCAAACAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTTAAAATTTTAAA
Found at i:16743464 original size:20 final size:21
Alignment explanation
Indices: 16743430--16743468 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16743420 CATTTTTCTA
*
16743430 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
16743451 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
16743469 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:16745660 original size:3 final size:3
Alignment explanation
Indices: 16745646--16745699 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
16745636 GCACAAAGAC
* * *
16745646 AAG AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAA AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
16745694 AAG AAG
1 AAG AAG
16745700 CACAAAAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16746471 original size:16 final size:16
Alignment explanation
Indices: 16746450--16746480 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16746440 AAAAAACATG
*
16746450 AGAAAAAGGAAGAAAA
1 AGAAAAAGAAAGAAAA
16746466 AGAAAAAGAAAGAAA
1 AGAAAAAGAAAGAAA
16746481 TTTTTGATAA
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAGAAAA
Found at i:16751834 original size:36 final size:35
Alignment explanation
Indices: 16751804--16752038 Score: 224
Period size: 36 Copynumber: 6.5 Consensus size: 35
16751794 ATGGCCTTAT
* *
16751804 GCTCTAACAGAGACATAAGCAATCACATGGCATTA-
1 GCTCTAAC-GAGACGTAAGCAATCACATAGCATTAC
* * *
16751839 GCTCTAACTGAGATGTAAGCAATCA-ATTAGCAATAT
1 GCTCTAAC-GAGACGTAAGCAATCACA-TAGCATTAC
* * *
16751875 GCTCTAATCGAGACATACA-CAATCACATAACATTAT
1 GCTCTAA-CGAGACGTA-AGCAATCACATAGCATTAC
* * *
16751911 GCTCTAATCGAGACGTAAGCAATTACTTAGCAATAC
1 GCTCTAA-CGAGACGTAAGCAATCACATAGCATTAC
*
16751947 GCTCTAACTGAGACGTACGCAATCACATAGCATTAC
1 GCTCTAAC-GAGACGTAAGCAATCACATAGCATTAC
* *
16751983 GCTTTAACCGAGACGTATGCAATCACATAGCATTAC
1 GCTCTAA-CGAGACGTAAGCAATCACATAGCATTAC
* *
16752019 GCTATAATCGAGACATAAGC
1 GCTCTAA-CGAGACGTAAGC
16752039 TCTTCATCGA
Statistics
Matches: 167, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
34 1 0.01
35 30 0.18
36 132 0.79
37 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (35 bp):
GCTCTAACGAGACGTAAGCAATCACATAGCATTAC
Found at i:16751995 original size:108 final size:107
Alignment explanation
Indices: 16751800--16752038 Score: 284
Period size: 108 Copynumber: 2.2 Consensus size: 107
16751790 TGAAATGGCC
* * *
16751800 TTATGCTCTAA-CAGAGACATAAGCAATCACATGGCATTAGCTCTAACTGAGATGTAAGCAATCA
1 TTATGCTCTAATC-GAGACATAAGCAATCACATAGCAATAGCTCTAACTGAGACGTAAGCAATCA
* *
16751864 ATTAGCAATATGCTCTAATCGAGACATACACAATCACATAACA
65 ATTAGCAATACGCTCTAACCGAGACATACACAATCACATAACA
* * * *
16751907 TTATGCTCTAATCGAGACGTAAGCAATTACTTAGCAATACGCTCTAACTGAGACGTACGCAATCA
1 TTATGCTCTAATCGAGACATAAGCAATCACATAGCAATA-GCTCTAACTGAGACGTAAGCAATCA
* * * ** *
16751972 CA-TAGCATTACGCTTTAACCGAGACGTATGCAATCACATAGCA
65 -ATTAGCAATACGCTCTAACCGAGACATACACAATCACATAACA
* *
16752015 TTACGCTATAATCGAGACATAAGC
1 TTATGCTCTAATCGAGACATAAGC
16752039 TCTTCATCGA
Statistics
Matches: 111, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
107 32 0.29
108 78 0.70
109 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (107 bp):
TTATGCTCTAATCGAGACATAAGCAATCACATAGCAATAGCTCTAACTGAGACGTAAGCAATCAA
TTAGCAATACGCTCTAACCGAGACATACACAATCACATAACA
Found at i:16758377 original size:31 final size:28
Alignment explanation
Indices: 16758342--16758410 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 28
16758332 ATGTCACATT
16758342 TGGTACTTATACTTTCATAAAATGTCCAACG
1 TGGTACTTATACTTTC--AAAATGT-CAACG
* * *
16758373 TGGTACATGTACTTTCAAAATGTCAATG
1 TGGTACTTATACTTTCAAAATGTCAACG
16758401 TGGTATCTTA
1 TGGTA-CTTA
16758411 ACTATTAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 9 0.28
29 9 0.28
31 14 0.44
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (28 bp):
TGGTACTTATACTTTCAAAATGTCAACG
Found at i:16758546 original size:92 final size:90
Alignment explanation
Indices: 16758339--16758614 Score: 356
Period size: 92 Copynumber: 3.0 Consensus size: 90
16758329 ATAATGTCAC
* *
16758339 ATTTGGTACTTATACTTTCATAAAATGTCCAACGTGGTACATGTACTTTCAAAATGTCAATGTGG
1 ATTTGGTACTTATACTTTCATAAAATGTACAATGTGGTACATGTACTTTCAAAATGTCAATGTGG
*
16758404 TATCTT-AACTATTAATTTGTGTATT
66 TA-CTTGAACTATCAATTTGTGTATT
* ** * * *
16758429 ATTTGGTACCTATACTTTCATAAAATGTTTAATGTGGTACCTGTACTTTTAAAATGTCCAATAAT
1 ATTTGGTACTTATACTTTCATAAAATGTACAATGTGGTACATGTACTTTCAAAATGT-CAAT-GT
16758494 GGTACTTGAACTATCAATTTGTGTATT
64 GGTACTTGAACTATCAATTTGTGTATT
* * * * * * *
16758521 ATTTGTTACTTTTACTTTCCTAAAATGTACAATGTGGTACTTATACTTTGAAAATATTCAATGTG
1 ATTTGGTACTTATACTTTCATAAAATGTACAATGTGGTACATGTACTTTCAAAAT-GTCAATGTG
*
16758586 GTACATGAACTATCAATTTGTGTATT
65 GTACTTGAACTATCAATTTGTGTATT
16758612 ATT
1 ATT
16758615 ATGGCATTTG
Statistics
Matches: 162, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
90 51 0.31
91 37 0.23
92 73 0.45
93 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (90 bp):
ATTTGGTACTTATACTTTCATAAAATGTACAATGTGGTACATGTACTTTCAAAATGTCAATGTGG
TACTTGAACTATCAATTTGTGTATT
Found at i:16760925 original size:6 final size:6
Alignment explanation
Indices: 16760900--16760938 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
16760890 ACAATTCATA
* * *
16760900 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
16760939 ATTTTGATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:16765273 original size:14 final size:15
Alignment explanation
Indices: 16765249--16765277 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
16765239 TGCACGATGC
16765249 TTTTTCTTCCTCCTT
1 TTTTTCTTCCTCCTT
16765264 TTTTTC-TCCTCCTT
1 TTTTTCTTCCTCCTT
16765278 GTGCTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTCTTCCTCCTT
Found at i:16766676 original size:51 final size:51
Alignment explanation
Indices: 16766599--16766703 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
16766589 GGATTAAACC
* *
16766599 TTCTCGAACAAAGATGAACTCTAACTCATGGTTATAAAGGTTAGCGTAAAA
1 TTCTCGAACAAAGATGAACTCCAACTCATGGTCATAAAGGTTAGCGTAAAA
16766650 TTCTCGAACAAAGATGAACTCCAACTCATGGTCATAAAGGTTAGCGTAAAA
1 TTCTCGAACAAAGATGAACTCCAACTCATGGTCATAAAGGTTAGCGTAAAA
16766701 TTC
1 TTC
16766704 GCATACCATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (51 bp):
TTCTCGAACAAAGATGAACTCCAACTCATGGTCATAAAGGTTAGCGTAAAA
Found at i:16779377 original size:6 final size:6
Alignment explanation
Indices: 16779343--16779404 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
16779333 TAATAGAGAT
* * * *
16779343 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
*
16779390 TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTT
16779405 TGAACACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 40 0.85
7 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:16784228 original size:40 final size:37
Alignment explanation
Indices: 16784161--16784253 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 37
16784151 CCAGAATGGT
*
16784161 ACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGGC
1 ACCCAGTGCCTCATCGGATAGTCCGAAG---TAAAGTGGC
* * *
16784201 ACCCAGTGTCTCATCGGCCTAG-CCGAAGTAAAGTGGT
1 ACCCAGTGCCTCATCGG-ATAGTCCGAAGTAAAGTGGC
*
16784238 ACCCAGTACCTCATCG
1 ACCCAGTGCCTCATCG
16784254 AATCTATCTG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
37 22 0.48
40 21 0.46
41 3 0.07
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (37 bp):
ACCCAGTGCCTCATCGGATAGTCCGAAGTAAAGTGGC
Found at i:16784242 original size:37 final size:38
Alignment explanation
Indices: 16784157--16784253 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 38
16784147 CACACCAGAA
*
16784157 TGGTACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAG
1 TGGTACCCAGTGCCTCATCGGATAGTCCGAAG--ATAAAG
* * *
16784197 TGGCACCCAGTGTCTCATCGGCCTAG-CCGAAG-TAAAG
1 TGGTACCCAGTGCCTCATCGG-ATAGTCCGAAGATAAAG
*
16784234 TGGTACCCAGTACCTCATCG
1 TGGTACCCAGTGCCTCATCG
16784254 AATCTATCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
37 22 0.45
40 24 0.49
41 3 0.06
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.22
Consensus pattern (38 bp):
TGGTACCCAGTGCCTCATCGGATAGTCCGAAGATAAAG
Found at i:16784413 original size:6 final size:6
Alignment explanation
Indices: 16784379--16784446 Score: 59
Period size: 6 Copynumber: 11.5 Consensus size: 6
16784369 TAATAGAGAT
* * * *
16784379 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* *
16784426 TTTCAC TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTT
16784447 TGATCACAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 46 0.87
7 3 0.06
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:16784421 original size:18 final size:18
Alignment explanation
Indices: 16784398--16784446 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
16784388 ACAATTCATA
16784398 TCACTTTCAATTTCAATT
1 TCACTTTCAATTTCAATT
* *
16784416 TCACTTTCACTTTCACTT
1 TCACTTTCAATTTCAATT
16784434 TCACTTTCAATTT
1 TCACTTTCAATTT
16784447 TGATCACAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (18 bp):
TCACTTTCAATTTCAATT
Found at i:16784423 original size:12 final size:12
Alignment explanation
Indices: 16784398--16784446 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
16784388 ACAATTCATA
16784398 TCACTTTCAATT
1 TCACTTTCAATT
* *
16784410 TCAATTTCACTT
1 TCACTTTCAATT
*
16784422 TCACTTTCACTT
1 TCACTTTCAATT
16784434 TCACTTTCAATT
1 TCACTTTCAATT
16784446 T
1 T
16784447 TGATCACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.22, C:0.27, G:0.00, T:0.51
Consensus pattern (12 bp):
TCACTTTCAATT
Found at i:16787802 original size:68 final size:67
Alignment explanation
Indices: 16787686--16787929 Score: 323
Period size: 68 Copynumber: 3.6 Consensus size: 67
16787676 GGCGGACTTT
* * *
16787686 TATTTGTTGCCATAGCCGAGCTATGGTCTTACACCTTGTAACCCCATGTTTATTGTCTTGGCATA
1 TATTGGTTGCCATAGCCGAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATGTCTTGACA-A
16787751 CTC
65 CTC
* * *
16787754 TATTGGGTGCCATAACCGAGCTATGGTCTTGCACCTTGTAACCCCATGTTTAATGTCTTGACGAA
1 TATTGGTTGCCATAGCCGAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATGTCTTGAC-AA
16787819 CTC
65 CTC
* * * *
16787822 TATTGGTTG---TCGCCGAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATATCCTGATAGA
1 TATTGGTTGCCATAGCCGAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATGTCTTGACA-A
16787884 CTC
65 CTC
* * *
16787887 TATTGGTTGTCATAGCCGAGCTATGGCCTTACACTTTGTAACC
1 TATTGGTTGCCATAGCCGAGCTATGGTCTTACACCTTGTAACC
16787930 TCTTTTGAGG
Statistics
Matches: 155, Mismatches: 16, Indels: 10
0.86 0.09 0.06
Matches are distributed among these distances:
64 1 0.01
65 57 0.37
68 96 0.62
69 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (67 bp):
TATTGGTTGCCATAGCCGAGCTATGGTCTTACACCTTGTAACCCCATGTTTAATGTCTTGACAAC
TC
Found at i:16789700 original size:90 final size:88
Alignment explanation
Indices: 16789598--16789887 Score: 304
Period size: 90 Copynumber: 3.2 Consensus size: 88
16789588 GAGAATTTGA
* *
16789598 GGTCAAAATGTAATTTATGGAAAATTTAGGGGGT-GAAATGTAATTTTTAGAAAGGTTCAAGGGT
1 GGTCAAAATGTAATTT-TGGAAAATTTA-GGGGTAAAAATGTAATTTTTAGAAA-GTTTAAGGGT
16789662 TAAAATGTAATTTTAGGAAGTTTAAG
63 TAAAATGTAATTTTAGGAAGTTTAAG
* * **
16789688 GGTCAAAATGTAATTTTAGG-AAGTTTAGGGGTCAAAATGTAATTTTGGGAAAGTTTAAGGGTTA
1 GGTCAAAATGTAATTTT-GGAAAATTTAGGGGTAAAAATGTAATTTTTAGAAAGTTTAAGGGTTA
*
16789752 AAATGTAATTTTAAGAAAGTTT-AG
65 AAATGTAATTTT-AGGAAGTTTAAG
* * * *
16789776 AGGTTAAAATATAATTTTGGAGAAGTTTTA-GGGTAAAAATGTAA-TTTTAGAAAAGTTTAGGGG
1 -GGTCAAAATGTAATTTTGGA-AA-ATTTAGGGGTAAAAATGTAATTTTTAG-AAAGTTTAAGGG
*** *
16789839 TTAAAACAAAATTTT-GGATAAATTTAAG
62 TTAAAATGTAATTTTAGG--AAGTTTAAG
16789867 GGTCAAAATGTAATTTTGGAA
1 GGTCAAAATGTAATTTTGGAA
16789888 GAGTTCAGGG
Statistics
Matches: 169, Mismatches: 20, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
88 33 0.20
89 51 0.30
90 79 0.47
91 6 0.04
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (88 bp):
GGTCAAAATGTAATTTTGGAAAATTTAGGGGTAAAAATGTAATTTTTAGAAAGTTTAAGGGTTAA
AATGTAATTTTAGGAAGTTTAAG
Found at i:16789739 original size:119 final size:118
Alignment explanation
Indices: 16789598--16789883 Score: 344
Period size: 119 Copynumber: 2.4 Consensus size: 118
16789588 GAGAATTTGA
* *
16789598 GGTCAAAATGTAATTTATGGAAAATTTAGGGGGTGAAATGTAATTTTTAGAAAGGTTCAAG-GGT
1 GGTCAAAATGTAATTT-TGGAAAATTTA-GGGGTAAAATGTAATTTTAAGAAA-GTT-AAGAGGT
* * *
16789662 TAAAATGTAATTTTAG-GAAGTTTAAGGGTCAAAATGTAATTTTAG-GAAGTTTAGG
62 TAAAATATAATTTTAGAGAAGTTTAAGGGTAAAAATGTAATTTTAGAAAAGTTTAGG
* * *
16789717 GGTCAAAATGTAATTTTGGGAAAGTTTAAGGGTTAAAATGTAATTTTAAGAAAGTTTAGAGGTTA
1 GGTCAAAATGTAATTTT-GGAAAATTT-AGGGGTAAAATGTAATTTTAAGAAAGTTAAGAGGTTA
* *
16789782 AAATATAATTTTGGAGAAGTTTTAGGGTAAAAATGTAATTTTAGAAAAGTTTAGG
64 AAATATAATTTTAGAGAAGTTTAAGGGTAAAAATGTAATTTTAGAAAAGTTTAGG
* *** *
16789837 GGTTAAAACAAAATTTTGGATAAATTTAAGGGTCAAAATGTAATTTT
1 GGTCAAAATGTAATTTTGGA-AAATTTAGGGGT-AAAATGTAATTTT
16789884 GGAAGAGTTC
Statistics
Matches: 143, Mismatches: 17, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
117 2 0.01
118 21 0.15
119 79 0.55
120 41 0.29
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.35
Consensus pattern (118 bp):
GGTCAAAATGTAATTTTGGAAAATTTAGGGGTAAAATGTAATTTTAAGAAAGTTAAGAGGTTAAA
ATATAATTTTAGAGAAGTTTAAGGGTAAAAATGTAATTTTAGAAAAGTTTAGG
Found at i:16789742 original size:30 final size:29
Alignment explanation
Indices: 16789598--16789898 Score: 259
Period size: 30 Copynumber: 10.1 Consensus size: 29
16789588 GAGAATTTGA
*
16789598 GGTCAAAATGTAATTTATGGAAAATTTAGGG
1 GGTCAAAATGTAATTT-TGGAAAGTTTA-GG
* * * *
16789629 GGT-GAAATGTAATTTTTAGAAAGGTTCAAG
1 GGTCAAAATGTAA-TTTTGGAAA-GTTTAGG
* *
16789659 GGTTAAAATGTAATTTTAGG-AAGTTTAAG
1 GGTCAAAATGTAATTTT-GGAAAGTTTAGG
16789688 GGTCAAAATGTAATTTTAGG-AAGTTTAGG
1 GGTCAAAATGTAATTTT-GGAAAGTTTAGG
*
16789717 GGTCAAAATGTAATTTTGGGAAAGTTTAAG
1 GGTCAAAATGTAATTTT-GGAAAGTTTAGG
* * *
16789747 GGTTAAAATGTAATTTTAAGAAAGTTTAGA
1 GGTCAAAATGTAATTTT-GGAAAGTTTAGG
* *
16789777 GGTTAAAATATAATTTTGGAGAAGTTTTA-G
1 GGTCAAAATGTAATTTTGGA-AAG-TTTAGG
* *
16789807 GGTAAAAATGTAATTTTAGAAAAGTTTAGG
1 GGTCAAAATGTAATTTT-GGAAAGTTTAGG
* *** * *
16789837 GGTTAAAACAAAATTTTGGATAAATTTAAG
1 GGTCAAAATGTAATTTTGGA-AAGTTTAGG
*
16789867 GGTCAAAATGTAATTTTGGAAGAGTTCAGG
1 GGTCAAAATGTAATTTTGGAA-AGTTTAGG
16789897 GG
1 GG
16789899 CTCTTTTATG
Statistics
Matches: 222, Mismatches: 37, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
29 61 0.27
30 137 0.62
31 24 0.11
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (29 bp):
GGTCAAAATGTAATTTTGGAAAGTTTAGG
Found at i:16789898 original size:60 final size:59
Alignment explanation
Indices: 16789602--16789883 Score: 302
Period size: 60 Copynumber: 4.7 Consensus size: 59
16789592 ATTTGAGGTC
* * * * * * *
16789602 AAAATGTAATTTATGGAAAATTTAGGGGGT-GAAATGTAATTTTTAGAAAGGTTCAAGGGTT
1 AAAATATAATTT-TGGAAAGTTTA-AGGGTCAAAATGTAATTTTAAGAAA-GTTTAGGGGTT
* * *
16789663 AAAATGTAATTTTAGG-AAGTTTAAGGGTCAAAATGTAATTTT-AGGAAGTTTAGGGGTC
1 AAAATATAATTTT-GGAAAGTTTAAGGGTCAAAATGTAATTTTAAGAAAGTTTAGGGGTT
* * *
16789721 AAAATGTAATTTTGGGAAAGTTTAAGGGTTAAAATGTAATTTTAAGAAAGTTTAGAGGTT
1 AAAATATAATTTT-GGAAAGTTTAAGGGTCAAAATGTAATTTTAAGAAAGTTTAGGGGTT
* *
16789781 AAAATATAATTTTGGAGAAGTTTTAGGGTAAAAATGTAATTTT-AGAAAAGTTTAGGGGTT
1 AAAATATAATTTTGGA-AAGTTTAAGGGTCAAAATGTAATTTTAAG-AAAGTTTAGGGGTT
* * *
16789841 AAAACAAAATTTTGGATAAATTTAAGGGTCAAAATGTAATTTT
1 AAAATATAATTTTGGA-AAGTTTAAGGGTCAAAATGTAATTTT
16789884 GGAAGAGTTC
Statistics
Matches: 193, Mismatches: 22, Indels: 13
0.85 0.10 0.06
Matches are distributed among these distances:
58 23 0.12
59 38 0.20
60 118 0.61
61 14 0.07
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (59 bp):
AAAATATAATTTTGGAAAGTTTAAGGGTCAAAATGTAATTTTAAGAAAGTTTAGGGGTT
Found at i:16791605 original size:39 final size:39
Alignment explanation
Indices: 16791562--16791718 Score: 107
Period size: 39 Copynumber: 4.0 Consensus size: 39
16791552 CTTCATTGTT
*
16791562 TTGGATAACTGCAATATACCCCATGATCGGGGTAAGAGA
1 TTGGATGACTGCAATATACCCCATGATCGGGGTAAGAGA
* ** * * * *
16791601 TTGGATGGCTGTGATCTGCCTCATGGTCGGGGTAAGAGA
1 TTGGATGACTGCAATATACCCCATGATCGGGGTAAGAGA
* *** * * *
16791640 TCGGATGACTGCAATCCGCCTCATGATCGAGGTGAGAGA
1 TTGGATGACTGCAATATACCCCATGATCGGGGTAAGAGA
* ** *** * *
16791679 TCGGATGGTTATGATCTACCCTATGATCGGGGTAAGAGA
1 TTGGATGACTGCAATATACCCCATGATCGGGGTAAGAGA
16791718 T
1 T
16791719 CGAGTAGTTG
Statistics
Matches: 91, Mismatches: 27, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
39 91 1.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (39 bp):
TTGGATGACTGCAATATACCCCATGATCGGGGTAAGAGA
Found at i:16791719 original size:39 final size:38
Alignment explanation
Indices: 16791584--16792239 Score: 174
Period size: 39 Copynumber: 16.8 Consensus size: 38
16791574 AATATACCCC
* * *
16791584 ATGATCGGGGTAAGAGATTGGATGGCTGTGATCTGCCT
1 ATGATCGGGGTAAGAGATCGGATGGTTGTGATCTCCCT
* ** **
16791622 CATGGTCGGGGTAAGAGATCGGATGACTGCAATC-CGCCT
1 -ATGATCGGGGTAAGAGATCGGATGGTTGTGATCTC-CCT
* * *
16791661 CATGATCGAGGTGAGAGATCGGATGGTTATGATCTACCCT
1 -ATGATCGGGGTAAGAGATCGGATGGTTGTGATCT-CCCT
* *
16791701 ATGATCGGGGTAAGAGATC-GAGTAGTTGTGATCTGCCTT
1 ATGATCGGGGTAAGAGATCGGA-TGGTTGTGATCT-CCCT
* * * *
16791740 ATCATCGGGGTAGGAGATC-GAGTAGTTGTGATTTGCCCT
1 ATGATCGGGGTAAGAGATCGGA-TGGTTGTGATCT-CCCT
* ** * * *
16791779 ATGATCGGGGTAAAAGATCAAATTGTCGTAATCTGCCTCT
1 ATGATCGGGGTAAGAGATCGGATGGTTGTGATCT-CC-CT
* * *** * *
16791819 ATCG--CGGGGTAAGAGATTGGCTGACGGTGACCTGCCCC
1 AT-GATCGGGGTAAGAGATCGGATGGTTGTGATCT-CCCT
* * * **
16791857 ATGATCAGGGTAAAAGATTC-AATGGTTGCAATCTGCCCCT
1 ATGATCGGGGTAAGAGA-TCGGATGGTTGTGATCT--CCCT
* * **** *
16791897 ATCG-T-GGGGTAAGATATTGG-TTAACGATGATCTGCCCC
1 AT-GATCGGGGTAAGAGATCGGATGGTTG-TGATCT-CCCT
* * *
16791935 ATGATCGGGGTAAAAGATCGAATGGTTGTAATCTATCCCT
1 ATGATCGGGGTAAGAGATCGGATGGTTGTGATC--TCCCT
* * * *** *
16791975 GTCG-T-GGGGTAAGAGATTGGCTGACGGTGATCTACCCC
1 AT-GATCGGGGTAAGAGATCGGATGGTTGTGATCT-CCCT
* * * * **
16792013 ATGATCCGGGTAAAAGATCAGATGATTGCAATCTGCCC-
1 ATGATCGGGGTAAGAGATCGGATGGTTGTGATCT-CCCT
* * * * * *
16792051 CTG-TCGCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCC
1 ATGAT--CGGGGTAAGAGATCGGATGGTTGTGATCT-CCCT
* * **
16792091 ATGATCGGGGTAAAAAATCGGATGGTTGCAATCTGCCCCT
1 ATGATCGGGGTAAGAGATCGGATGGTTGTGATCT--CCCT
* * * * ***
16792131 GTCA-CGGGGTAAGAGATTGGCTGACGGTGATCTGCCCT
1 ATGATCGGGGTAAGAGATCGGATGGTTGTGATCT-CCCT
* * * * *
16792169 ATGATTGGGGAAAAAGATCGAATGGTTGTAATCTGCCC-
1 ATGATCGGGGTAAGAGATCGGATGGTTGTGATCT-CCCT
* *
16792207 CTG-TCGTGGGGTAAGAGATTGGATGGTTGTGAT
1 ATGATC--GGGGTAAGAGATCGGATGGTTGTGAT
16792240 GTAACTTCAC
Statistics
Matches: 434, Mismatches: 152, Indels: 62
0.67 0.23 0.10
Matches are distributed among these distances:
37 6 0.01
38 29 0.07
39 364 0.84
40 29 0.07
41 6 0.01
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (38 bp):
ATGATCGGGGTAAGAGATCGGATGGTTGTGATCTCCCT
Found at i:16791855 original size:78 final size:78
Alignment explanation
Indices: 16791767--16792228 Score: 604
Period size: 78 Copynumber: 5.9 Consensus size: 78
16791757 TCGAGTAGTT
* * * * * * * *
16791767 GTGATTTGCCCTATGATCGGGGTAAAAGATCAAATTGTCGTAATCTGCCTCTATCGCGGGGTAAG
1 GTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCTGTCGCGGGGTAAG
16791832 AGATTGGCTGACG
66 AGATTGGCTGACG
* * * *
16791845 GTGACCTGCCCCATGATCAGGGTAAAAGATTC-AATGGTTGCAATCTGCCCCTATCGTGGGGTAA
1 GTGATCTGCCCCATGATCGGGGTAAAAGA-TCGAATGGTTGCAATCTGCCCCTGTCGCGGGGTAA
* * *
16791909 GATATTGGTTAACG
65 GAGATTGGCTGACG
* * ** *
16791923 ATGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGTAATCTATCCCTGTCGTGGGGTAAG
1 GTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCTGTCGCGGGGTAAG
16791988 AGATTGGCTGACG
66 AGATTGGCTGACG
* * *
16792001 GTGATCTACCCCATGATCCGGGTAAAAGATC-AGATGATTGCAATCTGCCCCTGTCGCGGGGTAA
1 GTGATCTGCCCCATGATCGGGGTAAAAGATCGA-ATGGTTGCAATCTGCCCCTGTCGCGGGGTAA
*
16792065 GAGATTGGCTGATG
65 GAGATTGGCTGACG
* * *
16792079 GTGATCTGCCCCATGATCGGGGTAAAAAATCGGATGGTTGCAATCTGCCCCTGTCACGGGGTAAG
1 GTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCTGTCGCGGGGTAAG
16792144 AGATTGGCTGACG
66 AGATTGGCTGACG
* * * * *
16792157 GTGATCTGCCCTATGATTGGGGAAAAAGATCGAATGGTTGTAATCTGCCCCTGTCGTGGGGTAAG
1 GTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCTGTCGCGGGGTAAG
16792222 AGATTGG
66 AGATTGG
16792229 ATGGTTGTGA
Statistics
Matches: 334, Mismatches: 46, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
77 3 0.01
78 329 0.99
79 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.26
Consensus pattern (78 bp):
GTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCTGTCGCGGGGTAAG
AGATTGGCTGACG
Found at i:16792239 original size:156 final size:155
Alignment explanation
Indices: 16791590--16792239 Score: 599
Period size: 156 Copynumber: 4.2 Consensus size: 155
16791580 CCCCATGATC
* * * * * **
16791590 GGGGTAAGAGATTGGATGGCTGTGATCTGCCTCATGGTCGGGGTAAGAGATCGGATGACTGCAAT
1 GGGGTAAGAGATTGGATGGTTGTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAAT
* * * * * * **** * *
16791655 CCGCCTCATG--ATCGAGGTGAGAGATCGGATGGTTATGATCTACCCTATGATCGGGGTAAGAGA
66 CTGCC-CCTGTCA-CGGGGTAAGAGATTGGCTGACGGTGATCTACCCCATGATCGGGGTAAAAGA
* * ** * *
16791718 TCGAGTAGTTGTGATCTG-CCTTATCAT
129 TC-AATGGTTGCAATCTGCCCCTATCGT
* * * * * * * * *
16791745 CGGGGTAGGAGA-TCGAGTAGTTGTGATTTGCCCTATGATCGGGGTAAAAGATCAAATTGTCGTA
1 -GGGGTAAGAGATTGGA-TGGTTGTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCA
* * * * * *
16791809 ATCTGCCTCTATCGCGGGGTAAGAGATTGGCTGACGGTGACCTGCCCCATGATCAGGGTAAAAGA
64 ATCTGCCCCTGTCACGGGGTAAGAGATTGGCTGACGGTGATCTACCCCATGATCGGGGTAAAAGA
16791874 TTCAATGGTTGCAATCTGCCCCTATCGT
129 -TCAATGGTTGCAATCTGCCCCTATCGT
* **** *
16791902 GGGGTAAGATATTGG-TTAACGATGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGTAA
1 GGGGTAAGAGATTGGATGGTTG-TGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAA
** ** *
16791966 TCTATCCCTGTCGTGGGGTAAGAGATTGGCTGACGGTGATCTACCCCATGATCCGGGTAAAAGAT
65 TCTGCCCCTGTCACGGGGTAAGAGATTGGCTGACGGTGATCTACCCCATGATCGGGGTAAAAGAT
* * *
16792031 CAGATGATTGCAATCTGCCCCTGTCGC
130 CA-ATGGTTGCAATCTGCCCCTATCGT
* * * * *
16792058 GGGGTAAGAGATTGGCTGATGGTGATCTGCCCCATGATCGGGGTAAAAAATCGGATGGTTGCAAT
1 GGGGTAAGAGATTGGATGGTTGTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAAT
* * * *
16792123 CTGCCCCTGTCACGGGGTAAGAGATTGGCTGACGGTGATCTGCCCTATGATTGGGGAAAAAGATC
66 CTGCCCCTGTCACGGGGTAAGAGATTGGCTGACGGTGATCTACCCCATGATCGGGGTAAAAGATC
* *
16792188 GAATGGTTGTAATCTGCCCCTGTCGT
131 -AATGGTTGCAATCTGCCCCTATCGT
16792214 GGGGTAAGAGATTGGATGGTTGTGAT
1 GGGGTAAGAGATTGGATGGTTGTGAT
16792240 GTAACTTCAC
Statistics
Matches: 399, Mismatches: 85, Indels: 20
0.79 0.17 0.04
Matches are distributed among these distances:
155 9 0.02
156 375 0.94
157 15 0.04
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (155 bp):
GGGGTAAGAGATTGGATGGTTGTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTGCAAT
CTGCCCCTGTCACGGGGTAAGAGATTGGCTGACGGTGATCTACCCCATGATCGGGGTAAAAGATC
AATGGTTGCAATCTGCCCCTATCGT
Found at i:16795421 original size:59 final size:59
Alignment explanation
Indices: 16795329--16795448 Score: 240
Period size: 59 Copynumber: 2.0 Consensus size: 59
16795319 AGCTTTTCAA
16795329 TCGATGAGTACTTTATTTCACAATTGGTGAACTTTTTGCTGAGGTAGTATATGGCTCTT
1 TCGATGAGTACTTTATTTCACAATTGGTGAACTTTTTGCTGAGGTAGTATATGGCTCTT
16795388 TCGATGAGTACTTTATTTCACAATTGGTGAACTTTTTGCTGAGGTAGTATATGGCTCTT
1 TCGATGAGTACTTTATTTCACAATTGGTGAACTTTTTGCTGAGGTAGTATATGGCTCTT
16795447 TC
1 TC
16795449 TTTTCTTCCA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (59 bp):
TCGATGAGTACTTTATTTCACAATTGGTGAACTTTTTGCTGAGGTAGTATATGGCTCTT
Found at i:16798204 original size:21 final size:21
Alignment explanation
Indices: 16798174--16798217 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
16798164 GCTGACATTA
*
16798174 TTGACTAAGCGGTCTAATTTG
1 TTGACCAAGCGGTCTAATTTG
16798195 TTGACCAAGCGGTCTAATTTG
1 TTGACCAAGCGGTCTAATTTG
16798216 TT
1 TT
16798218 TACTGAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (21 bp):
TTGACCAAGCGGTCTAATTTG
Found at i:16804325 original size:30 final size:30
Alignment explanation
Indices: 16804288--16804606 Score: 266
Period size: 30 Copynumber: 10.7 Consensus size: 30
16804278 ATTTGAGGTC
*
16804288 AAAATGTAA-TTTATGGAAAATTTAGGGGGT
1 AAAATGTAATTTTA-GGAAAGTTTAGGGGGT
* *
16804318 GAAATGTAATTTTTA-GAAAGGTTT-GAGGGTT
1 AAAATGTAA-TTTTAGGAAA-GTTTAG-GGGGT
*
16804349 AAAATATAATTTTAGGAAAGTTTA-GGGGT
1 AAAATGTAATTTTAGGAAAGTTTAGGGGGT
* * * *
16804378 CAAATATAATTTT-GGAAAGTTTAAGGGTT
1 AAAATGTAATTTTAGGAAAGTTTAGGGGGT
*
16804407 AAAATGTAATTTTAGG-AAGTTT-GGGAGGC
1 AAAATGTAATTTTAGGAAAGTTTAGGG-GGT
* *
16804436 AAAATATAATTTTAGGAAAGTTTAGGGGTT
1 AAAATGTAATTTTAGGAAAGTTTAGGGGGT
* * * *
16804466 AAAATGTAATTTTAAGTAAGTTTAAGGGTT
1 AAAATGTAATTTTAGGAAAGTTTAGGGGGT
* *
16804496 AAAATGCAATTTT-GGAAAAGTTT-GAGGGT
1 AAAATGTAATTTTAGG-AAAGTTTAGGGGGT
*
16804525 AAAATGTAATTTTA-GAAATGTTTAGGGGTT
1 AAAATGTAATTTTAGGAAA-GTTTAGGGGGT
*** * *
16804555 AAAACAAAATTTTAGAAAAATTTA-GGGGT
1 AAAATGTAATTTTAGGAAAGTTTAGGGGGT
16804584 CAAAATGTAATTTT-GGAAGAGTT
1 -AAAATGTAATTTTAGGAA-AGTT
16804607 CAAAGGCTCT
Statistics
Matches: 231, Mismatches: 40, Indels: 36
0.75 0.13 0.12
Matches are distributed among these distances:
28 15 0.06
29 81 0.35
30 107 0.46
31 24 0.10
32 4 0.02
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTAGGAAAGTTTAGGGGGT
Done.