Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007790.1 Hibiscus syriacus cultivar Beakdansim tig00110076_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2956777
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:2856699 original size:58 final size:58
Alignment explanation
Indices: 2856557--2856719 Score: 175
Period size: 58 Copynumber: 2.8 Consensus size: 58
2856547 ACCGTTGACC
* **** *
2856557 GGTGTTATTTTGGGAATTAATTCGGTTTA-GTGCTATTCGGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAAAAGGTGCTATTCTGGGAATTAATTCGAAATG
* ** * * * *
2856614 GGTGCTATTTTGGAAATTTTTTTGAAAAAGGTGATATTCTGGGAATTAATTTGAAATT
1 GGTGCTATTTTGGGAATTAATTCGAAAAAGGTGCTATTCTGGGAATTAATTCGAAATG
* * *
2856672 GGTGCTATTTTGGGAATTAATTCGAAAAGGGTGCTATTTTGGTAATTA
1 GGTGCTATTTTGGGAATTAATTCGAAAAAGGTGCTATTCTGGGAATTA
2856720 TTTAAAAAAG
Statistics
Matches: 84, Mismatches: 21, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
57 20 0.24
58 64 0.76
ACGTcount: A:0.28, C:0.06, G:0.26, T:0.41
Consensus pattern (58 bp):
GGTGCTATTTTGGGAATTAATTCGAAAAAGGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:2856734 original size:27 final size:29
Alignment explanation
Indices: 2856562--2856737 Score: 115
Period size: 29 Copynumber: 6.2 Consensus size: 29
2856552 TGACCGGTGT
****
2856562 TATTTTGGGAATTAATTCG-GTTTAGTGC
1 TATTTTGGGAATTAATTCGAAAAAAGTGC
** ***
2856590 TATTCGGGGAATTAATTCGAAATGGGTGC
1 TATTTTGGGAATTAATTCGAAAAAAGTGC
* ** * * *
2856619 TATTTTGGAAATTTTTTTGAAAAAGGTGA
1 TATTTTGGGAATTAATTCGAAAAAAGTGC
* * ***
2856648 TATTCTGGGAATTAATTTGAAATTGGTGC
1 TATTTTGGGAATTAATTCGAAAAAAGTGC
**
2856677 TATTTTGGGAATTAATTCGAAAAGGGTGC
1 TATTTTGGGAATTAATTCGAAAAAAGTGC
* *
2856706 TATTTTGGTAATT-ATT-TAAAAAAGTGC
1 TATTTTGGGAATTAATTCGAAAAAAGTGC
2856733 TATTT
1 TATTT
2856738 GTGTAAAATG
Statistics
Matches: 117, Mismatches: 30, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
27 13 0.11
28 20 0.17
29 84 0.72
ACGTcount: A:0.30, C:0.06, G:0.23, T:0.41
Consensus pattern (29 bp):
TATTTTGGGAATTAATTCGAAAAAAGTGC
Found at i:2856785 original size:12 final size:11
Alignment explanation
Indices: 2856768--2856821 Score: 58
Period size: 10 Copynumber: 4.9 Consensus size: 11
2856758 TGTTGACCTC
2856768 CTTTGACCAGAA
1 CTTTGACCAG-A
*
2856780 CTTTGACC-GG
1 CTTTGACCAGA
2856790 CTTTGACCAGAA
1 CTTTGACCAG-A
*
2856802 CTTTGACC-GG
1 CTTTGACCAGA
2856812 CTTTGACCAG
1 CTTTGACCAG
2856822 CTATTAAACG
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
10 16 0.44
11 4 0.11
12 16 0.44
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (11 bp):
CTTTGACCAGA
Found at i:2856787 original size:22 final size:22
Alignment explanation
Indices: 2856768--2856821 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
2856758 TGTTGACCTC
2856768 CTTTGACCAGAACTTTGACCGG
1 CTTTGACCAGAACTTTGACCGG
2856790 CTTTGACCAGAACTTTGACCGG
1 CTTTGACCAGAACTTTGACCGG
2856812 CTTTGACCAG
1 CTTTGACCAG
2856822 CTATTAAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (22 bp):
CTTTGACCAGAACTTTGACCGG
Found at i:2863806 original size:19 final size:18
Alignment explanation
Indices: 2863782--2863837 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
2863772 GAACGCTGAA
2863782 AACCGGATTTGACCGGTTT
1 AACCGG-TTTGACCGGTTT
2863801 AACCGGTTTTGAACCGGTTTT
1 AACCGG-TTTG-ACCGG-TTT
*
2863822 GACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
2863838 CTCGACCCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 15 0.45
20 9 0.27
21 8 0.24
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (18 bp):
AACCGGTTTGACCGGTTT
Found at i:2863817 original size:11 final size:11
Alignment explanation
Indices: 2863782--2863830 Score: 61
Period size: 10 Copynumber: 4.8 Consensus size: 11
2863772 GAACGCTGAA
*
2863782 AACCGGATTTG
1 AACCGGTTTTG
2863793 -ACCGG-TTT-
1 AACCGGTTTTG
2863801 AACCGGTTTTG
1 AACCGGTTTTG
2863812 AACCGGTTTTG
1 AACCGGTTTTG
2863823 -ACCGGTTT
1 AACCGGTTT
2863831 GACCGGTCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:2863833 original size:9 final size:10
Alignment explanation
Indices: 2863783--2863837 Score: 69
Period size: 9 Copynumber: 5.6 Consensus size: 10
2863773 AACGCTGAAA
*
2863783 ACCGGATTTG
1 ACCGGTTTTG
*
2863793 ACCGG-TTTA
1 ACCGGTTTTG
2863802 ACCGGTTTTG
1 ACCGGTTTTG
2863812 AACCGGTTTTG
1 -ACCGGTTTTG
2863823 ACCGG-TTTG
1 ACCGGTTTTG
2863832 ACCGGT
1 ACCGGT
2863838 CTCGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:2863870 original size:17 final size:17
Alignment explanation
Indices: 2863848--2863899 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 17
2863838 CTCGACCCGT
*
2863848 TGACCCTACCGTTGACC
1 TGACCCGACCGTTGACC
2863865 TGACCCGACCGTTGACC
1 TGACCCGACCGTTGACC
*
2863882 CGACCCGACCCGTTGACC
1 TGACCCGA-CCGTTGACC
2863900 GGTGTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 23 0.72
18 9 0.28
ACGTcount: A:0.17, C:0.44, G:0.21, T:0.17
Consensus pattern (17 bp):
TGACCCGACCGTTGACC
Found at i:2863974 original size:29 final size:28
Alignment explanation
Indices: 2863900--2864060 Score: 126
Period size: 28 Copynumber: 5.7 Consensus size: 28
2863890 CCCGTTGACC
* ***
2863900 GGTGTTATTTTGGGAATTAATTCGGTTT
1 GGTGCTATTTTGGGAATTAATTCGAAAT
* **
2863928 AGTGCTATTCGGGGAATTAATTCGAAAT
1 GGTGCTATTTTGGGAATTAATTCGAAAT
* ** * *
2863956 GAGTGCTATTTTGGTAATTTTTTTGAAAA
1 G-GTGCTATTTTGGGAATTAATTCGAAAT
* * * *
2863985 GGTGATATTCTGGGAATTAATCCAAAATT
1 GGTGCTATTTTGGGAATTAATTCGAAA-T
*
2864014 GGTGCTATTTTGGGAATTAATTCGAAAAG
1 GGTGCTATTTTGGGAATTAATTCG-AAAT
*
2864043 GGTGCTA-TTTGGTAATTA
1 GGTGCTATTTTGGGAATTA
2864061 TTTTAAAAAA
Statistics
Matches: 100, Mismatches: 30, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
28 49 0.49
29 48 0.48
30 3 0.03
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (28 bp):
GGTGCTATTTTGGGAATTAATTCGAAAT
Found at i:2864041 original size:57 final size:56
Alignment explanation
Indices: 2863900--2864060 Score: 155
Period size: 57 Copynumber: 2.8 Consensus size: 56
2863890 CCCGTTGACC
* *** * * *
2863900 GGTGTTATTTTGGGAATTAATTCGGTTTA-GTGCTATTCGGGGAATTAATTCGAAAT
1 GGTGCTATTTTGGGAATTAATTC-GAAAAGGTGCTATTCTGGGAATTAATCCAAAAT
* ** * *
2863956 GAGTGCTATTTTGGTAATTTTTTTGAAAAGGTGATATTCTGGGAATTAATCCAAAATT
1 G-GTGCTATTTTGGGAATTAATTCGAAAAGGTGCTATTCTGGGAATTAATCCAAAA-T
*
2864014 GGTGCTATTTTGGGAATTAATTCGAAAAGGGTGCTATT-TGGTAATTA
1 GGTGCTATTTTGGGAATTAATTCGAAAA-GGTGCTATTCTGGGAATTA
2864061 TTTTAAAAAA
Statistics
Matches: 83, Mismatches: 18, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
56 3 0.04
57 70 0.84
58 10 0.12
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (56 bp):
GGTGCTATTTTGGGAATTAATTCGAAAAGGTGCTATTCTGGGAATTAATCCAAAAT
Found at i:2864069 original size:28 final size:27
Alignment explanation
Indices: 2863942--2864085 Score: 90
Period size: 29 Copynumber: 5.1 Consensus size: 27
2863932 CTATTCGGGG
* *
2863942 AATTAATTCGAAATGAGTGCTATTTTGGT
1 AATTAATTCAAAAAG-GTGCTA-TTTGGT
** ** * *
2863971 AATTTTTTTGAAAAGGTGATATTCTGGG
1 AATTAATTCAAAAAGGTGCTATT-TGGT
* * *
2863999 AATTAATCCAAAATTGGTGCTATTTTGGG
1 AATTAATTCAAAA-AGGTGCTA-TTTGGT
*
2864028 AATTAATTCGAAAAGGGTGCTATTTGGT
1 AATTAATTC-AAAAAGGTGCTATTTGGT
* * *
2864056 AATTATTTTAAAAAAGTGCTATTTGTGT
1 AATTAATTCAAAAAGGTGCTATTTG-GT
2864084 AA
1 AA
2864086 AATGTTTGAC
Statistics
Matches: 90, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
27 16 0.18
28 32 0.36
29 36 0.40
30 6 0.07
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (27 bp):
AATTAATTCAAAAAGGTGCTATTTGGT
Found at i:2867506 original size:31 final size:29
Alignment explanation
Indices: 2867470--2867546 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 29
2867460 TTTACTCATA
* *
2867470 ATTCTAATAATATGAT-ATTTTATTCTTTAAT
1 ATTCTAATAATAT-ATAATATTATACTTT--T
*
2867501 ATTCTAATGATATATAATATTATACTTTT
1 ATTCTAATAATATATAATATTATACTTTT
*
2867530 ATTTTAATAATATATAA
1 ATTCTAATAATATATAA
2867547 CGAATTTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 16 0.40
30 2 0.05
31 22 0.55
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (29 bp):
ATTCTAATAATATATAATATTATACTTTT
Found at i:2871956 original size:24 final size:24
Alignment explanation
Indices: 2871848--2871956 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
2871838 GAATGTTTTA
* *
2871848 TCTGATTT-TCGATTTGAATTATGT
1 TCTGATTTCT-GATCTGAATTCTGT
* * * *
2871872 TCTGATTTTTTATTTGAATTTTGT
1 TCTGATTTCTGATCTGAATTCTGT
* * *
2871896 TCTGATTTCTAATCTGGATTCTTT
1 TCTGATTTCTGATCTGAATTCTGT
*
2871920 TTTGATATT-TGATCTGAATTCTGT
1 TCTGAT-TTCTGATCTGAATTCTGT
*
2871944 TTTGATTTCTGAT
1 TCTGATTTCTGAT
2871957 ATCTCCGTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
23 2 0.03
24 65 0.93
25 3 0.04
ACGTcount: A:0.18, C:0.09, G:0.15, T:0.58
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:2876609 original size:24 final size:24
Alignment explanation
Indices: 2876561--2876640 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
2876551 GAATATTTTA
* * *
2876561 TCTGATTTCCGATTTGAATTATGT
1 TCTGATTTCTGATATGAATTCTGT
* * *
2876585 TGTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* *
2876609 TCTGATATCTAATATGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
2876633 TTTGATTT
1 TCTGATTT
2876641 ATGACATCTT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.51
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:2882891 original size:19 final size:20
Alignment explanation
Indices: 2882869--2882908 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2882859 ATTATTATTT
*
2882869 TCAATAGTA-ATTAATATAA
1 TCAATAATATATTAATATAA
*
2882888 TCAATAATATATTATTATAA
1 TCAATAATATATTAATATAA
2882908 T
1 T
2882909 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (20 bp):
TCAATAATATATTAATATAA
Found at i:2887866 original size:523 final size:525
Alignment explanation
Indices: 2886867--2887928 Score: 1833
Period size: 523 Copynumber: 2.0 Consensus size: 525
2886857 AAGAGGATCA
* *
2886867 AATGCCTCTATATTTTCGATCGTTTTTGGAGTCATTTGACCTAAGGTTTGCATCTATAGAGTCCT
1 AATGCCTCCATATTTTCGATCGTTTTTGGAGTCATTTGACCTAAGGTTTGCATCTATAGAGTCCC
2886932 ATCTAACTACTTTAGGGGATCAACAATGGGAGATGAACGAACGTTTAGATGTGCTCACACTCGAC
66 ATCTAACTACTTTAGGGGATCAACAATGGGAGATGAACGAAC---T--A---G-T---ACTCGAC
* *
2886997 ATGCGAGCACGTTATCCTCCTCTTCCCGATTCTCCTTTGGATGACTAGACCTATCTTGCTTTAGT
119 ATGCGAGCACGTTATCATCCTCTTCCCGATCCTCCTTTGGATGACTAGACCTATCTTGCTTTAGT
2887062 TTTCAAGGATTTAGTACCTATTGTTAAACATTTTGAATGTTTTTGGATTTATATTTTGGATGATT
184 TTTCAAGGATTTAGTACCTATTGTTAAACATTTTGAATGTTTTTGGATTTATATTTTGGATGATT
2887127 GTGGATTGATGTTTTTGGATTATTTTTATTTTGAATGTTTGGATGTTTGAACTTATATTTATATA
249 GTGGATTGATGTTTTTGGATTATTTTTATTTTGAATGTTTGGATGTTTGAACTTATATTTATATA
*
2887192 TTTGGCTTGGTTTGAATTTTCAATTTGAGCTTAATGTTTATTAGTTTTGCATCATTTACATATTA
314 TTTGGATTGGTTTGAATTTTCAATTTGAGCTTAATGTTTATTAGTTTTGCATCATTTACATATTA
* * *
2887257 GTTTCATTATGACCAATTTACCATTTCACTTTTGTTTATGAATATTGATTTATGAAACTAATGGC
379 GTTGCATTATGACCAATTTACCATTGCACATTTGTTTATGAATATTGATTTATGAAACTAATGGC
2887322 TAACCTTTCTCTTGCTTTTGATCTTAGCAGCTTAAGTTATATTTATTTAAAATCAATTGGCTAAG
444 TAACCTTTCTCTTGCTTTTGATCTTAGCAGCTTAAGTTATATTTATTTAAAATCAATTGGCTAAG
*
2887387 TTTTGCAAAATCTTGTTT
509 -TTTCCAAAATCTTGTTT
*
2887405 AATGCCTCCATATTTTCGATCGTTTTTGGAGTCATTTGACCTAAGGTTTGCATCTATAGATTCCC
1 AATGCCTCCATATTTTCGATCGTTTTTGGAGTCATTTGACCTAAGGTTTGCATCTATAGAGTCCC
* * * *
2887470 ATCTTACTACTTTGGGGGCTCAACAATGGGAGATGAACGAAC-A-T-CTCGAGATGCGAGCACGT
66 ATCTAACTACTTTAGGGGATCAACAATGGGAGATGAACGAACTAGTACTCGACATGCGAGCACGT
*
2887532 TATCATCCTCTTCCCGATCCTCCTTTGGATGACTAGACCTATCTTGCTTTAGTTTTCATGGATTT
131 TATCATCCTCTTCCCGATCCTCCTTTGGATGACTAGACCTATCTTGCTTTAGTTTTCAAGGATTT
2887597 AGTACCTATTGTTAAACATTTTGAATGTTTTTGGATTTATATTTTGGATGATTGTGGATTGATGT
196 AGTACCTATTGTTAAACATTTTGAATGTTTTTGGATTTATATTTTGGATGATTGTGGATTGATGT
*
2887662 TTTTGGATTATTTTTATTTTGAATGTTTGGATGTTTGAACTTATTTTTATATATTTGGATTGGTT
261 TTTTGGATTATTTTTATTTTGAATGTTTGGATGTTTGAACTTATATTTATATATTTGGATTGGTT
2887727 TGAATTTTCAATTTGAGCTTAATGTTTATTAGTTTTGCATCATTTACATATTAGTTGCATTATGA
326 TGAATTTTCAATTTGAGCTTAATGTTTATTAGTTTTGCATCATTTACATATTAGTTGCATTATGA
2887792 CCAATTTACCATTGCACATTTGTTTATGAATATTGATTTATGAAACTAATGGCTAACCTTTCTCT
391 CCAATTTACCATTGCACATTTGTTTATGAATATTGATTTATGAAACTAATGGCTAACCTTTCTCT
*
2887857 TGCTTTTGATCTTAGCAGTTTAAGTTATATTTATTTAAAATCAATTGGCTAAGTTTCCAAAATCT
456 TGCTTTTGATCTTAGCAGCTTAAGTTATATTTATTTAAAATCAATTGGCTAAGTTTCCAAAATCT
2887922 TGTTT
521 TGTTT
2887927 AA
1 AA
2887929 AAACGTTTTA
Statistics
Matches: 507, Mismatches: 17, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
522 18 0.04
523 386 0.76
527 1 0.00
532 1 0.00
538 101 0.20
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (525 bp):
AATGCCTCCATATTTTCGATCGTTTTTGGAGTCATTTGACCTAAGGTTTGCATCTATAGAGTCCC
ATCTAACTACTTTAGGGGATCAACAATGGGAGATGAACGAACTAGTACTCGACATGCGAGCACGT
TATCATCCTCTTCCCGATCCTCCTTTGGATGACTAGACCTATCTTGCTTTAGTTTTCAAGGATTT
AGTACCTATTGTTAAACATTTTGAATGTTTTTGGATTTATATTTTGGATGATTGTGGATTGATGT
TTTTGGATTATTTTTATTTTGAATGTTTGGATGTTTGAACTTATATTTATATATTTGGATTGGTT
TGAATTTTCAATTTGAGCTTAATGTTTATTAGTTTTGCATCATTTACATATTAGTTGCATTATGA
CCAATTTACCATTGCACATTTGTTTATGAATATTGATTTATGAAACTAATGGCTAACCTTTCTCT
TGCTTTTGATCTTAGCAGCTTAAGTTATATTTATTTAAAATCAATTGGCTAAGTTTCCAAAATCT
TGTTT
Found at i:2889325 original size:65 final size:64
Alignment explanation
Indices: 2889221--2889373 Score: 175
Period size: 65 Copynumber: 2.4 Consensus size: 64
2889211 ACCCATTTCT
* * * * *
2889221 AATGCATTTTGTGTACCGATACGCAAGCCAAGCATCGATGCACTCTTGAATATTTTGAAACATCG
1 AATGCATTTTATGTACCGATGCACAAGCCAAGCATCGATGCACTCCTGAAT-CTTTGAAACATCG
* **
2889286 AATGCATTTTATGTACCGATGCACATA-CCATGCATCGATGCACTCCTGGCTCTTTGAAACATCG
1 AATGCATTTTATGTACCGATGCACA-AGCCAAGCATCGATGCACTCCTGAATCTTTGAAACATCG
* *
2889350 AATGTA-ATTAGTGTACCGATGCAC
1 AATGCATTTTA-TGTACCGATGCAC
2889374 CCCTAGTGTA
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 3 0.04
64 30 0.39
65 42 0.55
66 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (64 bp):
AATGCATTTTATGTACCGATGCACAAGCCAAGCATCGATGCACTCCTGAATCTTTGAAACATCG
Found at i:2889352 original size:851 final size:850
Alignment explanation
Indices: 2887712--2889419 Score: 3274
Period size: 851 Copynumber: 2.0 Consensus size: 850
2887702 TTATTTTTAT
*
2887712 ATATTTGGATTGGTTTGAATTTTCAATTTGAGCTTAATGTTTATTAGTTTTGCATCATTTACATA
1 ATATTTGGATTGGTTTGAATTTTCAATTTGAGCTTAATGTTTATTAGTTTTGCAACATTTACATA
2887777 TTAGTTGCATTATGACCAATTTACCATTGCACATTTGTTTATGAATATTGATTTATGAAACTAAT
66 TTAGTTGCATTATGACCAATTTACCATTGCACATTTGTTTATGAATATTGATTTATGAAACTAAT
*
2887842 GGCTAACCTTTCTCTTGCTTTTGATCTTAGCAGTTTAAGTTATATTTATTTAAAATCAATTGGCT
131 GGCTAACCTTTCTCTTGCTTTTGATCTTAGCAGCTTAAGTTATATTTATTTAAAATCAATTGGCT
*
2887907 AAGTTTCCAAAATCTTGTTTAAAAACGTTTTATAGAGTATTTTTTATTTAATAAAAATTGGGAGA
196 AAGTTTCCAAAATCTTGTTTAAAAACGTTTTATAGAGTATTTTTTATTTAATAAAAATGGGGAGA
*
2887972 AGGTGTGTTATAGTAAGGGGGGAATTTTACAAAAATTGTTTTCAAAAATGCTTTTCAAAGAAAGA
261 AGGTGTGTTATAGTAAGGGGGGAATTTTACAAAAATTGTTTTCAAAAATGCTTTTCAAAGAAAAA
2888037 CTTAAAATTACTTAAATGTTTTGTTATATCAAAAAGGGGGAGATTTTTGAAAACATTTTGATGTT
326 CTTAAAATTACTTAAATGTTTTGTTATATCAAAAAGGGGGAGATTTTTGAAAACATTTTGATGTT
*
2888102 TCGATATAACAAATTAAGGGTTATTGAATTATAAGATTTCACAATCATTTTTAAAGTATTTTCGA
391 TCGATATAACAAATTAAGGGTTATTGAATTATAAGATTTCACAATCATTTTTAAAGTATATTCGA
2888167 TTCAATTATTCGAATATCAAAATATTACTCCAAGTTTTTCAAAGATCAATTTCAATCCTTACTAA
456 TTCAATTATTCGAATATCAAAATATTACTCCAAGTTTTTCAAAGATCAATTTCAATCCTTACTAA
*
2888232 AGTGTAAAATTGTGTTTTAAACTTATAATATTTTTGAAGCAATTTTACAAAGTATTTCGAAATAA
521 AGTGTAAAACTGTGTTTTAAACTTATAATATTTTTGAAGCAATTTTACAAAGTATTTCGAAATAA
*
2888297 AATCGAGCCAAAAATCAAATTTACAAAGTGATGTACCGATGCACTACATGATGCATAGATGCATA
586 AATCGAGCCAAAAATCAAATTTACAAAGTGATGTACCGATGCACTACATGATACATAGATGCATA
2888362 CCCATTTCTAATGCATTTTGTGTACCGATACGCAAGCCAAGCATCGATGCACTCTTGAATATTTT
651 CCCATTTCTAATGCATTTTGTGTACCGATACGCAAGCCAAGCATCGATGCACTCTTGAATATTTT
2888427 GAAACATCGAATCATTTTATGTACCAATGCACATACCATGCATCGATGCACTCCTGGCTCTTTGA
716 GAAACATCGAATCATTTTATGTACCAATGCACATACCATGCATCGATGCACTCCTGGCTCTTTGA
2888492 AACATCGAATGTAATTAGTGTACCGATGCACCCCTAGTGTACTGATGCACTAAGTCTTATAACGG
781 AACATCGAATGTAATTAGTGTACCGATGCACCCCTAGTGTACTGATGCACTAAGTCTTATAACGG
2888557 TCGAA
846 TCGAA
*
2888562 ATATTTGGATTGGTTTTAATTTTCAATTTGAGCTTAATGTTTATTAGTTTTGCAACATTTACATA
1 ATATTTGGATTGGTTTGAATTTTCAATTTGAGCTTAATGTTTATTAGTTTTGCAACATTTACATA
2888627 TTAGTTGCATTATGACCAATTTACCATTGCACATTTGTTTATGAATATTGATTTATGAAACTAAT
66 TTAGTTGCATTATGACCAATTTACCATTGCACATTTGTTTATGAATATTGATTTATGAAACTAAT
*
2888692 GGCTAACCTTTCTCTTGCTTTTGATCTTAGCAGCTTAAGTTATATTTATTTTAAATCAATTGGCT
131 GGCTAACCTTTCTCTTGCTTTTGATCTTAGCAGCTTAAGTTATATTTATTTAAAATCAATTGGCT
* *
2888757 AAGTTTTCCAAAATCTTGTTTAAAAATGTTTTATAGAGTATTTTTTATTTAATAAAAATGGGGAT
196 AAG-TTTCCAAAATCTTGTTTAAAAACGTTTTATAGAGTATTTTTTATTTAATAAAAATGGGGAG
*
2888822 AAGGTGTGTTATAGTAAGGGGGGAATTTTGCAAAAATTGTTTTCAAAAATGCTTTTCAAAGAAAA
260 AAGGTGTGTTATAGTAAGGGGGGAATTTTACAAAAATTGTTTTCAAAAATGCTTTTCAAAGAAAA
2888887 ACTTAAAATTACTTAAATGTTTTGTTATATCAAAAAGGGGGAGATTTTTGAAAACATTTTGATGT
325 ACTTAAAATTACTTAAATGTTTTGTTATATCAAAAAGGGGGAGATTTTTGAAAACATTTTGATGT
2888952 TTCGATATAACAAATTAAGGGTTATTGAATTATAAGATTTCACAATCATTTTTAAAGTATATTCG
390 TTCGATATAACAAATTAAGGGTTATTGAATTATAAGATTTCACAATCATTTTTAAAGTATATTCG
2889017 ATTCAATTATTCGAATATCAAAATATTACTCCAAGTTTTTCAAAGATCAATTTCAATCCTTACTA
455 ATTCAATTATTCGAATATCAAAATATTACTCCAAGTTTTTCAAAGATCAATTTCAATCCTTACTA
2889082 AAGTGTAAAACTGTGTTTTAAACTTATAATA-TTTTGAAGCAATTTTACAAAGTATTTCGAAATA
520 AAGTGTAAAACTGTGTTTTAAACTTATAATATTTTTGAAGCAATTTTACAAAGTATTTCGAAATA
2889146 AAATCGAGCCAAAAATCAAATTTACAAAGTGATGTACCGATGCACTACATGATACATAGATGCAT
585 AAATCGAGCCAAAAATCAAATTTACAAAGTGATGTACCGATGCACTACATGATACATAGATGCAT
2889211 ACCCATTTCTAATGCATTTTGTGTACCGATACGCAAGCCAAGCATCGATGCACTCTTGAATATTT
650 ACCCATTTCTAATGCATTTTGTGTACCGATACGCAAGCCAAGCATCGATGCACTCTTGAATATTT
*
2889276 TGAAACATCGAATGCATTTTATGTACCGATGCACATACCATGCATCGATGCACTCCTGGCTCTTT
715 TGAAACATCGAAT-CATTTTATGTACCAATGCACATACCATGCATCGATGCACTCCTGGCTCTTT
2889341 GAAACATCGAATGTAATTAGTGTACCGATGCACCCCTAGTGTACTGATGCACTAAGTCTTATAAC
779 GAAACATCGAATGTAATTAGTGTACCGATGCACCCCTAGTGTACTGATGCACTAAGTCTTATAAC
2889406 GGTCGAA
844 GGTCGAA
2889413 ATATTTG
1 ATATTTG
2889420 AATTTTACAC
Statistics
Matches: 843, Mismatches: 13, Indels: 3
0.98 0.02 0.00
Matches are distributed among these distances:
850 369 0.44
851 474 0.56
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.38
Consensus pattern (850 bp):
ATATTTGGATTGGTTTGAATTTTCAATTTGAGCTTAATGTTTATTAGTTTTGCAACATTTACATA
TTAGTTGCATTATGACCAATTTACCATTGCACATTTGTTTATGAATATTGATTTATGAAACTAAT
GGCTAACCTTTCTCTTGCTTTTGATCTTAGCAGCTTAAGTTATATTTATTTAAAATCAATTGGCT
AAGTTTCCAAAATCTTGTTTAAAAACGTTTTATAGAGTATTTTTTATTTAATAAAAATGGGGAGA
AGGTGTGTTATAGTAAGGGGGGAATTTTACAAAAATTGTTTTCAAAAATGCTTTTCAAAGAAAAA
CTTAAAATTACTTAAATGTTTTGTTATATCAAAAAGGGGGAGATTTTTGAAAACATTTTGATGTT
TCGATATAACAAATTAAGGGTTATTGAATTATAAGATTTCACAATCATTTTTAAAGTATATTCGA
TTCAATTATTCGAATATCAAAATATTACTCCAAGTTTTTCAAAGATCAATTTCAATCCTTACTAA
AGTGTAAAACTGTGTTTTAAACTTATAATATTTTTGAAGCAATTTTACAAAGTATTTCGAAATAA
AATCGAGCCAAAAATCAAATTTACAAAGTGATGTACCGATGCACTACATGATACATAGATGCATA
CCCATTTCTAATGCATTTTGTGTACCGATACGCAAGCCAAGCATCGATGCACTCTTGAATATTTT
GAAACATCGAATCATTTTATGTACCAATGCACATACCATGCATCGATGCACTCCTGGCTCTTTGA
AACATCGAATGTAATTAGTGTACCGATGCACCCCTAGTGTACTGATGCACTAAGTCTTATAACGG
TCGAA
Found at i:2892444 original size:18 final size:18
Alignment explanation
Indices: 2892417--2892456 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2892407 GAGGACTTTT
*
2892417 ATATTATTTATAAAAATA
1 ATATTATTTAGAAAAATA
*
2892435 ATATTTTTTAGAAAAATA
1 ATATTATTTAGAAAAATA
2892453 ATAT
1 ATAT
2892457 AGATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
ATATTATTTAGAAAAATA
Found at i:2892999 original size:27 final size:30
Alignment explanation
Indices: 2892946--2893000 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
2892936 ACTTTTATTT
*
2892946 TAATATTATATAATAAATTTTCAATAAAAA
1 TAATATTATATAATAAATTTACAATAAAAA
*
2892976 TAATATTAT-TCATAAA-TTAC-ATAAA
1 TAATATTATATAATAAATTTACAATAAA
2893001 TGTATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 3 0.13
29 6 0.26
30 9 0.39
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (30 bp):
TAATATTATATAATAAATTTACAATAAAAA
Found at i:2895378 original size:43 final size:43
Alignment explanation
Indices: 2895347--2895563 Score: 330
Period size: 43 Copynumber: 5.0 Consensus size: 43
2895337 AAAAAGAGCT
* * * *
2895347 TGGGGAAACTCTAAGGCTTACCCTTGCACATAGCAAAGGAACC
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGAAAAGGGACC
* *
2895390 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACA
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGAAAAGGGACC
2895433 TGGGGAAACTGTAAGGCTTACCCTTGCACACA-ATAAAGGGACC
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGA-AAAGGGACC
*
2895476 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACC
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGAAAAGGGACC
*
2895519 TGGGGAAACTGTAAGGCTTACCCTTGTACACA-ACAAAGGGACC
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAGA-AAAGGGACC
2895562 TG
1 TG
2895564 TTGTAACGGT
Statistics
Matches: 162, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
43 162 1.00
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (43 bp):
TGGGGAAACTGTAAGGCTTACCCTTGCACACAGAAAAGGGACC
Found at i:2895448 original size:86 final size:86
Alignment explanation
Indices: 2895347--2895563 Score: 371
Period size: 86 Copynumber: 2.5 Consensus size: 86
2895337 AAAAAGAGCT
* * * *
2895347 TGGGGAAACTCTAAGGCTTACCCTTGCACATAGCAAAGGAACCTGGGGAAACTGTAAGGCTTACC
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTGTAAGGCTTACC
2895412 CTTGCACACAGCAAAGGGACA
66 CTTGCACACAGCAAAGGGACA
*
2895433 TGGGGAAACTGTAAGGCTTACCCTTGCACACAATAAAGGGACCTGGGGAAACTGTAAGGCTTACC
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTGTAAGGCTTACC
*
2895498 CTTGCACACAGCAAAGGGACC
66 CTTGCACACAGCAAAGGGACA
*
2895519 TGGGGAAACTGTAAGGCTTACCCTTGTACACAACAAAGGGACCTG
1 TGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
2895564 TTGTAACGGT
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 123 1.00
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (86 bp):
TGGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGAAACTGTAAGGCTTACC
CTTGCACACAGCAAAGGGACA
Found at i:2902034 original size:18 final size:19
Alignment explanation
Indices: 2902007--2902054 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2901997 GAGTAATTTT
*
2902007 ATATTATTTA-TAAAAATA
1 ATATTATTTAGAAAAAATA
*
2902025 ATATTTTTTAGAAAAAATA
1 ATATTATTTAGAAAAAATA
2902044 ATATATATTTA
1 ATAT-TATTTA
2902055 TATATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.36
19 11 0.44
20 5 0.20
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATTATTTAGAAAAAATA
Found at i:2902049 original size:2 final size:2
Alignment explanation
Indices: 2902044--2902079 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2902034 AGAAAAAATA
*
2902044 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2902080 CAAGAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2905048 original size:17 final size:20
Alignment explanation
Indices: 2905016--2905053 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
2905006 ATATATTTAT
2905016 ATATATATCAAGAA-TTAAA
1 ATATATATCAAGAATTTAAA
2905035 ATATATAT-AA-AATTTAAA
1 ATATATATCAAGAATTTAAA
2905053 A
1 A
2905054 ATAGAAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 8 0.44
19 8 0.44
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (20 bp):
ATATATATCAAGAATTTAAA
Found at i:2905525 original size:20 final size:20
Alignment explanation
Indices: 2905489--2905526 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2905479 TTATACTTTT
*
2905489 ATTTTAATAATATATAATGA
1 ATTTTAATAATAAATAATGA
2905509 ATTTTCAATAA-AAATAAT
1 ATTTT-AATAATAAATAAT
2905527 ACTATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTTTAATAATAAATAATGA
Found at i:2908955 original size:24 final size:24
Alignment explanation
Indices: 2908928--2909021 Score: 109
Period size: 24 Copynumber: 3.9 Consensus size: 24
2908918 ATTTTCAATT
2908928 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTGATA
* *
2908952 TGAA-TCATGTTCTAATTTCTAATA
1 TGAATTC-TGTTCTGATTTCTGATA
* * * *
2908976 TGGATTTTGTTCTGATATCTGATC
1 TGAATTCTGTTCTGATTTCTGATA
*
2909000 TGAATTCTGTTTTGATTTCTGA
1 TGAATTCTGTTCTGATTTCTGA
2909022 CATCTCTGTT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
23 2 0.04
24 53 0.95
25 1 0.02
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATA
Found at i:2912189 original size:22 final size:20
Alignment explanation
Indices: 2912147--2912191 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
2912137 ATTATTATTA
*
2912147 TTATTAAAATTTAATATAAT
1 TTATTAAAATTTAATAAAAT
*
2912167 TTATTCAAAGTTTCAATAAAAT
1 TTATT-AAAATTT-AATAAAAT
2912189 TTA
1 TTA
2912192 ATAATCTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 6 0.29
22 10 0.48
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
TTATTAAAATTTAATAAAAT
Found at i:2914898 original size:28 final size:29
Alignment explanation
Indices: 2914846--2914913 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
2914836 CTCATAATTC
* *
2914846 TAATAATAT-GATATTATATTCTTTAATAT
1 TAATAATATATATATTATACTCTTT-ATAT
*
2914875 T-ATAATATATATATTATACT-TTTATTT
1 TAATAATATATATATTATACTCTTTATAT
2914902 TAATAATATATA
1 TAATAATATATA
2914914 ATGATTTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 4 0.12
28 20 0.59
29 10 0.29
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (29 bp):
TAATAATATATATATTATACTCTTTATAT
Found at i:2919777 original size:13 final size:13
Alignment explanation
Indices: 2919747--2919781 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2919737 AGGGGGAGTA
2919747 ATTTTGCAAAATTG
1 ATTTT-CAAAATTG
2919761 -TTTTCAAAATTG
1 ATTTTCAAAATTG
2919773 ATTTTCAAA
1 ATTTTCAAA
2919782 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (13 bp):
ATTTTCAAAATTG
Found at i:2920208 original size:65 final size:64
Alignment explanation
Indices: 2920126--2920274 Score: 183
Period size: 65 Copynumber: 2.3 Consensus size: 64
2920116 ATTTCTAATG
* * *
2920126 CATTTTGTGTACAGATGCACA-AGCCAAGCATCGATGCACTCTTGAATATTTTGAAACATCAAAT
1 CATTTTGTGTACCGATGCACATA-CCAAGCATCGATGCACTCATGAAT-CTTTGAAACATCAAAT
2920190 A
64 A
* ** *
2920191 CATTTTGTGTACCGATGCACATACCATGCATCGATGCACTCATGGCTCTTTGAAACATCAAATG
1 CATTTTGTGTACCGATGCACATACCAAGCATCGATGCACTCATGAATCTTTGAAACATCAAATA
* * *
2920255 TAATTAGTGTACCGATGCAC
1 CATTTTGTGTACCGATGCAC
2920275 CCCTAGTGTA
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 32 0.44
65 40 0.55
66 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.30
Consensus pattern (64 bp):
CATTTTGTGTACCGATGCACATACCAAGCATCGATGCACTCATGAATCTTTGAAACATCAAATA
Found at i:2923923 original size:21 final size:21
Alignment explanation
Indices: 2923897--2923987 Score: 109
Period size: 21 Copynumber: 4.3 Consensus size: 21
2923887 AATAGTAATT
2923897 AAAATATATAATGATATTTTA
1 AAAATATATAATGATATTTTA
2923918 AAAATATATAATGATATTTTA
1 AAAATATATAATGATATTTTA
2923939 ATAATATATAATAATGAT-TTTTCA
1 A-AA-ATAT-ATAATGATATTTT-A
*
2923963 ATAATATAT-A--ATATTTTA
1 AAAATATATAATGATATTTTA
2923981 AAAATAT
1 AAAATAT
2923988 TATTCTTTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 13
0.81 0.03 0.17
Matches are distributed among these distances:
18 9 0.14
19 4 0.06
20 1 0.02
21 24 0.38
22 6 0.10
23 9 0.14
24 10 0.16
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (21 bp):
AAAATATATAATGATATTTTA
Found at i:2923977 original size:42 final size:41
Alignment explanation
Indices: 2923855--2923987 Score: 120
Period size: 42 Copynumber: 3.3 Consensus size: 41
2923845 ATTATACTTT
* *
2923855 TATTTTAAT-A-ATAT-ATAATGATTTTCAATAA-AAATAG
1 TATTTTAATAATATATAATAATGATTTTCAATAATATATAA
* * *
2923892 TA-ATTAA-AATATATAATGAT-ATTTT-AAAAATATATAATGA
1 TATTTTAATAATATATAATAATGATTTTCAATAATATAT-A--A
2923932 TATTTTAATAATATATAATAATGATTTTTCAATAATATATAA
1 TATTTTAATAATATATAATAATGA-TTTTCAATAATATATAA
*
2923974 TATTTTAAAAATAT
1 TATTTTAATAATAT
2923988 TATTCTTTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
36 9 0.12
37 14 0.19
38 5 0.07
40 2 0.03
41 4 0.05
42 26 0.35
43 1 0.01
44 5 0.07
45 9 0.12
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (41 bp):
TATTTTAATAATATATAATAATGATTTTCAATAATATATAA
Found at i:2930335 original size:2 final size:2
Alignment explanation
Indices: 2930328--2930354 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2930318 TTTCTTGGAA
2930328 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2930355 AGATATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2932261 original size:20 final size:20
Alignment explanation
Indices: 2932225--2932262 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2932215 TTATACTTTT
*
2932225 ATTTTAATAATATATAATGA
1 ATTTTAATAATAAATAATGA
2932245 ATTTTCAATAA-AAATAAT
1 ATTTT-AATAATAAATAAT
2932263 ACTAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTTTAATAATAAATAATGA
Found at i:2935672 original size:12 final size:12
Alignment explanation
Indices: 2935655--2935693 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2935645 ATGTTTTATC
*
2935655 TGATTTCCGATA
1 TGATTTCTGATA
* *
2935667 TGATTTCTGTTC
1 TGATTTCTGATA
2935679 TGATTTCTGATA
1 TGATTTCTGATA
2935691 TGA
1 TGA
2935694 ATCATATTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.49
Consensus pattern (12 bp):
TGATTTCTGATA
Found at i:2935680 original size:24 final size:24
Alignment explanation
Indices: 2935653--2935760 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
2935643 GAATGTTTTA
* *
2935653 TCTGATTTCCGATATGATTTCTGT
1 TCTGATTTCTGATATGATTTCTAT
*
2935677 TCTGATTTCTGATATGA-ATCATAT
1 TCTGATTTCTGATATGATTTC-TAT
*
2935701 TCTGATTTCTGATATGGATTT-TGT
1 TCTGATTTCTGATAT-GATTTCTAT
* * *
2935725 TCTGATATCTGATCTGAATTCTAT
1 TCTGATTTCTGATATGATTTCTAT
*
2935749 TTTGATTTCTGA
1 TCTGATTTCTGA
2935761 CATCTCTGTT
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
23 6 0.09
24 60 0.87
25 2 0.03
26 1 0.01
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATATGATTTCTAT
Found at i:2935758 original size:48 final size:48
Alignment explanation
Indices: 2935653--2935760 Score: 148
Period size: 48 Copynumber: 2.2 Consensus size: 48
2935643 GAATGTTTTA
* *
2935653 TCTGATTTCCGATATGATTTCTGTTCTGATTTCTGATATGAATCATAT
1 TCTGATTTCTGATATGATTTCTGTTCTGATATCTGATATGAATCATAT
*
2935701 TCTGATTTCTGATATGGATTT-TGTTCTGATATCTGATCTGAATTC-TAT
1 TCTGATTTCTGATAT-GATTTCTGTTCTGATATCTGATATGAA-TCATAT
*
2935749 TTTGATTTCTGA
1 TCTGATTTCTGA
2935761 CATCTCTGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
48 47 0.87
49 7 0.13
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATATGATTTCTGTTCTGATATCTGATATGAATCATAT
Found at i:2938708 original size:18 final size:18
Alignment explanation
Indices: 2938655--2938712 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
2938645 ATATTTACTC
* *
2938655 ATAATTCTA-ATAATATG
1 ATAATTATATATAATATT
2938672 AT-ATTATATTATGTAATATT
1 ATAATTATA-TA--TAATATT
2938692 ATAATTATATATAATATT
1 ATAATTATATATAATATT
2938710 ATA
1 ATA
2938713 CTTTTATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 5 0.15
17 2 0.06
18 11 0.32
20 10 0.29
21 6 0.18
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (18 bp):
ATAATTATATATAATATT
Found at i:2938961 original size:22 final size:20
Alignment explanation
Indices: 2938919--2938963 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
2938909 ATTATTATTA
*
2938919 TTATTAAAATTTAATATAAT
1 TTATTAAAATTTAATAAAAT
*
2938939 TTATTCAAAGTTTCAATAAAAT
1 TTATT-AAAATTT-AATAAAAT
2938961 TTA
1 TTA
2938964 ATAATCTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 6 0.29
22 10 0.48
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
TTATTAAAATTTAATAAAAT
Found at i:2940055 original size:2 final size:2
Alignment explanation
Indices: 2940048--2940078 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2940038 TTTCTTGGAA
2940048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2940079 AGATATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2941958 original size:31 final size:31
Alignment explanation
Indices: 2941887--2941958 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
2941877 CTCATAATTC
*
2941887 TAATA-ATATGATATTATATTCTTTTATATTA
1 TAATATATATAATATTATA-TCTTTTATATTA
*
2941918 TAATGATATATAATATTATA-CTTTTATTTTAA
1 TAAT-ATATATAATATTATATCTTTTATATT-A
2941950 TAATATATA
1 TAATATATA
2941959 ATGATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
31 18 0.50
32 6 0.17
33 12 0.33
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (31 bp):
TAATATATATAATATTATATCTTTTATATTA
Found at i:2946607 original size:14 final size:14
Alignment explanation
Indices: 2946590--2946630 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
2946580 ACCATTGCAC
*
2946590 ATTTGTTTATGAAT
1 ATTTATTTATGAAT
2946604 ATTTATTTATGAAT
1 ATTTATTTATGAAT
2946618 ATTTATTTATGAA
1 ATTTATTTATGAA
2946631 ACTAATGGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (14 bp):
ATTTATTTATGAAT
Found at i:2946809 original size:22 final size:22
Alignment explanation
Indices: 2946761--2946809 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
2946751 TAAGAAAAAT
2946761 GGGGAGAAGGTGTGTTATAGTAA
1 GGGG-GAAGGTGTGTTATAGTAA
*
2946784 --GGGAATGTGTGTTATAGTAA
1 GGGGGAAGGTGTGTTATAGTAA
2946804 GGGGGA
1 GGGGGA
2946810 GTAATTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.27
Consensus pattern (22 bp):
GGGGGAAGGTGTGTTATAGTAA
Found at i:2946843 original size:13 final size:13
Alignment explanation
Indices: 2946813--2946847 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2946803 AGGGGGAGTA
2946813 ATTTTGCAAAATTG
1 ATTTT-CAAAATTG
2946827 -TTTTCAAAATTG
1 ATTTTCAAAATTG
2946839 ATTTTCAAA
1 ATTTTCAAA
2946848 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (13 bp):
ATTTTCAAAATTG
Found at i:2947339 original size:64 final size:65
Alignment explanation
Indices: 2947198--2947340 Score: 155
Period size: 65 Copynumber: 2.2 Consensus size: 65
2947188 AATGCATTTT
* * * * *
2947198 GTGTATCGATGCACAAGCCAAGCATCGATGCACTCTTGAATATTTTGAAACATCAAATACATTTT
1 GTGTACCGATGCACAAGCCAAGCATCGATGCACTCATGAATACTTTGAAACATCAAATACAATTA
* ** * **
2947263 GTGTACCGATGCACATA-CCATGCATCGATGCACTCATGGCT-CTTTGAAACATCGAATGTAATT
1 GTGTACCGATGCACA-AGCCAAGCATCGATGCACTCATGAATACTTTGAAACATCAAATACAATT
2947326 A
65 A
*
2947327 GTGTACTGATGCAC
1 GTGTACCGATGCAC
2947341 CCCTAGTGTA
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
64 30 0.46
65 34 0.52
66 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (65 bp):
GTGTACCGATGCACAAGCCAAGCATCGATGCACTCATGAATACTTTGAAACATCAAATACAATTA
Found at i:2949042 original size:2 final size:2
Alignment explanation
Indices: 2949035--2949064 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2949025 TTTCTTGGAA
2949035 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2949065 TTTTTTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2954242 original size:20 final size:21
Alignment explanation
Indices: 2954196--2954242 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
2954186 TTAAACAATC
*
2954196 TATTGAAGTTTATTCAAACTA
1 TATTGAAATTTATTCAAACTA
* *
2954217 TA-TGAAATTTATT-ACAGTA
1 TATTGAAATTTATTCAAACTA
2954236 TATTGAA
1 TATTGAA
2954243 TTAAATGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 6 0.27
20 14 0.64
21 2 0.09
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (21 bp):
TATTGAAATTTATTCAAACTA
Found at i:2956243 original size:2 final size:2
Alignment explanation
Indices: 2956238--2956269 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2956228 TAAAAAAATA
2956238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2956270 CAAGAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2956721 original size:25 final size:26
Alignment explanation
Indices: 2956684--2956732 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
2956674 TTCCAATAAT
**
2956684 ATGATATTGTATT-CTTTAATTTATA
1 ATGATATAATATTACTTTAATTTATA
*
2956709 ATGATATAATATTACTTTTATTTA
1 ATGATATAATATTACTTTAATTTA
2956733 ATATATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (26 bp):
ATGATATAATATTACTTTAATTTATA
Done.