Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006455.1 Hibiscus syriacus cultivar Beakdansim tig00015637_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: 107365
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:6767 original size:40 final size:40
Alignment explanation
Indices: 6723--6800 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
6713 ATCTTACGTG
**
6723 CTCACCCGCAACTATGTGCGACTCTGCCACTGATTATGTA
1 CTCACCCGCAACTATGTGCGACTCCACCACTGATTATGTA
* *
6763 CTCACCCGCAATTATGTGCGACTCCATCACTGATTATG
1 CTCACCCGCAACTATGTGCGACTCCACCACTGATTATG
6801 AGCTATCACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (40 bp):
CTCACCCGCAACTATGTGCGACTCCACCACTGATTATGTA
Found at i:6954 original size:60 final size:60
Alignment explanation
Indices: 6873--7060 Score: 215
Period size: 60 Copynumber: 3.1 Consensus size: 60
6863 TGCATCATAT
* * *
6873 ATCCTTAAACTATGACTCTCATTTTAAATTGGTCCTTCAACTTTTAAACATTCTAATTTC
1 ATCCCTAAACTATGACTCTCATTCTAAATTAGTCCTTCAACTTTTAAACATTCTAATTTC
* * * *
6933 ATCCCTAAATTATGACTCTCATTCTAAATTATTCCTTAAACTTTTAAACATT-TCAATTTT
1 ATCCCTAAACTATGACTCTCATTCTAAATTAGTCCTTCAACTTTTAAACATTCT-AATTTC
* * *
6993 ATCCCCAAACTATAGA-TCTCATTCTAAATTAGTCC--CAAACTTTTGAATCTTTC-AATTTC
1 ATCCCTAAACTAT-GACTCTCATTCTAAATTAGTCCTTC-AACTTTT-AAACATTCTAATTTC
7052 ATCCCTAAA
1 ATCCCTAAA
7061 TTTATTCAAA
Statistics
Matches: 108, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
59 21 0.19
60 85 0.79
61 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (60 bp):
ATCCCTAAACTATGACTCTCATTCTAAATTAGTCCTTCAACTTTTAAACATTCTAATTTC
Found at i:9361 original size:29 final size:29
Alignment explanation
Indices: 9319--9375 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
9309 AGTGTTGGCC
9319 GTAGGTCGCCATGCACTCCGGACGACCTT
1 GTAGGTCGCCATGCACTCCGGACGACCTT
*
9348 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGACGACCT
9376 ACCCTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.16, C:0.35, G:0.30, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGACGACCTT
Found at i:9489 original size:50 final size:49
Alignment explanation
Indices: 9413--9510 Score: 169
Period size: 50 Copynumber: 2.0 Consensus size: 49
9403 GTGTTGCATG
* *
9413 GCACATGCACGTCCAACACATAGGTCGCCATGCCCTCCGGGCGACCTAT
1 GCACATGCACGTCCAACAAATAGGTCGCCATACCCTCCGGGCGACCTAT
9462 GCACATGCACGTCCCAACAAATAGGTCGCCATACCCTCCGGGCGACCTA
1 GCACATGCACGT-CCAACAAATAGGTCGCCATACCCTCCGGGCGACCTA
9511 CCCTCGCTCG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 12 0.26
50 34 0.74
ACGTcount: A:0.24, C:0.39, G:0.21, T:0.15
Consensus pattern (49 bp):
GCACATGCACGTCCAACAAATAGGTCGCCATACCCTCCGGGCGACCTAT
Found at i:9550 original size:33 final size:33
Alignment explanation
Indices: 9513--9606 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
9503 GCGACCTACC
* *
9513 CTCGCTCGGCTT-CCCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGACCTCGGATGCCCTCGCATAG
9546 CTCGCTCGGTTGACCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGACCTCGGATGCCCTCGCATAG
* * * *
9579 CTCGTTCGGATGGCCTCGGATGCTCTCG
1 CTCGCTCGGTTGACCTCGGATGCCCTCG
9607 GATGACCTCG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 2 0.04
33 52 0.96
ACGTcount: A:0.10, C:0.37, G:0.27, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGTTGACCTCGGATGCCCTCGCATAG
Found at i:9572 original size:10 final size:10
Alignment explanation
Indices: 9525--9647 Score: 75
Period size: 10 Copynumber: 11.7 Consensus size: 10
9515 CGCTCGGCTT
*
9525 CCCTCGGATT
1 CCCTCGGATG
*
9535 CCCTCGCATAG
1 CCCTCGGAT-G
*
9546 CTCGCTCGGTTG
1 C-C-CTCGGATG
*
9558 ACCTCGGATG
1 CCCTCGGATG
*
9568 CCCTCGCATAG
1 CCCTCGGAT-G
*
9579 CTCGTTCGGATG
1 C-C-CTCGGATG
*
9591 GCCTCGGATG
1 CCCTCGGATG
*
9601 CTCTCGGATG
1 CCCTCGGATG
*
9611 ACCTCGGATG
1 CCCTCGGATG
**
9621 CTTTCGGATG
1 CCCTCGGATG
*
9631 CTCTCGGATG
1 CCCTCGGATG
*
9641 GCCTCGG
1 CCCTCGG
9648 TCGGATGGCC
Statistics
Matches: 85, Mismatches: 22, Indels: 12
0.71 0.18 0.10
Matches are distributed among these distances:
10 66 0.78
11 5 0.06
12 4 0.05
13 10 0.12
ACGTcount: A:0.11, C:0.33, G:0.29, T:0.26
Consensus pattern (10 bp):
CCCTCGGATG
Found at i:9609 original size:20 final size:20
Alignment explanation
Indices: 9560--9665 Score: 88
Period size: 20 Copynumber: 5.0 Consensus size: 20
9550 CTCGGTTGAC
* *
9560 CTCGGATGCCCTCGCATAGCT
1 CTCGGATGGCCTCGGAT-GCT
9581 CGTTCGGATGGCCTCGGATGCT
1 C--TCGGATGGCCTCGGATGCT
*
9603 CTCGGATGACCTCGGATGCT
1 CTCGGATGGCCTCGGATGCT
*
9623 TTCGGAT-GCTCTCGGATGGCCT
1 CTCGGATGGC-CTCGGAT-G-CT
*
9645 CGGTCGGATGGCCTCAGATGC
1 C--TCGGATGGCCTCGGATGC
9666 CCAGCGTGTT
Statistics
Matches: 70, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
19 1 0.01
20 31 0.44
21 2 0.03
22 7 0.10
23 15 0.21
24 12 0.17
25 2 0.03
ACGTcount: A:0.12, C:0.30, G:0.32, T:0.25
Consensus pattern (20 bp):
CTCGGATGGCCTCGGATGCT
Found at i:9620 original size:30 final size:30
Alignment explanation
Indices: 9584--9647 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
9574 CATAGCTCGT
9584 TCGGATGGC-CTCGGATGCTCTCGGATGACC
1 TCGGAT-GCTCTCGGATGCTCTCGGATGACC
* *
9614 TCGGATGCTTTCGGATGCTCTCGGATGGCC
1 TCGGATGCTCTCGGATGCTCTCGGATGACC
9644 TCGG
1 TCGG
9648 TCGGATGGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.11, C:0.28, G:0.34, T:0.27
Consensus pattern (30 bp):
TCGGATGCTCTCGGATGCTCTCGGATGACC
Found at i:9741 original size:29 final size:29
Alignment explanation
Indices: 9704--9761 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
9694 GCAATCTCTT
*
9704 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* * *
9733 GTAGGTCGCCCTGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
9762 CGACCAACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.22, C:0.28, G:0.34, T:0.16
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:11564 original size:228 final size:226
Alignment explanation
Indices: 11082--11635 Score: 578
Period size: 228 Copynumber: 2.4 Consensus size: 226
11072 TTGAATTCCA
* * *
11082 AGACTCCTTTTGAATGTTGTAGTCTGCAAGGGTTAGACCATCCTCAAGCTGTTTCCTGGCAAAAA
1 AGACTCCTTTTGAATGTTGTA-TCAGCAAGGGTTCGACCATCCTCGAGCTGTTTCCTGGCAAAAA
* * *
11147 TTAACCTCTGCTGGTCTGGTGGAACCCCTCCTTGTCTTGGATCTTGGCCTTGACATTATCAATTG
65 TGAACCTCTGCTGGTCTGGGGGAACCCCTCCTTGTCTTGGATCTTGGCCTTGACATTATCAATCG
* * * * *
11212 TATCGGAACTCTCGACCTCTAAGGTTATGGCCTTTCCAGTAAGGGTTTTCACAAATATCTGCATA
130 TATCAGAACTCTCCACCACTAAGGTTATGGCCTTGCCAGTAAGGGTTTTCACAAAAATCTGCATA
* * *
11277 CCACCCCTCAGACGAAGGACAAGGTGGAAGGC
195 CCACCACGCAGACGAAGCACAAGGTGGAAGGC
* * * *
11309 GGACT-CTTTCTGGATGTTGTAATCAGCAAGGCTTCGGCCATCCTCGAGCTGTTTACC-GGCAAA
1 AGACTCCTTT-TGAATGTTGT-ATCAGCAAGGGTTCGACCATCCTCGAGCTGTTT-CCTGGCAAA
* * * * * * *
11372 GATGAGCCTCTGTTGGTCTGGAGGGATCCCTTCTTTGTCTTGGATCTTGGCCTTGACATTATCTA
63 AATGAACCTCTGCTGGTCTGG-GGGAACCCCTCCTTGTCTTGGATCTTGGCCTTGACATTATCAA
* * * *
11437 TCGTATCAGAGCTTTCCACCAC-AAGAGTTATGGTCTTGCCAGTAAGGGTTTTCACAAAAATTTG
127 TCGTATCAGAACTCTCCACCACTAAG-GTTATGGCCTTGCCAGTAAGGGTTTTCACAAAAATCTG
* * * * * * *
11501 CATGCCTCCACGGAGATGTAGCACCAA-GTGGAGGGT
191 CATACCACCACGCAGACGAAGCA-CAAGGTGGAAGGC
* * * * **
11537 AGACTCCTTTTGAATGTTTTGATCAGCAAGGGTCCGACCATCTTCGAGCTGCTTCCCAG-AAAAA
1 AGACTCCTTTTGAATGTTGT-ATCAGCAAGGGTTCGACCATCCTCGAGCTGTTTCCTGGCAAAAA
* * * *
11601 TTAACCTCTGCTGATCTGGTGGAATACCCTCCTTG
65 TGAACCTCTGCTGGTCTGGGGGAA-CCCCTCCTTG
11636 CCTTTTCTGC
Statistics
Matches: 262, Mismatches: 56, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
226 7 0.03
227 94 0.36
228 154 0.59
229 7 0.03
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (226 bp):
AGACTCCTTTTGAATGTTGTATCAGCAAGGGTTCGACCATCCTCGAGCTGTTTCCTGGCAAAAAT
GAACCTCTGCTGGTCTGGGGGAACCCCTCCTTGTCTTGGATCTTGGCCTTGACATTATCAATCGT
ATCAGAACTCTCCACCACTAAGGTTATGGCCTTGCCAGTAAGGGTTTTCACAAAAATCTGCATAC
CACCACGCAGACGAAGCACAAGGTGGAAGGC
Found at i:11650 original size:34 final size:34
Alignment explanation
Indices: 11607--11674 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
11597 AAAATTAACC
11607 TCTGCTGATCTGGTGGAATACCCTCCTTGCCTTT
1 TCTGCTGATCTGGTGGAATACCCTCCTTGCCTTT
*
11641 TCTGCTGATCTGGTGGAATACCCTCCTTGTCTTT
1 TCTGCTGATCTGGTGGAATACCCTCCTTGCCTTT
11675 GATCTTGGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.12, C:0.28, G:0.21, T:0.40
Consensus pattern (34 bp):
TCTGCTGATCTGGTGGAATACCCTCCTTGCCTTT
Found at i:18174 original size:39 final size:39
Alignment explanation
Indices: 18128--18207 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
18118 AAATTTTAAT
*
18128 TTTATATTCAATTATTGTATTTCATCGTATAATCAATGA
1 TTTATATTCAATTATTGTATTTCATCATATAATCAATGA
* *
18167 TTTATATTCAATTATTTTATTTCGTCATATAATCAATGA
1 TTTATATTCAATTATTGTATTTCATCATATAATCAATGA
18206 TT
1 TT
18208 GTTGATCTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (39 bp):
TTTATATTCAATTATTGTATTTCATCATATAATCAATGA
Found at i:25580 original size:65 final size:64
Alignment explanation
Indices: 25495--25625 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 64
25485 ATTAAATGCA
25495 GAAAAAAATTAAGAAATTAGGTGTGAAGACTTATGGCATATTAATAATTCTTTTTGATAGTTTG
1 GAAAAAAATTAAGAAATTAGGTGTGAAGACTTATGGCATATTAATAATTCTTTTTGATAGTTTG
* *
25559 GAAATAAAATTAAGAAATTAGGTGTGATGATTTATGGCATATTAATAATTCTTTTTGATAGTTTG
1 GAAA-AAAATTAAGAAATTAGGTGTGAAGACTTATGGCATATTAATAATTCTTTTTGATAGTTTG
25624 GA
1 GA
25626 TGACCAAAGT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 4 0.06
65 60 0.94
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (64 bp):
GAAAAAAATTAAGAAATTAGGTGTGAAGACTTATGGCATATTAATAATTCTTTTTGATAGTTTG
Found at i:31150 original size:2 final size:2
Alignment explanation
Indices: 31143--31170 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31133 TATACTAATA
31143 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
31171 TAAATTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33569 original size:30 final size:33
Alignment explanation
Indices: 33533--33607 Score: 122
Period size: 30 Copynumber: 2.4 Consensus size: 33
33523 ACCATAAATT
33533 ATAAACCCTAAACT-TTATAACTTATATA-A-C
1 ATAAACCCTAAACTCTTATAACTTATATATATC
33563 ATAAACCCTAAA-TCTTATAACTTATATATATC
1 ATAAACCCTAAACTCTTATAACTTATATATATC
33595 ATAAACCCTAAAC
1 ATAAACCCTAAAC
33608 CCTAATATAG
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
29 1 0.02
30 26 0.63
31 1 0.02
32 13 0.32
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (33 bp):
ATAAACCCTAAACTCTTATAACTTATATATATC
Found at i:40543 original size:59 final size:58
Alignment explanation
Indices: 40451--40570 Score: 222
Period size: 59 Copynumber: 2.1 Consensus size: 58
40441 CCTAAAAGTG
40451 AAATTTTCAAAGGAATTTATTAATTTTATTAAAAATAGAAAATATCCAAAATTATATAT
1 AAATTTTCAAAGGAATTTATTAATTTTATTAAAAATAGAAAATATCCAAAATTATA-AT
*
40510 AAATTTTCAAAGGAATTTATTAATTTTATTAAAAATAGAAAATATCTAAAATTATAAT
1 AAATTTTCAAAGGAATTTATTAATTTTATTAAAAATAGAAAATATCCAAAATTATAAT
40568 AAA
1 AAA
40571 GATTTATAAG
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 5 0.08
59 55 0.92
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (58 bp):
AAATTTTCAAAGGAATTTATTAATTTTATTAAAAATAGAAAATATCCAAAATTATAAT
Found at i:47054 original size:10 final size:10
Alignment explanation
Indices: 47039--47074 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
47029 ATTCATTGAA
*
47039 TTCGTTTACG
1 TTCGTTTATG
*
47049 TTCGTTTGTG
1 TTCGTTTATG
47059 TTCGTTTATG
1 TTCGTTTATG
47069 TTCGTT
1 TTCGTT
47075 CATTTGTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.06, C:0.14, G:0.22, T:0.58
Consensus pattern (10 bp):
TTCGTTTATG
Found at i:47861 original size:36 final size:36
Alignment explanation
Indices: 47814--47885 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
47804 GGGGACGGGG
*
47814 AAAACCGTTTATGCTAAACGGGGACGGAGACGGGAA
1 AAAACCGTTTATGCTAAACGGAGACGGAGACGGGAA
* * *
47850 AAAATCGTTTATGCTAAACGGAGATGGGGACGGGAA
1 AAAACCGTTTATGCTAAACGGAGACGGAGACGGGAA
47886 TAGGTTTGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.36, C:0.14, G:0.33, T:0.17
Consensus pattern (36 bp):
AAAACCGTTTATGCTAAACGGAGACGGAGACGGGAA
Found at i:47997 original size:34 final size:34
Alignment explanation
Indices: 47933--48037 Score: 92
Period size: 34 Copynumber: 3.0 Consensus size: 34
47923 CGGCCCGATA
* *
47933 AATATTAAAAAATAATTAATTTATA-T-ATATATAT
1 AATATTAATAAAT--TTAATTTAAATTAATATATAT
47967 AATATTAATAAATTTAATTTAAATTAATATATAT
1 AATATTAATAAATTTAATTTAAATTAATATATAT
* *
48001 -ATATATAAT-ATTTATATATTTAATTTAAATATATAT
1 AATAT-TAATAAATT-TA-ATTTAAATT-AATATATAT
48037 A
1 A
48038 CCCGACCCGA
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
32 9 0.15
33 8 0.13
34 26 0.43
35 8 0.13
36 9 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (34 bp):
AATATTAATAAATTTAATTTAAATTAATATATAT
Found at i:48009 original size:40 final size:38
Alignment explanation
Indices: 47954--48037 Score: 132
Period size: 40 Copynumber: 2.2 Consensus size: 38
47944 ATAATTAATT
47954 TATATATATATATAATATTAATAAATTTAATTTAAATTAA
1 TATATATATATATAATATTAATAAATTTAATTTAAA-T-A
* *
47994 TATATATATATATAATATTTATATATTTAATTTAAATA
1 TATATATATATATAATATTAATAAATTTAATTTAAATA
48032 TATATA
1 TATATA
48038 CCCGACCCGA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
38 7 0.17
39 1 0.02
40 34 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (38 bp):
TATATATATATATAATATTAATAAATTTAATTTAAATA
Found at i:51751 original size:30 final size:30
Alignment explanation
Indices: 51711--51774 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
51701 ATTCTTCTAC
* * *
51711 TTTATTTATTTTTTCATTATTATTTATTTAT
1 TTTATTTATTTTCTCATTATT-TTCATTAAT
51742 TTTA-TTATTTTCTCATTATTTTCATTAAT
1 TTTATTTATTTTCTCATTATTTTCATTAAT
51771 TTTA
1 TTTA
51775 ATGCCCTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 11 0.37
30 15 0.50
31 4 0.13
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (30 bp):
TTTATTTATTTTCTCATTATTTTCATTAAT
Found at i:53623 original size:2 final size:2
Alignment explanation
Indices: 53616--53666 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
53606 TGTTATTTGA
53616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53658 AT AT AT AT A
1 AT AT AT AT A
53667 CCGTAAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53834 original size:22 final size:24
Alignment explanation
Indices: 53803--53856 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
53793 AAACCTTTTC
*
53803 TTTTAATTTCAATA-TTATGT-TT
1 TTTTATTTTCAATATTTATGTATT
*
53825 TTTTATTTTCATTATTTATGTATT
1 TTTTATTTTCAATATTTATGTATT
53849 TATTTATT
1 T-TTTATT
53857 ATTGGAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 12 0.44
23 6 0.22
24 3 0.11
25 6 0.22
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTTATTTTCAATATTTATGTATT
Found at i:58343 original size:22 final size:21
Alignment explanation
Indices: 58297--58350 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
58287 CTAAATTATA
* *
58297 AACCCTAAACTATAACCTTGT
1 AACCCTAAACCATAACATTGT
58318 AACCTCTAAACCATGAACATTG-
1 AACC-CTAAACCAT-AACATTGT
*
58340 AACCATAAACC
1 AACCCTAAACC
58351 CCAACTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 10 0.36
22 12 0.43
23 6 0.21
ACGTcount: A:0.43, C:0.30, G:0.06, T:0.22
Consensus pattern (21 bp):
AACCCTAAACCATAACATTGT
Found at i:63080 original size:20 final size:19
Alignment explanation
Indices: 63045--63105 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
63035 AAATATAAAA
63045 ATAATA-AAATTATATATT
1 ATAATATAAATTATATATT
*
63063 ATAATATAAATTCGTATATT
1 ATAATATAAATT-ATATATT
* *
63083 AAAATTTAAATTA-ATTATT
1 ATAATATAAATTATA-TATT
63102 ATAA
1 ATAA
63106 CAAAAAACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.20
19 12 0.34
20 16 0.46
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
ATAATATAAATTATATATT
Found at i:76997 original size:31 final size:31
Alignment explanation
Indices: 76962--77022 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
76952 TATACGGTCA
*
76962 CTTTCGTTTTCATTTAATTAAGATATGATCC
1 CTTTCGTTTTCATTTAACTAAGATATGATCC
* * *
76993 CTTTCGTTTTTATTTAGCTAAGATGTGATC
1 CTTTCGTTTTCATTTAACTAAGATATGATC
77023 ACTACATGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (31 bp):
CTTTCGTTTTCATTTAACTAAGATATGATCC
Found at i:80838 original size:2 final size:2
Alignment explanation
Indices: 80831--80866 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
80821 GCATGTTTAG
80831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80867 GTGCCAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85919 original size:71 final size:71
Alignment explanation
Indices: 85777--85924 Score: 158
Period size: 71 Copynumber: 2.1 Consensus size: 71
85767 TTGGGGCAAC
* * * * * * *
85777 AATAGTGGCGTTTTTTAACAAACGCCGCAATAGGTCCATTTATAGTGACGTTTTTTAAATAGAGT
1 AATATTGGCGTTTTTTAACAAACGACGCAATAAGTCAATCTATAGTGACGTTTTTGAAATAGAGC
*
85842 CGCTAT
66 CACTAT
*
85848 AATATTGGCGTTTCTTTTA-AAACGACGCAATAAGTCAATCTATAGTGACGTTTATTGAAA-A-A
1 AATATTGGCGTTT-TTTAACAAACGACGCAATAAGTCAATCTATAGTGACGTTT-TTGAAATAGA
85910 CGCCACTAT
64 -GCCACTAT
85919 AGATAT
1 A-ATAT
85925 ATTTTTTTGA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
70 1 0.02
71 50 0.78
72 13 0.20
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (71 bp):
AATATTGGCGTTTTTTAACAAACGACGCAATAAGTCAATCTATAGTGACGTTTTTGAAATAGAGC
CACTAT
Found at i:87381 original size:24 final size:24
Alignment explanation
Indices: 87354--87429 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
87344 TAGGTGTATA
*
87354 TATATAT-ATATATTATTAGTTATT
1 TATATATGATATATTATTA-TTAAT
*
87378 TATATATGTTATATTATTATTAAT
1 TATATATGATATATTATTATTAAT
* * * *
87402 TATATAGGTTA-ATTATTGTTTAT
1 TATATATGATATATTATTATTAAT
87425 TATAT
1 TATAT
87430 TTAGTTATCC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.33
24 21 0.46
25 10 0.22
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.58
Consensus pattern (24 bp):
TATATATGATATATTATTATTAAT
Found at i:87395 original size:28 final size:28
Alignment explanation
Indices: 87350--87404 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
87340 CATTTAGGTG
*
87350 TATATATATATATATATTATTAGTTATT
1 TATATATATATATATATTATTAATTATT
*
87378 TATATATGT-TATATTATTATTAATTAT
1 TATATATATATATA-TATTATTAATTAT
87405 ATAGGTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (28 bp):
TATATATATATATATATTATTAATTATT
Found at i:87415 original size:13 final size:12
Alignment explanation
Indices: 87365--87429 Score: 50
Period size: 13 Copynumber: 5.6 Consensus size: 12
87355 ATATATATAT
87365 ATTAT-TAGTTA
1 ATTATATAGTTA
*
87376 TTTATATATGTTA
1 ATTATATA-GTTA
87389 TATTAT-TA-TTA
1 -ATTATATAGTTA
87400 ATTATATAGGTTA
1 ATTATATA-GTTA
*
87413 ATTAT-T-GTTT
1 ATTATATAGTTA
87423 ATTATAT
1 ATTATAT
87430 TTAGTTATCC
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
10 13 0.30
11 10 0.23
12 3 0.07
13 14 0.32
14 4 0.09
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (12 bp):
ATTATATAGTTA
Found at i:87426 original size:23 final size:24
Alignment explanation
Indices: 87362--87429 Score: 84
Period size: 23 Copynumber: 2.8 Consensus size: 24
87352 TATATATATA
* *
87362 TATATTATTAGTTATTTATATATGT
1 TATATTATTA-TTAATTATATAGGT
87387 TATATTATTATTAATTATATAGGT
1 TATATTATTATTAATTATATAGGT
* *
87411 TA-ATTATTGTTTATTATAT
1 TATATTATTATTAATTATAT
87430 TTAGTTATCC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.38
24 14 0.36
25 10 0.26
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (24 bp):
TATATTATTATTAATTATATAGGT
Found at i:89809 original size:2 final size:2
Alignment explanation
Indices: 89802--89830 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
89792 ATAACATAAT
89802 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
89831 TTATGCAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:91297 original size:37 final size:38
Alignment explanation
Indices: 91225--91297 Score: 96
Period size: 36 Copynumber: 1.9 Consensus size: 38
91215 TATATTTTTT
*
91225 ATTTTGTAAAAAAAATTATATAAATATTATGAATTTAA
1 ATTTTGTAAAAAAAATTATATAAATATTATCAATTTAA
* *
91263 ATTTT-TAAAGAAAA-TATATAAATATTTTACAATTT
1 ATTTTGTAAAAAAAATTATATAAATATTAT-CAATTT
91298 GTAATATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 13 0.42
37 13 0.42
38 5 0.16
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (38 bp):
ATTTTGTAAAAAAAATTATATAAATATTATCAATTTAA
Found at i:91479 original size:20 final size:20
Alignment explanation
Indices: 91443--91480 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
91433 ATCATATTCC
**
91443 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
91463 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
91481 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:94013 original size:21 final size:21
Alignment explanation
Indices: 93980--94142 Score: 124
Period size: 21 Copynumber: 7.9 Consensus size: 21
93970 TCCAAAATCA
*
93980 TTGCGATAACACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
94001 TTGTGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
** *
94022 TTGCGATAGTC-CAAATTC-GCG
1 TTGCGATAG-CAC-TGTTCACCG
* ***
94043 TTGCGGTAGTC-CAAAATCA---
1 TTGCGATAG-CAC-TGTTCACCG
*
94062 TTGCGATAGCACTGTTCA-CA
1 TTGCGATAGCACTGTTCACCG
*
94082 TTGCGATAACACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
* *
94103 TTGCGATAACACTGTTCACCA
1 TTGCGATAGCACTGTTCACCG
94124 TTGCGATAGCACTGTTCAC
1 TTGCGATAGCACTGTTCAC
94143 ATTGCGAATT
Statistics
Matches: 119, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
18 4 0.03
19 9 0.08
20 17 0.14
21 85 0.71
22 4 0.03
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACCG
Found at i:94078 original size:82 final size:81
Alignment explanation
Indices: 93941--94110 Score: 277
Period size: 82 Copynumber: 2.1 Consensus size: 81
93931 ACTATCGCAA
* * *
93941 TGCGATAGTCCGAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACCGTTGTG
1 TGCGATAGTCCAAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCA-CATTGCG
*
94006 ATAGCACTGTTCACCGT
65 ATAACACTGTTCACCGT
* *
94023 TGCGATAGTCCAAATTCGCGTTGCGGTAGTCCAAAATCATTGCGATAGCACTGTTCACATTGCGA
1 TGCGATAGTCCAAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACATTGCGA
94088 TAACACTGTTCACCGT
66 TAACACTGTTCACCGT
94104 TGCGATA
1 TGCGATA
94111 ACACTGTTCA
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
81 28 0.34
82 54 0.66
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (81 bp):
TGCGATAGTCCAAATTCGCGTTGCGATAGTCCAAAATCATTGCGATAACACTGTTCACATTGCGA
TAACACTGTTCACCGT
Found at i:94085 original size:20 final size:21
Alignment explanation
Indices: 94060--94149 Score: 139
Period size: 21 Copynumber: 4.4 Consensus size: 21
94050 AGTCCAAAAT
*
94060 CATTGCGATAGCACTGTTCA-
1 CATTGCGATAACACTGTTCAC
94080 CATTGCGATAACACTGTTCAC
1 CATTGCGATAACACTGTTCAC
*
94101 CGTTGCGATAACACTGTTCAC
1 CATTGCGATAACACTGTTCAC
*
94122 CATTGCGATAGCACTGTTCA-
1 CATTGCGATAACACTGTTCAC
94142 CATTGCGA
1 CATTGCGA
94150 ATTTGCGATA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
20 27 0.42
21 38 0.58
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (21 bp):
CATTGCGATAACACTGTTCAC
Found at i:94627 original size:16 final size:17
Alignment explanation
Indices: 94598--94649 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
94588 ATCATAAATA
*
94598 ATTTAGAATTTATATTT
1 ATTTAAAATTTATATTT
*
94615 ATTT-AATTTTATA-TT
1 ATTTAAAATTTATATTT
94630 ATTTAAAATTTATAGTTT
1 ATTTAAAATTTATA-TTT
94648 AT
1 AT
94650 CATAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 15 0.52
17 4 0.14
18 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
ATTTAAAATTTATATTT
Found at i:94831 original size:21 final size:21
Alignment explanation
Indices: 94802--94951 Score: 214
Period size: 21 Copynumber: 7.2 Consensus size: 21
94792 CGCAAATTCA
*
94802 CAAT-GTGAACAGTGCTATCG
1 CAATGGTGAACAGTGTTATCG
94822 CAATGGTGAACAGTGTTATCG
1 CAATGGTGAACAGTGTTATCG
**
94843 CAACAGTGAACAGTGTTATCG
1 CAATGGTGAACAGTGTTATCG
*
94864 CAATAGTGAACAGTGTTATCG
1 CAATGGTGAACAGTGTTATCG
* *
94885 CAAT-GTGAACAGTGCTATCA
1 CAATGGTGAACAGTGTTATCG
*
94905 CAATGGTGAACATTGTTATCG
1 CAATGGTGAACAGTGTTATCG
*
94926 CAACGGTGAACAGTGTTATCG
1 CAATGGTGAACAGTGTTATCG
94947 CAATG
1 CAATG
94952 ATTTTGGACT
Statistics
Matches: 116, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
20 22 0.19
21 94 0.81
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (21 bp):
CAATGGTGAACAGTGTTATCG
Found at i:94922 original size:62 final size:61
Alignment explanation
Indices: 94802--94951 Score: 210
Period size: 62 Copynumber: 2.4 Consensus size: 61
94792 CGCAAATTCA
* * *
94802 CAATGTGAACAGTGCTATCGCAATGGTGAACAGTGTTATCGCAACAGTGAACAGTGTTATCG
1 CAATGTGAACAGTGTTATCGCAAT-GTGAACAGTGCTATCACAACAGTGAACAGTGTTATCG
** *
94864 CAATAGTGAACAGTGTTATCGCAATGTGAACAGTGCTATCACAATGGTGAACATTGTTATCG
1 CAAT-GTGAACAGTGTTATCGCAATGTGAACAGTGCTATCACAACAGTGAACAGTGTTATCG
*
94926 CAACGGTGAACAGTGTTATCGCAATG
1 CAA-TGTGAACAGTGTTATCGCAATG
94952 ATTTTGGACT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
62 60 0.76
63 19 0.24
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (61 bp):
CAATGTGAACAGTGTTATCGCAATGTGAACAGTGCTATCACAACAGTGAACAGTGTTATCG
Found at i:95006 original size:21 final size:21
Alignment explanation
Indices: 94942--95009 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
94932 TGAACAGTGT
*
94942 TATCGCAA--TGATTTTGGAC
1 TATCGCAACGTGAATTTGGAC
* * *
94961 TATAGCAACGCGAATTCGGAC
1 TATCGCAACGTGAATTTGGAC
94982 TATCGCAACGTGAATTTGGAC
1 TATCGCAACGTGAATTTGGAC
95003 TATCGCA
1 TATCGCA
95010 TTGCGATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 7 0.17
21 33 0.82
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (21 bp):
TATCGCAACGTGAATTTGGAC
Found at i:95074 original size:20 final size:19
Alignment explanation
Indices: 95051--95096 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
95041 GAAAACTTAT
* *
95051 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
95071 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
95090 TTGCGAT
1 TTGCGAT
95097 TTTTATTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:95086 original size:19 final size:19
Alignment explanation
Indices: 95062--95098 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
95052 TGCGATACTG
*
95062 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
95081 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
95099 TTATTGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:101760 original size:38 final size:38
Alignment explanation
Indices: 101718--101793 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
101708 GGAATATCAA
101718 AGGTGTGAGTCTTCAATTGCCAAATGGCTGAAAGTTAT
1 AGGTGTGAGTCTTCAATTGCCAAATGGCTGAAAGTTAT
* *
101756 AGGTGTGAGTCTTCAATTGTCAAATGGTTGAAAGTTAT
1 AGGTGTGAGTCTTCAATTGCCAAATGGCTGAAAGTTAT
101794 CTTTGAACAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (38 bp):
AGGTGTGAGTCTTCAATTGCCAAATGGCTGAAAGTTAT
Found at i:102043 original size:24 final size:26
Alignment explanation
Indices: 101998--102049 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
101988 CGTTCGTGAA
*
101998 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
102024 CGTTC-ATT-TATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
102048 CG
1 CG
102050 AACAGAGGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.54
Consensus pattern (26 bp):
CGTTCGATTATATGTTCATTTATGTT
Found at i:102335 original size:12 final size:12
Alignment explanation
Indices: 102318--102342 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
102308 GTTGTTCGTT
102318 TGTTCGTTTATG
1 TGTTCGTTTATG
102330 TGTTCGTTTATG
1 TGTTCGTTTATG
102342 T
1 T
102343 TCGTTCGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.24, T:0.60
Consensus pattern (12 bp):
TGTTCGTTTATG
Done.