Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008896.1 Hibiscus syriacus cultivar Beakdansim tig00112165_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: 70573
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2930 original size:23 final size:23
Alignment explanation
Indices: 2904--2964 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
2894 TCCCCTGTGG
2904 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
* * *
2927 -GGGGAATCGGTTCCCTTTGAAC
1 GGGGGAATCGGTTCCCCTTCAAA
* *
2949 GGGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
2965 TCTGCACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 19 0.59
23 13 0.41
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.25
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Found at i:8836 original size:21 final size:21
Alignment explanation
Indices: 8791--8830 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
8781 TAACAAAGGT
8791 AGTACCGATACTCCCTATATG
1 AGTACCGATACTCCCTATATG
*
8812 AGTACTGATACTCCCTATA
1 AGTACCGATACTCCCTATA
8831 GAAGTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (21 bp):
AGTACCGATACTCCCTATATG
Found at i:9937 original size:26 final size:26
Alignment explanation
Indices: 9907--9960 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
9897 ACTTAATGCA
9907 TATGGAGGGCACAAACTTATGTGTAT
1 TATGGAGGGCACAAACTTATGTGTAT
* * *
9933 TATGGCGGGCACGACCTTATGTGTAT
1 TATGGAGGGCACAAACTTATGTGTAT
9959 TA
1 TA
9961 ATACTTCGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (26 bp):
TATGGAGGGCACAAACTTATGTGTAT
Found at i:18633 original size:21 final size:21
Alignment explanation
Indices: 18577--18634 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
18567 TCCTTAAGGA
* *
18577 GTGGTCCTTCGGGAAATCTAT
1 GTGGTCCTTCGGGACATATAT
* *
18598 GTGGTCATTTGGGACATATAT
1 GTGGTCCTTCGGGACATATAT
18619 GTGGTCCTTCGGGACA
1 GTGGTCCTTCGGGACA
18635 AATTCTATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATATAT
Found at i:22626 original size:34 final size:35
Alignment explanation
Indices: 22548--22642 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 35
22538 AACATAATCA
22548 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
* **
22583 TCAATTACATTCTAAACCTCAAATTTTAAAATAC-
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
* **
22617 TCAATTACATGCCCAACCCCAAATTC
1 TCAATTACATTCTAAACCCCAAATTC
22643 ATAATCAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
34 21 0.40
35 31 0.60
ACGTcount: A:0.41, C:0.28, G:0.01, T:0.29
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATACT
Found at i:23302 original size:148 final size:148
Alignment explanation
Indices: 23120--23414 Score: 536
Period size: 148 Copynumber: 2.0 Consensus size: 148
23110 AAAAACTATT
* * * *
23120 TAAATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCG
1 TAAATTAGAATCAAATAATATTATAATATAATAAATATTTATAATTAAATTTAAACAAAAACTCA
*
23185 AAAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAA
66 AAAATTCAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAA
23250 CTATTTTATAAACTGAAC
131 CTATTTTATAAACTGAAC
23268 TAAATTAGAATCAAATAATATTATAATATAATAAATATTTATAATTAAATTTAAACAAAAACTCA
1 TAAATTAGAATCAAATAATATTATAATATAATAAATATTTATAATTAAATTTAAACAAAAACTCA
*
23333 AAAATTCAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTCAA
66 AAAATTCAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAA
23398 CTATTTTATAAACTGAA
131 CTATTTTATAAACTGAA
23415 TTGAGTATTT
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
148 141 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (148 bp):
TAAATTAGAATCAAATAATATTATAATATAATAAATATTTATAATTAAATTTAAACAAAAACTCA
AAAATTCAATTCAATTCAACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTCGAGTAAA
CTATTTTATAAACTGAAC
Found at i:25510 original size:32 final size:29
Alignment explanation
Indices: 25474--25569 Score: 75
Period size: 32 Copynumber: 3.0 Consensus size: 29
25464 GGTGATTATC
25474 GGATCAGTTGTTTTTCGGCTCGGATCAATATT
1 GGATC-GTTGTTTTT-GGCTCGG-TCAATATT
* *
25506 GGATCGATTGATTTTTGGTTCAGGTCAATATC
1 GGATCG-TTG-TTTTTGGCTC-GGTCAATATT
* *
25538 GGATCTGTTATATTTTGGGTCGGGTCAATATT
1 GGATC-GTTGT-TTTTGGCTC-GGTCAATATT
25570 AGGTCGAGTC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
31 2 0.04
32 43 0.81
33 8 0.15
ACGTcount: A:0.20, C:0.12, G:0.26, T:0.42
Consensus pattern (29 bp):
GGATCGTTGTTTTTGGCTCGGTCAATATT
Found at i:26368 original size:16 final size:16
Alignment explanation
Indices: 26347--26385 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
26337 TGGGTTAAAA
26347 TTCGGTTCGGGTTAAT
1 TTCGGTTCGGGTTAAT
* *
26363 TTCGGTTCGTGTTACT
1 TTCGGTTCGGGTTAAT
26379 TTCGGTT
1 TTCGGTT
26386 TCACTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.08, C:0.15, G:0.28, T:0.49
Consensus pattern (16 bp):
TTCGGTTCGGGTTAAT
Found at i:31432 original size:2 final size:2
Alignment explanation
Indices: 31425--31466 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
31415 GTAGGTATTA
31425 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
31467 GCAAACAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35697 original size:19 final size:19
Alignment explanation
Indices: 35673--35722 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
35663 AAGAATCAAT
***
35673 TAAATTGATTTTAAAACTG
1 TAAATTGATTTTAAAAAAC
35692 TAAATTGATTTTAAAAAAC
1 TAAATTGATTTTAAAAAAC
35711 TAAATTGATTTT
1 TAAATTGATTTT
35723 TCTCAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (19 bp):
TAAATTGATTTTAAAAAAC
Found at i:36360 original size:21 final size:22
Alignment explanation
Indices: 36331--36374 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
36321 AAACATTTTC
36331 TTAAGATAATGAA-A-ATTTATT
1 TTAAGATAAT-AAGATATTTATT
*
36352 TTAATATAATAAGATATTTATT
1 TTAAGATAATAAGATATTTATT
36374 T
1 T
36375 ATTCAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 10 0.50
22 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTAAGATAATAAGATATTTATT
Found at i:39387 original size:135 final size:135
Alignment explanation
Indices: 39143--39632 Score: 743
Period size: 135 Copynumber: 3.6 Consensus size: 135
39133 TTGTTAGATT
* * * * * * *
39143 GAACAAGTTCTTCGCATTATGAAATTCTTCTCTCT-TTTGGATGATTTTTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
* * * * * *
39207 TTCACTGAAAATGTTGATCCCTCAAGCGAGGCGTCCCTGACTCGAAATG-CTGTGAATCGAGTGA
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTC-ATGAATCGAGTGA
39271 TAGGTC
130 TAGGTC
39277 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
39342 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
39407 AGGTC
131 AGGTC
**
39412 GAACAAGCTCTTCTCATTATGAACTTCTTCT-CCTTTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTT-GGATGAGTTCTTCTCATTATGAACT
* ** *
39476 CTCCATTGGAAATGTCAATTCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
65 CTCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
39541 TAGGTC
130 TAGGTC
*
39547 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTC-GTTGGATGAGTTCTTCTCATTATGAACT
*
39612 CTCCATTGAAAATGCTGATCC
65 CTCCATTGAAAATGTTGATCC
39633 ACCTATTTTT
Statistics
Matches: 324, Mismatches: 27, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
134 36 0.11
135 242 0.75
136 45 0.14
137 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (135 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
AGGTC
Found at i:40618 original size:14 final size:14
Alignment explanation
Indices: 40599--40643 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
40589 TCCTTCTTCA
40599 TTTTTTCTTTCTTT
1 TTTTTTCTTTCTTT
40613 TTTTTTC-TTCTTT
1 TTTTTTCTTTCTTT
*
40626 TTATTT-TTTCATTT
1 TTTTTTCTTTC-TTT
40640 TTTT
1 TTTT
40644 CTTCAAGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 14 0.52
14 13 0.48
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTCTTTCTTT
Found at i:40621 original size:25 final size:25
Alignment explanation
Indices: 40592--40648 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
40582 CGAACCCTCC
*
40592 TTCTTCATTTT-TTCTTTCTTTTTTT
1 TTCTTCATTTTATTCTTTC-ATTTTT
* *
40617 TTCTTCTTTTTATTTTTTCATTTTT
1 TTCTTCATTTTATTCTTTCATTTTT
40642 TTCTTCA
1 TTCTTCA
40649 AGCATAGTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 21 0.78
26 6 0.22
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (25 bp):
TTCTTCATTTTATTCTTTCATTTTT
Found at i:40625 original size:17 final size:16
Alignment explanation
Indices: 40598--40635 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
40588 CTCCTTCTTC
*
40598 ATTTTTTCTT-TCTTT
1 ATTTTTTCTTCTTTTT
40613 -TTTTTTCTTCTTTTT
1 ATTTTTTCTTCTTTTT
40628 ATTTTTTC
1 ATTTTTTC
40636 ATTTTTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 4 0.20
16 7 0.35
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (16 bp):
ATTTTTTCTTCTTTTT
Found at i:52667 original size:2 final size:2
Alignment explanation
Indices: 52660--52697 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
52650 TCAAATAATT
52660 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52698 AAAGAACTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54542 original size:2 final size:2
Alignment explanation
Indices: 54537--54583 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
54527 TAAAAAAGAT
54537 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54579 TA TA T
1 TA TA T
54584 GACTGATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55906 original size:3 final size:3
Alignment explanation
Indices: 55900--55958 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
55890 AATAATTATT
* *
55900 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
55943 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
55959 TTAAGTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 6 0.12
3 39 0.81
4 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:56210 original size:76 final size:76
Alignment explanation
Indices: 56112--56895 Score: 1364
Period size: 76 Copynumber: 10.4 Consensus size: 76
56102 GAGGTCTTAA
* * *
56112 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAATAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
56177 AGGCTTTTTGG
66 AGGCTTTTTGG
56188 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
56253 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
56264 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGTCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
56329 AGGCTTTTTGG
66 AGGCTTTTTGG
56340 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
56405 AGGCTTTTTGG
66 AGGCTTTTTGG
*
56416 -AA-A-CATGCACTGCAGGACTTACAGATG-CCCTAAGCCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
56477 AGGCTTTTTGG
66 AGGCTTTTTGG
56488 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
56552 AAGCTTTTTGG
66 AGGCTTTTTGG
*
56563 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
56627 AGGCTTTTTGG
66 AGGCTTTTTGG
*
56638 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
56703 AGGCTTTTTGG
66 AGGCTTTTTGG
* * **
56714 AAACATCTTGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCTTGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
56779 AGGCTTTTTGG
66 AGGCTTTTTGG
* * * *
56790 AAACAGCGTGCACTGTAGGACTTACAGATGAACCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
56855 AGGCTTTTTGG
66 AGGCTTTTTGG
*
56866 AAACATCATGCTCTGCAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
56896 TGGGAAATAG
Statistics
Matches: 679, Mismatches: 24, Indels: 10
0.95 0.03 0.01
Matches are distributed among these distances:
72 44 0.06
73 26 0.04
74 2 0.00
75 173 0.25
76 434 0.64
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:58123 original size:54 final size:54
Alignment explanation
Indices: 57997--58154 Score: 209
Period size: 54 Copynumber: 3.0 Consensus size: 54
57987 AGAATAACTG
* * *
57997 GTTCGTAAAACATTTGACAACACATGCAT-CATCTCATGTGGTTTCTGCTC--A-
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTC-TGTGGTTTCTGCTCAAAT
* *
58048 GAT-GTAAAACACTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAAAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAAAT
* *
58101 GTTCGTAAATCATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAAAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAAAT
58155 TTCTCAATCA
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
50 37 0.40
51 6 0.06
52 1 0.01
53 2 0.02
54 47 0.51
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCTCAAAT
Found at i:59988 original size:31 final size:31
Alignment explanation
Indices: 59953--60015 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
59943 AGATGTGGTC
59953 TGAATTCATCAATTGCAGAGTTGACAGATTT
1 TGAATTCATCAATTGCAGAGTTGACAGATTT
*
59984 TGAATTCATCAATTGTAGAGTTGACAGATTT
1 TGAATTCATCAATTGCAGAGTTGACAGATTT
60015 T
1 T
60016 ATATGTGCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (31 bp):
TGAATTCATCAATTGCAGAGTTGACAGATTT
Found at i:62466 original size:8 final size:8
Alignment explanation
Indices: 62453--62575 Score: 121
Period size: 8 Copynumber: 15.4 Consensus size: 8
62443 AATTTCTCCC
62453 CTTTTTTT
1 CTTTTTTT
62461 CTTTTTTTT
1 C-TTTTTTT
62470 CTTTTTTT
1 CTTTTTTT
62478 C-TTTTTT
1 CTTTTTTT
62485 C-TTTTTT
1 CTTTTTTT
62492 C-TTTTTT
1 CTTTTTTT
62499 C-TTTTTT
1 CTTTTTTT
*
62506 CTTTTTTC
1 CTTTTTTT
*
62514 CTTTTTCAT
1 CTTTTT-TT
62523 CTTTTTTT
1 CTTTTTTT
62531 CTTTTTTT
1 CTTTTTTT
*
62539 CTTTCTTTG
1 CTTT-TTTT
*
62548 CTGGATTTTT
1 CT--TTTTTT
62558 C-TTTTTT
1 CTTTTTTT
*
62565 CTTTCTTT
1 CTTTTTTT
62573 CTT
1 CTT
62576 GGATGAGTAT
Statistics
Matches: 99, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
7 34 0.34
8 41 0.41
9 19 0.19
10 4 0.04
11 1 0.01
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (8 bp):
CTTTTTTT
Found at i:62467 original size:7 final size:7
Alignment explanation
Indices: 62464--62575 Score: 116
Period size: 7 Copynumber: 14.3 Consensus size: 7
62454 TTTTTTTCTT
62464 TTTTTTC
1 TTTTTTC
62471 TTTTTTTC
1 -TTTTTTC
62479 TTTTTTC
1 TTTTTTC
62486 TTTTTTC
1 TTTTTTC
62493 TTTTTTC
1 TTTTTTC
62500 TTTTTTC
1 TTTTTTC
62507 TTTTTTCC
1 TTTTTT-C
62515 TTTTTCATC
1 TTTTT--TC
62524 TTTTTTTC
1 -TTTTTTC
62532 TTTTTTTC
1 -TTTTTTC
62540 TTTCTTTGC
1 TTT-TTT-C
62549 TGGATTTTTC
1 T---TTTTTC
62559 TTTTTTC
1 TTTTTTC
62566 TTTCTTTC
1 TTT-TTTC
62574 TT
1 TT
62576 GGATGAGTAT
Statistics
Matches: 94, Mismatches: 0, Indels: 20
0.82 0.00 0.18
Matches are distributed among these distances:
7 46 0.49
8 32 0.34
9 3 0.03
10 8 0.09
11 3 0.03
12 2 0.02
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:62482 original size:14 final size:14
Alignment explanation
Indices: 62456--62536 Score: 74
Period size: 15 Copynumber: 5.4 Consensus size: 14
62446 TTCTCCCCTT
62456 TTTTTCTTTTTTTTC
1 TTTTTC-TTTTTTTC
*
62471 TTTTTTTCTTTTTTC
1 TTTTTCT-TTTTTTC
62486 TTTTT-TCTTTTTTC
1 TTTTTCT-TTTTTTC
*
62500 TTTTTTCTTTTTTCC
1 -TTTTTCTTTTTTTC
62515 TTTTTCATCTTTTTTTC
1 -TTTT--TCTTTTTTTC
62532 TTTTT
1 TTTTT
62537 TTCTTTCTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.19
15 33 0.57
16 5 0.09
17 9 0.16
ACGTcount: A:0.01, C:0.15, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:62526 original size:53 final size:57
Alignment explanation
Indices: 62453--62573 Score: 160
Period size: 53 Copynumber: 2.1 Consensus size: 57
62443 AATTTCTCCC
* **
62453 CTTTTTTTCTTTTTTTTCTTTTTTTC-TTTTTTCTTT-TTT-CT-TTTTTCTTTTTT
1 CTTTTTTCCTTTTTCATCTTTTTTTCTTTTTTTCTTTCTTTGCTGTTTTTCTTTTTT
62506 CTTTTTTCCTTTTTCATCTTTTTTTCTTTTTTTCTTTCTTTGCTGGATTTTTCTTTTTT
1 CTTTTTTCCTTTTTCATCTTTTTTTCTTTTTTTCTTTCTTTGCT-G-TTTTTCTTTTTT
62565 CTTTCTTTC
1 CTTT-TTTC
62574 TTGGATGAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
53 23 0.40
54 10 0.17
55 3 0.05
56 2 0.03
59 16 0.28
60 4 0.07
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (57 bp):
CTTTTTTCCTTTTTCATCTTTTTTTCTTTTTTTCTTTCTTTGCTGTTTTTCTTTTTT
Found at i:62530 original size:1 final size:1
Alignment explanation
Indices: 62454--62512 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
62444 ATTTCTCCCC
* * * * * * *
62454 TTTTTTTCTTTTTTTTCTTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
62513 CCTTTTTCAT
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:65509 original size:23 final size:23
Alignment explanation
Indices: 65483--65527 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
65473 AAAAGTATGA
65483 ATGCAAAAATGAAAAATAAAAAG
1 ATGCAAAAATGAAAAATAAAAAG
* *
65506 ATGCAAAGATGAAAAATGAAAA
1 ATGCAAAAATGAAAAATAAAAA
65528 TGCATATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.67, C:0.04, G:0.16, T:0.13
Consensus pattern (23 bp):
ATGCAAAAATGAAAAATAAAAAG
Found at i:65538 original size:21 final size:21
Alignment explanation
Indices: 65482--65541 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 21
65472 TAAAAGTATG
65482 AATGCAAAAATGAAAAATAAAA
1 AATGCAAAAATGAAAAAT-AAA
* *
65504 AGATGCAAAGATGAAAAATGAA
1 A-ATGCAAAAATGAAAAATAAA
* *
65526 AATGCATATATGAAAA
1 AATGCAAAAATGAAAA
65542 GGTGTTTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 13 0.39
22 4 0.12
23 16 0.48
ACGTcount: A:0.63, C:0.05, G:0.15, T:0.17
Consensus pattern (21 bp):
AATGCAAAAATGAAAAATAAA
Found at i:68695 original size:132 final size:131
Alignment explanation
Indices: 68436--68675 Score: 290
Period size: 132 Copynumber: 1.8 Consensus size: 131
68426 ATTTATTTAG
* *
68436 AAATATCAGAAAGGACTTCTAGGTGCCTTAAGACAGCTCTTTCTTCGATATTAAAAATAAATAAA
1 AAATATCAAAAAGGACTTCTAGGTACCTTAAGACAGCTCTTTCTTCGATATTAAAAATAAATAAA
** ** * *
68501 TGACTAAAACATTTTCTTAAGATAATGAAAATTTATTTTAATATAGTAAGATATTTATTTATTCA
66 TGACTAAAACATTTTAATAAGATAATGAAAATAAATTATAATATAGTAAGATATTTAATTATTCA
68566 A
131 A
*
68567 AAATATCATAAAAGGGCTTCTAGGTACCTTAAGACAGCTCTTTTCTTCGATATTAATAAATAAAA
1 AAATATCA-AAAAGGACTTCTAGGTACCTTAAGACAGCTC-TTTCTTCGATATTAA-AAAT-AAA
* **
68632 TAAAT-A-TTAAA-ATTTTAATAATTTAAAT-AAAACTAAATTATAAT
62 TAAATGACTAAAACATTTTAATAAGAT-AATGAAAA-TAAATTATAAT
68676 TTTTATAATG
Statistics
Matches: 92, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
131 8 0.09
132 41 0.45
133 30 0.33
134 5 0.05
135 8 0.09
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.36
Consensus pattern (131 bp):
AAATATCAAAAAGGACTTCTAGGTACCTTAAGACAGCTCTTTCTTCGATATTAAAAATAAATAAA
TGACTAAAACATTTTAATAAGATAATGAAAATAAATTATAATATAGTAAGATATTTAATTATTCA
A
Found at i:68787 original size:2 final size:2
Alignment explanation
Indices: 68780--68837 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
68770 TATTTAAAAG
68780 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
68822 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
68838 GACTGATATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70141 original size:3 final size:3
Alignment explanation
Indices: 70135--70205 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
70125 AATAATTATT
* *
70135 TAA TAA TAA T-A TAA TATA TATA TAA T-A TAA TAA T-A TAT TTA TAA
1 TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
70179 T-A TAA TAA TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
70206 TTAAGTAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
2 8 0.15
3 40 0.73
4 7 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:70148 original size:19 final size:19
Alignment explanation
Indices: 70124--70205 Score: 80
Period size: 19 Copynumber: 4.2 Consensus size: 19
70114 TTTGGGCTTG
70124 TAATAATTATTTAATAATA
1 TAATAATTATTTAATAATA
*
70143 -ATATAA-TATATATATAATA
1 TA-ATAATTATTTA-ATAATA
70162 TAATAATATATTT-ATAATA
1 TAATAAT-TATTTAATAATA
*
70181 TAATAATAATTTTAATAATAA
1 TAATAATTA-TTTAATAAT-A
70202 TAAT
1 TAAT
70206 TTAAGTAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
18 7 0.13
19 30 0.58
20 6 0.12
21 9 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAATAATTATTTAATAATA
Found at i:70149 original size:11 final size:11
Alignment explanation
Indices: 70124--70203 Score: 72
Period size: 11 Copynumber: 7.0 Consensus size: 11
70114 TTTGGGCTTG
* *
70124 TAATAATTATT
1 TAATAATAATA
70135 TAATAATAATA
1 TAATAATAATA
70146 TAAT-ATATATA
1 TAATAATA-ATA
70157 TAATATAATAATA
1 T-A-ATAATAATA
* *
70170 TATTTATAATA
1 TAATAATAATA
*
70181 TAATAATAATTT
1 TAATAATAA-TA
70193 TAATAATAATA
1 TAATAATAATA
70204 ATTTAAGTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
10 3 0.05
11 32 0.57
12 12 0.21
13 6 0.11
14 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TAATAATAATA
Found at i:70161 original size:16 final size:17
Alignment explanation
Indices: 70140--70203 Score: 69
Period size: 17 Copynumber: 3.6 Consensus size: 17
70130 TTATTTAATA
70140 ATAATATAATATATA-T
1 ATAATATAATATATATT
70156 ATAATATAATAATATATTT
1 ATAATATAAT-ATATA-TT
70175 ATAATATAATA-ATAATT
1 ATAATATAATATAT-ATT
*
70192 TTAATAATAATA
1 ATAAT-ATAATA
70204 ATTTAAGTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 10 0.24
17 13 0.31
18 8 0.19
19 11 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAATATAATATATATT
Found at i:70169 original size:24 final size:25
Alignment explanation
Indices: 70138--70190 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
70128 AATTATTTAA
70138 TAATAATATA-ATATATATATAAT-A
1 TAATAATATATATATA-ATATAATAA
*
70162 TAATAATATATTTATAATATAATAA
1 TAATAATATATATATAATATAATAA
70187 TAAT
1 TAAT
70191 TTTAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TAATAATATATATATAATATAATAA
Done.