Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005631.1 Hibiscus syriacus cultivar Beakdansim tig00013127_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: 84833
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:6938 original size:27 final size:27
Alignment explanation
Indices: 6907--6959 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
6897 AAGATATATC
6907 CAGTGATGAATCCGAAGATGATCTATT
1 CAGTGATGAATCCGAAGATGATCTATT
* *
6934 CAGTGATGATTTCGAAGATGATCTAT
1 CAGTGATGAATCCGAAGATGATCTAT
6960 GGATAAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (27 bp):
CAGTGATGAATCCGAAGATGATCTATT
Found at i:7505 original size:24 final size:24
Alignment explanation
Indices: 7473--7531 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
7463 TTCTGATTTA
*
7473 TGATTTCTGATCTGGATTCTGTTC
1 TGATTTCTGATCTGAATTCTGTTC
* *
7497 TGATATCTGATCTGAATTCTGTTT
1 TGATTTCTGATCTGAATTCTGTTC
7521 TGATTTCTGAT
1 TGATTTCTGAT
7532 ATCTCAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.51
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTCTGTTC
Found at i:7528 original size:12 final size:12
Alignment explanation
Indices: 7473--7529 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
7463 TTCTGATTTA
*
7473 TGATTTCTGATC
1 TGATTTCTGTTC
7485 TGGA-TTCTGTTC
1 T-GATTTCTGTTC
* *
7497 TGATATCTGATC
1 TGATTTCTGTTC
* *
7509 TGAATTCTGTTT
1 TGATTTCTGTTC
7521 TGATTTCTG
1 TGATTTCTG
7530 ATATCTCAGT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
11 2 0.06
12 31 0.89
13 2 0.06
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (12 bp):
TGATTTCTGTTC
Found at i:7695 original size:2 final size:2
Alignment explanation
Indices: 7688--7717 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7678 AATGATGGGC
7688 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
7718 GTTTTAAAAA
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:11610 original size:16 final size:16
Alignment explanation
Indices: 11589--11619 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
11579 ACTACTCTCA
11589 ATCCATTATACCCTTT
1 ATCCATTATACCCTTT
11605 ATCCATTATACCCTT
1 ATCCATTATACCCTT
11620 GCAATGCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (16 bp):
ATCCATTATACCCTTT
Found at i:18002 original size:18 final size:18
Alignment explanation
Indices: 17979--18049 Score: 115
Period size: 18 Copynumber: 3.9 Consensus size: 18
17969 ACTGAATATT
*
17979 TGTCCCAAAGGACCACTA
1 TGTCCCGAAGGACCACTA
17997 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
18015 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
18033 TATCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
18050 GATAATCCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.30, C:0.32, G:0.20, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:22336 original size:39 final size:39
Alignment explanation
Indices: 22254--22397 Score: 128
Period size: 39 Copynumber: 3.7 Consensus size: 39
22244 CTGTACACCT
* * * * ** *
22254 AGTAAAGACTTACCCTGTGCATAAAGAAGAGGAGTTTGT
1 AGTAAGGACTTACCATGTGCACAAAGCAGAGGAGCCTGC
* *
22293 AGTAAGGTCTTATCATGTGCACAAAGCAGAGGAGCCTGC
1 AGTAAGGACTTACCATGTGCACAAAGCAGAGGAGCCTGC
* * * * *
22332 AGTAAGGACTTACCCTGAGCACAAAGCCGAGGAACTTG-
1 AGTAAGGACTTACCATGTGCACAAAGCAGAGGAGCCTGC
* *
22370 AGGTAAGGACTTACCCTGAGCACAAAGC
1 A-GTAAGGACTTACCATGTGCACAAAGC
22398 CGATGAGTCT
Statistics
Matches: 88, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
38 1 0.01
39 87 0.99
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.19
Consensus pattern (39 bp):
AGTAAGGACTTACCATGTGCACAAAGCAGAGGAGCCTGC
Found at i:22398 original size:39 final size:39
Alignment explanation
Indices: 22293--22400 Score: 137
Period size: 39 Copynumber: 2.8 Consensus size: 39
22283 AGGAGTTTGT
* * * * * *
22293 AGTAAGGTCTTATCATGTGCACAAAGCAGAGGAGCCTGC
1 AGTAAGGACTTACCCTGAGCACAAAGCCGAGGAACCTGC
*
22332 AGTAAGGACTTACCCTGAGCACAAAGCCGAGGAACTTG-
1 AGTAAGGACTTACCCTGAGCACAAAGCCGAGGAACCTGC
22370 AGGTAAGGACTTACCCTGAGCACAAAGCCGA
1 A-GTAAGGACTTACCCTGAGCACAAAGCCGA
22401 TGAGTCTGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 1 0.02
39 60 0.98
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (39 bp):
AGTAAGGACTTACCCTGAGCACAAAGCCGAGGAACCTGC
Found at i:23197 original size:20 final size:20
Alignment explanation
Indices: 23172--23226 Score: 101
Period size: 20 Copynumber: 2.7 Consensus size: 20
23162 TCGACTTTTT
23172 GGTCAAAGTCAACGATCAAC
1 GGTCAAAGTCAACGATCAAC
23192 GGTCAAAGTCAACGATCAAC
1 GGTCAAAGTCAACGATCAAC
23212 GGTCAACAGTCAACG
1 GGTCAA-AGTCAACG
23227 GTAAGTCCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (20 bp):
GGTCAAAGTCAACGATCAAC
Found at i:23216 original size:14 final size:13
Alignment explanation
Indices: 23172--23228 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
23162 TCGACTTTTT
*
23172 GGTCAAAGTCAAC
1 GGTCAACGTCAAC
*
23185 GATCAACGGTCAA-
1 GGTCAAC-GTCAAC
*
23198 AGTCAACGATCAAC
1 GGTCAACG-TCAAC
23212 GGTCAACAGTCAAC
1 GGTCAAC-GTCAAC
23226 GGT
1 GGT
23229 AAGTCCAGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
12 1 0.03
13 14 0.40
14 19 0.54
15 1 0.03
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.16
Consensus pattern (13 bp):
GGTCAACGTCAAC
Found at i:23637 original size:15 final size:16
Alignment explanation
Indices: 23617--23649 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23607 TTTTTTTCTA
*
23617 AAAGAG-GAAAATATT
1 AAAGAGAGAAAAAATT
23632 AAAGAGAGAAAAAATT
1 AAAGAGAGAAAAAATT
23648 AA
1 AA
23650 TTAATTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (16 bp):
AAAGAGAGAAAAAATT
Found at i:28392 original size:2 final size:2
Alignment explanation
Indices: 28385--28420 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28375 TATTTAAATG
28385 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
28421 GAAGCATTGG
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):
TA
Found at i:30281 original size:2 final size:2
Alignment explanation
Indices: 30276--30301 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30266 AAAACGGCAC
30276 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
30302 AGGAATTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:31278 original size:26 final size:26
Alignment explanation
Indices: 31249--31311 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
31239 TAAAAATTAA
* *
31249 AATTT-ATATTTTATAATTATTTTTTT
1 AATTTGATATTTAATAATTA-TATTTT
* *
31275 AATTTGAAATTTAATTATTATATTTT
1 AATTTGATATTTAATAATTATATTTT
31301 AATTTGATATT
1 AATTTGATATT
31312 AATTTAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (26 bp):
AATTTGATATTTAATAATTATATTTT
Found at i:32350 original size:2 final size:2
Alignment explanation
Indices: 32343--32369 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
32333 TAATGATTGG
32343 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
32370 ACTATAATTA
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:32444 original size:28 final size:27
Alignment explanation
Indices: 32400--32452 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
32390 TTAAACAAAA
*
32400 AAATTTAACTTTGTTATATTTTTAAAGT
1 AAATTTAACTTTGTTAT-TTTCTAAAGT
*
32428 AAATTTAA-TATTTTTATTTTCTAAA
1 AAATTTAACT-TTGTTATTTTCTAAA
32453 TTTGTAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (27 bp):
AAATTTAACTTTGTTATTTTCTAAAGT
Found at i:34223 original size:21 final size:20
Alignment explanation
Indices: 34166--34281 Score: 129
Period size: 21 Copynumber: 6.0 Consensus size: 20
34156 CAGATTGTCT
34166 AGGGGGAACAGATTCCCCCC
1 AGGGGGAACAGATTCCCCCC
*
34186 A-GGGGTACAGATTCCCCCC
1 AGGGGGAACAGATTCCCCCC
34205 AGGGGGAACAGATTCCCCCCC
1 AGGGGGAACAGATT-CCCCCC
*
34226 AGGGGGTATC-GATT--CCCC
1 AGGGGG-AACAGATTCCCCCC
34244 ---GGGAACAGATTCCCCCCC
1 AGGGGGAACAGATT-CCCCCC
*
34262 AGGGGGTACAGATTCCCCCC
1 AGGGGGAACAGATTCCCCCC
34282 TGAATGGTTT
Statistics
Matches: 81, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
14 2 0.02
15 7 0.09
18 8 0.10
19 18 0.22
20 18 0.22
21 26 0.32
22 2 0.02
ACGTcount: A:0.22, C:0.36, G:0.28, T:0.14
Consensus pattern (20 bp):
AGGGGGAACAGATTCCCCCC
Found at i:34255 original size:36 final size:37
Alignment explanation
Indices: 34168--34279 Score: 151
Period size: 36 Copynumber: 3.0 Consensus size: 37
34158 GATTGTCTAG
34168 GGGGAACAGATT-CCCCCCA-GGGGTACAGATTCCCCCC
1 GGGGAACAGATTCCCCCCCAGGGGGTACAGATT--CCCC
34205 AGGGGGAACAGATTCCCCCCCAGGGGGTATC-GATTCCCC
1 --GGGGAACAGATTCCCCCCCAGGGGGTA-CAGATTCCCC
34244 -GGGAACAGATTCCCCCCCAGGGGGTACAGATTCCCC
1 GGGGAACAGATTCCCCCCCAGGGGGTACAGATTCCCC
34280 CCTGAATGGT
Statistics
Matches: 69, Mismatches: 0, Indels: 11
0.86 0.00 0.14
Matches are distributed among these distances:
35 1 0.01
36 34 0.49
39 16 0.23
40 7 0.10
41 10 0.14
42 1 0.01
ACGTcount: A:0.21, C:0.36, G:0.29, T:0.14
Consensus pattern (37 bp):
GGGGAACAGATTCCCCCCCAGGGGGTACAGATTCCCC
Found at i:34420 original size:21 final size:21
Alignment explanation
Indices: 34394--34435 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
34384 ATTTGAATAT
*
34394 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
34415 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
34436 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:34497 original size:21 final size:21
Alignment explanation
Indices: 34464--34503 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
34454 TTTTTGTAGA
*
34464 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
34486 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
34504 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:35670 original size:19 final size:20
Alignment explanation
Indices: 35646--35693 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
35636 AACGATTTTC
*
35646 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
35665 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
35685 TTTTGAAAA
1 TTTTGAAAA
35694 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:37185 original size:21 final size:20
Alignment explanation
Indices: 37143--37221 Score: 131
Period size: 20 Copynumber: 3.9 Consensus size: 20
37133 CAGATTGCCT
*
37143 AGGGGGAATAGATTCCCCCC
1 AGGGGGAACAGATTCCCCCC
*
37163 AGGGGGTACAGATTCCCCTCC
1 AGGGGGAACAGATTCCCC-CC
37184 AGGGGGAACAGATTCCCCCC
1 AGGGGGAACAGATTCCCCCC
37204 AGGGGGAACAGATTCCCC
1 AGGGGGAACAGATTCCCC
37222 TTGAATGGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 36 0.65
21 19 0.35
ACGTcount: A:0.24, C:0.32, G:0.30, T:0.14
Consensus pattern (20 bp):
AGGGGGAACAGATTCCCCCC
Found at i:37189 original size:41 final size:41
Alignment explanation
Indices: 37143--37222 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
37133 CAGATTGCCT
* *
37143 AGGGGGAATAGATTCCCCCCAGGGGGTACAGATTCCCCTCC
1 AGGGGGAACAGATTCCCCCCAGGGGGAACAGATTCCCCTCC
37184 AGGGGGAACAGATTCCCCCCAGGGGGAACAGATTCCCCT
1 AGGGGGAACAGATTCCCCCCAGGGGGAACAGATTCCCCT
37223 TGAATGGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.24, C:0.31, G:0.30, T:0.15
Consensus pattern (41 bp):
AGGGGGAACAGATTCCCCCCAGGGGGAACAGATTCCCCTCC
Found at i:37361 original size:21 final size:21
Alignment explanation
Indices: 37335--37376 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
37325 ATTTGAATAT
*
37335 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
37356 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
37377 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:37438 original size:21 final size:21
Alignment explanation
Indices: 37405--37444 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
37395 TTTTTGCAGA
*
37405 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
37427 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
37445 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:40476 original size:2 final size:2
Alignment explanation
Indices: 40460--40499 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
40450 TAGCATTAAC
40460 TA TA -A TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40500 AAGTTATTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:40782 original size:22 final size:24
Alignment explanation
Indices: 40748--40791 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
40738 AGATAAGATT
40748 TTTCATTTCTAAT-TTTAAAATTA
1 TTTCATTTCTAATCTTTAAAATTA
*
40771 TTTCA-TTCTAATCTTTTAAAT
1 TTTCATTTCTAATCTTTAAAAT
40792 CTCTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTCATTTCTAATCTTTAAAATTA
Found at i:41642 original size:2 final size:2
Alignment explanation
Indices: 41626--41667 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
41616 TAGCATTAAC
41626 TA TA -A TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41668 AAGTTATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:41950 original size:22 final size:24
Alignment explanation
Indices: 41916--41959 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
41906 AGATAAGATT
41916 TTTCATTTCTAAT-TTTAAAATTA
1 TTTCATTTCTAATCTTTAAAATTA
*
41939 TTTCA-TTCTAATCTTTTAAAT
1 TTTCATTTCTAATCTTTAAAAT
41960 CTCTAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTCATTTCTAATCTTTAAAATTA
Found at i:45159 original size:24 final size:24
Alignment explanation
Indices: 45132--45178 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
45122 CACCATAGCT
* *
45132 CGTATAAATTACACCGAAGTACCG
1 CGTAGAAAATACACCGAAGTACCG
*
45156 CGTAGAAAATGCACCGAAGTACC
1 CGTAGAAAATACACCGAAGTACC
45179 ACATAGAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (24 bp):
CGTAGAAAATACACCGAAGTACCG
Found at i:45239 original size:23 final size:23
Alignment explanation
Indices: 45145--45266 Score: 117
Period size: 23 Copynumber: 5.4 Consensus size: 23
45135 ATAAATTACA
* *
45145 CCGAAGTACCGCGTAGAAAATG-C
1 CCGAAGGACCACGTAG-AAATGTC
* *
45168 ACCGAAGTACCACATAG-AATGTC
1 -CCGAAGGACCACGTAGAAATGTC
* *
45191 CCGAAGGACCACATAG--ATGTT
1 CCGAAGGACCACGTAGAAATGTC
* *
45212 TCGAAGGACCGCGTAGAAATGTC
1 CCGAAGGACCACGTAGAAATGTC
*
45235 CCGAAGGACCACGTAGAATTGTC
1 CCGAAGGACCACGTAGAAATGTC
45258 CCGAAGGAC
1 CCGAAGGAC
45267 TGTGTAGAAC
Statistics
Matches: 84, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
21 17 0.20
22 19 0.23
23 34 0.40
24 14 0.17
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.16
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAAATGTC
Found at i:55109 original size:23 final size:23
Alignment explanation
Indices: 55081--55125 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
55071 TAGATGTCTC
*
55081 GAAGGACCGCATAGAAATATCCT
1 GAAGGACCACATAGAAATATCCT
* *
55104 GAAGGACCACGTAGAATTATCC
1 GAAGGACCACATAGAAATATCC
55126 CAAATGACCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (23 bp):
GAAGGACCACATAGAAATATCCT
Found at i:63599 original size:17 final size:17
Alignment explanation
Indices: 63577--63610 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
63567 TTTTATCAGA
63577 TTAAAAACCGGTTTTTT
1 TTAAAAACCGGTTTTTT
*
63594 TTAAAAACCTGTTTTTT
1 TTAAAAACCGGTTTTTT
63611 CAAACCGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (17 bp):
TTAAAAACCGGTTTTTT
Found at i:64210 original size:25 final size:26
Alignment explanation
Indices: 64182--64239 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
64172 ATTATTAATT
64182 ATATTAATTACT-TATT-AAAATAAGA
1 ATATTAATTA-TATATTAAAAATAAGA
*
64207 ATATT-ATTATAATATTAAAAATTAGA
1 ATATTAATTAT-ATATTAAAAATAAGA
64233 ATATTAA
1 ATATTAA
64240 AAAATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
23 1 0.04
24 4 0.14
25 9 0.32
26 13 0.46
27 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (26 bp):
ATATTAATTATATATTAAAAATAAGA
Found at i:64235 original size:15 final size:15
Alignment explanation
Indices: 64212--64242 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
64202 TAAGAATATT
*
64212 ATTATAATATTAAAA
1 ATTAGAATATTAAAA
64227 ATTAGAATATTAAAA
1 ATTAGAATATTAAAA
64242 A
1 A
64243 ATATTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
ATTAGAATATTAAAA
Found at i:69777 original size:27 final size:28
Alignment explanation
Indices: 69725--69778 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
69715 CACCTGTTGT
* * *
69725 TTTCAAGCACTGACTTGACGATATAATG
1 TTTCAAGCACTGACTCGACAACATAATG
69753 TTTCAA-CACTGACTCGACAACATAAT
1 TTTCAAGCACTGACTCGACAACATAAT
69779 ATAACTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (28 bp):
TTTCAAGCACTGACTCGACAACATAATG
Found at i:75236 original size:13 final size:13
Alignment explanation
Indices: 75218--75251 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
75208 TAAGATTTTC
*
75218 TTTGAAAATCATT
1 TTTGAAAATCAGT
75231 TTTG-AAATCAGT
1 TTTGAAAATCAGT
75243 TTTGAAAAT
1 TTTGAAAAT
75252 TACTCCCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAGT
Found at i:76997 original size:12 final size:13
Alignment explanation
Indices: 76980--77012 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
76970 TTGGGCAAAA
*
76980 TTTGAAAACTAT-
1 TTTGAAAACAATG
76992 TTTGAAAACAATG
1 TTTGAAAACAATG
77005 TTTGAAAA
1 TTTGAAAA
77013 ACCATAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:83476 original size:14 final size:14
Alignment explanation
Indices: 83457--83484 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
83447 AAGACTAAAA
83457 CACAATTTTACACT
1 CACAATTTTACACT
83471 CACAATTTTACACT
1 CACAATTTTACACT
83485 TAAGTAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (14 bp):
CACAATTTTACACT
Done.