Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002023.1 Hibiscus syriacus cultivar Beakdansim tig00004132_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: 70086
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:9906 original size:18 final size:18
Alignment explanation
Indices: 9883--9955 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
9873 ACTAAATATT
9883 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
9901 TGTCCCGAATGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
9920 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
9939 TATCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
9956 GATAATCCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 30 0.65
19 2 0.04
20 14 0.30
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:9938 original size:38 final size:38
Alignment explanation
Indices: 9882--9958 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
9872 CACTAAATAT
* * *
9882 TTGTCCCGAAGGACCACTATGTCCCGAATGACCACTGA
1 TTGTCCCGAAGAACCACTATATCCCGAAGGACCACTGA
*
9920 TTGTTCCGAAGAACCACTATATCCCGAAGGACCACTGA
1 TTGTCCCGAAGAACCACTATATCCCGAAGGACCACTGA
9958 T
1 T
9959 AATCCCTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (38 bp):
TTGTCCCGAAGAACCACTATATCCCGAAGGACCACTGA
Found at i:10613 original size:19 final size:19
Alignment explanation
Indices: 10589--10640 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
10579 TTTAAGCAGG
*
10589 TGCATCGCTGCACTCCTTA
1 TGCATCGATGCACTCCTTA
*
10608 TGCATCGATGTACTCCTTA
1 TGCATCGATGCACTCCTTA
10627 TGCATCGATGCACT
1 TGCATCGATGCACT
10641 AATTACATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:17617 original size:23 final size:22
Alignment explanation
Indices: 17569--17617 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
17559 CCAGAATGTC
17569 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
17590 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
17613 AAGGA
1 AAGGA
17618 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:18495 original size:103 final size:103
Alignment explanation
Indices: 18311--18528 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
18301 GTCGAGGGTC
18311 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
18376 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
18414 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
18479 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
18517 TATGTGGTCCTT
1 TATGTGGTCCTT
18529 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:18578 original size:23 final size:23
Alignment explanation
Indices: 18545--18677 Score: 149
Period size: 23 Copynumber: 5.7 Consensus size: 23
18535 ATTATTATAT
*
18545 GGCACTACGGTACAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * ***
18568 GGCACTTCGGTGCAATTATTATAT
1 GGCACTACGGTGCAATT-CTACGC
18592 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
18615 GGCACTCCGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * * *
18638 GGCACTCCGGTGCAATTATATGT
1 GGCACTACGGTGCAATTCTACGC
*
18661 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
18678 ATATGAGTTG
Statistics
Matches: 93, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
23 75 0.81
24 18 0.19
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:18589 original size:47 final size:47
Alignment explanation
Indices: 18535--18679 Score: 193
Period size: 47 Copynumber: 3.1 Consensus size: 47
18525 CCTTATGGAC
*
18535 ATTATTATATGGCACTACGGTACAATTCTACGCGGCACTTCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTTCGGTGCA
*
18582 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTTCGGTGCA
* *** * * * *
18629 ATT-CTACGCGGCACTCCGGTGCAATTATATGTGGCACTTCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTTCGGTGCA
18675 ATTAT
1 ATTAT
18680 ATGAGTTGTG
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
46 37 0.44
47 48 0.56
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTTCGGTGCA
Found at i:24373 original size:103 final size:103
Alignment explanation
Indices: 24148--24365 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
24138 GTCGAGGGTC
*
24148 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
24213 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
24251 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
24316 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
24354 TATGTGGTCCTT
1 TATGTGGTCCTT
24366 ATAGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:24426 original size:47 final size:47
Alignment explanation
Indices: 24372--24491 Score: 188
Period size: 47 Copynumber: 2.6 Consensus size: 47
24362 CCTTATAGAC
* *
24372 ATTATTATATGGAACTACGGTGCAATTCTACGCGGCACTCCGGTACA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGACACTCCGGTACA
*
24419 ATTATTATATGGCACTACGGTGCAATTCTACGCGACACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGACACTCCGGTACA
* *
24466 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
24492 ATATGAGCTG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 20 0.29
47 48 0.71
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGACACTCCGGTACA
Found at i:24439 original size:24 final size:24
Alignment explanation
Indices: 24372--24493 Score: 88
Period size: 23 Copynumber: 5.2 Consensus size: 24
24362 CCTTATAGAC
*
24372 ATTATTATATGGAACTACGGTGCA
1 ATTATTATATGGCACTACGGTGCA
* *** * *
24396 ATT-CTACGCGGCACTCCGGTACA
1 ATTATTATATGGCACTACGGTGCA
24419 ATTATTATATGGCACTACGGTGCA
1 ATTATTATATGGCACTACGGTGCA
* *** * *
24443 ATT-CTACGCGACACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCA
* *
24466 ATTA-TATGTGGCACTTCGGTGCA
1 ATTATTATATGGCACTACGGTGCA
24489 ATTAT
1 ATTAT
24494 ATGAGCTGTG
Statistics
Matches: 72, Mismatches: 23, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
23 52 0.72
24 20 0.28
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (24 bp):
ATTATTATATGGCACTACGGTGCA
Found at i:24492 original size:23 final size:23
Alignment explanation
Indices: 24389--24496 Score: 108
Period size: 23 Copynumber: 4.7 Consensus size: 23
24379 TATGGAACTA
* *
24389 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTATATGCGGCACTC
* ** *
24412 CGGTACAATTATTATATGGCACTA
1 CGGTGCAATTA-TATGCGGCACTC
* * *
24436 CGGTGCAATTCTACGCGACACTC
1 CGGTGCAATTATATGCGGCACTC
* *
24459 CGGTGCAATTATATGTGGCACTT
1 CGGTGCAATTATATGCGGCACTC
24482 CGGTGCAATTATATG
1 CGGTGCAATTATATG
24497 AGCTGTGGTG
Statistics
Matches: 66, Mismatches: 18, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
23 49 0.74
24 17 0.26
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (23 bp):
CGGTGCAATTATATGCGGCACTC
Found at i:26085 original size:19 final size:19
Alignment explanation
Indices: 26038--26087 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
26028 TTTAAGCAGG
* *
26038 TGCATCGCTACACTCCTTA
1 TGCATCGATGCACTCCTTA
26057 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
26076 TGCATCGATGCA
1 TGCATCGATGCA
26088 TTAATTGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.22, C:0.32, G:0.16, T:0.30
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:28853 original size:108 final size:107
Alignment explanation
Indices: 28664--28913 Score: 353
Period size: 108 Copynumber: 2.3 Consensus size: 107
28654 GTTCATATGG
* *
28664 TACCGATACCAAAGGTATCGGAAGTATCGATACTCACAAGATAGTATTGATACTACCAACATTGC
1 TACCGATACCAAAGGTATCAGAAGTATCGATACTCACAAGATAGTATCGATACTACCAACATTGC
*
28729 TCAAATTCCAGAATGCAAAAATGGTACCTGATATCC-AAAGGGA
66 TCAAATTCCAGAATGCAAAAATGATACC-GATA-CCAAAAGGGA
*
28772 TACCGATACCAAAGGTATCAGAAGTATTGATACTCACAATG-TAGTATCGATACTACCAACATTG
1 TACCGATACCAAAGGTATCAGAAGTATCGATACTCACAA-GATAGTATCGATACTACCAACATTG
* * *
28836 CTCAAATTCCAGAATGCAAAAATGATATCGGTACCAAAAGGGG
65 CTCAAATTCCAGAATGCAAAAATGATACCGATACCAAAAGGGA
* * *
28879 TACCGATACCAAACGTAAT-GGAGGTATCGATACTC
1 TACCGATACCAAAGGT-ATCAGAAGTATCGATACTC
28914 CCTTTGGTAT
Statistics
Matches: 128, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
106 2 0.02
107 37 0.29
108 88 0.69
109 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.23
Consensus pattern (107 bp):
TACCGATACCAAAGGTATCAGAAGTATCGATACTCACAAGATAGTATCGATACTACCAACATTGC
TCAAATTCCAGAATGCAAAAATGATACCGATACCAAAAGGGA
Found at i:37134 original size:9 final size:9
Alignment explanation
Indices: 37120--37213 Score: 71
Period size: 10 Copynumber: 9.8 Consensus size: 9
37110 GGCTGCTGGA
37120 AACCGGTTT
1 AACCGGTTT
37129 AACCGGTTTT
1 AACCGG-TTT
*
37139 CAACCGATTCT
1 -AACCGGTT-T
*
37150 GACCGGTTT
1 AACCGGTTT
*
37159 GACCGGTTT
1 AACCGGTTT
*
37168 CAACCGGTTCG
1 -AACCGGTT-T
37179 AACCGGTTT
1 AACCGGTTT
* *
37188 GACCGGTCTG
1 AACCGGT-TT
37198 AACCGGTTT
1 AACCGGTTT
*
37207 GACCGGT
1 AACCGGT
37214 CTGACCCGAC
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
9 29 0.43
10 33 0.49
11 6 0.09
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:37183 original size:29 final size:28
Alignment explanation
Indices: 37121--37219 Score: 117
Period size: 29 Copynumber: 3.4 Consensus size: 28
37111 GCTGCTGGAA
* *
37121 ACCGGTTTAACCGGTTTTCAACCGATTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
37151 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * *
37179 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
*
37208 ACCGGTCTGACC
1 ACCGGTTTGACC
37220 CGACCCGACC
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 12 0.19
29 37 0.60
30 13 0.21
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.28
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:37214 original size:19 final size:19
Alignment explanation
Indices: 37120--37217 Score: 92
Period size: 19 Copynumber: 5.1 Consensus size: 19
37110 GGCTGCTGGA
* * *
37120 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG-TCTG
* *
37140 AACCGATTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
*
37160 -ACCGGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
37179 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
37198 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
37217 A
1 A
37218 CCCGACCCGA
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
18 2 0.03
19 40 0.60
20 19 0.28
21 6 0.09
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:37218 original size:9 final size:9
Alignment explanation
Indices: 37121--37219 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
37111 GCTGCTGGAA
*
37121 ACCGGTTTA
1 ACCGGTTTG
*
37130 ACCGGTTTTCA
1 ACCGG-TTT-G
*
37141 ACCGATTCTG
1 ACCGGTT-TG
37151 ACCGGTTTG
1 ACCGGTTTG
*
37160 ACCGGTTTCA
1 ACCGGTTT-G
*
37170 ACCGGTTCG
1 ACCGGTTTG
37179 AACCGGTTTG
1 -ACCGGTTTG
*
37189 ACCGGTCTG
1 ACCGGTTTG
37198 AACCGGTTTG
1 -ACCGGTTTG
*
37208 ACCGGTCTG
1 ACCGGTTTG
37217 ACC
1 ACC
37220 CGACCCGACC
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
9 34 0.46
10 34 0.46
11 6 0.08
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:37226 original size:5 final size:5
Alignment explanation
Indices: 37216--37272 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
37206 TGACCGGTCT
* *
37216 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GA-CC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
37264 GACCC GACC
1 GACCC GACC
37273 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 4 0.09
5 31 0.72
7 8 0.19
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:37242 original size:22 final size:22
Alignment explanation
Indices: 37216--37279 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
37206 TGACCGGTCT
37216 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
37238 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
37260 GA-CCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
37280 GTTGACTTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 18 0.43
22 24 0.57
ACGTcount: A:0.19, C:0.48, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:44486 original size:17 final size:17
Alignment explanation
Indices: 44464--44496 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
44454 TTGACCGGTC
44464 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
44481 TGACCCGACCCGACCG
1 TGACCCGACCCGACCG
44497 ACCCGACCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.48, G:0.24, T:0.09
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:48399 original size:48 final size:48
Alignment explanation
Indices: 48328--48434 Score: 196
Period size: 48 Copynumber: 2.2 Consensus size: 48
48318 TTCCATGCCA
*
48328 AGGAAGTATTTGAGATTCCCCAAATCTTTAAGCTCAAATTCTGTGCTG
1 AGGAAGTCTTTGAGATTCCCCAAATCTTTAAGCTCAAATTCTGTGCTG
*
48376 AGGAAGTCTTTGAGATTCCCCAAATTTTTAAGCTCAAATTCTGTGCTG
1 AGGAAGTCTTTGAGATTCCCCAAATCTTTAAGCTCAAATTCTGTGCTG
48424 AGGAAGTCTTT
1 AGGAAGTCTTT
48435 TAGTTTCAAC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (48 bp):
AGGAAGTCTTTGAGATTCCCCAAATCTTTAAGCTCAAATTCTGTGCTG
Found at i:50266 original size:2 final size:2
Alignment explanation
Indices: 50254--50299 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
50244 TACACAACAG
50254 TA TA T- 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
50295 TA TA T
1 TA TA T
50300 CATACCTCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57491 original size:26 final size:26
Alignment explanation
Indices: 57441--57492 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
57431 ATTAGGAGAA
* *
57441 TATTTTATTTAAAAGTATTTAATTTT
1 TATTTTATTTAAAAATATATAATTTT
57467 TATTTTCATTTAAAAATATAT-ATTTT
1 TATTTT-ATTTAAAAATATATAATTTT
57493 ATGTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (26 bp):
TATTTTATTTAAAAATATATAATTTT
Found at i:59475 original size:5 final size:5
Alignment explanation
Indices: 59465--59498 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
59455 ATTTATTTAC
* *
59465 AAAAT AAAAT AAAAT AAAAT AATAC AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
59499 AAATAGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:59493 original size:25 final size:25
Alignment explanation
Indices: 59462--59520 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
59452 CACATTTATT
59462 TACAAAATAAAATAAAATAAAAT-AA
1 TACAAAATAAAA-AAAATAAAATAAA
*
59487 TACAAAAT-AAAAAAATAGAATGAAA
1 TACAAAATAAAAAAAATAAAAT-AAA
59512 TACAAAATA
1 TACAAAATA
59521 TGGAAACATG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 9 0.30
24 3 0.10
25 18 0.60
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (25 bp):
TACAAAATAAAAAAAATAAAATAAA
Found at i:60703 original size:11 final size:11
Alignment explanation
Indices: 60675--60733 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
60665 GAGAGCTTTC
*
60675 TCTGTTTTTCGT
1 TCTGTTTTT-TT
60687 TC-GTTTTTTT
1 TCTGTTTTTTT
60697 TCTGTTTTTTT
1 TCTGTTTTTTT
**
60708 TCT-TCGATTTT
1 TCTGT-TTTTTT
*
60719 TCTCTTTTTTT
1 TCTGTTTTTTT
60730 TCTG
1 TCTG
60734 CCCTCTCCCC
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
10 4 0.11
11 31 0.82
12 3 0.08
ACGTcount: A:0.02, C:0.15, G:0.10, T:0.73
Consensus pattern (11 bp):
TCTGTTTTTTT
Found at i:60706 original size:24 final size:23
Alignment explanation
Indices: 60679--60730 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
60669 GCTTTCTCTG
* *
60679 TTTTTCGTTCGTTTTTTTTCTGTTT
1 TTTTTC-TTCGATTTTTCTCT-TTT
60704 TTTTTCTTCGATTTTTCTCTTTT
1 TTTTTCTTCGATTTTTCTCTTTT
60727 TTTT
1 TTTT
60731 CTGCCCTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
24 12 0.48
25 6 0.24
ACGTcount: A:0.02, C:0.13, G:0.08, T:0.77
Consensus pattern (23 bp):
TTTTTCTTCGATTTTTCTCTTTT
Found at i:60718 original size:13 final size:13
Alignment explanation
Indices: 60679--60724 Score: 51
Period size: 11 Copynumber: 3.6 Consensus size: 13
60669 GCTTTCTCTG
60679 TTTTTCGTTCGTTT
1 TTTTTC-TTCGTTT
60693 TTTTTC-T-GTTT
1 TTTTTCTTCGTTT
*
60704 TTTTTCTTCGATT
1 TTTTTCTTCGTTT
*
60717 TTTCTCTT
1 TTTTTCTT
60725 TTTTTTCTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.36
12 2 0.07
13 10 0.36
14 6 0.21
ACGTcount: A:0.02, C:0.15, G:0.09, T:0.74
Consensus pattern (13 bp):
TTTTTCTTCGTTT
Found at i:62094 original size:15 final size:15
Alignment explanation
Indices: 62074--62131 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
62064 AAATTTGTAA
62074 AATAAAATAATTAAT
1 AATAAAATAATTAAT
*
62089 AATAAAATAGTTAA-
1 AATAAAATAATTAAT
62103 AATAATAATAATATTAAT
1 AATAA-AAT-A-ATTAAT
*
62121 AATAAATTAAT
1 AATAAAATAAT
62132 AAAACGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 5 0.14
15 18 0.50
16 2 0.06
17 6 0.17
18 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (15 bp):
AATAAAATAATTAAT
Found at i:62120 original size:12 final size:11
Alignment explanation
Indices: 62082--62133 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
62072 AAAATAAAAT
62082 AATTAATAATA
1 AATTAATAATA
* *
62093 AAATAGT--TA
1 AATTAATAATA
*
62102 AAATAATAATA
1 AATTAATAATA
62113 ATATTAATAATA
1 A-ATTAATAATA
62125 AATTAATAA
1 AATTAATAA
62134 AACGAAAACC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 8 0.24
11 16 0.47
12 10 0.29
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
AATTAATAATA
Found at i:63520 original size:203 final size:204
Alignment explanation
Indices: 63132--63527 Score: 607
Period size: 203 Copynumber: 1.9 Consensus size: 204
63122 TATATAAAGT
* * *
63132 TTTGAGAAATCATAAAAGCGTTGTTCTCTCAAAACTTTCTTATCTTCCTTTTTGTGTTAGTTCTC
1 TTTGAGAAATCATAAAAGCATTGTTCTCTCAAAACTTTCTTATCTTCCATTTTGTGCTAGTTCTC
* * *
63197 TTGTCTAGCTTTCGTCGAGATTCTAAGCATCTTTGCTTGGGATATTTTCATGCTTACTTAGCCGC
66 TTGTCTAGCTTCCGTCGAGATTCTAAGCATCCTTGCTTGGGATATTTTCAGGCTTACTTAGCCGC
* * *
63262 AATCACTGAGAAGGCGACTAAGACCGCACGTTCTGTGGCGCCGAAGTTCTAAGGGCGTGACAAGA
131 AATCACTGAGAAGGCGACTAAGACCGCACGTTCCGAGACGCCGAAGTTCTAAGGGCGTGACAAGA
63327 CTCCTTCAC
196 CTCCTTCAC
* * ** *
63336 TTTGAGAAATCATAAGAGCATT-TTCTCTTAAAGTTTTTTTATCTTCCATTTTGTGCTAGTTCTC
1 TTTGAGAAATCATAAAAGCATTGTTCTCTCAAAACTTTCTTATCTTCCATTTTGTGCTAGTTCTC
*
63400 TTGTCTAGCTTCCGTCGAGATTCTAAGCATCCTTGTTTGGGATATTTTCAGGCTTACTTAGCCGC
66 TTGTCTAGCTTCCGTCGAGATTCTAAGCATCCTTGCTTGGGATATTTTCAGGCTTACTTAGCCGC
* * *
63465 AATTACTGAGAATGCGACTAA-AGCCGCACGTTCCGAGACGTCGAAGTTCTAAGGGCGTGACAA
131 AATCACTGAGAAGGCGACTAAGA-CCGCACGTTCCGAGACGCCGAAGTTCTAAGGGCGTGACAA
63528 TAAGATGAGT
Statistics
Matches: 173, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
202 1 0.01
203 152 0.88
204 20 0.12
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.35
Consensus pattern (204 bp):
TTTGAGAAATCATAAAAGCATTGTTCTCTCAAAACTTTCTTATCTTCCATTTTGTGCTAGTTCTC
TTGTCTAGCTTCCGTCGAGATTCTAAGCATCCTTGCTTGGGATATTTTCAGGCTTACTTAGCCGC
AATCACTGAGAAGGCGACTAAGACCGCACGTTCCGAGACGCCGAAGTTCTAAGGGCGTGACAAGA
CTCCTTCAC
Found at i:66600 original size:23 final size:22
Alignment explanation
Indices: 66562--66612 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
66552 ACATAATTTA
66562 ATTT-AAAAATATTTTATTTTT
1 ATTTAAAAAATATTTTATTTTT
66583 ATTTAAAAATATATTTTATTTTT
1 ATTTAAAAA-ATATTTTATTTTT
*
66606 ATCTAAA
1 ATTTAAA
66613 CTTTTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 4 0.15
22 4 0.15
23 19 0.70
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTAAAAAATATTTTATTTTT
Found at i:66620 original size:31 final size:30
Alignment explanation
Indices: 66584--66707 Score: 103
Period size: 31 Copynumber: 4.2 Consensus size: 30
66574 TTTATTTTTA
*
66584 TTTAAAAATATATTTTATTTTTATCTAAACT
1 TTTAAAAATATATTTTATTATTATCTAAA-T
* *
66615 TTTAAAAATATATTTTATTATTATTTTAAT
1 TTTAAAAATATATTTTATTATTATCTAAAT
* * *
66645 TTTCAAAAT-TA-TATATT-TTATCT-TAT
1 TTTAAAAATATATTTTATTATTATCTAAAT
** ** *
66671 TTTATTAATATATTACATTATTATTTAAAT
1 TTTAAAAATATATTTTATTATTATCTAAAT
66701 TATTAAA
1 T-TTAAA
66708 TATTCAATTC
Statistics
Matches: 73, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
26 8 0.11
27 7 0.10
28 10 0.14
29 7 0.10
30 12 0.16
31 29 0.40
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (30 bp):
TTTAAAAATATATTTTATTATTATCTAAAT
Found at i:66664 original size:33 final size:31
Alignment explanation
Indices: 66584--66674 Score: 105
Period size: 31 Copynumber: 2.9 Consensus size: 31
66574 TTTATTTTTA
* * *
66584 TTTAAAAATATATTTTATTTTTATCTAAACT
1 TTTAAAAATATATTTTATTATTATTTTAACT
66615 TTTAAAAATATATTTTATTATTATTTTAA-T
1 TTTAAAAATATATTTTATTATTATTTTAACT
*
66645 TTTCAAAATTATATATTTTA-TCTTATTTTA
1 TTT-AAAA--ATATATTTTATTATTATTTTA
66675 TTAATATATT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
30 4 0.08
31 30 0.57
32 9 0.17
33 10 0.19
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.58
Consensus pattern (31 bp):
TTTAAAAATATATTTTATTATTATTTTAACT
Found at i:66773 original size:25 final size:24
Alignment explanation
Indices: 66745--66826 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 24
66735 TATTTTAATA
66745 TAATATATATATATTTAAATTAAGT
1 TAATATATATATATTT-AATTAAGT
* *
66770 TAATAATAAAATATATTTAA-TAATT
1 TAAT-AT-ATATATATTTAATTAAGT
* *
66795 TAATATA-AAATATTT-TTTAGAGT
1 TAATATATATATATTTAATTA-AGT
66818 TAATATATA
1 TAATATATA
66827 AATAAATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 9 0.19
23 10 0.21
24 3 0.06
25 12 0.26
26 4 0.09
27 9 0.19
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
TAATATATATATATTTAATTAAGT
Found at i:66827 original size:25 final size:25
Alignment explanation
Indices: 66767--66828 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 25
66757 ATTTAAATTA
*
66767 AGTTAATA-ATAAAATATATTTAAT
1 AGTTAATATATAAAATATATTTAAG
* * * *
66791 AATTTA-ATATAAAATATTTTTTAG
1 AGTTAATATATAAAATATATTTAAG
66815 AGTTAATATATAAA
1 AGTTAATATATAAA
66829 TAAATTATGA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
23 1 0.03
24 21 0.72
25 7 0.24
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (25 bp):
AGTTAATATATAAAATATATTTAAG
Found at i:70051 original size:20 final size:20
Alignment explanation
Indices: 70026--70065 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
70016 TTTTCCAAAA
70026 TGCTACAGGGTATCGATACC
1 TGCTACAGGGTATCGATACC
* *
70046 TGCTACAGTGTATTGATACC
1 TGCTACAGGGTATCGATACC
70066 CTTGCTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (20 bp):
TGCTACAGGGTATCGATACC
Done.