Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006796.1 Hibiscus syriacus cultivar Beakdansim tig00017242_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: 74196
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1557 original size:21 final size:21
Alignment explanation
Indices: 1497--1588 Score: 60
Period size: 21 Copynumber: 4.4 Consensus size: 21
1487 GTGAATCGGG
* * * *
1497 CTCTAGAATGTTGGGAGGGAC
1 CTCTTGAATGGTGAGAGGGGC
* * * *
1518 CTCTTCAACGATGACAGGGGC
1 CTCTTGAATGGTGAGAGGGGC
* *
1539 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGAGAGGGGC
* *
1560 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAATGG-TGAGAGGGGC
1581 CTCTTGAA
1 CTCTTGAA
1589 CAATAGAGGA
Statistics
Matches: 52, Mismatches: 17, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.92
22 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.24
Consensus pattern (21 bp):
CTCTTGAATGGTGAGAGGGGC
Found at i:1564 original size:42 final size:42
Alignment explanation
Indices: 1497--1588 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
1487 GTGAATCGGG
* *
1497 CTCTAGAATGTTGGGAGGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
* ** *
1539 CTCTTGAATGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGGGGC
1581 CTCTTGAA
1 CTCTTGAA
1589 CAATAGAGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 39 0.91
43 4 0.09
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.24
Consensus pattern (42 bp):
CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
Found at i:1615 original size:42 final size:42
Alignment explanation
Indices: 1511--1619 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
1501 AGAATGTTGG
* * *** *
1511 GAGGGACCTCTTCAACGATGACAGGGGCCTCTTGAATGGTGG
1 GAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACAATGA
* ** *
1553 GAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACAAT-A
1 GAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACAATGA
1594 GAGGAGGCCTCTTGAACGATGACAGG
1 GAGG-GGCCTCTTGAACGATGACAGG
1620 TGAGTCGGCC
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
41 4 0.08
42 48 0.92
ACGTcount: A:0.25, C:0.18, G:0.37, T:0.20
Consensus pattern (42 bp):
GAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACAATGA
Found at i:2122 original size:20 final size:20
Alignment explanation
Indices: 2099--2167 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
2089 GAAACTTAAA
**
2099 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAATTTGACT
*
2119 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
2139 ATCACAATGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
2159 ATCGCAACG
1 ATCGCAACG
2168 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:2242 original size:19 final size:20
Alignment explanation
Indices: 2210--2262 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
2200 GCGATTCTTT
*
2210 CATTGCGATAGTCAAATTCG
1 CATTACGATAGTCAAATTCG
**
2230 CATTACG-TAGTCATTTTCG
1 CATTACGATAGTCAAATTCG
*
2249 CATTTCGATAGTCA
1 CATTACGATAGTCA
2263 TTTTCGCGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (20 bp):
CATTACGATAGTCAAATTCG
Found at i:2262 original size:20 final size:20
Alignment explanation
Indices: 2210--2364 Score: 111
Period size: 20 Copynumber: 7.6 Consensus size: 20
2200 GCGATTCTTT
**
2210 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
*
2230 CATTACG-TAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
2249 CATTTCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
* *
2269 CGTTGCGATGTTGTTGCGATTTT--
1 CATTGCGA--TAG-T-C-ATTTTCG
* * * *
2292 CATTTCGCATTG-CGATTCTCT
1 CATTGCG-ATAGTC-ATTTTCG
*
2313 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
2333 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
2353 CATTGCGATAGT
1 CATTGCGATAGT
2365 AAACTATTCT
Statistics
Matches: 109, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
19 22 0.20
20 63 0.58
21 6 0.06
22 5 0.05
23 6 0.06
24 2 0.02
25 5 0.05
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:4275 original size:20 final size:20
Alignment explanation
Indices: 4252--4305 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
4242 GAAACTTAAA
*
4252 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
4272 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
4292 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
4306 TGAAAATCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:4687 original size:22 final size:22
Alignment explanation
Indices: 4662--4713 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
4652 AATGATTTGC
4662 CGGAGATGGAGACTGATATCGT
1 CGGAGATGGAGACTGATATCGT
* *
4684 CGGAGATGGGGACTGATTTCGT
1 CGGAGATGGAGACTGATATCGT
4706 CGGAGATG
1 CGGAGATG
4714 TGGACGGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.23, C:0.13, G:0.40, T:0.23
Consensus pattern (22 bp):
CGGAGATGGAGACTGATATCGT
Found at i:4718 original size:22 final size:21
Alignment explanation
Indices: 4654--4718 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
4644 TGATCGTGAA
*
4654 TGATTT-GCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGG-GAC
*
4675 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGAT-GGGAC
4697 TGATTTCGTCGGAGATGTGGAC
1 TGATTTCGTCGGAGATG-GGAC
4719 GGATGTCGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
21 6 0.16
22 30 0.79
23 2 0.05
ACGTcount: A:0.22, C:0.14, G:0.38, T:0.26
Consensus pattern (21 bp):
TGATTTCGTCGGAGATGGGAC
Found at i:4943 original size:40 final size:39
Alignment explanation
Indices: 4915--5026 Score: 188
Period size: 39 Copynumber: 2.8 Consensus size: 39
4905 CGATAGTCAG
* *
4915 ATTCGCGTTGCGATTTACGTATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA-TTACGT
4955 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTACGT
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTACGT
*
4994 ATTCACATTGCGATTTACGTATTCGCATTGCGA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA
5027 ATTAGGAAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 38 0.55
40 31 0.45
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (39 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTACGT
Found at i:4945 original size:20 final size:20
Alignment explanation
Indices: 4915--5026 Score: 190
Period size: 20 Copynumber: 5.7 Consensus size: 20
4905 CGATAGTCAG
*
4915 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
4935 ATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
4955 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
4975 ATTCGCATTGCGA-TTACGT
1 ATTCGCATTGCGATTTACGT
*
4994 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
5014 ATTCGCATTGCGA
1 ATTCGCATTGCGA
5027 ATTAGGAAAG
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
19 18 0.21
20 68 0.79
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:5047 original size:21 final size:21
Alignment explanation
Indices: 5023--5068 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5013 TATTCGCATT
*
5023 GCGAATTAGGAAAGTCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
5044 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
5065 GCGA
1 GCGA
5069 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:9672 original size:14 final size:15
Alignment explanation
Indices: 9637--9677 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
9627 CTGTTGTTTT
9637 TGTAGAAAACAGACTG
1 TGTAGAAAACAGAC-G
9653 TGTAGAAAACAGAC-
1 TGTAGAAAACAGACG
9667 TGTAGAAAACA
1 TGTAGAAAACA
9678 AACAAGTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 11 0.44
16 14 0.56
ACGTcount: A:0.49, C:0.12, G:0.22, T:0.17
Consensus pattern (15 bp):
TGTAGAAAACAGACG
Found at i:11989 original size:51 final size:51
Alignment explanation
Indices: 11913--12009 Score: 167
Period size: 51 Copynumber: 1.9 Consensus size: 51
11903 GAAAGGATAA
* * *
11913 GCTGTAAAGAAATATCGGTTTGAACATGTTGAAATTCCTTGTAACTAATAG
1 GCTGTAAAGAAATATAGGTTTGAACAGGCTGAAATTCCTTGTAACTAATAG
11964 GCTGTAAAGAAATATAGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 GCTGTAAAGAAATATAGGTTTGAACAGGCTGAAATTCCTTGTAACT
12010 CTCCCCTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (51 bp):
GCTGTAAAGAAATATAGGTTTGAACAGGCTGAAATTCCTTGTAACTAATAG
Found at i:13800 original size:14 final size:16
Alignment explanation
Indices: 13763--13806 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
13753 CCTGATACCA
13763 TGTAGAAAACAGACTG
1 TGTAGAAAACAGACTG
13779 TGTAGAAAACAGACT-
1 TGTAGAAAACAGACTG
13794 T-TAGAAAACAGAC
1 TGTAGAAAACAGAC
13807 AAGTCTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 12 0.43
15 1 0.04
16 15 0.54
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (16 bp):
TGTAGAAAACAGACTG
Found at i:15598 original size:50 final size:50
Alignment explanation
Indices: 15543--15641 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
15533 TTATCCACTC
*
15543 TCTTCTGATCCCTTTTTCATTAGTTTTTATCTCTTAGTTCATAAATTTCT
1 TCTTCTGATCCCTTTTTCATTAGTTTTCATCTCTTAGTTCATAAATTTCT
*
15593 TCTTCTGATCCCTTTTTCATTAGTTTTCATCTCTTGGTTCATAAATTTC
1 TCTTCTGATCCCTTTTTCATTAGTTTTCATCTCTTAGTTCATAAATTTC
15642 AAACCTTACC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.55
Consensus pattern (50 bp):
TCTTCTGATCCCTTTTTCATTAGTTTTCATCTCTTAGTTCATAAATTTCT
Found at i:18735 original size:51 final size:51
Alignment explanation
Indices: 18659--18755 Score: 167
Period size: 51 Copynumber: 1.9 Consensus size: 51
18649 GAAAGGATAA
* * *
18659 GCTGTAAAGAAATATCGGTTTGAACATGTTGAAATTCCTTGTAACTAATAG
1 GCTGTAAAGAAATATAGGTTTGAACAGGCTGAAATTCCTTGTAACTAATAG
18710 GCTGTAAAGAAATATAGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 GCTGTAAAGAAATATAGGTTTGAACAGGCTGAAATTCCTTGTAACT
18756 CTCCCCCTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (51 bp):
GCTGTAAAGAAATATAGGTTTGAACAGGCTGAAATTCCTTGTAACTAATAG
Found at i:20549 original size:14 final size:16
Alignment explanation
Indices: 20512--20552 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
20502 CCTGATACCA
20512 TGTAGAAAACAGACTG
1 TGTAGAAAACAGACTG
20528 TGTAGAAAACAGACT-
1 TGTAGAAAACAGACTG
20543 T-TAGAAAACA
1 TGTAGAAAACA
20553 ACAAGTCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.36
15 1 0.04
16 15 0.60
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.20
Consensus pattern (16 bp):
TGTAGAAAACAGACTG
Found at i:22343 original size:50 final size:50
Alignment explanation
Indices: 22288--22386 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
22278 TTATCCACTC
*
22288 TCTTCTGATCCCTTTTTCATTAGTTTTTATCTCTTAGTTCATAAATTTCT
1 TCTTCTGATCCCTTTTTCATTAGTTTTCATCTCTTAGTTCATAAATTTCT
*
22338 TCTTCTGATCCCTTTTTCATTAGTTTTCATCTCTTGGTTCATAAATTTC
1 TCTTCTGATCCCTTTTTCATTAGTTTTCATCTCTTAGTTCATAAATTTC
22387 AAACCTTACC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.17, C:0.21, G:0.07, T:0.55
Consensus pattern (50 bp):
TCTTCTGATCCCTTTTTCATTAGTTTTCATCTCTTAGTTCATAAATTTCT
Found at i:30136 original size:12 final size:11
Alignment explanation
Indices: 30119--30157 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 11
30109 TAATCTCATC
30119 TATTAGTCCATG
1 TATTAG-CCATG
30131 TATTAGCCAATG
1 TATTAGCC-ATG
30143 TATTAGCCCATG
1 TATTAG-CCATG
30155 TAT
1 TAT
30158 AGTACTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (11 bp):
TATTAGCCATG
Found at i:30318 original size:38 final size:39
Alignment explanation
Indices: 30261--30371 Score: 129
Period size: 38 Copynumber: 2.9 Consensus size: 39
30251 CTCGTATAAA
*
30261 CTGTGTCCCGAAGGTCCTATCATCCC-ATAGGATGTC-AT
1 CTGTGTCCCGAAGGACCTATCATCCCGA-AGGATGTCAAT
* *
30299 CTGTTTCCCGTAGGACCTATCATCCCGAAGGATG-CAAT
1 CTGTGTCCCGAAGGACCTATCATCCCGAAGGATGTCAAT
* * * *
30337 CTGTGTCTCGGAGAACCTGTCATCCCGAAGGATGT
1 CTGTGTCCCGAAGGACCTATCATCCCGAAGGATGT
30372 AGCCCTCGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
37 1 0.02
38 60 0.97
39 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (39 bp):
CTGTGTCCCGAAGGACCTATCATCCCGAAGGATGTCAAT
Found at i:31417 original size:9 final size:9
Alignment explanation
Indices: 31400--31441 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
31390 CTTACATTTT
*
31400 AAATACCAG
1 AAATTCCAG
31409 AAATTCCAG
1 AAATTCCAG
*
31418 AAATTCAAG
1 AAATTCCAG
31427 AAATTCCAG
1 AAATTCCAG
*
31436 TAATTC
1 AAATTC
31442 TGGTAATGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.24
Consensus pattern (9 bp):
AAATTCCAG
Found at i:32704 original size:30 final size:30
Alignment explanation
Indices: 32668--32725 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
32658 TTTGGTACCT
* *
32668 AAACTTTTCAAAATTTATACTTTAGTCACC
1 AAACTTTACAAAATTTATAATTTAGTCACC
* *
32698 AAACTTTACCAAATTTATAATTTGGTCA
1 AAACTTTACAAAATTTATAATTTAGTCA
32726 TTAAATAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (30 bp):
AAACTTTACAAAATTTATAATTTAGTCACC
Found at i:33211 original size:17 final size:16
Alignment explanation
Indices: 33189--33222 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
33179 TAAAGACAGT
33189 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
33206 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
33222 A
1 A
33223 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:33741 original size:24 final size:24
Alignment explanation
Indices: 33697--33743 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
33687 ATAAAGAACC
*
33697 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
33721 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
33744 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:37058 original size:19 final size:20
Alignment explanation
Indices: 37036--37079 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
37026 GAGAAAAGGT
37036 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
37055 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
37075 AAAAG
1 AAAAG
37080 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:43460 original size:17 final size:16
Alignment explanation
Indices: 43438--43471 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
43428 TAAAGACAGT
43438 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
43455 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
43471 A
1 A
43472 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:43990 original size:24 final size:24
Alignment explanation
Indices: 43946--43992 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
43936 GTAAAGAACC
*
43946 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
43970 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
43993 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:52877 original size:15 final size:14
Alignment explanation
Indices: 52850--52935 Score: 61
Period size: 15 Copynumber: 6.1 Consensus size: 14
52840 ATCTCTCATC
52850 TCATCTTTTTTTTTT
1 TCAT-TTTTTTTTTT
52865 TCATTTTTATTTTTT
1 TCATTTTT-TTTTTT
**
52880 TCA-TTCATTTTTT
1 TCATTTTTTTTTTT
*** *
52893 TCAAAATTTTTTAT
1 TCATTTTTTTTTTT
*
52907 TC--TTTTTCTTTT
1 TCATTTTTTTTTTT
52919 TCATTTTCTTTTTTT
1 TCATTTT-TTTTTTT
52934 TC
1 TC
52936 TTTGTTTTCT
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
12 8 0.15
13 9 0.17
14 16 0.30
15 21 0.39
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (14 bp):
TCATTTTTTTTTTT
Found at i:55474 original size:12 final size:12
Alignment explanation
Indices: 55457--55500 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
55447 TTTTATAATC
55457 CCATGTATTAGT
1 CCATGTATTAGT
55469 CCATGTATTAGT
1 CCATGTATTAGT
* *
55481 CAATGTATTAGC
1 CCATGTATTAGT
55493 CCATGTAT
1 CCATGTAT
55501 AGTACTGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (12 bp):
CCATGTATTAGT
Found at i:55659 original size:38 final size:38
Alignment explanation
Indices: 55607--55716 Score: 139
Period size: 38 Copynumber: 2.9 Consensus size: 38
55597 GTATAAACTG
* * * *
55607 TGTCCCGAATGACCTATCATCCCGCATGATGTCATCTA
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTA
* * *
55645 TGTCCCGTAGGACCTATCATCCTGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTA
* *
55683 TGTCCCGGAGGACCTGTCATCCCGAAGGATGTAA
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGTAA
55717 CCCTCGACTC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 62 1.00
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGTAATCTA
Found at i:57296 original size:12 final size:12
Alignment explanation
Indices: 57279--57320 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
57269 TTATAATCCT
57279 ATGTATTAGTCC
1 ATGTATTAGTCC
*
57291 ATGTATTAGTCA
1 ATGTATTAGTCC
*
57303 ATGTATTAGCCC
1 ATGTATTAGTCC
57315 ATGTAT
1 ATGTAT
57321 AGTACTGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (12 bp):
ATGTATTAGTCC
Found at i:57478 original size:38 final size:38
Alignment explanation
Indices: 57427--57536 Score: 148
Period size: 38 Copynumber: 2.9 Consensus size: 38
57417 GTATAAACTG
* * *
57427 TGTCCCGAAGGACCTATCATCCCGCAGGATGTCATCTA
1 TGTCCCGGAGGACCTATCATCCCGAAGGATGTAATCTA
* * *
57465 TGTCCTGTAGGACCTATCATCCCGAAGGATGTAATCTG
1 TGTCCCGGAGGACCTATCATCCCGAAGGATGTAATCTA
* *
57503 TGTCCCGGAGAACCTGTCATCCCGAAGGATGTAA
1 TGTCCCGGAGGACCTATCATCCCGAAGGATGTAA
57537 CCCTCGACTC
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 63 1.00
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (38 bp):
TGTCCCGGAGGACCTATCATCCCGAAGGATGTAATCTA
Found at i:59100 original size:12 final size:12
Alignment explanation
Indices: 59083--59126 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
59073 TTTTATAATC
*
59083 CCATGTATTATT
1 CCATGTATTAGT
59095 CCATGTATTAGT
1 CCATGTATTAGT
* *
59107 CAATGTATTAGC
1 CCATGTATTAGT
59119 CCATGTAT
1 CCATGTAT
59127 AGTACTGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (12 bp):
CCATGTATTAGT
Found at i:59285 original size:38 final size:38
Alignment explanation
Indices: 59243--59342 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 38
59233 TGTCCTGAAG
* * *
59243 GACCTATCATCCCGCAGGATGTCATCTATGTCCCGTAA
1 GACCTATCATCCCGAAGGATGTAATCTATGTCCCGGAA
* * *
59281 GACCTATCATCCCGAAGGATATAATCTGTGTCCCGGAG
1 GACCTATCATCCCGAAGGATGTAATCTATGTCCCGGAA
* *
59319 GACCTGTCATCCCAAAGGATGTAA
1 GACCTATCATCCCGAAGGATGTAA
59343 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (38 bp):
GACCTATCATCCCGAAGGATGTAATCTATGTCCCGGAA
Found at i:60329 original size:76 final size:76
Alignment explanation
Indices: 60221--60413 Score: 302
Period size: 76 Copynumber: 2.6 Consensus size: 76
60211 TTTATTTAGT
* *
60221 ATGGTATCGATACCCCCATATAGGGTACCGATACCCCTATGAACATTTTGGTTT-CGAGAAATAA
1 ATGGTACCGATACCCCCCTATAGGGTACCGATACCCCTATGAACATTTT-GTTTCCGAGAAATAA
*
60285 CAGAATGCTTGG
65 CAGAATGCTCGG
60297 ATGGTACCGATACCCCCCTATAGGGTACCGATACCCCTATGAACATTTTGTTTCCGAGAAATAAC
1 ATGGTACCGATACCCCCCTATAGGGTACCGATACCCCTATGAACATTTTGTTTCCGAGAAATAAC
60362 AGAATGCTCGG
66 AGAATGCTCGG
* *
60373 ATGGTACCGATA-CCCCCTAGTA-GGTATCGATACCCCCATGA
1 ATGGTACCGATACCCCCCTA-TAGGGTACCGATACCCCTATGA
60414 TATGGTATCG
Statistics
Matches: 110, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
75 28 0.25
76 82 0.75
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (76 bp):
ATGGTACCGATACCCCCCTATAGGGTACCGATACCCCTATGAACATTTTGTTTCCGAGAAATAAC
AGAATGCTCGG
Found at i:60423 original size:22 final size:21
Alignment explanation
Indices: 60373--60450 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 21
60363 GAATGCTCGG
*
60373 ATGGTACCGATACCCCCTAGT
1 ATGGTATCGATACCCCCTAGT
60394 A-GGTATCGATACCCCC-ATGAT
1 ATGGTATCGATACCCCCTA-G-T
*
60415 ATGGTATCGATACCCCCTACT
1 ATGGTATCGATACCCCCTAGT
*
60436 -TAGGTACCGATACCC
1 AT-GGTATCGATACCC
60451 TCAGACATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
19 1 0.02
20 16 0.33
21 16 0.33
22 15 0.31
23 1 0.02
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (21 bp):
ATGGTATCGATACCCCCTAGT
Found at i:60441 original size:21 final size:20
Alignment explanation
Indices: 60375--60450 Score: 82
Period size: 22 Copynumber: 3.6 Consensus size: 20
60365 ATGCTCGGAT
*
60375 GGTACCGATACCCCCTAGTA
1 GGTACCGATACCCCCTATTA
*
60395 GGTATCGATACCCCC-ATGATA
1 GGTACCGATACCCCCTAT--TA
*
60416 TGGTATCGATACCCCCTACTTA
1 -GGTACCGATACCCCCTA-TTA
60438 GGTACCGATACCC
1 GGTACCGATACCC
60451 TCAGACATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
19 1 0.02
20 14 0.29
21 14 0.29
22 17 0.35
23 1 0.02
24 1 0.02
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (20 bp):
GGTACCGATACCCCCTATTA
Found at i:64791 original size:103 final size:103
Alignment explanation
Indices: 64611--64836 Score: 443
Period size: 103 Copynumber: 2.2 Consensus size: 103
64601 GTCGAGGGTC
64611 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
64676 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTGGCATATGTATATGATTCTTAAGGAATGA
64714 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
64779 TTGATCCCTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTGGCATATGTATATGATTCTTAAGGAATGA
64817 TATGTGGTCCTTCGGGACAT
1 TATGTGGTCCTTCGGGACAT
64837 TATTATATGG
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 122 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:64878 original size:23 final size:23
Alignment explanation
Indices: 64845--64907 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
64835 ATTATTATAT
64845 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
64868 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
64891 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
64908 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:69627 original size:62 final size:65
Alignment explanation
Indices: 69539--69659 Score: 144
Period size: 62 Copynumber: 1.9 Consensus size: 65
69529 TAAAATAAAT
* *
69539 ACATCGAATGCAATTAGTTCATCGATGC-TAAGGCA-TGCATCGATGCAT-CC-CATTAATAACA
1 ACATCGAATGCAATTAGTGCACCGATGCATAA-GCAGTGCATCGATGCATACCTCATTAATAACA
69600 A
65 A
* * *
69601 ACATCGAATGCATTTTA-TGCACCGATGCATCAGTAGTGCATCGATGCATACCTCATTAA
1 ACATCGAATGCA-ATTAGTGCACCGATGCATAAGCAGTGCATCGATGCATACCTCATTAA
69660 AAGATGAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
62 23 0.47
63 18 0.37
64 2 0.04
65 6 0.12
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (65 bp):
ACATCGAATGCAATTAGTGCACCGATGCATAAGCAGTGCATCGATGCATACCTCATTAATAACAA
Found at i:70546 original size:100 final size:102
Alignment explanation
Indices: 70371--70597 Score: 354
Period size: 100 Copynumber: 2.2 Consensus size: 102
70361 GTCGAGGGTC
* *
70371 TATGTGGTCCTTCAGGAC--ATATGCATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
*
70434 TTGATCCTTGGCATATG-TAT-ATTCTTAAGGAATGA
66 TTGATCCCTGGCATATGATATGATTCTTAAGGAATGA
*
70469 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
70534 TTGATCCCTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTGGCATATG-ATATGATTCTTAAGGAATGA
* *
70572 TATGTGGTCTTTTGGGACATTATATG
1 TATGTGGTCCTTCGGGACA-TATATG
70598 GCACTACGGT
Statistics
Matches: 117, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
98 17 0.15
100 59 0.50
102 3 0.03
103 32 0.27
104 6 0.05
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACATATATGCATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
TTGATCCCTGGCATATGATATGATTCTTAAGGAATGA
Found at i:70639 original size:22 final size:23
Alignment explanation
Indices: 70597--70658 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
70587 GACATTATAT
70597 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
70620 GGCACTCCGGTGC-ATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
70642 GGCACTTCAGTGCAATT
1 GGCACTACGGTGCAATT
70659 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 19 0.56
23 15 0.44
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Done.