Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008764.1 Hibiscus syriacus cultivar Beakdansim tig00111857_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: 68921
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:377 original size:33 final size:35
Alignment explanation
Indices: 154--388 Score: 143
Period size: 37 Copynumber: 6.9 Consensus size: 35
144 AGATTTTGTG
* * *
154 TTTCAA-GGTAACTGTCTCAAGATAGACGAAAATTGA
1 TTTCAAGGGAAACTGTCTCAAGAGAGAC--AAATTTA
* *
190 -TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGAC-AAATTTA
* ** * *
225 GTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTG
1 -TTTCAAGGGAAACTGTCTCAAGAGAGAC-AAATTTA
* * * * * *
262 TTTCAAAGAAAACATAT-TC---A-A-A-TATTTTG
1 TTTCAAGGGAAAC-TGTCTCAAGAGAGACAAATTTA
* * *
291 TTTCAAGGGAAACTGTCTCAAGATAGACGAATTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAATTTA
*
326 TTTCAA-AGAAACTGTCTC-AGAGAGA-AAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAATTTA
*
358 TTTCAAGGGAAACTTTCTCAAGAGAGACAAA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAA
389 AATCTTCTAG
Statistics
Matches: 156, Mismatches: 29, Indels: 29
0.73 0.14 0.14
Matches are distributed among these distances:
28 2 0.01
29 18 0.12
31 1 0.01
32 13 0.08
33 17 0.11
34 19 0.12
35 25 0.16
36 30 0.19
37 31 0.20
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.26
Consensus pattern (35 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAATTTA
Found at i:885 original size:17 final size:18
Alignment explanation
Indices: 853--887 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
843 ATGATGAATC
*
853 CCAAAGATGCCTCAATAT
1 CCAAAGATGCCCCAATAT
871 CCAAA-ATGCCCCAATAT
1 CCAAAGATGCCCCAATAT
888 TTGATATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.40, C:0.31, G:0.09, T:0.20
Consensus pattern (18 bp):
CCAAAGATGCCCCAATAT
Found at i:1294 original size:21 final size:22
Alignment explanation
Indices: 1270--1319 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
1260 TTGTGTTTGG
*
1270 TCAAGGGTTTGGCATTTGA-GC
1 TCAAAGGTTTGGCATTTGATGC
*
1291 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1313 TCAAAGG
1 TCAAAGG
1320 ATTGATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.24, C:0.12, G:0.30, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1959 original size:22 final size:22
Alignment explanation
Indices: 1934--1976 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1924 TTGCATGTGC
*
1934 TTTTGTCCCTTTTTCTTTTTGAT
1 TTTTG-CCCTTTTTCCTTTTGAT
*
1957 TTTTGCTCTTTTTCCTTTTG
1 TTTTGCCCTTTTTCCTTTTG
1977 TTCTTGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.02, C:0.19, G:0.09, T:0.70
Consensus pattern (22 bp):
TTTTGCCCTTTTTCCTTTTGAT
Found at i:6421 original size:5 final size:5
Alignment explanation
Indices: 6411--6490 Score: 53
Period size: 5 Copynumber: 16.6 Consensus size: 5
6401 TAGATATAAA
* ** * * *
6411 AAAAT AAAAT AAAAT AAAAA ATAAAT AAATAT TCAAC CAAAT AAAA- GAAAT
1 AAAAT AAAAT AAAAT AAAAT A-AAAT AAA-AT AAAAT AAAAT AAAAT AAAAT
6462 AAAAT AAAAT -AAAT -AAAT -AAAT -AAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
6491 GCATAGAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
4 19 0.32
5 34 0.57
6 7 0.12
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:6438 original size:4 final size:4
Alignment explanation
Indices: 6406--6490 Score: 57
Period size: 4 Copynumber: 20.2 Consensus size: 4
6396 CATTTTAGAT
* * **
6406 ATAA AAAA ATAAA ATAAA ATAA A-AA ATAA ATAA AT-A TTCAA CCAA ATAAA
1 ATAA ATAA AT-AA AT-AA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA AT-AA
*
6456 AGAA ATAAA ATAAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA AT-AA AT-AA ATAA ATAA ATAA ATAA ATAA A
6491 GCATAGAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
3 5 0.08
4 39 0.59
5 22 0.33
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (4 bp):
ATAA
Found at i:6468 original size:14 final size:13
Alignment explanation
Indices: 6449--6482 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
6439 ATATTCAACC
6449 AAATAAAAGAAAT
1 AAATAAAAGAAAT
*
6462 AAAATAAAATAAAT
1 -AAATAAAAGAAAT
6476 AAATAAA
1 AAATAAA
6483 TAAATAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (13 bp):
AAATAAAAGAAAT
Found at i:6513 original size:51 final size:51
Alignment explanation
Indices: 6403--6533 Score: 123
Period size: 51 Copynumber: 2.6 Consensus size: 51
6393 GAACATTTTA
* *
6403 GATA-TAAA-AAAATAAAATAAAATAAA-AAATAAATAAATATTCAACCAAAT
1 GATAGTAAATAAAATAAAAT-AAATAAATAAATAAATAAACATACAA-CAAAT
* * *
6453 AAAAG-AAATAAAATAAAATAAATAAATAAATAAATAAAGCATAGAA-AAAT
1 GATAGTAAATAAAATAAAATAAATAAATAAATAAATAAA-CATACAACAAAT
6503 GATAGTAAATAATAATATAAAT--ATAAATAAA
1 GATAGTAAATAA-AATA-AAATAAATAAATAAA
6534 AAAAAGGTAA
Statistics
Matches: 67, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
50 19 0.28
51 36 0.54
52 8 0.12
53 4 0.06
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (51 bp):
GATAGTAAATAAAATAAAATAAATAAATAAATAAATAAACATACAACAAAT
Found at i:7280 original size:34 final size:35
Alignment explanation
Indices: 7190--7291 Score: 136
Period size: 38 Copynumber: 2.9 Consensus size: 35
7180 AATAGTAAAC
7190 TCTATCCTATTTTTAGGAGTTTGAATCCTAACAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCT-A-AAAAT
*
7227 T-TCATCCTATTTTTTAGGAGTTTGAATCCT-GAAAT
1 TCT-ATCCTA-TTTTTAGGAGTTTGAATCCTAAAAAT
*
7262 TCTATCCTATTTTTAGGAGTTCGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
7292 GTAGGACGAA
Statistics
Matches: 59, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
34 19 0.32
35 11 0.19
36 2 0.03
37 7 0.12
38 20 0.34
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
Found at i:10502 original size:20 final size:20
Alignment explanation
Indices: 10474--10511 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10464 AACTCTACCT
10474 CCTGAATCTAAATGATATGA
1 CCTGAATCTAAATGATATGA
* *
10494 CCTGGATCTGAATGATAT
1 CCTGAATCTAAATGATAT
10512 CGCCTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (20 bp):
CCTGAATCTAAATGATATGA
Found at i:14609 original size:39 final size:39
Alignment explanation
Indices: 14548--14688 Score: 153
Period size: 39 Copynumber: 3.7 Consensus size: 39
14538 AAAGACATAG
* * *
14548 GGTAAGGACTTACCTTGTGCACAAAGCAGAGGAGCTTGC
1 GGTAAGGACTTACCATGAGCACAAAGCAGAGGAGCCTGC
* *
14587 GGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGC
1 GGTAAGGACTTACCATGAGCACAAAGCAGAGGAGCCTGC
* * ** *
14626 AGTAAGAACTTACCATGAGCACAAAGTTGAGAAG---GC
1 GGTAAGGACTTACCATGAGCACAAAGCAGAGGAGCCTGC
* *
14662 GTTAAGAACTTACCATGAGCACAAAGC
1 GGTAAGGACTTACCATGAGCACAAAGC
14689 CAATGAGCAT
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
36 26 0.29
39 63 0.71
ACGTcount: A:0.34, C:0.22, G:0.27, T:0.17
Consensus pattern (39 bp):
GGTAAGGACTTACCATGAGCACAAAGCAGAGGAGCCTGC
Found at i:18174 original size:20 final size:20
Alignment explanation
Indices: 18149--18186 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18139 CCAAATTTGC
18149 AACGCGAATATGTAAATCGT
1 AACGCGAATATGTAAATCGT
*
18169 AACGCGAATCTGTAAATC
1 AACGCGAATATGTAAATC
18187 ACGTTGCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (20 bp):
AACGCGAATATGTAAATCGT
Found at i:18217 original size:20 final size:20
Alignment explanation
Indices: 18192--18275 Score: 100
Period size: 20 Copynumber: 4.2 Consensus size: 20
18182 AAATCACGTT
18192 GCGATTTCCAAATTCGCAAC
1 GCGATTTCCAAATTCGCAAC
18212 GCGATTTCCAAATTCGCAAC
1 GCGATTTCCAAATTCGCAAC
*
18232 ACTGAATTT-CAAATTCGCAAC
1 GC-G-ATTTCCAAATTCGCAAC
* **
18253 TCGA-TTCTGAATTCGCAAC
1 GCGATTTCCAAATTCGCAAC
18272 GCGA
1 GCGA
18276 ATTTGTTGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
18 2 0.04
19 14 0.25
20 22 0.39
21 14 0.25
22 4 0.07
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.26
Consensus pattern (20 bp):
GCGATTTCCAAATTCGCAAC
Found at i:19135 original size:12 final size:12
Alignment explanation
Indices: 19114--19147 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19104 ACCACATTTC
*
19114 CAATACCAAACA
1 CAATATCAAACA
19126 CAATATCAAACA
1 CAATATCAAACA
*
19138 CAATCTCAAA
1 CAATATCAAA
19148 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:19289 original size:24 final size:24
Alignment explanation
Indices: 19268--19314 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
19258 AGGCAATATT
19268 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
* *
19292 CGGACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
19315 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:19319 original size:24 final size:24
Alignment explanation
Indices: 19273--19326 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
19263 ATATTCGAAA
19273 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
19297 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
19321 TTTGAT
1 TTTGAT
19327 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:21570 original size:12 final size:12
Alignment explanation
Indices: 21553--21599 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
21543 AGCAAAAGGA
21553 AATCAAAATCGC
1 AATCAAAATCGC
**
21565 AATCAAAATCAA
1 AATCAAAATCGC
*
21577 AATCAAAATCCC
1 AATCAAAATCGC
*
21589 AATCACAATCG
1 AATCAAAATCG
21600 ACTTCACCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.53, C:0.26, G:0.04, T:0.17
Consensus pattern (12 bp):
AATCAAAATCGC
Found at i:21574 original size:6 final size:6
Alignment explanation
Indices: 21552--21586 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
21542 AAGCAAAAGG
* *
21552 AAATCA AAATCG CAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
21587 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:21803 original size:29 final size:29
Alignment explanation
Indices: 21766--21821 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
21756 GATTTTTTTG
* *
21766 TTGCGATTGTTGCGAAAGTCAAATTCGCA
1 TTGCAATTGTTGCAAAAGTCAAATTCGCA
21795 TTGCAATTGTTGCAAAAGTCAAATTCG
1 TTGCAATTGTTGCAAAAGTCAAATTCG
21822 AAATACGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (29 bp):
TTGCAATTGTTGCAAAAGTCAAATTCGCA
Found at i:21873 original size:20 final size:20
Alignment explanation
Indices: 21846--21896 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
21836 CAACGTGAAG
21846 TTGACTTTCGCGTTGCAAAT
1 TTGACTTTCGCGTTGCAAAT
* * *
21866 TTGGCTTTCACGTTGCGAAT
1 TTGACTTTCGCGTTGCAAAT
21886 TTGACTTTCGC
1 TTGACTTTCGC
21897 AACCATCGCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGACTTTCGCGTTGCAAAT
Found at i:22066 original size:13 final size:12
Alignment explanation
Indices: 22048--22077 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
22038 TTATTTACAC
22048 ATCAATTAAACAA
1 ATCAATTAAAC-A
22061 ATCAATTAAACA
1 ATCAATTAAACA
22073 ATCAA
1 ATCAA
22078 AAAATAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (12 bp):
ATCAATTAAACA
Found at i:22073 original size:50 final size:50
Alignment explanation
Indices: 22007--22115 Score: 164
Period size: 50 Copynumber: 2.2 Consensus size: 50
21997 ATCAACTTTT
22007 ACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAA
1 ACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAA
* *** * *
22057 ACAAATCAATTAAACAATCAAAAAATAATTCTTATTTCCTCATCAATTAA
1 ACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAA
22107 ACAAATCAA
1 ACAAATCAA
22116 CTTTTACAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.27
Consensus pattern (50 bp):
ACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAA
Found at i:23326 original size:21 final size:21
Alignment explanation
Indices: 23302--23413 Score: 125
Period size: 21 Copynumber: 5.3 Consensus size: 21
23292 CGGGCTCTCA
* *
23302 AACGGTGGGAGGGACCTCTTG
1 AACGATGGGAGGGGCCTCTTG
**
23323 AACGATGATAGGGGCCTCTTG
1 AACGATGGGAGGGGCCTCTTG
*
23344 AACGGTGGGAGGGGCCTCTTG
1 AACGATGGGAGGGGCCTCTTG
* **
23365 AATGATGATAGGGGCCTCTTG
1 AACGATGGGAGGGGCCTCTTG
* * *
23386 AATGATAGGAGAGGCCTCTTG
1 AACGATGGGAGGGGCCTCTTG
23407 AACGATG
1 AACGATG
23414 ACAGGTGATT
Statistics
Matches: 74, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (21 bp):
AACGATGGGAGGGGCCTCTTG
Found at i:23362 original size:42 final size:42
Alignment explanation
Indices: 23302--23414 Score: 172
Period size: 42 Copynumber: 2.7 Consensus size: 42
23292 CGGGCTCTCA
*
23302 AACGGTGGGAGGGACCTCTTGAACGATGATAGGGGCCTCTTG
1 AACGGTGGGAGGGGCCTCTTGAACGATGATAGGGGCCTCTTG
*
23344 AACGGTGGGAGGGGCCTCTTGAATGATGATAGGGGCCTCTTG
1 AACGGTGGGAGGGGCCTCTTGAACGATGATAGGGGCCTCTTG
* * * *
23386 AATGATAGGAGAGGCCTCTTGAACGATGA
1 AACGGTGGGAGGGGCCTCTTGAACGATGA
23415 CAGGTGATTC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.22
Consensus pattern (42 bp):
AACGGTGGGAGGGGCCTCTTGAACGATGATAGGGGCCTCTTG
Found at i:23733 original size:21 final size:21
Alignment explanation
Indices: 23709--23748 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
23699 ATAGATATGC
*
23709 TACCTCATCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
23730 TACCTCACCACGTAAAGTA
1 TACCTCACCACGTAAAGTA
23749 CCATTGTCAT
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:0.38, C:0.28, G:0.12, T:0.23
Consensus pattern (21 bp):
TACCTCACCACGTAAAGTAGA
Found at i:29984 original size:16 final size:16
Alignment explanation
Indices: 29963--30004 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
29953 AAAATGTTGA
29963 AAAAAAAATAGCAGTTCG
1 AAAAAAAA-A-CAGTTCG
*
29981 AAAAAAAAACTGTTCG
1 AAAAAAAAACAGTTCG
29997 AAAAAAAA
1 AAAAAAAA
30005 GACTTGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.61
17 1 0.04
18 8 0.35
ACGTcount: A:0.64, C:0.10, G:0.12, T:0.14
Consensus pattern (16 bp):
AAAAAAAAACAGTTCG
Found at i:32789 original size:20 final size:20
Alignment explanation
Indices: 32764--32833 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
32754 TCTTAAACTT
32764 AAAATCGCAATGCGAAAATG
1 AAAATCGCAATGCGAAAATG
32784 AAAATCGCAATGCGAAAATG
1 AAAATCGCAATGCGAAAATG
*
32804 AAAATCGCAACGCG-AAATG
1 AAAATCGCAATGCGAAAATG
*
32823 AAAATCACAAT
1 AAAATCGCAAT
32834 AGTCTTCTGC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 14 0.30
20 33 0.70
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAATCGCAATGCGAAAATG
Found at i:33183 original size:22 final size:22
Alignment explanation
Indices: 33155--33213 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
33145 AGATGGAGAT
33155 AGACGGATTTCGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
* *
33177 GGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
*
33199 AGACGGATGTCGCCG
1 AGACGGATTTCGCCG
33214 TAGAGGGTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.20, C:0.19, G:0.42, T:0.19
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATGG
Found at i:33339 original size:19 final size:20
Alignment explanation
Indices: 33317--33354 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33307 AATATTGTGT
33317 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
33336 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
33355 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:33386 original size:20 final size:20
Alignment explanation
Indices: 33361--33411 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
33351 TAAACGCGCT
33361 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
*
33381 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTATGTG
33401 TTGCGAATTTG
1 TTGCGAATTTG
33412 GAAAATCGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.18, C:0.12, G:0.25, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:33429 original size:21 final size:21
Alignment explanation
Indices: 33403--33469 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
33393 CTTCTGTGTT
33403 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
*
33424 GCGAATTTGGAAAATCACAAC
1 GCGAATTTGGAAAATCGCAAC
*
33445 GCGAATTTGGAAAATCGCAAT
1 GCGAATTTGGAAAATCGCAAC
33466 GCGA
1 GCGA
33470 TTTACATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:36565 original size:11 final size:11
Alignment explanation
Indices: 36549--36577 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
36539 AACAGCGAAG
36549 TGATGATGCAA
1 TGATGATGCAA
36560 TGATGATGCAA
1 TGATGATGCAA
36571 TG-TGATG
1 TGATGATG
36578 GGGTGTGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.31
Consensus pattern (11 bp):
TGATGATGCAA
Found at i:36619 original size:9 final size:11
Alignment explanation
Indices: 36591--36646 Score: 103
Period size: 11 Copynumber: 5.1 Consensus size: 11
36581 TGTGGGTGTG
36591 AGGGAGAGAGA
1 AGGGAGAGAGA
*
36602 AGGAAGAGAGA
1 AGGGAGAGAGA
36613 AGGGAGAGAGA
1 AGGGAGAGAGA
36624 AGGGAGAGAGA
1 AGGGAGAGAGA
36635 AGGGAGAGAGA
1 AGGGAGAGAGA
36646 A
1 A
36647 TTGGTAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 43 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (11 bp):
AGGGAGAGAGA
Found at i:41840 original size:15 final size:16
Alignment explanation
Indices: 41815--41849 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
41805 GCAAACCAAT
41815 TTTTGTCTTAAAATGA
1 TTTTGTCTTAAAATGA
*
41831 TTTT-TCTTAAAATTA
1 TTTTGTCTTAAAATGA
41846 TTTT
1 TTTT
41850 AAAGAACGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.60
Consensus pattern (16 bp):
TTTTGTCTTAAAATGA
Found at i:41965 original size:22 final size:21
Alignment explanation
Indices: 41919--41964 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
41909 AAATCAATTC
41919 AAAATCACTAATTTTTCTAATA
1 AAAATCACTAATTTTTCTAA-A
* *
41941 AAAGTCA-TAATTTTTTTAAA
1 AAAATCACTAATTTTTCTAAA
41961 AAAA
1 AAAA
41965 ATATTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAATCACTAATTTTTCTAAA
Found at i:47116 original size:37 final size:36
Alignment explanation
Indices: 47053--47182 Score: 100
Period size: 37 Copynumber: 3.6 Consensus size: 36
47043 CAAAGTGTTA
** * * *
47053 TCTCGCTTGAGATTGTTTTATTTAAAAGCAAATTTTG
1 TCTCGCTTGAGACAGTTTTCTCTAAAA-CCAATTTTG
* *
47090 TCTCGCTTGAGACAGTTTTCTCTAAAAACCGATTTTA
1 TCTCGCTTGAGACAGTTTTCTCT-AAAACCAATTTTG
* * * * *
47127 TCTAGCTTAAGACA-ATTTCGCTCATAACCAATTTTG
1 TCTCGCTTGAGACAGTTTTCTCT-AAAACCAATTTTG
* *
47163 TCTTGCTTGAGACATTTTTC
1 TCTCGCTTGAGACAGTTTTC
47183 CTTTGAGATA
Statistics
Matches: 73, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
36 28 0.38
37 41 0.56
38 4 0.05
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (36 bp):
TCTCGCTTGAGACAGTTTTCTCTAAAACCAATTTTG
Found at i:47176 original size:36 final size:37
Alignment explanation
Indices: 47083--47176 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 37
47073 TTTAAAAGCA
* * *
47083 AATTTTGTCTCGCTTGAGACAGTTTTCTCTAAAAACC
1 AATTTTGTCTAGCTTGAGACAGATTTCGCTAAAAACC
* * * * *
47120 GATTTTATCTAGCTTAAGACA-ATTTCGCTCATAACC
1 AATTTTGTCTAGCTTGAGACAGATTTCGCTAAAAACC
*
47156 AATTTTGTCTTGCTTGAGACA
1 AATTTTGTCTAGCTTGAGACA
47177 TTTTTCCTTT
Statistics
Matches: 45, Mismatches: 12, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
36 28 0.62
37 17 0.38
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (37 bp):
AATTTTGTCTAGCTTGAGACAGATTTCGCTAAAAACC
Found at i:47535 original size:134 final size:134
Alignment explanation
Indices: 47290--47632 Score: 418
Period size: 134 Copynumber: 2.6 Consensus size: 134
47280 TTGAAATATT
* *
47290 ATCCCTAAAGATGGCCA-ACTATCCTCATCACGTAGGAACTGTGTCATCCACCGACCAAATCTCC
1 ATCCCTAAAGATGGCCAGTC-ATCCTCATCACGTAGGAACAGTGTCATCCACCGACCAAATCTCC
* ** * * * *
47354 TCATCACGTAGGAGTTGCGTCAACCTTAGATAACCAACCGTCCTCATCACGTAGGAACCATGTTA
65 TCATCACGTAAGAGTCACATCAACCTTAGATAACCAACCATCATCATCACATAGGAACCATGTTA
*
47419 TCATC
130 TCAAC
* * * * * * *
47424 ATCCCTAAAGTTGGCCAGTCATCCTCATCGCTTAGGAACGGTGTTATCCACTGACCATATCTCCT
1 ATCCCTAAAGATGGCCAGTCATCCTCATCACGTAGGAACAGTGTCATCCACCGACCAAATCTCCT
* * * **
47489 CATCACTTAAGAGTCACATCAACCTTAGATATCCAGCCATCATCATCACATAGGAACTGTGTTAT
66 CATCACGTAAGAGTCACATCAACCTTAGATAACCAACCATCATCATCACATAGGAACCATGTTAT
47554 CAAC
131 CAAC
* * * * *
47558 ATCCCTAAAGATGACCAAGTCATCCTCATCAAGTAGGAACAATGTCATCCACCGACTAGATCTCC
1 ATCCCTAAAGATGGCC-AGTCATCCTCATCACGTAGGAACAGTGTCATCCACCGACCAAATCTCC
47623 TCATCACGTA
65 TCATCACGTA
47633 GGAGCCGTGT
Statistics
Matches: 174, Mismatches: 33, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
134 125 0.72
135 49 0.28
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (134 bp):
ATCCCTAAAGATGGCCAGTCATCCTCATCACGTAGGAACAGTGTCATCCACCGACCAAATCTCCT
CATCACGTAAGAGTCACATCAACCTTAGATAACCAACCATCATCATCACATAGGAACCATGTTAT
CAAC
Found at i:47892 original size:3 final size:3
Alignment explanation
Indices: 47884--47915 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
47874 TCTGAGTCTT
47884 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
47916 TAAATATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.