Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001632.1 Hibiscus syriacus cultivar Beakdansim tig00003253_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: 66248
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:76 original size:24 final size:24
Alignment explanation
Indices: 26--92 Score: 118
Period size: 24 Copynumber: 2.8 Consensus size: 24
16 AAGTAAAGGG
*
26 TCTACGCGGTCCTTCGGG-CAAAT
1 TCTACGTGGTCCTTCGGGACAAAT
49 TCTACGTGGTCCTTCGGGACAAAT
1 TCTACGTGGTCCTTCGGGACAAAT
73 TCTACGTGGTCCTTCGGGAC
1 TCTACGTGGTCCTTCGGGAC
93 GTATGTATTC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
23 17 0.40
24 25 0.60
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.28
Consensus pattern (24 bp):
TCTACGTGGTCCTTCGGGACAAAT
Found at i:233 original size:23 final size:23
Alignment explanation
Indices: 199--284 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
189 ACATATTATA
199 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
222 TGGCACTTCGGTGTATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
245 CGGTC-CTTCGG-ACAAAATTCTACG
1 TGG-CACTACGGTGC--AATTCTACG
269 TGGCACTACGGTGCAA
1 TGGCACTACGGTGCAA
285 ATTTATAGCT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
23 31 0.65
24 16 0.33
25 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:5768 original size:16 final size:17
Alignment explanation
Indices: 5734--5773 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
5724 TTATATGAAA
*
5734 TGATATGTGCTTATATG
1 TGATATGTGATTATATG
*
5751 TGCTATGTGATT-TATG
1 TGATATGTGATTATATG
5767 TGATATG
1 TGATATG
5774 CCATATGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (17 bp):
TGATATGTGATTATATG
Found at i:6369 original size:23 final size:23
Alignment explanation
Indices: 6335--6421 Score: 81
Period size: 23 Copynumber: 3.7 Consensus size: 23
6325 ACATATTATA
*
6335 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
6358 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
6381 CGGTC-CTTCGG-GACAAAATTCTACG
1 TGG-CACTTCGGTG-C--AATTCTACG
6406 TGGCA-TTACGGTGCAA
1 TGGCACTT-CGGTGCAA
6422 ATTTATACGA
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
22 1 0.02
23 32 0.62
24 4 0.08
25 14 0.27
26 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:7268 original size:7 final size:7
Alignment explanation
Indices: 7252--7287 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
7242 TGTTCATCGT
7252 ACTATTC
1 ACTATTC
*
7259 ACTGTTC
1 ACTATTC
*
7266 ACTATTT
1 ACTATTC
7273 ACTATTC
1 ACTATTC
7280 ACTATTC
1 ACTATTC
7287 A
1 A
7288 TATAGTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.25, G:0.03, T:0.44
Consensus pattern (7 bp):
ACTATTC
Found at i:7653 original size:21 final size:22
Alignment explanation
Indices: 7621--7665 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
7611 GAGTTGGTAA
7621 GGTTATTGTTAGAGA-TTTTAT
1 GGTTATTGTTAGAGATTTTTAT
*
7642 GGTTGATT-TTAGGGATTTTTAT
1 GGTT-ATTGTTAGAGATTTTTAT
7664 GG
1 GG
7666 ATTTGAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (22 bp):
GGTTATTGTTAGAGATTTTTAT
Found at i:11752 original size:24 final size:24
Alignment explanation
Indices: 11724--11771 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
11714 AACAGTGCCA
*
11724 TAGTAAAACTCAATTCTGTAAGTG
1 TAGTAAAACTCAATTCTATAAGTG
11748 TAGTAAAACTCAATTCTATAAGTG
1 TAGTAAAACTCAATTCTATAAGTG
11772 AAATCTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (24 bp):
TAGTAAAACTCAATTCTATAAGTG
Found at i:12638 original size:50 final size:51
Alignment explanation
Indices: 12574--12669 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 51
12564 AAATATGAAA
12574 AAAAATACTGAATTTAATTTAGAA-ATATAAAAAT-AATAAATTTTAATATG
1 AAAAATACTGAATTTAATTTA-AATATATAAAAATAAATAAATTTTAATATG
* * * * *
12624 AAAAATATTTAATTTAGTTTAAATATGTAAATATAAATAAATTTTA
1 AAAAATACTGAATTTAATTTAAATATATAAAAATAAATAAATTTTA
12670 TTTTAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
49 2 0.05
50 26 0.67
51 11 0.28
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (51 bp):
AAAAATACTGAATTTAATTTAAATATATAAAAATAAATAAATTTTAATATG
Found at i:15661 original size:17 final size:17
Alignment explanation
Indices: 15628--15668 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
15618 GAGAAAGGGT
15628 AAGAAGAAAAAATGGAG
1 AAGAAGAAAAAATGGAG
*
15645 AAGAATGAAATAA-GGAG
1 AAGAA-GAAAAAATGGAG
15662 AAGAAGA
1 AAGAAGA
15669 TGAAGAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 14 0.64
18 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.29, T:0.07
Consensus pattern (17 bp):
AAGAAGAAAAAATGGAG
Found at i:16407 original size:17 final size:19
Alignment explanation
Indices: 16369--16409 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
16359 TTTAGGATAA
16369 TTTAGGATCTTTTTATTAT
1 TTTAGGATCTTTTTATTAT
*
16388 TTTAGGAT-TTTTT-TTCT
1 TTTAGGATCTTTTTATTAT
16405 TTTAG
1 TTTAG
16410 TTAGTGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 5 0.24
19 8 0.38
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.66
Consensus pattern (19 bp):
TTTAGGATCTTTTTATTAT
Found at i:16646 original size:4 final size:4
Alignment explanation
Indices: 16637--16674 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
16627 CTCTATTCTC
16637 TTTA TTTA TTTA TTTA TTTA TTTA -TTA -TTA TTTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTT
16675 TGTTTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 6 0.19
4 23 0.72
5 3 0.09
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:17346 original size:15 final size:17
Alignment explanation
Indices: 17323--17356 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
17313 TTCTTATTTA
17323 TTTATTTTTTCTT-AAT
1 TTTATTTTTTCTTCAAT
17339 TTTA-TTTTTCTTCAAT
1 TTTATTTTTTCTTCAAT
17355 TT
1 TT
17357 ATTATGATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTTTTCTTCAAT
Found at i:17357 original size:15 final size:14
Alignment explanation
Indices: 17300--17359 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 14
17290 TAAAATTTCA
17300 TTTCTTAATTGT-TT
1 TTTCTTAATT-TATT
* *
17314 TCTTATTTATTTATTT
1 T-TTCTTAATTTA-TT
17330 TTTCTTAATTTTATT
1 TTTCTTAA-TTTATT
17345 TTTCTTCAATTTATT
1 TTTCTT-AATTTATT
17360 ATGATTGAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
14 2 0.05
15 26 0.70
16 9 0.24
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCTTAATTTATT
Found at i:19014 original size:35 final size:36
Alignment explanation
Indices: 18934--19014 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 36
18924 ACAAACATAC
* *
18934 AAGTAAGTATGCAAGTTCAGGATGAATATGAAACAT
1 AAGTAAATATGCAAGTTCAAGATGAATATGAAACAT
*
18970 AAGTAAATATGCATAGTTTAAGATGAA-ATGAAA-AT
1 AAGTAAATATGCA-AGTTCAAGATGAATATGAAACAT
19005 AAGTAAATAT
1 AAGTAAATAT
19015 AATGATCTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
35 12 0.29
36 18 0.44
37 11 0.27
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (36 bp):
AAGTAAATATGCAAGTTCAAGATGAATATGAAACAT
Found at i:26830 original size:3 final size:3
Alignment explanation
Indices: 26824--26902 Score: 115
Period size: 3 Copynumber: 26.0 Consensus size: 3
26814 ATTTATTATT
*
26824 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
26872 TAT TAAA TAA TAA TAA -AA TTAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA -TAA TAA TAA TAA
26903 ATAAAAAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
2 2 0.03
3 63 0.91
4 4 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:27444 original size:139 final size:139
Alignment explanation
Indices: 27123--27464 Score: 429
Period size: 139 Copynumber: 2.5 Consensus size: 139
27113 CAAAAAGTTA
*
27123 AACAAATTCTTCTCATTATGAACTTCTTCTTCTTTTTCAGATGAGTTCTTCTCATTATGAAC-TC
1 AACAAATTCTTCTCATTATGAACTTCTTCTTCATTTTCAGATGAGTTCTTCTCATTATGAACTTC
* * * * * * * *
27187 CTTCTGGAAATGCTGATCTTCAAAAGAGTGATTTGTTGATTCAACTCCCTATGTGATGAATTAAG
66 CTTCTGAAAATACTGATCCTCAAAAGAGTGATTTGTTCATTCAACTCCATAGGAGATGAATCAAG
** *
27252 GTAATGTTG
131 ACAAGGTTG
* * *
27261 AACAAATTCTTCTTATTATGAACTTCTTCTTCATCTTCATATGAGTTCTTCTCATTATGAACTTC
1 AACAAATTCTTCTCATTATGAACTTCTTCTTCATTTTCAGATGAGTTCTTCTCATTATGAACTTC
* * * *
27326 C-TCTGAAAATATTGATCCTCAAATGAGGTTATTCT-TTCATTCAATTCCATAGGAGATGAATCA
66 CTTCTGAAAATACTGATCCTCAAAAGA-GTGATT-TGTTCATTCAACTCCATAGGAGATGAATCA
*
27389 ATACAAGGTTG
129 AGACAAGGTTG
* * *
27400 AACAAATTCTTCTCATTATGAACTTCTCCTTCCTTTTCAGATGAGTTTTTCTCATTAATGAACTT
1 AACAAATTCTTCTCATTATGAACTTCTTCTTCATTTTCAGATGAGTTCTTCTCATT-ATGAACTT
27465 TACCTGGAAA
Statistics
Matches: 174, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
138 78 0.45
139 87 0.50
140 9 0.05
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (139 bp):
AACAAATTCTTCTCATTATGAACTTCTTCTTCATTTTCAGATGAGTTCTTCTCATTATGAACTTC
CTTCTGAAAATACTGATCCTCAAAAGAGTGATTTGTTCATTCAACTCCATAGGAGATGAATCAAG
ACAAGGTTG
Found at i:27738 original size:112 final size:113
Alignment explanation
Indices: 27579--27788 Score: 316
Period size: 112 Copynumber: 1.9 Consensus size: 113
27569 CTCTGGAAAC
*** ** * * *
27579 GCTGATCCATCGGGTGATGAATTTGAGCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTT-TT
1 GCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT
27643 CTTTCC-TCTTCAAATGAGTTCTTCTCATTATGAGCTCGACCTGACAAT
66 C-TTCCTTCTTCAAATGAGTTCTTCTCATTATGAGCTCGACCTGACAAT
27691 GCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT
1 GCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT
*
27756 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
66 CTTCCTTCTTCAAATGAGTTCTTCTCATTATGA
27789 ACTTTCTCCG
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
112 58 0.67
113 29 0.33
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
GCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT
CTTCCTTCTTCAAATGAGTTCTTCTCATTATGAGCTCGACCTGACAAT
Found at i:27857 original size:124 final size:124
Alignment explanation
Indices: 27718--28171 Score: 737
Period size: 124 Copynumber: 3.7 Consensus size: 124
27708 TGAATTCAAA
*
27718 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
27783 TTATGAACTTTCTCCGGAAAAGTTAATGCTGATCCATCTCCTTTTGTGATAGAGTCATG
66 TTATGAACTTTCTCTGGAAAAGTTAATGCTGATCCATCTCCTTTTGTGATAGAGTCATG
* *
27842 CAAAAGGTTGAACAAACTCTTCTCATTATGAAATTCTTTTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
27907 TTATGAACTTCCTTTGGAAAAGTTAATGCTGATCCATCTCCTTTTGTGATAGAGTCATG
66 TTATGAACTTTCTCTGGAAAAGTTAATGCTGATCCATCTCCTTTTGTGATAGAGTCATG
** *
27966 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * ** *
28031 TTATGAACTTTCTCTGGAAAAGTTGATGATGATATATCTCCTTCTGTGATAGAGTCATG
66 TTATGAACTTTCTCTGGAAAAGTTAATGCTGATCCATCTCCTTTTGTGATAGAGTCATG
* * * *
28090 CAAAAGGTTGAACAAGCTATTCTCATTATTAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
28155 TTATGAACTCTCTCTGG
66 TTATGAACTTTCTCTGG
28172 CATGTTGATC
Statistics
Matches: 306, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
124 306 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (124 bp):
CAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGTTAATGCTGATCCATCTCCTTTTGTGATAGAGTCATG
Found at i:29701 original size:9 final size:9
Alignment explanation
Indices: 29689--29728 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
29679 TCATTTTTTA
29689 TTTTTTCTC
1 TTTTTTCTC
*
29698 TTTTTTTTC
1 TTTTTTCTC
29707 TTTTTT-TC
1 TTTTTTCTC
29715 -TTTTTCTC
1 TTTTTTCTC
29723 TTTTTT
1 TTTTTT
29729 TTCTATTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 5 0.18
8 4 0.14
9 19 0.68
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:29704 original size:17 final size:17
Alignment explanation
Indices: 29682--29746 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
29672 TTGACCCTCA
29682 TTTTTTATTTTTTCTCT
1 TTTTTTATTTTTTCTCT
*
29699 TTTTTT-TCTTTTTTTCT
1 TTTTTTAT-TTTTTCTCT
* * *
29716 TTTTCTCTTTTTTTTC-
1 TTTTTTATTTTTTCTCT
* *
29732 TATTTCATTTTTTCT
1 TTTTTTATTTTTTCT
29747 TCAAGCATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
16 11 0.28
17 27 0.69
18 1 0.03
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTATTTTTTCTCT
Found at i:29710 original size:25 final size:25
Alignment explanation
Indices: 29682--29746 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
29672 TTGACCCTCA
29682 TTTTTTATTTTTTCTCTTTTTTTTC
1 TTTTTTATTTTTTCTCTTTTTTTTC
29707 TTTTTT-TCTTTTTCTCTTTTTTTTC
1 TTTTTTAT-TTTTTCTCTTTTTTTTC
* *
29732 TATTTCATTTTTTCT
1 TTTTTTATTTTTTCT
29747 TCAAGCATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 1 0.03
25 34 0.94
26 1 0.03
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTTTATTTTTTCTCTTTTTTTTC
Found at i:37073 original size:15 final size:15
Alignment explanation
Indices: 37055--37088 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
37045 AATGCAATGA
37055 AAAATGAATGTATGC
1 AAAATGAATGTATGC
*
37070 AAAATGCATGTATGC
1 AAAATGAATGTATGC
37085 AAAA
1 AAAA
37089 GGTATTGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.24
Consensus pattern (15 bp):
AAAATGAATGTATGC
Found at i:41323 original size:22 final size:22
Alignment explanation
Indices: 41272--41329 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
41262 AAATAATAAT
* *
41272 AATAATT-AAATATAAACATAT
1 AATAATTAAAATATAAACAAAC
*
41293 AA-AATTTAAAATATAAATAAAC
1 AATAA-TTAAAATATAAACAAAC
41315 AATAATTAAAATATA
1 AATAATTAAAATATA
41330 CATTAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.06
21 4 0.13
22 23 0.74
23 2 0.06
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAATTAAAATATAAACAAAC
Found at i:42624 original size:3 final size:3
Alignment explanation
Indices: 42611--42677 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
42601 ATTTATTATT
* * * *
42611 TAA TAA AAA TAA TAA AAA TAA TAT TAA TAA TAA TAT TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
42657 TAA -AA TTAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA
42678 AAAAAGAGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 47 0.89
4 4 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:42652 original size:28 final size:28
Alignment explanation
Indices: 42611--42682 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
42601 ATTTATTATT
* *
42611 TAATAAAAAT-AATAAAAATAATATTAA
1 TAATAATAATAAATAAAAATAAAATTAA
* *
42638 TAATAATATTAAATAATAATAAAATTAA
1 TAATAATAATAAATAAAAATAAAATTAA
42666 TAATAATAATAAA-AAAA
1 TAATAATAATAAATAAAA
42683 GAGTATCTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 11 0.29
28 27 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (28 bp):
TAATAATAATAAATAAAAATAAAATTAA
Found at i:43739 original size:15 final size:16
Alignment explanation
Indices: 43712--43743 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
43702 GTAATTTAGG
43712 ATATTTTTATTATTTT
1 ATATTTTTATTATTTT
43728 ATATTTTT-TTATTTT
1 ATATTTTTATTATTTT
43743 A
1 A
43744 ATTAGTGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
ATATTTTTATTATTTT
Found at i:46127 original size:16 final size:16
Alignment explanation
Indices: 46106--46161 Score: 112
Period size: 16 Copynumber: 3.5 Consensus size: 16
46096 CGCAAATGCA
46106 CTATGACTTAAAGGTT
1 CTATGACTTAAAGGTT
46122 CTATGACTTAAAGGTT
1 CTATGACTTAAAGGTT
46138 CTATGACTTAAAGGTT
1 CTATGACTTAAAGGTT
46154 CTATGACT
1 CTATGACT
46162 CTACGGACTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (16 bp):
CTATGACTTAAAGGTT
Found at i:46295 original size:19 final size:19
Alignment explanation
Indices: 46271--46307 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
46261 ATAAACTCTG
*
46271 GTCAAAGCCAATGGGTCAT
1 GTCAAAGCCAACGGGTCAT
*
46290 GTCAAAGTCAACGGGTCA
1 GTCAAAGCCAACGGGTCA
46308 GTTGGGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (19 bp):
GTCAAAGCCAACGGGTCAT
Found at i:49503 original size:53 final size:53
Alignment explanation
Indices: 49346--49506 Score: 270
Period size: 53 Copynumber: 3.0 Consensus size: 53
49336 GTATTATAGA
49346 CACTATGTGTGCATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTC-G
1 CACTATGTGTGCATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCAG
* * *
49398 ACAATATGTGTGCATCCCTGGAATTCATAATGAGTTTGTGAATTATCATTTCAG
1 -CACTATGTGTGCATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCAG
*
49452 CACTATGTGTGCATCCATGGAATTCATAATTAGTTTGTGAATTACCATTTCAG
1 CACTATGTGTGCATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCAG
49505 CA
1 CA
49507 ATTAGGTGCA
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 99 0.99
54 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (53 bp):
CACTATGTGTGCATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCAG
Found at i:52434 original size:25 final size:25
Alignment explanation
Indices: 52400--52457 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
52390 GAATCTTGGA
52400 TGGATTTATGTCATGTTTTCCATGC
1 TGGATTTATGTCATGTTTTCCATGC
52425 TGGATTTATGTCATGTTTTCCATGC
1 TGGATTTATGTCATGTTTTCCATGC
*
52450 TAGATTTA
1 TGGATTTA
52458 GTTCAACAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (25 bp):
TGGATTTATGTCATGTTTTCCATGC
Found at i:53757 original size:10 final size:10
Alignment explanation
Indices: 53742--53775 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
53732 TATTGAGCAA
53742 ATGCAAAATT
1 ATGCAAAATT
53752 ATGCAAAATT
1 ATGCAAAATT
*
53762 AAGCAAAATT
1 ATGCAAAATT
53772 ATGC
1 ATGC
53776 TAAGTTTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (10 bp):
ATGCAAAATT
Found at i:56859 original size:26 final size:26
Alignment explanation
Indices: 56805--56855 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
56795 AAATAAATAA
* *
56805 AAAGTAAATGGTATAAATTAAAATAT
1 AAAGTAAATGGTATAAAATAAAAGAT
56831 AAAGTAAA-GG-ACTAAAATAAAAGAT
1 AAAGTAAATGGTA-TAAAATAAAAGAT
56856 TAAAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 1 0.05
25 13 0.59
26 8 0.36
ACGTcount: A:0.61, C:0.02, G:0.14, T:0.24
Consensus pattern (26 bp):
AAAGTAAATGGTATAAAATAAAAGAT
Found at i:58210 original size:136 final size:137
Alignment explanation
Indices: 58063--58327 Score: 415
Period size: 136 Copynumber: 1.9 Consensus size: 137
58053 TATCAAAGAA
* * *
58063 TGACACGACTCCTTCGTGATGAGGAGTTTTGATTGGTAGATGACATTGTTCCTTTGTGATGAGGA
1 TGACACGACTCCTTCGTGATGAGGAGTTCTGATTAGTAGATGACATTGTTCCTTCGTGATGAGGA
*
58128 CATCTGACCATCTTT-AAGATATCTGAGATAACACGGTTCCTTCGTGATGAGGACATCTAGTTAT
66 CATCTGACCATCTTTAAACATATCTGAGATAACACGGTTCCTTCGTGATGAGGACATCTAGTTAT
58192 ATAAGGC
131 ATAAGGC
* * *
58199 TGACATGACTCCTTCGTGATGAGGAGTTCTGATTATTAGATGACATTGTTCGTTCGTGATGAGGA
1 TGACACGACTCCTTCGTGATGAGGAGTTCTGATTAGTAGATGACATTGTTCCTTCGTGATGAGGA
* * ** *
58264 CATCTGGCCATCTTTAAACATATTTGAGATAACATTGTTCCTTCGTGATGAGGACATCTGGTTA
66 CATCTGACCATCTTTAAACATATCTGAGATAACACGGTTCCTTCGTGATGAGGACATCTAGTTA
58328 CCTAAGACAT
Statistics
Matches: 116, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
136 73 0.63
137 43 0.37
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (137 bp):
TGACACGACTCCTTCGTGATGAGGAGTTCTGATTAGTAGATGACATTGTTCCTTCGTGATGAGGA
CATCTGACCATCTTTAAACATATCTGAGATAACACGGTTCCTTCGTGATGAGGACATCTAGTTAT
ATAAGGC
Found at i:58363 original size:53 final size:53
Alignment explanation
Indices: 58236--58386 Score: 178
Period size: 53 Copynumber: 2.8 Consensus size: 53
58226 TCTGATTATT
* * * ** *
58236 AGATGACATTGTTCGTTCGTGATGAGGACATCTGGCCATCTTTAA-ACATATTTG
1 AGATAACATAGTTCCTTCGTGATGAGGACATCTGGTTA-C-CTAAGACATATTTG
* *
58290 AGATAACATTGTTCCTTCGTGATGAGGACATCTGGTTACCTAAGACATTTTTG
1 AGATAACATAGTTCCTTCGTGATGAGGACATCTGGTTACCTAAGACATATTTG
* **
58343 AGATAACATAGTTTCTTCGTGATGAGGACGCCTGGTTACCTAAG
1 AGATAACATAGTTCCTTCGTGATGAGGACATCTGGTTACCTAAG
58387 GATGACACGA
Statistics
Matches: 86, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
52 3 0.03
53 49 0.57
54 34 0.40
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (53 bp):
AGATAACATAGTTCCTTCGTGATGAGGACATCTGGTTACCTAAGACATATTTG
Found at i:58431 original size:190 final size:190
Alignment explanation
Indices: 58151--58523 Score: 557
Period size: 190 Copynumber: 2.0 Consensus size: 190
58141 TTAAGATATC
* * * * *
58151 TGAGATAACACGGTTCCTTCGTGATGAGGACATCTAGTTATATAAGGCTGACATGACTCCTTCGT
1 TGAGATAACACAGTTCCTTCGTGATGAGGACACCTAGTTACATAAGGATGACACGACTCCTTCGT
* * *
58216 GATGAGGAGTTCTGATTATTAGATGACATTGTTCGTTCGTGATGAGGACATCTGGCCATCTTTAA
66 GATGAAGAGTTCTGATTAGTAGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAA
**
58281 ACATATTTGAGATAACATTGTTCCTTCGTGATGAGGACATCTGGTTACCTAAGACATTTT
131 ACATATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGTTACCTAAGACATTTT
* * * * *
58341 TGAGATAACATAGTTTCTTCGTGATGAGGACGCCTGGTTACCTAAGGATGACACGACTCCTTCGT
1 TGAGATAACACAGTTCCTTCGTGATGAGGACACCTAGTTACATAAGGATGACACGACTCCTTCGT
* *
58406 GATGAAGAGTTCTGATTGGTAGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTGA
66 GATGAAGAGTTCTGATTAGTAGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAA
* * * *
58471 AGATATTTGAGATAACACGGTTCCTTCGTGATGAGGACGTCTTGTTATCTAAG
131 ACATATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGTTACCTAAG
58524 GATTTTGTTT
Statistics
Matches: 162, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
190 162 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (190 bp):
TGAGATAACACAGTTCCTTCGTGATGAGGACACCTAGTTACATAAGGATGACACGACTCCTTCGT
GATGAAGAGTTCTGATTAGTAGATGACATTGTTCCTTCGTGATGAGGACATCTGGCCATCTTTAA
ACATATTTGAGATAACACGGTTCCTTCGTGATGAGGACATCTGGTTACCTAAGACATTTT
Done.