Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004734.1 Hibiscus syriacus cultivar Beakdansim tig00010689_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: 57928
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:314 original size:21 final size:21
Alignment explanation
Indices: 290--333 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
280 GAGCCGGAGG
* *
290 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
311 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
332 AG
1 AG
334 CTCCCGAGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:9776 original size:21 final size:21
Alignment explanation
Indices: 9746--9834 Score: 151
Period size: 21 Copynumber: 4.2 Consensus size: 21
9736 AATTTGTTGT
*
9746 ATTAATTTATTCTTGAATTAA
1 ATTAACTTATTCTTGAATTAA
9767 ATTAACTTATTCTTGAATTAA
1 ATTAACTTATTCTTGAATTAA
9788 ATTAACTTATTCTTGAATTAA
1 ATTAACTTATTCTTGAATTAA
* *
9809 ATTAACTTACTCTTAAATTAA
1 ATTAACTTATTCTTGAATTAA
9830 ATTAA
1 ATTAA
9835 TATATCTATA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.47
Consensus pattern (21 bp):
ATTAACTTATTCTTGAATTAA
Found at i:12651 original size:21 final size:21
Alignment explanation
Indices: 12625--12689 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
12615 TAGTTTGTTG
*
12625 TATTAATTTATTCTTGAATTA
1 TATTAATTTATTCTTAAATTA
12646 TATTAATTTATTCTTAAATTA
1 TATTAATTTATTCTTAAATTA
*
12667 TATCAATTTATTCTTAAATTA
1 TATTAATTTATTCTTAAATTA
12688 TA
1 TA
12690 GTGTTGTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTAATTTATTCTTAAATTA
Found at i:14485 original size:264 final size:264
Alignment explanation
Indices: 14015--14544 Score: 1060
Period size: 264 Copynumber: 2.0 Consensus size: 264
14005 TTTTTTGCTC
14015 CATAAATATCTTATAATTAGCTTGCCTTCATAGCTTAGTTGTTTAATCCGAAGTTAATATTTTTA
1 CATAAATATCTTATAATTAGCTTGCCTTCATAGCTTAGTTGTTTAATCCGAAGTTAATATTTTTA
14080 ACATATTCATAGTATGTATCAGTTCAGTCATACTTTCTGAGGAAGCTTTAGTTTAATGTCATACT
66 ACATATTCATAGTATGTATCAGTTCAGTCATACTTTCTGAGGAAGCTTTAGTTTAATGTCATACT
14145 TCTTGATCTATAGTCAAAATTCATCTTTATTAACAAATAAATATTGAGAGTTGTGACTGCTTAGC
131 TCTTGATCTATAGTCAAAATTCATCTTTATTAACAAATAAATATTGAGAGTTGTGACTGCTTAGC
14210 ATATTTGTTGTGACTTCTTGACCAAAGCCCTGATTCTTTATATGATCTTTTAGGTAGATCTAACT
196 ATATTTGTTGTGACTTCTTGACCAAAGCCCTGATTCTTTATATGATCTTTTAGGTAGATCTAACT
14275 TGAT
261 TGAT
14279 CATAAATATCTTATAATTAGCTTGCCTTCATAGCTTAGTTGTTTAATCCGAAGTTAATATTTTTA
1 CATAAATATCTTATAATTAGCTTGCCTTCATAGCTTAGTTGTTTAATCCGAAGTTAATATTTTTA
14344 ACATATTCATAGTATGTATCAGTTCAGTCATACTTTCTGAGGAAGCTTTAGTTTAATGTCATACT
66 ACATATTCATAGTATGTATCAGTTCAGTCATACTTTCTGAGGAAGCTTTAGTTTAATGTCATACT
14409 TCTTGATCTATAGTCAAAATTCATCTTTATTAACAAATAAATATTGAGAGTTGTGACTGCTTAGC
131 TCTTGATCTATAGTCAAAATTCATCTTTATTAACAAATAAATATTGAGAGTTGTGACTGCTTAGC
14474 ATATTTGTTGTGACTTCTTGACCAAAGCCCTGATTCTTTATATGATCTTTTAGGTAGATCTAACT
196 ATATTTGTTGTGACTTCTTGACCAAAGCCCTGATTCTTTATATGATCTTTTAGGTAGATCTAACT
14539 TGAT
261 TGAT
14543 CA
1 CA
14545 CCTCTGTCAG
Statistics
Matches: 266, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
264 266 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.42
Consensus pattern (264 bp):
CATAAATATCTTATAATTAGCTTGCCTTCATAGCTTAGTTGTTTAATCCGAAGTTAATATTTTTA
ACATATTCATAGTATGTATCAGTTCAGTCATACTTTCTGAGGAAGCTTTAGTTTAATGTCATACT
TCTTGATCTATAGTCAAAATTCATCTTTATTAACAAATAAATATTGAGAGTTGTGACTGCTTAGC
ATATTTGTTGTGACTTCTTGACCAAAGCCCTGATTCTTTATATGATCTTTTAGGTAGATCTAACT
TGAT
Found at i:15933 original size:51 final size:51
Alignment explanation
Indices: 15869--15998 Score: 188
Period size: 51 Copynumber: 2.5 Consensus size: 51
15859 CCTTTGCAGA
* * * *
15869 AAGGCGCGACCCATGCACCGTGCCTTACGTTGATGTGGCGCCACGTGGGGT
1 AAGGCGCGGCCCATGCACCGCGCCTTACGCTGATGTGGCGCCACATGGGGT
* *
15920 AAGGCGCGGCCCATGCACCGCGCCTTACGCTGATGTGGCGCCATATGGGTT
1 AAGGCGCGGCCCATGCACCGCGCCTTACGCTGATGTGGCGCCACATGGGGT
**
15971 AAGGCATGGCCCATGCACCGCGCCTTAC
1 AAGGCGCGGCCCATGCACCGCGCCTTAC
15999 AGCAGCTGGA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 71 1.00
ACGTcount: A:0.17, C:0.32, G:0.32, T:0.18
Consensus pattern (51 bp):
AAGGCGCGGCCCATGCACCGCGCCTTACGCTGATGTGGCGCCACATGGGGT
Found at i:16143 original size:23 final size:23
Alignment explanation
Indices: 16114--16191 Score: 129
Period size: 23 Copynumber: 3.4 Consensus size: 23
16104 TAATCCGGAC
16114 CGTTCACACTCCCCTTATCCGAT
1 CGTTCACACTCCCCTTATCCGAT
* *
16137 CCTTCACACTCCCCTTATCTGAT
1 CGTTCACACTCCCCTTATCCGAT
*
16160 CGTTCACACTCACCTTATCCGAT
1 CGTTCACACTCCCCTTATCCGAT
16183 CGTTCACAC
1 CGTTCACAC
16192 CCCATCCCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.19, C:0.42, G:0.08, T:0.31
Consensus pattern (23 bp):
CGTTCACACTCCCCTTATCCGAT
Found at i:20407 original size:43 final size:46
Alignment explanation
Indices: 20285--20410 Score: 147
Period size: 47 Copynumber: 2.8 Consensus size: 46
20275 TATAAAATCT
20285 CTTACCATTT-A-TCCTATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCC-ATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
20330 TTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATAA-A
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAA-AATA
* *
20377 CTTGCCA-TT-ATT-CATAAGCTCATAAGCTTATTTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTT
20411 CATACTTACC
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
43 21 0.29
44 3 0.04
45 9 0.12
46 2 0.03
47 32 0.44
48 5 0.07
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:23403 original size:30 final size:30
Alignment explanation
Indices: 23367--23430 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
23357 ATCAAAGATA
23367 AGAGGATTGTTGGGTGATGTTTACGGGTTG
1 AGAGGATTGTTGGGTGATGTTTACGGGTTG
* *
23397 AGAGGATTGTTGTGTGATGTTTATGGGTTG
1 AGAGGATTGTTGGGTGATGTTTACGGGTTG
23427 AGAG
1 AGAG
23431 AGTATCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.02, G:0.42, T:0.38
Consensus pattern (30 bp):
AGAGGATTGTTGGGTGATGTTTACGGGTTG
Found at i:24250 original size:34 final size:32
Alignment explanation
Indices: 24170--24258 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
24160 TTAGTATTTT
* * *
24170 TTTAAATAGTTATTATTTTTTATATTAATATA
1 TTTATATAATTATTATTTTTTATATAAATATA
* *
24202 TTTATGTAAATATTATTTTATTAT-TAAAATAATA
1 TTTATATAATTATTATTTT-TTATAT-AAAT-ATA
24236 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTT-TTTA
24259 GAATTATTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
32 16 0.35
33 7 0.15
34 22 0.48
35 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (32 bp):
TTTATATAATTATTATTTTTTATATAAATATA
Found at i:26009 original size:21 final size:21
Alignment explanation
Indices: 25979--26026 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
25969 GCAGGGGTAC
* *
25979 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
26000 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
26021 ATGCCA
1 ATGCCA
26027 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:26056 original size:21 final size:21
Alignment explanation
Indices: 26030--26123 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
26020 TATGCCATCT
* *
26030 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
26051 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
26072 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
26093 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
26114 CCGCAGGGTT
1 CCGCAGGGTT
26124 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:26705 original size:33 final size:34
Alignment explanation
Indices: 26646--26742 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
26636 AAATGTTTTT
*
26646 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
26680 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
26713 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
26743 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:26749 original size:34 final size:33
Alignment explanation
Indices: 26644--26749 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
26634 ATAAATGTTT
*
26644 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
26678 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
26710 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
26745 TTAAA
1 TTAAA
26750 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:27355 original size:126 final size:126
Alignment explanation
Indices: 27130--27356 Score: 454
Period size: 126 Copynumber: 1.8 Consensus size: 126
27120 TTTAAGTTAT
27130 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
27195 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTATTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTATTGATATATCTAGTG
27256 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
27321 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
27357 CCGATTATAG
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 101 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTATTGATATATCTAGTG
Found at i:27437 original size:8 final size:8
Alignment explanation
Indices: 27424--27464 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
27414 TCACAATCTT
27424 TCAAATTC
1 TCAAATTC
27432 TCAAATTC
1 TCAAATTC
* *
27440 CCAAACTC
1 TCAAATTC
27448 T-AAATTC
1 TCAAATTC
27455 TCAAATTC
1 TCAAATTC
27463 TC
1 TC
27465 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:29133 original size:23 final size:23
Alignment explanation
Indices: 29095--29152 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
29085 TAGTTATAAT
29095 TTTTACAT--TATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
29116 TTTTACATAATATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
29139 TTTTACATAATATA
1 TTTTACATAATATA
29153 TTATTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (23 bp):
TTTTACATAATATAATCGAAACA
Found at i:31129 original size:22 final size:22
Alignment explanation
Indices: 31104--31172 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
31094 CCAAATATTA
31104 CATTACCAAAATCCATTTAACC
1 CATTACCAAAATCCATTTAACC
** *
31126 CATTACCCCAATACAATTT-ACC
1 CATTACCAAAAT-CCATTTAACC
* *
31148 CATTA-CATAAT-CAATTAACC
1 CATTACCAAAATCCATTTAACC
31168 CATTA
1 CATTA
31173 ACATAACATA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
19 3 0.08
20 8 0.21
21 4 0.11
22 18 0.47
23 5 0.13
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.29
Consensus pattern (22 bp):
CATTACCAAAATCCATTTAACC
Found at i:32402 original size:29 final size:29
Alignment explanation
Indices: 32370--32458 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
32360 TATTTTTAAT
* *
32370 TATTTACATTTCAACCCTTTAATTTTTTG
1 TATTTACATTTCAACCCTTTAATTTCTAG
* *
32399 TATTTTTA-ATTTCAGCCCTTAAATTTCTAG
1 TA--TTTACATTTCAACCCTTTAATTTCTAG
* *
32429 CATTTACATTTTAATCCC-TTAATTTCTAG
1 TATTTACATTTCAA-CCCTTTAATTTCTAG
32458 T
1 T
32459 TTTTCTTTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
28 4 0.09
29 17 0.36
30 22 0.47
31 4 0.09
ACGTcount: A:0.26, C:0.18, G:0.04, T:0.52
Consensus pattern (29 bp):
TATTTACATTTCAACCCTTTAATTTCTAG
Found at i:32882 original size:138 final size:136
Alignment explanation
Indices: 32737--33146 Score: 445
Period size: 138 Copynumber: 2.9 Consensus size: 136
32727 TCTTTTTAAT
32737 TTAGTCCTTTAATTTAGGAGAATTTTTAATTTGGTTCTCGCTTTTGCTCGAGGTTTCATTTTAAT
1 TTAGTCCTTTAATTTAGG-GAATTTTTAATTTGGTTCTCGCTTTTGCTCGAGGTTTCATTTTAAT
* *
32802 TATTTGAATCAATAATTGATTAAAAATGAATAGGATAATATTTAGAGCCTCCATTTTAGGTTTAA
65 TATTTGAATCAATAATTGATTAAAATTGAATAGGATAATA-TTAGAACCTCCATTTTAGGTTTAA
*
32867 TTTTA-AA
129 TTTCATAA
* *
32874 CTTAGTCCTTTAA-TTAGGTGGAATTTTTAATTTGG-TCATCGCTTTTGCTTGAGGTTTCTTTTT
1 -TTAGTCCTTTAATTTA-G-GGAATTTTTAATTTGGTTC-TCGCTTTTGCTCGAGGTTTCATTTT
* * * * * * *
32937 AATTATTCGATTAAATAATTTATTAAAATTGACTATGTTAATAATAATTAGAACCTCCACTTTAG
62 AATTATTTGAATCAATAATTGATTAAAATTGAATA-G--GATAAT-ATTAGAACCTCCATTTTAG
33002 GTTTAATTTCATAA
123 GTTTAATTTCATAA
* * *
33016 TTAGTCCTTTAGTTTAGGGAATTCTTAATTT-GTTCCTCGCTTTTGCTCAAGG-TTCTATTTTAA
1 TTAGTCCTTTAATTTAGGGAATTTTTAATTTGGTT-CTCGCTTTTGCTCGAGGTTTC-ATTTTAA
* * * * * **
33079 TTA-TTCAATTCAATAATTGGTTAAGAATTGAATTGGTTAATATTAGATCCTATATTTTTAGGTT
64 TTATTTGAA-TCAATAATTGATTAA-AATTGAATAGGATAATATTAGAACCTCCA-TTTTAGGTT
33143 TAAT
126 TAAT
33147 CCCCTAATCT
Statistics
Matches: 226, Mismatches: 31, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
137 15 0.07
138 96 0.42
139 8 0.04
140 50 0.22
141 51 0.23
142 6 0.03
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (136 bp):
TTAGTCCTTTAATTTAGGGAATTTTTAATTTGGTTCTCGCTTTTGCTCGAGGTTTCATTTTAATT
ATTTGAATCAATAATTGATTAAAATTGAATAGGATAATATTAGAACCTCCATTTTAGGTTTAATT
TCATAA
Found at i:37828 original size:29 final size:28
Alignment explanation
Indices: 37791--37845 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
37781 TTTTTGTATT
37791 TTTAATTTT-AGCCCTTAAATTTCCAGCA
1 TTTAATTTTAAGCCCTT-AATTTCCAGCA
*
37819 TTTACATTTTAATCCCTTAATTTCCAG
1 TTTA-ATTTTAAGCCCTTAATTTCCAG
37846 TTTTTCTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 4 0.17
29 14 0.58
30 6 0.25
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.45
Consensus pattern (28 bp):
TTTAATTTTAAGCCCTTAATTTCCAGCA
Found at i:38290 original size:137 final size:136
Alignment explanation
Indices: 38130--38537 Score: 434
Period size: 137 Copynumber: 2.9 Consensus size: 136
38120 CTTTTTAATT
* *
38130 TAGTCCTTTAATTTTGGAGAATTTTTAATTTGGTTCTCGCTTTTGCTCGAGGTTTCATTTTAATT
1 TAGTCCTTTAACTTAGG-GAATTTTTAATTTGGTTCTCGCTTTTGCTCGAGGTTTCATTTTAATT
*
38195 ATTCGAATCAATAATTGATTAAAATTGAATAGGATAATATTTAGAGCCTCCATTTTAGGTTTAAT
65 ATTCGAATCAATAATTGATTAAAATTGAATAGGATAATA-TTAGAACCTCCATTTTAGGTTTAAT
*
38260 TTTA-AAC
129 TTCATAAC
* * *
38267 TTAG-CCTTT-ACTTAGGTGGAATTTTTAATATGG-TCATCGCTTTTGCTTGAGGTTTCGTTTTA
1 -TAGTCCTTTAACTTA-G-GGAATTTTTAATTTGGTTC-TCGCTTTTGCTCGAGGTTTCATTTTA
* * * * *
38329 ATTATTCGATTAAATAATTTATTAAAATTGACTAGGTTAATAATAATTAGAACCTCCACTTTAGG
62 ATTATTCGAATCAATAATTGATTAAAATTGAATAGG---ATAAT-ATTAGAACCTCCATTTTAGG
* *
38394 CTCAATTTCATAAC
123 TTTAATTTCATAAC
* * *
38408 TAGTCCTTTAATTTAGGGAATTCTTAATTT-GTTCCTCGCTTTTGCTCAAGG-TTCTATTTTAAT
1 TAGTCCTTTAACTTAGGGAATTTTTAATTTGGTT-CTCGCTTTTGCTCGAGGTTTC-ATTTTAAT
* * * * *
38471 TATTC-AATTCAATAATTGGTTAAGAATTGAATTGGTTAATATTAGATCCTACATTTTTAGGTTT
64 TATTCGAA-TCAATAATTGATTAA-AATTGAATAGGATAATATTAGAACCTCCA-TTTTAGGTTT
38535 AAT
126 AAT
38538 CCCTAAGCTC
Statistics
Matches: 222, Mismatches: 32, Indels: 32
0.78 0.11 0.11
Matches are distributed among these distances:
136 5 0.02
137 87 0.39
138 18 0.08
139 5 0.02
140 83 0.37
141 20 0.09
142 4 0.02
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (136 bp):
TAGTCCTTTAACTTAGGGAATTTTTAATTTGGTTCTCGCTTTTGCTCGAGGTTTCATTTTAATTA
TTCGAATCAATAATTGATTAAAATTGAATAGGATAATATTAGAACCTCCATTTTAGGTTTAATTT
CATAAC
Found at i:38450 original size:140 final size:140
Alignment explanation
Indices: 38129--38511 Score: 449
Period size: 140 Copynumber: 2.7 Consensus size: 140
38119 TCTTTTTAAT
*
38129 TTAGTCCTTTAATTTTGGAGAATTTTTAATTTGGTT-CTCGCTTTTGCTCGAGGTTTCATTTTAA
1 TTAGTCCTTTAATTTAGG-GAATTTTTAATTT-GTTCCTCGCTTTTGCTCGAGGTTTCATTTTAA
* * * * *
38193 TTATTCGAATCAATAATTGATTAAAATTGAATAGG---ATAATATTTAGAGCCTCCATTTTAGGT
64 TTATTCGATTCAATAATTGATTAAAATTGAATAGGTTAATAATAATTAGAACCTCCACTTTAGGC
* *
38255 TTAATTTTAAAC
129 TCAATTTCAAAC
* * * * * *
38267 TTAG-CCTTT-ACTTAGGTGGAATTTTTAATATGGTCATCGCTTTTGCTTGAGGTTTCGTTTTAA
1 TTAGTCCTTTAATTTA-G-GGAATTTTTAATTTGTTCCTCGCTTTTGCTCGAGGTTTCATTTTAA
* * *
38330 TTATTCGATTAAATAATTTATTAAAATTGACTAGGTTAATAATAATTAGAACCTCCACTTTAGGC
64 TTATTCGATTCAATAATTGATTAAAATTGAATAGGTTAATAATAATTAGAACCTCCACTTTAGGC
38395 TCAATTTCATAAC
129 TCAATTTCA-AAC
* *
38408 -TAGTCCTTTAATTTAGGGAATTCTTAATTTGTTCCTCGCTTTTGCTCAAGG-TTCTATTTTAAT
1 TTAGTCCTTTAATTTAGGGAATTTTTAATTTGTTCCTCGCTTTTGCTCGAGGTTTC-ATTTTAAT
* * *
38471 TATTCAATTCAATAATTGGTTAAGAATTGAATTGGTTAATA
65 TATTCGATTCAATAATTGATTAA-AATTGAATAGGTTAATA
38512 TTAGATCCTA
Statistics
Matches: 203, Mismatches: 31, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
136 5 0.02
137 74 0.36
138 5 0.02
139 3 0.01
140 88 0.43
141 24 0.12
142 4 0.02
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (140 bp):
TTAGTCCTTTAATTTAGGGAATTTTTAATTTGTTCCTCGCTTTTGCTCGAGGTTTCATTTTAATT
ATTCGATTCAATAATTGATTAAAATTGAATAGGTTAATAATAATTAGAACCTCCACTTTAGGCTC
AATTTCAAAC
Found at i:43857 original size:21 final size:21
Alignment explanation
Indices: 43833--43885 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
43823 CCCTATCTTA
43833 TATTCTATCATTTATACATTC
1 TATTCTATCATTTATACATTC
43854 TATTCTATCATTTATACATTC
1 TATTCTATCATTTATACATTC
43875 TATTCTATCAT
1 TATTCTATCAT
43886 AAGCATGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTCTATCATTTATACATTC
Found at i:44336 original size:20 final size:20
Alignment explanation
Indices: 44300--44338 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
44290 TCATCACATA
*
44300 AGGAGCTTAAACTTAGCTGG
1 AGGAGCTTAAAATTAGCTGG
44320 AGGAGC-TAAAATGTAGCTG
1 AGGAGCTTAAAAT-TAGCTG
44339 AACTTAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.33, C:0.13, G:0.31, T:0.23
Consensus pattern (20 bp):
AGGAGCTTAAAATTAGCTGG
Found at i:46981 original size:80 final size:81
Alignment explanation
Indices: 46879--47065 Score: 213
Period size: 81 Copynumber: 2.3 Consensus size: 81
46869 CAAATTGAAA
* * *
46879 ATGACATTGTTCCTTCACGTTGAGGACAT-GAATCATATTTC-AATGATTCATTCT-CTT-GTTT
1 ATGACATTGTTCCTTCATGTTGAGGACATCGAATCACA-TTCGAATGATT--TGCTCCTTCGTTT
46940 GAGGATGT-AAATCTTGTTG
63 GAGGATGTCAAAT-TTGTTG
* * * * *
46959 ATGACATTGTTCCTTCATGTTGAGGACTTCTAGTCACATTCGGATGATTTGCTCCTTCTTTTGAG
1 ATGACATTGTTCCTTCATGTTGAGGACATCGAATCACATTCGAATGATTTGCTCCTTCGTTTGAG
47024 GATGTCAAATTTGTTG
66 GATGTCAAATTTGTTG
* *
47040 ACGACATTGTTGCTTCATGTTGAGGA
1 ATGACATTGTTCCTTCATGTTGAGGA
47066 TGTCTAGTCG
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
79 3 0.03
80 33 0.36
81 52 0.57
82 4 0.04
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (81 bp):
ATGACATTGTTCCTTCATGTTGAGGACATCGAATCACATTCGAATGATTTGCTCCTTCGTTTGAG
GATGTCAAATTTGTTG
Found at i:46982 original size:40 final size:41
Alignment explanation
Indices: 46938--47069 Score: 112
Period size: 40 Copynumber: 3.3 Consensus size: 41
46928 ATTCTCTTGT
46938 TTGAGGATGT-AAATCTTGTTGATGACATTGTTCCTTCATG
1 TTGAGGATGTCAAATCTTGTTGATGACATTGTTCCTTCATG
* * *** * * *
46978 TTGAGGACT-TCTAGTCACATTCGGATGA-TTTGCTCCTTC-TT
1 TTGAGGA-TGTCAAATCTTGTT--GATGACATTGTTCCTTCATG
* *
47019 TTGAGGATGTCAAAT-TTGTTGACGACATTGTTGCTTCATG
1 TTGAGGATGTCAAATCTTGTTGATGACATTGTTCCTTCATG
47059 TTGAGGATGTC
1 TTGAGGATGTC
47070 TAGTCGCATT
Statistics
Matches: 67, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
38 4 0.06
39 8 0.12
40 23 0.34
41 18 0.27
42 9 0.13
43 5 0.07
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.41
Consensus pattern (41 bp):
TTGAGGATGTCAAATCTTGTTGATGACATTGTTCCTTCATG
Found at i:47046 original size:81 final size:81
Alignment explanation
Indices: 46937--47089 Score: 229
Period size: 81 Copynumber: 1.9 Consensus size: 81
46927 CATTCTCTTG
* *
46937 TTTGAGGATGTAAATCTTGTTGATGACATTGTTCCTTCATGTTGAGGACT-TCTAGTCACATTCG
1 TTTGAGGATGTAAATCTTGTTGACGACATTGTTCCTTCATGTTGAGGA-TGTCTAGTCACATTCA
47001 GATGATTTGCTCCTTCT
65 GATGATTTGCTCCTTCT
* * *
47018 TTTGAGGATGTCAAAT-TTGTTGACGACATTGTTGCTTCATGTTGAGGATGTCTAGTCGCATTTA
1 TTTGAGGATGT-AAATCTTGTTGACGACATTGTTCCTTCATGTTGAGGATGTCTAGTCACATTCA
47082 GATGATTT
65 GATGATTT
47090 TTTCCTACAT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
80 1 0.02
81 60 0.92
82 4 0.06
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (81 bp):
TTTGAGGATGTAAATCTTGTTGACGACATTGTTCCTTCATGTTGAGGATGTCTAGTCACATTCAG
ATGATTTGCTCCTTCT
Found at i:47113 original size:81 final size:82
Alignment explanation
Indices: 46948--47116 Score: 207
Period size: 81 Copynumber: 2.1 Consensus size: 82
46938 TTGAGGATGT
* *
46948 AAATCTTGTTGATGACATTGTTCCTTCATGTTGAGGACTTCTAGTCACATTCGGATGATTTGCTC
1 AAATCTTGTTGACGACATTGTTCCTTCATGTTGAGGACTTCTAGTCACATTCAGATGATTTGCTC
* * **
47013 CTTCTTTTGAGGATGTC
66 CTACATTTGAGGACATC
* * * **
47030 AAAT-TTGTTGACGACATTGTTGCTTCATGTTGAGGA-TGTCTAGTCGCATTTAGATGATTTTTT
1 AAATCTTGTTGACGACATTGTTCCTTCATGTTGAGGACT-TCTAGTCACATTCAGATGATTTGCT
*
47093 CCTACATTTGATGACATC
65 CCTACATTTGAGGACATC
47111 AAATCT
1 AAATCT
47117 GAAAATGACT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
80 1 0.01
81 67 0.92
82 5 0.07
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (82 bp):
AAATCTTGTTGACGACATTGTTCCTTCATGTTGAGGACTTCTAGTCACATTCAGATGATTTGCTC
CTACATTTGAGGACATC
Found at i:47847 original size:19 final size:20
Alignment explanation
Indices: 47823--47866 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
47813 AGGTACGACA
* *
47823 TATAAAATA-ATTTTAAAAT
1 TATAAAATATATGTAAAAAT
47842 TAT-AAATATATGTAAAAAT
1 TATAAAATATATGTAAAAAT
47861 TATAAA
1 TATAAA
47867 TAAAGTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 5 0.24
19 14 0.67
20 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TATAAAATATATGTAAAAAT
Found at i:51121 original size:130 final size:130
Alignment explanation
Indices: 50888--51192 Score: 452
Period size: 130 Copynumber: 2.4 Consensus size: 130
50878 ATAGCACTAA
* *
50888 GAGAGAAAATGATAATATCTAATTATTTCGAAACGAGAATAAATGACCTCCCATGCCTTAAAGCA
1 GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCCCATGCCTTAAAGCA
* * * *
50953 GTCATTTATTACTCGAATCGAAATGAAGAGATATCACTATTTCGTCTT-AAATTCAATATTGATT
66 GTCATTTATTACTCCAATCGAAATGAAGAAATATCACTATTTCATCTTAAAAATCAATATTGATT
* * ** *
51017 CGAGAGAAAATGATAATAACTAATTATTTCCAATTGAGAATAAATGACCTCTTATGCCTTAAAGT
1 -GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCCCATGCCTTAAAGC
*
51082 AGTCATTTATTACTCCAATCGAAATGAAGAAATATCACTATTTCATCTTAAAAATCAATATTGGT
65 AGTCATTTATTACTCCAATCGAAATGAAGAAATATCACTATTTCATCTTAAAAATCAATATTGAT
51147 T
130 T
* * *
51148 TA-AGAGAACGATAATATCTAATTATTTCCAATCGAGAATAAATGA
1 GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGA
51193 ACCCTCGTGC
Statistics
Matches: 157, Mismatches: 17, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
129 39 0.25
130 104 0.66
131 14 0.09
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (130 bp):
GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCCCATGCCTTAAAGCA
GTCATTTATTACTCCAATCGAAATGAAGAAATATCACTATTTCATCTTAAAAATCAATATTGATT
Found at i:52715 original size:17 final size:17
Alignment explanation
Indices: 52693--52726 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52683 CGAAAAAACA
*
52693 TAAAATATGACTTTTTG
1 TAAAATATAACTTTTTG
*
52710 TAAAATTTAACTTTTTG
1 TAAAATATAACTTTTTG
52727 GTTAAAGTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (17 bp):
TAAAATATAACTTTTTG
Found at i:57186 original size:18 final size:19
Alignment explanation
Indices: 57134--57199 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
57124 ACGATTCATG
* * *
57134 TCAAATTCAACAAGTCAGT
1 TCAAAGTCAACAGGTCAGA
* *
57153 TAAAAGCCAACAGGTCAGA
1 TCAAAGTCAACAGGTCAGA
* *
57172 TC-AAGTCAACGGGTCAGG
1 TCAAAGTCAACAGGTCAGA
57190 TCAAAGTCAA
1 TCAAAGTCAA
57200 TGAGTCAGAC
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
18 15 0.41
19 22 0.59
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (19 bp):
TCAAAGTCAACAGGTCAGA
Done.