Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015958.1 Corchorus capsularis cultivar CVL-1 contig15979, 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: 34909
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:2964 original size:2 final size:2
Alignment explanation
Indices: 2957--2987 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2947 TTTTCCAATA
2957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2988 CTGCATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6937 original size:22 final size:22
Alignment explanation
Indices: 6912--6958 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
6902 TTTGGTACCC
*
6912 TATCCGGTATTCAGAGTTTTGT
1 TATCCGGTATCCAGAGTTTTGT
6934 TATCCGGTATCCAGAGTTTTGT
1 TATCCGGTATCCAGAGTTTTGT
6956 TAT
1 TAT
6959 AACTAATCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.45
Consensus pattern (22 bp):
TATCCGGTATCCAGAGTTTTGT
Found at i:16955 original size:54 final size:54
Alignment explanation
Indices: 16889--18362 Score: 1788
Period size: 54 Copynumber: 26.9 Consensus size: 54
16879 CATTAAGTGA
* * * ** *
16889 TAATTAGTAATTAGTTTAATTCTGAGCAATTAAGCTAAAGCGTAAAAGAAAAAG
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
* * **
16943 TAATCAATAATTAGTTTAATTCAGAATAATTAAGCTAAAAAACATAAAG-AAGAG
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTA-AAAGAAAGAG
* * * *
16997 TAATCAGTATTTAGTTTAAATTCAGAGAAATTAAGCTAAAAAAAGTAAAGGAAGGAG
1 TAATCAGTAATTAGTTT-AATTCAGAGTAATTAAGCT--AAAAAGTAAAAGAAAGAG
* * * *
17054 TAATCAGCAAATAAGTTTAATTCAGAGTAATTAGGCTAAAAAGTAAAGGAAAGAG
1 TAATCAG-TAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
* *
17109 TAATCAGTAGATAAGTTTTATTCAGAGTAATTAAGCTAAAAAGGGTAAAAGAAAGAG
1 TAATCAGTA-ATTAGTTTAATTCAGAGTAATTAAGCTAAAAA--GTAAAAGAAAGAG
**
17166 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAACATAAAG-AAGAG
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTA-AAAGAAAGAG
* * *
17220 TAATCAGTAATTAGTTTAAATTCAGAGAAATTAAGCTAAAAAAAGTAAAGGAAGGAG
1 TAATCAGTAATTAGTTT-AATTCAGAGTAATTAAGCT--AAAAAGTAAAAGAAAGAG
* * * * *
17277 TAATCAGCAGATAAGTTTAATTTAGAGTAATTAGGCTAAAAAGTAAAGGAAAGAG
1 TAATCAGTA-ATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
* *
17332 TAATCAGTAGATAAGTTTAATTCAGAGTAATTAAGCTAAAAAGGGTAAAAGAAAGAC
1 TAATCAGTA-ATTAGTTTAATTCAGAGTAATTAAGCTAAAAA--GTAAAAGAAAGAG
* *
17389 TAATCAGTAATTAGTTTAATTC--AGTAATTAAGCTAAAGAGGGTAAAAGAAGGAG
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAA-A-AGTAAAAGAAAGAG
* * *
17443 TGATCAGTAAATAGTTTAATTCAGAGTAATTAAGCTAAAAAAGGTAAAAGAAAAAG
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCT-AAAAA-GTAAAAGAAAGAG
* * *
17499 TAATAAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAGGAAGGAG
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
* * * * *
17553 TAATCAGCAGATAAGTTTAATTCAAAGTAATTAAGCTAAAAAGTAAAGGAAGGAG
1 TAATCAGTA-ATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
* * * *
17608 TAATCAGCAGATAAGTTTAATTCAGAGTAATTAGGCTAAAAAGTAAAAGAAAAAG
1 TAATCAGTA-ATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
*
17663 TAATCAGTAGA-TAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAAAG
1 TAATCAGTA-ATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
* * *
17717 TAACCAGTAATTAGTTTAATTCAGAGTAATTAAACTAAAAAGGTGAAAGAAAGAG
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAA-GTAAAAGAAAGAG
*
17772 TAATCAGTAGATTAGTTTAATTCAGAGTAATTAAACTAAAAAGAGTAAAAGAAAGAG
1 TAATCAGTA-ATTAGTTTAATTCAGAGTAATTAAGCT-AAAA-AGTAAAAGAAAGAG
* * * *
17829 TAATTAGTACA-TAGTTTAATTCAGAGTAATTAAGCTAAACAGTAAAAGAAAAAA
1 TAATCAGTA-ATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
* * *
17883 TAATCAGTAATTACTTTAATTCAGAGTAATTAAGCTAAACAGTAAAAGAAAAAG
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
* * * * *
17937 TAATCAGTAACTAGTTTAATTCGGAGTAATTAAACTAAACAGTAAAAGAAAAAG
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
* *
17991 TAATCAGTAATTAGTTTAATTCTGAGTAATTAAGCTAAAAAGTAAAAGAAAAAG
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
*
18045 TAATCAGTAATTAGTTTAATTCTGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
* * *
18099 TAATCAGTAGA-TAGTTTAATTTAGAGAAATTAAACTAAAAAGTAAAAGAAAGAG
1 TAATCAGTA-ATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
* *
18153 TAATCAGT-ATATAATTTAATTCAGAGTAAATTAATCTAAAAAGTAAAAGAAAGAG
1 TAATCAGTAAT-TAGTTTAATTCAGAGT-AATTAAGCTAAAAAGTAAAAGAAAGAG
18208 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAAGGGTAAAAGAAAGAG
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCT-AAAAA--GTAAAAGAAAGAG
* * *
18265 TAATCAGTAGTTAG-TTAA-TCAGAGTAATTAAACTAAAAAG-AGTAAA-AATG-G
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTA--AAAGAAAGAG
* * * *
18316 TAATTAGTAATT-GACTTGATTCAGAGTAATTAAGTTAAAAAGTAAAA
1 TAATCAGTAATTAG-TTTAATTCAGAGTAATTAAGCTAAAAAGTAAAA
18363 ATAGTAATAA
Statistics
Matches: 1259, Mismatches: 117, Indels: 90
0.86 0.08 0.06
Matches are distributed among these distances:
50 1 0.00
51 12 0.01
52 11 0.01
53 25 0.02
54 516 0.41
55 354 0.28
56 162 0.13
57 163 0.13
58 15 0.01
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (54 bp):
TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
Found at i:17223 original size:166 final size:162
Alignment explanation
Indices: 16889--18362 Score: 1808
Period size: 166 Copynumber: 9.0 Consensus size: 162
16879 CATTAAGTGA
* * * ** * *
16889 TAATTAGTAATTAGTTTAATTCTGAGCAATTAAGCTAAAGCGTAAAAGAAAAAGTAATCAATA-A
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAGA
* ** *
16953 TTAGTTTAATTCAGAATAATTAAGCTAAAAAACATAAAG-AAGAGTAATCAGTATTTAGTTTAAA
66 -TAGTTTAATTCAGAGTAATTAAGCTAAAAAGTA-AAAGAAAGAGTAATCAGTAATTAGTTT-AA
* * *
17017 TTCAGAGAAATTAAGCTAAAAAAAGTAAAGGAAGGAG
128 TTCAGAGTAATTAAGCT--AAAAAGTAAAAGAAAGAG
* * * *
17054 TAATCAGCAAATAAGTTTAATTCAGAGTAATTAGGCTAAAAAGTAAAGGAAAGAGTAATCAGTAG
1 TAATCAG-TAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAG
*
17119 ATAAGTTTTATTCAGAGTAATTAAGCTAAAAAGGGTAAAAGAAAGAGTAATCAGTAATTAGTTTA
65 AT-AGTTTAATTCAGAGTAATTAAGCTAAAAA--GTAAAAGAAAGAGTAATCAGTAATTAGTTTA
**
17184 ATTCAGAGTAATTAAGCTAAAAAACATAAAG-AAGAG
127 ATTCAGAGTAATTAAGCTAAAAAGTA-AAAGAAAGAG
* * * *
17220 TAATCAGTAATTAGTTTAAATTCAGAGAAATTAAGCTAAAAAAAGTAAAGGAAGGAGTAATCAGC
1 TAATCAGTAATTAGTTT-AATTCAGAGTAATTAAGCT--AAAAAGTAAAAGAAAGAGTAATCAGT
* * * *
17285 AGATAAGTTTAATTTAGAGTAATTAGGCTAAAAAGTAAAGGAAAGAGTAATCAGTAGATAAGTTT
63 AGAT-AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTA-ATTAGTTT
*
17350 AATTCAGAGTAATTAAGCTAAAAAGGGTAAAAGAAAGAC
126 AATTCAGAGTAATTAAGCTAAAAA--GTAAAAGAAAGAG
* * *
17389 TAATCAGTAATTAGTTTAATTC--AGTAATTAAGCTAAAGAGGGTAAAAGAAGGAGTGATCAGTA
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAA-A-AGTAAAAGAAAGAGTAATCAGTA
* * *
17452 AATAGTTTAATTCAGAGTAATTAAGCTAAAAAAGGTAAAAGAAAAAGTAATAAGTAATTAGTTTA
64 GATAGTTTAATTCAGAGTAATTAAGCT-AAAAA-GTAAAAGAAAGAGTAATCAGTAATTAGTTTA
* *
17517 ATTCAGAGTAATTAAGCTAAAAAGTAAAGGAAGGAG
127 ATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
* * * * * *
17553 TAATCAGCAGATAAGTTTAATTCAAAGTAATTAAGCTAAAAAGTAAAGGAAGGAGTAATCAGCAG
1 TAATCAGTA-ATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAG
* *
17618 ATAAGTTTAATTCAGAGTAATTAGGCTAAAAAGTAAAAGAAAAAGTAATCAGTAGA-TAGTTTAA
65 AT-AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTA-ATTAGTTTAA
*
17682 TTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAAAG
128 TTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
* * *
17717 TAACCAGTAATTAGTTTAATTCAGAGTAATTAAACTAAAAAGGTGAAAGAAAGAGTAATCAGTAG
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAA-GTAAAAGAAAGAGTAATCAGTAG
* *
17782 ATTAGTTTAATTCAGAGTAATTAAACTAAAAAGAGTAAAAGAAAGAGTAATTAGTACA-TAGTTT
65 A-TAGTTTAATTCAGAGTAATTAAGCT-AAAA-AGTAAAAGAAAGAGTAATCAGTA-ATTAGTTT
* * *
17846 AATTCAGAGTAATTAAGCTAAACAGTAAAAGAAAAAA
126 AATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
* * *
17883 TAATCAGTAATTACTTTAATTCAGAGTAATTAAGCTAAACAGTAAAAGAAAAAGTAATCAGTA-A
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAGA
* * * *
17947 CTAGTTTAATTCGGAGTAATTAAACTAAACAGTAAAAGAAAAAGTAATCAGTAATTAGTTTAATT
66 -TAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATT
* *
18012 CTGAGTAATTAAGCTAAAAAGTAAAAGAAAAAG
130 CAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
*
18045 TAATCAGTAATTAGTTTAATTCTGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAGA
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAGA
* * * *
18110 TAGTTTAATTTAGAGAAATTAAACTAAAAAGTAAAAGAAAGAGTAATCAGT-ATATAATTTAATT
66 TAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAAT-TAGTTTAATT
*
18174 CAGAGTAAATTAATCTAAAAAGTAAAAGAAAGAG
130 CAGAGT-AATTAAGCTAAAAAGTAAAAGAAAGAG
18208 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAAGGGTAAAAGAAAGAGTAATCAGT
1 TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCT-AAAAA--GTAAAAGAAAGAGTAATCAGT
* * * * *
18273 AGTTAG-TTAA-TCAGAGTAATTAAACTAAAAAG-AGTAAA-AATG-GTAATTAGTAATT-GACT
63 AGATAGTTTAATTCAGAGTAATTAAGCTAAAAAGTA--AAAGAAAGAGTAATCAGTAATTAG-TT
* *
18332 TGATTCAGAGTAATTAAGTTAAAAAGTAAAA
125 TAATTCAGAGTAATTAAGCTAAAAAGTAAAA
18363 ATAGTAATAA
Statistics
Matches: 1155, Mismatches: 116, Indels: 79
0.86 0.09 0.06
Matches are distributed among these distances:
161 3 0.00
162 198 0.17
163 114 0.10
164 186 0.16
165 108 0.09
166 320 0.28
167 96 0.08
168 86 0.07
169 44 0.04
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (162 bp):
TAATCAGTAATTAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAGA
TAGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAATTAGTTTAATTC
AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAG
Found at i:17554 original size:28 final size:28
Alignment explanation
Indices: 17522--17611 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
17512 GTTTAATTCA
17522 GAGTAATTAAGCTAAAAAGTAAAGGAAG
1 GAGTAATTAAGCTAAAAAGTAAAGGAAG
* * ***
17550 GAGTAA-TCAGC-AGATAAGTTTAATTCAA-
1 GAGTAATTAAGCTA-AAAAG--TAAAGGAAG
17578 -AGTAATTAAGCTAAAAAGTAAAGGAAG
1 GAGTAATTAAGCTAAAAAGTAAAGGAAG
17605 GAGTAAT
1 GAGTAAT
17612 CAGCAGATAA
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
26 6 0.13
27 13 0.29
28 20 0.44
29 6 0.13
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (28 bp):
GAGTAATTAAGCTAAAAAGTAAAGGAAG
Found at i:17635 original size:27 final size:27
Alignment explanation
Indices: 17550--17638 Score: 74
Period size: 27 Copynumber: 3.3 Consensus size: 27
17540 GTAAAGGAAG
17550 GAGTAATCAGCAGATAAGTTTAATTCA
1 GAGTAATCAGCAGATAAGTTTAATTCA
* * * * ***
17577 AAGTAATTAAGCTA-AAAAG-TAAAGGAA
1 GAGTAA-TCAGC-AGATAAGTTTAATTCA
17604 GGAGTAATCAGCAGATAAGTTTAATTCA
1 -GAGTAATCAGCAGATAAGTTTAATTCA
17632 GAGTAAT
1 GAGTAAT
17639 TAGGCTAAAA
Statistics
Matches: 43, Mismatches: 14, Indels: 10
0.64 0.21 0.15
Matches are distributed among these distances:
26 1 0.02
27 24 0.56
28 17 0.40
29 1 0.02
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.26
Consensus pattern (27 bp):
GAGTAATCAGCAGATAAGTTTAATTCA
Found at i:21169 original size:442 final size:437
Alignment explanation
Indices: 20335--21395 Score: 1387
Period size: 442 Copynumber: 2.4 Consensus size: 437
20325 AGTTGTGCGA
* * * * *
20335 AATCGGATATATGCATC-AAAATTATATAATATTTAAA-AGACCGTCAATCGAAACCATAAAATT
1 AATCGGACATGTGGATCGAAAATTATATAATA-TTAAATAGACCGACAATCGAAACCACAAAATT
* * * *
20398 TCGGAAGCATTTTTTAGAAATGAAACATAAAAATTAGCTTTTGAGTCCTTAATGAAAGTTGTAGA
65 TCGGAAGCATTTTTTTGAATTGAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAGA
* * * * * *
20463 TCATGAAATTACCTTT--TAGACACCTGAATTACATTGATTGAACAAATAGAACAAAGAAAAAAA
130 TCATGAAATTACTTTTAATAGATACCTGAATCACATTAATCGGACAAATAGAACAAAGAAAAAAA
* * *
20526 AAAGCCAAAGCATTCAATCGAGTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAA
195 AAAGCCAAAGCATTAAATCGAGTAAGATAGAATTAGTAAAGGACTAAGTAGTATAAAGTAAAAAA
* ** * * *
20591 CTATAAGGGTCATTTGACAAATAATCCAAATAATAAAATGCTTGTTGGTGGAGATCTTGAAATAT
260 ATATAAGAATCATTTGACAAATAATCCAAATAAGAAAATGCTTGTTGATGGAGATCTTGAAACAT
* * * *
20656 AAAAATTCCCTTTTGGACCCTTAATGAAACTCGTAGATCAAATTCAGCTTTCGGGTCCTTCATGA
325 AAAAATTCCCTTCTGAACCCTTAACGAAACTCGTAGATCAAATTCAGCTTTCGGGTCCTTCATAA
* *
20721 AAGTCGTAGATCATGCAATAACCTTTTAACCGACACTTGAATAACTTT
390 AAGTCGTAGATCATGCAATAACCTTTTAACCGACACTTAAATAACTCT
* *
20769 AATCGGACATGTGGATCGAAAATTATATGATATTAAATAGACCGACAATCGAAACCACAAAATCT
1 AATCGGACATGTGGATCGAAAATTATATAATATTAAATAGACCGACAATCGAAACCACAAAATTT
* * * * * *
20834 CGGAAGCTTTTTTTTGAATTGAAATATAAAAATTGGCTTTTAAGTCATTCATGAAAGTTATAGGT
66 CGGAAGCATTTTTTTGAATTGAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAGAT
* *
20899 CATGAAATTATCTTTTAATAGATACCTGAATCACCTTAATCGGACAAATATAACAAAGAAAATAA
131 CATGAAATTA-CTTTTAATAGATACCTGAATCACATTAATCGGACAAATAGAACAAAG---A-AA
** * *
20964 AAAAAAAGCTTAAGCGTTAAATCGATTAAGATAGAATTAGTAAAGGACTAAGTAGTATAAAGTAA
191 AAAAAAAGCCAAAGCATTAAATCGAGTAAGATAGAATTAGTAAAGGACTAAGTAGTATAAAGTAA
* *
21029 AAAAATATGAGAATCATTTGATAAATAATCCAAATAAGAAAATG-TTCGTTGATGGAGATCTTGA
256 AAAAATATAAGAATCATTTGACAAATAATCCAAATAAGAAAATGCTT-GTTGATGGAGATCTTGA
* *
21093 AACATAAAAATTCCCTTCTGAACCCTTCACGAAACTCGTAGATCAAATTTAGCTTTCGGGTCCTT
320 AACATAAAAATTCCCTTCTGAACCCTTAACGAAACTCGTAGATCAAATTCAGCTTTCGGGTCCTT
*
21158 CATAAAAGTCGTAGATCATGTAATAACCTTTTAACCGACACTTAAATAACTCT
385 CATAAAAGTCGTAGATCATGCAATAACCTTTTAACCGACACTTAAATAACTCT
* * * * *
21211 AATTGGACATGTGGATCGAAACTTATATAATATATAAGTAGACTGGCAATCGAAATTAACCACAA
1 AATCGGACATGTGGATCGAAAATTATATAATAT-TAAATAGACCGACAATCG--A--AACCACAA
** ** *
21276 AATTTTAGAAGCATTTTTTTGAATCAAAACATAAAATTTGGCTTTTGAGTCCTTCATGAAAGTTG
61 AATTTCGGAAGCATTTTTTTGAATTGAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAGTTG
* * * *
21341 TAAATCATGAAATTACCTTTTAATAGACT-CCTTAATCACTTTAATCAGACAAATA
126 TAGATCATGAAATTA-CTTTTAATAGA-TACCTGAATCACATTAATCGGACAAATA
21396 AAGCTAAAAT
Statistics
Matches: 539, Mismatches: 72, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
434 19 0.04
435 102 0.19
436 4 0.01
438 33 0.06
441 3 0.01
442 252 0.47
443 15 0.03
445 1 0.00
447 109 0.20
448 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (437 bp):
AATCGGACATGTGGATCGAAAATTATATAATATTAAATAGACCGACAATCGAAACCACAAAATTT
CGGAAGCATTTTTTTGAATTGAAACATAAAAATTGGCTTTTGAGTCCTTCATGAAAGTTGTAGAT
CATGAAATTACTTTTAATAGATACCTGAATCACATTAATCGGACAAATAGAACAAAGAAAAAAAA
AAGCCAAAGCATTAAATCGAGTAAGATAGAATTAGTAAAGGACTAAGTAGTATAAAGTAAAAAAA
TATAAGAATCATTTGACAAATAATCCAAATAAGAAAATGCTTGTTGATGGAGATCTTGAAACATA
AAAATTCCCTTCTGAACCCTTAACGAAACTCGTAGATCAAATTCAGCTTTCGGGTCCTTCATAAA
AGTCGTAGATCATGCAATAACCTTTTAACCGACACTTAAATAACTCT
Found at i:26108 original size:50 final size:50
Alignment explanation
Indices: 26033--26138 Score: 203
Period size: 50 Copynumber: 2.1 Consensus size: 50
26023 CCAAGTTGAA
26033 TATGTTCTAAGGCATCCGGCTACCTTTTAATTGTAAAACCTAATAAGGCC
1 TATGTTCTAAGGCATCCGGCTACCTTTTAATTGTAAAACCTAATAAGGCC
26083 TATGTTCTAAGGCATCCGGCTACCTTTTAATTGTAAAACCTAATAAGGCC
1 TATGTTCTAAGGCATCCGGCTACCTTTTAATTGTAAAACCTAATAAGGCC
26133 TGATGT
1 T-ATGT
26139 CCAAATTGGG
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 51 0.93
51 4 0.07
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (50 bp):
TATGTTCTAAGGCATCCGGCTACCTTTTAATTGTAAAACCTAATAAGGCC
Found at i:26212 original size:29 final size:30
Alignment explanation
Indices: 26139--26243 Score: 79
Period size: 31 Copynumber: 3.5 Consensus size: 30
26129 GGCCTGATGT
* *
26139 CCAAATTGGGTCTAAACCTTTTCAAACTTA
1 CCAAATTGGGCCTAAACCTTTTCAAACTGA
** *
26169 CTCATTTTGAGCCTAAACC-TTT-AAACATGA
1 C-CAAATTGGGCCTAAACCTTTTCAAAC-TGA
* ** *
26199 CCAAATTGGGCCTAAACGTTAGCAAATTGCA
1 CCAAATTGGGCCTAAACCTTTTCAAACTG-A
*
26230 CCAAATTGAGCCTA
1 CCAAATTGGGCCTA
26244 TTTTAGACGG
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
29 17 0.30
30 10 0.18
31 30 0.53
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (30 bp):
CCAAATTGGGCCTAAACCTTTTCAAACTGA
Found at i:27003 original size:29 final size:30
Alignment explanation
Indices: 26970--27032 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
26960 TTTTTTAAAA
* * *
26970 ATTTAATTTTTAT-ATACACAACATTATTC
1 ATTTAATTTGTATAAAAAACAACATTATTC
*
26999 ATTT-ATTTGTATAAAAAAGAACATTATTC
1 ATTTAATTTGTATAAAAAACAACATTATTC
27028 ATTTA
1 ATTTA
27033 TAGGTTGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (30 bp):
ATTTAATTTGTATAAAAAACAACATTATTC
Found at i:28523 original size:22 final size:22
Alignment explanation
Indices: 28499--28540 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
28489 GTTTGTTTGT
*
28499 TTTTTTCTTTTT-TTCTTTTCC
1 TTTTTCCTTTTTATTCTTTTCC
28520 TTTTTCCTTTTTATTCTTTTC
1 TTTTTCCTTTTTATTCTTTTC
28541 TCTTATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTCCTTTTTATTCTTTTCC
Found at i:28552 original size:22 final size:21
Alignment explanation
Indices: 28505--28559 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
28495 TTGTTTTTTT
*
28505 CTTTTTTTCTTTTCCTTTTTC
1 CTTTTTTTCTTTTCCTTTATC
28526 CTTTTTATTCTTTT-CTCTTATC
1 CTTTTT-TTCTTTTCCT-TTATC
*
28548 TTTTTCTTTCTT
1 CTTTT-TTTCTT
28560 CCCATCACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 8 0.28
22 20 0.69
23 1 0.03
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.75
Consensus pattern (21 bp):
CTTTTTTTCTTTTCCTTTATC
Found at i:34850 original size:30 final size:29
Alignment explanation
Indices: 34750--34850 Score: 103
Period size: 29 Copynumber: 3.4 Consensus size: 29
34740 TAAACAACCA
** * *
34750 TTTTGCCCCCTGAACTTGTAGCGTTTTGACG
1 TTTTGCCCCCTGAACTTCAATC--TTGGACG
* *
34781 TTTTGCCCCCCGAACTTCAATCTTGGACA
1 TTTTGCCCCCTGAACTTCAATCTTGGACG
* *
34810 TTTTGTCCCCTGAACTTCAATTTTGGGACG
1 TTTTGCCCCCTGAACTTCAATCTT-GGACG
34840 TTTTGCCCCCT
1 TTTTGCCCCCT
34851 CAACCTAACG
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
29 26 0.45
30 14 0.24
31 18 0.31
ACGTcount: A:0.15, C:0.30, G:0.18, T:0.38
Consensus pattern (29 bp):
TTTTGCCCCCTGAACTTCAATCTTGGACG
Done.