Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013211.1 Corchorus olitorius cultivar O-4 contig13244, 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: 70907
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:4063 original size:15 final size:16
Alignment explanation
Indices: 4034--4063 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4024 GTGTGAATTC
4034 AAATTGATCTTTTGAA
1 AAATTGATCTTTTGAA
4050 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
4064 TAAACTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (16 bp):
AAATTGATCTTTTGAA
Found at i:10433 original size:36 final size:36
Alignment explanation
Indices: 10393--10461 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
10383 TGATCGTATA
* *
10393 AGTTTAAGTGATGATCAAGAAGTTAAAAAAGATTCG
1 AGTTTAAGTGACGATCAAGAAGCTAAAAAAGATTCG
* *
10429 AGTTTAAGTGACGATCACGAAGCTCAAAAAGAT
1 AGTTTAAGTGACGATCAAGAAGCTAAAAAAGAT
10462 CCAGATTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (36 bp):
AGTTTAAGTGACGATCAAGAAGCTAAAAAAGATTCG
Found at i:10556 original size:32 final size:33
Alignment explanation
Indices: 10515--10584 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 33
10505 ACAAAGTTTA
* *
10515 TTTAACATGCATAATCTCTTC-TTCTACCTTTC
1 TTTATCATGCATAATCTCCTCTTTCTACCTTTC
*
10547 TTTATCATGCATAATCTCCTCTTTCTACGTTTC
1 TTTATCATGCATAATCTCCTCTTTCTACCTTTC
10580 TTTAT
1 TTTAT
10585 GATTAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 19 0.56
33 15 0.44
ACGTcount: A:0.20, C:0.26, G:0.04, T:0.50
Consensus pattern (33 bp):
TTTATCATGCATAATCTCCTCTTTCTACCTTTC
Found at i:12109 original size:38 final size:38
Alignment explanation
Indices: 12058--12131 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
12048 CTATATCGGG
12058 TGTGCAAATTTGATTGAAGGCTCCGGAAGAGCTAGTCT
1 TGTGCAAATTTGATTGAAGGCTCCGGAAGAGCTAGTCT
*
12096 TGTGCAAATTTGATTGAATGCTCCGGAAGAGCTAGT
1 TGTGCAAATTTGATTGAAGGCTCCGGAAGAGCTAGT
12132 ATCGTTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (38 bp):
TGTGCAAATTTGATTGAAGGCTCCGGAAGAGCTAGTCT
Found at i:17931 original size:31 final size:32
Alignment explanation
Indices: 17878--18042 Score: 183
Period size: 32 Copynumber: 5.2 Consensus size: 32
17868 ACTATTTAGC
17878 GGCGTTTTGTTCTGA-AGACGCCGCTAAATAAG
1 GGCGTTTTGTTCT-ATAGACGCCGCTAAATAAG
* *
17910 GGCGTTTT-TTGTTTAGACGCCGCTAAATAAG
1 GGCGTTTTGTTCTATAGACGCCGCTAAATAAG
* *
17941 GGCGTTTTG-TCTTTTAAACGCCGCTAAATAAG
1 GGCGTTTTGTTC-TATAGACGCCGCTAAATAAG
* * * * *
17973 GGCATTTTCTTCTATAGACGACGCTAAATTAT
1 GGCGTTTTGTTCTATAGACGCCGCTAAATAAG
* * *
18005 GGCATTTTGTTCCATAGACGCCGCTATATAAG
1 GGCGTTTTGTTCTATAGACGCCGCTAAATAAG
18037 GGCGTT
1 GGCGTT
18043 CTGAAACTTG
Statistics
Matches: 111, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
31 29 0.26
32 80 0.72
33 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (32 bp):
GGCGTTTTGTTCTATAGACGCCGCTAAATAAG
Found at i:22897 original size:32 final size:31
Alignment explanation
Indices: 22841--22902 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
22831 AAGATTATAT
*
22841 ATAGCGGTGTTTACTCTAGAAACGCCGCTAA
1 ATAGCGGCGTTTACTCTAGAAACGCCGCTAA
22872 ATAGCGGCGTTTCAC-CTATGAAACGCCGCTA
1 ATAGCGGCGTTT-ACTCTA-GAAACGCCGCTA
22903 TTCCCATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (31 bp):
ATAGCGGCGTTTACTCTAGAAACGCCGCTAA
Found at i:22966 original size:124 final size:123
Alignment explanation
Indices: 22801--23400 Score: 866
Period size: 124 Copynumber: 4.8 Consensus size: 123
22791 GGTGTTTTTA
*
22801 TTAGTTTCACCAAATTTCTATTCTTTGGATAAGATTATATATAGCGGTGTTTACTCTAGAAACGC
1 TTAGTTTCACCAAATTTCTATTCTTTGGATAAGATTATATATAGCGGCGTTTACTCTAGAAACGC
* ** *** * *
22866 CGCTAAATAGCGGCGTTTCACCTATGAAACGCCGCTATTCCCATCAAGTAATAATGTTT
66 CACTATTTAGCGGCGTTTCAGGGATGAAACGCCGCTATT-CCAACAAGAAATAATGTTT
*
22925 TTAGTTTCGCCAAATTTCTATTCTTTGGATAAGATTATATATAGCGGCGTTTACT-TGAGAAACG
1 TTAGTTTCACCAAATTTCTATTCTTTGGATAAGATTATATATAGCGGCGTTTACTCT-AGAAACG
* * *
22989 CCACTATTTAGCGGCGTTTTTAGGGCTGAAACGCCGTTATTCCAACAAGAAATAATGTTT
65 CCACTATTTAGCGGCG-TTTCAGGGATGAAACGCCGCTATTCCAACAAGAAATAATGTTT
23049 TTAGTTTCACCAAATTTCTATTCTTTGGATAAGATTATATATAGCGGCGTTTACTCTAGAAACGC
1 TTAGTTTCACCAAATTTCTATTCTTTGGATAAGATTATATATAGCGGCGTTTACTCTAGAAACGC
* * *
23114 CACTATTTAGCGGCGTTTCATAGGA-GAAACGCCGCTATTCCTATCAAGTAATAATGTTT
66 CACTATTTAGCGGCGTTTCA-GGGATGAAACGCCGCTATTCC-AACAAGAAATAATGTTT
* * *
23173 TTAGTTTCGCCAAATTTCTATTCTTTGGATAAGATTATACATAGCGGCCTTTACT-TGAGAAACG
1 TTAGTTTCACCAAATTTCTATTCTTTGGATAAGATTATATATAGCGGCGTTTACTCT-AGAAACG
* *
23237 CCACTATTTAGCGGCGTTTTTAGGGCTGAAACGCCGCTATTCCAACAAGAAATAATGTTT
65 CCACTATTTAGCGGCG-TTTCAGGGATGAAACGCCGCTATTCCAACAAGAAATAATGTTT
* *
23297 TTAGTTTCACCAAATTTCTATTCTTTGGATAAGATTATATATAGCGACGTTTACCCTAGAAACGC
1 TTAGTTTCACCAAATTTCTATTCTTTGGATAAGATTATATATAGCGGCGTTTACTCTAGAAACGC
** *
23362 CACTATTTAGCGGCGTCTTTTGTGA-GAAACGCCGCTATT
66 CACTATTTAGCGGCGT-TTCAGGGATGAAACGCCGCTATT
23401 GTATTTAGAA
Statistics
Matches: 430, Mismatches: 36, Indels: 21
0.88 0.07 0.04
Matches are distributed among these distances:
123 36 0.08
124 354 0.82
125 40 0.09
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (123 bp):
TTAGTTTCACCAAATTTCTATTCTTTGGATAAGATTATATATAGCGGCGTTTACTCTAGAAACGC
CACTATTTAGCGGCGTTTCAGGGATGAAACGCCGCTATTCCAACAAGAAATAATGTTT
Found at i:23239 original size:248 final size:248
Alignment explanation
Indices: 22764--23400 Score: 1030
Period size: 248 Copynumber: 2.6 Consensus size: 248
22754 TTTCATAGGA
* * **
22764 GAAACGCCATTATTTCCATCAAGAAATGGTGTTTTTATTAGTTTCACCAAATTTCTATTCTTTGG
1 GAAACGCCGTTA-TTCCAACAAGAAATAATG--TTT-TTAGTTTCACCAAATTTCTATTCTTTGG
* * ** *
22829 ATAAGATTATATATAGCGGTGTTTACTCTAGAAACGCCGCTAAATAGCGGCGTTTCACCTA--TG
62 ATAAGATTATATATAGCGGCGTTTACTCTAGAAACGCCACTATTTAGCGGCGTTTCA--TAGGAG
22892 AAACGCCGCTATTCCCATCAAGTAATAATGTTTTTAGTTTCGCCAAATTTCTATTCTTTGGATAA
125 AAACGCCGCTATTCCCATCAAGTAATAATGTTTTTAGTTTCGCCAAATTTCTATTCTTTGGATAA
* *
22957 GATTATATATAGCGGCGTTTACTTGAGAAACGCCACTATTTAGCGGCGTTTTTAGGGCT
190 GATTATACATAGCGGCCTTTACTTGAGAAACGCCACTATTTAGCGGCGTTTTTAGGGCT
23016 GAAACGCCGTTATTCCAACAAGAAATAATGTTTTTAGTTTCACCAAATTTCTATTCTTTGGATAA
1 GAAACGCCGTTATTCCAACAAGAAATAATGTTTTTAGTTTCACCAAATTTCTATTCTTTGGATAA
23081 GATTATATATAGCGGCGTTTACTCTAGAAACGCCACTATTTAGCGGCGTTTCATAGGAGAAACGC
66 GATTATATATAGCGGCGTTTACTCTAGAAACGCCACTATTTAGCGGCGTTTCATAGGAGAAACGC
*
23146 CGCTATTCCTATCAAGTAATAATGTTTTTAGTTTCGCCAAATTTCTATTCTTTGGATAAGATTAT
131 CGCTATTCCCATCAAGTAATAATGTTTTTAGTTTCGCCAAATTTCTATTCTTTGGATAAGATTAT
23211 ACATAGCGGCCTTTACTTGAGAAACGCCACTATTTAGCGGCGTTTTTAGGGCT
196 ACATAGCGGCCTTTACTTGAGAAACGCCACTATTTAGCGGCGTTTTTAGGGCT
*
23264 GAAACGCCGCTATTCCAACAAGAAATAATGTTTTTAGTTTCACCAAATTTCTATTCTTTGGATAA
1 GAAACGCCGTTATTCCAACAAGAAATAATGTTTTTAGTTTCACCAAATTTCTATTCTTTGGATAA
* * *
23329 GATTATATATAGCGACGTTTACCCTAGAAACGCCACTATTTAGCGGCGTCTT--TTGTGAGAAAC
66 GATTATATATAGCGGCGTTTACTCTAGAAACGCCACTATTTAGCGGCGT-TTCATAG-GAGAAAC
23392 GCCGCTATT
129 GCCGCTATT
23401 GTATTTAGAA
Statistics
Matches: 365, Mismatches: 16, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
246 2 0.01
247 2 0.01
248 330 0.90
249 5 0.01
251 15 0.04
252 11 0.03
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (248 bp):
GAAACGCCGTTATTCCAACAAGAAATAATGTTTTTAGTTTCACCAAATTTCTATTCTTTGGATAA
GATTATATATAGCGGCGTTTACTCTAGAAACGCCACTATTTAGCGGCGTTTCATAGGAGAAACGC
CGCTATTCCCATCAAGTAATAATGTTTTTAGTTTCGCCAAATTTCTATTCTTTGGATAAGATTAT
ACATAGCGGCCTTTACTTGAGAAACGCCACTATTTAGCGGCGTTTTTAGGGCT
Found at i:40732 original size:2 final size:2
Alignment explanation
Indices: 40725--40754 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40715 TTAAACTCGA
40725 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40755 TACTAGTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43573 original size:42 final size:42
Alignment explanation
Indices: 43526--43650 Score: 232
Period size: 42 Copynumber: 3.0 Consensus size: 42
43516 TAAATTCTAG
* *
43526 TACTCCATCTCTAGGTAATTCATCAGAATAAAGCTAATATTC
1 TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTC
43568 TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTC
1 TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTC
43610 TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
1 TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
43651 AATTGTTACT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (42 bp):
TACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTC
Found at i:43586 original size:23 final size:23
Alignment explanation
Indices: 43560--43628 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
43550 AGAATAAAGC
43560 TAATATTCTACTCCATCTCTAGA
1 TAATATTCTACTCCATCTCTAGA
* ** ** *
43583 T-A-ATTC-A-TCAAAATAAAGC
1 TAATATTCTACTCCATCTCTAGA
43602 TAATATTCTACTCCATCTCTAGA
1 TAATATTCTACTCCATCTCTAGA
43625 TAAT
1 TAAT
43629 TCATCAAAAT
Statistics
Matches: 30, Mismatches: 12, Indels: 8
0.60 0.24 0.16
Matches are distributed among these distances:
19 7 0.23
20 2 0.07
21 8 0.27
22 2 0.07
23 11 0.37
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (23 bp):
TAATATTCTACTCCATCTCTAGA
Found at i:52335 original size:41 final size:41
Alignment explanation
Indices: 52204--52340 Score: 177
Period size: 41 Copynumber: 3.3 Consensus size: 41
52194 AATAATATTG
*
52204 AAAATTACCTTTGACACCAGAAGTTGTCACTTTGGTAAATT
1 AAAATTACCTTTGACACCAAAAGTTGTCACTTTGGTAAATT
* * * * * *
52245 AAAATTA-CTGCTAACACTAAAAGTCGTCACCTTAGTAAATT
1 AAAATTACCT-TTGACACCAAAAGTTGTCACTTTGGTAAATT
* *
52286 AAAGTTACCTTTGACACCAAAAGTTGTCAATTTGGTAAATT
1 AAAATTACCTTTGACACCAAAAGTTGTCACTTTGGTAAATT
52327 AAAATTACCTTTGA
1 AAAATTACCTTTGA
52341 TATCAGAAGT
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 2 0.03
41 74 0.95
42 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (41 bp):
AAAATTACCTTTGACACCAAAAGTTGTCACTTTGGTAAATT
Found at i:57330 original size:7 final size:7
Alignment explanation
Indices: 57297--57329 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
57287 ATATCGAAAA
57297 TCTC-TC
1 TCTCTTC
57303 TCTCTTC
1 TCTCTTC
57310 TCTCTTC
1 TCTCTTC
*
57317 TCTCTTT
1 TCTCTTC
57324 TCTCTT
1 TCTCTT
57330 TCTTGGTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 4 0.16
7 21 0.84
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (7 bp):
TCTCTTC
Found at i:58246 original size:18 final size:18
Alignment explanation
Indices: 58213--58251 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
58203 AATTTGCAGG
**
58213 ATGTTCAGGTTGAAGACA
1 ATGTTCAGGTACAAGACA
*
58231 ATGTTCAGGTACAAGATA
1 ATGTTCAGGTACAAGACA
58249 ATG
1 ATG
58252 ATGATTTAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (18 bp):
ATGTTCAGGTACAAGACA
Found at i:69903 original size:20 final size:20
Alignment explanation
Indices: 69878--69921 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
69868 AAGCTTTGTA
69878 GTATATGGTTATGGTTAAGC
1 GTATATGGTTATGGTTAAGC
69898 GTATATGGTTATGGTTAAGC
1 GTATATGGTTATGGTTAAGC
69918 GTAT
1 GTAT
69922 CCTTGGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.05, G:0.30, T:0.41
Consensus pattern (20 bp):
GTATATGGTTATGGTTAAGC
Done.