Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011246.1 Corchorus olitorius cultivar O-4 contig11279, 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: 38343
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
38 ACTTTATTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:10963 original size:14 final size:14
Alignment explanation
Indices: 10946--10981 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
10936 AAAAACTTGA
10946 TTTTGAAAAAGTGC
1 TTTTGAAAAAGTGC
10960 TTTTG-AAAAGTGC
1 TTTTGAAAAAGTGC
*
10973 TTTTTAAAA
1 TTTTGAAAA
10982 TTGGGGTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.42
Consensus pattern (14 bp):
TTTTGAAAAAGTGC
Found at i:13889 original size:19 final size:20
Alignment explanation
Indices: 13867--13918 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
13857 GGGCTGAAAT
13867 TAATTAATTATTAAATA-AA
1 TAATTAATTATTAAATAGAA
**
13886 TAA-TAATTATTTTATAGAA
1 TAATTAATTATTAAATAGAA
13905 TAATT-ATTATTAAA
1 TAATTAATTATTAAA
13919 AATAGCACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 11 0.41
19 15 0.56
20 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TAATTAATTATTAAATAGAA
Found at i:13922 original size:16 final size:16
Alignment explanation
Indices: 13871--13922 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
13861 TGAAATTAAT
*
13871 TAATTATTAAATAAATAA
1 TAATTATT-ATTAAA-AA
*
13889 TAATTATT-TTATAGAA
1 TAATTATTATTA-AAAA
13905 TAATTATTATTAAAAA
1 TAATTATTATTAAAAA
13921 TA
1 TA
13923 GCACATGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 17 0.59
17 4 0.14
18 8 0.28
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TAATTATTATTAAAAA
Found at i:15363 original size:51 final size:50
Alignment explanation
Indices: 15262--15363 Score: 111
Period size: 51 Copynumber: 2.0 Consensus size: 50
15252 GTTCATCAAC
* **
15262 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
*
15312 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATACAAACACT-GTACACGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTGT
15363 T
1 T
15364 CTTCATTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
50 8 0.18
51 35 0.80
52 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
Found at i:17441 original size:30 final size:30
Alignment explanation
Indices: 17405--17463 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
17395 CTTCAAAACC
* *
17405 AGGAATGAATGGTGAAACAAGTTTTGAACA
1 AGGAATGAATAGTGAAACAAGTTTGGAACA
*
17435 AGGAATGAATAGTGATACAAGTTTGGAAC
1 AGGAATGAATAGTGAAACAAGTTTGGAAC
17464 CTGATAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.42, C:0.07, G:0.27, T:0.24
Consensus pattern (30 bp):
AGGAATGAATAGTGAAACAAGTTTGGAACA
Found at i:17598 original size:21 final size:20
Alignment explanation
Indices: 17560--17599 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
17550 ACTGTTTTGT
*
17560 TTTTTTCTTTCTGCATTTAG
1 TTTTTTCTTTCTGAATTTAG
*
17580 TTTTTTCTTTTGTGAATTTA
1 TTTTTTC-TTTCTGAATTTA
17600 AAGTTTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.12, C:0.10, G:0.10, T:0.68
Consensus pattern (20 bp):
TTTTTTCTTTCTGAATTTAG
Found at i:31090 original size:33 final size:33
Alignment explanation
Indices: 31048--31115 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
31038 ATGCCAACAA
31048 CAGGATCAAGAATTTGGGTTTGGATATTGATTT
1 CAGGATCAAGAATTTGGGTTTGGATATTGATTT
31081 CAGGATCAAGAATTTGGGTTTGGATATTGATTT
1 CAGGATCAAGAATTTGGGTTTGGATATTGATTT
31114 CA
1 CA
31116 ACAGCGCCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.07, G:0.26, T:0.38
Consensus pattern (33 bp):
CAGGATCAAGAATTTGGGTTTGGATATTGATTT
Found at i:34744 original size:20 final size:20
Alignment explanation
Indices: 34703--34745 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
34693 CTCTCACAAG
* *
34703 TTTCTAGCCGTTTGAGCTCT
1 TTTCTAGCCGTTTGAACACT
34723 TTTCTAGCCGTTAT-AACACT
1 TTTCTAGCCGTT-TGAACACT
34743 TTT
1 TTT
34746 TCCACTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.47
Consensus pattern (20 bp):
TTTCTAGCCGTTTGAACACT
Found at i:35393 original size:32 final size:32
Alignment explanation
Indices: 35353--35671 Score: 440
Period size: 32 Copynumber: 9.9 Consensus size: 32
35343 ATTAAAGAAA
* *
35353 AACGCCACAGATTGGTGGCGTTTTCTTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* * *
35385 TACGCCACAAATTAGTGGCATTTTCTTCCAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* *
35417 AACGCCACAAATTAGTGGCGTTTTCTTTAAAA
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
35449 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
*
35481 TACGCCACAAATTAGTGGCGTTTTCTTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* * * * *
35513 TACGCCACTAATTTGTGGCATTTTCTTCCAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
*
35545 AACGCCACAAATTAGTGGCGTTTTTCTTTAAAG
1 AACGCCACAAATTAGTGGCG-TTTTCTTCAAAG
* *
35578 AACGCCACAGATTAGTGGCGTTTTCTTTAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
35610 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* ** * *
35642 AACGTCACTGATTTGTGGCGTTTTATTCAA
1 AACGCCACAAATTAGTGGCGTTTTCTTCAA
35672 TAAACACCAT
Statistics
Matches: 255, Mismatches: 31, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
32 226 0.89
33 29 0.11
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (32 bp):
AACGCCACAAATTAGTGGCGTTTTCTTCAAAG
Found at i:35698 original size:129 final size:129
Alignment explanation
Indices: 35353--35680 Score: 426
Period size: 129 Copynumber: 2.6 Consensus size: 129
35343 ATTAAAGAAA
* * * * * * *
35353 AACGCCACAGATTGGTGGCGTTTTCTTCAAAGTACGCCACAAATTAGTGGCATTTTCTTCCAAGA
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAGAACGCCACTAATTTGTGGCATTTTATTCCAAAA
* * *
35418 ACGCCACAAATTAGT-GGCGTTTTCTTTAAAAAACGCCACAAATTAGTGGCGTTTTCTTCAAAG
66 ACACCACAAATTAGTAGCCTTTTTCTTTAAAAAACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* * * *
35481 TACGCCACAAATTAGTGGCGTTTTCTTCAAAGTACGCCACTAATTTGTGGCATTTTCTTCCAAGA
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAGAACGCCACTAATTTGTGGCATTTTATTCCAAAA
* * * * * *
35546 ACGCCACAAATTAGTGGCGTTTTTCTTTAAAGAACGCCACAGATTAGTGGCGTTTTCTTTAAAG
66 ACACCACAAATTAGTAGCCTTTTTCTTTAAAAAACGCCACAAATTAGTGGCGTTTTCTTCAAAG
* * *
35610 AACGCCACAAATTAGTGGCGTTTTCTTCAAAGAACGTCACTGATTTGTGGCGTTTTATT-CAATA
1 AACGCCACAAATTAGTGGCGTTTTCTTCAAAGAACGCCACTAATTTGTGGCATTTTATTCCAA-A
35674 AACACCA
65 AACACCA
35681 TGAATTTTCA
Statistics
Matches: 179, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
128 78 0.44
129 101 0.56
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (129 bp):
AACGCCACAAATTAGTGGCGTTTTCTTCAAAGAACGCCACTAATTTGTGGCATTTTATTCCAAAA
ACACCACAAATTAGTAGCCTTTTTCTTTAAAAAACGCCACAAATTAGTGGCGTTTTCTTCAAAG
Found at i:35732 original size:161 final size:161
Alignment explanation
Indices: 35390--35680 Score: 415
Period size: 161 Copynumber: 1.8 Consensus size: 161
35380 CAAAGTACGC
* *
35390 CACAAATTAGTGGC-ATTTTCTTCCAAGAACGCCACAAATTAGTGGCGTTTTCTTTAAAAAACGC
1 CACAAATTAGTGGCGTTTTTCTTCAAAGAACGCCACAAATTAGTGGCGTTTTCTTTAAAAAACGC
* * * *
35454 CACAAATTAGTGGCGTTTTCTTCAAAGTACGCCACAAATTAGTGGCGTTTTCTTCAAAGTACGCC
66 CACAAATTAGTGGCGTTTTCTTCAAAGAACGCCACAAATTAGTGGCGTTTTATTCAAAGAACACC
* **
35519 ACTAATTTGTGGCATTTTCTTCCAAGAACGC
131 ACTAATTTGTGCCATTTTCTTCCAAGAACAA
* * *
35550 CACAAATTAGTGGCGTTTTTCTTTAAAGAACGCCACAGATTAGTGGCGTTTTCTTTAAAGAACGC
1 CACAAATTAGTGGCGTTTTTCTTCAAAGAACGCCACAAATTAGTGGCGTTTTCTTTAAAAAACGC
* ** *
35615 CACAAATTAGTGGCGTTTTCTTCAAAGAACGTCACTGATTTGTGGCGTTTTATTCAATA-AACAC
66 CACAAATTAGTGGCGTTTTCTTCAAAGAACGCCACAAATTAGTGGCGTTTTATTCAA-AGAACAC
35679 CA
130 CA
35681 TGAATTTTCA
Statistics
Matches: 116, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
160 14 0.12
161 101 0.87
162 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (161 bp):
CACAAATTAGTGGCGTTTTTCTTCAAAGAACGCCACAAATTAGTGGCGTTTTCTTTAAAAAACGC
CACAAATTAGTGGCGTTTTCTTCAAAGAACGCCACAAATTAGTGGCGTTTTATTCAAAGAACACC
ACTAATTTGTGCCATTTTCTTCCAAGAACAA
Found at i:36480 original size:33 final size:33
Alignment explanation
Indices: 36364--36480 Score: 148
Period size: 33 Copynumber: 3.5 Consensus size: 33
36354 TAATCTCATT
* * *
36364 TCTTCTGTCTTCTTCAAGGCGAGCTAGCTCATT-
1 TCTTCTATCTTCTTCAATGCGAGCCAGCTC-TTG
*
36397 TCTTCTCTCTTCTTCAACT-CGAGCCAGCTCTTG
1 TCTTCTATCTTCTTCAA-TGCGAGCCAGCTCTTG
*
36430 TCGTCTATCTTCTTCAATGCGAGCCAGCTCTTG
1 TCTTCTATCTTCTTCAATGCGAGCCAGCTCTTG
*
36463 TCTTCTTTCTTCTTCAAT
1 TCTTCTATCTTCTTCAAT
36481 TCTTGCAAGC
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
32 3 0.04
33 71 0.96
ACGTcount: A:0.14, C:0.31, G:0.14, T:0.42
Consensus pattern (33 bp):
TCTTCTATCTTCTTCAATGCGAGCCAGCTCTTG
Found at i:36492 original size:33 final size:33
Alignment explanation
Indices: 36364--36496 Score: 142
Period size: 33 Copynumber: 4.0 Consensus size: 33
36354 TAATCTCATT
* ** *
36364 TCTTCTGTCTTCTTCAAGGCGAGCTAGCTCATT-
1 TCTTCTATCTTCTTCAATTCGAGCCAGCTC-TTG
* *
36397 TCTTCTCTCTTCTTCAACTCGAGCCAGCTCTTG
1 TCTTCTATCTTCTTCAATTCGAGCCAGCTCTTG
* *
36430 TCGTCTATCTTCTTCAATGCGAGCCAGCTCTTG
1 TCTTCTATCTTCTTCAATTCGAGCCAGCTCTTG
* ** *
36463 TCTTCTTTCTTCTTCAATTCTTGCAAGCTCTTG
1 TCTTCTATCTTCTTCAATTCGAGCCAGCTCTTG
36496 T
1 T
36497 TGCCTTTCTA
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
32 2 0.02
33 83 0.98
ACGTcount: A:0.14, C:0.30, G:0.14, T:0.42
Consensus pattern (33 bp):
TCTTCTATCTTCTTCAATTCGAGCCAGCTCTTG
Found at i:36492 original size:66 final size:66
Alignment explanation
Indices: 36371--36496 Score: 173
Period size: 66 Copynumber: 1.9 Consensus size: 66
36361 ATTTCTTCTG
* *
36371 TCTTCTTCAAGGCGAGCTAGCTCATTTCTTCTCTCTTCTTCAACTCGAGCCAGCTCTTGTCGTCT
1 TCTTCTTCAAGGCGAGCCAGCTCATTTCTTCTCTCTTCTTCAACTCGAGCAAGCTCTTGTCGTCT
36436 A
66 A
* * * **
36437 TCTTCTTCAATGCGAGCCAGCTC-TTGTCTTCTTTCTTCTTCAATTCTTGCAAGCTCTTGT
1 TCTTCTTCAAGGCGAGCCAGCTCATT-TCTTCTCTCTTCTTCAACTCGAGCAAGCTCTTGT
36497 TGCCTTTCTA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
65 2 0.04
66 50 0.96
ACGTcount: A:0.14, C:0.30, G:0.14, T:0.41
Consensus pattern (66 bp):
TCTTCTTCAAGGCGAGCCAGCTCATTTCTTCTCTCTTCTTCAACTCGAGCAAGCTCTTGTCGTCT
A
Done.