Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021230.1 Corchorus olitorius cultivar O-4 contig21263, 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: 60359
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7228 original size:14 final size:14
Alignment explanation
Indices: 7204--7263 Score: 59
Period size: 14 Copynumber: 4.1 Consensus size: 14
7194 CGCTATATTC
*
7204 AAATTTTATTTTCT
1 AAATATTATTTTCT
*
7218 AAATATCATTTT-T
1 AAATATTATTTTCT
*
7231 AAACATTTATAATTTCT
1 AAATA-TTAT--TTTCT
7248 AAATATTATTTTCT
1 AAATATTATTTTCT
7262 AA
1 AA
7264 TTATAATTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 5 0.14
14 20 0.54
16 7 0.19
17 5 0.14
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.53
Consensus pattern (14 bp):
AAATATTATTTTCT
Found at i:7289 original size:44 final size:44
Alignment explanation
Indices: 7241--7334 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
7231 AAACATTTAT
* * * *
7241 AATTTCTAAATATTATTTTCTAATTATAATTTCATTACATATAC
1 AATTTCTAAATAATATTTACAAAATATAATTTCATTACATATAC
* * * *
7285 AATTTCTATATAATGTTTAGAAAATATAATTTCATTACATATAT
1 AATTTCTAAATAATATTTACAAAATATAATTTCATTACATATAC
7329 AATTTC
1 AATTTC
7335 ATTACATATA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (44 bp):
AATTTCTAAATAATATTTACAAAATATAATTTCATTACATATAC
Found at i:7330 original size:17 final size:17
Alignment explanation
Indices: 7308--7395 Score: 109
Period size: 17 Copynumber: 5.6 Consensus size: 17
7298 TGTTTAGAAA
7308 ATATAATTTCATTACAT
1 ATATAATTTCATTACAT
7325 ATATAATTTCATTACAT
1 ATATAATTTCATTACAT
7342 ATATAATTT-A-TA-A-
1 ATATAATTTCATTACAT
* *
7355 ATATTATTTC-CTA-AT
1 ATATAATTTCATTACAT
7370 -TATAATTTCATTACAT
1 ATATAATTTCATTACAT
7386 ATATAATTTC
1 ATATAATTTC
7396 TAAAAATTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
13 8 0.13
14 12 0.19
15 4 0.06
16 3 0.05
17 35 0.56
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATAATTTCATTACAT
Found at i:7334 original size:61 final size:61
Alignment explanation
Indices: 7265--7395 Score: 181
Period size: 61 Copynumber: 2.1 Consensus size: 61
7255 ATTTTCTAAT
* * * *
7265 TATAATTTCATTACATATACAATTTCTATATAATGTTTAGAAAATATAATTTCATTACATA
1 TATAATTTCATTACATATACAATTTATAAATAATATTTACAAAATATAATTTCATTACATA
* * * * *
7326 TATAATTTCATTACATATATAATTTATAAATATTATTTCCTAATTATAATTTCATTACATA
1 TATAATTTCATTACATATACAATTTATAAATAATATTTACAAAATATAATTTCATTACATA
7387 TATAATTTC
1 TATAATTTC
7396 TAAAAATTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (61 bp):
TATAATTTCATTACATATACAATTTATAAATAATATTTACAAAATATAATTTCATTACATA
Found at i:7374 original size:44 final size:44
Alignment explanation
Indices: 7326--7430 Score: 158
Period size: 44 Copynumber: 2.4 Consensus size: 44
7316 TCATTACATA
*
7326 TATAATTTCATTACATATATAATTTATAAATATTATTTCCTAAT
1 TATAATTTCATTACATATATAATTTATAAAAATTATTTCCTAAT
* * *
7370 TATAATTTCATTACATATATAATTTCTAAAAATTATTTTCTCAT
1 TATAATTTCATTACATATATAATTTATAAAAATTATTTCCTAAT
*
7414 TATAATTTC-TTAAATAT
1 TATAATTTCATTACATAT
7431 GGGGGCAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 7 0.12
44 49 0.88
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (44 bp):
TATAATTTCATTACATATATAATTTATAAAAATTATTTCCTAAT
Found at i:7420 original size:105 final size:104
Alignment explanation
Indices: 7233--7430 Score: 263
Period size: 105 Copynumber: 1.9 Consensus size: 104
7223 TCATTTTTAA
* * * *
7233 ACATTTATAATTTCTAAATATTATTTTCTAATTATAATTTCATTACATATACAATTTCTATATAA
1 ACATATATAATTTATAAATATTATTTCCTAATTATAATTTCATTACATATACAATTTCTATAAAA
* * *
7298 TGTTTAGAAAATATAATTTCATTACATATATAATTTCATT
66 TATTTACAAAATATAATTTC-TTAAATATATAATTTCATT
*
7338 ACATATATAATTTATAAATATTATTTCCTAATTATAATTTCATTACATATATAATTTCTA-AAAA
1 ACATATATAATTTATAAATATTATTTCCTAATTATAATTTCATTACATATACAATTTCTATAAAA
* ** *
7402 TTATTTTCTCATTATAATTTCTTAAATAT
66 -TATTTACAAAATATAATTTCTTAAATAT
7431 GGGGGCAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
104 10 0.12
105 70 0.88
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (104 bp):
ACATATATAATTTATAAATATTATTTCCTAATTATAATTTCATTACATATACAATTTCTATAAAA
TATTTACAAAATATAATTTCTTAAATATATAATTTCATT
Found at i:8048 original size:20 final size:21
Alignment explanation
Indices: 8009--8048 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7999 CGTTAAAGTC
* *
8009 TCGATTTGTTGTTGTAGGTTT
1 TCGATTTATGGTTGTAGGTTT
8030 TCGATTTATGGTT-TAGGTT
1 TCGATTTATGGTTGTAGGTT
8049 GAAAATCCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.05, G:0.28, T:0.55
Consensus pattern (21 bp):
TCGATTTATGGTTGTAGGTTT
Found at i:11401 original size:17 final size:17
Alignment explanation
Indices: 11379--11411 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11369 TCATTACATC
11379 AATTAA-AATTATAAATT
1 AATTAATAA-TATAAATT
11396 AATTAATAATATAAAT
1 AATTAATAATATAAAT
11412 ATCCATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATTAATAATATAAATT
Found at i:12537 original size:17 final size:16
Alignment explanation
Indices: 12513--12551 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
12503 GCTTTTGATC
12513 TTAGGTCACTCAGGTT
1 TTAGGTCACTCAGGTT
* *
12529 TTCAGGTCATTCGGGTT
1 TT-AGGTCACTCAGGTT
12546 TTAGGT
1 TTAGGT
12552 TTTTCGGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.41
Consensus pattern (16 bp):
TTAGGTCACTCAGGTT
Found at i:17478 original size:14 final size:14
Alignment explanation
Indices: 17459--17487 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17449 GGATTTTCGT
17459 AGATCTGAGCCGAC
1 AGATCTGAGCCGAC
17473 AGATCTGAGCCGAC
1 AGATCTGAGCCGAC
17487 A
1 A
17488 ATCGCGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.14
Consensus pattern (14 bp):
AGATCTGAGCCGAC
Found at i:31789 original size:48 final size:47
Alignment explanation
Indices: 31718--31813 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 47
31708 TAAATTTTTT
31718 ATTAAAAAATATTAATTTATGAAGTGAGAATGAAGGGTTAA-AAAAAGA
1 ATTAAAAAATATTAATTTATGAAGTGAGAAT--AGGGTTAATAAAAAGA
* *
31766 ATTAAAAACTATTAATTTATGAAGTGAGAATTGGGTTAATAAAAAGA
1 ATTAAAAAATATTAATTTATGAAGTGAGAATAGGGTTAATAAAAAGA
31813 A
1 A
31814 AGGAAAAGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
46 7 0.16
47 8 0.18
48 30 0.67
ACGTcount: A:0.52, C:0.01, G:0.18, T:0.29
Consensus pattern (47 bp):
ATTAAAAAATATTAATTTATGAAGTGAGAATAGGGTTAATAAAAAGA
Found at i:36821 original size:30 final size:30
Alignment explanation
Indices: 36785--36847 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
36775 TCTTCAAGGG
*
36785 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATAATGCG-CCAAGGACTTATCAT
36815 GGAGGGAATAATGCGCCAAGGACTTATCAT
1 GGAGGGAATAATGCGCCAAGGACTTATCAT
36845 GGA
1 GGA
36848 CTTGAAGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.19
Consensus pattern (30 bp):
GGAGGGAATAATGCGCCAAGGACTTATCAT
Found at i:43794 original size:15 final size:15
Alignment explanation
Indices: 43774--43817 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
43764 CTTCCAGTTG
43774 GATGCAGCTTGGTTA
1 GATGCAGCTTGGTTA
*
43789 GATGCAGCTTGGTTT
1 GATGCAGCTTGGTTA
**
43804 GATGTTGCTTGGTT
1 GATGCAGCTTGGTT
43818 GGAGGTTGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.14, C:0.11, G:0.34, T:0.41
Consensus pattern (15 bp):
GATGCAGCTTGGTTA
Found at i:43816 original size:30 final size:30
Alignment explanation
Indices: 43780--43838 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
43770 GTTGGATGCA
*
43780 GCTTGGTTAGATGCAGCTTGGTTTGATGTT
1 GCTTGGTTAGAGGCAGCTTGGTTTGATGTT
* **
43810 GCTTGGTTGGAGGTTGCTTGGTTTGATGT
1 GCTTGGTTAGAGGCAGCTTGGTTTGATGT
43839 GGATGCAGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.10, C:0.08, G:0.37, T:0.44
Consensus pattern (30 bp):
GCTTGGTTAGAGGCAGCTTGGTTTGATGTT
Found at i:43825 original size:15 final size:15
Alignment explanation
Indices: 43795--43832 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
43785 GTTAGATGCA
* *
43795 GCTTGGTTTGATGTT
1 GCTTGGTTGGAGGTT
43810 GCTTGGTTGGAGGTT
1 GCTTGGTTGGAGGTT
43825 GCTTGGTT
1 GCTTGGTT
43833 TGATGTGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.08, G:0.39, T:0.47
Consensus pattern (15 bp):
GCTTGGTTGGAGGTT
Found at i:46097 original size:15 final size:15
Alignment explanation
Indices: 46079--46178 Score: 146
Period size: 15 Copynumber: 6.7 Consensus size: 15
46069 CCGATATGAG
* *
46079 GAATCCACACTATCA
1 GAATCCCCATTATCA
*
46094 GAATCCCCATAATCA
1 GAATCCCCATTATCA
*
46109 GGATCCCCATTATCA
1 GAATCCCCATTATCA
46124 GAATCCCCATTATCA
1 GAATCCCCATTATCA
*
46139 GGATCCCCATTATCA
1 GAATCCCCATTATCA
*
46154 GGATCCCCATTATCA
1 GAATCCCCATTATCA
46169 GAATCCCCAT
1 GAATCCCCAT
46179 CCTCAACTTG
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 77 1.00
ACGTcount: A:0.32, C:0.34, G:0.10, T:0.24
Consensus pattern (15 bp):
GAATCCCCATTATCA
Found at i:46138 original size:45 final size:45
Alignment explanation
Indices: 46079--46178 Score: 164
Period size: 45 Copynumber: 2.2 Consensus size: 45
46069 CCGATATGAG
* *
46079 GAATCCACACTATCAGAATCCCCATAATCAGGATCCCCATTATCA
1 GAATCCCCATTATCAGAATCCCCATAATCAGGATCCCCATTATCA
* *
46124 GAATCCCCATTATCAGGATCCCCATTATCAGGATCCCCATTATCA
1 GAATCCCCATTATCAGAATCCCCATAATCAGGATCCCCATTATCA
46169 GAATCCCCAT
1 GAATCCCCAT
46179 CCTCAACTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.32, C:0.34, G:0.10, T:0.24
Consensus pattern (45 bp):
GAATCCCCATTATCAGAATCCCCATAATCAGGATCCCCATTATCA
Found at i:46382 original size:18 final size:18
Alignment explanation
Indices: 46359--46404 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
46349 TTATTGTGAG
*
46359 CATTCTCAGCTTCCTCAC
1 CATTCTCACCTTCCTCAC
* *
46377 CATTCTCACCTTGCTGAC
1 CATTCTCACCTTCCTCAC
46395 CATTCTCACC
1 CATTCTCACC
46405 ATCATTCGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.17, C:0.43, G:0.07, T:0.33
Consensus pattern (18 bp):
CATTCTCACCTTCCTCAC
Found at i:46846 original size:33 final size:34
Alignment explanation
Indices: 46797--46864 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 34
46787 AGACAACACA
* *
46797 AAAATAAATAGTTTATTAAACACATATAA-CAGAC
1 AAAACAAATAGTTTATTAAACAAATA-AACCAGAC
*
46831 AAAACAAATA-TTTATTCAACAAATAAACCAGAC
1 AAAACAAATAGTTTATTAAACAAATAAACCAGAC
46864 A
1 A
46865 TTAAACATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 2 0.07
33 19 0.63
34 9 0.30
ACGTcount: A:0.57, C:0.15, G:0.04, T:0.24
Consensus pattern (34 bp):
AAAACAAATAGTTTATTAAACAAATAAACCAGAC
Found at i:47000 original size:26 final size:28
Alignment explanation
Indices: 46971--47023 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 28
46961 CAATTTGCAA
46971 AACCCATAAAAAACAATA-A-AAAAACG
1 AACCCATAAAAAACAATACATAAAAACG
46997 AACCCATAAAAAACAATACATAAAAAC
1 AACCCATAAAAAACAATACATAAAAAC
47024 CAAATACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 18 0.72
27 1 0.04
28 6 0.24
ACGTcount: A:0.68, C:0.21, G:0.02, T:0.09
Consensus pattern (28 bp):
AACCCATAAAAAACAATACATAAAAACG
Found at i:47022 original size:15 final size:15
Alignment explanation
Indices: 47001--47036 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
46991 AAAACGAACC
47001 CATAAAAAAC-AATA
1 CATAAAAAACAAATA
*
47015 CATAAAAACCAAATA
1 CATAAAAAACAAATA
47030 CATAAAA
1 CATAAAA
47037 CTTACCTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (15 bp):
CATAAAAAACAAATA
Found at i:49956 original size:11 final size:11
Alignment explanation
Indices: 49940--49968 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
49930 ATGCACAAAG
49940 TAAATAAATAA
1 TAAATAAATAA
49951 TAAATAAATAA
1 TAAATAAATAA
49962 T-AATAAA
1 TAAATAAA
49969 AAAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:53465 original size:41 final size:40
Alignment explanation
Indices: 53380--53466 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 40
53370 TAGTTGCCTT
* *
53380 TGCTTTATGTAGAAATTGCCTCTTAGCCACGTTAAGTTTG
1 TGCTTTATGTAGAAATTGCCTCCTAGCCACATTAAGTTTG
* ***
53420 TGCTTTATGTAGAACATTGTCTCCTAGCTGTATTAAGTTTG
1 TGCTTTATGTAGAA-ATTGCCTCCTAGCCACATTAAGTTTG
53461 TGCTTT
1 TGCTTT
53467 TACAACATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 14 0.35
41 26 0.65
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.44
Consensus pattern (40 bp):
TGCTTTATGTAGAAATTGCCTCCTAGCCACATTAAGTTTG
Done.