Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022745.1 Corchorus olitorius cultivar O-4 contig22778, 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: 9793
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:234 original size:29 final size:29
Alignment explanation
Indices: 201--274 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 29
191 GCACTTGAAG
* *
201 TGACCAAAATGCCCCCTAGATGTGTAAAA
1 TGACCAAAATGCCCCCTAGATATGCAAAA
*
230 TGACCAAAATG-CCCCTGGATATGCAAAA
1 TGACCAAAATGCCCCCTAGATATGCAAAA
* *
258 GGACCAAAATCCCCCCT
1 TGACCAAAATGCCCCCT
275 TAAGTGACCC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 23 0.59
29 16 0.41
ACGTcount: A:0.36, C:0.30, G:0.16, T:0.18
Consensus pattern (29 bp):
TGACCAAAATGCCCCCTAGATATGCAAAA
Found at i:4350 original size:29 final size:29
Alignment explanation
Indices: 4278--4351 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 29
4268 GGGTCACTTA
* *
4278 AGGGGGCATTTTGGTCATTCTGCATATCT
1 AGGGGGCATTTTGGTCATTCTACACATCT
* *
4307 A-GGGGCATTTTGGTCATTTTATACATCT
1 AGGGGGCATTTTGGTCATTCTACACATCT
4335 AGGGGGCATTTTGGTCA
1 AGGGGGCATTTTGGTCA
4352 CTTCAAGTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 24 0.60
29 16 0.40
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (29 bp):
AGGGGGCATTTTGGTCATTCTACACATCT
Found at i:4732 original size:22 final size:22
Alignment explanation
Indices: 4705--4755 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
4695 TTAGTAATAG
*
4705 TTGCATTTTTGCATGGCACCTT
1 TTGCATTTTTGCACGGCACCTT
* *
4727 TTGCATTTTTGCACGGTATCTT
1 TTGCATTTTTGCACGGCACCTT
4749 TTGCATT
1 TTGCATT
4756 CATCCTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.49
Consensus pattern (22 bp):
TTGCATTTTTGCACGGCACCTT
Found at i:6569 original size:16 final size:16
Alignment explanation
Indices: 6535--6606 Score: 85
Period size: 16 Copynumber: 4.6 Consensus size: 16
6525 CGGGCTCGGG
*
6535 CGGGTTCGGGTA-CTT
1 CGGGTTCGGGTATTTT
*
6550 CGGGTTGGGGTATTTT
1 CGGGTTCGGGTATTTT
*
6566 CGGGTTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
*
6582 CGGGTTTGGGTATTTT
1 CGGGTTCGGGTATTTT
6598 CGGGTTCGG
1 CGGGTTCGG
6607 TCTCGGGTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
15 12 0.26
16 34 0.72
17 1 0.02
ACGTcount: A:0.06, C:0.12, G:0.43, T:0.39
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:6593 original size:32 final size:31
Alignment explanation
Indices: 6535--6606 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 31
6525 CGGGCTCGGG
6535 CGGGTTCGGGTACTTCGGGTTGGGGTATTTT
1 CGGGTTCGGGTACTTCGGGTTGGGGTATTTT
*
6566 CGGGTTCGGGTTA-TGTCGGGTTTGGGTATTTT
1 CGGGTTCGGG-TACT-TCGGGTTGGGGTATTTT
6598 CGGGTTCGG
1 CGGGTTCGG
6607 TCTCGGGTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
31 11 0.29
32 27 0.71
ACGTcount: A:0.06, C:0.12, G:0.43, T:0.39
Consensus pattern (31 bp):
CGGGTTCGGGTACTTCGGGTTGGGGTATTTT
Found at i:6605 original size:6 final size:6
Alignment explanation
Indices: 6596--6655 Score: 63
Period size: 6 Copynumber: 10.3 Consensus size: 6
6586 TTTGGGTATT
* *
6596 TTCGGG TTC-GG TCTCGGG -TAGGG TTCGGG TTCGGG CTCGGG -TCGGG
1 TTCGGG TTCGGG T-TCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG
*
6642 TTCGGG CTCGGG TT
1 TTCGGG TTCGGG TT
6656 TGATTTCGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
5 12 0.27
6 31 0.69
7 2 0.04
ACGTcount: A:0.02, C:0.20, G:0.48, T:0.30
Consensus pattern (6 bp):
TTCGGG
Found at i:6626 original size:23 final size:23
Alignment explanation
Indices: 6596--6653 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
6586 TTTGGGTATT
*
6596 TTCGGGTTCGGTCTCGGGTAGGG
1 TTCGGGTTCGGGCTCGGGTAGGG
*
6619 TTCGGGTTCGGGCTCGGGTCGGG
1 TTCGGGTTCGGGCTCGGGTAGGG
*
6642 TTCGGGCTCGGG
1 TTCGGGTTCGGG
6654 TTTGATTTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.02, C:0.21, G:0.50, T:0.28
Consensus pattern (23 bp):
TTCGGGTTCGGGCTCGGGTAGGG
Found at i:6629 original size:17 final size:18
Alignment explanation
Indices: 6599--6655 Score: 66
Period size: 17 Copynumber: 3.3 Consensus size: 18
6589 GGGTATTTTC
6599 GGGTTC-GGTCTCGGG-TA
1 GGGTTCGGGT-TCGGGCTA
*
6616 GGGTTCGGGTTCGGGCTC
1 GGGTTCGGGTTCGGGCTA
*
6634 GGG-TCGGGTTCGGGCTC
1 GGGTTCGGGTTCGGGCTA
6651 GGGTT
1 GGGTT
6656 TGATTTCGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
17 28 0.78
18 8 0.22
ACGTcount: A:0.02, C:0.19, G:0.51, T:0.28
Consensus pattern (18 bp):
GGGTTCGGGTTCGGGCTA
Found at i:6788 original size:8 final size:8
Alignment explanation
Indices: 6768--6801 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
6758 AAGTTTATTT
6768 ATAATAT-
1 ATAATATA
6775 ATAATATA
1 ATAATATA
6783 ATAATATA
1 ATAATATA
6791 ATAATATA
1 ATAATATA
6799 ATA
1 ATA
6802 TAACATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAATATA
Found at i:6791 original size:13 final size:13
Alignment explanation
Indices: 6767--6804 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
6757 TAAGTTTATT
6767 TATAAT-ATATAA
1 TATAATAATATAA
6779 TATAATAATATAA
1 TATAATAATATAA
6792 TA-ATATAATATAA
1 TATA-ATAATATAA
6805 CATTATTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATAATAATATAA
Found at i:7111 original size:31 final size:31
Alignment explanation
Indices: 7076--7147 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
7066 TAAATTATTG
*
7076 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
7107 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
7138 CAAATTAAAA
1 CAAATTAAAA
7148 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:7402 original size:14 final size:15
Alignment explanation
Indices: 7375--7406 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
7365 TGTTTTAAGT
7375 TATATAAGTTATATA
1 TATATAAGTTATATA
7390 TATATAA-TTATATA
1 TATATAAGTTATATA
7404 TAT
1 TAT
7407 TTAGTAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TATATAAGTTATATA
Found at i:7610 original size:17 final size:17
Alignment explanation
Indices: 7584--7634 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
7574 TCAAATTATT
7584 TCGGGTTCGGGCTCGGG
1 TCGGGTTCGGGCTCGGG
*
7601 TCGGGATCGGGCTCGGG
1 TCGGGTTCGGGCTCGGG
7618 TCGGGTTCGGGCTCGGG
1 TCGGGTTCGGGCTCGGG
7635 CTGCCTCGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.02, C:0.24, G:0.53, T:0.22
Consensus pattern (17 bp):
TCGGGTTCGGGCTCGGG
Found at i:7616 original size:23 final size:23
Alignment explanation
Indices: 7584--7677 Score: 77
Period size: 23 Copynumber: 4.0 Consensus size: 23
7574 TCAAATTATT
*
7584 TCGGGTTCGGGCTCGGG-TCGGGA
1 TCGGGCTCGGG-TCGGGTTCGGGA
*
7607 TCGGGCTCGGGTCGGGTTCGGGC
1 TCGGGCTCGGGTCGGGTTCGGGA
**
7630 TCGGGCT-GCCTCGGGTTCGGGTA
1 TCGGGCTCGGGTCGGGTTCGGG-A
*
7653 TTTTCGGGCTCGGG-CAGGTTCGGGA
1 ---TCGGGCTCGGGTCGGGTTCGGGA
7678 CGTTGACTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
22 17 0.30
23 22 0.39
25 1 0.02
26 16 0.28
27 1 0.02
ACGTcount: A:0.04, C:0.23, G:0.48, T:0.24
Consensus pattern (23 bp):
TCGGGCTCGGGTCGGGTTCGGGA
Found at i:7643 original size:22 final size:23
Alignment explanation
Indices: 7595--7650 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
7585 CGGGTTCGGG
*
7595 CTCGGG-TCGGGATCGGGCTCGG
1 CTCGGGTTCGGGATCGGGCTCGC
* *
7617 GTCGGGTTCGGGCTCGGGCT-GC
1 CTCGGGTTCGGGATCGGGCTCGC
7639 CTCGGGTTCGGG
1 CTCGGGTTCGGG
7651 TATTTTCGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 17 0.59
23 12 0.41
ACGTcount: A:0.02, C:0.27, G:0.50, T:0.21
Consensus pattern (23 bp):
CTCGGGTTCGGGATCGGGCTCGC
Found at i:7651 original size:6 final size:6
Alignment explanation
Indices: 7584--7636 Score: 65
Period size: 6 Copynumber: 9.2 Consensus size: 6
7574 TCAAATTATT
* * *
7584 TCGGGT TCGGGC TCGGG- TCGGGA TCGGGC TCGGG- TCGGGT TCGGGC
1 TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC TCGGGC
7630 TCGGGC T
1 TCGGGC T
7637 GCCTCGGGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
5 10 0.24
6 32 0.76
ACGTcount: A:0.02, C:0.25, G:0.51, T:0.23
Consensus pattern (6 bp):
TCGGGC
Found at i:7674 original size:16 final size:16
Alignment explanation
Indices: 7587--7676 Score: 72
Period size: 16 Copynumber: 5.5 Consensus size: 16
7577 AATTATTTCG
*
7587 GGTTCGGGCTCGGGTCG
1 GGTTCGGGCTCGGG-CA
* *
7604 GGATCGGGCTCGGGTCG
1 GGTTCGGGCTCGGG-CA
*
7621 GGTTCGGGCTCGGGCT
1 GGTTCGGGCTCGGGCA
** * *
7637 GCCTCGGGTTCGGGTA
1 GGTTCGGGCTCGGGCA
**
7653 TTTTCGGGCTCGGGCA
1 GGTTCGGGCTCGGGCA
7669 GGTTCGGG
1 GGTTCGGG
7677 ACGTTGACTT
Statistics
Matches: 58, Mismatches: 15, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
16 29 0.50
17 29 0.50
ACGTcount: A:0.03, C:0.23, G:0.49, T:0.24
Consensus pattern (16 bp):
GGTTCGGGCTCGGGCA
Found at i:8148 original size:41 final size:42
Alignment explanation
Indices: 8062--8168 Score: 153
Period size: 41 Copynumber: 2.6 Consensus size: 42
8052 GTGTGATTTC
*
8062 ATTCAATTTTATCCCTAATTTAGACTAATTATTTATTTATTG
1 ATTCAATTTTGTCCCTAATTTAGACTAATTATTTATTTATTG
* *
8104 ATTCAATTTTGTCCCTAATTTAGAGTAA-TATTTTTTTATTG
1 ATTCAATTTTGTCCCTAATTTAGACTAATTATTTATTTATTG
* **
8145 ATTCAATTTCGTCCCGGATTTAGA
1 ATTCAATTTTGTCCCTAATTTAGA
8169 ATTTTATCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 33 0.56
42 26 0.44
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (42 bp):
ATTCAATTTTGTCCCTAATTTAGACTAATTATTTATTTATTG
Done.