Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014268.1 Corchorus capsularis cultivar CVL-1 contig14289, 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: 50735
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2363 original size:35 final size:35
Alignment explanation
Indices: 2317--2777 Score: 703
Period size: 35 Copynumber: 13.2 Consensus size: 35
2307 TCCAGAGCGG
* *
2317 TCATTTTAAGAAGTTTTTAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
2352 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
2387 TCATATCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* *
2422 TCATTTCAAGAAGTTTTCAGAAGCCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
2457 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* *
2492 TCATTCCAAGAAGTTTTTAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
2527 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* *
2562 TCATATCAAGAAGTTTTTAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
2597 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATA
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
2632 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
2667 TCATATCAAGAAGTTTTCAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* **
2702 TCATTTCAAGAAGTTTCCA-ACTATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATC
* * *
2737 TCATTTTC-AGTAGTTTCCA-ACGATCAGAGTTGATC
1 TCA-TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATC
*
2772 GCATTT
1 TCATTT
2778 TCAGTATTTT
Statistics
Matches: 396, Mismatches: 28, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
34 4 0.01
35 388 0.98
36 4 0.01
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (35 bp):
TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
Found at i:2752 original size:105 final size:105
Alignment explanation
Indices: 2317--2946 Score: 694
Period size: 105 Copynumber: 6.0 Consensus size: 105
2307 TCCAGAGCGG
* *
2317 TCATTTTAAGAAGTTTTTAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGT
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGT
* * *
2382 TGATCTCATATCAAGAAGTTTTCAGAGGTCAGAGTTGATC
66 TGATCTCATTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
* *
2422 TCATTTCAAGAAGTTTTCAGAAGCCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGT
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGT
* ** *
2487 TGATCTCATTCCAAGAAGTTTTTAGAGGTCAGAGTTGATC
66 TGATCTCATTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
* *
2527 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATCAAGAAGTTTTTAGAGGTCAGAGT
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGT
* * *
2592 TGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATA
66 TGATCTCATTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
* *
2632 TCATTCCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATATCAAGAAGTTTTCAGAGGTCAGAGT
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGT
*
2697 TGATCTCATTTCAAGAAGTTTCCA-ACTATCAGAGTTGATC
66 TGATCTCATTTCAAGAAGTTTCCAGA-GATCAGAGTTGATC
* * * * * *
2737 TCATTTTC-AGTAGTTTCCA-ACGATCAGAGTTGATCGCATTTTC-AGTA-TTTTCCA-ACGATC
1 TCA-TTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATCTCA-TTTCAAGAAGTTTT-CAGA-GGTC
* *
2797 AGAGTTGATCGCATTTTC-AGTAGTTTCCA-ACGATCAGAGTTGATC
61 AGAGTTGATCTCA-TTTCAAGAAGTTTCCAGA-GATCAGAGTTGATC
* * * * * * ** *
2842 GCATTTTC-AGTA-TTTTCCA-ACGATCAGAGTTGATCGCATTTTC-AGTAGTTTCCA-ACAATT
1 TCA-TTTCAAGAAGTTTT-CAGA-GGTCAGAGTTGATCTCA-TTTCAAGAAGTTTTCAGA-GGTC
* *
2902 AGAGGTGATCTCATTTCAAGAAATTTCC-GATGATCAGAGTTGATC
61 AGAGTTGATCTCATTTCAAGAAGTTTCCAGA-GATCAGAGTTGATC
2947 CAGAGGAGTT
Statistics
Matches: 473, Mismatches: 41, Indels: 22
0.88 0.08 0.04
Matches are distributed among these distances:
104 14 0.03
105 446 0.94
106 13 0.03
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (105 bp):
TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGT
TGATCTCATTTCAAGAAGTTTCCAGAGATCAGAGTTGATC
Found at i:2778 original size:35 final size:35
Alignment explanation
Indices: 2690--2946 Score: 356
Period size: 35 Copynumber: 7.3 Consensus size: 35
2680 TTTTCAGAGG
* * *
2690 TCAGAGTTGATCTCA-TTTCAAGAAGTTTCCAACTA
1 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGA
*
2725 TCAGAGTTGATCTCATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
2760 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
2795 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
2830 TCAGAGTTGATCGCATTTTCAGTATTTTCCAACGA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
*
2865 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACAA
1 TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
* * * * * * *
2900 TTAGAGGTGATCTCA-TTTCAAGAAATTTCCGATGA
1 TCAGAGTTGATCGCATTTTC-AGTAGTTTCCAACGA
2935 TCAGAGTTGATC
1 TCAGAGTTGATC
2947 CAGAGGAGTT
Statistics
Matches: 202, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
34 4 0.02
35 194 0.96
36 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (35 bp):
TCAGAGTTGATCGCATTTTCAGTAGTTTCCAACGA
Found at i:4290 original size:87 final size:85
Alignment explanation
Indices: 4110--4293 Score: 230
Period size: 87 Copynumber: 2.1 Consensus size: 85
4100 TAATAAAATT
*
4110 GATAAAGATTTAAAGAGAATATTTTCCAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTG
1 GATAAATA-TTAAAGAGAATATTTTCCAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTG
*
4175 AAGAAATAAATAAATAATAAA
65 AAGAAATAAATAAAAAATAAA
* * *
4196 AATTAAATATTAATGAGAATATTTCTCCAAATCTTGCCAGATTGTGGGAGATTTAGGAGATA-TT
1 GA-TAAATATTAAAGAGAATATTT-TCCAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTT
*
4260 -AA-ATAATAGTAATAAAAAAGTTAA
64 GAAGA-AATA--AATAAAAAA-TAAA
4284 GATAAATATT
1 GATAAATATT
4294 TACATAATTA
Statistics
Matches: 85, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
84 1 0.01
85 6 0.07
86 17 0.20
87 57 0.67
88 4 0.05
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (85 bp):
GATAAATATTAAAGAGAATATTTTCCAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTGA
AGAAATAAATAAAAAATAAA
Found at i:15409 original size:25 final size:26
Alignment explanation
Indices: 15381--15439 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
15371 TTCTACTTCT
*
15381 ATATTAATTA-GACAATTTCACCATA
1 ATATTAATTACAACAATTTCACCATA
*
15406 ATATTTTAATTACAATAATTTCACCATA
1 ATA--TTAATTACAACAATTTCACCATA
*
15434 AAATTA
1 ATATTA
15440 TTATTTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 3 0.11
26 3 0.11
27 7 0.25
28 15 0.54
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.39
Consensus pattern (26 bp):
ATATTAATTACAACAATTTCACCATA
Found at i:20375 original size:11 final size:10
Alignment explanation
Indices: 20352--20390 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
20342 TAAACATACT
20352 AAAAAGAATAA
1 AAAAAGAA-AA
*
20363 AAATAGAAAA
1 AAAAAGAAAA
20373 AAAAAGATAAA
1 AAAAAGA-AAA
20384 AAAAAGA
1 AAAAAGA
20391 GAAGACACGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:26204 original size:87 final size:85
Alignment explanation
Indices: 26050--26320 Score: 366
Period size: 87 Copynumber: 3.2 Consensus size: 85
26040 ACCTAATAAC
* ****
26050 CAAAGTCCCCAAACACATTTATAACACAACAACAACTCTCTTTCTAAAGTCCTCAAGCACATTTA
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAACTCTCTTTCTAAAGTCCTCAAGCACATTTA
26115 TAACACAGAGGCATCTATAT
66 TAACACAGAGGCATCTATAT
*
26135 CAAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTCTCTCTAAAGTCCTCAAGCACATT
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAA--CTCTCTTTCTAAAGTCCTCAAGCACATT
*
26200 TATAACACAGAGACAT-TCATAT
64 TATAACACAGAGGCATCT-ATAT
* * * *
26222 CAAAGTCCCCAAGCACAATTATAACACAGGGGCACCTCTATTTC-AAAGTTCTCAAGCACATTTA
1 CAAAGTCCCCAAACACAATTATAACACAGGGGCAACTCTCTTTCTAAAGTCCTCAAGCACATTTA
* * *
26286 TAACACAGGGGCATCTCTAC
66 TAACACAGAGGCATCTATAT
*
26306 CAAAGTCCCTAAACA
1 CAAAGTCCCCAAACA
26321 TATGTAACAC
Statistics
Matches: 164, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
84 46 0.28
85 38 0.23
86 1 0.01
87 79 0.48
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.23
Consensus pattern (85 bp):
CAAAGTCCCCAAACACAATTATAACACAGGGGCAACTCTCTTTCTAAAGTCCTCAAGCACATTTA
TAACACAGAGGCATCTATAT
Found at i:26279 original size:43 final size:42
Alignment explanation
Indices: 26050--26313 Score: 237
Period size: 41 Copynumber: 6.2 Consensus size: 42
26040 ACCTAATAAC
* * **** * *
26050 CAAAGTCCCCAAACACATTTATAACACAACAACAACTCTCTTT
1 CAAAGTCCTCAAGCACATTTATAACACAGGGGC-ACTCTATAT
*
26093 CTAAAGTCCTCAAGCACATTTATAACACAGAGGCA-TCTATAT
1 C-AAAGTCCTCAAGCACATTTATAACACAGGGGCACTCTATAT
* * * * *
26135 CAAAGTCCCCAAACACAATTATAACACAGGGGCAATTCTCTCTCT
1 CAAAGTCCTCAAGCACATTTATAACACAGGGGC-A--CTCTATAT
* * *
26180 CTAAAGTCCTCAAGCACATTTATAACACAGAGACATTC-ATAT
1 C-AAAGTCCTCAAGCACATTTATAACACAGGGGCACTCTATAT
* * *
26222 CAAAGTCCCCAAGCACAATTATAACACAGGGGCACCTCTATTT
1 CAAAGTCCTCAAGCACATTTATAACACAGGGGCA-CTCTATAT
* * *
26265 CAAAGTTCTCAAGCACATTTATAACACAGGGGCA-TCTCTAC
1 CAAAGTCCTCAAGCACATTTATAACACAGGGGCACTCTATAT
26306 CAAAGTCC
1 CAAAGTCC
26314 CTAAACATAT
Statistics
Matches: 178, Mismatches: 35, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
41 68 0.38
42 12 0.07
43 38 0.21
44 26 0.15
45 7 0.04
46 27 0.15
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (42 bp):
CAAAGTCCTCAAGCACATTTATAACACAGGGGCACTCTATAT
Found at i:29538 original size:19 final size:18
Alignment explanation
Indices: 29514--29549 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29504 TGAAGATTTA
29514 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
29533 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
29550 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:39637 original size:18 final size:18
Alignment explanation
Indices: 39614--39655 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
39604 TCCTCGACCT
*
39614 TTCCTCCTCGTTGGCCTC
1 TTCCTCCTCGTCGGCCTC
39632 TTCCTCCTCGTCGGCCTC
1 TTCCTCCTCGTCGGCCTC
39650 TTCCTC
1 TTCCTC
39656 TGGATGGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.14, T:0.38
Consensus pattern (18 bp):
TTCCTCCTCGTCGGCCTC
Found at i:44120 original size:19 final size:19
Alignment explanation
Indices: 44096--44139 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
44086 ATGACACGCG
* *
44096 CCGTTAAGTCTATTTTTTT
1 CCGTTAAGTCCAATTTTTT
44115 CCGTTAAGTCCAATTTTTT
1 CCGTTAAGTCCAATTTTTT
44134 CCGTTA
1 CCGTTA
44140 CACACGTGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.11, T:0.50
Consensus pattern (19 bp):
CCGTTAAGTCCAATTTTTT
Found at i:49649 original size:11 final size:10
Alignment explanation
Indices: 49631--49664 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
49621 AATTGTCTTC
49631 AAATCTTCAA
1 AAATCTTCAA
49641 AATATCTTCAA
1 AA-ATCTTCAA
49652 GAAATCTTCAA
1 -AAATCTTCAA
49663 AA
1 AA
49665 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Done.