Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010167.1 Corchorus capsularis cultivar CVL-1 contig10188, 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: 4264
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:2019 original size:37 final size:38
Alignment explanation
Indices: 1971--2333 Score: 384
Period size: 37 Copynumber: 9.8 Consensus size: 38
1961 CATTCTCGTC
*
1971 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCA
1 AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
* * * *
2009 AAAT-CTTGTTTAAGATGCCTGTTTAGGTTTCTTAT-G
1 AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
* * *
2045 AAATCCTTGTTTAAGGTCCCTATTTTAGGTGTCTCGTCA
1 AAATCCTTGTTTAAGATCCCT-GTTTAGGTGTCTCATCA
* * * * *
2084 AAAT-CTTGTTTAAGATTCCTGTTTAGATTTCTTAT-T
1 AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
* *
2120 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCGTCA
1 AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
* * * * **
2158 AAAT-CTTGTTTAAGATTCCTATTTAGGTTTCT-TTTT
1 AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
*
2194 AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCTCGTCA
1 AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
* * * * *
2232 AAAT-CTTGTTTAAGATTCCTGTTTAGATTTCTTAT-T
1 AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
*
2268 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCA
1 AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
* *
2306 AAAT-CTTATTTAAGATTCCTGTTTAGGT
1 AAATCCTTGTTTAAGATCCCTGTTTAGGT
2334 TTAACAAATC
Statistics
Matches: 261, Mismatches: 55, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
36 17 0.07
37 198 0.76
38 42 0.16
39 4 0.02
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (38 bp):
AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
Found at i:2062 original size:74 final size:74
Alignment explanation
Indices: 1971--2335 Score: 622
Period size: 74 Copynumber: 4.9 Consensus size: 74
1961 CATTCTCGTC
* *
1971 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTGTTTAAGATGCCTGTTTAGG
1 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGG
*
2036 TTTCTTATG
66 TTTCTTATT
*
2045 AAATCCTTGTTTAAGGTCCCTATTTTAGGTGTCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAG
1 AAATCCTTGTTTAAGGTCCCT-GTTTAGGTGTCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAG
*
2110 ATTTCTTATT
65 GTTTCTTATT
*
2120 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCGTCAAAATCTTGTTTAAGATTCCTATTTAGG
1 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGG
*
2185 TTTCTTTTT
66 TTTCTTATT
* *
2194 AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGA
1 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGG
2259 TTTCTTATT
66 TTTCTTATT
* *
2268 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAATCTTATTTAAGATTCCTGTTTAGG
1 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGG
2333 TTT
66 TTT
2336 AACAAATCCT
Statistics
Matches: 273, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
74 204 0.75
75 69 0.25
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (74 bp):
AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGG
TTTCTTATT
Found at i:2514 original size:62 final size:59
Alignment explanation
Indices: 2446--2568 Score: 158
Period size: 59 Copynumber: 2.0 Consensus size: 59
2436 TTCTTCAAAA
* * *
2446 ATCAAAATTCAAAAC-TCTCATTTCAGCATTCCATTATTCGAAAATCAAAGTTCAATATTTGC
1 ATCAAAATTCAAAACAT-GCATTTCAGCATTCC---ATCCGAAAATCAAAGTTCAAAATTTGC
* *
2508 ATCAAAATTCAAAACATGCATTTTAGTATTCCATCCGAAAATCAAAGTTCAAAATTTGC
1 ATCAAAATTCAAAACATGCATTTCAGCATTCCATCCGAAAATCAAAGTTCAAAATTTGC
2567 AT
1 AT
2569 TTCATTATTC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
59 27 0.49
62 27 0.49
63 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.33
Consensus pattern (59 bp):
ATCAAAATTCAAAACATGCATTTCAGCATTCCATCCGAAAATCAAAGTTCAAAATTTGC
Found at i:2615 original size:28 final size:27
Alignment explanation
Indices: 2584--2641 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
2574 TATTCAAAAA
*
2584 TCAAAATTCAAAATCAGCATCTCATGGT
1 TCAAAATTCAAAACCAGCATCTCAT-GT
* *
2612 TCAAAATTCAAAACCTGCATTTCATGT
1 TCAAAATTCAAAACCAGCATCTCATGT
2639 TCA
1 TCA
2642 TTCTTGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (27 bp):
TCAAAATTCAAAACCAGCATCTCATGT
Found at i:2660 original size:41 final size:43
Alignment explanation
Indices: 2612--2725 Score: 146
Period size: 43 Copynumber: 2.7 Consensus size: 43
2602 ATCTCATGGT
*
2612 TCAAAATTCAAAACCTGCATTTCATG-TTC-ATTCTT-GAAAA
1 TCAAAATTCAAAACTTGCATTTCATGATTCTATTCTTCGAAAA
2652 GTCAAAATTCAAAACTTGCATTTCA-GCATTCTATTCTTCGAAAA
1 -TCAAAATTCAAAACTTGCATTTCATG-ATTCTATTCTTCGAAAA
* * *
2696 TCAAAGTTCAAAATTTGCATTTCATTATTC
1 TCAAAATTCAAAACTTGCATTTCATGATTC
2726 AAAAATCAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
40 1 0.02
41 23 0.36
42 3 0.05
43 32 0.50
44 5 0.08
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (43 bp):
TCAAAATTCAAAACTTGCATTTCATGATTCTATTCTTCGAAAA
Found at i:2723 original size:147 final size:146
Alignment explanation
Indices: 2509--2912 Score: 590
Period size: 147 Copynumber: 2.8 Consensus size: 146
2499 AATATTTGCA
* * *
2509 TCAAAATTCAAAACATGCATTTTAGTATTCCATC--CGAAAATCAAAGTTCAAAATTTGCATTTC
1 TCAAAATTCAAAACTTGCATTTCAGCATT-CATCTTCGAAAATCAAAGTTCAAAATTTGCATTTC
*
2572 ATTATTCAAAAATCAAAATTCAAAATCAGCATCTCATGGTTCAAAATTCAAAACCTGCATTTCA-
65 ATTATTCAAAAATCAAAGTTCAAAATCAGCATCTCATGGTTCAAAATTCAAAACCTGCATTTCAC
** *
2636 TGTTCATTCTTGAAAAG
130 AATTCATTCTTCAAAAG
2653 TCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTT
1 TCAAAATTCAAAACTTGCATTTCAGCATTC-A-TCTTCGAAAATCAAAGTTCAAAATTTGCATTT
**
2718 CATTATTCAAAAATCAAAGTTTGAAATCAGCATCTCATGGTTCAAAATTCAAAACCTGCATTTCA
64 CATTATTCAAAAATCAAAGTTCAAAATCAGCATCTCATGGTTCAAAATTCAAAACCTGCATTTCA
*
2783 CAATTTATTCTTCAAAAG
129 CAATTCATTCTTCAAAAG
* *
2801 TCAAAATTCAAAACTTGCATTTCAGCATTCCT-TTCGAAAATCAAAATTC-AAATTTGCATTTCA
1 TCAAAATTCAAAACTTGCATTTCAGCATTCATCTTCGAAAATCAAAGTTCAAAATTTGCATTTCA
* * *
2864 -T-TTCAAAATTCAAAGTTCAAAATCTGCATCTCAT-GTTCAAAACTCAAAA
66 TTATTCAAAAATCAAAGTTCAAAATCAGCATCTCATGGTTCAAAATTCAAAA
2913 TCCAGAATCT
Statistics
Matches: 238, Mismatches: 17, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
141 14 0.06
142 29 0.12
143 2 0.01
144 41 0.17
145 18 0.08
146 1 0.00
147 90 0.38
148 43 0.18
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (146 bp):
TCAAAATTCAAAACTTGCATTTCAGCATTCATCTTCGAAAATCAAAGTTCAAAATTTGCATTTCA
TTATTCAAAAATCAAAGTTCAAAATCAGCATCTCATGGTTCAAAATTCAAAACCTGCATTTCACA
ATTCATTCTTCAAAAG
Found at i:2911 original size:34 final size:34
Alignment explanation
Indices: 2837--2983 Score: 192
Period size: 34 Copynumber: 4.4 Consensus size: 34
2827 ATTCCTTTCG
* * *
2837 AAAA-TCAAAATTC-AAATTTGCATTTCAT-TTC
1 AAAACTCAAAATCCAAAATCTGCATCTCATGTTC
* * *
2868 AAAATTCAAAGTTCAAAATCTGCATCTCATGTTC
1 AAAACTCAAAATCCAAAATCTGCATCTCATGTTC
*
2902 AAAACTCAAAATCCAGAATCTGCATCTCATGTTC
1 AAAACTCAAAATCCAAAATCTGCATCTCATGTTC
* *
2936 AAAACTCAAAATCCAGAATCTGCATTTCATGTTC
1 AAAACTCAAAATCCAAAATCTGCATCTCATGTTC
2970 AAAACTCAAAATCC
1 AAAACTCAAAATCC
2984 TAATTGTTGG
Statistics
Matches: 105, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
31 4 0.04
32 8 0.08
33 13 0.12
34 80 0.76
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (34 bp):
AAAACTCAAAATCCAAAATCTGCATCTCATGTTC
Done.