Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013086.1 Corchorus capsularis cultivar CVL-1 contig13107, 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: 7939
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2067 original size:35 final size:34
Alignment explanation
Indices: 2009--2278 Score: 249
Period size: 35 Copynumber: 7.7 Consensus size: 34
1999 TCGATCACCT
* *
2009 AGGGTGGTCTTTCTTCAGTTTATTTAGGTTGATCC
1 AGGGCGGTCTTTCTTCAGTTTATTTA-GTTGACCC
* *
2044 AGGGCGGTCTTTCGTCAGCTTATTTTAGTTGACCC
1 AGGGCGGTCTTTCTTCAGTTTA-TTTAGTTGACCC
* *
2079 AGGGCGGTTTTTCTTCAGTTTATTTCTGTTGACCC
1 AGGGCGGTCTTTCTTCAGTTTATTT-AGTTGACCC
* *
2114 AGGGCAGTTTTTCTTCAGTTTATTTCAGTTGACCC
1 AGGGCGGTCTTTCTTCAGTTTATTT-AGTTGACCC
* * **
2149 AGGGCGGTCTTT-TGTCAGTTCATTTCAGTTAACGT
1 AGGGCGGTCTTTCT-TCAGTTTATTT-AGTTGACCC
* * * ** * *
2184 AGAGCGGTCTTTCATAAACTTATTTCAATTGTA-AC
1 AGGGCGGTCTTTCTTCAGTTTATTT-AGTTG-ACCC
*
2219 AGGGCAGTCTTTC-TCAAGTTTATTTCAGTTGACCC
1 AGGGCGGTCTTTCTTC-AGTTTATTT-AGTTGACCC
2254 AGGGCGGTCTTTCTTCAGTTTATTT
1 AGGGCGGTCTTTCTTCAGTTTATTT
2279 TAGTGCACCA
Statistics
Matches: 193, Mismatches: 34, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
34 6 0.03
35 180 0.93
36 7 0.04
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.41
Consensus pattern (34 bp):
AGGGCGGTCTTTCTTCAGTTTATTTAGTTGACCC
Found at i:2137 original size:70 final size:70
Alignment explanation
Indices: 2009--2278 Score: 287
Period size: 70 Copynumber: 3.9 Consensus size: 70
1999 TCGATCACCT
* * * *
2009 AGGGTGGTCTTTCTTCAGTTTATTT-AGGTTGATCCAGGGCGGTCTTTCGTCAGCTTATTTTAGT
1 AGGGCGGTCTTTCTTCAGTTTATTTCA-GTTGACCCAGGGCGGTCTTTCTTCAGCTTATTTCAGT
2073 TGACCC
65 TGACCC
* * * * *
2079 AGGGCGGTTTTTCTTCAGTTTATTTCTGTTGACCCAGGGCAGTTTTTCTTCAGTTTATTTCAGTT
1 AGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGCTTATTTCAGTT
2144 GACCC
66 GACCC
* * ** * * * * *
2149 AGGGCGGTCTTT-TGTCAGTTCATTTCAGTTAACGTAGAGCGGTCTTTCATAAACTTATTTCAAT
1 AGGGCGGTCTTTCT-TCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGCTTATTTCAGT
*
2213 TGTA-AC
65 TG-ACCC
* *
2219 AGGGCAGTCTTTC-TCAAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTT
1 AGGGCGGTCTTTCTTC-AGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGCTTATTT
2279 TAGTGCACCA
Statistics
Matches: 161, Mismatches: 34, Indels: 10
0.79 0.17 0.05
Matches are distributed among these distances:
69 3 0.02
70 157 0.98
71 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.41
Consensus pattern (70 bp):
AGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGCTTATTTCAGTT
GACCC
Found at i:2207 original size:105 final size:104
Alignment explanation
Indices: 2015--2278 Score: 293
Period size: 105 Copynumber: 2.5 Consensus size: 104
2005 ACCTAGGGTG
* * * *
2015 GTCTTTCTTCAGTTTATTT-AGGTTGATCCAGGGCGGTCTTTCGTCAGCTTATTTTAGTTGACCC
1 GTCTTTCTTCAGTTTATTTCA-GTTGACCCAGGGCGGTCTTTTGTCAG-TTATTTCAGTTAACCC
* * * * ** ** *
2079 AGGGCGGTTTTTCTTCAGTTTATTTCTGTTG-ACCCAGGGCA
64 AGAGCGGTCTTTCATAAACTTATTTCAATTGTA-ACAGGGCA
* **
2120 GTTTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTTGTCAGTTCATTTCAGTTAACGTA
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTTGTCAGTT-ATTTCAGTTAACCCA
2185 GAGCGGTCTTTCATAAACTTATTTCAATTGTAACAGGGCA
65 GAGCGGTCTTTCATAAACTTATTTCAATTGTAACAGGGCA
2225 GTCTTTC-TCAAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCT-TCAGTTTATTT
1 GTCTTTCTTC-AGTTTATTTCAGTTGACCCAGGGCGGTCTTT-TGTCAG-TTATTT
2279 TAGTGCACCA
Statistics
Matches: 136, Mismatches: 17, Indels: 12
0.82 0.10 0.07
Matches are distributed among these distances:
104 4 0.03
105 127 0.93
106 5 0.04
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.42
Consensus pattern (104 bp):
GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTTGTCAGTTATTTCAGTTAACCCAG
AGCGGTCTTTCATAAACTTATTTCAATTGTAACAGGGCA
Found at i:2302 original size:35 final size:35
Alignment explanation
Indices: 2009--2311 Score: 161
Period size: 35 Copynumber: 8.7 Consensus size: 35
1999 TCGATCACCT
* * *
2009 AGGGTGGTCTTTCTTCAGTTTATTT-AGGTTGATCC-
1 AGGGCGGTATTTCTCCAGTTTATTTCA-GTTGA-CCA
* * * *
2044 AGGGCGGTCTTTCGT-CAGCTTATTTTAGTTGACCC
1 AGGGCGGTATTTC-TCCAGTTTATTTCAGTTGACCA
* * * *
2079 AGGGCGGTTTTTCTTCAGTTTATTTCTGTTGACCC
1 AGGGCGGTATTTCTCCAGTTTATTTCAGTTGACCA
* * * *
2114 AGGGCAGTTTTTCTTCAGTTTATTTCAGTTGACCC
1 AGGGCGGTATTTCTCCAGTTTATTTCAGTTGACCA
* * * * **
2149 AGGGCGGTCTTT-TGTCAGTTCATTTCAGTTAACGT
1 AGGGCGGTATTTCT-CCAGTTTATTTCAGTTGACCA
* * * ** * *
2184 AGAGCGGTCTTTCAT-AAACTTATTTCAATTGTAAC-
1 AGGGCGGTATTTC-TCCAGTTTATTTCAGTTG-ACCA
* * * *
2219 AGGGCAGTCTTTCTCAAGTTTATTTCAGTTGACCC
1 AGGGCGGTATTTCTCCAGTTTATTTCAGTTGACCA
* * *
2254 AGGGCGGTCTTTCTTCAGTTTATTTTAG-TGCACCA
1 AGGGCGGTATTTCTCCAGTTTATTTCAGTTG-ACCA
* *
2289 AGGGTGGTATTTCTCCAATTTAT
1 AGGGCGGTATTTCTCCAGTTTAT
2312 GTCTATTTGA
Statistics
Matches: 219, Mismatches: 38, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
34 9 0.04
35 206 0.94
36 3 0.01
37 1 0.00
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (35 bp):
AGGGCGGTATTTCTCCAGTTTATTTCAGTTGACCA
Found at i:2442 original size:99 final size:100
Alignment explanation
Indices: 2308--2493 Score: 218
Period size: 99 Copynumber: 1.9 Consensus size: 100
2298 TTTCTCCAAT
* * * *
2308 TTATGTCTATTTGATCTAGGGTCGTTAGTTATTCAAT-GTGTT-TTGATCCAAGGTGGTCGTTCT
1 TTATGTCAATTTGATCTAGGGTCGTCAGTTATTCAATAATGTTATTGATCCAAGGTGGTCATTCT
2371 TCAGTTTATTTCGATCCAGGGCGATCATTATCCAGC
66 TCAGTTTATTT-GATCCAGGGCGATCATTATCCAGC
* * * *
2407 TTATGTCAATTTGAT-TCAGGGT-GCTCAGTTCTTCAATACATTTTAATTGATCCAGGGTGGTTA
1 TTATGTCAATTTGATCT-AGGGTCG-TCAGTTATTCAATA-ATGTT-ATTGATCCAAGGTGGTCA
*
2470 TTCTTTAGTTTATTTGATCCAGGG
62 TTCTTCAGTTTATTTGATCCAGGG
2494 AGGTCATTCT
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
98 2 0.03
99 30 0.42
101 3 0.04
102 9 0.12
103 28 0.39
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (100 bp):
TTATGTCAATTTGATCTAGGGTCGTCAGTTATTCAATAATGTTATTGATCCAAGGTGGTCATTCT
TCAGTTTATTTGATCCAGGGCGATCATTATCCAGC
Found at i:2791 original size:121 final size:121
Alignment explanation
Indices: 2566--2793 Score: 277
Period size: 121 Copynumber: 1.9 Consensus size: 121
2556 TTTTGTTGGG
* * **
2566 TCCGGGCAATTGGTAAATCCTCCGAGTACCATTTCATTTCATCAAGTTGTCATCAAAGATTCATG
1 TCCGGGCAATTGGTAAAACCTCCGAGTACCATTTCATTTCATCAAGTTGTCATCAAAAAACCATG
* *
2631 TTTAAGTTTAAAATTCTTGTTAAAGGTCTCTATTCAGAGTTTGCATTGATAAGTCC
66 TTTAAGTTTAAAATTCCTGTTAAAGGTCTCTAGTCAGAGTTTGCATTGATAAGTCC
* *
2687 TCCGGGCAATTGGTAAAACCTCC-AGGTACCATTTCATTTCATCAAGTTTTTCAT-AAAAAACCT
1 TCCGGGCAATTGGTAAAACCTCCGA-GTACCATTTCATTTCATCAAG-TTGTCATCAAAAAACCA
* * *
2750 TGTTT-CGTTTTCAAA-TCCTGCTT-GAGGTCTCTAGTCGAGAGTTT
64 TGTTTAAG-TTTAAAATTCCTG-TTAAAGGTCTCTAGTC-AGAGTTT
2794 TCAATCCAAA
Statistics
Matches: 91, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
120 17 0.19
121 68 0.75
122 6 0.07
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (121 bp):
TCCGGGCAATTGGTAAAACCTCCGAGTACCATTTCATTTCATCAAGTTGTCATCAAAAAACCATG
TTTAAGTTTAAAATTCCTGTTAAAGGTCTCTAGTCAGAGTTTGCATTGATAAGTCC
Found at i:2875 original size:64 final size:63
Alignment explanation
Indices: 2748--3188 Score: 486
Period size: 63 Copynumber: 7.1 Consensus size: 63
2738 CATAAAAAAC
** * *
2748 CTTGTTTCGTTTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAG-----T-TTTCAATCCAAAAT
1 CTTGTTTCG-TTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAGT
* ** *
2806 TTTGTTTCGTTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTCTTGTTTCAATCCAAAGT
1 CTTGTTTCGTTTCAAATCCTAATCGAGGTCTCTAGTCGAGAG-TTTCTTGTTTCAATCCAAAGT
* ** * *
2870 CTTGTTTCATTTCAAATCCTGCTTGAGGTGTCTAGTCGAGAGTTTTCTTGTTTCAATCCAAAGT
1 CTTGTTTCGTTTCAAATCCTAATCGAGGTCTCTAGTCGAGAG-TTTCTTGTTTCAATCCAAAGT
* *
2934 CTTGTTTCGTTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTCCAATCTAAAGT
1 CTTGTTTCGTTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAGT
* * *
2997 CTTGTTTCCTTTCAAATCCTAATTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTAAAGT
1 CTTGTTTCGTTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAGT
* * * *
3060 CTTGCTTCGTTTAAAATCCTAATCGAGGTCTTTAGTCGAGAGTTTCTTGTTTCAATTCCAAAAT
1 CTTGTTTCGTTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCCAAAGT
* * * * *** * * *
3124 CATG-TTCATTTTAAATCTTGCCCGAGGACTCTAG-CAGAGAGTTT-TTGTTTCAATCTAAAAT
1 CTTGTTTCGTTTCAAATCCTAATCGAGGTCTCTAGTC-GAGAGTTTCTTGTTTCAATCCAAAGT
3185 CTTG
1 CTTG
3189 CTCGAGAGTT
Statistics
Matches: 341, Mismatches: 33, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
57 33 0.10
58 8 0.02
61 10 0.03
62 10 0.03
63 160 0.47
64 120 0.35
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.41
Consensus pattern (63 bp):
CTTGTTTCGTTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAGT
Found at i:3010 original size:63 final size:63
Alignment explanation
Indices: 2748--3121 Score: 499
Period size: 63 Copynumber: 6.0 Consensus size: 63
2738 CATAAAAAAC
** *
2748 CTTGTTTCGTTTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAG-----T-TTTCAATCCAAAAT
1 CTTGTTTCG-TTTCAAATCCTAATTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAGT
* **
2806 TTTGTTTCGTTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTCTTGTTTCAATCCAAAGT
1 CTTGTTTCGTTTCAAATCCTAATTGAGGTCTCTAGTCGAGAG-TTTCTTGTTTCAATCCAAAGT
* ** *
2870 CTTGTTTCATTTCAAATCCTGCTTGAGGTGTCTAGTCGAGAGTTTTCTTGTTTCAATCCAAAGT
1 CTTGTTTCGTTTCAAATCCTAATTGAGGTCTCTAGTCGAGAG-TTTCTTGTTTCAATCCAAAGT
* * *
2934 CTTGTTTCGTTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTCCAATCTAAAGT
1 CTTGTTTCGTTTCAAATCCTAATTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAGT
* *
2997 CTTGTTTCCTTTCAAATCCTAATTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTAAAGT
1 CTTGTTTCGTTTCAAATCCTAATTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAGT
* * * *
3060 CTTGCTTCGTTTAAAATCCTAATCGAGGTCTTTAGTCGAGAGTTTCTTGTTTCAATTCCAAA
1 CTTGTTTCGTTTCAAATCCTAATTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCCAAA
3122 ATCATGTTCA
Statistics
Matches: 287, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
57 33 0.11
58 8 0.03
63 130 0.45
64 116 0.40
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (63 bp):
CTTGTTTCGTTTCAAATCCTAATTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAGT
Found at i:3102 original size:126 final size:125
Alignment explanation
Indices: 2748--3190 Score: 540
Period size: 126 Copynumber: 3.5 Consensus size: 125
2738 CATAAAAAAC
* *
2748 CTTGTTTCGTTTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAG----T-TTTCAATCCAAAATTT
1 CTTGTTTC-ATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTTGTTTCAATCCAAAATCT
* ** *
2808 TGTTTCGTTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTCTTGTTTCAATCCAAAGT
65 TGCTTCGTTTCAAATCCTAATCGAGGTCTCTAGTCGAGAG-TTTCTTGTTTCAATCCAAAGT
* *
2870 CTTGTTTCATTTCAAATCCTGCTTGAGGTGTCTAGTCGAGAGTTTTCTTGTTTCAATCCAAAGTC
1 CTTGTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAG-TTT-TTGTTTCAATCCAAAATC
* * *
2935 TTGTTTCGTTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTCCAATCTAAAGT
64 TTGCTTCGTTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAGT
* ** * *
2997 CTTGTTTCCTTTCAAATCCTAATTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTAAAGTCT
1 CTTGTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTT-TTGTTTCAATCCAAAATCT
* * *
3062 TGCTTCGTTTAAAATCCTAATCGAGGTCTTTAGTCGAGAGTTTCTTGTTTCAATTCCAAAAT
65 TGCTTCGTTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCCAAAGT
* * * ** * *
3124 CATG-TTCATTTTAAATCTTGCCCGAGGACTCTAG-CAGAGAGTTTTTGTTTCAATCTAAAATCT
1 CTTGTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTC-GAGAGTTTTTGTTTCAATCCAAAATCT
3187 TGCT
65 TGCT
3191 CGAGAGTTTT
Statistics
Matches: 282, Mismatches: 30, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
121 32 0.11
122 8 0.03
125 23 0.08
126 101 0.36
127 67 0.24
128 51 0.18
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.41
Consensus pattern (125 bp):
CTTGTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTTTGTTTCAATCCAAAATCTT
GCTTCGTTTCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAGT
Done.