Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014604.1 Corchorus capsularis cultivar CVL-1 contig14625, 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: 31066
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Found at i:83 original size:49 final size:49
Alignment explanation
Indices: 11--106 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
1 AGTTTATCCA
* *
11 AGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGTCTTTCTCC
1 AGTTTATGTTAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTCC
60 AGTTTAT-TTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCT
1 AGTTTATGTT-AGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCT
107 TTAGTAGCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 2 0.05
49 42 0.95
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (49 bp):
AGTTTATGTTAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTCC
Found at i:216 original size:49 final size:49
Alignment explanation
Indices: 135--230 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 49
125 ATCCAAGTCT
* * * * *
135 ATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGTTTTTCTTCAGTTC
1 ATGTCAGAATGATCGACTCAGTCGACCAAGGGTGGTCTTTCTTCAGTTC
*
184 ATGTCAGAATGATCGACTCGGTCGACCAAGGGTGGTCTTTCTTCAGT
1 ATGTCAGAATGATCGACTCAGTCGACCAAGGGTGGTCTTTCTTCAGT
231 AGTTTCCGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (49 bp):
ATGTCAGAATGATCGACTCAGTCGACCAAGGGTGGTCTTTCTTCAGTTC
Found at i:221 original size:119 final size:119
Alignment explanation
Indices: 1--301 Score: 440
Period size: 119 Copynumber: 2.5 Consensus size: 119
* *
1 AGTTTATCCAAGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGTCTTTCTCCAGTTTA
1 AGTTTATCCAAGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTCA
* * * *
66 TTTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTTAGTAGCTTCCA
66 TGTCAGAATGATCGACTCAGTCGACCAAGGGCGGTCTTTCTTCAGTAGCTTCCA
* *
120 AGTTTATCCAAGTCTATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGTTTTTCTTCAGTTCA
1 AGTTTATCCAAGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTCA
* * * *
185 TGTCAGAATGATCGACTCGGTCGACCAAGGGTGGTCTTTCTTCAGTAGTTTCCG
66 TGTCAGAATGATCGACTCAGTCGACCAAGGGCGGTCTTTCTTCAGTAGCTTCCA
* * * * * *
239 TGTTTATCCAAGTTTATGTCAGAATGATCGATTCAGTCGATCTAGGGCGGTCTTTCTTCAGTT
1 AGTTTATCCAAGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGTCTTTCTTCAGTT
302 GTTTCCAAGT
Statistics
Matches: 162, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
119 162 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (119 bp):
AGTTTATCCAAGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTCA
TGTCAGAATGATCGACTCAGTCGACCAAGGGCGGTCTTTCTTCAGTAGCTTCCA
Found at i:297 original size:70 final size:70
Alignment explanation
Indices: 179--881 Score: 994
Period size: 70 Copynumber: 10.0 Consensus size: 70
169 GTTTTTCTTC
* * * * * * **
179 AGTTCATGTCAGAATGATCGACTCGGTCGACCAAGGGTGGTCTTTCTTCAGTAGTTTCCGTGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
244 ATCCA
66 ATCCA
*
249 AGTTTATGTCAGAATGATCGATTCAGTCGATCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
314 ATCCA
66 ATCCA
* * * ** * *
319 AGTTTGTGTCAGAATGATCGATTCGGTCGACCCAGGGTTGTCTTTCTTAAGTAGTTTCCACA-TT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCA-AGTT
383 TATCCA
65 TATCCA
389 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
454 ATCCA
66 ATCCA
* * * *
459 AGTTTGTGTCAGAATGATCGATTCGGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
*
524 ATTCGA
66 A-TCCA
* *
530 AGTTTATGTCAGAATGATCGATTCAGTTGACCTAGGGCGGTCTTTCTTGAGTTGTTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
595 ATCCA
66 ATCCA
* * *
600 AGTTTGTGTCAGAATGATCGATTCGGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
*
665 ATTCGA
66 A-TCCA
* * *
671 AGTTTATGTCAGAATGATCGATTCAGTTGACCTAGGGCGGTCTTTGTTCACTTGTTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
736 ATTCCA
66 A-TCCA
* * * * *
742 AGTTTATGTCAGAATGATCGATTTAGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
807 ATCCA
66 ATCCA
* * * * * *
812 AGTTTATGTCAGAATGATCAATTCAGCCGACCCAGGGCGGTTTTTCATCAGTTGTTTCCAAGTTG
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
877 ATCCA
66 ATCCA
882 GGGTGGTCTT
Statistics
Matches: 563, Mismatches: 66, Indels: 8
0.88 0.10 0.01
Matches are distributed among these distances:
69 1 0.00
70 373 0.66
71 189 0.34
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (70 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
ATCCA
Found at i:620 original size:141 final size:140
Alignment explanation
Indices: 185--881 Score: 1072
Period size: 141 Copynumber: 5.0 Consensus size: 140
175 CTTCAGTTCA
* * **
185 TGTCAGAATGATCGACTCGGTCGACCAAGGGTGGTCTTTCTTCAGTAGTTTCCGTGTTTATCCAA
1 TGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCAAGTTTATCCAA
*
250 GTTTATGTCAGAATGATCGATTCAGTCGATCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTA
66 GTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTA
315 TCCAAGTTTG
131 TCCAAGTTTG
* *
325 TGTCAGAATGATCGATTCGGTCGACCCAGGGTTGTCTTTCTTAAGTAGTTTCCACA-TTTATCCA
1 TGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCA-AGTTTATCCA
389 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
65 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
454 ATCCAAGTTTG
130 ATCCAAGTTTG
* * * *
465 TGTCAGAATGATCGATTCGGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTTATTCGA
1 TGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCAAGTTTA-TCCA
* *
530 AGTTTATGTCAGAATGATCGATTCAGTTGACCTAGGGCGGTCTTTCTTGAGTTGTTTCCAAGTTT
65 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
595 ATCCAAGTTTG
130 ATCCAAGTTTG
* * * * *
606 TGTCAGAATGATCGATTCGGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTTATTCGA
1 TGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCAAGTTTA-TCCA
* * *
671 AGTTTATGTCAGAATGATCGATTCAGTTGACCTAGGGCGGTCTTTGTTCACTTGTTTCCAAGTTT
65 AGTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
*
736 ATTCCAAGTTTA
130 A-TCCAAGTTTG
** *
748 TGTCAGAATGATCGATTTAGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTTTATCCAA
1 TGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCAAGTTTATCCAA
* * * * * *
813 GTTTATGTCAGAATGATCAATTCAGCCGACCCAGGGCGGTTTTTCATCAGTTGTTTCCAAGTTGA
66 GTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTA
878 TCCA
131 TCCA
882 GGGTGGTCTT
Statistics
Matches: 516, Mismatches: 37, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
139 1 0.00
140 189 0.37
141 264 0.51
142 62 0.12
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (140 bp):
TGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCAAGTTTATCCAA
GTTTATGTCAGAATGATCGATTCAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTA
TCCAAGTTTG
Found at i:1297 original size:27 final size:27
Alignment explanation
Indices: 1267--1340 Score: 130
Period size: 27 Copynumber: 2.7 Consensus size: 27
1257 AGGGTCATCT
1267 AGGGGCATTTTGGTCATTTTTACATTC
1 AGGGGCATTTTGGTCATTTTTACATTC
* *
1294 AGGGGCATTTAGGTCATTTTTGCATTC
1 AGGGGCATTTTGGTCATTTTTACATTC
1321 AGGGGCATTTTGGTCATTTT
1 AGGGGCATTTTGGTCATTTT
1341 AAGTCCACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.18, C:0.14, G:0.26, T:0.43
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTTACATTC
Found at i:11363 original size:3 final size:3
Alignment explanation
Indices: 11355--11390 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
11345 TCTTGATGCA
11355 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11391 TACTTGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12391 original size:33 final size:33
Alignment explanation
Indices: 12345--12407 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
12335 AAAAAGGTTT
* * *
12345 CAATGCAAATTTCCACCCCGGTAGGAGTGATTA
1 CAATGCAAATTTCCAACCCGGCAAGAGTGATTA
*
12378 CAATGCAATTTTCCAACCCGGCAAGAGTGA
1 CAATGCAAATTTCCAACCCGGCAAGAGTGA
12408 GCACACATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (33 bp):
CAATGCAAATTTCCAACCCGGCAAGAGTGATTA
Found at i:14901 original size:22 final size:22
Alignment explanation
Indices: 14864--14922 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
14854 ATTTCTTACC
* *
14864 TTTATCTTTATCTTTTCGTTATT-
1 TTTATTTTTAT-TTTTAGTT-TTG
*
14887 TTTCTTTTTATTTTTAGTTTTG
1 TTTATTTTTATTTTTAGTTTTG
14909 TTTATTTTTATTTT
1 TTTATTTTTATTTT
14923 CCTTTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 2 0.06
22 20 0.65
23 9 0.29
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (22 bp):
TTTATTTTTATTTTTAGTTTTG
Found at i:14912 original size:16 final size:15
Alignment explanation
Indices: 14893--14936 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
14883 TATTTTTCTT
14893 TTTATTTTTAGTTTTG
1 TTTATTTTTA-TTTTG
*
14909 TTTATTTTTATTTTC
1 TTTATTTTTATTTTG
*
14924 CTT-TTTTTATTTT
1 TTTATTTTTATTTT
14937 TCTTTGGTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 10 0.38
15 6 0.23
16 10 0.38
ACGTcount: A:0.11, C:0.05, G:0.05, T:0.80
Consensus pattern (15 bp):
TTTATTTTTATTTTG
Found at i:16102 original size:21 final size:21
Alignment explanation
Indices: 16063--16111 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
16053 TCAATGCTTT
** *
16063 AGGAATGCAAGAGGGATTTCGA
1 AGGAA-GCAAGAGCCATTTCCA
16085 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCCA
16106 A-GAAGC
1 AGGAAGC
16112 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.39, C:0.16, G:0.31, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCCA
Found at i:20192 original size:15 final size:17
Alignment explanation
Indices: 20169--20206 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
20159 ATTTTTATTT
*
20169 TTATTTTTATTT-G-TC
1 TTATGTTTATTTGGATC
20184 TTATGTTTATTTGGATC
1 TTATGTTTATTTGGATC
20201 TTATGT
1 TTATGT
20207 AAGACTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 1 0.05
17 8 0.40
ACGTcount: A:0.16, C:0.05, G:0.13, T:0.66
Consensus pattern (17 bp):
TTATGTTTATTTGGATC
Found at i:24402 original size:78 final size:75
Alignment explanation
Indices: 24251--24405 Score: 179
Period size: 78 Copynumber: 2.0 Consensus size: 75
24241 AATTAGATTA
* * **
24251 AAAAAGCTTTAAATTCTTGTTAAAAATAAAGAATTAATTTTAATCACAATAAATTAAACTATTAA
1 AAAAAGCTTCAAATTCTTGTTAAAAAGAAAGAATTAATTTTAATCACAATAAATTAAACTACCAA
**
24316 TATGCACTCC
66 TACACACTCC
* *
24326 AAAAA-CTTCAAATTCTTGTTAGAAAGGAAAGAA-TACATTTTAATCATCACAATAATTTAAACT
1 AAAAAGCTTCAAATTCTTGTTA-AAAAGAAAGAATTA-ATTTT-A--ATCACAATAAATTAAACT
24389 ACCAATACACACTCC
61 ACCAATACACACTCC
24404 AA
1 AA
24406 GAATAGAAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
74 17 0.25
75 19 0.28
76 1 0.01
78 30 0.45
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (75 bp):
AAAAAGCTTCAAATTCTTGTTAAAAAGAAAGAATTAATTTTAATCACAATAAATTAAACTACCAA
TACACACTCC
Found at i:26456 original size:17 final size:17
Alignment explanation
Indices: 26436--26469 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
26426 GCTAATAATG
26436 ATTATGAAATAATTATT
1 ATTATGAAATAATTATT
**
26453 ATTATTCAATAATTATT
1 ATTATGAAATAATTATT
26470 CCTATATTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTATGAAATAATTATT
Done.