Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015678.1 Corchorus capsularis cultivar CVL-1 contig15699, 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: 16597
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Found at i:2108 original size:115 final size:113
Alignment explanation
Indices: 1879--2309 Score: 594
Period size: 115 Copynumber: 3.8 Consensus size: 113
1869 TTAAAAGTAG
* * * * * *
1879 ATTAAAGATGGCGGCGTCTTGTGGTTCAGACGCCTCCATTTAGCGTCGTCTCGGGGTCC-AGACG
1 ATTAAAGATGGCGGCGTCTCGGGGTCCATACGCCTCCATTTAGTGGCGTCT---GG-CCAAGACG
* * * **
1943 CCGCTATAATTTAGCCTTCTTTTTTCACCAAATTTAACTTTCTCGGAGAAAA
62 CCGCTATATTTTAGCCTTCATTTTTCACCCAATTTGCCTTTCTCGGAGAAAA
* *
1995 ATTAAAGATGGCGGCGTCTTGGGGTTCATACGCCTCCATTTAGTGGCGTCTGGGCCTAAGACGCC
1 ATTAAAGATGGCGGCGTCTCGGGGTCCATACGCCTCCATTTAGTGGCGTCT-GGCC-AAGACGCC
2060 GCTATATTTTAGCCTTCATTTTTCACCCAATTTGCCTTTCTCGGAGAAAA
64 GCTATATTTTAGCCTTCATTTTTCACCCAATTTGCCTTTCTCGGAGAAAA
2110 ATTAAAGATGGCGGCGTCTCGGGGTCCATACGCCTCCATTTAGTGGCGTCTGGCCCAAGACGCCG
1 ATTAAAGATGGCGGCGTCTCGGGGTCCATACGCCTCCATTTAGTGGCGTCTGG-CCAAGACGCCG
2175 CTATATTTTAGCCTTCATTTTTCACCCAATTTGCCTTTCTCGGAG-AAA
65 CTATATTTTAGCCTTCATTTTTCACCCAATTTGCCTTTCTCGGAGAAAA
* *
2223 ATTAAAGATGGCGGCGTCTCAGGGTCCATACGCCTCCA-TTA-----G-C-GGCCCAGACGCCGC
1 ATTAAAGATGGCGGCGTCTCGGGGTCCATACGCCTCCATTTAGTGGCGTCTGGCCAAGACGCCGC
2280 TATATTTTAGCCTTCATTTTTCACCCAATT
66 TATATTTTAGCCTTCATTTTTCACCCAATT
2310 AAAGATGGCA
Statistics
Matches: 299, Mismatches: 13, Indels: 18
0.91 0.04 0.05
Matches are distributed among these distances:
104 41 0.14
105 2 0.01
106 1 0.00
107 1 0.00
112 3 0.01
113 42 0.14
114 59 0.20
115 103 0.34
116 47 0.16
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (113 bp):
ATTAAAGATGGCGGCGTCTCGGGGTCCATACGCCTCCATTTAGTGGCGTCTGGCCAAGACGCCGC
TATATTTTAGCCTTCATTTTTCACCCAATTTGCCTTTCTCGGAGAAAA
Found at i:2357 original size:229 final size:224
Alignment explanation
Indices: 1879--2309 Score: 561
Period size: 229 Copynumber: 1.9 Consensus size: 224
1869 TTAAAAGTAG
* * * * * *
1879 ATTAAAGATGGCGGCGTCTTGTGGTTCAGACGCCTCCATTTAGCGTCGTCTCGGGGTCCAGACGC
1 ATTAAAGATAGCGGCGTCTCGGGGTCCAGACGCCTCCATTTAGCGGCGTCT--GGGCCCAGACGC
*
1944 CGCTATAATTTAGCCTTCTTTTTTCACCAAATTTAACTTTCTCGGAGAAAAATTAAAGATGGCGG
64 CGCTATAATTTAGCCTTCATTTTTCACCAAATTTAACTTTCTCGGAGAAAAATTAAAGATGGCGG
** *
2009 CGTCTTGGGGTTCATACGCCTCCATTTAGTGGCGTCTGGGCCTAAGACGCCGCTATATTTTAGCC
129 CGTCTCAGGGTCCATACGCCTCCATTTA---G-GTC-GGGCCTAAGACGCCGCTATATTTTAGCC
* *
2074 TTCATTTTTCACCCAATTTGCCTTTCTCGGAGAAAA
189 TTCATTTTTCACCCAATTTGCCTGTCTAGGAGAAAA
* * *
2110 ATTAAAGATGGCGGCGTCTCGGGGTCCATACGCCTCCATTTAGTGGCGTCT-GGCCCAAGACGCC
1 ATTAAAGATAGCGGCGTCTCGGGGTCCAGACGCCTCCATTTAGCGGCGTCTGGGCCC-AGACGCC
* * **
2174 GCTATATTTTAGCCTTCATTTTTCACCCAATTTGCCTTTCTCGGAG-AAAATTAAAGATGGCGGC
65 GCTATAATTTAGCCTTCATTTTTCACCAAATTTAACTTTCTCGGAGAAAAATTAAAGATGGCGGC
*
2238 GTCTCAGGGTCCATACGCCTCCA-TTA-G-C-GGCC-CAGACGCCGCTATATTTTAGCCTTCATT
130 GTCTCAGGGTCCATACGCCTCCATTTAGGTCGGGCCTAAGACGCCGCTATATTTTAGCCTTCATT
2298 TTTCACCCAATT
195 TTTCACCCAATT
2310 AAAGATGGCA
Statistics
Matches: 183, Mismatches: 16, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
218 39 0.21
219 4 0.02
221 1 0.01
222 1 0.01
227 3 0.02
228 42 0.23
229 48 0.26
231 45 0.25
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (224 bp):
ATTAAAGATAGCGGCGTCTCGGGGTCCAGACGCCTCCATTTAGCGGCGTCTGGGCCCAGACGCCG
CTATAATTTAGCCTTCATTTTTCACCAAATTTAACTTTCTCGGAGAAAAATTAAAGATGGCGGCG
TCTCAGGGTCCATACGCCTCCATTTAGGTCGGGCCTAAGACGCCGCTATATTTTAGCCTTCATTT
TTCACCCAATTTGCCTGTCTAGGAGAAAA
Found at i:3328 original size:19 final size:19
Alignment explanation
Indices: 3239--3329 Score: 92
Period size: 19 Copynumber: 4.8 Consensus size: 19
3229 ATGTGTGGAT
* *
3239 TATTCATATGTGTATGGAA
1 TATTCATATGTGTGTGAAA
* * * * *
3258 TATCCATATATGCGAGGAA
1 TATTCATATGTGTGTGAAA
* *
3277 TATTCATATATGTGTGGAA
1 TATTCATATGTGTGTGAAA
3296 TATTCATATGTGTGTGAAA
1 TATTCATATGTGTGTGAAA
*
3315 TATTCATGTGTGTGT
1 TATTCATATGTGTGT
3330 TAGGTGCAGC
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 61 1.00
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.41
Consensus pattern (19 bp):
TATTCATATGTGTGTGAAA
Found at i:3329 original size:38 final size:38
Alignment explanation
Indices: 3228--3329 Score: 123
Period size: 38 Copynumber: 2.7 Consensus size: 38
3218 AGGATATTTT
* *
3228 TATGTGTGGATTATTCATATGTGTATGGAATATCCATA
1 TATGTGTGGAATATTCATATGTGTGTGGAATATCCATA
* * * *
3266 TATGCGAGGAATATTCATATATGTGTGGAATATTCATA
1 TATGTGTGGAATATTCATATGTGTGTGGAATATCCATA
* * *
3304 TGTGTGTGAAATATTCATGTGTGTGT
1 TATGTGTGGAATATTCATATGTGTGT
3330 TAGGTGCAGC
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (38 bp):
TATGTGTGGAATATTCATATGTGTGTGGAATATCCATA
Found at i:12377 original size:7 final size:7
Alignment explanation
Indices: 12365--12405 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
12355 AAATTGTAAC
12365 TAATAAT
1 TAATAAT
12372 TAATAAT
1 TAATAAT
12379 TACATAAT
1 TA-ATAAT
12387 TAATAA-
1 TAATAAT
12393 TAATCAA-
1 TAAT-AAT
12400 TAATAA
1 TAATAA
12406 AAAAAATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.19
7 19 0.59
8 7 0.22
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (7 bp):
TAATAAT
Found at i:12387 original size:28 final size:25
Alignment explanation
Indices: 12346--12403 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
12336 ATTAAATTTC
* *
12346 ATAATTTCAAAATTGTAACTAATAATTA
1 ATAATTACAAAA-T-TAA-TAATAATCA
*
12374 ATAATTACATAATTAATAATAATCA
1 ATAATTACAAAATTAATAATAATCA
12399 ATAAT
1 ATAAT
12404 AAAAAAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 13 0.48
26 3 0.11
27 1 0.04
28 10 0.37
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (25 bp):
ATAATTACAAAATTAATAATAATCA
Found at i:12513 original size:32 final size:32
Alignment explanation
Indices: 12473--12557 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 32
12463 CCATGGATTG
* *
12473 TGCCGCCCTAGTGGGACGGCTTGTCCATGGCA
1 TGCCGCCCTACTGGGACGGCATGTCCATGGCA
* *
12505 TGTCGCCCTCCTGGGACGGCATGTCCATGGCA
1 TGCCGCCCTACTGGGACGGCATGTCCATGGCA
* *
12537 TGCCGCCCTCCTGGGGCGGCA
1 TGCCGCCCTACTGGGACGGCA
12558 CTGCACCGAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.11, C:0.35, G:0.34, T:0.20
Consensus pattern (32 bp):
TGCCGCCCTACTGGGACGGCATGTCCATGGCA
Found at i:12609 original size:13 final size:13
Alignment explanation
Indices: 12593--12617 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12583 TTCCTTTATT
12593 TTAGATCTACAAC
1 TTAGATCTACAAC
12606 TTAGATCTACAA
1 TTAGATCTACAA
12618 AATAACAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
TTAGATCTACAAC
Found at i:12891 original size:19 final size:18
Alignment explanation
Indices: 12867--12902 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
12857 TGAAGATTTC
12867 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
12886 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
12903 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:15940 original size:6 final size:6
Alignment explanation
Indices: 15929--15961 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
15919 AAAGCAAAGC
*
15929 AAATCT AAATCT AAACCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT AAA
15962 GCAGATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (6 bp):
AAATCT
Found at i:15973 original size:12 final size:13
Alignment explanation
Indices: 15958--15991 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
15948 AATCTAAATC
*
15958 TAAAGCAGATT-A
1 TAAAGCAAATTAA
15970 TAAAGCAAATTAA
1 TAAAGCAAATTAA
15983 TAAAGCAAA
1 TAAAGCAAA
15992 CAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (13 bp):
TAAAGCAAATTAA
Done.