Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015305.1 Corchorus capsularis cultivar CVL-1 contig15326, 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: 34885
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:628 original size:332 final size:332
Alignment explanation
Indices: 27--672 Score: 842
Period size: 333 Copynumber: 1.9 Consensus size: 332
17 TCGGATTGAG
* * * *
27 ATGCTCGTAAAAAGAAATTCTTAAATCCAATGTGGCTGATATTAAGTTAGATAAATATAGATATT
1 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTAAGTTAGATAAATATAGATATT
* * *
92 TCAATGAGTCTTGGCGCAAAAATCATGCAAAACTGAGCCGGAGTCCCATAACGCGTTTTTAGCCA
66 TCAATGAGACTTGGCGCAAAAATCATGCAAAACTGAGCCGGAGTCCCAGAACGCGTTTTAAGCCA
* *
157 AAAACAGTGATAGTTAATACACGATTTCAGCTAAAATTTTGTAAAAATTGACCCGAAATAATTTT
131 AAAACAGTGATAGTTAATACACGATTTCAACTAAAATTTTGCAAAAATTGACCCGAAATAATTTT
* * * * * *
222 CCTCAATTTTTGTCCACGATACTCATAAAAAAATATATAATTCAACACCAAAAATATTGAAAGGA
196 CCTCAATTTTAGTCCACAATACTAATAAAAAAATATATAACTCAACACCAAAAAGACTGAAAGGA
*
287 TATTCACGCTTCTAAATATCG-TACTTCCTA-TTTTTCTGAATTAATTCCTAATTGAATCGAAAC
261 TATTCACGCTTCT-AATATCGCT-CTTCCTACTTTTTCCGAATTAATTCCTAATTGAATCGAAAC
350 ATGATTCAT
324 ATGATTCAT
* ** **
359 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGGTAAGATTTGGTTAGATGGATATAGATATT
1 ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTAAGTTAGATAAATATAGATATT
* * * * *
424 TCAATGAGACTTGGCGCCAAAAATCTTGCAAAGCTGAGCCGGTG-CTCCGGAACGCGTTTTAAGT
66 TCAATGAGACTTGGCG-CAAAAATCATGCAAAACTGAGCCGGAGTC-CCAGAACGCGTTTTAAGC
* * *
488 CAAAAATC-GTGATGGTTAGTACACGATTTCAACTAAAATTTTGCAAAAATTGACCCGAGA-AAT
129 CAAAAA-CAGTGATAGTTAATACACGATTTCAACTAAAATTTTGCAAAAATTGACCCGAAATAAT
**
551 TTATCCTCAATTTTAAG-CCACAATACTAAT-AAAAAATATATAACTCAACGTCAAAAAGACTG-
193 TT-TCCTCAATTTT-AGTCCACAATACTAATAAAAAAATATATAACTCAACACCAAAAAGACTGA
* *
613 AAGTGCT-TCTCACGCTTCTAATATCGCTCTTCCTACCTTTTTCCGAATTAATTTCTAATT
256 AAG-GATAT-TCACGCTTCTAATATCGCTCTTCCTA-CTTTTTCCGAATTAATTCCTAATT
673 TAAAAATTAT
Statistics
Matches: 271, Mismatches: 33, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
331 18 0.07
332 117 0.43
333 134 0.49
334 2 0.01
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (332 bp):
ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTAAGTTAGATAAATATAGATATT
TCAATGAGACTTGGCGCAAAAATCATGCAAAACTGAGCCGGAGTCCCAGAACGCGTTTTAAGCCA
AAAACAGTGATAGTTAATACACGATTTCAACTAAAATTTTGCAAAAATTGACCCGAAATAATTTT
CCTCAATTTTAGTCCACAATACTAATAAAAAAATATATAACTCAACACCAAAAAGACTGAAAGGA
TATTCACGCTTCTAATATCGCTCTTCCTACTTTTTCCGAATTAATTCCTAATTGAATCGAAACAT
GATTCAT
Found at i:891 original size:94 final size:96
Alignment explanation
Indices: 717--896 Score: 249
Period size: 94 Copynumber: 1.9 Consensus size: 96
707 AAATATATTT
* * * *
717 GAAAAAAATACAGAAAATTATATTTTAATAATTGTATAGTTAAAATATATTTTAATGATGAAAAT
1 GAAAAAAATACAGAAAATTATATTCTAATAATTGCATAATTAAAATATATTTTAATAATGAAAAT
782 TTAAAAATATATTTGAAAAAATAGTACAATC
66 TTAAAAATATATTTGAAAAAATAGTACAATC
* * * *
813 GAAAAATATACATAAGATTATATTCTAATAA-TGACATAATT-AAA-ATATTTTAATAATGACAA
1 GAAAAAAATACAGAAAATTATATTCTAATAATTG-CATAATTAAAATATATTTTAATAATGAAAA
*
875 TTTAGAAATATATTTGAAAAAA
65 TTTAAAAATATATTTGAAAAAA
897 GGGGTATAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
94 37 0.50
95 5 0.07
96 32 0.43
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (96 bp):
GAAAAAAATACAGAAAATTATATTCTAATAATTGCATAATTAAAATATATTTTAATAATGAAAAT
TTAAAAATATATTTGAAAAAATAGTACAATC
Found at i:1261 original size:15 final size:15
Alignment explanation
Indices: 1241--1291 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
1231 TATATAGTCT
1241 AATAATTAATAATGG
1 AATAATTAATAATGG
* * *
1256 AATAATTTATGATTG
1 AATAATTAATAATGG
1271 AA-AA--AATAATGG
1 AATAATTAATAATGG
1283 AATAATTAA
1 AATAATTAA
1292 AATATTATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
12 7 0.26
13 2 0.07
14 2 0.07
15 16 0.59
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (15 bp):
AATAATTAATAATGG
Found at i:1351 original size:30 final size:31
Alignment explanation
Indices: 1317--1381 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
1307 TGGCAATTTA
*
1317 GAAATATGTTTTAAAAA-AAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
1347 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
1378 GAAA
1 GAAA
1382 ACATAAAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.28
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:1983 original size:168 final size:165
Alignment explanation
Indices: 1595--2039 Score: 615
Period size: 168 Copynumber: 2.7 Consensus size: 165
1585 TGAGTCATTT
*
1595 GTCAATTGAGAAATAACCAAAAAGTTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * ** * *
1660 TTAAGTAATCTGCCAAGTAGGTAAAGATGAAAAAGATTAGTTCTCTAGCTCATCATCAATCCTTG
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTTG
* * *
1725 ATGGGAATCTTTTATTAATTCACTACTCTAGTTCAA
130 ATAGGAATCTTTTAGTAATTCACTACTCTAGTTAAA
* *
1761 GTCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* *
1826 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAAATAAGTTCTCTAACTCCAAAAGCAAGCTT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACG-AAAAAAATTAGTTCTCTAACT-CAAAAGCAAGCCT
*
1891 TGGTAGGAATCTTTTAGTAATTCCACTACTCTA-TTAAA
128 TGATAGGAATCTTTTAGTAATT-CACTACTCTAGTTAAA
* **
1929 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGGTAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* *
1994 TTAAGTAATCGGTCAAGT-GTGAAAAGACGAAAAAAATTAGTTCTCT
65 TTAAGTAATCTGCCAAGTAG-GAAAAGACGAAAAAAATTAGTTCTCT
2040 CGCTCCTCAT
Statistics
Matches: 249, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
166 88 0.35
167 36 0.14
168 115 0.46
169 10 0.04
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTAATTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAAATTAGTTCTCTAACTCAAAAGCAAGCCTTGA
TAGGAATCTTTTAGTAATTCACTACTCTAGTTAAA
Found at i:17367 original size:10 final size:10
Alignment explanation
Indices: 17341--17370 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
17331 GAGGGACTTT
17341 AAAAAAA-AA
1 AAAAAAAGAA
17350 AAAAAAAGAA
1 AAAAAAAGAA
17360 AAAAAAAGAA
1 AAAAAAAGAA
17370 A
1 A
17371 TACATCTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.35
10 13 0.65
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:33093 original size:21 final size:21
Alignment explanation
Indices: 33067--33112 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
33057 CTATGTTATT
**
33067 TTAGATCACATTGATCATTCA
1 TTAGATCACATAAATCATTCA
33088 TTAGATCACATAAATCATTCA
1 TTAGATCACATAAATCATTCA
33109 TTAG
1 TTAG
33113 TTTGGTAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (21 bp):
TTAGATCACATAAATCATTCA
Done.