Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008671.1 Corchorus capsularis cultivar CVL-1 contig08692, 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: 24005
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:234 original size:49 final size:49
Alignment explanation
Indices: 114--401 Score: 287
Period size: 49 Copynumber: 5.9 Consensus size: 49
104 AATTTTTCGG
*
114 TTTTTACCTGCTATTTCCCAAAATG-CCTTCCCGGATGGAAGGCACTCT-
1 TTTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACT-TA
* * * ** * *
162 TTTTCAGCC-GCTATCTCCGAAAATGCCCTTCCCAAACGGAATGCATTTA
1 TTTTTA-CCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * *
211 TTTTTACCTACTATTTCCCAAAATACCCTTCCCAGACGGAAGGCACTTA
1 TTTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * * *
260 -TTTTACTTGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGACGCTTA
1 TTTTTACCTGCTA-TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * * * * *
309 TTTTTGCTTACTTTTTCCCAAAGTGCCCTTCCCGGACGGAAGGCACTAA
1 TTTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * * * *
358 TTTTTACTTGCTTTTTCCTAAAACGCCCTTCCCGGATGGAAGGC
1 TTTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGC
402 GTTAGTCTTA
Statistics
Matches: 197, Mismatches: 37, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
48 32 0.16
49 156 0.79
50 9 0.05
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (49 bp):
TTTTTACCTGCTATTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
Found at i:434 original size:48 final size:49
Alignment explanation
Indices: 114--450 Score: 279
Period size: 49 Copynumber: 6.9 Consensus size: 49
104 AATTTTTCGG
* * * *
114 TTTTTACCTGCTATTTCCCAAAATG-CCTTCCCGGATGGAAGGCACTCT-
1 TTTTTACTTGCTTTTTCCTAAAATGCCCTTCCCGGACGGAAGGCACT-TA
* * * * * ** * *
162 TTTTCAGC-CGCTATCTCCGAAAATGCCCTTCCCAAACGGAATGCATTTA
1 TTTTTA-CTTGCTTTTTCCTAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * * * * *
211 TTTTTACCTACTATTTCCCAAAATACCCTTCCCAGACGGAAGGCACTTA
1 TTTTTACTTGCTTTTTCCTAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * *
260 -TTTTACTTGCTATTTTCCAAAAATGCCCTTCCCGGACGGAAGACGCTTA
1 TTTTTACTTGCT-TTTTCCTAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * * * *
309 TTTTTGCTTACTTTTTCCCAAAGTGCCCTTCCCGGACGGAAGGCACTAA
1 TTTTTACTTGCTTTTTCCTAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * *
358 TTTTTACTTGCTTTTTCCTAAAACGCCCTTCCCGGATGGAAGGC-GTTA
1 TTTTTACTTGCTTTTTCCTAAAATGCCCTTCCCGGACGGAAGGCACTTA
* * * * ** *
406 GTCTTACTCGCTTTTTCTTAAAATGCCCTTTTCGGACGAAAGGCA
1 TTTTTACTTGCTTTTTCCTAAAATGCCCTTCCCGGACGGAAGGCA
451 AGTTCACTTT
Statistics
Matches: 232, Mismatches: 50, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
48 67 0.29
49 156 0.67
50 9 0.04
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (49 bp):
TTTTTACTTGCTTTTTCCTAAAATGCCCTTCCCGGACGGAAGGCACTTA
Found at i:9088 original size:24 final size:24
Alignment explanation
Indices: 9061--9116 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
9051 AAAGCAAAAA
9061 AGCAACAGAAGAAGAAAAA-GAGTG
1 AGCAACAGAAGAAGAAAAAGGA-TG
*
9085 AGCAACAGCAGAAGAAAAAGGATG
1 AGCAACAGAAGAAGAAAAAGGATG
9109 AGCAACAG
1 AGCAACAG
9117 GAAAAAGCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 28 0.93
25 2 0.07
ACGTcount: A:0.55, C:0.12, G:0.29, T:0.04
Consensus pattern (24 bp):
AGCAACAGAAGAAGAAAAAGGATG
Found at i:10048 original size:2 final size:2
Alignment explanation
Indices: 10041--10113 Score: 55
Period size: 2 Copynumber: 37.5 Consensus size: 2
10031 GAATATCTGT
** *
10041 TA TA TA TA TA TA TA TA TA TA TA TGA GC T- TA T- TGA -A TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA T-A TA TA TA TA
* *
10082 T- TA TA TA TA TA CA TA TA CA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10114 GTTGTGCAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
1 4 0.07
2 51 0.91
3 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:10080 original size:42 final size:42
Alignment explanation
Indices: 10021--10105 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
10011 AATGGTGAAT
* * *
10021 TGAGCTTATTGAATATCTGTTATATATATATATATATATATA
1 TGAGCTTATTGAATATCTATTATATATATACATATACATATA
10063 TGAGCTTATTGAATATCTATTATATATATACATATACATATA
1 TGAGCTTATTGAATATCTATTATATATATACATATACATATA
10105 T
1 T
10106 ATATATATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (42 bp):
TGAGCTTATTGAATATCTATTATATATATACATATACATATA
Found at i:13699 original size:20 final size:21
Alignment explanation
Indices: 13674--13715 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
13664 ATTTTTATGG
*
13674 CTATTTTTCTATAC-TTTTTA
1 CTATTTTTATATACATTTTTA
*
13694 CTATTTTTATATGCATTTTTA
1 CTATTTTTATATACATTTTTA
13715 C
1 C
13716 CTTATTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.21, C:0.14, G:0.02, T:0.62
Consensus pattern (21 bp):
CTATTTTTATATACATTTTTA
Found at i:13904 original size:19 final size:18
Alignment explanation
Indices: 13880--13915 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
13870 TGAAGATTTC
13880 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
13899 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
13916 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:15194 original size:15 final size:16
Alignment explanation
Indices: 15176--15212 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
15166 CTTGATTGCT
15176 CTTTTAGTTA-ATTTA
1 CTTTTAGTTAGATTTA
15191 CTTTTAGTTAGATTTA
1 CTTTTAGTTAGATTTA
*
15207 ATTTTA
1 CTTTTA
15213 ATTCTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.27, C:0.05, G:0.08, T:0.59
Consensus pattern (16 bp):
CTTTTAGTTAGATTTA
Found at i:15211 original size:16 final size:15
Alignment explanation
Indices: 15177--15212 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
15167 TTGATTGCTC
*
15177 TTTTAGTTAATTTAC
1 TTTTAGTTAATTTAA
15192 TTTTAGTTAGATTTAA
1 TTTTAGTTA-ATTTAA
15208 TTTTA
1 TTTTA
15213 ATTCTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.61
Consensus pattern (15 bp):
TTTTAGTTAATTTAA
Found at i:15833 original size:30 final size:30
Alignment explanation
Indices: 15778--15835 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
15768 AAATAATATA
*
15778 AATATAATAAATGAAATATTATAATTTTGT
1 AATATAATAAATGAAATAATATAATTTTGT
15808 AATATATATAAGATG-AATAAT-TAATTTT
1 AATATA-ATAA-ATGAAATAATATAATTTT
15836 TATAAATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 13 0.52
31 9 0.36
32 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (30 bp):
AATATAATAAATGAAATAATATAATTTTGT
Found at i:21191 original size:38 final size:38
Alignment explanation
Indices: 21140--21216 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
21130 CCGTTAGATT
21140 TTACTTTGCTTGCAAGTAAAGCAGATTAGCATTAAATG
1 TTACTTTGCTTGCAAGTAAAGCAGATTAGCATTAAATG
21178 TTACTTTGCTTGCAAGTAAAGCAGATTAGCATTAAATG
1 TTACTTTGCTTGCAAGTAAAGCAGATTAGCATTAAATG
21216 T
1 T
21217 AAAGGGGATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (38 bp):
TTACTTTGCTTGCAAGTAAAGCAGATTAGCATTAAATG
Found at i:22403 original size:30 final size:30
Alignment explanation
Indices: 22367--22798 Score: 594
Period size: 30 Copynumber: 14.2 Consensus size: 30
22357 AATGACACCT
* *
22367 TTGTCATGATTTTGCAATTGACACAAGAAG
1 TTGTCATGATTTTACAATTGACACCAGAAG
22397 TTGTCATGATTTTACAATTGACACCAGAAG
1 TTGTCATGATTTTACAATTGACACCAGAAG
* * * *
22427 TTGTCAATAATCTTACAAATGACACCAGAAA
1 TTGTC-ATGATTTTACAATTGACACCAGAAG
22458 TTGTCATGATTTTACAATTGACACCAGAAG
1 TTGTCATGATTTTACAATTGACACCAGAAG
* * * * *
22488 TAGTCAATAATCTTACAAATGACACCATAAG
1 TTGTC-ATGATTTTACAATTGACACCAGAAG
* * *
22519 TTGTCATGGTCTTACAAATGACACCAGAAG
1 TTGTCATGATTTTACAATTGACACCAGAAG
22549 TTGTCATGATTTTACAATTGACACCAGAAG
1 TTGTCATGATTTTACAATTGACACCAGAAG
* * * *
22579 TTGTCAATAATCTTACAAATGACACTAGAAG
1 TTGTC-ATGATTTTACAATTGACACCAGAAG
* *
22610 TTGTCATGATTTTGCAATTGACACTAGAAG
1 TTGTCATGATTTTACAATTGACACCAGAAG
*
22640 TTGTCATGATTTTGCAATTGACACCAGAAG
1 TTGTCATGATTTTACAATTGACACCAGAAG
*
22670 TTGTCATGATTTTGCAATTGACACCAGAAG
1 TTGTCATGATTTTACAATTGACACCAGAAG
*
22700 TTGTCATGATTTATTCAATTGACACCAGAAG
1 TTGTCATGATTT-TACAATTGACACCAGAAG
*
22731 TTGTCATGATTTTGCAATTGACACCAGAAG
1 TTGTCATGATTTTACAATTGACACCAGAAG
*
22761 TTGTCATGATTTATTCAATTGACACCAGAAG
1 TTGTCATGATTT-TACAATTGACACCAGAAG
22792 TTGTCAT
1 TTGTCAT
22799 ATACACCATG
Statistics
Matches: 363, Mismatches: 34, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
30 233 0.64
31 130 0.36
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (30 bp):
TTGTCATGATTTTACAATTGACACCAGAAG
Found at i:22462 original size:61 final size:60
Alignment explanation
Indices: 22367--22798 Score: 594
Period size: 61 Copynumber: 7.1 Consensus size: 60
22357 AATGACACCT
* *
22367 TTGTCATGATTTTGCAATTGACACAAGAAGTTGTCATGATTTTACAATTGACACCAGAAG
1 TTGTCATGATTTTACAATTGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAG
* * * *
22427 TTGTCAATAATCTTACAAATGACACCAGAAATTGTCATGATTTTACAATTGACACCAGAAG
1 TTGTC-ATGATTTTACAATTGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAG
* * * * * * * *
22488 TAGTCAATAATCTTACAAATGACACCATAAGTTGTCATGGTCTTACAAATGACACCAGAAG
1 TTGTC-ATGATTTTACAATTGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAG
* * * *
22549 TTGTCATGATTTTACAATTGACACCAGAAGTTGTCAATAATCTTACAAATGACACTAGAAG
1 TTGTCATGATTTTACAATTGACACCAGAAGTTGTC-ATGATTTTACAATTGACACCAGAAG
* * *
22610 TTGTCATGATTTTGCAATTGACACTAGAAGTTGTCATGATTTTGCAATTGACACCAGAAG
1 TTGTCATGATTTTACAATTGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAG
* *
22670 TTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTATTCAATTGACACCAGAAG
1 TTGTCATGATTTTACAATTGACACCAGAAGTTGTCATGATTT-TACAATTGACACCAGAAG
* *
22731 TTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTATTCAATTGACACCAGAAG
1 TTGTCATGATTTTACAATTGACACCAGAAGTTGTCATGATTT-TACAATTGACACCAGAAG
22792 TTGTCAT
1 TTGTCAT
22799 ATACACCATG
Statistics
Matches: 340, Mismatches: 29, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
60 92 0.27
61 248 0.73
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (60 bp):
TTGTCATGATTTTACAATTGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAG
Found at i:22532 original size:91 final size:90
Alignment explanation
Indices: 22367--22798 Score: 598
Period size: 91 Copynumber: 4.7 Consensus size: 90
22357 AATGACACCT
* *
22367 TTGTCATGATTTTGCAATTGACACAAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTC
1 TTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTC
* *
22432 AATAATCTTACAAATGACACCAGAAA
66 -ATGATCTTACAAATGACACCAGAAG
* * * * *
22458 TTGTCATGATTTTACAATTGACACCAGAAGTAGTCAATAATCTTACAAATGACACCATAAGTTGT
1 TTGTCATGATTTTGCAATTGACACCAGAAGTTGTC-ATGATCTTACAATTGACACCAGAAGTTGT
*
22523 CATGGTCTTACAAATGACACCAGAAG
65 CATGATCTTACAAATGACACCAGAAG
* * * *
22549 TTGTCATGATTTTACAATTGACACCAGAAGTTGTCAATAATCTTACAAATGACACTAGAAGTTGT
1 TTGTCATGATTTTGCAATTGACACCAGAAGTTGTC-ATGATCTTACAATTGACACCAGAAGTTGT
* * * *
22614 CATGATTTTGCAATTGACACTAGAAG
65 CATGATCTTACAAATGACACCAGAAG
* *
22640 TTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTC
1 TTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTC
*
22705 ATGAT-TTATTCAATTGACACCAGAAG
66 ATGATCTTA--CAAATGACACCAGAAG
22731 TTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGAT-TTATTCAATTGACACCAGAAGTTG
1 TTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATCTTA--CAATTGACACCAGAAGTTG
22795 TCAT
64 TCAT
22799 ATACACCATG
Statistics
Matches: 309, Mismatches: 27, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
89 2 0.01
90 32 0.10
91 226 0.73
92 49 0.16
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (90 bp):
TTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTC
ATGATCTTACAAATGACACCAGAAG
Done.