Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013707.1 Corchorus capsularis cultivar CVL-1 contig13728, 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: 40972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:11565 original size:53 final size:53
Alignment explanation
Indices: 11479--11582 Score: 156
Period size: 53 Copynumber: 2.0 Consensus size: 53
11469 CGACGTGGCA
* * *
11479 TGCCACGTGTACCAATAAGTGACATGTGGCACGCCACGTGTACCAAAAAGTTG
1 TGCCACATGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTTG
*
11532 TGCCACATGTACCAAAAAGTGACA-GATGTCACGCCACATGTACCAAAAAGT
1 TGCCACATGTACCAAAAAGTGACATG-TGGCACGCCACATGTACCAAAAAGT
11583 GACATGTGGC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 1 0.02
53 45 0.98
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (53 bp):
TGCCACATGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTTG
Found at i:11571 original size:31 final size:31
Alignment explanation
Indices: 11533--11630 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 31
11523 AAAAAGTTGT
*
11533 GCCACATGTACCAAAAAGTGACA-GATGTCAC
1 GCCACATGTACCAAAAAGTGACATG-TGGCAC
*
11564 GCCACATGTACCAAAAAGTGACATGTGGCAT
1 GCCACATGTACCAAAAAGTGACATGTGGCAC
** * ** *
11595 GCCACATGTTTCAAAAAATGGTATGTGGCAT
1 GCCACATGTACCAAAAAGTGACATGTGGCAC
11626 GCCAC
1 GCCAC
11631 GTGCACAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.20
Consensus pattern (31 bp):
GCCACATGTACCAAAAAGTGACATGTGGCAC
Found at i:15005 original size:60 final size:61
Alignment explanation
Indices: 14911--15051 Score: 196
Period size: 60 Copynumber: 2.3 Consensus size: 61
14901 GTTAATTGCT
* * *
14911 CAAATAAGGGTCTAACGTT-TGCTAAAATGCTCAAATAAGGGCATGATCTTTTAATTTGAC
1 CAAATAAGGGTCTAACGTTATGCGAAAATGATCAAATAAGGGCACGATCTTTTAATTTGAC
* * * *
14971 CAAATAAGGGTCTAATGTTAT-CGAAGATGATCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGTCTAACGTTATGCGAAAATGATCAAATAAGGGCACGATCTTTTAATTTGAC
*
15031 CAAATAAGGATCTAACGTTAT
1 CAAATAAGGGTCTAACGTTAT
15052 TGAAAATACT
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 70 0.99
61 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.30
Consensus pattern (61 bp):
CAAATAAGGGTCTAACGTTATGCGAAAATGATCAAATAAGGGCACGATCTTTTAATTTGAC
Found at i:15065 original size:60 final size:60
Alignment explanation
Indices: 14911--15069 Score: 191
Period size: 60 Copynumber: 2.7 Consensus size: 60
14901 GTTAATTGCT
* *
14911 CAAATAAGGGTCTAACG-T-TTGCTAAAATGCTCAAATAAGGGCATGATCTTTTAATTTGAC
1 CAAATAAGGGTCTAACGTTATTG--AAAATACTCAAATAAGGGCACGATCTTTTAATTTGAC
* * * * *
14971 CAAATAAGGGTCTAATGTTATCGAAGATGA-TCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGTCTAACGTTATTGAAAAT-ACTCAAATAAGGGCACGATCTTTTAATTTGAC
*
15031 CAAATAAGGATCTAACGTTATTGAAAATACTCAAA-AAGG
1 CAAATAAGGGTCTAACGTTATTGAAAATACTCAAATAAGG
15070 ACCTGGTGTC
Statistics
Matches: 84, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
59 5 0.06
60 76 0.90
61 1 0.01
62 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (60 bp):
CAAATAAGGGTCTAACGTTATTGAAAATACTCAAATAAGGGCACGATCTTTTAATTTGAC
Found at i:15219 original size:58 final size:59
Alignment explanation
Indices: 15117--15229 Score: 174
Period size: 58 Copynumber: 1.9 Consensus size: 59
15107 ATGTCATAAC
** * *
15117 CTTATTTGAGCATTTTTTATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGGCT
1 CTTATTTGAGCATTTTCGACAAC-TTAGGCCCTTATTTGACCAAATTAAAAGATCGGGCT
15177 CTTATTTGAGCATTTTCGACAA-TTAGGCCCTTATTTGACCAAATTAAAAGATC
1 CTTATTTGAGCATTTTCGACAACTTAGGCCCTTATTTGACCAAATTAAAAGATC
15230 AAACCCTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 30 0.61
60 19 0.39
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (59 bp):
CTTATTTGAGCATTTTCGACAACTTAGGCCCTTATTTGACCAAATTAAAAGATCGGGCT
Found at i:15239 original size:58 final size:59
Alignment explanation
Indices: 15116--15250 Score: 173
Period size: 58 Copynumber: 2.3 Consensus size: 59
15106 GATGTCATAA
** * * ***
15116 CCTTATTTGAGCATTTTTTATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGGC
1 CCTTATTTGAGCATTTTCGACAAC-TTAGGCCCTTATTTGACCAAATTAAAAGATCAAAC
*
15176 TCTTATTTGAGCATTTTCGACAA-TTAGGCCCTTATTTGACCAAATTAAAAGATCAAAC
1 CCTTATTTGAGCATTTTCGACAACTTAGGCCCTTATTTGACCAAATTAAAAGATCAAAC
*
15234 CCTTATTTGAACATTTT
1 CCTTATTTGAGCATTTT
15251 GATAAATATT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 46 0.71
60 19 0.29
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (59 bp):
CCTTATTTGAGCATTTTCGACAACTTAGGCCCTTATTTGACCAAATTAAAAGATCAAAC
Found at i:21748 original size:30 final size:30
Alignment explanation
Indices: 21707--21768 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
21697 TATAATTTTT
*
21707 AATCATTAAACTTTTATCTATTAATTATAA
1 AATCATCAAACTTTTATCTATTAATTATAA
*
21737 AATCATCAAACTTTTATTTATTAATTATAA
1 AATCATCAAACTTTTATCTATTAATTATAA
21767 AA
1 AA
21769 AGATATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (30 bp):
AATCATCAAACTTTTATCTATTAATTATAA
Found at i:22229 original size:22 final size:21
Alignment explanation
Indices: 22190--22258 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 21
22180 GAATTGTTAG
*
22190 TAATCACACATTGGAATTTTGA
1 TAATCACAC-TTGAAATTTTGA
*
22212 TAATCACACTGTGAAATTATGA
1 TAATCACACT-TGAAATTTTGA
*
22234 TAA-CATCACTACGAAATTTTGA
1 TAATCA-CACT-TGAAATTTTGA
22256 TAA
1 TAA
22259 ATCTTCCTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.08
22 37 0.93
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (21 bp):
TAATCACACTTGAAATTTTGA
Found at i:22275 original size:23 final size:23
Alignment explanation
Indices: 22247--22326 Score: 110
Period size: 23 Copynumber: 3.5 Consensus size: 23
22237 CATCACTACG
22247 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
*
22270 AAATTTTGATAAATCTCCCTATA
1 AAATTTTGATAAATCTTCCTATA
*
22293 AAATTTTGAT-AA-CTTGCTTATA
1 AAATTTTGATAAATCTT-CCTATA
*
22315 AAATCTTGATAA
1 AAATTTTGATAA
22327 CTACAAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.04
22 16 0.31
23 33 0.65
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:22359 original size:22 final size:22
Alignment explanation
Indices: 22331--22516 Score: 108
Period size: 22 Copynumber: 8.7 Consensus size: 22
22321 TGATAACTAC
22331 AAATTTTGATAACCTCATTATG
1 AAATTTTGATAACCTCATTATG
* * **
22353 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCATTATG
22375 AAATTTTGAT---CTACATATATG
1 AAATTTTGATAACCT-CAT-TATG
22396 AAATTTTGATAACCCTC-TTATG
1 AAATTTTGATAA-CCTCATTATG
* * *
22418 AAATTTTGA-AAACTAAATTATA
1 AAATTTTGATAACCT-CATTATG
* *
22440 AAATTTTGATTA-CTCCATTATA
1 AAATTTTGATAACCT-CATTATG
* * **
22462 AAAGTTTAATAACCT--TCCT-
1 AAATTTTGATAACCTCATTATG
*
22481 -AATTTTG-TAACCAT-ACTATG
1 AAATTTTGATAACC-TCATTATG
22501 AAATTTTGATAACCTC
1 AAATTTTGATAACCTC
22517 CCCATAAATA
Statistics
Matches: 125, Mismatches: 23, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
17 5 0.04
18 6 0.05
19 3 0.02
20 5 0.04
21 24 0.19
22 75 0.60
23 4 0.03
24 1 0.01
25 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTCATTATG
Found at i:22581 original size:44 final size:44
Alignment explanation
Indices: 22531--22673 Score: 114
Period size: 44 Copynumber: 3.2 Consensus size: 44
22521 TAAATACCAC
*
22531 TATGAAATTTTTGTAATCACATTTTTAAAATTTGATAACCTCTT
1 TATGAAATTTTTGTAATCACATTTATAAAATTTGATAACCTCTT
** * * * *
22575 TATGAAA-TTTTGATAGCCTC-TTTATAAAAGTTTGTTGACCCCTT
1 TATGAAATTTTTG-TAATCACATTTATAAAA-TTTGATAACCTCTT
* * * * *
22619 TATGAAATTCTTATAATCACA-TTATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTTGTAATCACATTTAT-AAAATTTGATAACCTC-TT
22664 T-TGAAATTTT
1 TATGAAATTTT
22674 GATAACAACA
Statistics
Matches: 74, Mismatches: 19, Indels: 12
0.70 0.18 0.11
Matches are distributed among these distances:
43 13 0.18
44 54 0.73
45 7 0.09
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.45
Consensus pattern (44 bp):
TATGAAATTTTTGTAATCACATTTATAAAATTTGATAACCTCTT
Found at i:22588 original size:22 final size:22
Alignment explanation
Indices: 22561--22746 Score: 121
Period size: 22 Copynumber: 8.4 Consensus size: 22
22551 ATTTTTAAAA
22561 TTTGATAACCTCTTTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
* * *
22583 TTTGATAGCCTCTTTATAAAAG
1 TTTGATAACCTCTTTATGAAAT
* * *
22605 TTTGTTGACCCCTTTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
* * * *
22627 TCTT-ATAATCACATTATGTAAT
1 T-TTGATAACCTCTTTATGAAAT
*
22649 TTTGATAACCTCGCTT-TGAAAT
1 TTTGATAACCTC-TTTATGAAAT
** **
22671 TTTGATAACAACACTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
22693 TTTGATAA--TCTTCCTAT-AAAT
1 TTTGATAACCTCTT--TATGAAAT
*
22714 TTTGATAATCCGATCTCTATGAAAT
1 TTTGATAA-CC--TCTTTATGAAAT
*
22739 TTCGATAA
1 TTTGATAA
22747 TCACTATTTG
Statistics
Matches: 124, Mismatches: 28, Indels: 21
0.72 0.16 0.12
Matches are distributed among these distances:
20 1 0.01
21 15 0.12
22 87 0.70
23 4 0.03
24 3 0.02
25 11 0.09
26 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (22 bp):
TTTGATAACCTCTTTATGAAAT
Found at i:22869 original size:44 final size:44
Alignment explanation
Indices: 22814--22919 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 44
22804 ACTTTTATAA
* * *
22814 CTATAAAATTTTGATAACCTCCCCATGAAA-TATTAGTAACCTC-
1 CTATGAAATTTTGATAACCACACCATGAAATTATTA-TAACCTCG
* * *
22857 CTAATGAAATTTTGTTAACCACACTATGAAATTCTTATAACCTCG
1 CT-ATGAAATTTTGATAACCACACCATGAAATTATTATAACCTCG
**
22902 CTATGTCATTTTGATAAC
1 CTATGAAATTTTGATAAC
22920 ATCTTTGATA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
43 2 0.04
44 43 0.84
45 6 0.12
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.36
Consensus pattern (44 bp):
CTATGAAATTTTGATAACCACACCATGAAATTATTATAACCTCG
Found at i:22875 original size:22 final size:20
Alignment explanation
Indices: 22814--22906 Score: 69
Period size: 22 Copynumber: 4.2 Consensus size: 20
22804 ACTTTTATAA
*
22814 CTATAAAATTTTGATAACCTCC
1 CTATGAAATTTTG-TAACCT-C
* *
22836 CCATGAAATATTAGTAACCTC
1 CTATGAAAT-TTTGTAACCTC
*
22857 CTAATGAAATTTTGTTAACCAC
1 CT-ATGAAATTTTG-TAACCTC
*
22879 ACTATGAAATTCTTATAACCTC
1 -CTATGAAATT-TTGTAACCTC
22901 GCTATG
1 -CTATG
22907 TCATTTTGAT
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
21 5 0.09
22 45 0.79
23 7 0.12
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (20 bp):
CTATGAAATTTTGTAACCTC
Found at i:23026 original size:46 final size:43
Alignment explanation
Indices: 22961--23091 Score: 120
Period size: 44 Copynumber: 3.0 Consensus size: 43
22951 AATTAATCAC
***
22961 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTGGTAACCAGA-CTAAGAAATTTTAATAA-CT--T
* *
23007 CCTATGAAATTTTGGTAACCAGACTATGAAATTTTGATAACTT
1 CCTATGAAATTTTGGTAACCAGACTAAGAAATTTTAATAACTT
* * * * *
23050 CCATATGAAATTTTGGTAATCACACTATGGAATTTTGATAAC
1 CC-TATGAAATTTTGGTAACCAGACTAAGAAATTTTAATAAC
23092 CACATAAAGA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
43 3 0.04
44 36 0.48
45 2 0.03
46 33 0.44
47 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Consensus pattern (43 bp):
CCTATGAAATTTTGGTAACCAGACTAAGAAATTTTAATAACTT
Found at i:23036 original size:22 final size:22
Alignment explanation
Indices: 22962--23095 Score: 105
Period size: 22 Copynumber: 6.0 Consensus size: 22
22952 ATTAATCACC
**
22962 CTATGAAATTTCAATAACCA-A
1 CTATGAAATTTTGATAACCACA
* *
22983 CCTAAGAAATTTTAATAACCTGATC-
1 -CTATGAAATTTTGATAACC--A-CA
* *
23008 CTATGAAATTTTGGTAACCAGA
1 CTATGAAATTTTGATAACCACA
23030 CTATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
* *
23053 -TATGAAATTTTGGTAATCACA
1 CTATGAAATTTTGATAACCACA
*
23074 CTATGGAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
23096 TAAAGACAAG
Statistics
Matches: 90, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 68 0.76
23 1 0.01
24 18 0.20
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:23461 original size:20 final size:20
Alignment explanation
Indices: 23438--23481 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
23428 CATTTAACCT
23438 TTTTATTATTATAA-TAATAA
1 TTTTATTATTATAATTAAT-A
*
23458 TTTTATTATTTTAATTAATA
1 TTTTATTATTATAATTAATA
23478 TTTT
1 TTTT
23482 CTTTTTAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTATTATTATAATTAATA
Found at i:24217 original size:14 final size:14
Alignment explanation
Indices: 24198--24229 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
24188 TAACAATTGC
24198 GACTGTAACAAAAA
1 GACTGTAACAAAAA
*
24212 GACTGTAACGAAAA
1 GACTGTAACAAAAA
24226 GACT
1 GACT
24230 ATATAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.16, G:0.19, T:0.16
Consensus pattern (14 bp):
GACTGTAACAAAAA
Found at i:34380 original size:29 final size:31
Alignment explanation
Indices: 34334--34392 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
34324 AAAGGTAACA
*
34334 ATGTTCTAAATTT-TTAAACTTGAGAAGCCC
1 ATGTTCTAAATTTCTAAAACTTGAGAAGCCC
34364 ATGTTCT-AATTTCTAAAACTTGAGAAGCC
1 ATGTTCTAAATTTCTAAAACTTGAGAAGCC
34393 TAAATATCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (31 bp):
ATGTTCTAAATTTCTAAAACTTGAGAAGCCC
Found at i:38863 original size:20 final size:19
Alignment explanation
Indices: 38835--38873 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
38825 GTTTAGAATG
*
38835 TACAGCAAAATAGAAAAGAA
1 TACAGCAAAA-ACAAAAGAA
*
38855 TACATCAAAAACAAAAGAA
1 TACAGCAAAAACAAAAGAA
38874 GAGAGAGACG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.67, C:0.13, G:0.10, T:0.10
Consensus pattern (19 bp):
TACAGCAAAAACAAAAGAA
Done.