Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016429.1 Corchorus capsularis cultivar CVL-1 contig16450, 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: 58127
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:945 original size:29 final size:30
Alignment explanation
Indices: 903--974 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
893 ACTTTGCCAT
* *
903 AAATCTCAAATAAGGG-TCTGAAC-TTTAGA
1 AAATGTCAAATAAGGGCTC-CAACTTTTAGA
932 AAATGTCAAATAAGGGCTCCAACTTTTAGA
1 AAATGTCAAATAAGGGCTCCAACTTTTAGA
*
962 AAAGGCTCAAATA
1 AAATG-TCAAATA
975 GGTCCAATCC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 18 0.49
30 12 0.32
31 7 0.19
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (30 bp):
AAATGTCAAATAAGGGCTCCAACTTTTAGA
Found at i:2717 original size:18 final size:17
Alignment explanation
Indices: 2685--2723 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
2675 AAAATAAGAA
2685 AAAT-GAAAAAGAAATT
1 AAATAGAAAAAGAAATT
2701 AAATAGAAAATAGAAATT
1 AAATAGAAAA-AGAAATT
2719 AAATA
1 AAATA
2724 AAATGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.19
17 5 0.24
18 12 0.57
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (17 bp):
AAATAGAAAAAGAAATT
Found at i:2867 original size:29 final size:31
Alignment explanation
Indices: 2809--2873 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
2799 TGGGTGGACC
*
2809 TATTTGAGCCTTCTCTAAAAGTTGGAGCCCT
1 TATTTGAGCCTTCTCTAAAAGTTAGAGCCCT
*
2840 TATTTGA-CCTTTTCT-AAAGTTCAG-GCCCT
1 TATTTGAGCCTTCTCTAAAAGTT-AGAGCCCT
2869 TATTT
1 TATTT
2874 AAGATTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 16 0.52
30 8 0.26
31 7 0.23
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.42
Consensus pattern (31 bp):
TATTTGAGCCTTCTCTAAAAGTTAGAGCCCT
Found at i:10988 original size:6 final size:6
Alignment explanation
Indices: 10979--11083 Score: 90
Period size: 6 Copynumber: 17.5 Consensus size: 6
10969 TTTGTTGAGA
* * *
10979 CTGTTG CTGTTG CTGATG CTG-AG ACTGTTG CTGTTG CTGATG CTGATT-
1 CTGTTG CTGTTG CTGTTG CTGTTG -CTGTTG CTGTTG CTGTTG CTG-TTG
* * * *
11027 CTGTTG CTGTTG CTGATG CTGATT- CTGTTG CTGCTG CTGATG CTGCTG
1 CTGTTG CTGTTG CTGTTG CTG-TTG CTGTTG CTGTTG CTGTTG CTGTTG
*
11075 CTGCTG CTG
1 CTGTTG CTG
11084 CGGATGCTGT
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
5 5 0.06
6 75 0.90
7 3 0.04
ACGTcount: A:0.08, C:0.20, G:0.31, T:0.41
Consensus pattern (6 bp):
CTGTTG
Found at i:11001 original size:24 final size:24
Alignment explanation
Indices: 10974--11071 Score: 151
Period size: 24 Copynumber: 4.1 Consensus size: 24
10964 TTGTGTTTGT
10974 TGAGACTGTTGCTGTTGCTGATGC
1 TGAGACTGTTGCTGTTGCTGATGC
10998 TGAGACTGTTGCTGTTGCTGATGC
1 TGAGACTGTTGCTGTTGCTGATGC
**
11022 TGATTCTGTTGCTGTTGCTGATGC
1 TGAGACTGTTGCTGTTGCTGATGC
** *
11046 TGATTCTGTTGCTGCTGCTGATGC
1 TGAGACTGTTGCTGTTGCTGATGC
11070 TG
1 TG
11072 CTGCTGCTGC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.10, C:0.17, G:0.32, T:0.41
Consensus pattern (24 bp):
TGAGACTGTTGCTGTTGCTGATGC
Found at i:11084 original size:24 final size:24
Alignment explanation
Indices: 10979--11083 Score: 149
Period size: 24 Copynumber: 4.4 Consensus size: 24
10969 TTTGTTGAGA
10979 CTGTTGCTGTTGCTGATGCTGA-G
1 CTGTTGCTGTTGCTGATGCTGATG
*
11002 ACTGTTGCTGTTGCTGATGCTGATT
1 -CTGTTGCTGTTGCTGATGCTGATG
*
11027 CTGTTGCTGTTGCTGATGCTGATT
1 CTGTTGCTGTTGCTGATGCTGATG
* *
11051 CTGTTGCTGCTGCTGATGCTGCTG
1 CTGTTGCTGTTGCTGATGCTGATG
*
11075 CTGCTGCTG
1 CTGTTGCTG
11084 CGGATGCTGT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
24 75 1.00
ACGTcount: A:0.08, C:0.20, G:0.31, T:0.41
Consensus pattern (24 bp):
CTGTTGCTGTTGCTGATGCTGATG
Found at i:15684 original size:7 final size:7
Alignment explanation
Indices: 15672--15702 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
15662 GAAGCTCAGA
15672 TCTTGCT
1 TCTTGCT
15679 TCTTGCT
1 TCTTGCT
15686 TCTTGCT
1 TCTTGCT
*
15693 TCTTACT
1 TCTTGCT
15700 TCT
1 TCT
15703 CGTTACATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.03, C:0.29, G:0.10, T:0.58
Consensus pattern (7 bp):
TCTTGCT
Found at i:17553 original size:29 final size:30
Alignment explanation
Indices: 17501--17565 Score: 105
Period size: 29 Copynumber: 2.2 Consensus size: 30
17491 AGGATACATA
* *
17501 CCACGTGTCATTTTTTGTCCACGTGGCATG
1 CCACATGTAATTTTTTGTCCACGTGGCATG
17531 CCACATGTAATTTTTT-TCCACGTGGCATG
1 CCACATGTAATTTTTTGTCCACGTGGCATG
17560 CCACAT
1 CCACAT
17566 CGGACGTCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.35
Consensus pattern (30 bp):
CCACATGTAATTTTTTGTCCACGTGGCATG
Found at i:24819 original size:12 final size:12
Alignment explanation
Indices: 24802--24827 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
24792 TTTTTTGGTT
24802 TTTACATTATTA
1 TTTACATTATTA
24814 TTTACATTATTA
1 TTTACATTATTA
24826 TT
1 TT
24828 ATTAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTACATTATTA
Found at i:24828 original size:18 final size:17
Alignment explanation
Indices: 24807--24840 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
24797 TGGTTTTTAC
*
24807 ATTATTATTTACATTATT
1 ATTATTAATTA-ATTATT
24825 ATTATTAATTAATTAT
1 ATTATTAATTAATTAT
24841 ACTATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTATTAATTAATTATT
Found at i:35575 original size:99 final size:99
Alignment explanation
Indices: 35399--35748 Score: 583
Period size: 99 Copynumber: 3.5 Consensus size: 99
35389 CTGACGCTCG
* ** * *
35399 ACTTAGTTTCAATGTTCTCATTGGGAGTCCGGATCGAAATCCAAGGTCAAATACGAACGTTGCCG
1 ACTTAGTTTCGATGTTCTCACGGGGAGTCCGGATCGAAATCTAAGGTCAATTACGAACGTTGCCG
* *
35464 TTCTCACAAAGAGTCCGGGGCTCACGTTCGGCCA
66 TTCTCACGAAGAGTCCAGGGCTCACGTTCGGCCA
* *
35498 ACTTAGTTTCGATGTTCTCACGGAGAGTCCGGATCGAAATCTAAGGTCAATTACGAACGTTGCCA
1 ACTTAGTTTCGATGTTCTCACGGGGAGTCCGGATCGAAATCTAAGGTCAATTACGAACGTTGCCG
*
35563 TTCTCACGAAGAGTCCAGGGTTCACGTTCGGCCA
66 TTCTCACGAAGAGTCCAGGGCTCACGTTCGGCCA
*
35597 ACTTAGATTCGATGTTCTCACGGGGAGTCCGGATCGAAATCTAAGGTCAATTACGAACGTTGCCG
1 ACTTAGTTTCGATGTTCTCACGGGGAGTCCGGATCGAAATCTAAGGTCAATTACGAACGTTGCCG
*
35662 TTCTCACGAAGAGTCCAGGGCTCACGTCCGGCCA
66 TTCTCACGAAGAGTCCAGGGCTCACGTTCGGCCA
*
35696 ACTTAGTTTCGATGTTCTCACGGGGAGTCCGGATCGAAATCTAGGGTCAATTA
1 ACTTAGTTTCGATGTTCTCACGGGGAGTCCGGATCGAAATCTAAGGTCAATTA
35749 AAAATTTCTA
Statistics
Matches: 234, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 234 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (99 bp):
ACTTAGTTTCGATGTTCTCACGGGGAGTCCGGATCGAAATCTAAGGTCAATTACGAACGTTGCCG
TTCTCACGAAGAGTCCAGGGCTCACGTTCGGCCA
Found at i:35576 original size:51 final size:50
Alignment explanation
Indices: 35512--35677 Score: 146
Period size: 51 Copynumber: 3.3 Consensus size: 50
35502 AGTTTCGATG
*
35512 TTCTCACGGAGAGTCCGGATCGAAATCTAAGGTCAATTACGAACGTTGCC
1 TTCTCACGAAGAGTCCGGATCGAAATCTAAGGTCAATTACGAACGTTGCC
* ** * * * *
35562 ATTCTCACGAAGAGTCCAGGGTTC-ACGT-T-CGGCCAACTTA-GATTCGATG--
1 -TTCTCACGAAGAGTCC--GGATCGAAATCTAAGGTCAA-TTACGA-ACGTTGCC
**
35611 TTCTCACGGGGAGTCCGGATCGAAATCTAAGGTCAATTACGAACGTTGCC
1 TTCTCACGAAGAGTCCGGATCGAAATCTAAGGTCAATTACGAACGTTGCC
35661 GTTCTCACGAAGAGTCC
1 -TTCTCACGAAGAGTCC
35678 AGGGCTCACG
Statistics
Matches: 85, Mismatches: 19, Indels: 22
0.67 0.15 0.17
Matches are distributed among these distances:
46 4 0.05
47 2 0.02
48 22 0.26
49 7 0.08
50 7 0.08
51 37 0.44
52 2 0.02
53 4 0.05
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (50 bp):
TTCTCACGAAGAGTCCGGATCGAAATCTAAGGTCAATTACGAACGTTGCC
Found at i:37325 original size:27 final size:27
Alignment explanation
Indices: 37282--37340 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
37272 CATCTCTAGA
*
37282 ACAAAGCTTCCAATACCTTGCCGAGCT
1 ACAAAGCTCCCAATACCTTGCCGAGCT
* *
37309 ACAAAGCTCCCATTACCTTGCCGGGCT
1 ACAAAGCTCCCAATACCTTGCCGAGCT
37336 ACAAA
1 ACAAA
37341 ACCAACATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.34, G:0.15, T:0.20
Consensus pattern (27 bp):
ACAAAGCTCCCAATACCTTGCCGAGCT
Found at i:41077 original size:112 final size:112
Alignment explanation
Indices: 40875--41104 Score: 442
Period size: 112 Copynumber: 2.1 Consensus size: 112
40865 CAAAGAAAAA
*
40875 TGAAAGAGAGGTCAAACAATGCTGAGAACCATCATAATTAAGCAACTTAAAAAGAAATTCCAAAC
1 TGAATGAGAGGTCAAACAATGCTGAGAACCATCATAATTAAGCAACTTAAAAAGAAATTCCAAAC
40940 ACTGGTTAGAACTTAATATGATGATTATGCAAAATGAAAACATAAGT
66 ACTGGTTAGAACTTAATATGATGATTATGCAAAATGAAAACATAAGT
*
40987 TGAATGAGAGGTCAAACAATGCTGAGAACCATCATAATTAAGCAACTTATAAAGAAATTCCAAAC
1 TGAATGAGAGGTCAAACAATGCTGAGAACCATCATAATTAAGCAACTTAAAAAGAAATTCCAAAC
41052 ACTGGTTAGAACTTAATATGATGATTATGCAAAATGAAAACATAAGT
66 ACTGGTTAGAACTTAATATGATGATTATGCAAAATGAAAACATAAGT
41099 TGAATG
1 TGAATG
41105 CTTCAAGTAG
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 116 1.00
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (112 bp):
TGAATGAGAGGTCAAACAATGCTGAGAACCATCATAATTAAGCAACTTAAAAAGAAATTCCAAAC
ACTGGTTAGAACTTAATATGATGATTATGCAAAATGAAAACATAAGT
Found at i:44796 original size:16 final size:16
Alignment explanation
Indices: 44771--44803 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
44761 TGAACGATGA
44771 ACTTACATCACTAGTG
1 ACTTACATCACTAGTG
*
44787 ACTTAGATCACTAGTG
1 ACTTACATCACTAGTG
44803 A
1 A
44804 TCTGGGGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (16 bp):
ACTTACATCACTAGTG
Found at i:46247 original size:1 final size:1
Alignment explanation
Indices: 46241--46284 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
46231 TGTCACAAGC
* * * *
46241 AAAAAAAAAAAAAAAAAAAAAGAAGAAAAAGAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
46285 CTTAATTAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:46496 original size:11 final size:11
Alignment explanation
Indices: 46453--46490 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
46443 TTCCTATATA
*
46453 AAATAAATTAT
1 AAATTAATTAT
46464 CAAA-TAATTAT
1 -AAATTAATTAT
46475 AAATTAATTAT
1 AAATTAATTAT
46486 AAATT
1 AAATT
46491 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:47221 original size:31 final size:31
Alignment explanation
Indices: 47169--47307 Score: 149
Period size: 31 Copynumber: 4.6 Consensus size: 31
47159 GATGTGACGT
* **
47169 GCCACGTGGA-CAAAAAATGACACGTGGCAC
1 GCCACGTGTACCAAAAGGTGACACGTGGCAC
*
47199 GCCACGTGTACCAAAAGGTGACATGTGGCAC
1 GCCACGTGTACCAAAAGGTGACACGTGGCAC
* * * *
47230 GCCATGTGTTCCAAAAGGTGACACGTGTCGC
1 GCCACGTGTACCAAAAGGTGACACGTGGCAC
* *
47261 GCCACGTGTACCAAAA-GTGACACGTAGCAT
1 GCCACGTGTACCAAAAGGTGACACGTGGCAC
* *
47291 GTCACGTGCA-CAAAAGG
1 GCCACGTGTACCAAAAGG
47308 ACATGTGCCA
Statistics
Matches: 90, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
29 5 0.06
30 28 0.31
31 57 0.63
ACGTcount: A:0.31, C:0.26, G:0.27, T:0.16
Consensus pattern (31 bp):
GCCACGTGTACCAAAAGGTGACACGTGGCAC
Found at i:47853 original size:11 final size:11
Alignment explanation
Indices: 47810--47847 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
47800 TCTATATATA
*
47810 AAATAAATTAT
1 AAATTAATTAT
47821 CAAA-TAATTAT
1 -AAATTAATTAT
47832 AAATTAATTAT
1 AAATTAATTAT
47843 AAATT
1 AAATT
47848 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:48841 original size:107 final size:107
Alignment explanation
Indices: 48677--48942 Score: 496
Period size: 107 Copynumber: 2.5 Consensus size: 107
48667 AGTTTAGCCT
* *
48677 TAATTTCATTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTAAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTAAAAATC
48742 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
48784 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATC
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTAAAAATC
*
48849 AATAATTTATTGTTATATGGTTTTAGAAATAAAATACAAAAC
66 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
48891 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
48943 TAGAAAAATT
Statistics
Matches: 155, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 155 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (107 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTAAAAATC
AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:55140 original size:113 final size:109
Alignment explanation
Indices: 55015--55236 Score: 372
Period size: 109 Copynumber: 2.0 Consensus size: 109
55005 TCTATTACAT
*
55015 ATATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGTACACATATATACCAAA
1 ATATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAA--ACAC--ACATACCAAA
* *
55080 CAATACAAAATGTAATGAACTATTGGATTTAAAGAAAAATACAAGCAC
62 CAACACAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCAC
55128 ATATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAACACACATACCAAACAAC
1 ATATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAACACACATACCAAACAAC
*
55193 ACAAAGTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCAC
66 ACAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCAC
55237 CAAAATGGCT
Statistics
Matches: 105, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
109 54 0.51
111 4 0.04
113 47 0.45
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (109 bp):
ATATTATTATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAACACACATACCAAACAAC
ACAAAATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCAC
Done.