Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009168.1 Corchorus capsularis cultivar CVL-1 contig09189, 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: 33477
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:418 original size:46 final size:46
Alignment explanation
Indices: 361--498 Score: 249
Period size: 46 Copynumber: 3.0 Consensus size: 46
351 AAAGTTTAAG
*
361 AAGATATTTTAGATATTTCCATTTATATTAAATTACATATTAACCA
1 AAGATATTTTAGATATTTCCATTTATATTAAATTACTTATTAACCA
* *
407 AAGATAGTTTAGATATTTCCATTTATATTAAATTTCTTATTAACCA
1 AAGATATTTTAGATATTTCCATTTATATTAAATTACTTATTAACCA
453 AAGATATTTTAGATATTTCCATTTATATTAAATTACTTATTAACCA
1 AAGATATTTTAGATATTTCCATTTATATTAAATTACTTATTAACCA
499 TTAAAACTTA
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (46 bp):
AAGATATTTTAGATATTTCCATTTATATTAAATTACTTATTAACCA
Found at i:499 original size:25 final size:25
Alignment explanation
Indices: 425--500 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
415 TTAGATATTT
*
425 CCATTTATATTAAATTTCTTATTAA
1 CCATTTATATTAAATTACTTATTAA
*** ** *
450 CCAAAGATATT---TTAGATATT-T
1 CCATTTATATTAAATTACTTATTAA
471 CCATTTATATTAAATTACTTATTAA
1 CCATTTATATTAAATTACTTATTAA
496 CCATT
1 CCATT
501 AAAACTTACT
Statistics
Matches: 34, Mismatches: 13, Indels: 8
0.62 0.24 0.15
Matches are distributed among these distances:
21 8 0.24
22 6 0.18
24 7 0.21
25 13 0.38
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (25 bp):
CCATTTATATTAAATTACTTATTAA
Found at i:739 original size:45 final size:44
Alignment explanation
Indices: 687--772 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 44
677 AGAAAAGATG
*
687 AATCTGAGACAACTGAGAAAGTTGCCAAGGACGAGGAGAGGACCA
1 AATCTGAGAAAACTGAGAAAGTTGCCAAGGACGA-GAGAGGACCA
* *
732 AATCTGAGAAAACTGAGAAAGTTGCGAAGGAGGAGAGAGGA
1 AATCTGAGAAAACTGAGAAAGTTGCCAAGGACGAGAGAGGA
773 TTGAATCCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 7 0.18
45 31 0.82
ACGTcount: A:0.42, C:0.13, G:0.34, T:0.12
Consensus pattern (44 bp):
AATCTGAGAAAACTGAGAAAGTTGCCAAGGACGAGAGAGGACCA
Found at i:1844 original size:12 final size:12
Alignment explanation
Indices: 1824--1859 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
1814 TAATATCATC
*
1824 ACTTCACTTTAA
1 ACTTGACTTTAA
1836 ACTTGACTTTTAA
1 ACTTGAC-TTTAA
1849 ACTTGACTTTA
1 ACTTGACTTTA
1860 TGAGGTTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (12 bp):
ACTTGACTTTAA
Found at i:1849 original size:13 final size:13
Alignment explanation
Indices: 1831--1858 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1821 ATCACTTCAC
1831 TTTAAACTTGACT
1 TTTAAACTTGACT
1844 TTTAAACTTGACT
1 TTTAAACTTGACT
1857 TT
1 TT
1859 ATGAGGTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (13 bp):
TTTAAACTTGACT
Found at i:3259 original size:38 final size:38
Alignment explanation
Indices: 3215--3297 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
3205 TCGTTATAAA
* * *
3215 CAAATTTTGTTAATTATTTTATCAATAATAGAATTTTT
1 CAAATTTTGTTAATCATTTTATCAATAATAGAACTTAT
*
3253 CAAATTTTGTTAATCATTTTTTCAATAATAGAACTTAT
1 CAAATTTTGTTAATCATTTTATCAATAATAGAACTTAT
3291 CAAATTT
1 CAAATTT
3298 ACAATAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.49
Consensus pattern (38 bp):
CAAATTTTGTTAATCATTTTATCAATAATAGAACTTAT
Found at i:4612 original size:31 final size:31
Alignment explanation
Indices: 4516--4685 Score: 187
Period size: 31 Copynumber: 5.4 Consensus size: 31
4506 TCCGACGTGG
* * ** *
4516 CATGCCATGTGTACCAAAAAATGACATGTGG
1 CATGCCACGTGTACCAAAAAGTGACACATGT
* **
4547 CATGCCACGTGTACAAAAAAGTGACATGTGT
1 CATGCCACGTGTACCAAAAAGTGACACATGT
* *
4578 CATGCCATGTGTACCAAAAAGTGACACATAT
1 CATGCCACGTGTACCAAAAAGTGACACATGT
*
4609 CATGCCACATGTACCAAAAAGTGACACATAGCAT
1 CATGCCACGTGTACCAAAAAGTGACACAT-G--T
* *
4643 GCATGCCACGTGTACCAGAAAGTGACACATGG
1 -CATGCCACGTGTACCAAAAAGTGACACATGT
4675 CATGCCACGTG
1 CATGCCACGTG
4686 CACAAAAGGA
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
31 91 0.76
34 2 0.02
35 27 0.22
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (31 bp):
CATGCCACGTGTACCAAAAAGTGACACATGT
Found at i:4613 original size:62 final size:64
Alignment explanation
Indices: 4515--4692 Score: 218
Period size: 62 Copynumber: 2.8 Consensus size: 64
4505 GTCCGACGTG
* **
4515 GCATGCCATGTGTACCAAAAAATGACATGTGGCATGCCACGTGTACAAAAAAGTG-ACAT-G-T
1 GCATGCCATGTGTACCAAAAAGTGACACATGGCATGCCACGTGTACAAAAAAGTGAACATAGAT
** * *
4576 GTCATGCCATGTGTACCAAAAAGTGACACATATCATGCCACATGTACCAAAAAGTGACACATAGC
1 G-CATGCCATGTGTACCAAAAAGTGACACATGGCATGCCACGTGTACAAAAAAGTGA-ACATAG-
4641 AT
63 AT
* * *
4643 GCATGCCACGTGTACCAGAAAGTGACACATGGCATGCCACGTGCACAAAA
1 GCATGCCATGTGTACCAAAAAGTGACACATGGCATGCCACGTGTACAAAA
4693 GGATACGTAC
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
61 1 0.01
62 47 0.48
64 4 0.04
65 1 0.01
66 42 0.43
67 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.19
Consensus pattern (64 bp):
GCATGCCATGTGTACCAAAAAGTGACACATGGCATGCCACGTGTACAAAAAAGTGAACATAGAT
Found at i:17654 original size:1 final size:1
Alignment explanation
Indices: 17650--17675 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
17640 GATTTTTCAC
17650 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
17676 GTAATTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:23101 original size:2 final size:2
Alignment explanation
Indices: 23094--23141 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
23084 CCATTATTAA
*
23094 AT AT AT AT AT AT A- AC AT AT ACT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
23135 AT A- AT AT
1 AT AT AT AT
23142 GTTAATGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
1 3 0.07
2 36 0.88
3 2 0.05
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:23952 original size:32 final size:33
Alignment explanation
Indices: 23916--23981 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
23906 TTATTTTACC
*
23916 TGCATAATCT-CTTCTTCTACCTTTCTTTATCA
1 TGCATAATCTCCTCCTTCTACCTTTCTTTATCA
23948 TGCATAATCTCCTCCTTCTACCTTTCTTTATCA
1 TGCATAATCTCCTCCTTCTACCTTTCTTTATCA
23981 T
1 T
23982 TAAAAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.18, C:0.30, G:0.03, T:0.48
Consensus pattern (33 bp):
TGCATAATCTCCTCCTTCTACCTTTCTTTATCA
Found at i:24061 original size:33 final size:33
Alignment explanation
Indices: 24012--24143 Score: 210
Period size: 33 Copynumber: 4.0 Consensus size: 33
24002 ATACTACCTT
* *
24012 GTATATTAGTAGCACCTGAAGTTGTCACATCAC
1 GTATATTAGTGGCACCTGAAGTTGTCACATCAA
* *
24045 GTGTATAAGTGGCACCTGAAGTTGTCACATCAA
1 GTATATTAGTGGCACCTGAAGTTGTCACATCAA
*
24078 GTATATTAGTGGCATCTGAAGTTGTCACATCAA
1 GTATATTAGTGGCACCTGAAGTTGTCACATCAA
*
24111 GCATATTAGTGGCACCTGAAGTTGTCACATCAA
1 GTATATTAGTGGCACCTGAAGTTGTCACATCAA
24144 AAATATAATA
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (33 bp):
GTATATTAGTGGCACCTGAAGTTGTCACATCAA
Found at i:25093 original size:42 final size:42
Alignment explanation
Indices: 25032--25115 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
25022 ATGGTCGCGG
* *
25032 TCGTGATCGTAGCTCTGGATATAATGGTGATCATTTGAAAAA
1 TCGTGATCGTAGCTATGGATATAATGGTGATCATTCGAAAAA
*
25074 TCGTGGTCGTAGCTATGGATATAATGGTGATCATTCGAAAAA
1 TCGTGATCGTAGCTATGGATATAATGGTGATCATTCGAAAAA
25116 CATATCTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32
Consensus pattern (42 bp):
TCGTGATCGTAGCTATGGATATAATGGTGATCATTCGAAAAA
Done.