Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020583.1 Corchorus olitorius cultivar O-4 contig20616, 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: 30986
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Found at i:28 original size:20 final size:20
Alignment explanation
Indices: 3--42 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1 AA
3 CTCTCACGGAATGTGAGTTT
1 CTCTCACGGAATGTGAGTTT
23 CTCTCACGGAATGTGAGTTT
1 CTCTCACGGAATGTGAGTTT
43 GTTTGTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CTCTCACGGAATGTGAGTTT
Found at i:2256 original size:2 final size:2
Alignment explanation
Indices: 2249--2278 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2239 AAAGTCAAAC
2249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2279 TTTGTTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4392 original size:21 final size:19
Alignment explanation
Indices: 4346--4385 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
4336 AATAAAAAAG
* *
4346 TTTT-TTTTTTAAATTTTA
1 TTTTATTTTTTAAAATTAA
4364 TTTTATTTTTTAAAATTAA
1 TTTTATTTTTTAAAATTAA
4383 TTT
1 TTT
4386 GTTATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTTTTTAAAATTAA
Found at i:7197 original size:93 final size:94
Alignment explanation
Indices: 7032--7214 Score: 278
Period size: 93 Copynumber: 2.0 Consensus size: 94
7022 CTGATACCAC
* * * * *
7032 TTGTTGGGAGAGGAAACCGGGCCCTGACTGCTTCAGCAAGGCCTATCGAGTAGCCCATATACATG
1 TTGTTGGGAGAGGAAACCGGGCCCTGACTACTCCAGCAAGGCCCACCGAGCAGCCCATATACATG
*
7097 TCAGACACCAACCTAAATCCAAAAGCCTT
66 TCAGACACCAACCTAAACCCAAAAGCCTT
* *
7126 TTGTTGGGAGAGG-AACCGGGCCCTGTCTACTCCAGCAAGGCCCACCGAGCAGCTCATATACATG
1 TTGTTGGGAGAGGAAACCGGGCCCTGACTACTCCAGCAAGGCCCACCGAGCAGCCCATATACATG
*
7190 TCGGACACCAACCTAAACCCAAAAG
66 TCAGACACCAACCTAAACCCAAAAG
7215 TCTAGACTAA
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 67 0.84
94 13 0.16
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.18
Consensus pattern (94 bp):
TTGTTGGGAGAGGAAACCGGGCCCTGACTACTCCAGCAAGGCCCACCGAGCAGCCCATATACATG
TCAGACACCAACCTAAACCCAAAAGCCTT
Found at i:8636 original size:29 final size:30
Alignment explanation
Indices: 8594--8661 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 30
8584 ATTTATTATG
*
8594 ACATTTTAATATATGTG-TAGTTTTTTTAA
1 ACATTTTAATATATATGTTAGTTTTTTTAA
*
8623 ACATTTTAATATATATGTTAGTTTTTTTTA
1 ACATTTTAATATATATGTTAGTTTTTTTAA
8653 ACATATTTA
1 ACAT-TTTA
8662 TAAGAAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 16 0.46
30 15 0.43
31 4 0.11
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.56
Consensus pattern (30 bp):
ACATTTTAATATATATGTTAGTTTTTTTAA
Found at i:8640 original size:31 final size:29
Alignment explanation
Indices: 8594--8661 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
8584 ATTTATTATG
8594 ACATTTT-AATATATGTGTAGTTTTTTTAA
1 ACATTTTAAATATATGT-TAGTTTTTTTAA
*
8623 ACATTTTAATATATATGTTAGTTTTTTTTA
1 ACATTTTAA-ATATATGTTAGTTTTTTTAA
8653 ACATATTTA
1 ACAT-TTTA
8662 TAAGAAAGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
29 7 0.20
30 16 0.46
31 12 0.34
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.56
Consensus pattern (29 bp):
ACATTTTAAATATATGTTAGTTTTTTTAA
Found at i:8687 original size:28 final size:30
Alignment explanation
Indices: 8656--8715 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
8646 TTTTTTAACA
* *
8656 TATTTAT-AAGAAAG-AATTAAAATGTTCT
1 TATTTATAAAAAAAGAAAGTAAAATGTTCT
8684 TA-TTATAAAAAAAGAAAGTAAAATGTTCT
1 TATTTATAAAAAAAGAAAGTAAAATGTTCT
8713 TAT
1 TAT
8716 ATTGAATTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.15
28 8 0.30
29 15 0.56
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.37
Consensus pattern (30 bp):
TATTTATAAAAAAAGAAAGTAAAATGTTCT
Found at i:17059 original size:200 final size:200
Alignment explanation
Indices: 16716--17116 Score: 784
Period size: 200 Copynumber: 2.0 Consensus size: 200
16706 GACTACGTTC
16716 AGTAGAGCGATGTGATTGGCTCCGTTTAAACTGAAATTGTAAGATTAAACACTGTACAGATCAAA
1 AGTAGAGCGATGTGATTGGCTCCGTTTAAACTGAAATTGTAAGATTAAACACTGTACAGATCAAA
*
16781 TTAGGTACGGTACAAATGACCGGTGAAAACGGAAATGTTAAGTGAGAACAGCGGTGGGGTGAGAT
66 TTAGGTACGGTACAAATGACCGGTGAAAACGGAAATGTTAAGTGAGAACAGCGGTAGGGTGAGAT
16846 TAAAATGTAAAATGACCTTTAAGGGTATTATTATTTAAAGGTATTGTATCATTTTATTTATTTTA
131 TAAAATGTAAAATGACCTTTAAGGGTATTATTATTTAAAGGTATTGTATCATTTTATTTATTTTA
16911 TTTAT
196 TTTAT
*
16916 AGTAGAGCGGTGTGATTGGCTCCGTTTAAACTGAAATTGTAAGATTAAACACTGTACAGATCAAA
1 AGTAGAGCGATGTGATTGGCTCCGTTTAAACTGAAATTGTAAGATTAAACACTGTACAGATCAAA
16981 TTAGGTACGGTACAAATGACCGGTGAAAACGGAAATGTTAAGTGAGAACAGCGGTAGGGTGAGAT
66 TTAGGTACGGTACAAATGACCGGTGAAAACGGAAATGTTAAGTGAGAACAGCGGTAGGGTGAGAT
17046 TAAAATGTAAAATGACCTTTAAGGGTATTATTATTTAAAGGTATTGTATCATTTTATTTATTTTA
131 TAAAATGTAAAATGACCTTTAAGGGTATTATTATTTAAAGGTATTGTATCATTTTATTTATTTTA
17111 TTTAT
196 TTTAT
17116 A
1 A
17117 TAATATTTAT
Statistics
Matches: 199, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 199 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.33
Consensus pattern (200 bp):
AGTAGAGCGATGTGATTGGCTCCGTTTAAACTGAAATTGTAAGATTAAACACTGTACAGATCAAA
TTAGGTACGGTACAAATGACCGGTGAAAACGGAAATGTTAAGTGAGAACAGCGGTAGGGTGAGAT
TAAAATGTAAAATGACCTTTAAGGGTATTATTATTTAAAGGTATTGTATCATTTTATTTATTTTA
TTTAT
Found at i:17290 original size:23 final size:22
Alignment explanation
Indices: 17264--17309 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
17254 AACTATTACT
17264 AAAAAAAATAAACAAAAGTAAAA
1 AAAAAAAATAAACAAAA-TAAAA
** *
17287 AAAATGAATAAATAAAATAAAA
1 AAAAAAAATAAACAAAATAAAA
17309 A
1 A
17310 TCCATTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.13
Consensus pattern (22 bp):
AAAAAAAATAAACAAAATAAAA
Found at i:17926 original size:31 final size:31
Alignment explanation
Indices: 17878--18092 Score: 188
Period size: 31 Copynumber: 7.1 Consensus size: 31
17868 GTGTCCGACA
* * *
17878 TGGCATGCCATGTGTACCAAAAAGCGACATG
1 TGGCACGCCACGTGTACCAAAAAGCGACACG
* *
17909 TGACACGCTC-CGTGTACCAAAAAACGACACG
1 TGGCACGC-CACGTGTACCAAAAAGCGACACG
* * *
17940 TGGCACGCCACATGTACCAAAAAGTGACACA
1 TGGCACGCCACGTGTACCAAAAAGCGACACG
* * * *
17971 TGGCACGCCACATGTACAAAAAAGTGACAAG
1 TGGCACGCCACGTGTACCAAAAAGCGACACG
* * **
18002 TGTCACGCCATGTGTACCAAAAAGTAACACG
1 TGGCACGCCACGTGTACCAAAAAGCGACACG
* * *
18033 TGGCATGCCTCGTGCA-CAAAAAG-GACACG
1 TGGCACGCCACGTGTACCAAAAAGCGACACG
* * *
18062 TGGCATGCCTCGTGCA-CAAAAAG-GACACG
1 TGGCACGCCACGTGTACCAAAAAGCGACACG
18091 TG
1 TG
18093 CCATGTGTCA
Statistics
Matches: 157, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
29 36 0.23
30 8 0.05
31 112 0.71
32 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.23, T:0.15
Consensus pattern (31 bp):
TGGCACGCCACGTGTACCAAAAAGCGACACG
Found at i:18060 original size:29 final size:29
Alignment explanation
Indices: 18019--18097 Score: 131
Period size: 29 Copynumber: 2.7 Consensus size: 29
18009 CCATGTGTAC
*
18019 CAAAAAGTAACACGTGGCATGCCTCGTGCA
1 CAAAAAG-GACACGTGGCATGCCTCGTGCA
18049 CAAAAAGGACACGTGGCATGCCTCGTGCA
1 CAAAAAGGACACGTGGCATGCCTCGTGCA
*
18078 CAAAAAGGACACGTGCCATG
1 CAAAAAGGACACGTGGCATG
18098 TGTCATTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 40 0.85
30 7 0.15
ACGTcount: A:0.34, C:0.27, G:0.25, T:0.14
Consensus pattern (29 bp):
CAAAAAGGACACGTGGCATGCCTCGTGCA
Found at i:20950 original size:2 final size:2
Alignment explanation
Indices: 20943--20974 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20933 CATTCTCTTG
20943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20975 TTTTCACACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29337 original size:15 final size:15
Alignment explanation
Indices: 29317--29347 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29307 TGAAGAAATG
29317 TCTCTGATCACGTTC
1 TCTCTGATCACGTTC
29332 TCTCTGATCACGTTC
1 TCTCTGATCACGTTC
29347 T
1 T
29348 ATAAATAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.32, G:0.13, T:0.42
Consensus pattern (15 bp):
TCTCTGATCACGTTC
Done.