Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012340.1 Corchorus olitorius cultivar O-4 contig12373, 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: 68634
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:294 original size:19 final size:19
Alignment explanation
Indices: 246--321 Score: 68
Period size: 19 Copynumber: 4.2 Consensus size: 19
236 CCAGAAACCA
* * *
246 ACCACTGCCGGCCACCACT
1 ACCACCGCCGGTCACCACC
* *
265 ACCGCCCCCGGTCACCACC
1 ACCACCGCCGGTCACCACC
284 ACCACCGCCGG-CA--ACC
1 ACCACCGCCGGTCACCACC
* *
300 ACCGCCGCCTGTCACCACC
1 ACCACCGCCGGTCACCACC
319 ACC
1 ACC
322 GCCGGTCACT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
16 12 0.27
17 2 0.04
18 2 0.04
19 29 0.64
ACGTcount: A:0.20, C:0.58, G:0.16, T:0.07
Consensus pattern (19 bp):
ACCACCGCCGGTCACCACC
Found at i:329 original size:16 final size:16
Alignment explanation
Indices: 280--330 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
270 CCCCGGTCAC
280 CACCACCACCGCCGG-
1 CACCACCACCGCCGGT
* *
295 CAACCACCGCCGCCTGT
1 C-ACCACCACCGCCGGT
312 CACCACCACCGCCGGT
1 CACCACCACCGCCGGT
328 CAC
1 CAC
331 TTTTCCGGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 1 0.03
16 28 0.93
17 1 0.03
ACGTcount: A:0.20, C:0.57, G:0.18, T:0.06
Consensus pattern (16 bp):
CACCACCACCGCCGGT
Found at i:571 original size:8 final size:8
Alignment explanation
Indices: 558--616 Score: 64
Period size: 8 Copynumber: 6.9 Consensus size: 8
548 CTTAATTTAT
558 TTTTTTTC
1 TTTTTTTC
566 TTTTTTTC
1 TTTTTTTC
*
574 TTTTTTCTT
1 TTTTTT-TC
583 TTTTTTTC
1 TTTTTTTC
591 ATTTTTTTC
1 -TTTTTTTC
*
600 TCCTTTTCTC
1 T--TTTTTTC
610 TTTTTTT
1 TTTTTTT
617 TTTATTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 21 0.49
9 15 0.35
10 7 0.16
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:577 original size:15 final size:15
Alignment explanation
Indices: 559--587 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
549 TTAATTTATT
559 TTTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTC
574 TTTTTTCTTTTTTT
1 TTTTTTCTTTTTTT
588 TTCATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTCTTTTTTTC
Found at i:605 original size:29 final size:27
Alignment explanation
Indices: 557--626 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 27
547 GCTTAATTTA
*
557 TTTTTTTTC--TTTTTTTCTTTTTTCT
1 TTTTTTTTCATTTTTTTTCTTTTCTCT
582 TTTTTTTTCATTTTTTTCTCCTTTTCTCT
1 TTTTTTTTCATTTTTTT-T-CTTTTCTCT
*
611 TTTTTTTTTATTTTTT
1 TTTTTTTTCATTTTTT
627 ATAAATGATG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
25 9 0.23
27 6 0.15
28 1 0.03
29 23 0.59
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (27 bp):
TTTTTTTTCATTTTTTTTCTTTTCTCT
Found at i:1206 original size:16 final size:16
Alignment explanation
Indices: 1169--1207 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1159 ACCACCGACG
*
1169 CCGCCGGCAACCACCG
1 CCGCCGGCAACCACCA
*
1185 CTGCCGGCAACCACCA
1 CCGCCGGCAACCACCA
1201 CCGCCGG
1 CCGCCGG
1208 TCACTTTTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.18, C:0.54, G:0.26, T:0.03
Consensus pattern (16 bp):
CCGCCGGCAACCACCA
Found at i:11057 original size:27 final size:27
Alignment explanation
Indices: 11016--11082 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
11006 TCAATTAAGA
* * *
11016 AAATGATCAACATACTCCTGAATGTGC
1 AAATGACCAAAATACCCCTGAATGTGC
*
11043 AAATGAGCAAAATACCCCTGAATGTGC
1 AAATGACCAAAATACCCCTGAATGTGC
11070 AAATGACCAAAAT
1 AAATGACCAAAAT
11083 GCAACTAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (27 bp):
AAATGACCAAAATACCCCTGAATGTGC
Found at i:23321 original size:21 final size:21
Alignment explanation
Indices: 23295--23354 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
23285 CCCAGCCATG
*
23295 GCCCGGTCAGCCGAGTCACCT
1 GCCCGGTCAGCCGAGCCACCT
*
23316 GCCCGGCCAGCCGAGCCACCT
1 GCCCGGTCAGCCGAGCCACCT
* *
23337 GCCCGGTCATCCGCGCCA
1 GCCCGGTCAGCCGAGCCA
23355 TTCCAGGCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.13, C:0.48, G:0.28, T:0.10
Consensus pattern (21 bp):
GCCCGGTCAGCCGAGCCACCT
Found at i:24451 original size:18 final size:18
Alignment explanation
Indices: 24428--24462 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24418 AAGTGTAGTT
* *
24428 AAAAAAATTGTTTTCATA
1 AAAAAAAGTGCTTTCATA
24446 AAAAAAAGTGCTTTCAT
1 AAAAAAAGTGCTTTCAT
24463 GCAAGAGGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (18 bp):
AAAAAAAGTGCTTTCATA
Found at i:30772 original size:11 final size:12
Alignment explanation
Indices: 30756--30787 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
30746 GAGGTTCTTG
30756 TTTGAAGACT-A
1 TTTGAAGACTAA
30767 TTTGAAGA-TAA
1 TTTGAAGACTAA
30778 TTTGAAGACT
1 TTTGAAGACT
30788 TAAAGACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 17 0.89
12 1 0.05
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTAA
Found at i:35692 original size:11 final size:10
Alignment explanation
Indices: 35672--35711 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
35662 CCAAGTTAGG
35672 ACCGGCCATC
1 ACCGGCCATC
35682 ACCGTGCCATC
1 ACCG-GCCATC
*
35693 ACCGTGCCATT
1 ACCG-GCCATC
35704 ACCGGCCA
1 ACCGGCCA
35712 AATGCTTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 8 0.29
11 20 0.71
ACGTcount: A:0.20, C:0.45, G:0.20, T:0.15
Consensus pattern (10 bp):
ACCGGCCATC
Found at i:36375 original size:26 final size:26
Alignment explanation
Indices: 36352--36403 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
36342 TTACATGCAT
36352 ATTGATCATAATCTTAATCAATGCTA
1 ATTGATCATAATCTTAATCAATGCTA
*
36378 ATTGATCATAATCTTAATCGATGCTA
1 ATTGATCATAATCTTAATCAATGCTA
36404 TAATTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (26 bp):
ATTGATCATAATCTTAATCAATGCTA
Found at i:39837 original size:19 final size:18
Alignment explanation
Indices: 39804--39839 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
39794 TTGAGATAAT
39804 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
39822 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
39840 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:41391 original size:30 final size:30
Alignment explanation
Indices: 41352--41410 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
41342 GTTTATTAAT
41352 GAAACTTGAAAATTAAAGACATAAAATAAAG
1 GAAACTTGAAAATTAAAG-CATAAAATAAAG
*
41383 GAAA-TTGAAAATTAAAGCATAAATTAAA
1 GAAACTTGAAAATTAAAGCATAAAATAAA
41411 TAACTAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.37
30 13 0.48
31 4 0.15
ACGTcount: A:0.61, C:0.05, G:0.12, T:0.22
Consensus pattern (30 bp):
GAAACTTGAAAATTAAAGCATAAAATAAAG
Found at i:47462 original size:28 final size:28
Alignment explanation
Indices: 47422--47503 Score: 103
Period size: 28 Copynumber: 3.0 Consensus size: 28
47412 CCCCCCCCCT
47422 TGGACGTGC-AAATGACCAAAATGCCCA
1 TGGACGTGCAAAATGACCAAAATGCCCA
* * *
47449 TGGAGGTGCAAAATGACCACAATGCCCT
1 TGGACGTGCAAAATGACCAAAATGCCCA
* * *
47477 TGGTCATGCAAAATGATCAAAATGCCC
1 TGGACGTGCAAAATGACCAAAATGCCC
47504 CCCCTTAAGT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
27 8 0.17
28 38 0.83
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.18
Consensus pattern (28 bp):
TGGACGTGCAAAATGACCAAAATGCCCA
Found at i:47775 original size:34 final size:35
Alignment explanation
Indices: 47735--47885 Score: 109
Period size: 35 Copynumber: 4.3 Consensus size: 35
47725 AGAAACACTG
47735 CACCGAGCCCA-CCGAG-TCCA-TATTGAAGATGCTA
1 CACCGAG-CCATCCGAGAT-CATTATTGAAGATGCTA
* * *
47769 CACCGAGTCATCCGAGATCATTTTTGAAGATGCTG
1 CACCGAGCCATCCGAGATCATTATTGAAGATGCTA
* * *
47804 CACCGAGTCATCCGA-ATTTATCT-TTGAAGATGCTG
1 CACCGAGCCATCCGAGA-TCAT-TATTGAAGATGCTA
* * *
47839 CACCGAGTCATCTGA-ATTCATCT-TTGAAGATGCTG
1 CACCGAGCCATCCGAGA-TCAT-TATTGAAGATGCTA
*
47874 CACCGAGTCATC
1 CACCGAGCCATC
47886 TGAATTCATC
Statistics
Matches: 106, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
33 2 0.02
34 15 0.14
35 88 0.83
36 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (35 bp):
CACCGAGCCATCCGAGATCATTATTGAAGATGCTA
Found at i:48026 original size:35 final size:35
Alignment explanation
Indices: 47757--48026 Score: 371
Period size: 35 Copynumber: 7.7 Consensus size: 35
47747 CGAGTCCATA
* * * *
47757 TTGAAGATGCTACACCGAGTCATCCGAGA-TCATTT
1 TTGAAGATGCTGCACCGAGTCAT-CTAAATTCATCT
** *
47792 TTGAAGATGCTGCACCGAGTCATCCGAATTTATCT
1 TTGAAGATGCTGCACCGAGTCATCTAAATTCATCT
*
47827 TTGAAGATGCTGCACCGAGTCATCTGAATTCATCT
1 TTGAAGATGCTGCACCGAGTCATCTAAATTCATCT
*
47862 TTGAAGATGCTGCACCGAGTCATCTGAATTCATCT
1 TTGAAGATGCTGCACCGAGTCATCTAAATTCATCT
* *
47897 TTGAAAATGCTGCATCGAGTCATCTAAATTCATCT
1 TTGAAGATGCTGCACCGAGTCATCTAAATTCATCT
* * * *
47932 TTGAATATGTTACACCGAGTCATCTAAATTCGTCT
1 TTGAAGATGCTGCACCGAGTCATCTAAATTCATCT
*
47967 TTGAAGATGCTACACCGAGTCATCTAAATTCATCT
1 TTGAAGATGCTGCACCGAGTCATCTAAATTCATCT
*
48002 TTGAAGATGTTGCACCGAGTCATCT
1 TTGAAGATGCTGCACCGAGTCATCT
48027 GATTTCCTGA
Statistics
Matches: 213, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
34 2 0.01
35 211 0.99
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (35 bp):
TTGAAGATGCTGCACCGAGTCATCTAAATTCATCT
Found at i:59891 original size:10 final size:10
Alignment explanation
Indices: 59872--59900 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
59862 AGTAGAACAT
59872 CAAA-CAAAA
1 CAAACCAAAA
59881 CAAACCAAAA
1 CAAACCAAAA
59891 CAAACCAAAA
1 CAAACCAAAA
59901 ATCAAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAACCAAAA
Found at i:65454 original size:11 final size:12
Alignment explanation
Indices: 65438--65469 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
65428 GAAGTTCGTG
65438 TTTGAAGACT-A
1 TTTGAAGACTAA
65449 TTTGAAGA-TAA
1 TTTGAAGACTAA
65460 TTTGAAGACT
1 TTTGAAGACT
65470 TGAAGACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 17 0.89
12 1 0.05
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (12 bp):
TTTGAAGACTAA
Done.