Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023871.1 Corchorus olitorius cultivar O-4 contig23904, 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: 132166
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1507 original size:21 final size:19
Alignment explanation
Indices: 1481--1539 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 19
1471 TGCTGCTCTA
1481 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
* *
1500 ACATAATCTAATTTGTACAGT
1 --ATAATCTCATCTGTACAGT
*
1521 GTAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
1540 TACCAAACAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:1527 original size:19 final size:19
Alignment explanation
Indices: 1482--1539 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1472 GCTGCTCTAA
* *
1482 TAATCTCATCTGTACAGTACA
1 TAATCTAATCTGTACAGT--G
*
1503 TAATCTAATTTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
1522 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
1540 TACCAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:20199 original size:19 final size:19
Alignment explanation
Indices: 20163--20199 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20153 CTGTTTAGCA
*
20163 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAAATTAC
*
20182 ACTGTACAGATTAAATTA
1 ACTGTACAGATGAAATTA
20200 GGTATTGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
ACTGTACAGATGAAATTAC
Found at i:41538 original size:28 final size:29
Alignment explanation
Indices: 41506--41580 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
41496 ACTTGTAGCG
* *
41506 TTTGGACGTTTTGTCCCTGAACT-TCAAT
1 TTTGGACGTTTTGCCCCTAAACTCTCAAT
*
41534 TTTGGACATTTTGCCCCTAAACTCTCAAT
1 TTTGGACGTTTTGCCCCTAAACTCTCAAT
41563 TTTGGACGTTTTGCCCCT
1 TTTGGACGTTTTGCCCCT
41581 CTCAAACGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 20 0.48
29 22 0.52
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.41
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCCTAAACTCTCAAT
Found at i:44406 original size:5 final size:5
Alignment explanation
Indices: 44391--44421 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
44381 GTATTCATCC
44391 TTTTGA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA
44422 AATCATCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:49704 original size:2 final size:2
Alignment explanation
Indices: 49697--49721 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
49687 AAAGAAAAGA
49697 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
49722 AGCAACTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:54484 original size:45 final size:44
Alignment explanation
Indices: 54435--54524 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 44
54425 TAAAATTTAG
*
54435 ATTCCATAAACGAATTATAAGGAATTGACACATACTTCATTTCTT
1 ATTCCACAAACGAATTATAAGGAATTGACACATA-TTCATTTCTT
*
54480 ATTCCACAAACGAGTTATAAGGAATTGACACATATTCATTTCTT
1 ATTCCACAAACGAATTATAAGGAATTGACACATATTCATTTCTT
54524 A
1 A
54525 ATTAATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
44 11 0.26
45 32 0.74
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (44 bp):
ATTCCACAAACGAATTATAAGGAATTGACACATATTCATTTCTT
Found at i:62286 original size:2 final size:2
Alignment explanation
Indices: 62279--62303 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
62269 GTTTATCTTT
62279 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
62304 GTTTTGATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:90498 original size:13 final size:12
Alignment explanation
Indices: 90480--90509 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
90470 ATTAATTAAT
90480 AATAAAATAAATA
1 AATAAAATAAA-A
90493 AATAAAATAAAA
1 AATAAAATAAAA
90505 AATAA
1 AATAA
90510 CGACTTCTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
AATAAAATAAAA
Found at i:100456 original size:68 final size:68
Alignment explanation
Indices: 100378--100514 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
100368 ACACATGTCC
100378 ATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTCACCCTTC
1 ATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTCACCCTTC
100443 AGA
66 AGA
100446 ATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTCACCCTTC
1 ATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTCACCCTTC
100511 AGA
66 AGA
100514 A
1 A
100515 CCCGCTTGTG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (68 bp):
ATTTTTTTAATTAATTAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTCACCCTTC
AGA
Found at i:100680 original size:17 final size:16
Alignment explanation
Indices: 100647--100684 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
100637 CTACTCGATC
*
100647 CCTTTCTTTTCTTCTT
1 CCTTCCTTTTCTTCTT
100663 CCTTCCTTTTCTTTCTT
1 CCTTCCTTTTC-TTCTT
100680 CCTTC
1 CCTTC
100685 ACCCGACAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (16 bp):
CCTTCCTTTTCTTCTT
Found at i:107021 original size:57 final size:55
Alignment explanation
Indices: 106929--107039 Score: 136
Period size: 57 Copynumber: 2.0 Consensus size: 55
106919 AATCGCGACC
*
106929 ATGTAAGATCTTAGTGATTTTTTTTCTCTACATAATATTTTATCCAAATCTCTTATT
1 ATGTAAGATCTTAGTGATTTTTTTTCACTACAT-A-ATTTTATCCAAATCTCTTATT
* * *
106986 ATGTAAGATCTTAGTGCAATTTTTTTT-AC-ATATAATTTTCTCCAAATCTTTTAT
1 ATGTAAGATCTTAGTG--ATTTTTTTTCACTACATAATTTTATCCAAATCTCTTAT
107040 ATCTTCAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
55 18 0.38
56 1 0.02
57 19 0.40
58 1 0.02
59 9 0.19
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (55 bp):
ATGTAAGATCTTAGTGATTTTTTTTCACTACATAATTTTATCCAAATCTCTTATT
Found at i:109772 original size:4 final size:4
Alignment explanation
Indices: 109763--109787 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
109753 GGCTCGTTTA
109763 TGTT TGTT TGTT TGTT TGTT TGTT T
1 TGTT TGTT TGTT TGTT TGTT TGTT T
109788 AATAAGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TGTT
Found at i:111646 original size:45 final size:45
Alignment explanation
Indices: 111595--111682 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
111585 CAGCAAATTA
*
111595 TTACTCTGGGGCTTATGGTTATGGAGATAAGGGAGTTGATAATAC
1 TTACTCTGGGGCTTATGCTTATGGAGATAAGGGAGTTGATAATAC
111640 TTACTCTGGGGCTTATGCTTATGGAGATAAGGGAGTTGATAAT
1 TTACTCTGGGGCTTATGCTTATGGAGATAAGGGAGTTGATAAT
111683 GCTGGGCAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.26, C:0.09, G:0.31, T:0.34
Consensus pattern (45 bp):
TTACTCTGGGGCTTATGCTTATGGAGATAAGGGAGTTGATAATAC
Found at i:123626 original size:31 final size:29
Alignment explanation
Indices: 123560--123630 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
123550 ATCATTTGAG
**
123560 AGGGGGCAAAACGTCCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCAAAATACAAGTTC
* *
123589 ATGGGGCAAAACGTCCAAACGCTACAAGTTC
1 AGGGGGCAAAACGTCCAAA--ATACAAGTTC
123620 AGGGGGCAAAA
1 AGGGGGCAAAA
123631 AAGGTATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 18 0.51
31 17 0.49
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.14
Consensus pattern (29 bp):
AGGGGGCAAAACGTCCAAAATACAAGTTC
Found at i:124426 original size:13 final size:13
Alignment explanation
Indices: 124410--124434 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
124400 TTGGATAAGT
124410 ATTTTTTTTTCTG
1 ATTTTTTTTTCTG
124423 ATTTTTTTTTCT
1 ATTTTTTTTTCT
124435 TTTGGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.80
Consensus pattern (13 bp):
ATTTTTTTTTCTG
Found at i:130546 original size:62 final size:62
Alignment explanation
Indices: 130434--130605 Score: 195
Period size: 62 Copynumber: 2.8 Consensus size: 62
130424 TTCGACGTGA
* * * * * * *
130434 CATGCCACGTGTACCAAAAAGCGACATGTGGCACGCCACGTGTACAAAAAAGTGACACGTAT
1 CATGCCATGTGTATCAAAAAGTGACACGTGGCATGCCACGTGTACAAAAAAGTGACACCTAG
* * *
130496 CATGCCATGTGTATCAAAAAGTGACACGTGGCATGCCATGTGTTTC-AAAAAGTGACACCTGG
1 CATGCCATGTGTATCAAAAAGTGACACGTGGCATGCCACGTG-TACAAAAAAGTGACACCTAG
* * * *
130558 CATGTCATGT-TTTCAAAAAGTGACACGTAGCATGCCACGTGCACAAAA
1 CATGCCATGTGTATCAAAAAGTGACACGTGGCATGCCACGTGTACAAAA
130606 GGATACGTGC
Statistics
Matches: 92, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
60 1 0.01
61 31 0.34
62 58 0.63
63 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (62 bp):
CATGCCATGTGTATCAAAAAGTGACACGTGGCATGCCACGTGTACAAAAAAGTGACACCTAG
Found at i:130605 original size:30 final size:30
Alignment explanation
Indices: 130428--130605 Score: 176
Period size: 31 Copynumber: 5.8 Consensus size: 30
130418 ACAGTGTTCG
* *
130428 ACGTGACATGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCATGCCACGTGTA-CAAAAAGTGAC
* *
130459 ATGTGGCACGCCACGTGTACAAAAAAGTGAC
1 ACGTGGCATGCCACGTGTAC-AAAAAGTGAC
** *
130490 ACGTATCATGCCATGTGTATCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTA-CAAAAAGTGAC
* *
130521 ACGTGGCATGCCATGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTG-TACAAAAAGTGAC
* * * * *
130552 ACCTGGCATGTCATGTTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACAAAAAGTGAC
* *
130582 ACGTAGCATGCCACGTGCACAAAA
1 ACGTGGCATGCCACGTGTACAAAA
130606 GGATACGTGC
Statistics
Matches: 122, Mismatches: 22, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
30 31 0.25
31 89 0.73
32 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (30 bp):
ACGTGGCATGCCACGTGTACAAAAAGTGAC
Done.