Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021567.1 Corchorus olitorius cultivar O-4 contig21600, 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: 53420
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:15 original size:3 final size:3
Alignment explanation
Indices: 1--76 Score: 143
Period size: 3 Copynumber: 25.0 Consensus size: 3
1 TAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
47 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
77 ATTGGATAAG
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 69 0.96
4 3 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:627 original size:3 final size:3
Alignment explanation
Indices: 614--652 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
604 TGAAAAACGG
* *
614 AAC ATAC AAC AAC AAC AAC AAG AAC AAC AAG AAC AAC AA
1 AAC A-AC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
653 GAATAGCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.26, G:0.05, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:653 original size:9 final size:9
Alignment explanation
Indices: 619--655 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
609 AACGGAACAT
*
619 ACAACAACA
1 ACAACAAGA
628 ACAACAAGA
1 ACAACAAGA
637 ACAACAAGA
1 ACAACAAGA
646 ACAACAAGA
1 ACAACAAGA
655 A
1 A
656 TAGCAAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.68, C:0.24, G:0.08, T:0.00
Consensus pattern (9 bp):
ACAACAAGA
Found at i:6445 original size:31 final size:30
Alignment explanation
Indices: 6390--6706 Score: 445
Period size: 31 Copynumber: 10.7 Consensus size: 30
6380 AATCTCCAAA
6390 TGACACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
6420 TGACACCAGAAGTTGTCAATGATCTTGCAAT
1 TGACACCAGAAGTTGTC-ATGATCTTGCAAT
6451 TGACACCAGAAGTTGTCAATGATCTTGCAAT
1 TGACACCAGAAGTTGTC-ATGATCTTGCAAT
6482 TGACACCAGAAGTTGTCAATGATCTTGCAAT
1 TGACACCAGAAGTTGTC-ATGATCTTGCAAT
*
6513 TGACACCAG-AGTTGTCATGCTCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
6542 TGATACCAGAAGTTGTCATGATCTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
6572 TGACACCAGAAGTTGTCATGATCTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
* *
6602 TGACACCAGAAGTTGTCAATGGTCTTACAAT
1 TGACACCAGAAGTTGTC-ATGATCTTGCAAT
* ** *
6633 TG--ACCAGAAGTTCTCA--AAATT-AAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
*
6658 TGACACCAGAAGTTGTCAT-A-ATT-CAAT
1 TGACACCAGAAGTTGTCATGATCTTGCAAT
6685 TGACACCAGAAGTTGTCATGAT
1 TGACACCAGAAGTTGTCATGAT
6707 TTTACCTTTC
Statistics
Matches: 266, Mismatches: 13, Indels: 17
0.90 0.04 0.06
Matches are distributed among these distances:
25 5 0.02
26 2 0.01
27 38 0.14
28 3 0.01
29 32 0.12
30 88 0.33
31 98 0.37
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTGCAAT
Found at i:16328 original size:14 final size:15
Alignment explanation
Indices: 16298--16330 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
16288 ACTGTCGAAA
16298 TCTTCTATTTAATTT
1 TCTTCTATTTAATTT
*
16313 TCTTCT-TTTCATTT
1 TCTTCTATTTAATTT
16327 TCTT
1 TCTT
16331 AAACTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (15 bp):
TCTTCTATTTAATTT
Found at i:23371 original size:15 final size:16
Alignment explanation
Indices: 23347--23386 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
23337 AGAGGTTGAA
*
23347 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
23362 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
23378 AGAAAACAA
1 AGAAAACAA
23387 AACAAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:28080 original size:27 final size:27
Alignment explanation
Indices: 28048--28113 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
28038 GTCAATTTAA
*
28048 AAAGCCCACTATAATGCGTGGCAATAC
1 AAAGCCCACTATAATACGTGGCAATAC
28075 AAAGCCCACTATAATACGTGGCAATAC
1 AAAGCCCACTATAATACGTGGCAATAC
28102 AAAGCCCACTAT
1 AAAGCCCACTAT
28114 GTGGCACATG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.39, C:0.27, G:0.15, T:0.18
Consensus pattern (27 bp):
AAAGCCCACTATAATACGTGGCAATAC
Found at i:28205 original size:53 final size:53
Alignment explanation
Indices: 28142--28248 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
28132 AATCATGATT
28142 AAGGGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTCCCACAGCCCG
1 AAGGGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTCCCACAGCCCG
*
28195 AAGGGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCTTTCCCACAGCCCG
1 AAGGGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTCCCACAGCCCG
28248 A
1 A
28249 GAAAGCGAGT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.21
Consensus pattern (53 bp):
AAGGGAGTGGTCAAGGGAGCTAAGAGTTTCTTACCTAGCCTTCCCACAGCCCG
Found at i:40403 original size:53 final size:53
Alignment explanation
Indices: 40346--40611 Score: 265
Period size: 53 Copynumber: 5.1 Consensus size: 53
40336 TGTTTATTCA
* *
40346 ATTGAACCTATTAAATAAGTACACATACCAAATAATAAAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
40399 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
** * * * * ** * * *** *** * *
40452 ATTGAA--TAATTCTATTA-TATA-TTA-TTATTATTA-ATTGTGTTGTTAATTCA
1 ATTGAACCT-ATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAA--CT
* *
40502 ATTGAACCTATTAAATAAGAACACATACCAAATAATACAAAATGTAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
40555 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
1 ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
40608 ATTG
1 ATTG
40612 GATTTAAAGA
Statistics
Matches: 165, Mismatches: 39, Indels: 18
0.74 0.18 0.08
Matches are distributed among these distances:
48 6 0.04
49 5 0.03
50 9 0.05
51 9 0.05
52 9 0.05
53 115 0.70
54 5 0.03
55 7 0.04
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (53 bp):
ATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAATGAACT
Found at i:40501 original size:156 final size:157
Alignment explanation
Indices: 40317--40611 Score: 547
Period size: 156 Copynumber: 1.9 Consensus size: 157
40307 ATAATAATTC
* *
40317 TATTATATATTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGTACACATACCAAATAAT
1 TATTATATATTAATTGTGTTGTTAATTCAATTGAACCTATTAAATAAGAACACATACCAAATAAT
40382 AAAAAATGCAATGAACTATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAAT
66 AAAAAATGCAATGAACTATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAAT
40447 GAACTATTGAATAATTCTATTATATAT
131 GAACTATTGAATAATTCTATTATATAT
40474 TATTAT-TATTAATTGTGTTGTTAATTCAATTGAACCTATTAAATAAGAACACATACCAAATAAT
1 TATTATATATTAATTGTGTTGTTAATTCAATTGAACCTATTAAATAAGAACACATACCAAATAAT
* *
40538 ACAAAATGTAATGAACTATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAAT
66 AAAAAATGCAATGAACTATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAAT
40603 GAACTATTG
131 GAACTATTG
40612 GATTTAAAGA
Statistics
Matches: 134, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
156 128 0.96
157 6 0.04
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (157 bp):
TATTATATATTAATTGTGTTGTTAATTCAATTGAACCTATTAAATAAGAACACATACCAAATAAT
AAAAAATGCAATGAACTATTGAACCTATTAAATAAGCACACATACCAAATAATACAAAATGCAAT
GAACTATTGAATAATTCTATTATATAT
Found at i:41434 original size:16 final size:16
Alignment explanation
Indices: 41413--41444 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41403 TATAATTATT
41413 TATATATTAATAATAA
1 TATATATTAATAATAA
*
41429 TATATATTATTAATAA
1 TATATATTAATAATAA
41445 AAATTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:41439 original size:19 final size:19
Alignment explanation
Indices: 41397--41444 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
41387 GTACGTTTGT
* *
41397 TTATTATATAATTATTTATA
1 TTATTA-ATAATAATATATA
41417 -TATTAATAATAATATATA
1 TTATTAATAATAATATATA
41435 TTATTAATAA
1 TTATTAATAA
41445 AAATTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTAATAATAATATATA
Found at i:41498 original size:29 final size:29
Alignment explanation
Indices: 41453--41508 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
41443 AAAAATTATA
*
41453 AAAATAATATTCTATTATCTA-ATATATTT
1 AAAATAAAATTCTATTAT-TATATATATTT
41482 AAAATAAAATT-TAATTATTATATATAT
1 AAAATAAAATTCT-ATTATTATATATAT
41509 ATATAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (29 bp):
AAAATAAAATTCTATTATTATATATATTT
Found at i:47855 original size:1 final size:1
Alignment explanation
Indices: 47849--47876 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
47839 ATGCTTTTGC
47849 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
47877 AAAGTTAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.