Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018332.1 Corchorus olitorius cultivar O-4 contig18365, 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: 35944
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:263 original size:15 final size:15
Alignment explanation
Indices: 245--291 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
235 TATTAATCAA
245 TATTTTAATTAATAT
1 TATTTTAATTAATAT
* * * *
260 TATTTCAA-AAAAAA
1 TATTTTAATTAATAT
274 TATTTTAATTAATAT
1 TATTTTAATTAATAT
289 TAT
1 TAT
292 ACTATAAGGG
Statistics
Matches: 23, Mismatches: 8, Indels: 2
0.70 0.24 0.06
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTTTAATTAATAT
Found at i:1524 original size:13 final size:14
Alignment explanation
Indices: 1508--1548 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
1498 TAGCAAATAA
*
1508 CAATATTAAT-TTT
1 CAATATTAATACTT
1521 CAATTATTAATACTT
1 CAA-TATTAATACTT
1536 CAA-ATTAATACTT
1 CAATATTAATACTT
1549 ATGGTCAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 13 0.52
14 7 0.28
15 5 0.20
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.46
Consensus pattern (14 bp):
CAATATTAATACTT
Found at i:3801 original size:21 final size:20
Alignment explanation
Indices: 3771--3819 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
3761 TAAAACTATC
3771 TAAGATTACTAAAAAGCTTAA
1 TAAG-TTACTAAAAAGCTTAA
* *
3792 TAAAGTTACTAAAATGCTTAC
1 T-AAGTTACTAAAAAGCTTAA
3813 TAAGTTA
1 TAAGTTA
3820 TATATTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 16 0.64
22 3 0.12
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (20 bp):
TAAGTTACTAAAAAGCTTAA
Found at i:4121 original size:22 final size:22
Alignment explanation
Indices: 4080--4131 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
4070 GCTTACAAGA
* *
4080 TTACT-AAAATTTTAATAAAGG
1 TTACTAAAAATTGTAACAAAGG
4101 TTACTAAAAATTGTAACAAAGG
1 TTACTAAAAATTGTAACAAAGG
4123 TTACTAAAA
1 TTACTAAAA
4132 CCTTTAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.33
Consensus pattern (22 bp):
TTACTAAAAATTGTAACAAAGG
Found at i:4464 original size:20 final size:22
Alignment explanation
Indices: 4419--4466 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
4409 AAAACACTCA
4419 ATAAGGTTACTAAAAAAAACTTC
1 ATAAGGTTACT-AAAAAAACTTC
*
4442 ATAAGGTTACT-ATAAAA-TTC
1 ATAAGGTTACTAAAAAAACTTC
4462 ATAAG
1 ATAAG
4467 TTAACGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 5 0.21
23 11 0.46
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.29
Consensus pattern (22 bp):
ATAAGGTTACTAAAAAAACTTC
Found at i:4476 original size:20 final size:21
Alignment explanation
Indices: 4434--4477 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
4424 GTTACTAAAA
*
4434 AAAACTTCATAAGGTTACTAT
1 AAAACTTCATAAGGTTACGAT
4455 AAAA-TTCATAA-GTTAACGAT
1 AAAACTTCATAAGGTT-ACGAT
4475 AAA
1 AAA
4478 TCTTACAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 14 0.67
21 4 0.19
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (21 bp):
AAAACTTCATAAGGTTACGAT
Found at i:4697 original size:85 final size:86
Alignment explanation
Indices: 4540--4717 Score: 313
Period size: 86 Copynumber: 2.1 Consensus size: 86
4530 TAAGATCACT
*
4540 AAAAATCTTAAATGAGGTGATTGAATAAATTTAAGAAAACTAATTAAAAAGATTTTAAGTTTAAT
1 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTAATTAAAAAGATTTTAAGTTTAAT
4605 GAAAAATTTATAAGCTTACCA
66 GAAAAATTTATAAGCTTACCA
* *
4626 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTATTTAAAAA-CTTTTAAGTTTAAT
1 AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTAATTAAAAAGATTTTAAGTTTAAT
4690 GAAAAATTTATAAGCTTACCA
66 GAAAAATTTATAAGCTTACCA
4711 AGAAAAT
1 A-AAAAT
4718 TTACAAGGTT
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
85 35 0.40
86 53 0.60
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (86 bp):
AAAAATCTTAAACGAGGTGATTGAATAAATTTAAGAAAACTAATTAAAAAGATTTTAAGTTTAAT
GAAAAATTTATAAGCTTACCA
Found at i:4800 original size:21 final size:20
Alignment explanation
Indices: 4753--4792 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
4743 CAATTACAAT
*
4753 AAAAGTTAAATAGTTTACTA
1 AAAAGTTAAATAGATTACTA
4773 AAAAGTTAAATAAGATTACT
1 AAAAGTTAAAT-AGATTACT
4793 TGAAAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (20 bp):
AAAAGTTAAATAGATTACTA
Found at i:5201 original size:27 final size:27
Alignment explanation
Indices: 5161--5213 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
5151 TAAGGTGACT
5161 AAAAAACTTTATAAGG-CCAAAAAAGG
1 AAAAAACTTTATAAGGTCCAAAAAAGG
*
5187 AAAAAAGTTTAATAAGGTCCAAAAAAG
1 AAAAAACTTT-ATAAGGTCCAAAAAAG
5214 CTCAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 9 0.38
27 6 0.25
28 9 0.38
ACGTcount: A:0.58, C:0.09, G:0.15, T:0.17
Consensus pattern (27 bp):
AAAAAACTTTATAAGGTCCAAAAAAGG
Found at i:5684 original size:16 final size:16
Alignment explanation
Indices: 5663--5693 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5653 AGAATTAATC
5663 ATAAAGACTTAGTAAA
1 ATAAAGACTTAGTAAA
*
5679 ATAAAGATTTAGTAA
1 ATAAAGACTTAGTAA
5694 TATTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (16 bp):
ATAAAGACTTAGTAAA
Found at i:6343 original size:38 final size:38
Alignment explanation
Indices: 6292--6366 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
6282 AGAAAATGTG
6292 ATAATTAAATCTCATGGATTACAATTCCCTAGTTAAAC
1 ATAATTAAATCTCATGGATTACAATTCCCTAGTTAAAC
6330 ATAATTAAATCTCATGGATTACAATTCCCTAGTTAAA
1 ATAATTAAATCTCATGGATTACAATTCCCTAGTTAAA
6367 ACTTCTAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (38 bp):
ATAATTAAATCTCATGGATTACAATTCCCTAGTTAAAC
Found at i:7130 original size:30 final size:30
Alignment explanation
Indices: 7094--7154 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
7084 ATAGCTTCAA
7094 CAAAATCCCATCAACAATAAGAAAAAGCCC
1 CAAAATCCCATCAACAATAAGAAAAAGCCC
7124 CAAAATCCCATCAACAATAAGAAAAAGCCC
1 CAAAATCCCATCAACAATAAGAAAAAGCCC
7154 C
1 C
7155 TTCTATACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.52, C:0.31, G:0.07, T:0.10
Consensus pattern (30 bp):
CAAAATCCCATCAACAATAAGAAAAAGCCC
Found at i:20942 original size:3 final size:3
Alignment explanation
Indices: 20930--20959 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
20920 AAAAGAAAAA
20930 AAT AATT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AA
20960 ATATAAATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:24932 original size:19 final size:19
Alignment explanation
Indices: 24908--24945 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
24898 CAACATATAC
24908 TACATATTAATTTGAAGAT
1 TACATATTAATTTGAAGAT
24927 TACATATTAATTTGAAGAT
1 TACATATTAATTTGAAGAT
24946 AAAAAACTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (19 bp):
TACATATTAATTTGAAGAT
Found at i:25137 original size:30 final size:30
Alignment explanation
Indices: 25101--25157 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
25091 GTTTTACGTT
25101 ACACGTTGTTAGAGTTTAAAATTTGGAAAA
1 ACACGTTGTTAGAGTTTAAAATTTGGAAAA
25131 ACACGTTGTTAGAGTTTAAAATTTGGA
1 ACACGTTGTTAGAGTTTAAAATTTGGA
25158 CGGACTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (30 bp):
ACACGTTGTTAGAGTTTAAAATTTGGAAAA
Found at i:27597 original size:73 final size:75
Alignment explanation
Indices: 27476--27622 Score: 226
Period size: 73 Copynumber: 2.0 Consensus size: 75
27466 TAAATTCCTT
* * *
27476 TTATATAATTTAGTGCTTTTGTAAATCATATGGAAGCTATTAAGTTCAT-A-ATTATCATAACTT
1 TTATATAATTTAGTGCTCTTGTAAAACATATGGAAGCTATTAAATTCATAAGATTATCATAACTT
27539 GGTAGAATTC
66 GGTAGAATTC
* *
27549 TTATATAGTTTAGTGCTCTTGTAAAACATATGGAAGCTATTAAATTCATAATGATTATTATAACT
1 TTATATAATTTAGTGCTCTTGTAAAACATATGGAAGCTATTAAATTCATAA-GATTATCATAACT
27614 TGGTAGAAT
65 TGGTAGAAT
27623 AATAAACAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
73 45 0.68
74 1 0.02
76 20 0.30
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.41
Consensus pattern (75 bp):
TTATATAATTTAGTGCTCTTGTAAAACATATGGAAGCTATTAAATTCATAAGATTATCATAACTT
GGTAGAATTC
Found at i:32725 original size:9 final size:9
Alignment explanation
Indices: 32711--32739 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
32701 ATTGACCAAA
32711 AAGAATATG
1 AAGAATATG
32720 AAGAATATG
1 AAGAATATG
32729 AAGAATATG
1 AAGAATATG
32738 AA
1 AA
32740 ACCACTCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (9 bp):
AAGAATATG
Done.