Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016184.1 Corchorus olitorius cultivar O-4 contig16217, 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: 18775
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:78 original size:22 final size:21
Alignment explanation
Indices: 29--78 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
19 GGTGCCTAAT
* * *
29 AATTAATTATTCATATTTTTA
1 AATTAATTATTAAAATTATTA
*
50 AACTAATTAGTTAAAATTATTA
1 AATTAATTA-TTAAAATTATTA
72 AATTAAT
1 AATTAAT
79 ATGTGATGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (21 bp):
AATTAATTATTAAAATTATTA
Found at i:496 original size:24 final size:25
Alignment explanation
Indices: 469--533 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
459 ATTGGGCCAG
*
469 TCTTGAATTTTTTTAATGT-TTAAT
1 TCTTAAATTTTTTTAATGTCTTAAT
*
493 TCTTAAATTTATTTAATGTCTTAAT
1 TCTTAAATTTTTTTAATGTCTTAAT
* *
518 TATTCAATTTATTTTA
1 TCTTAAATTT-TTTTA
534 CAATCCACTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 17 0.50
25 13 0.38
26 4 0.12
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.60
Consensus pattern (25 bp):
TCTTAAATTTTTTTAATGTCTTAAT
Found at i:526 original size:25 final size:24
Alignment explanation
Indices: 474--531 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
464 GCCAGTCTTG
* *
474 AATTTTTTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
498 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
523 AATTTATTT
1 AATTTATTT
532 TACAATCCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 13 0.43
25 17 0.57
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:2957 original size:61 final size:62
Alignment explanation
Indices: 2876--3006 Score: 201
Period size: 61 Copynumber: 2.1 Consensus size: 62
2866 TATTTAGGAA
* * * * *
2876 GGGATAAATTGTGTTTAGTTAAAAGATCCGGATTAGTCAGGGTTAAGTCCTTGATACCGGAT
1 GGGATAAACTGTCTTTAGTTAAAAGATCCGGATTAATCAGGGTTAAGTCCTGGATACCGAAT
*
2938 -GGATAAACTGTCTTTAGTTAAAAGATCCGGATTAATCATGGTTAAGTCCTGGATACCGAAT
1 GGGATAAACTGTCTTTAGTTAAAAGATCCGGATTAATCAGGGTTAAGTCCTGGATACCGAAT
2999 GGGATAAA
1 GGGATAAA
3007 AAAAATTATG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
61 55 0.89
62 7 0.11
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (62 bp):
GGGATAAACTGTCTTTAGTTAAAAGATCCGGATTAATCAGGGTTAAGTCCTGGATACCGAAT
Found at i:3698 original size:6 final size:6
Alignment explanation
Indices: 3687--3719 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
3677 TGTGGATAAA
3687 TTTTCT TTTTCT TTTTCT TTTT-T TTTTCAT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T TTT
3720 ATGCTGAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.20
6 16 0.64
7 4 0.16
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:5300 original size:48 final size:48
Alignment explanation
Indices: 5245--5350 Score: 194
Period size: 48 Copynumber: 2.2 Consensus size: 48
5235 GAAAGTGAAT
5245 TGCTCCTGGTGGAATTGTTCCTTGGGTTTACCACCACCCCCACCGCCA
1 TGCTCCTGGTGGAATTGTTCCTTGGGTTTACCACCACCCCCACCGCCA
*
5293 TGCTCCTGGTGGAATTGTTCCTTGGGTTTACCACCACCGCCACCGCCA
1 TGCTCCTGGTGGAATTGTTCCTTGGGTTTACCACCACCCCCACCGCCA
*
5341 TGCTCATGGT
1 TGCTCCTGGT
5351 ATGTTTTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.14, C:0.35, G:0.23, T:0.28
Consensus pattern (48 bp):
TGCTCCTGGTGGAATTGTTCCTTGGGTTTACCACCACCCCCACCGCCA
Found at i:6622 original size:2 final size:2
Alignment explanation
Indices: 6579--6611 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6569 ACCATATAAA
6579 AT AT A- 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 AT
6612 CAAAGTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6900 original size:114 final size:117
Alignment explanation
Indices: 6775--7004 Score: 376
Period size: 115 Copynumber: 2.0 Consensus size: 117
6765 TAATTATTCT
6775 ATTTTTACCATTTTACTATTTTAA-TTAAAAATTAAATATATTAGAATTTTTTAAATAAATTTCT
1 ATTTTTACCATTTTACTATTTTAATTTAAAAATTAAATATATTAGAATTTTTTAAATAAATTTCT
* *
6839 TAAATG-A-TATTGTTTAAACTTTACAGTTTTATTCTACTACAAACTCTTCC
66 TAAATGAACTATTGTTTAAACTTTACAGTTTTATTATACTAAAAACTCTTCC
* *
6889 ATTTTTACCATTTTACTATTTTAATTTAAAAATTAGATATATTAGAATTTTTTAAATATATTTCT
1 ATTTTTACCATTTTACTATTTTAATTTAAAAATTAAATATATTAGAATTTTTTAAATAAATTTCT
*
6954 TAAATGATACTTATTGTTTAAACTTTATAGTTTTATTATACTAAAAACTCT
66 TAAATGA-AC-TATTGTTTAAACTTTACAGTTTTATTATACTAAAAACTCT
7005 AATTTTATTT
Statistics
Matches: 106, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
114 24 0.23
115 44 0.42
117 1 0.01
119 37 0.35
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.50
Consensus pattern (117 bp):
ATTTTTACCATTTTACTATTTTAATTTAAAAATTAAATATATTAGAATTTTTTAAATAAATTTCT
TAAATGAACTATTGTTTAAACTTTACAGTTTTATTATACTAAAAACTCTTCC
Found at i:7078 original size:37 final size:37
Alignment explanation
Indices: 7006--7103 Score: 162
Period size: 37 Copynumber: 2.6 Consensus size: 37
6996 AAAAACTCTA
*
7006 ATTTTATTTAATTAAATTCAATATTTTTATCAACTAT
1 ATTTTATTTCATTAAATTCAATATTTTTATCAACTAT
7043 ATTTTAATTTCATTAAATTCAATATTTTTAT-AACTAT
1 ATTTT-ATTTCATTAAATTCAATATTTTTATCAACTAT
7080 ATTTTGATTTCATTAAATTCAATA
1 ATTTT-ATTTCATTAAATTCAATA
7104 GATCTGGACC
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
37 34 0.59
38 24 0.41
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (37 bp):
ATTTTATTTCATTAAATTCAATATTTTTATCAACTAT
Found at i:7136 original size:22 final size:22
Alignment explanation
Indices: 7111--7155 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
7101 ATAGATCTGG
*
7111 ACCCAACCGAATTATAATACAA
1 ACCCAACCCAATTATAATACAA
7133 ACCCAACCCAATTATAATACAA
1 ACCCAACCCAATTATAATACAA
7155 A
1 A
7156 TAGACATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.29, G:0.02, T:0.18
Consensus pattern (22 bp):
ACCCAACCCAATTATAATACAA
Found at i:9861 original size:162 final size:162
Alignment explanation
Indices: 9576--9974 Score: 604
Period size: 162 Copynumber: 2.5 Consensus size: 162
9566 AATGCGGATC
* *
9576 ATGACTAAACTTTGCAGGACTTCTTTCATAATGTTCATAAGCATATCACCATCTTCATGGAGCCA
1 ATGACCAAACTTTGCACGACTTCTTTCATAATGTTCATAAGCATATCACCATCTTCATGGAG-CA
* *
9641 A-TTTCACGCTCAAATCTTCCTATTCAAGTGTTTTGTCCTTAACTGAAAACCGAGTAAAAGTTAC
65 ATTTTCACGCTCAAATCTTCCTATTCAAGTGTTTTGTCCTTAACTAAAAACCAAGTAAAAGTTAC
* * *
9705 GT-TCTGCACCGGAATGATTCAGAATTTGTGGAA
130 -TCTATGCACCGGAATGAGTCAAAATTTGTGGAA
9738 ATGACCAAACTTTGCACGACTTCTTTCATAATGTTCATAAGCATATCACCATCTTCATGGAGCAA
1 ATGACCAAACTTTGCACGACTTCTTTCATAATGTTCATAAGCATATCACCATCTTCATGGAGCAA
* **
9803 TTTTCATGCTCAAATCTTCCTATTCTGGTGTTTTGTCCTTAACTAAAAACCAAGTAAAAGTTACT
66 TTTTCACGCTCAAATCTTCCTATTCAAGTGTTTTGTCCTTAACTAAAAACCAAGTAAAAGTTACT
* *
9868 CTATGCATCGGAATTAGTCAAAATTTGTGGAA
131 CTATGCACCGGAATGAGTCAAAATTTGTGGAA
* * * * *
9900 ATGACCAAACTTTTCACGACTTCTTTCATGATGTTCATAAGCACATTACCATCTTCATGGAGCCA
1 ATGACCAAACTTTGCACGACTTCTTTCATAATGTTCATAAGCATATCACCATCTTCATGGAGCAA
*
9965 TTTCCACGCT
66 TTTTCACGCT
9975 GGTGTTTTGT
Statistics
Matches: 216, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
161 4 0.02
162 212 0.98
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (162 bp):
ATGACCAAACTTTGCACGACTTCTTTCATAATGTTCATAAGCATATCACCATCTTCATGGAGCAA
TTTTCACGCTCAAATCTTCCTATTCAAGTGTTTTGTCCTTAACTAAAAACCAAGTAAAAGTTACT
CTATGCACCGGAATGAGTCAAAATTTGTGGAA
Found at i:12282 original size:2 final size:2
Alignment explanation
Indices: 12275--12308 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12265 CTAAGTCTAC
12275 AT 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 AT
12309 CTACTAAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12953 original size:13 final size:13
Alignment explanation
Indices: 12917--12942 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12907 AGCCCAATGG
12917 AAGGTAAGAAACA
1 AAGGTAAGAAACA
12930 AAGGTAAGAAACA
1 AAGGTAAGAAACA
12943 GAGAGTAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.23, T:0.08
Consensus pattern (13 bp):
AAGGTAAGAAACA
Found at i:14410 original size:36 final size:36
Alignment explanation
Indices: 14358--14430 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
14348 CTGTCTCTGC
* *
14358 GAGCCCTCTGATATCACCCTCCGTTACACGGCTGGA
1 GAGCCCTCTGACATCACCCTCCGTTACACGACTGGA
* * *
14394 GAGCCCTCTGACATCACCTTTCTTTACACGACTGGA
1 GAGCCCTCTGACATCACCCTCCGTTACACGACTGGA
14430 G
1 G
14431 CAGATGATTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.25
Consensus pattern (36 bp):
GAGCCCTCTGACATCACCCTCCGTTACACGACTGGA
Found at i:15435 original size:16 final size:16
Alignment explanation
Indices: 15408--15440 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
15398 ATAATATACC
15408 TATTTTTCCTTCTCTCT
1 TATTTTTCCTTCT-TCT
15425 TATTTTT-CTTCTTCT
1 TATTTTTCCTTCTTCT
15440 T
1 T
15441 CACGACCCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 5 0.31
17 7 0.44
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTTCCTTCTTCT
Found at i:16506 original size:19 final size:20
Alignment explanation
Indices: 16478--16518 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
16468 TTAAAGTGTG
*
16478 TTTGTGATTTT-TATTTAAT
1 TTTGTAATTTTATATTTAAT
*
16497 TTTGTAATTTTATTTTTAAT
1 TTTGTAATTTTATATTTAAT
16517 TT
1 TT
16519 CATAAATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (20 bp):
TTTGTAATTTTATATTTAAT
Found at i:17647 original size:114 final size:115
Alignment explanation
Indices: 17517--17738 Score: 374
Period size: 115 Copynumber: 1.9 Consensus size: 115
17507 TATTCTATTA
*
17517 TTACCATTTTACTATTTTAATT-AAAACTTAAATATATTAGAATTTTTTAAATAAATTTCTTAAA
1 TTACCATTTTACTATTTTAATTAAAAAATTAAATATATTAGAATTTTTTAAATAAATTTCTTAAA
* *
17581 TGATATTGTTTAAACTTTACAGTTTTATTCTACTACAAACTCTTCCATTT
66 TGATATTGTTTAAACTTTACAGTTTTATTATACTAAAAACTCTTCCATTT
* * *
17631 TTACCATTTTACTATTTTAATTAAAAAATTAGATATATTAGAATTTTTTAAATATATTTTTTAAA
1 TTACCATTTTACTATTTTAATTAAAAAATTAAATATATTAGAATTTTTTAAATAAATTTCTTAAA
*
17696 TGATATTGTTTAAACTTTATAGTTTTATTATACTAAAAACTCT
66 TGATATTGTTTAAACTTTACAGTTTTATTATACTAAAAACTCT
17739 AATTTTATTT
Statistics
Matches: 100, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
114 22 0.22
115 78 0.78
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.49
Consensus pattern (115 bp):
TTACCATTTTACTATTTTAATTAAAAAATTAAATATATTAGAATTTTTTAAATAAATTTCTTAAA
TGATATTGTTTAAACTTTACAGTTTTATTATACTAAAAACTCTTCCATTT
Found at i:17691 original size:13 final size:14
Alignment explanation
Indices: 17673--17709 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
17663 ATATATTAGA
17673 ATTTTTTAAAT-AT
1 ATTTTTTAAATGAT
17686 ATTTTTTAAATGAT
1 ATTTTTTAAATGAT
*
17700 ATTGTTTAAA
1 ATTTTTTAAA
17710 CTTTATAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (14 bp):
ATTTTTTAAATGAT
Found at i:17820 original size:37 final size:38
Alignment explanation
Indices: 17740--17834 Score: 137
Period size: 37 Copynumber: 2.6 Consensus size: 38
17730 AAAAACTCTA
* *
17740 ATTTT-ATTTAATTAAATTC---AATTTTATAAACTAT
1 ATTTTAATTTCATTAAATTCAATAATTTTATAAACCAT
17774 ATTTTAATTTCATTAAATTCAATAATTTTAT-AACCAT
1 ATTTTAATTTCATTAAATTCAATAATTTTATAAACCAT
17811 ATTTTAATTTCATTAAATTCAATA
1 ATTTTAATTTCATTAAATTCAATA
17835 GATCTGGACC
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
34 5 0.09
35 13 0.24
37 29 0.53
38 8 0.15
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (38 bp):
ATTTTAATTTCATTAAATTCAATAATTTTATAAACCAT
Done.