Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012152.1 Corchorus olitorius cultivar O-4 contig12185, 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: 20367
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2494 original size:7 final size:6
Alignment explanation
Indices: 2479--2561 Score: 66
Period size: 6 Copynumber: 13.7 Consensus size: 6
2469 TAATTTTCTA
*
2479 TTTTCTC TTATTTC TTATTTC TTTTTT TTCTTTC TTTTTTC TTTTTC -TTTT-
1 TTTT-TC TT-TTTC TT-TTTC TTTTTC TT-TTTC -TTTTTC TTTTTC TTTTTC
* *
2530 TTTTCC TTTTTC -TTTTC -TTTTC TTTTCC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
2562 CCCTTTTTCC
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
5 17 0.26
6 24 0.37
7 20 0.31
8 4 0.06
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:2514 original size:27 final size:26
Alignment explanation
Indices: 2484--2555 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 26
2474 TTCTATTTTC
2484 TCTTATTTCTTATTTCTTTTTTTTCTT
1 TCTTATTTCTT-TTTCTTTTTTTTCTT
*
2511 TCTTTTTTCTTTTTCTTTTTTTTCCTT
1 TCTTATTTCTTTTTCTTTTTTTT-CTT
*
2538 T-TTCTTT-TCTTTTCTTTT
1 TCTTATTTCT-TTTTCTTTT
2556 CCTTTTCCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
25 1 0.02
26 26 0.63
27 14 0.34
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (26 bp):
TCTTATTTCTTTTTCTTTTTTTTCTT
Found at i:2523 original size:16 final size:16
Alignment explanation
Indices: 2479--2561 Score: 87
Period size: 16 Copynumber: 5.1 Consensus size: 16
2469 TAATTTTCTA
*
2479 TTTTCTCTTATTTCTTAT
1 TTTTTTCTT-TTTCTT-T
*
2497 TTCTTT-TTTTTCTTT
1 TTTTTTCTTTTTCTTT
2512 CTTTTTTCTTTTTCTTT
1 -TTTTTTCTTTTTCTTT
*
2529 TTTTTCCTTTTTCTTT
1 TTTTTTCTTTTTCTTT
* *
2545 TCTTTTCTTTTCCTTT
1 TTTTTTCTTTTTCTTT
2561 T
1 T
2562 CCCTTTTTCC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
15 1 0.02
16 40 0.71
17 11 0.20
18 4 0.07
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTCTTTTTCTTT
Found at i:2674 original size:13 final size:12
Alignment explanation
Indices: 2643--2670 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2633 CGCTGGGCCG
2643 TTCTCTTTTTTT
1 TTCTCTTTTTTT
2655 TTCTCTTTTTTT
1 TTCTCTTTTTTT
2667 TTCT
1 TTCT
2671 TCTTCTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTCTCTTTTTTT
Found at i:3578 original size:2 final size:2
Alignment explanation
Indices: 3535--3564 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3525 AAATATATTC
3535 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
3565 CTTACTACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5479 original size:44 final size:43
Alignment explanation
Indices: 5411--5535 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 43
5401 TGACAATCAA
* * * * * *
5411 ACCAAAATTACATAGAAAGATTATCAAAATTCCGTAGTGTGGTT
1 ACCAAAATTTCATACAGAGGTTATCAAAATT-CATAGTGTAGTT
*
5455 ACCAAAATTTCATATAGAGGTTATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATACAGAGGTTATCAAAA-TTCATAGTGTAGTT
* *
5499 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATAG
1 ACCAAAATTTCATACAGAGGTTATCAAAA-TTCATAG
5536 GGAGGGAGGT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
44 68 0.97
45 2 0.03
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (43 bp):
ACCAAAATTTCATACAGAGGTTATCAAAATTCATAGTGTAGTT
Found at i:5540 original size:22 final size:22
Alignment explanation
Indices: 5411--5647 Score: 121
Period size: 22 Copynumber: 10.9 Consensus size: 22
5401 TGACAATCAA
* * *
5411 ACCAAAATTACATAGAAAGATT
1 ACCAAAATTTCATAGAGAGGTT
* * * * *
5433 ATCAAAATTCCGTAGTGTGGTT
1 ACCAAAATTTCATAGAGAGGTT
*
5455 ACCAAAATTTCATATAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
* * *
5477 ATCAAAACTTCATAGTGTA-GTT
1 ACCAAAATTTCATAGAG-AGGTT
* *
5499 ATCAAAATTTCATACAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
5521 ACCAAAATTTCATAGGGAGGGAGGTT
1 ACCAAAATTTCATA--GA--GAGGTT
* *
5547 ACCAAAA-TT--T---GTGCTT
1 ACCAAAATTTCATAGAGAGGTT
* *
5563 ATCAAAATTTCCTAGAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
* * *
5585 AACAAAATTTTATAGGGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
** * *
5607 ATGAAAATTTTATGGAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
* *
5629 ATCGAAAA-TACATAGAGAG
1 A-CCAAAATTTCATAGAGAG
5648 AGGATATCAT
Statistics
Matches: 163, Mismatches: 39, Indels: 26
0.71 0.17 0.11
Matches are distributed among these distances:
16 10 0.06
17 2 0.01
19 1 0.01
21 1 0.01
22 126 0.77
23 7 0.04
24 1 0.01
25 2 0.01
26 13 0.08
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.30
Consensus pattern (22 bp):
ACCAAAATTTCATAGAGAGGTT
Found at i:5793 original size:22 final size:21
Alignment explanation
Indices: 5768--5911 Score: 119
Period size: 22 Copynumber: 6.6 Consensus size: 21
5758 TATAGGCAGA
*
5768 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATA-TGAGG
*
5790 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATA-TGAGG
* * * *
5812 TTACCCAAATTTCACAGTGTGG
1 TTATCAAAATTTCATA-TGAGG
* *
5834 TTATCAAATTTTCATAGGTAGG
1 TTATCAAAATTTCATATG-AGG
*
5856 TTATCGAAATTTCATATGAGG
1 TTATCAAAATTTCATATGAGG
* *
5877 TTATC-AAATTTGCAAAATGTGG
1 TTATCAAAATTT-C-ATATGAGG
*
5899 TTATCAATATTTC
1 TTATCAAAATTTC
5912 TACATTGGAG
Statistics
Matches: 100, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
20 6 0.06
21 10 0.10
22 79 0.79
23 5 0.05
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (21 bp):
TTATCAAAATTTCATATGAGG
Found at i:5822 original size:44 final size:43
Alignment explanation
Indices: 5774--5901 Score: 143
Period size: 44 Copynumber: 2.9 Consensus size: 43
5764 CAGATTATCA
5774 AAATTTCACACTGAGGTTATCAAAATTTCATAGTGTGGTTACCC
1 AAATTTCACA-TGAGGTTATCAAAATTTCATAGTGTGGTTACCC
* * * *
5818 AAATTTCACAGTGTGGTTATCAAATTTTCATAG-GTAGGTTATCG
1 AAATTTCACA-TGAGGTTATCAAAATTTCATAGTGT-GGTTACCC
* * *
5862 AAATTTCATATGAGGTTATC-AAATTTGCAAAATGTGGTTA
1 AAATTTCACATGAGGTTATCAAAATTT-CATAGTGTGGTTA
5902 TCAATATTTC
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
42 5 0.07
43 19 0.27
44 47 0.66
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (43 bp):
AAATTTCACATGAGGTTATCAAAATTTCATAGTGTGGTTACCC
Found at i:10001 original size:32 final size:32
Alignment explanation
Indices: 9960--10036 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
9950 TTTTTTGTTG
*
9960 GAAACGCCACT-ATTTAGTTGCGTTTTACTTGA
1 GAAACGCCACTAATTT-GTGGCGTTTTACTTGA
* *
9992 GAAATGCCACTAATTTGTGGCGTTTTACTTTAA
1 GAAACGCCACTAATTTGTGGCGTTTTAC-TTGA
*
10025 AAAACGCCACTA
1 GAAACGCCACTA
10037 TTATATTAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
32 21 0.55
33 17 0.45
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (32 bp):
GAAACGCCACTAATTTGTGGCGTTTTACTTGA
Found at i:11401 original size:32 final size:32
Alignment explanation
Indices: 11365--11429 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
11355 GAAAAAACCA
** *
11365 AAATAGCAGCGTTTAGGTTCAGAAACGCCGCT
1 AAATAGCAGCGTTTACATACAGAAACGCCGCT
** *
11397 AAATAGTGGCGTTTCCATACAGAAACGCCGCT
1 AAATAGCAGCGTTTACATACAGAAACGCCGCT
11429 A
1 A
11430 TTTAGTGGCG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (32 bp):
AAATAGCAGCGTTTACATACAGAAACGCCGCT
Found at i:11455 original size:64 final size:64
Alignment explanation
Indices: 11387--11539 Score: 198
Period size: 64 Copynumber: 2.4 Consensus size: 64
11377 TTAGGTTCAG
** ** *
11387 AAACGCCGCTAAATAGTGGCGTTTCCATACAGAAACGCCGCTATTTAGTGGCGTTTCCGAACAT
1 AAACGCCGCTATTTAGTGGCGTTTCCATACAGAAACGCCAATATTTAGCGGCGTTTCCGAACAT
* * ** * * *
11451 AAACGCCACTATTTAGCGGCGTTTCTGTACGGACACGCCAATATTTAGCGGCGTTTCTGAACAT
1 AAACGCCGCTATTTAGTGGCGTTTCCATACAGAAACGCCAATATTTAGCGGCGTTTCCGAACAT
11515 AAACGCCGCTATTTAGTGGCGTTTC
1 AAACGCCGCTATTTAGTGGCGTTTC
11540 AGTGAAAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 75 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (64 bp):
AAACGCCGCTATTTAGTGGCGTTTCCATACAGAAACGCCAATATTTAGCGGCGTTTCCGAACAT
Found at i:11559 original size:32 final size:32
Alignment explanation
Indices: 11387--11539 Score: 155
Period size: 32 Copynumber: 4.8 Consensus size: 32
11377 TTAGGTTCAG
** * * *
11387 AAACGCCGCTAAATAGTGGCGTTTC-CATACAG
1 AAACGCCGCTATTTAGCGGCGTTTCTGA-ACAT
* *
11419 AAACGCCGCTATTTAGTGGCGTTTCCGAACAT
1 AAACGCCGCTATTTAGCGGCGTTTCTGAACAT
* * **
11451 AAACGCCACTATTTAGCGGCGTTTCTGTACGG
1 AAACGCCGCTATTTAGCGGCGTTTCTGAACAT
* **
11483 ACACGCCAATATTTAGCGGCGTTTCTGAACAT
1 AAACGCCGCTATTTAGCGGCGTTTCTGAACAT
*
11515 AAACGCCGCTATTTAGTGGCGTTTC
1 AAACGCCGCTATTTAGCGGCGTTTC
11540 AGTGAAAAAA
Statistics
Matches: 101, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
32 100 0.99
33 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (32 bp):
AAACGCCGCTATTTAGCGGCGTTTCTGAACAT
Found at i:12111 original size:7 final size:7
Alignment explanation
Indices: 12101--12132 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
12091 AATCTAAAAA
12101 AAAATTC
1 AAAATTC
12108 AAAATTC
1 AAAATTC
12115 AAAATTC
1 AAAATTC
12122 AAAATTC
1 AAAATTC
12129 AAAA
1 AAAA
12133 AAAGAATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAATTC
Found at i:12325 original size:37 final size:36
Alignment explanation
Indices: 12205--12415 Score: 255
Period size: 36 Copynumber: 5.8 Consensus size: 36
12195 AATTTAGCTG
12205 GTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTTAA
1 GTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTTAA
* *
12241 GTTTTAAAATTGGGAAAGATCCCATCAAGTTTTTAA
1 GTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTTAA
* * *
12277 GTTTTCAAATTGGGAAAGCTCCCATCCAGTTTTCAAA
1 GTTTTCAAATTGGGAAAGTTCCCATCAAGTTTT-TAA
*
12314 GTTTTCAAATTGGGAAAGTTCCCATC-AGATTTT-A
1 GTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTTAA
* * ** *
12348 GTTTTCAATTTAGGGAAAGTTCCCGTCATTTTCGGTTTTA
1 GTTTTCAAATT-GGGAAAGTTCCCATCAAGTT---TTTAA
*
12388 GTTTTCAAAATGGGAAAGTTCCCATCAA
1 GTTTTCAAATTGGGAAAGTTCCCATCAA
12416 AAGCATTTTT
Statistics
Matches: 150, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
34 11 0.07
35 14 0.09
36 70 0.47
37 27 0.18
39 18 0.12
40 10 0.07
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.37
Consensus pattern (36 bp):
GTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTTAA
Found at i:14249 original size:22 final size:23
Alignment explanation
Indices: 14210--14253 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
14200 TACAACAACT
14210 TTACAAATTAAATTTGAATGAAA
1 TTACAAATTAAATTTGAATGAAA
*
14233 TTACAAA-TATATTTGAATGAA
1 TTACAAATTAAATTTGAATGAA
14254 GATACGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (23 bp):
TTACAAATTAAATTTGAATGAAA
Found at i:19412 original size:2 final size:2
Alignment explanation
Indices: 19405--19432 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19395 TGACTTCTAG
19405 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
19433 CAATCTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.