Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024317.1 Corchorus olitorius cultivar O-4 contig24350, 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: 23701
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:5384 original size:18 final size:18
Alignment explanation
Indices: 5361--5399 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5351 TAACCTTAAA
* *
5361 AAAGGGAAAAGGAAAAGG
1 AAAGGGAAAAAGAAAAAG
5379 AAAGGGAAAAAGAAAAAG
1 AAAGGGAAAAAGAAAAAG
5397 AAA
1 AAA
5400 AACCTTACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
AAAGGGAAAAAGAAAAAG
Found at i:7786 original size:28 final size:28
Alignment explanation
Indices: 7730--7801 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
7720 ATCTAAAATT
*
7730 AAAAAGAAAATAGAAC--TTTTTAGAGG
1 AAAAAGAAAATACAACTTTTTTTAGAGG
*
7756 AAAAAGAAAATACAACTTTTTTTTTGA-G
1 AAAAAGAAAATACAAC-TTTTTTTAGAGG
7784 AAAAAGAAAATACAACTT
1 AAAAAGAAAATACAACTT
7802 AATTGTTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
26 15 0.37
27 2 0.05
28 17 0.41
29 7 0.17
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.26
Consensus pattern (28 bp):
AAAAAGAAAATACAACTTTTTTTAGAGG
Found at i:9366 original size:3 final size:3
Alignment explanation
Indices: 9360--9387 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
9350 AGCAGATGAT
9360 GCA GCA GCA GCA GCA GCA GCA GCA GCA G
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA G
9388 GAAGAGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.36, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:16907 original size:106 final size:105
Alignment explanation
Indices: 16790--17007 Score: 244
Period size: 107 Copynumber: 2.1 Consensus size: 105
16780 TTAACTCAAT
** **
16790 AAAAAAATTT-AATTAATTTCAAGAAATTTAGTTTCAAATTTAAAAAATTAATTCATTTAAAGAG
1 AAAAAAATTTAAAAGAATTTCAAGAAATTTAGTCCCAAATTTAAAAAA--AATTCATTTAAAGAG
16854 TAAG-TTGTAAAATAAAAGATTTATTATTAT-AGGATTTTAGA
64 TAAGTTTGTAAAATAAAAGATTTATTATTATAAGG-TTTTAGA
* ** * * * *
16895 AAAAAAATTTTAAAAAGAATTTTACTAAGTTTAGTCCCAAATTTAAAAGAAGTTCATTTAAAGGG
1 AAAAAAA-TTT-AAAAGAATTTCAAGAAATTTAGTCCCAAATTTAAAAAAAATTCATTTAAAGAG
* * *
16960 TAAGTTTGTGAAATTAAATATTTATTATTATAAGGTTTTAGA
64 TAAGTTTGTAAAATAAAAGATTTATTATTATAAGGTTTTAGA
17002 AAAAAA
1 AAAAAA
17008 TAAAAAACGG
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
105 7 0.07
106 20 0.21
107 36 0.38
108 31 0.33
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.38
Consensus pattern (105 bp):
AAAAAAATTTAAAAGAATTTCAAGAAATTTAGTCCCAAATTTAAAAAAAATTCATTTAAAGAGTA
AGTTTGTAAAATAAAAGATTTATTATTATAAGGTTTTAGA
Found at i:17152 original size:106 final size:102
Alignment explanation
Indices: 16960--17220 Score: 244
Period size: 104 Copynumber: 2.5 Consensus size: 102
16950 ATTTAAAGGG
* **
16960 TAAGTTTGTGAAATTAAATATTTATTATTATAAGG-TTTTAGAAAAAAATAAAAAACGGATTTCA
1 TAAG-TTGTGAAATTAAAAATTTATTATTAT-AGGATTTTAG--AAAAATAAAAAACAAATTTCA
* *
17024 CTGAATTTAACTCCAATGAAAAAAA-AAA-TCCAAGGGT-AAGTAC
62 CTGAATTTAACTCAAATAAAAAAAATAAACT-C-A-GGTCAAG--C
* * * *
17067 TAAGTTGTGAAATTAAAAATTTATTTTTATAGGATTTTAGAAAAAGAAAAAACAAATTTTA-TTA
1 TAAGTTGTGAAATTAAAAATTTATTATTATAGGATTTTAGAAAAATAAAAAACAAATTTCACTGA
* * ** *
17131 AGTTTAGCTTCAAATTAAAAAAAATTAACTCATTTCAAGG
66 A-TTTAAC-TCAAA-TAAAAAAAATAAACTCAGGTCAAGC
*
17171 TAAGTTGTGAAATTAAAAATTTATTATTATAGAATTTTAGAAAAATAAAA
1 TAAGTTGTGAAATTAAAAATTTATTATTATAGGATTTTAGAAAAATAAAA
17221 GGTAAGGATT
Statistics
Matches: 130, Mismatches: 17, Indels: 17
0.79 0.10 0.10
Matches are distributed among these distances:
103 3 0.02
104 69 0.53
105 8 0.06
106 42 0.32
107 7 0.05
108 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.34
Consensus pattern (102 bp):
TAAGTTGTGAAATTAAAAATTTATTATTATAGGATTTTAGAAAAATAAAAAACAAATTTCACTGA
ATTTAACTCAAATAAAAAAAATAAACTCAGGTCAAGC
Found at i:17505 original size:18 final size:17
Alignment explanation
Indices: 17459--17505 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
17449 TGATCAAGTG
*
17459 AAAAAGCAAAAGAAAAA
1 AAAAAGAAAAAGAAAAA
17476 AAACAAGAAAAAGAAATAA
1 AAA-AAGAAAAAGAAA-AA
17495 AAAAAGGAAAA
1 AAAAA-GAAAA
17506 CTTTGGCACG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 13 0.50
19 10 0.38
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAAA
Found at i:19264 original size:20 final size:21
Alignment explanation
Indices: 19241--19279 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
19231 GGTTTTCTAG
19241 TAATCTCGTGTGTT-TGTTCA
1 TAATCTCGTGTGTTATGTTCA
*
19261 TAATCTCTTGTGTTATGTT
1 TAATCTCGTGTGTTATGTT
19280 TTGAGGTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.15, C:0.13, G:0.18, T:0.54
Consensus pattern (21 bp):
TAATCTCGTGTGTTATGTTCA
Found at i:22716 original size:2 final size:2
Alignment explanation
Indices: 22704--22758 Score: 65
Period size: 2 Copynumber: 27.0 Consensus size: 2
22694 TACACCAATT
* * * *
22704 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TC TA TA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22746 TA TA TA CTA TA TA
1 TA TA TA -TA TA TA
22759 AGTCTAAACT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:23061 original size:18 final size:18
Alignment explanation
Indices: 23038--23124 Score: 63
Period size: 18 Copynumber: 4.7 Consensus size: 18
23028 TAATTTAAAC
23038 TTATTATTATTATAATAA
1 TTATTATTATTATAATAA
*
23056 TTATTAAACTTATTAT--TAG
1 TTATT--A-TTATTATAATAA
* *
23075 TGGTATTATAATTATTAA-AC
1 T--TATTATTATTA-TAATAA
23095 TTATTATTATTATAATAA
1 TTATTATTATTATAATAA
*
23113 TAATTATTATTA
1 TTATTATTATTA
23125 GTGGTATGTA
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
17 3 0.06
18 32 0.59
19 5 0.09
20 3 0.06
21 11 0.20
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (18 bp):
TTATTATTATTATAATAA
Found at i:23086 original size:30 final size:27
Alignment explanation
Indices: 23032--23118 Score: 129
Period size: 27 Copynumber: 3.1 Consensus size: 27
23022 TCACGTTAAT
23032 TTAAACTTATTATTATTATAATAATTA
1 TTAAACTTATTATTATTATAATAATTA
*
23059 TTAAACTTATTATTAGTGGTATTATAATTA
1 TTAAACTTATTATTA-T--TATAATAATTA
*
23089 TTAAACTTATTATTATTATAATAATAA
1 TTAAACTTATTATTATTATAATAATTA
23116 TTA
1 TTA
23119 TTATTAGTGG
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
27 27 0.50
28 1 0.02
29 1 0.02
30 25 0.46
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (27 bp):
TTAAACTTATTATTATTATAATAATTA
Found at i:23118 original size:15 final size:16
Alignment explanation
Indices: 23082--23122 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
23072 TAGTGGTATT
*
23082 ATAATTATTA-AACTT
1 ATAATTATTATAACTA
*
23097 ATTATTATTATAA-TA
1 ATAATTATTATAACTA
23112 ATAATTATTAT
1 ATAATTATTAT
23123 TAGTGGTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATAATTATTATAACTA
Found at i:23119 original size:30 final size:29
Alignment explanation
Indices: 23032--23121 Score: 121
Period size: 30 Copynumber: 3.1 Consensus size: 29
23022 TCACGTTAAT
23032 TTAAACTTATTATTA-T-TATAATAATTA
1 TTAAACTTATTATTATTATATAATAATTA
** *
23059 TTAAACTTATTATTAGTGGTATTATAATTA
1 TTAAACTTATTATTA-TTATATAATAATTA
23089 TTAAACTTATTATTATTATAATAATAATTA
1 TTAAACTTATTATTATTAT-ATAATAATTA
23119 TTA
1 TTA
23122 TTAGTGGTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
27 15 0.28
29 2 0.04
30 37 0.69
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.51
Consensus pattern (29 bp):
TTAAACTTATTATTATTATATAATAATTA
Done.