Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021769.1 Corchorus olitorius cultivar O-4 contig21802, 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: 18484
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:2740 original size:15 final size:15
Alignment explanation
Indices: 2703--2740 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2693 AAATGAAATA
2703 TGCAATTTTTGTTAG
1 TGCAATTTTTGTTAG
*
2718 TGGAATTTTTGTTAG
1 TGCAATTTTTGTTAG
*
2733 TGCCATTT
1 TGCAATTT
2741 CACGTTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.18, C:0.08, G:0.21, T:0.53
Consensus pattern (15 bp):
TGCAATTTTTGTTAG
Found at i:5610 original size:22 final size:22
Alignment explanation
Indices: 5556--5764 Score: 145
Period size: 22 Copynumber: 9.4 Consensus size: 22
5546 GTCTGTGTGA
* *
5556 TTATCAAAATTTTAT-GAGATGG
1 TTATCAAAATTTCATAGTGA-GG
* *
5578 TTATTATAATTTCATGAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* *
5600 TTATCAAAATTACATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* **
5622 TTATCAAAATTTCATGGAAAGG
1 TTATCAAAATTTCATAGTGAGG
* *
5644 TTATCTAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* *
5666 TTACCAAAATTTCATAGGATCAGG
1 TTATCAAAATTTCATA-G-TGAGG
* *
5690 TTATTAAAATTTCTTAG-GAAGG
1 TTATCAAAATTTCATAGTG-AGG
** * *
5712 TTATTGAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* * **
5734 TTATCACAATTTTATAGAAAGG
1 TTATCAAAATTTCATAGTGAGG
5756 TTATCAAAA
1 TTATCAAAA
5765 AGATTATCAA
Statistics
Matches: 144, Mismatches: 36, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
21 2 0.01
22 120 0.83
23 5 0.03
24 17 0.12
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:5722 original size:68 final size:68
Alignment explanation
Indices: 5556--5764 Score: 186
Period size: 66 Copynumber: 3.1 Consensus size: 68
5546 GTCTGTGTGA
* * * * *
5556 TTATCAAAATTTTAT-GAGATGGTTAT-TATAATTTCATGAG-GAGGTTATCAAAATTACATAGT
1 TTATCAAAATTTCATGGA-AAGGTTATCTA-AATTTCAT-AGTGTGGTTACCAAAATTTCATAG-
5618 G-T--GG
62 GATCAGG
5622 TTATCAAAATTTCATGGAAAGGTTATCTAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATC
1 TTATCAAAATTTCATGGAAAGGTTATCTAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATC
5687 AGG
66 AGG
* * * * * *
5690 TTATTAAAATTTCTTAGG-AAGGTTAT-TGAAATTTTATAGTGTGGTTATCACAATTTTATA-GA
1 TTATCAAAATTTCAT-GGAAAGGTTATCT-AAATTTCATAGTGTGGTTACCAAAATTTCATAGGA
*
5752 -AAGG
64 TCAGG
5756 TTATCAAAA
1 TTATCAAAA
5765 AGATTATCAA
Statistics
Matches: 122, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
65 3 0.02
66 59 0.48
67 7 0.06
68 51 0.42
69 2 0.02
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.39
Consensus pattern (68 bp):
TTATCAAAATTTCATGGAAAGGTTATCTAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATC
AGG
Found at i:5903 original size:22 final size:22
Alignment explanation
Indices: 5768--6186 Score: 185
Period size: 22 Copynumber: 18.9 Consensus size: 22
5758 ATCAAAAAGA
**
5768 TTATC-AAATTGTCATAACGAGG
1 TTATCAAAATT-TCATAGTGAGG
*
5790 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
*
5812 TTAACAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* * * *
5834 TTA-CTAATATTTTATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
*
5856 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
*
5878 TTATCAAAATTTCATA-TGAAGT
1 TTATCAAAATTTCATAGTG-AGG
*
5900 TTAT-AAAAGTCTCAATTTCA-TGAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * * *
5925 AGTACCAAAATTTGATAG-AATG
1 -TTATCAAAATTTCATAGTGAGG
* * * *
5947 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
5968 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGA--GG
*
5992 ATTATCAAAATTT-ATAG-GAAGA
1 -TTATCAAAATTTCATAGTG-AGG
**
6014 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* * *
6036 TTATCAAAATTTCAAAGCGGGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
6058 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
* *
6080 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
6102 ATAACAAAATTTTATAGAGAGT
1 TTATCAAAATTTCATAGTGAGG
* ** *
6124 TTATCAAATTTTCATAAAGAGT
1 TTATCAAAATTTCATAGTGAGG
* * * * *
6146 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
*
6168 TTACCAAAATTTCATAGTG
1 TTATCAAAATTTCATAGTG
6187 GTATTTTTGG
Statistics
Matches: 301, Mismatches: 72, Indels: 48
0.71 0.17 0.11
Matches are distributed among these distances:
20 9 0.03
21 28 0.09
22 219 0.73
23 13 0.04
24 6 0.02
25 15 0.05
26 7 0.02
27 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:5955 original size:20 final size:22
Alignment explanation
Indices: 5932--6030 Score: 89
Period size: 21 Copynumber: 4.5 Consensus size: 22
5922 AGGAGTACCA
*
5932 AAATTTGATAGAATG-TTATC-
1 AAATTTCATAGAATGATTATCG
* *
5952 AAATCTCATAGAGTGATTATCG
1 AAATTTCATAGAATGATTATCG
*
5974 AAATTTCATAGAGATCGGATTATCA
1 AAATTTCATAGA-AT--GATTATCG
*
5999 AAATTT-ATAGGAA-GATTATCA
1 AAATTTCATA-GAATGATTATCG
6020 AAATTTCATAG
1 AAATTTCATAG
6031 TGTTGTTATC
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
20 12 0.18
21 20 0.30
22 14 0.21
23 1 0.02
24 4 0.06
25 15 0.23
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.34
Consensus pattern (22 bp):
AAATTTCATAGAATGATTATCG
Found at i:6312 original size:22 final size:22
Alignment explanation
Indices: 6284--6511 Score: 136
Period size: 22 Copynumber: 10.6 Consensus size: 22
6274 TCGGGGAGGA
6284 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* *
6306 TATCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
6328 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
*
6349 AGATCAAAATTTCATAATG-AGGT
1 -TATCAAAATTTCAT-ATGAAGGT
* ** * * *
6372 TATAAAAAAATCATAAGGATGT
1 TATCAAAATTTCATATGAAGGT
*
6394 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* *
6410 TATCAAGATTTCATA-AAGAGGT
1 TATCAAAATTTCATATGA-AGGT
* * * *
6432 TATCAAAATTTTATAGGATGATT
1 TATCAAAATTTCATATGAAG-GT
6455 TATCAAAATTTCATA-GCAAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
6477 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
6499 TATCAAAATTTCA
1 TATCAAAATTTCA
6512 GGGTGTGATT
Statistics
Matches: 159, Mismatches: 31, Indels: 32
0.72 0.14 0.14
Matches are distributed among these distances:
16 9 0.06
17 2 0.01
18 2 0.01
20 2 0.01
21 6 0.04
22 114 0.72
23 22 0.14
24 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:6338 original size:44 final size:43
Alignment explanation
Indices: 6284--6511 Score: 166
Period size: 44 Copynumber: 5.3 Consensus size: 43
6274 TCGGGGAGGA
6284 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATA-GAAGGTTATCAAAATTTCATAAGAGGGT
* * *
6328 TATCAAAATTTCATAGTATGTAGATCAAAATTTCATAATGA-GGT
1 TATCAAAATTTCATAGAAGGT-TATCAAAATTTCATAA-GAGGGT
* ** * * *
6372 TATAAAAAAATCATAAGGATGTTATCAAAATTT-GT---A--GT
1 TATCAAAATTTCAT-AGAAGGTTATCAAAATTTCATAAGAGGGT
* * * * **
6410 TATCAAGATTTCATAAAGAGGTTATCAAAATTTTATAGGATGATT
1 TATCAAAATTTCATAGA-AGGTTATCAAAATTTCATAAGA-GGGT
* * *
6455 TATCAAAATTTCATAGCAAGGTTATCACAATTTCAT-AGTGTGAT
1 TATCAAAATTTCATAG-AAGGTTATCAAAATTTCATAAGAG-GGT
6499 TATCAAAATTTCA
1 TATCAAAATTTCA
6512 GGGTGTGATT
Statistics
Matches: 145, Mismatches: 26, Indels: 26
0.74 0.13 0.13
Matches are distributed among these distances:
37 1 0.01
38 26 0.18
39 2 0.01
42 1 0.01
43 6 0.04
44 69 0.48
45 39 0.27
46 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (43 bp):
TATCAAAATTTCATAGAAGGTTATCAAAATTTCATAAGAGGGT
Found at i:6460 original size:45 final size:44
Alignment explanation
Indices: 6409--6511 Score: 129
Period size: 45 Copynumber: 2.3 Consensus size: 44
6399 AAATTTGTAG
* *
6409 TTATCAAGATTTCATA-AAGAGGTTATCAAAATTTTATAG-GATGA
1 TTATCAAAATTTCATAGAA-AGGTTATCAAAATTTCATAGTG-TGA
* *
6453 TTTATCAAAATTTCATAGCAAGGTTATCACAATTTCATAGTGTGA
1 -TTATCAAAATTTCATAGAAAGGTTATCAAAATTTCATAGTGTGA
6498 TTATCAAAATTTCA
1 TTATCAAAATTTCA
6512 GGGTGTGATT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
44 14 0.27
45 36 0.69
46 2 0.04
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.38
Consensus pattern (44 bp):
TTATCAAAATTTCATAGAAAGGTTATCAAAATTTCATAGTGTGA
Found at i:6517 original size:22 final size:22
Alignment explanation
Indices: 6431--6522 Score: 69
Period size: 22 Copynumber: 4.1 Consensus size: 22
6421 CATAAAGAGG
* *
6431 TTATCAAAATTTTATAG-GATGA
1 TTATCAAAATTTCAGAGTG-TGA
* *** *
6453 TTTATCAAAATTTCATAGCAAGG
1 -TTATCAAAATTTCAGAGTGTGA
* *
6476 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
*
6498 TTATCAAAATTTCAGGGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
6520 TTA
1 TTA
6523 CTAACAATGC
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
22 39 0.70
23 17 0.30
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:6589 original size:22 final size:23
Alignment explanation
Indices: 6564--6615 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
6554 CATAACGTGG
*
6564 TTATCAATATATCATA-TGGAGA
1 TTATCAACATATCATAGTGGAGA
* **
6586 TTATCAACATCTCATAGTGTTGA
1 TTATCAACATATCATAGTGGAGA
6609 TTATCAA
1 TTATCAA
6616 AATTTCATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (23 bp):
TTATCAACATATCATAGTGGAGA
Found at i:15062 original size:28 final size:28
Alignment explanation
Indices: 15022--15079 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
15012 GTGCTATTGT
15022 GGAGTGTTCGTAGCTTGCACAACTCCAG
1 GGAGTGTTCGTAGCTTGCACAACTCCAG
*
15050 GGAGTGTTCGTAGCTTGCACCACTCCAG
1 GGAGTGTTCGTAGCTTGCACAACTCCAG
15078 GG
1 GG
15080 TTAAGTCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.24
Consensus pattern (28 bp):
GGAGTGTTCGTAGCTTGCACAACTCCAG
Found at i:17224 original size:31 final size:31
Alignment explanation
Indices: 17174--17252 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
17164 TTCAATTATT
* **
17174 ACATAAATATGGATT-TTTTTTT-CTGGCCAG
1 ACATAGATATGG-TTATTTTTTTGCTACCCAG
*
17204 ATCATAGATATGGTTATTTTTTTGCTACCCAT
1 A-CATAGATATGGTTATTTTTTTGCTACCCAG
*
17236 AGATAGATATGGTTATT
1 ACATAGATATGGTTATT
17253 AGTAAACTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 3 0.07
31 32 0.78
32 6 0.15
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.44
Consensus pattern (31 bp):
ACATAGATATGGTTATTTTTTTGCTACCCAG
Found at i:17960 original size:15 final size:15
Alignment explanation
Indices: 17902--17969 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
17892 ATGCAAGATT
*
17902 TTTG-AATTCAATAA
1 TTTGAAATTCTATAA
**
17916 TTTGAAATTCT-TTG
1 TTTGAAATTCTATAA
17930 TTTGGAAA-T-TAGTAA
1 TTT-GAAATTCTA-TAA
17945 TTTGAAATTCTATAA
1 TTTGAAATTCTATAA
*
17960 TTTCAAATTC
1 TTTGAAATTC
17970 ATTGTTTGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
13 1 0.02
14 13 0.31
15 26 0.62
16 2 0.05
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.47
Consensus pattern (15 bp):
TTTGAAATTCTATAA
Found at i:17967 original size:29 final size:29
Alignment explanation
Indices: 17913--17968 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
17903 TTGAATTCAA
** *
17913 TAATTTGAAATTCTTTGTTTGGAAATTAG
1 TAATTTGAAATTCTTAATTTGCAAATTAG
17942 TAATTTGAAATTCTATAATTT-CAAATT
1 TAATTTGAAATTCT-TAATTTGCAAATT
17969 CATTGTTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (29 bp):
TAATTTGAAATTCTTAATTTGCAAATTAG
Found at i:17992 original size:44 final size:43
Alignment explanation
Indices: 17902--17992 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
17892 ATGCAAGATT
* * * *
17902 TTTGAATTCAATAATTTGAAATTCTTTGTTTGGAAATTAGTAA
1 TTTGAATTCAATAATTTCAAATTCATTGTTTGGAAACTAATAA
* *
17945 TTTGAAATTCTATAATTTCAAATTCATTGTTTGGATGACTAAT-A
1 TTTG-AATTCAATAATTTCAAATTCATTGTTTGGA-AACTAATAA
17989 TTTG
1 TTTG
17993 GATTTGGATT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
43 4 0.10
44 32 0.80
45 4 0.10
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (43 bp):
TTTGAATTCAATAATTTCAAATTCATTGTTTGGAAACTAATAA
Found at i:17999 original size:6 final size:6
Alignment explanation
Indices: 17988--18016 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17978 GATGACTAAT
17988 ATTTGG ATTTGG ATTTGG ATTTGG ATTTG
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTTG
18017 AACTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (6 bp):
ATTTGG
Done.