Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022386.1 Corchorus olitorius cultivar O-4 contig22419, 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: 32637
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:147 original size:30 final size:27
Alignment explanation
Indices: 62--144 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 27
52 GTTAATTTAG
62 ACTTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTATAATAATTATTAA
*
89 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-T--TATAATAATTATTAA
*
119 ACTTATTATTATAATAATAATTATTA
1 ACTTATTATTATTATAATAATTATTA
145 TTAGTGGTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 23 0.46
28 1 0.02
29 1 0.02
30 25 0.50
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (27 bp):
ACTTATTATTATTATAATAATTATTAA
Found at i:5183 original size:25 final size:25
Alignment explanation
Indices: 5150--5213 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
5140 CTGCAGAGGA
*
5150 TGGCACAGGGCCT-AA-AAGAGAAAAG
1 TGGCGCAGGGCCTGAATAA-AG-AAAG
* *
5175 TGGCGCAGGGCTTGAATAAAGGAAG
1 TGGCGCAGGGCCTGAATAAAGAAAG
5200 TGGCGCAGGGCCTG
1 TGGCGCAGGGCCTG
5214 GAGAAGAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 27 0.82
26 4 0.12
27 2 0.06
ACGTcount: A:0.31, C:0.17, G:0.39, T:0.12
Consensus pattern (25 bp):
TGGCGCAGGGCCTGAATAAAGAAAG
Found at i:7517 original size:68 final size:68
Alignment explanation
Indices: 7408--7536 Score: 217
Period size: 68 Copynumber: 1.9 Consensus size: 68
7398 GCTTGAAATA
*
7408 CATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGGTG-TTCCTACCATTTTTTCTT
1 CATTGTCTTTATATGTAATGTTAGCATTTGGATGTAATTAATGGTGCTTCC-ACCATTTTTTCTT
7472 AGTG
65 AGTG
7476 CATTGTCTTTATATGTAATGTTAGCA-TTGAGATGTAATTAATGGTGCTTCCACCATTTTTT
1 CATTGTCTTTATATGTAATGTTAGCATTTG-GATGTAATTAATGGTGCTTCCACCATTTTTT
7537 TCTTTAGTTG
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
67 3 0.05
68 51 0.88
69 4 0.07
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.48
Consensus pattern (68 bp):
CATTGTCTTTATATGTAATGTTAGCATTTGGATGTAATTAATGGTGCTTCCACCATTTTTTCTTA
GTG
Found at i:21868 original size:17 final size:17
Alignment explanation
Indices: 21823--21870 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
21813 AATATCACAT
*
21823 GACTAGTAATGGTTTAG
1 GACTAGTAATGTTTTAG
* *
21840 GACTAGTCATGTTTTAT
1 GACTAGTAATGTTTTAG
*
21857 TACTAGTAATGTTT
1 GACTAGTAATGTTT
21871 CTCAAATCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (17 bp):
GACTAGTAATGTTTTAG
Found at i:23057 original size:20 final size:20
Alignment explanation
Indices: 23020--23058 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
23010 TTACTAATTT
23020 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
23040 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
23059 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:23120 original size:34 final size:34
Alignment explanation
Indices: 23082--23149 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
23072 AGATTAAACT
23082 AACACTAACACGTACAATACTATTGTTAGTGAAG
1 AACACTAACACGTACAATACTATTGTTAGTGAAG
23116 AACACTAACACGTACAATACTATTGTTAGTGAAG
1 AACACTAACACGTACAATACTATTGTTAGTGAAG
23150 CTCCATCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (34 bp):
AACACTAACACGTACAATACTATTGTTAGTGAAG
Found at i:23286 original size:22 final size:22
Alignment explanation
Indices: 23258--23410 Score: 105
Period size: 22 Copynumber: 6.9 Consensus size: 22
23248 TGTCTTTGTG
23258 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
23280 TGGTTATTATAATTTCATGAGG
1 TGGTTATCAAAATTTCATAAGA
* * * *
23302 CGGTTATTAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
23324 TGGTTACCAAAATTTCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
* *
23344 TGTAGTTACCAAAATTTCATAGGA
1 TG--GTTATCAAAATTTCATAAGA
* * *
23368 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAAGA
*
23392 AGGTTATCAAAATTTCATA
1 TGGTTATCAAAATTTCATA
23411 GTATTATCAC
Statistics
Matches: 106, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.02
21 2 0.02
22 82 0.77
23 1 0.01
24 18 0.17
26 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:23564 original size:24 final size:24
Alignment explanation
Indices: 23448--23599 Score: 128
Period size: 22 Copynumber: 6.7 Consensus size: 24
23438 ATCAAAAAGA
* *
23448 TTATCAAAATGTCATA--GCGAGG
1 TTATCAAAATTTCATAGTGTGAGG
23470 TTAT-AAGAATTTCATAGTGT--GG
1 TTATCAA-AATTTCATAGTGTGAGG
* *
23492 TTAACAAAATTTCATA-AG-GAGG
1 TTATCAAAATTTCATAGTGTGAGG
*
23514 TTA-CTAATATTTCAT-GTG-GAGG
1 TTATC-AAAATTTCATAGTGTGAGG
*
23536 TTATCAAAATTTCATAGTGTGTGG
1 TTATCAAAATTTCATAGTGTGAGG
**
23560 TTATCAAAATTTTTTAGTGT-ACGG
1 TTATCAAAATTTCATAGTGTGA-GG
23584 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
23600 TGAAGGTTAT
Statistics
Matches: 105, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
21 4 0.04
22 57 0.54
23 6 0.06
24 38 0.36
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.38
Consensus pattern (24 bp):
TTATCAAAATTTCATAGTGTGAGG
Found at i:23789 original size:22 final size:22
Alignment explanation
Indices: 23718--23914 Score: 105
Period size: 22 Copynumber: 8.9 Consensus size: 22
23708 TGCGCAGGGA
* *
23718 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAGTGAT--G
*
23742 ATTATCAAAATTT-ATAG-GAATA
1 -TTATCAAAATTTCATAGTG-ATG
*
23764 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGATG
* * * *
23786 TTATCAAATTTTCAAATTGAGG
1 TTATCAAAATTTCATAGTGATG
* *
23808 TTATCAAAATTACATAAT-ATG
1 TTATCAAAATTTCATAGTGATG
* **
23829 ATTATCAAAATTTCATAGAGGGG
1 -TTATCAAAATTTCATAGTGATG
* * * * *
23852 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGTGATG
* * * *
23874 TTATCGAATTTTCAAAATG-TG
1 TTATCAAAATTTCATAGTGATG
*
23895 ATTACCAAAATTTCATAGTG
1 -TTATCAAAATTTCATAGTG
23915 GTATTTCTGG
Statistics
Matches: 129, Mismatches: 37, Indels: 15
0.71 0.20 0.08
Matches are distributed among these distances:
21 15 0.12
22 94 0.73
23 3 0.02
24 6 0.05
25 11 0.09
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGATG
Found at i:23818 original size:44 final size:44
Alignment explanation
Indices: 23764--23914 Score: 126
Period size: 44 Copynumber: 3.4 Consensus size: 44
23754 TATAGGAATA
* *
23764 TTATCAAAATTTCATAGTGTTGTTATCAAATTTTCAAATTGAGG
1 TTATCAAAATTTCATAGTGATGTTATCAAATTTTCAAAATGAGG
* * * * *
23808 TTATCAAAATTACATAAT-ATGATTATCAAAATTTCATAGA-GGGG
1 TTATCAAAATTTCATAGTGATG-TTATCAAATTTTCA-AAATGAGG
* * * * * * * *
23852 TCAACAAAATTTTATAGAGAGGTTATCGAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGATGTTATCAAATTTTCAAAATGAGG
*
23896 TTACCAAAATTTCATAGTG
1 TTATCAAAATTTCATAGTG
23915 GTATTTCTGG
Statistics
Matches: 80, Mismatches: 23, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
43 4 0.05
44 73 0.91
45 3 0.04
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (44 bp):
TTATCAAAATTTCATAGTGATGTTATCAAATTTTCAAAATGAGG
Found at i:24269 original size:39 final size:39
Alignment explanation
Indices: 24215--24341 Score: 227
Period size: 39 Copynumber: 3.3 Consensus size: 39
24205 ATTAGGCTTT
*
24215 GTCGCGCGCGACCAAGGCTTGCGACCAAGCCACGGCTCG
1 GTCGCGCGCGACCAAGGCTTGCGACCAAGCCGCGGCTCG
24254 GTCGCGCGCGACCAAGGCTTGCGACCAAGCCGCGGCTCG
1 GTCGCGCGCGACCAAGGCTTGCGACCAAGCCGCGGCTCG
**
24293 GTCGCGCGCGACCAAGGCTTGCGACCAAGTTGCGGCTCG
1 GTCGCGCGCGACCAAGGCTTGCGACCAAGCCGCGGCTCG
24332 GTCGCGCGCG
1 GTCGCGCGCG
24342 GCTCATGACC
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.15, C:0.37, G:0.36, T:0.12
Consensus pattern (39 bp):
GTCGCGCGCGACCAAGGCTTGCGACCAAGCCGCGGCTCG
Found at i:24906 original size:22 final size:22
Alignment explanation
Indices: 24862--25134 Score: 121
Period size: 22 Copynumber: 12.6 Consensus size: 22
24852 TCAGGGAGAA
**
24862 TATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAGTAGAGT
*
24884 TTTCAAAATTTCATAAG-AGAGT
1 TATCAAAATTTCAT-AGTAGAGT
*
24906 TATCAAAATTTCATTGTATGTAG-
1 TATCAAAATTTCATAGTA-G-AGT
* *
24929 -ATCAAAATTCCATAG-GGAGAT
1 TATCAAAATTTCATAGTAGAG-T
* *
24950 TAACAAAATTTCATAAT-GAGGT
1 TATCAAAATTTCATAGTAGA-GT
** *
24972 TATCAAAAACTCATAG-GGAGGT
1 TATCAAAATTTCATAGTAGA-GT
24994 TATCAAAA-TT--T-GT--AGT
1 TATCAAAATTTCATAGTAGAGT
* *
25010 TATCAAGATTTCATAAGGAG-GT
1 TATCAAAATTTCAT-AGTAGAGT
* *
25032 TATCAAAATTTTATAG-GGAGGTT
1 TATCAAAATTTCATAGTAGA-G-T
* *
25055 TATCAAAATTTTATAGGA-AGGTT
1 TATCAAAATTTCATAGTAGA-G-T
*
25078 TATCAAAATTTTATAGT-GAGGT
1 TATCAAAATTTCATAGTAGA-GT
* *
25100 TATCACAATTTCATAGT-GTGAT
1 TATCAAAATTTCATAGTAGAG-T
*
25122 TATCAGAATTTCA
1 TATCAAAATTTCA
25135 GAGTGTGATT
Statistics
Matches: 200, Mismatches: 27, Indels: 48
0.73 0.10 0.17
Matches are distributed among these distances:
16 9 0.05
17 3 0.01
18 1 0.00
19 4 0.02
20 2 0.01
21 6 0.03
22 128 0.64
23 45 0.22
24 2 0.01
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATAGTAGAGT
Found at i:24977 original size:44 final size:44
Alignment explanation
Indices: 24843--25313 Score: 331
Period size: 44 Copynumber: 10.8 Consensus size: 44
24833 TTATGGAGTA
** *
24843 ATCAAAATTTC--AGGGAGAATATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAG-TGAGGTT
* * * * *
24885 TTCAAAATTTCATA-AGAGAGTTATCAAAATTTCATTGT-ATGTAG
1 ATCAAAATTTCATAGGGAG-GTTATCAAAATTTCATAGTGAGGT-T
* * * *
24929 ATCAAAATTCCATAGGGAGATTAACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGAGGTT
**
24973 ATCAAAAACTCATAGGGAGGTTATCAAAA-TT--T-GT-A-GTT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGAGGTT
* * * *
25011 ATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGAGG-TT
* * *
25056 ATCAAAATTTTATAGGAAGGTTTATCAAAATTTTATAGTGAGGTT
1 ATCAAAATTTCATAGGGAGG-TTATCAAAATTTCATAGTGAGGTT
* * * * * * * *
25101 ATCACAATTTCATAGTGTGATTATCAGAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGAGGTT
* * * * ** *
25145 A-CTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAACGTGGTT
1 ATC-AA-AATTTCATAGGGAGGTTATCAAAATTTCATAGTGAGGTT
* * * ** * *
25189 ATCAATATATCATATGGAGGTTATCATCATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTG-AGGTT
* *
25234 ATCAAAATTTCATTGGGAAGTTATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGAGGT-T
* * *
25279 -TCAAAATTCCTTAGGGAGGTTAACAAAATTTCATA
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATA
25314 AGAAGGTTAA
Statistics
Matches: 329, Mismatches: 79, Indels: 40
0.73 0.18 0.09
Matches are distributed among these distances:
38 28 0.09
39 3 0.01
40 1 0.00
41 2 0.01
42 12 0.04
43 11 0.03
44 171 0.52
45 80 0.24
46 21 0.06
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (44 bp):
ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGAGGTT
Found at i:25061 original size:23 final size:22
Alignment explanation
Indices: 24929--25309 Score: 154
Period size: 22 Copynumber: 17.5 Consensus size: 22
24919 TTGTATGTAG
** *
24929 ATCAAAATTCCATAGGGAGATT
1 ATCAAAATTTTATAGGGAGGTT
* * **
24951 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTTATAGGGAGGTT
** *
24973 ATCAAAAACTCATAGGGAGGTT
1 ATCAAAATTTTATAGGGAGGTT
*
24995 ATCAAAA--TT-T--GTA-GTT
1 ATCAAAATTTTATAGGGAGGTT
* * *
25011 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTTATAGGGAGGTT
25033 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTTATAGGGAGG-TT
*
25056 ATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTTATAGGGAGG-TT
*
25079 ATCAAAATTTTATAGTGAGGTT
1 ATCAAAATTTTATAGGGAGGTT
* * * * *
25101 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTTATAGGGAGGTT
* * * * * *
25123 ATCAGAATTTCAGAGTGTGATT
1 ATCAAAATTTTATAGGGAGGTT
* *
25145 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTTATAGGGAGGTT
** ** *
25167 -TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTT-ATAGGGAGGTT
* * * *
25189 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTTATAGGGAGGTT
** * * **
25211 ATCATCATCTCATAGTGTTGGTT
1 ATCAAAATTTTATAG-GGAGGTT
* * *
25234 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTTATAGGGAGGTT
* *
25256 ATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTTATAGGGAGGT-T
*
25279 -TCAAAATTCCT-TAGGGAGGTT
1 ATCAAAATT-TTATAGGGAGGTT
*
25300 AACAAAATTT
1 ATCAAAATTT
25310 CATAAGAAGG
Statistics
Matches: 274, Mismatches: 68, Indels: 35
0.73 0.18 0.09
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 1 0.00
19 2 0.01
20 3 0.01
21 7 0.03
22 184 0.67
23 66 0.24
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTTATAGGGAGGTT
Found at i:25320 original size:22 final size:22
Alignment explanation
Indices: 25295--25336 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
25285 TTCCTTAGGG
*
25295 AGGTT-AACAAAATTTCATAAGA
1 AGGTTAAAAAAAATTT-ATAAGA
25317 AGGTTAAAAAAAATTTATAA
1 AGGTTAAAAAAAATTTATAA
25337 CTGTTGCGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.29
Consensus pattern (22 bp):
AGGTTAAAAAAAATTTATAAGA
Found at i:27370 original size:23 final size:22
Alignment explanation
Indices: 27326--27370 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
27316 ATCGTTATTG
**
27326 AAATTTCATAGGAAGGTTGTCA
1 AAATTTCATAGGAAGGAAGTCA
*
27348 AAATTTCATAAGTAAGGAAGTCA
1 AAATTTCAT-AGGAAGGAAGTCA
27371 TCAAAAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (22 bp):
AAATTTCATAGGAAGGAAGTCA
Done.