Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020131.1 Corchorus olitorius cultivar O-4 contig20164, 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: 64074
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1359 original size:13 final size:12
Alignment explanation
Indices: 1341--1384 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 12
1331 TTTTATTATG
1341 GTTTTATTAAATT
1 GTTTTA-TAAATT
*
1354 GTTTTATAAATG
1 GTTTTATAAATT
1366 GTTTTAAATAAATT
1 GTTTT--ATAAATT
1380 GTTTT
1 GTTTT
1385 GGGTGCATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 10 0.37
13 6 0.22
14 11 0.41
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (12 bp):
GTTTTATAAATT
Found at i:1369 original size:12 final size:13
Alignment explanation
Indices: 1338--1371 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1328 CTATTTTATT
1338 ATGGTTTTATTAA
1 ATGGTTTTATTAA
*
1351 ATTGTTTTA-TAA
1 ATGGTTTTATTAA
1363 ATGGTTTTA
1 ATGGTTTTA
1372 AATAAATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (13 bp):
ATGGTTTTATTAA
Found at i:3155 original size:18 final size:17
Alignment explanation
Indices: 3113--3155 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
3103 ATGTGTCCCC
3113 TTATGGAATATTTATTAA
1 TTAT-GAATATTTATTAA
3131 -TATTGAATATTTAATTAA
1 TTA-TGAATATTT-ATTAA
3149 TTATGAA
1 TTATGAA
3156 ATATGTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 10 0.45
18 10 0.45
19 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (17 bp):
TTATGAATATTTATTAA
Found at i:3269 original size:198 final size:200
Alignment explanation
Indices: 2849--3430 Score: 857
Period size: 198 Copynumber: 2.9 Consensus size: 200
2839 AACTTTAGTG
* ** * * *
2849 CAATACACCGTCAGTGGAGTTTAATAAAATGCACGTGCGGGGTTTAAGGGTTGACATGTATCCCC
1 CAATACACCGTCAGTAGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCC
* *
2914 TTAGGGAATATGTATTAATATTAAATATTTGATTAATTATGAAATGTAGTATTTGTCAACTTCTT
66 TTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGTAGTATGTGTCAACTTCTT
*
2979 AAA-CCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAA
131 AAACCCGCTTATGGAGTCCAAAAATTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAA
3043 TTATA
196 TTATA
* * *
3048 CAATACACCGTCACTAGAGTTTAGCAGACTACACGTGCGGGGTTTAAAGGTTGACATGTGTCCCC
1 CAATACACCGTCAGTAGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCC
* * * *
3113 TTATGGAATATTTATTAATATTGAATATTTAATTAATTATGAAATAT-GTATGTGTCAACTT-TT
66 TTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGTAGTATGTGTCAACTTCTT
* * * *
3176 AAACCCGCTTATGGAGACCAAAAGTTGCACTGACAGTGTATTGTATAATAATCCTATAAGCAAAA
131 AAACCCGCTTATGGAGTCCAAAAATTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAA
*
3241 TTTTA
196 TTATA
* * **
3246 TAATACACCGTCAGTAGAGTTTAGCAGACTGTACGTGCATGGTTTAAGGGTTGACATGTGTCCCC
1 CAATACACCGTCAGTAGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCC
* *
3311 TTAGGGAATATGTATTAATATCAAATATTTAATTAATTATGAAATGTGGTATGTGTCAACTTCTT
66 TTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGTAGTATGTGTCAACTTCTT
* * *
3376 -AACCCGCTTATGAAGTCCAAAAATTACATTGATAGTGTATTTGTATAATAATCCT
131 AAACCCGCTTATGGAGTCCAAAAATTACACTGACAGTGTA-TTGTATAATAATCCT
3431 TATTATAAAG
Statistics
Matches: 341, Mismatches: 38, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
197 5 0.01
198 174 0.51
199 145 0.43
200 17 0.05
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (200 bp):
CAATACACCGTCAGTAGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCC
TTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGTAGTATGTGTCAACTTCTT
AAACCCGCTTATGGAGTCCAAAAATTACACTGACAGTGTATTGTATAATAATCCTATAAGAAAAA
TTATA
Found at i:3774 original size:16 final size:16
Alignment explanation
Indices: 3749--3779 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3739 TCTACATATT
3749 ATAAAGATTTAGTAAA
1 ATAAAGATTTAGTAAA
*
3765 ATAAATATTTAGTAA
1 ATAAAGATTTAGTAA
3780 TATTTTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
ATAAAGATTTAGTAAA
Found at i:5700 original size:49 final size:47
Alignment explanation
Indices: 5601--5734 Score: 155
Period size: 49 Copynumber: 2.8 Consensus size: 47
5591 ATCTTTTACA
*
5601 TTTCCTGCACTTTTTCTCAATTTTTACA-ACAAAATTGAACCTTTAAT
1 TTTCCTGCACTTTTTCTCAATTTTTA-AGACAAAATTGAACATTTAAT
**
5648 TTTCCTCGCACCTTTTTCTCAATTTTTAAGACAAAATTGAACATTTTCT
1 TTTCCT-GCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACATTTAAT
* * * *
5697 TTTCATTGCTCTTTTTATCAATTTTT-GGACAAAATTGA
1 TTTC-CTGCACTTTTTCTCAATTTTTAAGACAAAATTGA
5735 TTGGCACGCT
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
47 17 0.22
48 19 0.25
49 39 0.51
50 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46
Consensus pattern (47 bp):
TTTCCTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACATTTAAT
Found at i:8373 original size:15 final size:15
Alignment explanation
Indices: 8325--8374 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
8315 TGCTAGGGTG
*
8325 AATGGTGCAAACAAC
1 AATGGTGCGAACAAC
*
8340 AATGGTGCGAATAAC
1 AATGGTGCGAACAAC
* *
8355 AATGGTGTGAACAAT
1 AATGGTGCGAACAAC
8370 AATGG
1 AATGG
8375 AAACGGTGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.26, T:0.20
Consensus pattern (15 bp):
AATGGTGCGAACAAC
Found at i:13015 original size:31 final size:31
Alignment explanation
Indices: 12924--13026 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 31
12914 ACAAAAAAAA
* ** *
12924 TCAATTTAGTCCCTCTACTA--AAAAACCGA
1 TCAATTTAGTCCCTCTACTACTAAGAATGGG
**
12953 TCAATTTAGTCCCTCTACTTGTAAGAATGGG
1 TCAATTTAGTCCCTCTACTACTAAGAATGGG
* *
12984 TCAATTTAGTCCCTCTACTCACTCA-ATTGGG
1 TCAATTTAGTCCCTCTACT-ACTAAGAATGGG
*
13015 TCAATTAAGTCC
1 TCAATTTAGTCC
13027 AATCGATAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
29 19 0.31
31 40 0.66
32 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (31 bp):
TCAATTTAGTCCCTCTACTACTAAGAATGGG
Found at i:16919 original size:39 final size:39
Alignment explanation
Indices: 16865--16949 Score: 161
Period size: 39 Copynumber: 2.2 Consensus size: 39
16855 TTCTTAAGTT
*
16865 GTTCTTTTGAGCTAATTTGTGCAATTAACCCTATTTGGA
1 GTTCTTTTGAGCTAATTTGTGCAATTAACCCAATTTGGA
16904 GTTCTTTTGAGCTAATTTGTGCAATTAACCCAATTTGGA
1 GTTCTTTTGAGCTAATTTGTGCAATTAACCCAATTTGGA
16943 GTTCTTT
1 GTTCTTT
16950 GGTGCAATTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (39 bp):
GTTCTTTTGAGCTAATTTGTGCAATTAACCCAATTTGGA
Found at i:18053 original size:3 final size:3
Alignment explanation
Indices: 18045--18069 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18035 AAGCTCAATT
18045 ACC ACC ACC ACC ACC ACC ACC ACC A
1 ACC ACC ACC ACC ACC ACC ACC ACC A
18070 AGGGGAGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:22378 original size:30 final size:30
Alignment explanation
Indices: 22342--22400 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
22332 TCTTCAAGGG
22342 GGAGGGAATGATGCGCCCAAGG-CTTATCAT
1 GGAGGGAATGATGCG-CCAAGGACTTATCAT
22372 GGAGGGAATGATGCGCCAAGGACTTATCA
1 GGAGGGAATGATGCGCCAAGGACTTATCA
22401 AGGACATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.29, C:0.19, G:0.34, T:0.19
Consensus pattern (30 bp):
GGAGGGAATGATGCGCCAAGGACTTATCAT
Found at i:34666 original size:18 final size:18
Alignment explanation
Indices: 34643--34677 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34633 AAAAGGAATG
34643 GCGGC-ATCTGTCTTGTTA
1 GCGGCAATCT-TCTTGTTA
34661 GCGGCAATCTTCTTGTT
1 GCGGCAATCTTCTTGTT
34678 TTTTCCCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.11, C:0.23, G:0.26, T:0.40
Consensus pattern (18 bp):
GCGGCAATCTTCTTGTTA
Found at i:36283 original size:28 final size:27
Alignment explanation
Indices: 36258--36309 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
36248 AAATAAAAGG
36258 AATTTTTTTTATA-AAAACGCAAAAAAC
1 AATTTTTTTT-TAGAAAACGCAAAAAAC
36285 AATTTTTTTTTAGAAAACGCAAAAA
1 AATTTTTTTTTAGAAAACGCAAAAA
36310 CTCTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.35
Consensus pattern (27 bp):
AATTTTTTTTTAGAAAACGCAAAAAAC
Found at i:36317 original size:27 final size:26
Alignment explanation
Indices: 36259--36325 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 26
36249 AATAAAAGGA
36259 ATTTTTTTTATAAAAACGCAAAAAAC
1 ATTTTTTTTATAAAAACGCAAAAAAC
36285 AATTTTTTTT-TAGAAAACGC-AAAAAC
1 -ATTTTTTTTATA-AAAACGCAAAAAAC
* *
36311 -TCTTTTTTAAAAAAA
1 ATTTTTTTTATAAAAA
36326 ACGTAAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
24 11 0.31
25 1 0.03
26 8 0.22
27 16 0.44
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.37
Consensus pattern (26 bp):
ATTTTTTTTATAAAAACGCAAAAAAC
Found at i:39943 original size:19 final size:18
Alignment explanation
Indices: 39910--39945 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
39900 TTGAGATAAT
39910 TCTTCAATAATCTTCAAA
1 TCTTCAATAATCTTCAAA
*
39928 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
39946 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAA
Found at i:51179 original size:218 final size:210
Alignment explanation
Indices: 50727--51155 Score: 548
Period size: 218 Copynumber: 2.0 Consensus size: 210
50717 AGTAGTAGCA
* * * ***
50727 AAACTTG-TATAAATTATGTCCTGAACTCAATAAAAATTTTTTCCTTTCTCATCAATTTTTCCCT
1 AAACTTGTTA-AAATTCTGTCCTGAACTCAATAAAAATTATATCCTTTCTCATCAATTTCAACCT
* *
50791 TTCCTCTATTAACTCCTTTTCAACCATTGTTAACCCCTCCAAAAACCCAACAAATTGGTATCTAG
65 TTCCTCTATAAACTCCTTTTCAACCATTGTTAACCCCTCCAAAAACCCAACAAATTGGTAACTAG
50856 AGCTAACTTCTTAAGGGATCTGTTGTCAAAACCTTTGAAAACCTTCGAAACCAAACCTTGACAGA
130 AGCTAACTTCTTAAGGGATCTGTTG-----A---TTGAAAACCTTCGAAACCAAACCTTGACAGA
*
50921 AAGCCTGAAACTTTGAATCCTGTT
187 AAGCCTGAAACTTTGAATCCTATT
* *
50945 AAACTTGTTTAAATTCTGTCCTGAACTCAATGAAAAA-TATATCCTTTCTCATCAATTTCAACGT
1 AAACTTGTTAAAATTCTGTCCTGAACTCAAT-AAAAATTATATCCTTTCTCATCAATTTCAACCT
* *
51009 TTCCTCTGTAAACTCCCTTTTCAACCATTGTTAACCCCTCCAAAAACCCAAC-AATTGTTAACTA
65 TTCCTCTATAAACT-CCTTTTCAACCATTGTTAACCCCTCCAAAAACCCAACAAATTGGTAACTA
* * * *
51073 GAGCTGACTTCTTAAGGGA-CTTGTTG-TT-AAAACCTTTGAAACCAAGCCTTG-CAGAAAGCTT
129 GAGCTAACTTCTTAAGGGATC-TGTTGATTGAAAACCTTCGAAACCAAACCTTGACAGAAAGCCT
51134 GAAACTTTGAATCCTATT
193 GAAACTTTGAATCCTATT
51152 AAAC
1 AAAC
51156 CAATTTTCAA
Statistics
Matches: 190, Mismatches: 17, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
207 30 0.16
208 21 0.11
209 2 0.01
217 1 0.01
218 93 0.49
219 43 0.23
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.33
Consensus pattern (210 bp):
AAACTTGTTAAAATTCTGTCCTGAACTCAATAAAAATTATATCCTTTCTCATCAATTTCAACCTT
TCCTCTATAAACTCCTTTTCAACCATTGTTAACCCCTCCAAAAACCCAACAAATTGGTAACTAGA
GCTAACTTCTTAAGGGATCTGTTGATTGAAAACCTTCGAAACCAAACCTTGACAGAAAGCCTGAA
ACTTTGAATCCTATT
Found at i:52498 original size:17 final size:18
Alignment explanation
Indices: 52476--52510 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
52466 GCTTGTTAAG
52476 CCCTTTCAAAA-TTTCAA
1 CCCTTTCAAAACTTTCAA
*
52493 CCCTTTTAAAACTTTCAA
1 CCCTTTCAAAACTTTCAA
52511 TTTTTTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.37
Consensus pattern (18 bp):
CCCTTTCAAAACTTTCAA
Found at i:60612 original size:30 final size:31
Alignment explanation
Indices: 60574--60646 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
60564 TTTGATAGTA
60574 AAGGGATTTTTTTGCCCCAAAA-AAAAAGAT
1 AAGGGATTTTTTTGCCCCAAAATAAAAAGAT
** * * *
60604 CGGGGATTTATTTGTCCCAAAATAAAAAGGT
1 AAGGGATTTTTTTGCCCCAAAATAAAAAGAT
60635 AAGGGATTTTTT
1 AAGGGATTTTTT
60647 GGTATTTAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 18 0.53
31 16 0.47
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (31 bp):
AAGGGATTTTTTTGCCCCAAAATAAAAAGAT
Done.