Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021042.1 Corchorus olitorius cultivar O-4 contig21075, 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: 45164
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:3012 original size:28 final size:28
Alignment explanation
Indices: 2972--3030 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
2962 GCTCATAGAT
*
2972 TAGTATTTCAGTAATGTAGCTAATCATG
1 TAGTATTTCAGTAATGTAGCTAATAATG
*
3000 TAGTGTTTCAGTAATGTAGCTAATAATG
1 TAGTATTTCAGTAATGTAGCTAATAATG
3028 TAG
1 TAG
3031 CAGTGTACGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.39
Consensus pattern (28 bp):
TAGTATTTCAGTAATGTAGCTAATAATG
Found at i:3379 original size:3 final size:3
Alignment explanation
Indices: 3371--3434 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
3361 GTCTAGCCTT
3371 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3418 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
3435 CTCTTTTTGC
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4786 original size:16 final size:16
Alignment explanation
Indices: 4759--4800 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
4749 TTTGGTTGAG
4759 AGGAAA-GAAATAGGA
1 AGGAAAGGAAATAGGA
*
4774 AGGAAAGGAAATAGGG
1 AGGAAAGGAAATAGGA
*
4790 AGGAAGGGAAA
1 AGGAAAGGAAA
4801 GGTAGTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.55, C:0.00, G:0.40, T:0.05
Consensus pattern (16 bp):
AGGAAAGGAAATAGGA
Found at i:5473 original size:16 final size:15
Alignment explanation
Indices: 5452--5493 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
5442 AAGGGAAGCT
5452 TTTCTTTCCTTCCCC
1 TTTCTTTCCTTCCCC
*
5467 ATTTCTTTCC-GCCCC
1 -TTTCTTTCCTTCCCC
5482 TCTTCTTTCCTT
1 T-TTCTTTCCTT
5494 TCCATTTCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 1 0.05
15 12 0.55
16 9 0.41
ACGTcount: A:0.02, C:0.43, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTCTTTCCTTCCCC
Found at i:10685 original size:26 final size:26
Alignment explanation
Indices: 10652--10701 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
10642 GGCGCTCGAC
10652 CTCTGTCACCTCTTGAGGCCATAGCT
1 CTCTGTCACCTCTTGAGGCCATAGCT
10678 CTCTGTCACCTCTTGAGGCCATAG
1 CTCTGTCACCTCTTGAGGCCATAG
10702 GTTCATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.16, C:0.34, G:0.20, T:0.30
Consensus pattern (26 bp):
CTCTGTCACCTCTTGAGGCCATAGCT
Found at i:13975 original size:10 final size:10
Alignment explanation
Indices: 13957--13989 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
13947 AAACTCTTAA
13957 AAAAAAAAAC
1 AAAAAAAAAC
*
13967 AAAACAAAAC
1 AAAAAAAAAC
13977 AAAAAAAAAC
1 AAAAAAAAAC
13987 AAA
1 AAA
13990 GAAATGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:14683 original size:28 final size:28
Alignment explanation
Indices: 14628--14684 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
14618 GGTAGAGTAT
* * *
14628 TGGACTCTTAGTTCCAGTCTATCTAGAC
1 TGGACTCTTAGTTCCAGCCTACCCAGAC
14656 TGGACTCTTAGTTCCAGCCTACCCAGAC
1 TGGACTCTTAGTTCCAGCCTACCCAGAC
14684 T
1 T
14685 ATGAGGTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.32
Consensus pattern (28 bp):
TGGACTCTTAGTTCCAGCCTACCCAGAC
Found at i:15943 original size:21 final size:21
Alignment explanation
Indices: 15909--15948 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
15899 TTAATATTAA
*
15909 AAAAAATAAAATTTGAAAAAG
1 AAAAAAGAAAATTTGAAAAAG
* *
15930 AAAAAAGAATATTTTAAAA
1 AAAAAAGAAAATTTGAAAA
15949 GGTTTTTGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (21 bp):
AAAAAAGAAAATTTGAAAAAG
Found at i:17053 original size:24 final size:24
Alignment explanation
Indices: 16988--17053 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
16978 ATTCCTTTAA
*
16988 TTACATTTATATCCTT--TTTATAT
1 TTACATTTATAT-ATTGATTTATAT
*
17011 TTCACAATTTATATTTTGATTTATAT
1 TT-AC-ATTTATATATTGATTTATAT
17037 TTACATTTATATATTGA
1 TTACATTTATATATTGA
17054 ATAATTACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
23 2 0.05
24 16 0.43
25 10 0.27
26 9 0.24
ACGTcount: A:0.30, C:0.09, G:0.03, T:0.58
Consensus pattern (24 bp):
TTACATTTATATATTGATTTATAT
Found at i:17237 original size:13 final size:13
Alignment explanation
Indices: 17219--17262 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
17209 AAATATACTT
17219 AACTTAAAATTAC
1 AACTTAAAATTAC
17232 AACTT-AAA-TA-
1 AACTTAAAATTAC
*
17242 AAGTTAAAATTAC
1 AACTTAAAATTAC
17255 AACTTAAA
1 AACTTAAA
17263 TAAATTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 4 0.15
11 5 0.19
12 5 0.19
13 12 0.46
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (13 bp):
AACTTAAAATTAC
Found at i:17248 original size:23 final size:23
Alignment explanation
Indices: 17222--17273 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
17212 TATACTTAAC
17222 TTAAAATTACAACTTAAATAAAG
1 TTAAAATTACAACTTAAATAAAG
*
17245 TTAAAATTACAACTTAAATAAAT
1 TTAAAATTACAACTTAAATAAAG
17268 TTAAAA
1 TTAAAA
17274 AACAAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (23 bp):
TTAAAATTACAACTTAAATAAAG
Found at i:17284 original size:22 final size:23
Alignment explanation
Indices: 17222--17285 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
17212 TATACTTAAC
* **
17222 TTAAAATTACAACTTAAATAAAG
1 TTAAAATAACAAAATAAATAAAG
* ** *
17245 TTAAAATTACAACTTAAATAAAT
1 TTAAAATAACAAAATAAATAAAG
17268 TTAAAA-AACAAAATAAAT
1 TTAAAATAACAAAATAAAT
17286 TACACCATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 9 0.24
23 28 0.76
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.30
Consensus pattern (23 bp):
TTAAAATAACAAAATAAATAAAG
Found at i:18861 original size:136 final size:136
Alignment explanation
Indices: 18612--19376 Score: 1099
Period size: 136 Copynumber: 5.6 Consensus size: 136
18602 TAGACACAAT
* * * * * * *
18612 TGTGGAACAGATAAGGATTCAAA-CAACAGTCACATTTCAATCTCACTTTGAATCCAACGGTTGG
1 TGTGGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACTTTTAATCCAACGGTTGA
* * * * * * * * ** *
18676 ATTCAGATAATGTTAAATTATCATCAATTTATTGACTGTTGTGTTATTTTTTTTGACATATCTTG
66 ATTGAGATAAGGTTAGATTCTC-TAAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTG
18741 GATATTG
130 GATATTG
* *** * *
18748 TGTGGAAGAGATAA-GTTTTTCATCAACGGTCACATTTGAATC-CAACTTTT-ATCCAACGATTG
1 TGTGGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTC-ACTTTTAATCCAACGGTTG
* *
18810 GATTAAGATAAGGTTAGATTCTCTAAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTG
65 AATTGAGATAAGGTTAGATTCTCTAAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTG
18875 GATATTG
130 GATATTG
18882 TGTGGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACTTTTAATCCAACGGTTGA
1 TGTGGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACTTTTAATCCAACGGTTGA
* *
18947 ATTGAGATAAGGTTAGATTCTCTGAAATTATTGGCTATTGTGTTGGATTTTCTGACATATCTTGG
66 ATTGAGATAAGGTTAGATTCTCTAAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGG
19012 ATATTG
131 ATATTG
* * *
19018 TGTGGATGAGATAACGATTCAAATTGACGGTCACATTTGAATCTCACTTTTAATCCAACAGTTGA
1 TGTGGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACTTTTAATCCAACGGTTGA
** *
19083 ATTGAGATAAGGTTAGATTCTCTGGAATTATTGGCTATTGTGTTAGATTTTCTGAAATATCTTGG
66 ATTGAGATAAGGTTAGATTCTCTAAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGG
19148 ATATTG
131 ATATTG
19154 TGTGGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACTTTTAATCCAACGGTTGA
1 TGTGGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACTTTTAATCCAACGGTTGA
* *
19219 ATTGAGATAAGGTTAGATTCTTTAGAAATTATTGGCTATTGTGTTAGATTTTCTAACATATCTTG
66 ATTGAGATAAGGTTAGATTCTCTA-AAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTG
19284 GATATTG
130 GATATTG
* * *
19291 TGTGGAAAAGATAACGATTCAAATTAACAGTCATATTTGAATCTCACTTTTAATCCAACGGTT-A
1 TGTGGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACTTTTAATCCAACGGTTGA
*
19355 GATTGAGATAGGGTTAGATTCT
66 -ATTGAGATAAGGTTAGATTCT
19377 GTGAAGATAA
Statistics
Matches: 574, Mismatches: 48, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
134 56 0.10
135 64 0.11
136 330 0.57
137 124 0.22
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.38
Consensus pattern (136 bp):
TGTGGAAGAGATAACGATTCAAATTAACGGTCACATTTGAATCTCACTTTTAATCCAACGGTTGA
ATTGAGATAAGGTTAGATTCTCTAAAATTATTGGCTATTGTGTTAGATTTTCTGACATATCTTGG
ATATTG
Found at i:19001 original size:30 final size:30
Alignment explanation
Indices: 18962--19024 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
18952 GATAAGGTTA
*
18962 GATTCTCTGAAAT-TATTGGCTATTGTGTTG
1 GATTCTCTGAAATATATTGGATATTGTG-TG
* * *
18992 GATTTTCTGACATATCTTGGATATTGTGTG
1 GATTCTCTGAAATATATTGGATATTGTGTG
19022 GAT
1 GAT
19025 GAGATAACGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.21, C:0.10, G:0.24, T:0.46
Consensus pattern (30 bp):
GATTCTCTGAAATATATTGGATATTGTGTG
Found at i:19128 original size:30 final size:31
Alignment explanation
Indices: 19094--19156 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
19084 TTGAGATAAG
* *
19094 GTTAGATTCTCTGGAAT-TATTGGCTATTGT
1 GTTAGATTCTCTGAAATATATTGGATATTGT
* *
19124 GTTAGATTTTCTGAAATATCTTGGATATTGT
1 GTTAGATTCTCTGAAATATATTGGATATTGT
19155 GT
1 GT
19157 GGAAGAGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.48
Consensus pattern (31 bp):
GTTAGATTCTCTGAAATATATTGGATATTGT
Found at i:23171 original size:69 final size:69
Alignment explanation
Indices: 23054--23186 Score: 212
Period size: 69 Copynumber: 1.9 Consensus size: 69
23044 TCAAAGAATG
* *
23054 ATTAAGAAAATAATAGTAATTCTGTAAATTAGCTAAAACTCATAGATAAAATGGTAAAAACAATT
1 ATTAAGAAAATAATAGTAATTCTGTAAATAAGCTAAAACACATAGATAAAATGGTAAAAACAATT
23119 ATTA
66 ATTA
* * * *
23123 ATTAAGAAAGTAATTGTAATTCTGTAAATAAGCTAAAACACATGGATAAAATGGTGAAAACAAT
1 ATTAAGAAAATAATAGTAATTCTGTAAATAAGCTAAAACACATAGATAAAATGGTAAAAACAAT
23187 AATAGGAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.29
Consensus pattern (69 bp):
ATTAAGAAAATAATAGTAATTCTGTAAATAAGCTAAAACACATAGATAAAATGGTAAAAACAATT
ATTA
Found at i:23786 original size:23 final size:23
Alignment explanation
Indices: 23740--23786 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
23730 AATAACAAAC
23740 TTTAAAACTGAAAATAAACTTTT
1 TTTAAAACTGAAAATAAACTTTT
*
23763 TTTAAGAAGTGAAAATAAACTTTT
1 TTTAA-AACTGAAAATAAACTTTT
23787 GCCCAGCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (23 bp):
TTTAAAACTGAAAATAAACTTTT
Found at i:24673 original size:6 final size:6
Alignment explanation
Indices: 24662--24694 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
24652 TTGTTAATAG
24662 ATCCCA ATCCCA ATCCCA ATCCCA ATCCCA ATC
1 ATCCCA ATCCCA ATCCCA ATCCCA ATCCCA ATC
24695 TCATATATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.48, G:0.00, T:0.18
Consensus pattern (6 bp):
ATCCCA
Found at i:26892 original size:19 final size:19
Alignment explanation
Indices: 26868--26906 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
26858 CTAACAGTGT
26868 ATGGGATTCATGCACTATC
1 ATGGGATTCATGCACTATC
26887 ATGGGATTCATGCACTATC
1 ATGGGATTCATGCACTATC
26906 A
1 A
26907 GTGCATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (19 bp):
ATGGGATTCATGCACTATC
Found at i:29172 original size:2 final size:2
Alignment explanation
Indices: 29167--29192 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29157 GGAGTAGTTC
29167 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
29193 GTGTGGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30084 original size:22 final size:22
Alignment explanation
Indices: 30049--30130 Score: 64
Period size: 22 Copynumber: 3.9 Consensus size: 22
30039 AATCATAGGA
30049 AGGTTA-C-AAATTTCATAGTT
1 AGGTTATCAAAATTTCATAGTT
* *
30069 AGGTTATCAAAATTTCTTA-TGG
1 AGGTTATCAAAATTTCATAGT-T
* * * *
30091 AGTTTATCACAATTTTATAGGT
1 AGGTTATCAAAATTTCATAGTT
*
30113 A-ATTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
30131 TGGTGAGTAT
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
20 6 0.13
21 16 0.34
22 25 0.53
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGTT
Found at i:30142 original size:22 final size:22
Alignment explanation
Indices: 30072--30144 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 22
30062 CATAGTTAGG
* * *
30072 TTATCAAAATTTCTTATGGAGT
1 TTATCAAAATTTCATATGGTGA
* * *
30094 TTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTCATATGGTGA
30115 TTATCAAAATTTCATATGGTGA
1 TTATCAAAATTTCATATGGTGA
*
30137 GTATCAAA
1 TTATCAAA
30145 GGGTAGATAT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 16 0.40
22 24 0.60
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCATATGGTGA
Found at i:36213 original size:24 final size:24
Alignment explanation
Indices: 36185--36236 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
36175 CCTTTCAACA
*
36185 TTTTCAACTTCAACTTCAATAT-TC
1 TTTTCAACTGCAACTTCAAT-TGTC
* *
36209 TTTTCAGCTGCATCTTCAATTGTC
1 TTTTCAACTGCAACTTCAATTGTC
36233 TTTT
1 TTTT
36237 GAGCATCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.21, C:0.23, G:0.06, T:0.50
Consensus pattern (24 bp):
TTTTCAACTGCAACTTCAATTGTC
Done.