Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014415.1 Corchorus olitorius cultivar O-4 contig14448, 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: 35967
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:2407 original size:32 final size:32
Alignment explanation
Indices: 2351--2424 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
2341 TTGCTGGAAA
*
2351 ATAGCGGCGTCTACTGAAGAAAACGTCC-CTAT
1 ATAGCGGCGTCTACTGAAGAAAACG-CCGCTAC
* *
2383 TTAGCGGCGTCTATTGAA-AGAAACGCCGCTAC
1 ATAGCGGCGTCTACTGAAGA-AAACGCCGCTAC
2415 ATAGCGGCGT
1 ATAGCGGCGT
2425 TCACTAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 3 0.08
32 33 0.92
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (32 bp):
ATAGCGGCGTCTACTGAAGAAAACGCCGCTAC
Found at i:2657 original size:33 final size:33
Alignment explanation
Indices: 2620--2691 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
2610 AGGTGTAAAG
2620 CGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGA
1 CGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGA
2653 CGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGA
1 CGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGA
2686 CGCCGC
1 CGCCGC
2692 CATGTATAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (33 bp):
CGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGA
Found at i:2826 original size:109 final size:109
Alignment explanation
Indices: 2650--2874 Score: 450
Period size: 109 Copynumber: 2.1 Consensus size: 109
2640 TTCAGAGCTC
2650 AGACGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGACGCCGCCATGTATAGTAAAATTGAGGAAA
1 AGACGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGACGCCGCCATGTATAGTAAAATTGAGGAAA
2715 CTTCCTGGGTCAATTTCACTATATATGGCGGCGTCTGAGCTGTG
66 CTTCCTGGGTCAATTTCACTATATATGGCGGCGTCTGAGCTGTG
2759 AGACGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGACGCCGCCATGTATAGTAAAATTGAGGAAA
1 AGACGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGACGCCGCCATGTATAGTAAAATTGAGGAAA
2824 CTTCCTGGGTCAATTTCACTATATATGGCGGCGTCTGAGCTGTG
66 CTTCCTGGGTCAATTTCACTATATATGGCGGCGTCTGAGCTGTG
2868 AGACGCC
1 AGACGCC
2875 ACTAAAATAG
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 116 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.28
Consensus pattern (109 bp):
AGACGCCGCTATTTTAGTGGCGTTTCAGAGCTCAGACGCCGCCATGTATAGTAAAATTGAGGAAA
CTTCCTGGGTCAATTTCACTATATATGGCGGCGTCTGAGCTGTG
Found at i:9110 original size:29 final size:27
Alignment explanation
Indices: 9007--9106 Score: 69
Period size: 29 Copynumber: 3.5 Consensus size: 27
8997 TCCATTTTTA
9007 CTTTCATTCTCTTCCTCT-TCCCTCTTCT
1 CTTTC-TTCTCTTCCTCTGTCCC-CTTCT
* *
9035 CTTTCTCTCTGCTTCCTTTGAT-CCTTTCT
1 CTTTCT-TCT-CTTCCTCTG-TCCCCTTCT
* * *
9064 ACCTTCTTCTCTCCTCTCTGTCCCGTTCT
1 -CTTTCTTCTCTTC-CTCTGTCCCCTTCT
9093 CTTTCTTCTGCTTC
1 CTTTCTTCT-CTTC
9107 TCTCCTTCAT
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
27 1 0.02
28 20 0.36
29 27 0.48
30 7 0.12
31 1 0.02
ACGTcount: A:0.03, C:0.40, G:0.05, T:0.52
Consensus pattern (27 bp):
CTTTCTTCTCTTCCTCTGTCCCCTTCT
Found at i:9382 original size:16 final size:17
Alignment explanation
Indices: 9363--9418 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
9353 TATTGTTTTT
9363 TATAATATTA-TATTAG
1 TATAATATTATTATTAG
*
9379 TATATTATTATTATTA-
1 TATAATATTATTATTAG
*
9395 T-TATTATTATTATTA-
1 TATAATATTATTATTAG
*
9410 TATATTATT
1 TATAATATT
9419 TTTTATATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
15 15 0.41
16 17 0.46
17 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TATAATATTATTATTAG
Found at i:9387 original size:31 final size:29
Alignment explanation
Indices: 9353--9424 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
9343 TTTTTCTTCT
* *
9353 TATTGTTTTTTA-TAATATTA-TATTAGTA
1 TATTATTTTTTATTATTATTATTATTA-TA
9381 TATTATTATTATTATTATTATTATTATTATA
1 TATTATT-TT-TTATTATTATTATTATTATA
9412 TATTATTTTTTAT
1 TATTATTTTTTAT
9425 ATTTACAGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 6 0.16
29 6 0.16
30 5 0.13
31 16 0.42
32 5 0.13
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (29 bp):
TATTATTTTTTATTATTATTATTATTATA
Found at i:9389 original size:3 final size:3
Alignment explanation
Indices: 9368--9418 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
9358 TTTTTTATAA
*
9368 TAT TA- TAT TAG TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
9415 TAT T
1 TAT T
9419 TTTTATATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:9425 original size:12 final size:13
Alignment explanation
Indices: 9370--9427 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 13
9360 TTTTATAATA
* *
9370 TTATATTAGTATA
1 TTATATTATTATT
9383 TTATTATTATTATT
1 TTA-TATTATTATT
*
9397 AT-TATTATTATT
1 TTATATTATTATT
*
9409 ATATATTATT-TT
1 TTATATTATTATT
9421 TTATATT
1 TTATATT
9428 TACAGGTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
12 20 0.51
13 10 0.26
14 9 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (13 bp):
TTATATTATTATT
Found at i:11342 original size:26 final size:27
Alignment explanation
Indices: 11306--11366 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
11296 TCTAACAGCA
*
11306 ATTTTTTTTA-GAAAATAATCATTTTC
1 ATTTCTTTTAGGAAAATAATCATTTTC
**
11332 ATTTCTTTTAGTGGTAATAATCATTTTC
1 ATTTCTTTTAG-GAAAATAATCATTTTC
*
11360 ATCTCTT
1 ATTTCTT
11367 CGTTCAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 9 0.31
28 20 0.69
ACGTcount: A:0.28, C:0.11, G:0.07, T:0.54
Consensus pattern (27 bp):
ATTTCTTTTAGGAAAATAATCATTTTC
Found at i:11637 original size:137 final size:137
Alignment explanation
Indices: 11474--11755 Score: 530
Period size: 137 Copynumber: 2.1 Consensus size: 137
11464 CCCTTCCCCA
11474 ACAAAC-AAACCCAATGAAATCTCATTACAATTCAAATAAATCTTTATGACCAAATATCTAAATG
1 ACAAACAAAACCCAATGAAATCTCATTACAATTCAAATAAATCTTTATGACCAAATATCTAAATG
11538 AGAATTCAACCCAAAATAGAAACTATACCGTAAATAAACTACCTACTTACCAAATACACAAACAA
66 AGAATTCAACCCAAAATAGAAACTATACCGTAAATAAACTACCTACTTACCAAATACACAAACAA
*
11603 ATAAATT
131 ACAAATT
*
11610 ACAAACAAAACCCAATGAAATCTCATTACAATTCAAATAAATCTTTATGCCCAAATATCTAAATG
1 ACAAACAAAACCCAATGAAATCTCATTACAATTCAAATAAATCTTTATGACCAAATATCTAAATG
*
11675 AGAATTCAACCCAAAATAGAAATTATACCGTAAATAAACTACCTACTTACCAAATACACAAACAA
66 AGAATTCAACCCAAAATAGAAACTATACCGTAAATAAACTACCTACTTACCAAATACACAAACAA
11740 ACAAATT
131 ACAAATT
11747 ACAAACAAA
1 ACAAACAAA
11756 CTTACATTCG
Statistics
Matches: 142, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
136 6 0.04
137 136 0.96
ACGTcount: A:0.51, C:0.22, G:0.04, T:0.23
Consensus pattern (137 bp):
ACAAACAAAACCCAATGAAATCTCATTACAATTCAAATAAATCTTTATGACCAAATATCTAAATG
AGAATTCAACCCAAAATAGAAACTATACCGTAAATAAACTACCTACTTACCAAATACACAAACAA
ACAAATT
Found at i:18066 original size:16 final size:15
Alignment explanation
Indices: 18047--18133 Score: 93
Period size: 16 Copynumber: 5.5 Consensus size: 15
18037 AGAGCTTGGG
18047 CGGGTTCGGGCTTTTT
1 CGGGTTCGGG-TTTTT
*
18063 CGGGTTCGGGTTCTGT
1 CGGGTTCGGGTT-TTT
*
18079 CGGGTTTGGGTTTTT
1 CGGGTTCGGGTTTTT
* * *
18094 TGGGCTCGGGTTATAT
1 CGGGTTCGGGTT-TTT
18110 CGGGTTCGGGTATTTT
1 CGGGTTCGGGT-TTTT
18126 CGGGTTCG
1 CGGGTTCG
18134 AGCTCGGGTA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
15 13 0.22
16 44 0.76
17 1 0.02
ACGTcount: A:0.03, C:0.15, G:0.40, T:0.41
Consensus pattern (15 bp):
CGGGTTCGGGTTTTT
Found at i:18103 original size:31 final size:31
Alignment explanation
Indices: 18047--18125 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
18037 AGAGCTTGGG
* * * *
18047 CGGGTTCGGGCTTTTTCGGGTTCGGGTTCTGT
1 CGGGTTCGGG-TTTTTTGGGCTCGGGTTATAT
*
18079 CGGGTTTGGGTTTTTTGGGCTCGGGTTATAT
1 CGGGTTCGGGTTTTTTGGGCTCGGGTTATAT
*
18110 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTTTTTT
18126 CGGGTTCGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 31 0.77
32 9 0.22
ACGTcount: A:0.04, C:0.14, G:0.39, T:0.43
Consensus pattern (31 bp):
CGGGTTCGGGTTTTTTGGGCTCGGGTTATAT
Found at i:21173 original size:32 final size:32
Alignment explanation
Indices: 21128--21199 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
21118 GTATATTAAT
*
21128 ATGGCGGCGTCTTTCTATCAAAACGCCACTAA
1 ATGGCGGCATCTTTCTATCAAAACGCCACTAA
21160 ATGGCGGCATCTTTCTATCAAAACGCCACTAA
1 ATGGCGGCATCTTTCTATCAAAACGCCACTAA
21192 ATGGCGGC
1 ATGGCGGC
21200 GTCTACATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (32 bp):
ATGGCGGCATCTTTCTATCAAAACGCCACTAA
Found at i:28069 original size:17 final size:17
Alignment explanation
Indices: 28047--28080 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28037 ATTGATTTCT
28047 TTACCCAAAATCTACAG
1 TTACCCAAAATCTACAG
28064 TTACCCAAAATCTACAG
1 TTACCCAAAATCTACAG
28081 GATTGGCTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.29, G:0.06, T:0.24
Consensus pattern (17 bp):
TTACCCAAAATCTACAG
Found at i:29371 original size:83 final size:84
Alignment explanation
Indices: 29214--29371 Score: 221
Period size: 83 Copynumber: 1.9 Consensus size: 84
29204 GGTTTCATGT
* * * *
29214 AATAAATAATAAAGTTGAATAATAATGAGAATATTTTCTAGATCTTGGCAAATTGTGGAAGGTTT
1 AATAAATAATAAAGAT-AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTT
*
29279 AGGAGATATTTTAAGAAATA
65 AGGAAATATTTTAAGAAATA
* *
29299 AATAAATTATAAAGAT-ATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTT-
1 AATAAATAATAAAGATAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTA
29362 GGAAAATATT
66 GG-AAATATT
29372 AGATAAAATA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
82 2 0.03
83 49 0.75
85 14 0.22
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (84 bp):
AATAAATAATAAAGATAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTA
GGAAATATTTTAAGAAATA
Found at i:34123 original size:31 final size:30
Alignment explanation
Indices: 34083--34145 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
34073 AAGGCAAGGT
* *
34083 CACTGCACACCAACCCTTGCACACTGCACA
1 CACTGCACACCAACCCTTACAAACTGCACA
34113 CACTGTCACACCAACCCTTACAAACTGCACA
1 CACTG-CACACCAACCCTTACAAACTGCACA
34144 CA
1 CA
34146 ACAAACAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.33, C:0.44, G:0.08, T:0.14
Consensus pattern (30 bp):
CACTGCACACCAACCCTTACAAACTGCACA
Done.