Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015858.1 Corchorus olitorius cultivar O-4 contig15891, 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: 60986
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2378 original size:12 final size:12
Alignment explanation
Indices: 2361--2385 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2351 TATAGTAAAC
2361 GGATATAAGTAT
1 GGATATAAGTAT
2373 GGATATAAGTAT
1 GGATATAAGTAT
2385 G
1 G
2386 AAAGAGAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (12 bp):
GGATATAAGTAT
Found at i:2599 original size:22 final size:22
Alignment explanation
Indices: 2556--2599 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2546 CTTCTTCTTT
* *
2556 CTCCCCCCACTAACTCTTTCTC
1 CTCCCCCCACTAACTATCTCTC
* *
2578 CTCCTCCCACTCACTATCTCTC
1 CTCCCCCCACTAACTATCTCTC
2600 TTCATAAATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.55, G:0.00, T:0.32
Consensus pattern (22 bp):
CTCCCCCCACTAACTATCTCTC
Found at i:3897 original size:55 final size:55
Alignment explanation
Indices: 3779--3985 Score: 234
Period size: 57 Copynumber: 3.7 Consensus size: 55
3769 TGGGGGTTGC
* * * * * * *
3779 CTATTAAAATTTGGGGTTTGATCATACATATACAATAAAATGCTTTTTGTGGTTTGA
1 CTATCAAACTTTGGGGTTTGACCATGCATGTACAATGATAT--TTTTTGTGGTTTGA
* * *
3836 TTATCAAACTTTGGGGTTTGACCATCCATGTACAATGATATTTTTTGTGGTTTAA
1 CTATCAAACTTTGGGGTTTGACCATGCATGTACAATGATATTTTTTGTGGTTTGA
* * *
3891 CTATCAAACTTTGGGGTTTGACCATGCATGTACATTGTTTTTTTTTTGTGGTTTTGA
1 CTATCAAACTTTGGGGTTTGACCATGCATGTACAATG-ATATTTTTTGTGG-TTTGA
* * *
3948 CTATTAAACTTTGGAGTTTCACCATGCATGTACAATGA
1 CTATCAAACTTTGGGGTTTGACCATGCATGTACAATGA
3986 AATGCTTTTC
Statistics
Matches: 128, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
55 47 0.37
56 11 0.09
57 70 0.55
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (55 bp):
CTATCAAACTTTGGGGTTTGACCATGCATGTACAATGATATTTTTTGTGGTTTGA
Found at i:4089 original size:21 final size:21
Alignment explanation
Indices: 4042--4090 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
4032 GGTTTAACGT
* *
4042 GATTTGGCTATCAAACTTCGG
1 GATTTGACTATCAAAATTCGG
* * *
4063 GGTTTGACTATTAAAATTTGG
1 GATTTGACTATCAAAATTCGG
4084 GATTTGA
1 GATTTGA
4091 TCATGCATAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39
Consensus pattern (21 bp):
GATTTGACTATCAAAATTCGG
Found at i:4188 original size:55 final size:56
Alignment explanation
Indices: 4063--4211 Score: 174
Period size: 57 Copynumber: 2.6 Consensus size: 56
4053 CAAACTTCGG
* * *
4063 GGTTTGACTATTAAAATTTGGGATTTGATCATGCATATACAATGAAATGCTTTTTGT
1 GGTTTGACTATCAAACTTTGGG-TTTGACCATGCATATACAATGAAATGCTTTTTGT
* * * **
4120 GGTTTGATTATCAAACTTTGGGTTTGACCGTGCATATACAATG-ATTTTTTTTTGT
1 GGTTTGACTATCAAACTTTGGGTTTGACCATGCATATACAATGAAATGCTTTTTGT
* *
4175 GTTTTGACTATCAAACTTTAGCGTTTTGACCATGCAT
1 GGTTTGACTATCAAACTTT-G-GGTTTGACCATGCAT
4212 GTACCATCGG
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
55 26 0.33
56 20 0.26
57 32 0.41
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.44
Consensus pattern (56 bp):
GGTTTGACTATCAAACTTTGGGTTTGACCATGCATATACAATGAAATGCTTTTTGT
Found at i:5484 original size:57 final size:55
Alignment explanation
Indices: 5396--5509 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 55
5386 TATCAGTTTC
*
5396 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCCCTATCTCTGCTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTAT--CCCCTATCTCTACTTAATTATT
* * *
5453 CTTTCACATAATAAATGTTATAATAAATCCTATCCCTTATCTCTACTTAGTTATT
1 CTTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATT
5508 CT
1 CT
5510 ACAAAATAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
55 21 0.40
57 32 0.60
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.41
Consensus pattern (55 bp):
CTTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATT
Found at i:5623 original size:42 final size:42
Alignment explanation
Indices: 5575--5655 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
5565 TAAGAATTAG
5575 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
5617 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
5656 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:8985 original size:19 final size:18
Alignment explanation
Indices: 8944--8985 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
8934 TTAGGGTTCT
* *
8944 TAATTTGTGCAATTGAGC
1 TAATTTGTGCAATTAACC
8962 TAATTTGTGCAATTAACCC
1 TAATTTGTGCAATTAA-CC
8981 TAATT
1 TAATT
8986 GGAGTTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (18 bp):
TAATTTGTGCAATTAACC
Found at i:9150 original size:9 final size:9
Alignment explanation
Indices: 9136--9171 Score: 72
Period size: 9 Copynumber: 4.0 Consensus size: 9
9126 GTTCTTGATT
9136 GTTGAATTG
1 GTTGAATTG
9145 GTTGAATTG
1 GTTGAATTG
9154 GTTGAATTG
1 GTTGAATTG
9163 GTTGAATTG
1 GTTGAATTG
9172 TGTTTTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (9 bp):
GTTGAATTG
Found at i:18323 original size:36 final size:36
Alignment explanation
Indices: 18276--18348 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
18266 ACAAATATGG
18276 AGAGTTAGTATATGAAACCACTTTCTCAACCATCAA
1 AGAGTTAGTATATGAAACCACTTTCTCAACCATCAA
18312 AGAGTTAGTATATGAAACCACTTTCTCAACCATCAA
1 AGAGTTAGTATATGAAACCACTTTCTCAACCATCAA
18348 A
1 A
18349 TGCCCCAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (36 bp):
AGAGTTAGTATATGAAACCACTTTCTCAACCATCAA
Found at i:27025 original size:30 final size:31
Alignment explanation
Indices: 26982--27092 Score: 95
Period size: 30 Copynumber: 3.7 Consensus size: 31
26972 TTATTCTTCC
* * *
26982 ATTGTTGCGATTTGAGGC-TGA-AGTTATTTG
1 ATTGATGCAATTTGAGGCTTGATA-TTACTTG
*
27012 ATTGCTGCAATTTG-GGCTTGATATTACTTG
1 ATTGATGCAATTTGAGGCTTGATATTACTTG
* * * * *
27042 ATTGATGCAATTTGAGACTGGTTA-TGCTTA
1 ATTGATGCAATTTGAGGCTTGATATTACTTG
*
27072 ATTTATGCAATTTGAGGCTTG
1 ATTGATGCAATTTGAGGCTTG
27093 TTTGGGTGTG
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
29 3 0.05
30 56 0.85
31 7 0.11
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (31 bp):
ATTGATGCAATTTGAGGCTTGATATTACTTG
Found at i:31734 original size:13 final size:14
Alignment explanation
Indices: 31716--31744 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
31706 ATAATTGAAC
31716 TTTGCATTCAT-CA
1 TTTGCATTCATGCA
31729 TTTGCATTCATGCA
1 TTTGCATTCATGCA
31743 TT
1 TT
31745 AATCTAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTGCATTCATGCA
Found at i:36100 original size:111 final size:111
Alignment explanation
Indices: 35901--36113 Score: 365
Period size: 111 Copynumber: 1.9 Consensus size: 111
35891 TCATTCAACA
*
35901 AAGCGAATTTCTGGCCTTATTGAGAAACTTATTTCAAGCTAACCAACCAGTCTAAATATCCACCC
1 AAGCCAATTTCTGGCCTTATTGAGAAACTTATTTCAAGCTAACCAACCAGTCTAAATATCCACCC
35966 TTCGCCAGCCATGTCATCAGCATTGTTTCCTTCTCTTTGAAGAACG
66 TTCGCCAGCCATGTCATCAGCATTGTTTCCTTCTCTTTGAAGAACG
* * * *
36012 AAGCCAATTTTTGGCGC-TATTGATAAACTTATTTCAAGCTAACCAAGCAGTTTAAATATCCACC
1 AAGCCAATTTCTGGC-CTTATTGAGAAACTTATTTCAAGCTAACCAACCAGTCTAAATATCCACC
36076 CTTCGCCAGCCATGTCATCAGCATTGTTTCCTTCTCTT
65 CTTCGCCAGCCATGTCATCAGCATTGTTTCCTTCTCTT
36114 CGAATAACTT
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
111 95 0.99
112 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (111 bp):
AAGCCAATTTCTGGCCTTATTGAGAAACTTATTTCAAGCTAACCAACCAGTCTAAATATCCACCC
TTCGCCAGCCATGTCATCAGCATTGTTTCCTTCTCTTTGAAGAACG
Found at i:36789 original size:33 final size:34
Alignment explanation
Indices: 36722--36791 Score: 115
Period size: 35 Copynumber: 2.1 Consensus size: 34
36712 CTTGCTGAGC
*
36722 GTATTATTGCACCTGATATGTATATATTTAATGGT
1 GTATTATTGCACCTGATA-GTATACATTTAATGGT
36757 GTATTATTGCACCTGATA-TATACATTTAATGGT
1 GTATTATTGCACCTGATAGTATACATTTAATGGT
36790 GT
1 GT
36792 GCTAGATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 16 0.47
35 18 0.53
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (34 bp):
GTATTATTGCACCTGATAGTATACATTTAATGGT
Found at i:37354 original size:37 final size:37
Alignment explanation
Indices: 37313--37426 Score: 219
Period size: 37 Copynumber: 3.1 Consensus size: 37
37303 AATCAGTCCC
*
37313 AAAACAAATCAAAATTCAAAATACCCTTATCTAAATT
1 AAAACAAATCAAAATTCAAAGTACCCTTATCTAAATT
37350 AAAACAAATCAAAATTCAAAGTACCCTTATCTAAATT
1 AAAACAAATCAAAATTCAAAGTACCCTTATCTAAATT
37387 AAAACAAATCAAAATTCAAAGTACCCTTATCTAAATT
1 AAAACAAATCAAAATTCAAAGTACCCTTATCTAAATT
37424 AAA
1 AAA
37427 CGTAAAACTA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 76 1.00
ACGTcount: A:0.54, C:0.18, G:0.02, T:0.26
Consensus pattern (37 bp):
AAAACAAATCAAAATTCAAAGTACCCTTATCTAAATT
Found at i:38095 original size:106 final size:106
Alignment explanation
Indices: 37910--38121 Score: 388
Period size: 106 Copynumber: 2.0 Consensus size: 106
37900 CCTACACGTG
*
37910 AATAATCGAGACTGGGCAAATTAGGGACAGATGGACTGTCGTCAGCAAATCACAAAAATAATCCC
1 AATAATCGAGACTGGACAAATTAGGGACAGATGGACTGTCGTCAGCAAATCACAAAAATAATCCC
*
37975 CACAAATCCTTGCTAAGTAGATACGGTAAGTAGGGGTCGTA
66 CACAAATCCTTGCTAAGTAGATACGGTAAGTAAGGGTCGTA
* *
38016 AATAATCGAGACTGGACAAATTAGGGACATATGGCCTGTCGTCAGCAAATCACAAAAATAATCCC
1 AATAATCGAGACTGGACAAATTAGGGACAGATGGACTGTCGTCAGCAAATCACAAAAATAATCCC
38081 CACAAATCCTTGCTAAGTAGATACGGTAAGTAAGGGTCGTA
66 CACAAATCCTTGCTAAGTAGATACGGTAAGTAAGGGTCGTA
38122 TCCAATAGAG
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (106 bp):
AATAATCGAGACTGGACAAATTAGGGACAGATGGACTGTCGTCAGCAAATCACAAAAATAATCCC
CACAAATCCTTGCTAAGTAGATACGGTAAGTAAGGGTCGTA
Found at i:40618 original size:31 final size:31
Alignment explanation
Indices: 40583--40645 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
40573 AAGAAACTTG
* *
40583 ATGATCTTGGTTTCAAAGTTGAGTTTGATTC
1 ATGATCATGATTTCAAAGTTGAGTTTGATTC
40614 ATGATCATGATTTCAAAGTTGAGTTTGATTC
1 ATGATCATGATTTCAAAGTTGAGTTTGATTC
40645 A
1 A
40646 CAAAAAGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.43
Consensus pattern (31 bp):
ATGATCATGATTTCAAAGTTGAGTTTGATTC
Found at i:40887 original size:27 final size:27
Alignment explanation
Indices: 40857--40964 Score: 171
Period size: 27 Copynumber: 4.0 Consensus size: 27
40847 TTGGCATTAG
*
40857 GCACATTCAGGGGCATTTTGGTCATTT
1 GCACATCCAGGGGCATTTTGGTCATTT
* *
40884 GCACATTCAGGGGCATTTTGGTCGTTT
1 GCACATCCAGGGGCATTTTGGTCATTT
*
40911 GCACATCCAAGGGCATTTTGGTCATTT
1 GCACATCCAGGGGCATTTTGGTCATTT
*
40938 GCACGTCCAGGGGCATTTTGGTCATTT
1 GCACATCCAGGGGCATTTTGGTCATTT
40965 CAAGTTCACT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (27 bp):
GCACATCCAGGGGCATTTTGGTCATTT
Found at i:45987 original size:21 final size:21
Alignment explanation
Indices: 45958--46006 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
45948 GGCTTGGAAT
* **
45958 GGTGATGGCACGGGCTTGGCC
1 GGTGGTGGCACGGGCTTAACC
45979 GGTGGTGGCACGGGCTTAACC
1 GGTGGTGGCACGGGCTTAACC
46000 GGTGGTG
1 GGTGGTG
46007 TGGCAATCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.10, C:0.20, G:0.49, T:0.20
Consensus pattern (21 bp):
GGTGGTGGCACGGGCTTAACC
Found at i:51419 original size:113 final size:113
Alignment explanation
Indices: 51221--51442 Score: 417
Period size: 113 Copynumber: 2.0 Consensus size: 113
51211 TTAAAGGGTT
* *
51221 TTGACACAGCATTTTCAAAATTTCTTCCCGGTGCGGAAGAGTCAACAAGAGAACAAACAGTAAAA
1 TTGACACAGAATTTTCAAAATTTCTTCCCAGTGCGGAAGAGTCAACAAGAGAACAAACAGTAAAA
*
51286 GAGAATCGAGACAGAATTGATCGACGGTGTTCGGTCATATTCTTTTGA
66 GAGAATCGAGACAGAATTGATCGACGGTATTCGGTCATATTCTTTTGA
51334 TTGACACAGAATTTTCAAAATTTCTTCCCAGTGCGGAAGAGTCAACAAGAGAACAAACAGTAAAA
1 TTGACACAGAATTTTCAAAATTTCTTCCCAGTGCGGAAGAGTCAACAAGAGAACAAACAGTAAAA
51399 GAGAATCGAGACAGAATTGATCGACGGTATTCGGTCATATTCTT
66 GAGAATCGAGACAGAATTGATCGACGGTATTCGGTCATATTCTT
51443 CGAATTCCCG
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 106 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (113 bp):
TTGACACAGAATTTTCAAAATTTCTTCCCAGTGCGGAAGAGTCAACAAGAGAACAAACAGTAAAA
GAGAATCGAGACAGAATTGATCGACGGTATTCGGTCATATTCTTTTGA
Done.