Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023065.1 Corchorus olitorius cultivar O-4 contig23098, 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: 76090
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3384 original size:12 final size:12
Alignment explanation
Indices: 3369--3393 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3359 ATACATTAAT
3369 AAATAATAATAA
1 AAATAATAATAA
3381 AAATAATAATAA
1 AAATAATAATAA
3393 A
1 A
3394 TATTACAACT
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAATAATAA
Found at i:3895 original size:31 final size:31
Alignment explanation
Indices: 3857--3922 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
3847 TTGAATCCAT
3857 GTCAATCAACCAAGGGAAGTTTCGGAATAAA
1 GTCAATCAACCAAGGGAAGTTTCGGAATAAA
3888 GTCAATCAACCAAGGGAAGTTTCGGAATAAA
1 GTCAATCAACCAAGGGAAGTTTCGGAATAAA
3919 GTCA
1 GTCA
3923 TTGATTCTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.20
Consensus pattern (31 bp):
GTCAATCAACCAAGGGAAGTTTCGGAATAAA
Found at i:6001 original size:30 final size:31
Alignment explanation
Indices: 5962--6022 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
5952 CAATTCTTCC
*
5962 TCTTGAAATAAATCTTCAAAG-GTCTTCAAA
1 TCTTCAAATAAATCTTCAAAGAGTCTTCAAA
* *
5992 TCTTCAAATAAGTCTTCAATGAGTCTTCAAA
1 TCTTCAAATAAATCTTCAAAGAGTCTTCAAA
6023 CACGAACTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (31 bp):
TCTTCAAATAAATCTTCAAAGAGTCTTCAAA
Found at i:6607 original size:30 final size:30
Alignment explanation
Indices: 6550--6608 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
6540 TCGCCCTCTA
* **
6550 AGGGCGGCATGGCCATGGTTACACCGCCCT
1 AGGGCGGCATGACCATGGCCACACCGCCCT
*
6580 AGGGCGGCATGACCATGGCCACGCCGCCC
1 AGGGCGGCATGACCATGGCCACACCGCCC
6609 ACCGAGGGCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.17, C:0.37, G:0.34, T:0.12
Consensus pattern (30 bp):
AGGGCGGCATGACCATGGCCACACCGCCCT
Found at i:6622 original size:33 final size:33
Alignment explanation
Indices: 6580--6654 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
6570 ACACCGCCCT
* *
6580 AGGGCGGCATGACCATGGCCACGCCGCCCACCG
1 AGGGCGGCATCACCATGGCCACGCCACCCACCG
* *
6613 AGGGCGGCATCCCCATGGCCATGCCACCCACCG
1 AGGGCGGCATCACCATGGCCACGCCACCCACCG
6646 AGGGCGGCA
1 AGGGCGGCA
6655 CCGACCATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.19, C:0.41, G:0.33, T:0.07
Consensus pattern (33 bp):
AGGGCGGCATCACCATGGCCACGCCACCCACCG
Found at i:17197 original size:31 final size:31
Alignment explanation
Indices: 17155--17230 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
17145 CGTTTCTATT
* *
17155 TTTAGACTCAAATTG-GTCAATTTTTTAAAGG
1 TTTAGACTCAAATTGAG-CAACTTTTGAAAGG
*
17186 TTTAGATTCAAATTGAGCAACTTTTGAAAGG
1 TTTAGACTCAAATTGAGCAACTTTTGAAAGG
* *
17217 TTTTGACTCGAATT
1 TTTAGACTCAAATT
17231 AGTGGCTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 37 0.97
32 1 0.03
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.41
Consensus pattern (31 bp):
TTTAGACTCAAATTGAGCAACTTTTGAAAGG
Found at i:20935 original size:22 final size:23
Alignment explanation
Indices: 20895--20937 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
20885 GATTTTGATT
* *
20895 TTTTGGGATGAATTTCTTTTGGG
1 TTTTGGGATAAATTACTTTTGGG
20918 TTTTGGGA-AAATTACTTTTG
1 TTTTGGGATAAATTACTTTTG
20938 TCATGTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.19, C:0.05, G:0.26, T:0.51
Consensus pattern (23 bp):
TTTTGGGATAAATTACTTTTGGG
Found at i:20994 original size:14 final size:14
Alignment explanation
Indices: 20953--20995 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
20943 TTGTTCGAAA
*
20953 TTATAAAAATTATC
1 TTATAAAAATTATT
*
20967 TTATAGAAATTATT
1 TTATAAAAATTATT
20981 TTATAAAAATTATT
1 TTATAAAAATTATT
20995 T
1 T
20996 GGCAAAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (14 bp):
TTATAAAAATTATT
Found at i:28362 original size:14 final size:15
Alignment explanation
Indices: 28345--28376 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28335 TATAGAATAT
28345 AAAA-TATTACCATG
1 AAAAGTATTACCATG
28359 AAAAGTATTACCATG
1 AAAAGTATTACCATG
28374 AAA
1 AAA
28377 TCATGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.25
Consensus pattern (15 bp):
AAAAGTATTACCATG
Found at i:42666 original size:46 final size:46
Alignment explanation
Indices: 42594--42697 Score: 181
Period size: 46 Copynumber: 2.2 Consensus size: 46
42584 TCTAAGGGTG
*
42594 ATCTGGATTACCACCATAAACCCATGTAATATTTGAATCACCGGTA
1 ATCTAGATTACCACCATAAACCCATGTAATATTTGAATCACCGGTA
42640 ATCTAGATTACCACCATAAACCCATGTAATATTTGAATCACCGGTA
1 ATCTAGATTACCACCATAAACCCATGTAATATTTGAATCACCGGTA
*
42686 ATTTTAGATTAC
1 A-TCTAGATTAC
42698 TAGTGATTTG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
46 46 0.84
47 9 0.16
ACGTcount: A:0.36, C:0.22, G:0.12, T:0.31
Consensus pattern (46 bp):
ATCTAGATTACCACCATAAACCCATGTAATATTTGAATCACCGGTA
Found at i:66641 original size:252 final size:252
Alignment explanation
Indices: 66181--66679 Score: 786
Period size: 252 Copynumber: 2.0 Consensus size: 252
66171 TATTTTGTTA
* * * *
66181 TGTAACTTTTTATATGGCTAAAGTCTGCTGCTCCATTGAGATAGAGCCTATAACTTTGAACCAAG
1 TGTAACTTTTTATATGGCTAAAGACTGCTGCTCCATTGAGATAGAACCTAGAACTTTGAACAAAG
* * * *
66246 GCAAACTCAACCATGCTAGGGTCATGGGTACACAGGTCACAGTTGTGCAAACATCACAACAAATG
66 GCAAACTCAACCATGCTAGGGTCATGGGTACACAAGTCACACTTATGAAAACATCACAACAAAT-
*** * * **
66311 AGAAAGCTCGCTCGCGGATGAATGTGGCAGCTTGGACTTCCGGGCTCAACGTGAAGAAGACGGGA
130 AGAAAGCTCGCTCGCGGATGAATGCAACAGCTTAGACTTCCGGGCTCAACGCGAAGAAGACAAGA
66376 TCTCTCTTCTTCAGCTTATCCAGTTCATCTTTTGCCGCAAGGTTGTGGTTCCAGATTC
195 TCTCTCTTCTTCAGCTTATCCAGTTCATCTTTTGCCGCAAGGTTGTGGTTCCAGATTC
*
66434 TGTAACTTTTTTTATGGCTAAAGACTGCTGCTCCATTGAGATAGAACCTAGAACTTTGAACAAAG
1 TGTAACTTTTTATATGGCTAAAGACTGCTGCTCCATTGAGATAGAACCTAGAACTTTGAACAAAG
* * *
66499 GCCAACTCAACCAATGCTAGGGTCATGGGTACACAAGTCATACTTATGAAAACATCACAGCAAAT
66 GCAAACTCAACC-ATGCTAGGGTCATGGGTACACAAGTCACACTTATGAAAACATCACAACAAAT
66564 -GAAAGCTTC-CTCGCGGATGAATGCAACAGCTTAGACTTCCGGGCTCAACGCGAAGAAGACAAG
130 AGAAAGC-TCGCTCGCGGATGAATGCAACAGCTTAGACTTCCGGGCTCAACGCGAAGAAGACAAG
66627 ATCTCTCTTCTTCAGCTTATCCAGTTCATCTTTTGCCGCAAGGTTGTGGTTCC
194 ATCTCTCTTCTTCAGCTTATCCAGTTCATCTTTTGCCGCAAGGTTGTGGTTCC
66680 TTTTGAGTTC
Statistics
Matches: 225, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
252 106 0.47
253 73 0.32
254 46 0.20
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (252 bp):
TGTAACTTTTTATATGGCTAAAGACTGCTGCTCCATTGAGATAGAACCTAGAACTTTGAACAAAG
GCAAACTCAACCATGCTAGGGTCATGGGTACACAAGTCACACTTATGAAAACATCACAACAAATA
GAAAGCTCGCTCGCGGATGAATGCAACAGCTTAGACTTCCGGGCTCAACGCGAAGAAGACAAGAT
CTCTCTTCTTCAGCTTATCCAGTTCATCTTTTGCCGCAAGGTTGTGGTTCCAGATTC
Found at i:66833 original size:2 final size:2
Alignment explanation
Indices: 66826--66853 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
66816 ATTAAAAGGC
66826 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66854 GATGGGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71614 original size:28 final size:27
Alignment explanation
Indices: 71572--71625 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
71562 TTTTTATTTG
*
71572 AGTTTGTTTTTGAGTCGGTTT-GAGTC
1 AGTTTGTTTTTGAGTCAGTTTCGAGTC
71598 AGTTTGTTTTTTCGAGTCAGTTTCGAGT
1 AGTTTG-TTTTT-GAGTCAGTTTCGAGT
71626 ATAGTCTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 6 0.25
27 5 0.21
28 9 0.38
29 4 0.17
ACGTcount: A:0.13, C:0.09, G:0.28, T:0.50
Consensus pattern (27 bp):
AGTTTGTTTTTGAGTCAGTTTCGAGTC
Found at i:74465 original size:178 final size:178
Alignment explanation
Indices: 74188--74528 Score: 449
Period size: 178 Copynumber: 1.9 Consensus size: 178
74178 TATCCGATTA
* ** *
74188 AGATGATTTAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACTTGACAA
1 AGATGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACACGAAAA
* *
74253 CTAAATTTAATGTTTCAAGTATCAAAAATGCTTCCGAAA-AATTTGTTGTTTCGGTT-AACGAGA
66 CTAAATTTAATGTTTCAAGTATCAAAAATGCTTCC-AAAGAATTAGTTGTTTCGGTTAAAGGA-A
*
74316 ATAGACGATCCACTTAATATTATATAACTTT-TGCTCCAGATGTGTAATTG
129 ATAGACGATCCACTTAATATTACATAA-TTTGTGCTCCAGATGTGTAATTG
* * * * * * *
74366 AGATGATTCAAGTGTCTCTTGAAAGGTTTTTCCATGATCTACAACTTTTATGAAGGGCACGAAAA
1 AGATGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACACGAAAA
*
74431 CTAAATTTAATG-TTCGAGGTAT-AAAAATTGCTTCCAAAGAATTAGTTGTTTCGGTTAAAGGAA
66 CTAAATTTAATGTTTC-AAGTATCAAAAA-TGCTTCCAAAGAATTAGTTGTTTCGGTTAAAGGAA
* *
74494 ATAGACGGTCTACTTAATATTACATAATTTGTGCT
129 ATAGACGATCCACTTAATATTACATAATTTGTGCT
74529 TATGGTGGAA
Statistics
Matches: 141, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
177 14 0.10
178 123 0.87
179 4 0.03
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (178 bp):
AGATGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACACGAAAA
CTAAATTTAATGTTTCAAGTATCAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAAAGGAAAT
AGACGATCCACTTAATATTACATAATTTGTGCTCCAGATGTGTAATTG
Found at i:75465 original size:13 final size:11
Alignment explanation
Indices: 75347--75460 Score: 69
Period size: 11 Copynumber: 10.8 Consensus size: 11
75337 ATTATGCTAT
*
75347 TATATATCAAA
1 TATATATAAAA
*
75358 TATAT-TAATGA
1 TATATATAA-AA
75369 TATATATAAAA
1 TATATATAAAA
*
75380 TATAT-T-TAA
1 TATATATAAAA
* **
75389 T-TATTTATGA
1 TATATATAAAA
75399 TATATATAAAA
1 TATATATAAAA
* *
75410 TACATGT-AAA
1 TATATATAAAA
*
75420 -ATATATAAAT
1 TATATATAAAA
* **
75430 TATATTTATGA
1 TATATATAAAA
75441 TATATATAAAA
1 TATATATAAAA
75452 TATATATAA
1 TATATATAA
75461 CAAATTTTTT
Statistics
Matches: 76, Mismatches: 20, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
8 3 0.04
9 8 0.11
10 11 0.14
11 51 0.67
12 3 0.04
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (11 bp):
TATATATAAAA
Found at i:75591 original size:10 final size:10
Alignment explanation
Indices: 75576--75600 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
75566 ATTTCCTATT
75576 TTAAAACCGA
1 TTAAAACCGA
75586 TTAAAACCGA
1 TTAAAACCGA
75596 TTAAA
1 TTAAA
75601 TTAAATTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (10 bp):
TTAAAACCGA
Done.