Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020253.1 Corchorus olitorius cultivar O-4 contig20286, 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: 87606
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3112 original size:2 final size:2
Alignment explanation
Indices: 3105--3146 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3095 GACTTTTGAA
3105 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
3147 GCCTGACTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4533 original size:27 final size:27
Alignment explanation
Indices: 4476--4533 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
4466 CTTGTTGATC
* * *
4476 TTTTAGGACTAGAATAGCCAGTGCTAA
1 TTTTAGGACTAGAAAAGCCAGAGCCAA
* *
4503 TTTTAGGACTAGAAAAGCTAGAGCCAG
1 TTTTAGGACTAGAAAAGCCAGAGCCAA
4530 TTTT
1 TTTT
4534 TCTAGCAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (27 bp):
TTTTAGGACTAGAAAAGCCAGAGCCAA
Found at i:8883 original size:107 final size:107
Alignment explanation
Indices: 8685--8922 Score: 458
Period size: 107 Copynumber: 2.2 Consensus size: 107
8675 GCGGGTTGGA
*
8685 CGGGTTCTCAGATCATTCGGGTTTCGGCTCATCTAGATTCAGGTCATTCGGGTCTCGGGTCTGCT
1 CGGGTTCTGAG-TCATTCGGGTTTCGGCTCATCTAGATTCAGGTCATTCGGGTCTCGGGTCTGCT
8750 GGATTTAGGGTCATGCATGTTCGGGTTTTGGCCTCAGGTTACT
65 GGATTTAGGGTCATGCATGTTCGGGTTTTGGCCTCAGGTTACT
8793 CGGGTTCTGAGTCATTCGGGTTTCGGCTCATCTAGATTCAGGTCATTCGGGTCTCGGGTCTGCTG
1 CGGGTTCTGAGTCATTCGGGTTTCGGCTCATCTAGATTCAGGTCATTCGGGTCTCGGGTCTGCTG
8858 GATTTAGGGTCATGCATGTTCGGGTTTTGGCCTCAGGTTACT
66 GATTTAGGGTCATGCATGTTCGGGTTTTGGCCTCAGGTTACT
8900 CGGGTTCTGAGTCATTCGGGTTT
1 CGGGTTCTGAGTCATTCGGGTTT
8923 TGGATTTTTC
Statistics
Matches: 129, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
107 119 0.92
108 10 0.08
ACGTcount: A:0.12, C:0.21, G:0.32, T:0.36
Consensus pattern (107 bp):
CGGGTTCTGAGTCATTCGGGTTTCGGCTCATCTAGATTCAGGTCATTCGGGTCTCGGGTCTGCTG
GATTTAGGGTCATGCATGTTCGGGTTTTGGCCTCAGGTTACT
Found at i:9009 original size:26 final size:23
Alignment explanation
Indices: 8963--9009 Score: 58
Period size: 26 Copynumber: 1.9 Consensus size: 23
8953 TTAAGTCAAC
*
8963 CTTAAATTTTTAAATGTTTAATT
1 CTTAAATTTTTAAATGGTTAATT
8986 CTTAAATTTATTTAAAATGGTTAA
1 CTTAAA-TT-TTT-AAATGGTTAA
9010 AATTATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 2 0.10
25 3 0.15
26 9 0.45
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.51
Consensus pattern (23 bp):
CTTAAATTTTTAAATGGTTAATT
Found at i:13961 original size:27 final size:27
Alignment explanation
Indices: 13923--13977 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
13913 AGTAAGTCCC
13923 TAAATTTAGGACATTAATTGGCTAGGG
1 TAAATTTAGGACATTAATTGGCTAGGG
13950 TAAATTTAGGACATTAATTGGCTAGGG
1 TAAATTTAGGACATTAATTGGCTAGGG
13977 T
1 T
13978 TTTAGAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (27 bp):
TAAATTTAGGACATTAATTGGCTAGGG
Found at i:15555 original size:2 final size:2
Alignment explanation
Indices: 15548--15575 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15538 TCTTTTTGTG
15548 TA 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 TA
15576 AGTAGTAACT
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):
TA
Found at i:31033 original size:243 final size:234
Alignment explanation
Indices: 30569--31052 Score: 571
Period size: 243 Copynumber: 2.0 Consensus size: 234
30559 AAGGGGTTGG
* * * *
30569 AAGGATATGCGTGGAAACAAGAGGATTGCCGATAGTGAGGATGAATATGAAGATGATATTGTGCG
1 AAGGATATACATGGAAACAAGAGAACTGCCGATAGTGAGGATGAATATGAAGATGATATTGTGCG
* * *
30634 TGCTGCTGAATTGGATTCCCCCTATGCTGGTGGTTTGAGTGAGAGTGAGAATGATGATGATTCTG
66 CGCTGCTGAATTGGATTCCCACAATGCTGGTGGTTTGAGTGAGAGTGAGAATGATGATGATTCTG
*
30699 AAGAAGCTTTTGAGTTCAAGAGATCAAGAGTAGAAAACAGAAAGCAATATAAAATCGGAAGGTGG
131 AAGAAGCTTTTGAGTTCAAGAGATCAAGAGTAGAAAACAGAAAGCAAGATAAAATCGGAAGGTGG
*
30764 AATAACTCTAATAACTCTTTAGGTTTCAGACAAAATGCAGGAGGT
196 AATAAC-C----AAC-CTGTAGGTTTCAGACAAAATGCAGGAGGT
* *
30809 AAGGATATACATGGAAGCAAGAGAACTGCTGATAGTGAGGATGAATATGAAGATGATGATATTGT
1 AAGGATATACATGGAAACAAGAGAACTGCCGATAGTGAGGATGAATATG-A-A-GATGATATTGT
* * * *
30874 GGGCGGTTCTGAATTGGATTTCCACAATGCTGGTGGTTTGAGTGAGAGTGGGAGTGATGATGATA
63 GCGCGCTGCTGAATTGGATTCCCACAATGCTGGTGGTTTGAGTGAGAGT--GA--GA--ATG---
* * * *
30939 ATGATGATTCTGAAGAAGCTTTTGAGTTCAAGAGTTCTAGAGTAGAGAATAGAAAGCAAGAT-AA
119 ATGATGATTCTGAAGAAGCTTTTGAGTTCAAGAGATCAAGAGTAGAAAACAGAAAGCAAGATAAA
* * *
31003 AGCTGGAAGGTGGAATAA-C-A-CTGTAGGTTTCAGACGAAGTGCAGGAGGT
184 ATC-GGAAGGTGGAATAACCAACCTGTAGGTTTCAGACAAAATGCAGGAGGT
31052 A
1 A
31053 GTAATAAACA
Statistics
Matches: 209, Mismatches: 22, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
240 43 0.21
241 1 0.00
242 1 0.00
243 80 0.38
245 3 0.01
247 2 0.01
249 3 0.01
250 1 0.00
251 4 0.02
252 71 0.34
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.26
Consensus pattern (234 bp):
AAGGATATACATGGAAACAAGAGAACTGCCGATAGTGAGGATGAATATGAAGATGATATTGTGCG
CGCTGCTGAATTGGATTCCCACAATGCTGGTGGTTTGAGTGAGAGTGAGAATGATGATGATTCTG
AAGAAGCTTTTGAGTTCAAGAGATCAAGAGTAGAAAACAGAAAGCAAGATAAAATCGGAAGGTGG
AATAACCAACCTGTAGGTTTCAGACAAAATGCAGGAGGT
Found at i:34473 original size:64 final size:65
Alignment explanation
Indices: 34372--34502 Score: 246
Period size: 64 Copynumber: 2.0 Consensus size: 65
34362 AGAGGTGATA
34372 TGTAAGATTTTGCAAACCCAATAATCTACTTCTTCCCTGTTAGGAAAACCGTAA-GGAACGGCTT
1 TGTAAGATTTTGCAAACCCAATAATCTACTTCTTCCCTGTTAGGAAAACCGTAATGGAACGGCTT
*
34436 TGTAAGATTTTGCAAACCCAATAATCTACTTCTTCCCTGTTAGGAAAACTGTAATGGAACGGCTT
1 TGTAAGATTTTGCAAACCCAATAATCTACTTCTTCCCTGTTAGGAAAACCGTAATGGAACGGCTT
34501 TG
1 TG
34503 AGGCGTGGTT
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
64 53 0.82
65 12 0.18
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (65 bp):
TGTAAGATTTTGCAAACCCAATAATCTACTTCTTCCCTGTTAGGAAAACCGTAATGGAACGGCTT
Found at i:35699 original size:288 final size:288
Alignment explanation
Indices: 35183--35759 Score: 1109
Period size: 288 Copynumber: 2.0 Consensus size: 288
35173 TGGGCAATCT
35183 ATCCAAAATAGTCATCCAACTCACAATAGAATGCTAAGGCTGATTACACGAAAACCATGTGAGCC
1 ATCCAAAATAGTCATCCAACTCACAATAGAATGCTAAGGCTGATTACACGAAAACCATGTGAGCC
35248 TCTACCAATTCACACGAGGGTTCCTATGTCTCATCTGATCATAAACAAGAGAACGCTTAAAGGTG
66 TCTACCAATTCACACGAGGGTTCCTATGTCTCATCTGATCATAAACAAGAGAACGCTTAAAGGTG
35313 TAGCCAGGTAGATTCCAGTCATGAATAACCTGAGCTGCCTTACTTCTCAATTTGAGTAGTTTTTT
131 TAGCCAGGTAGATTCCAGTCATGAATAACCTGAGCTGCCTTACTTCTCAATTTGAGTAGTTTTTT
35378 CAAGTTCCAACTGTATCTCTGTAGGCATGGTATTTCCATAATATTCCTCCCTTTAAGAATATACA
196 CAAGTTCCAACTGTATCTCTGTAGGCATGGTATTTCCATAATATTCCTCCCTTTAAGAATATACA
35443 GCTGGATCCAGGCTATCCACAATGAACC
261 GCTGGATCCAGGCTATCCACAATGAACC
*
35471 ATCCAAAATAGTCATCCAACTCACAATAGAATGCTTAGGCTGATTACACGAAAACCATGTGAGCC
1 ATCCAAAATAGTCATCCAACTCACAATAGAATGCTAAGGCTGATTACACGAAAACCATGTGAGCC
* * *
35536 TCTGCCAATTCACACGGGGGTTCCTATGTCTCATCTGATCATAAACAAGAGAATGCTTAAAGGTG
66 TCTACCAATTCACACGAGGGTTCCTATGTCTCATCTGATCATAAACAAGAGAACGCTTAAAGGTG
35601 TAGCCAGGTAGATTCCAGTCATGAATAACCTGAGCTGCCTTACTTCTCAATTTGAGTAGTTTTTT
131 TAGCCAGGTAGATTCCAGTCATGAATAACCTGAGCTGCCTTACTTCTCAATTTGAGTAGTTTTTT
*
35666 CAAGTTCCAACTGTATCTCTGTAGGCATGGTATTTCCATAATATTCCTCCCTTTAAGAATATACT
196 CAAGTTCCAACTGTATCTCTGTAGGCATGGTATTTCCATAATATTCCTCCCTTTAAGAATATACA
35731 GCTGGATCCAGGCTATCCACAATGAACC
261 GCTGGATCCAGGCTATCCACAATGAACC
35759 A
1 A
35760 GACAACATAT
Statistics
Matches: 284, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
288 284 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (288 bp):
ATCCAAAATAGTCATCCAACTCACAATAGAATGCTAAGGCTGATTACACGAAAACCATGTGAGCC
TCTACCAATTCACACGAGGGTTCCTATGTCTCATCTGATCATAAACAAGAGAACGCTTAAAGGTG
TAGCCAGGTAGATTCCAGTCATGAATAACCTGAGCTGCCTTACTTCTCAATTTGAGTAGTTTTTT
CAAGTTCCAACTGTATCTCTGTAGGCATGGTATTTCCATAATATTCCTCCCTTTAAGAATATACA
GCTGGATCCAGGCTATCCACAATGAACC
Found at i:38277 original size:30 final size:30
Alignment explanation
Indices: 38243--38300 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
38233 TTATCTTGAT
*
38243 TTTCCTTTTATACCCTCAAATTTTAATAAC
1 TTTCCTCTTATACCCTCAAATTTTAATAAC
38273 TTTCCTCTTATACCCTCAAATTTTAATA
1 TTTCCTCTTATACCCTCAAATTTTAATA
38301 TATTATGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (30 bp):
TTTCCTCTTATACCCTCAAATTTTAATAAC
Found at i:46875 original size:45 final size:42
Alignment explanation
Indices: 46799--46892 Score: 109
Period size: 45 Copynumber: 2.2 Consensus size: 42
46789 AACAACAATT
* * ** *
46799 AATATTAACTTTATTTTGATGAATTATCTAGAGATTAAGGAGTAG
1 AATATTAGCTTTATTTTAATGAACGACCTAGAGA-T--GGAGTAG
46844 AATATTAGCTTTATTTTAATGAACGACCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTAATGAACGACCTAGAGATGGAGTAG
46886 AAT-TTAG
1 AATATTAG
46893 GTAATACACT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 4 0.09
42 10 0.23
44 1 0.02
45 29 0.66
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.37
Consensus pattern (42 bp):
AATATTAGCTTTATTTTAATGAACGACCTAGAGATGGAGTAG
Found at i:49373 original size:17 final size:17
Alignment explanation
Indices: 49333--49373 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
49323 TTAACGTGTC
*
49333 ATTAGAAAGGTGCTAAA
1 ATTAAAAAGGTGCTAAA
49350 A-TAAAAAGGTGCTAAA
1 ATTAAAAAGGTGCTAAA
49366 ATTAAAAA
1 ATTAAAAA
49374 AAAAACGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.56, C:0.05, G:0.17, T:0.22
Consensus pattern (17 bp):
ATTAAAAAGGTGCTAAA
Found at i:52200 original size:2 final size:2
Alignment explanation
Indices: 52189--52220 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
52179 AATAATCACT
52189 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52221 TAATGACTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58162 original size:12 final size:12
Alignment explanation
Indices: 58145--58169 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58135 CCCTGCTTCG
58145 TTTTTGTTTTTT
1 TTTTTGTTTTTT
58157 TTTTTGTTTTTT
1 TTTTTGTTTTTT
58169 T
1 T
58170 CCTTCTGCAC
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTTGTTTTTT
Found at i:58381 original size:1 final size:1
Alignment explanation
Indices: 58377--58428 Score: 86
Period size: 1 Copynumber: 52.0 Consensus size: 1
58367 TTCTGGTTTG
* *
58377 TTTTTTTGTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
58429 AAATTTCTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.04, T:0.96
Consensus pattern (1 bp):
T
Found at i:63276 original size:16 final size:16
Alignment explanation
Indices: 63255--63295 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
63245 AAAATTCTGG
63255 TTTTTATTTAATTTTA
1 TTTTTATTTAATTTTA
63271 TTTTTATTTAATTTTA
1 TTTTTATTTAATTTTA
63287 TTTTTATTT
1 TTTTTATTT
63296 TTAATGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTATTTAATTTTA
Done.