Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022991.1 Corchorus olitorius cultivar O-4 contig23024, 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: 59918
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:9392 original size:147 final size:147
Alignment explanation
Indices: 9133--9425 Score: 568
Period size: 147 Copynumber: 2.0 Consensus size: 147
9123 AACTTGACTC
*
9133 AAAACAGAAGCAGCTTGAAGCTATGCAAAAATCTCAGAAACAACTCTCTGATGAACTTGAGTCAA
1 AAAACAGAAGCAGCTTGAAGCTATACAAAAATCTCAGAAACAACTCTCTGATGAACTTGAGTCAA
*
9198 AAGAAAAGCAATTGGGTTTGATGGAGAAGGCATGCAATGAACGCCAATTGGAGGCTGATGTCAAG
66 AAGAAAAGCAATTGGGTTTGATGGAGAAGGCATGCAATGAACGCCAATTGGAGGCTGATGCCAAG
9263 GAGAAGGGTCTTGATTT
131 GAGAAGGGTCTTGATTT
9280 AAAACAGAAGCAGCTTGAAGCTATACAAAAATCTCAGAAACAACTCTCTGATGAACTTGAGTCAA
1 AAAACAGAAGCAGCTTGAAGCTATACAAAAATCTCAGAAACAACTCTCTGATGAACTTGAGTCAA
9345 AAGAAAAGCAATTGGGTTTGATGGAGAAGGCATGCAATGAACGCCAATTGGAGGCTGATGCCAAG
66 AAGAAAAGCAATTGGGTTTGATGGAGAAGGCATGCAATGAACGCCAATTGGAGGCTGATGCCAAG
9410 GAGAAGGGTCTTGATT
131 GAGAAGGGTCTTGATT
9426 CGCTCAAAAG
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 144 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (147 bp):
AAAACAGAAGCAGCTTGAAGCTATACAAAAATCTCAGAAACAACTCTCTGATGAACTTGAGTCAA
AAGAAAAGCAATTGGGTTTGATGGAGAAGGCATGCAATGAACGCCAATTGGAGGCTGATGCCAAG
GAGAAGGGTCTTGATTT
Found at i:9600 original size:117 final size:117
Alignment explanation
Indices: 9383--9619 Score: 307
Period size: 117 Copynumber: 2.0 Consensus size: 117
9373 GGCATGCAAT
* * * *
9383 GAACGCCAATTGGAGGCTGATGCCAAGGAGAAGGGTCTTGATTCGCTCAAAAGATCACTAGAGGA
1 GAACGCCAACTGGAGGCTGATGCCAAGGAGAAGAGTCTTGATTCACTCAAAAGATCAATAGAGGA
* * *
9448 ACGCTCTGAAAAACTAGAAGCTGAAAAGAGGCAATTTGAAGCTCGCGTCAAG
66 ACGCTCTGAAAAACTAGAAGCAGAAAAGAGCCAATTCGAAGCTCGCGTCAAG
* ** *
9500 GAACTCCAACTGGAGGCTGATGTGAAGGCA-AAGAGTCTTGATTCACGT-GAAAGATCAATAGAG
1 GAACGCCAACTGGAGGCTGATGCCAAGG-AGAAGAGTCTTGATTCAC-TCAAAAGATCAATAGAG
* * * *
9563 GAGCGCTCTGCAAAACTAGAAGCAGAAAAGAGCCAATTCGAAGCTCGTGTGAAG
64 GAACGCTCTGAAAAACTAGAAGCAGAAAAGAGCCAATTCGAAGCTCGCGTCAAG
9617 GAA
1 GAA
9620 TTTGAAACTC
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
117 101 0.98
118 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.18
Consensus pattern (117 bp):
GAACGCCAACTGGAGGCTGATGCCAAGGAGAAGAGTCTTGATTCACTCAAAAGATCAATAGAGGA
ACGCTCTGAAAAACTAGAAGCAGAAAAGAGCCAATTCGAAGCTCGCGTCAAG
Found at i:11382 original size:2 final size:2
Alignment explanation
Indices: 11377--11412 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11367 TATATATATA
11377 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
11413 ATAAATCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:17200 original size:28 final size:28
Alignment explanation
Indices: 17160--17229 Score: 140
Period size: 28 Copynumber: 2.5 Consensus size: 28
17150 AAATGAAGGG
17160 GATTGTCGGATCAGTATGCAGTTGTTCA
1 GATTGTCGGATCAGTATGCAGTTGTTCA
17188 GATTGTCGGATCAGTATGCAGTTGTTCA
1 GATTGTCGGATCAGTATGCAGTTGTTCA
17216 GATTGTCGGATCAG
1 GATTGTCGGATCAG
17230 CATTTATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.21, C:0.14, G:0.30, T:0.34
Consensus pattern (28 bp):
GATTGTCGGATCAGTATGCAGTTGTTCA
Found at i:26710 original size:1 final size:1
Alignment explanation
Indices: 26704--26745 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
26694 CCAACGCTAG
26704 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
26746 CTACTCATGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:26849 original size:26 final size:26
Alignment explanation
Indices: 26820--26870 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
26810 TGAAATAATT
*
26820 GGGTTTAAG-CTTTAGATCATTTGGAA
1 GGGTTTAAGTC-TCAGATCATTTGGAA
26846 GGGTTTAAGTCTCAGATCATTTGGA
1 GGGTTTAAGTCTCAGATCATTTGGA
26871 TTTAGGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.37
Consensus pattern (26 bp):
GGGTTTAAGTCTCAGATCATTTGGAA
Found at i:27098 original size:31 final size:31
Alignment explanation
Indices: 27060--27121 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
27050 GAGTTTTGTA
*
27060 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
*
27091 AAACTTTTGAATCGCCTATCATATCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
27122 TTAGTCAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATCATACCCTTATT
Found at i:27290 original size:93 final size:93
Alignment explanation
Indices: 27120--27296 Score: 277
Period size: 93 Copynumber: 1.9 Consensus size: 93
27110 CATATCCTTA
* *
27120 TTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAATTTTTTTACTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAATTATTTTACTT
* *
27185 TTACCATTTTACTATTTTACTTTTATAG
66 TTACCATATTACTAATTTACTTTTATAG
27213 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAT-ATCTATTTTA-T
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAT-TATTTTACT
*
27276 TTTAACGATATTACTAATTTA
65 TTT-ACCATATTACTAATTTA
27297 ATTAAAAAGT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
92 6 0.08
93 71 0.92
ACGTcount: A:0.33, C:0.13, G:0.02, T:0.52
Consensus pattern (93 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAATTATTTTACTT
TTACCATATTACTAATTTACTTTTATAG
Found at i:29908 original size:63 final size:63
Alignment explanation
Indices: 29777--29911 Score: 157
Period size: 63 Copynumber: 2.1 Consensus size: 63
29767 AGAGTTATAG
* * * * *
29777 AGAGTTTGAGCAGAGAAAGGAGCAATTTGGGTTAATAGAGCAGCGTTTTGAGAAACTTTTGAT
1 AGAGTTTGAACAGAGAAAGAAGCAATTTGGGTTAATAGAGCAGAGTTTTGAGAAACCTTTGAA
* * * *
29840 GGAGTTTGAACTGAGACAGAAGCAATTTGGGTTGAA-AGAGCAGAGTTTTGAGAATCGCTTT-AA
1 AGAGTTTGAACAGAGAAAGAAGCAATTTGGGTT-AATAGAGCAGAGTTTTGAGAAAC-CTTTGAA
29903 AGAGTTTGA
1 AGAGTTTGA
29912 GTTGGAAGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 55 0.92
64 5 0.08
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.28
Consensus pattern (63 bp):
AGAGTTTGAACAGAGAAAGAAGCAATTTGGGTTAATAGAGCAGAGTTTTGAGAAACCTTTGAA
Found at i:30376 original size:15 final size:17
Alignment explanation
Indices: 30342--30374 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
30332 AGAATGCTTG
*
30342 AGAGAAATCAAATTGAA
1 AGAGAAATCAAATAGAA
30359 AGAGAAA-CAAATAGAA
1 AGAGAAATCAAATAGAA
30375 GAATCATCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.64, C:0.06, G:0.18, T:0.12
Consensus pattern (17 bp):
AGAGAAATCAAATAGAA
Found at i:40367 original size:45 final size:45
Alignment explanation
Indices: 40303--40391 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
40293 AGAGTCAATT
*
40303 TAAGTCCCTAACGTTTTGGGGTTTATTAGGTTGTCAATTTGACGC
1 TAAGTCCCTAACGTTTTGGGGTTTATTAGGCTGTCAATTTGACGC
*
40348 TAAGTCCCTAATGTTTTGGGGTTTATTAGGCTGTCAATTTGACG
1 TAAGTCCCTAACGTTTTGGGGTTTATTAGGCTGTCAATTTGACG
40392 TCAGGGACTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.40
Consensus pattern (45 bp):
TAAGTCCCTAACGTTTTGGGGTTTATTAGGCTGTCAATTTGACGC
Found at i:41373 original size:36 final size:36
Alignment explanation
Indices: 41333--41405 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
41323 GATTGTGGGT
*
41333 GGCCAATGCCTTTGAGTGGCTGTAAGTAGGACCTTA
1 GGCCAATGCCTTTGAGTGGCTGTAAATAGGACCTTA
*
41369 GGCCAATGCCTTTTAGTGGCTGTAAATAGGACCTTA
1 GGCCAATGCCTTTGAGTGGCTGTAAATAGGACCTTA
41405 G
1 G
41406 TGCAATTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (36 bp):
GGCCAATGCCTTTGAGTGGCTGTAAATAGGACCTTA
Found at i:41787 original size:34 final size:34
Alignment explanation
Indices: 41744--41810 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
41734 AACCCACTCA
41744 CCCAAACTCAACCTGAAAAAATCCGATTGACTAG
1 CCCAAACTCAACCTGAAAAAATCCGATTGACTAG
* * *
41778 CCCAAACTCAACTTGAAAAGATTCGATTGACTA
1 CCCAAACTCAACCTGAAAAAATCCGATTGACTA
41811 AAAAAGTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.40, C:0.27, G:0.12, T:0.21
Consensus pattern (34 bp):
CCCAAACTCAACCTGAAAAAATCCGATTGACTAG
Found at i:41859 original size:15 final size:16
Alignment explanation
Indices: 41828--41863 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 16
41818 TTAACTACTT
41828 GAATCCAAAGGAAACCC
1 GAATCCAAA-GAAACCC
41845 GAATCCAAA-AAACCC
1 GAATCCAAAGAAACCC
41860 GAAT
1 GAAT
41864 TCAATACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.53
17 9 0.47
ACGTcount: A:0.50, C:0.28, G:0.14, T:0.08
Consensus pattern (16 bp):
GAATCCAAAGAAACCC
Found at i:42275 original size:19 final size:19
Alignment explanation
Indices: 42243--42284 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
42233 TGGTCTATTC
*
42243 AACTCGTTCAAAAAAAAAA
1 AACTCATTCAAAAAAAAAA
42262 AACTCATTCCAAAAAAAAAA
1 AACTCATT-CAAAAAAAAAA
42282 AAC
1 AAC
42285 CCTCTAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.64, C:0.19, G:0.02, T:0.14
Consensus pattern (19 bp):
AACTCATTCAAAAAAAAAA
Found at i:48630 original size:18 final size:19
Alignment explanation
Indices: 48603--48641 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
48593 TCTTATATGT
*
48603 TTCATGACCT-TAAACTAC
1 TTCATAACCTCTAAACTAC
*
48621 TTCATAACCTCTAAATTAC
1 TTCATAACCTCTAAACTAC
48640 TT
1 TT
48642 TAGGCCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (19 bp):
TTCATAACCTCTAAACTAC
Found at i:49957 original size:26 final size:26
Alignment explanation
Indices: 49921--49977 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
49911 TTCACCATTG
49921 CCAACTATAGTAACTTATAGGTACTA
1 CCAACTATAGTAACTTATAGGTACTA
49947 CCAACTATAGTAACTTATAGGTACTA
1 CCAACTATAGTAACTTATAGGTACTA
49973 CCAAC
1 CCAAC
49978 CTAGTTGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.28
Consensus pattern (26 bp):
CCAACTATAGTAACTTATAGGTACTA
Done.