Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014156.1 Corchorus olitorius cultivar O-4 contig14189, 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: 88862
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:726 original size:19 final size:18
Alignment explanation
Indices: 702--737 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
692 TGAAGACTTA
702 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
721 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
738 ATAATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:8216 original size:20 final size:21
Alignment explanation
Indices: 8172--8232 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
8162 TAGTCGACTA
*
8172 AAGCAATTACCGACCTAAGAGG
1 AAGCAATTATCGA-CTAAGAGG
*
8194 AAGCAATTATCGACTTA-AGG
1 AAGCAATTATCGACTAAGAGG
*
8214 AAGTAATTAGTCGAC-AAGA
1 AAGCAATTA-TCGACTAAGA
8233 AAGAAATCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 12 0.36
21 9 0.27
22 12 0.36
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
AAGCAATTATCGACTAAGAGG
Found at i:10792 original size:11 final size:12
Alignment explanation
Indices: 10775--10807 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
10765 CGAAGTTCGT
10775 GTTTGAAGACTA
1 GTTTGAAGACTA
10787 -TTTGAAGA-TA
1 GTTTGAAGACTA
10797 GTTTGAAGACT
1 GTTTGAAGACT
10808 TGAAGATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.11
11 16 0.84
12 1 0.05
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (12 bp):
GTTTGAAGACTA
Found at i:43838 original size:47 final size:47
Alignment explanation
Indices: 43769--43862 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
43759 CAGATTGGTG
43769 TTTAATTGTTAATGACCAATGAGAACTTATAACTTAAATTATTGCTA
1 TTTAATTGTTAATGACCAATGAGAACTTATAACTTAAATTATTGCTA
*
43816 TTTAATTGTTAATGACCAATGAGAACTTATAAGTTAAATTATTGCTA
1 TTTAATTGTTAATGACCAATGAGAACTTATAACTTAAATTATTGCTA
43863 AAACGCTTGG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (47 bp):
TTTAATTGTTAATGACCAATGAGAACTTATAACTTAAATTATTGCTA
Found at i:46902 original size:1 final size:1
Alignment explanation
Indices: 46896--46920 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
46886 AAGCAATGAC
46896 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
46921 CACAAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:51194 original size:16 final size:17
Alignment explanation
Indices: 51173--51208 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
51163 TACAGCACTA
51173 ATTATTACTCTATT-TT
1 ATTATTACTCTATTATT
*
51189 ATTATTACTTTATTATT
1 ATTATTACTCTATTATT
51206 ATT
1 ATT
51209 GCATTAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTATTACTCTATTATT
Found at i:52583 original size:19 final size:19
Alignment explanation
Indices: 52541--52601 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
52531 GTAAATTTTT
52541 ATTACACTCAAA-ATTGATACC
1 ATTACAC-CAAATATTGAT--C
52562 ATTACACCAAATGA-TGATC
1 ATTACACCAAAT-ATTGATC
*
52581 ATTATACCAAATATTGATC
1 ATTACACCAAATATTGATC
52600 AT
1 AT
52602 ATTTTGCTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 1 0.03
19 19 0.53
20 4 0.11
21 11 0.31
22 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.31
Consensus pattern (19 bp):
ATTACACCAAATATTGATC
Found at i:53371 original size:66 final size:66
Alignment explanation
Indices: 53258--53383 Score: 159
Period size: 66 Copynumber: 1.9 Consensus size: 66
53248 TGAATATTTT
* * * * *
53258 TATGAAATTTTGATAACCATCCTATTAAATTTTGATAACCACGCTATGAAATTTTGATAATTTAC
1 TATGAAATTGTGATAAACATCCTATTAAACTTTGATAACCACACTATGAAATTTTAATAATTTAC
53323 C
66 C
53324 TATGAAATTGTGATAAAC-TCC-ATGTGAAACTTTGATAACCTA-ACTATGAAATTTTAATAA
1 TATGAAATTGTGATAAACATCCTAT-T-AAACTTTGATAACC-ACACTATGAAATTTTAATAA
53384 ACCTTCCTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
64 2 0.04
65 4 0.08
66 45 0.87
67 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37
Consensus pattern (66 bp):
TATGAAATTGTGATAAACATCCTATTAAACTTTGATAACCACACTATGAAATTTTAATAATTTAC
C
Found at i:53412 original size:21 final size:21
Alignment explanation
Indices: 53258--53463 Score: 98
Period size: 22 Copynumber: 9.5 Consensus size: 21
53248 TGAATATTTT
* *
53258 TATGAAATTTTGATAACCATCC
1 TATG-AATTTTGATAATCTTCC
* **
53280 TATTAAATTTTGATAA-CCACGC
1 TA-TGAATTTTGATAATCTTC-C
53302 TATGAAATTTTGATAAT-TTACC
1 TATG-AATTTTGATAATCTT-CC
* *
53324 TATGAAATTGTGATAAAC-TCC
1 TATG-AATTTTGATAATCTTCC
* * * **
53345 ATGTGAAACTTTGATAACCTAAC
1 -TATG-AATTTTGATAATCTTCC
* *
53368 TATGAAATTTTAATAAACCTTCC
1 TATG-AATTTTGAT-AATCTTCC
53391 TATGCAATTTTG-TAATCTTCC
1 TATG-AATTTTGATAATCTTCC
* * *
53412 TATGATTTTTGATAACCTACC
1 TATGAATTTTGATAATCTTCC
* *
53433 TATGAGATTTTGTTAATCTCCC
1 TATGA-ATTTTGATAATCTTCC
53455 TAT-AATTTT
1 TATGAATTTT
53464 TTATACTATA
Statistics
Matches: 144, Mismatches: 29, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
20 11 0.08
21 29 0.20
22 85 0.59
23 19 0.13
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (21 bp):
TATGAATTTTGATAATCTTCC
Found at i:53429 original size:42 final size:43
Alignment explanation
Indices: 53383--53464 Score: 114
Period size: 42 Copynumber: 1.9 Consensus size: 43
53373 AATTTTAATA
* * *
53383 AACCTTCCTATGCA-ATTTTG-TAATCTTCCTATGATTTTTGAT
1 AACCTACCTATG-AGATTTTGTTAATCTCCCTATAATTTTTGAT
53425 AACCTACCTATGAGATTTTGTTAATCTCCCTATAATTTTT
1 AACCTACCTATGAGATTTTGTTAATCTCCCTATAATTTTT
53465 TATACTATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 1 0.03
42 17 0.49
43 17 0.49
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.46
Consensus pattern (43 bp):
AACCTACCTATGAGATTTTGTTAATCTCCCTATAATTTTTGAT
Found at i:56353 original size:28 final size:28
Alignment explanation
Indices: 56321--56381 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
56311 CTAAATTTTC
56321 ATTATTTTAATAATGGAATAATTA-AAAT
1 ATTATTTTAATAATGGAA-AATTATAAAT
* *
56349 ATTA-TTTATTAATGGAAATTTATAAAT
1 ATTATTTTAATAATGGAAAATTATAAAT
56376 A-TATTT
1 ATTATTT
56382 GAAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 6 0.21
27 19 0.66
28 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (28 bp):
ATTATTTTAATAATGGAAAATTATAAAT
Found at i:57245 original size:13 final size:13
Alignment explanation
Indices: 57223--57258 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
57213 AAAATTCTAT
57223 TTGACCCTCCAAA
1 TTGACCCTCCAAA
* *
57236 TTGTCCCTCCAAC
1 TTGACCCTCCAAA
57249 TTGACCCTCC
1 TTGACCCTCC
57259 TAATAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.44, G:0.08, T:0.28
Consensus pattern (13 bp):
TTGACCCTCCAAA
Found at i:65042 original size:2 final size:2
Alignment explanation
Indices: 65035--65061 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
65025 AAAAGAATTG
65035 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
65062 TCTGTTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:68558 original size:18 final size:18
Alignment explanation
Indices: 68535--68572 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
68525 AATTTCTAGT
68535 AATGCCTTTTGGCTTGAC
1 AATGCCTTTTGGCTTGAC
68553 AATGCCTTTTGGCTTGAC
1 AATGCCTTTTGGCTTGAC
68571 AA
1 AA
68573 ACGTTCCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (18 bp):
AATGCCTTTTGGCTTGAC
Found at i:72781 original size:27 final size:28
Alignment explanation
Indices: 72741--72809 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
72731 GGTGTGATTG
*
72741 GGGAAAAA-AGAAAACAAG-AAAGAGAAA
1 GGGAAAAAGAAAAAACAAGAAAAG-GAAA
* *
72768 -GGAAATAGAAAAAAGAAGAAAAGGAAA
1 GGGAAAAAGAAAAAACAAGAAAAGGAAA
72795 GGGAAAAAGAAAAAA
1 GGGAAAAAGAAAAAA
72810 AAATTAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 6 0.17
27 12 0.34
28 17 0.49
ACGTcount: A:0.71, C:0.01, G:0.26, T:0.01
Consensus pattern (28 bp):
GGGAAAAAGAAAAAACAAGAAAAGGAAA
Found at i:72800 original size:28 final size:27
Alignment explanation
Indices: 72742--72809 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
72732 GTGTGATTGG
*
72742 GGAAAAA-AGAAAACAAGAAAGAGAAA
1 GGAAAAAGAAAAAACAAGAAAGAGAAA
* *
72768 GGAAATAGAAAAAAGAAGAAA-AGGAAA
1 GGAAAAAGAAAAAACAAGAAAGA-GAAA
72795 GGGAAAAAGAAAAAA
1 -GGAAAAAGAAAAAA
72810 AAATTAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 7 0.20
27 15 0.43
28 13 0.37
ACGTcount: A:0.72, C:0.01, G:0.25, T:0.01
Consensus pattern (27 bp):
GGAAAAAGAAAAAACAAGAAAGAGAAA
Found at i:72818 original size:29 final size:27
Alignment explanation
Indices: 72742--72821 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
72732 GTGTGATTGG
* *
72742 GGAAAAA-AGAAAACAAG-AAAGAGAAA
1 GGAAAAAGAAAAAAAAAGAAAAG-GAAA
* *
72768 GGAAATAGAAAAAAGAAGAAAAGGAAA
1 GGAAAAAGAAAAAAAAAGAAAAGGAAA
*
72795 GGGAAAAAGAAAAAAAAATTAAAAGGA
1 -GGAAAAAGAAAAAAAAA-GAAAAGGA
72822 CGTCATTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 6 0.14
27 12 0.27
28 19 0.43
29 7 0.16
ACGTcount: A:0.71, C:0.01, G:0.24, T:0.04
Consensus pattern (27 bp):
GGAAAAAGAAAAAAAAAGAAAAGGAAA
Found at i:72897 original size:13 final size:13
Alignment explanation
Indices: 72881--72907 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
72871 TGAATTTTCT
72881 TCCACTTAATTGA
1 TCCACTTAATTGA
72894 TCCACTTAATTGA
1 TCCACTTAATTGA
72907 T
1 T
72908 TATACGTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (13 bp):
TCCACTTAATTGA
Found at i:76021 original size:90 final size:90
Alignment explanation
Indices: 75868--76032 Score: 312
Period size: 90 Copynumber: 1.8 Consensus size: 90
75858 GGTTCAGGCT
*
75868 TCATTAAAGTGCTCTTAAGTACCATAAAGCTAAAACCGATGACACTTATTATATATTGAACTCAA
1 TCATTAAAGTGCTCTTAAGTACCATAAAACTAAAACCGATGACACTTATTATATATTGAACTCAA
75933 ATTAGTTTATCATGTATATTGATTC
66 ATTAGTTTATCATGTATATTGATTC
*
75958 TCATTAAAGTGCTCTTAAGTACCATAAAACTAAAACCGATGACACTTATTATCTATTGAACTCAA
1 TCATTAAAGTGCTCTTAAGTACCATAAAACTAAAACCGATGACACTTATTATATATTGAACTCAA
76023 ATTAGTTTAT
66 ATTAGTTTAT
76033 TTATACGTAC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 73 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (90 bp):
TCATTAAAGTGCTCTTAAGTACCATAAAACTAAAACCGATGACACTTATTATATATTGAACTCAA
ATTAGTTTATCATGTATATTGATTC
Found at i:86357 original size:21 final size:21
Alignment explanation
Indices: 86332--86414 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
86322 TATCTTAGAT
86332 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
86353 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
86374 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
86396 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
86415 TTACTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:86365 original size:25 final size:25
Alignment explanation
Indices: 86334--86382 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
86324 TCTTAGATAT
*
86334 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
86359 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
86383 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Done.