Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018357.1 Corchorus olitorius cultivar O-4 contig18390, 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: 91429
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:11128 original size:40 final size:40
Alignment explanation
Indices: 11066--11146 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
11056 ACTTGACCCT
* *
11066 CCTAATAATTAAGGAAATAAATTAAATCTAGGTTTAGCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCC
*
11106 CCTAATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCC
11146 C
1 C
11147 TAGTTATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (40 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCC
Found at i:11266 original size:13 final size:13
Alignment explanation
Indices: 11248--11277 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11238 ACACGTCAGA
11248 AGGGACAAATTGG
1 AGGGACAAATTGG
*
11261 AGGGACAAGTTGG
1 AGGGACAAATTGG
11274 AGGG
1 AGGG
11278 TCATGTAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.47, T:0.13
Consensus pattern (13 bp):
AGGGACAAATTGG
Found at i:34911 original size:2 final size:2
Alignment explanation
Indices: 34904--34929 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34894 CAAGATTAAG
34904 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
34930 TATGGGGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41313 original size:21 final size:21
Alignment explanation
Indices: 41288--41327 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
41278 GTTGCTCTAA
*
41288 TAATCTCATCTGTACAGTACC
1 TAATCTAATCTGTACAGTACC
41309 TAATCTAATCTGTACAGTA
1 TAATCTAATCTGTACAGTA
41328 TAATCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.35
Consensus pattern (21 bp):
TAATCTAATCTGTACAGTACC
Found at i:56620 original size:15 final size:15
Alignment explanation
Indices: 56602--56630 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
56592 AAATTAAAAC
56602 ATGTTTAATTGAATA
1 ATGTTTAATTGAATA
56617 ATGTTTAATTGAAT
1 ATGTTTAATTGAAT
56631 CTATCTAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (15 bp):
ATGTTTAATTGAATA
Found at i:63337 original size:9 final size:8
Alignment explanation
Indices: 63312--63357 Score: 67
Period size: 8 Copynumber: 5.8 Consensus size: 8
63302 AACATAACCT
63312 AAAA-GAA
1 AAAATGAA
*
63319 AAAAAGAA
1 AAAATGAA
63327 AAAATGAA
1 AAAATGAA
63335 AAAATGAA
1 AAAATGAA
63343 AAAATGAA
1 AAAATGAA
63351 AACAATG
1 AA-AATG
63358 TTCCTGCTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
7 4 0.11
8 28 0.78
9 4 0.11
ACGTcount: A:0.76, C:0.02, G:0.13, T:0.09
Consensus pattern (8 bp):
AAAATGAA
Found at i:65705 original size:21 final size:21
Alignment explanation
Indices: 65679--65718 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
65669 TGCTATCCTA
65679 CAATGGTGACTTCCGTGGCTC
1 CAATGGTGACTTCCGTGGCTC
65700 CAATGGTGACTTCCGTGGC
1 CAATGGTGACTTCCGTGGC
65719 CCCCAGAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.28
Consensus pattern (21 bp):
CAATGGTGACTTCCGTGGCTC
Found at i:72771 original size:60 final size:60
Alignment explanation
Indices: 72706--72867 Score: 209
Period size: 60 Copynumber: 2.7 Consensus size: 60
72696 GTTAATTGCT
*** * ***
72706 CAAATAAGGGCCTAGTGTTTGTCAAAATGTTCAAATAAGGGTTTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACATTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
*
72766 TAAATAAGGGCCTAACATTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACATTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
* * *
72826 CAAATAAGGGCCTAAC-GTTATCGAAAATGCTCAATTAAGGGC
1 CAAATAAGGGCCTAACATTTGTC-AAAATGCTCAAATAAGGGC
72868 TTGGTGTAGA
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
59 4 0.04
60 85 0.96
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (60 bp):
CAAATAAGGGCCTAACATTTGTCAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:72805 original size:31 final size:30
Alignment explanation
Indices: 72702--72867 Score: 92
Period size: 31 Copynumber: 5.5 Consensus size: 30
72692 TTTGGTTAAT
**
72702 TGCTCAAATAAGGGCCTAGTGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTA-ACTTTGTCAAAA
* ** * **
72733 TGTTCAAATAAGGGTTTGATCTTT-T-AATT
1 TGCTCAAATAAGGGCCT-AACTTTGTCAAAA
72762 TGGCT-AAATAAGGGCCTAACATTTGTCAAAA
1 T-GCTCAAATAAGGGCCTAAC-TTTGTCAAAA
* * **
72793 TGCTCAAATAAGGGCCCGATCTTT-T-AATT
1 TGCTCAAATAAGGG-CCTAACTTTGTCAAAA
* *
72822 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGCCTAACTTTGTC-AAAA
*
72853 TGCTCAATTAAGGGC
1 TGCTCAAATAAGGGC
72868 TTGGTGTAGA
Statistics
Matches: 101, Mismatches: 22, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
28 8 0.08
29 30 0.30
30 12 0.12
31 46 0.46
32 5 0.05
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACTTTGTCAAAA
Found at i:73057 original size:60 final size:60
Alignment explanation
Indices: 72907--73068 Score: 191
Period size: 60 Copynumber: 2.7 Consensus size: 60
72897 AAACGGCATA
* *
72907 CCCTTATTTGAGCATTTTCGATAACATTAGACTCTTATTTGACCAAATTAAAAGATCAAG
1 CCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCAAG
* * * ***
72967 CCCTTATTTGAGCATTTCCGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATTGTG
1 CCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCAAG
* * * * *
73027 GCCTTATTTAAGCATTTTGGCA-AATATTAGGCCTTTATTTGA
1 CCCTTATTTGAGCATTTTCG-ATAACATTAGGCCCTTATTTGA
73069 GCAATTAGCC
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
60 84 0.99
61 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCAAG
Found at i:76024 original size:38 final size:38
Alignment explanation
Indices: 75980--76057 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
75970 CCATGATGAG
75980 AGCTAAAAATGGAATTAGAATAACAGGTAAAGCGCCAT
1 AGCTAAAAATGGAATTAGAATAACAGGTAAAGCGCCAT
76018 AGCTAAAAATGGAATTAGAATAACAGGTAAAGCGCCAT
1 AGCTAAAAATGGAATTAGAATAACAGGTAAAGCGCCAT
76056 AG
1 AG
76058 GTGAAACCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.47, C:0.13, G:0.22, T:0.18
Consensus pattern (38 bp):
AGCTAAAAATGGAATTAGAATAACAGGTAAAGCGCCAT
Found at i:78448 original size:27 final size:27
Alignment explanation
Indices: 78398--78449 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
78388 TGAACAAGTT
**
78398 AATAAAAAGTTTGATTTTTTTTTAAGG
1 AATAAAAAGTTTGATTTTAATTTAAGG
*
78425 AATAAAAGGTTTGATTTTAATTTAA
1 AATAAAAAGTTTGATTTTAATTTAA
78450 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.46
Consensus pattern (27 bp):
AATAAAAAGTTTGATTTTAATTTAAGG
Found at i:83574 original size:10 final size:11
Alignment explanation
Indices: 83534--83576 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
83524 GAAAGTTTAG
83534 AGAGAAAAGAA
1 AGAGAAAAGAA
83545 AGAGAAAAGAA
1 AGAGAAAAGAA
*
83556 GCGAGAGAAAGAA
1 -AGAGA-AAAGAA
83569 AGAGAAAA
1 AGAGAAAA
83577 ATTGGGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 14 0.50
12 8 0.29
13 6 0.21
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.00
Consensus pattern (11 bp):
AGAGAAAAGAA
Done.