Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018687.1 Corchorus olitorius cultivar O-4 contig18720, 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: 28879
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:9019 original size:32 final size:31
Alignment explanation
Indices: 8945--9003 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
8935 TTAAGAGATA
8945 AAAGTGGGAAAATTGTCCCGATTTTGATAATTT
1 AAAG-GGGAAAATTGTCCC-ATTTTGATAATTT
8978 AAAGGGGAAAATTGTCCC-TTTT-ATAA
1 AAAGGGGAAAATTGTCCCATTTTGATAA
9004 AAGTTTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 4 0.15
30 4 0.15
32 14 0.54
33 4 0.15
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (31 bp):
AAAGGGGAAAATTGTCCCATTTTGATAATTT
Found at i:10696 original size:3 final size:3
Alignment explanation
Indices: 10688--10733 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
10678 GCCACCCTGC
10688 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
10734 GTTTCAACAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:10786 original size:20 final size:20
Alignment explanation
Indices: 10761--10800 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
10751 AAAAGTCATC
10761 AATTAAATAGTATTAAAGTT
1 AATTAAATAGTATTAAAGTT
10781 AATTAAATAGTATTAAAGTT
1 AATTAAATAGTATTAAAGTT
10801 TTTGGCATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (20 bp):
AATTAAATAGTATTAAAGTT
Found at i:16867 original size:29 final size:30
Alignment explanation
Indices: 16805--16881 Score: 122
Period size: 29 Copynumber: 2.6 Consensus size: 30
16795 TGAATGTAAC
16805 AAGATGAACCATTCTCATAACATCTATATG
1 AAGATGAACCATTCTCATAACATCTATATG
*
16835 AAGATGAACCATTC-CATCACATCTATA-G
1 AAGATGAACCATTCTCATAACATCTATATG
16863 AAAGATGAACCATTCTCAT
1 -AAGATGAACCATTCTCAT
16882 TAATCACATA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
28 1 0.02
29 26 0.59
30 17 0.39
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.27
Consensus pattern (30 bp):
AAGATGAACCATTCTCATAACATCTATATG
Found at i:17394 original size:3 final size:3
Alignment explanation
Indices: 17386--17418 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
17376 TCTTGTCTGG
*
17386 CAA CAA CAA CAA CAA TAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
17419 AAAAAAAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.30, G:0.00, T:0.03
Consensus pattern (3 bp):
CAA
Found at i:21721 original size:16 final size:16
Alignment explanation
Indices: 21702--21735 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21692 GAGCCGAAAA
21702 ACCCAAAACCCGAATG
1 ACCCAAAACCCGAATG
* *
21718 ACCCGAAACCCGAGTG
1 ACCCAAAACCCGAATG
21734 AC
1 AC
21736 TTGAGGCTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.38, G:0.18, T:0.06
Consensus pattern (16 bp):
ACCCAAAACCCGAATG
Found at i:23061 original size:92 final size:93
Alignment explanation
Indices: 22950--23132 Score: 237
Period size: 93 Copynumber: 2.0 Consensus size: 93
22940 GCTTTTTAAT
* * * *
22950 TAAATTAGTAATATCGTAAAAAT-AAATAGGTATGAG-GATATTAGATTTAATTAAATAAAACA-
1 TAAAATAGTAAAATCGTAAAAATAAAATAAGTATAAGAG-TATTAGATTTAATTAAATAAAA-AT
* *
23012 ATAGTTTTTAGTGGAGTAAAACTATAAAAG
64 AGAGTTTTTAGTGGACTAAAACTATAAAAG
* *
23042 TAAAATAGTAAAATGGTAAAAATAAAATAATTATAAGAGTATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATCGTAAAAATAAAATAAGTATAAGAGTATTAGATTTAATTAAATAAAAATAG
* *
23107 AGTTTTTAGTTGACTGAAACTATAAA
66 AGTTTTTAGTGGACTAAAACTATAAA
23133 TATATTCGAA
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
92 21 0.27
93 56 0.72
94 1 0.01
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.33
Consensus pattern (93 bp):
TAAAATAGTAAAATCGTAAAAATAAAATAAGTATAAGAGTATTAGATTTAATTAAATAAAAATAG
AGTTTTTAGTGGACTAAAACTATAAAAG
Found at i:24232 original size:60 final size:60
Alignment explanation
Indices: 24145--24277 Score: 176
Period size: 60 Copynumber: 2.2 Consensus size: 60
24135 GTTAATTGCT
* * * **
24145 CAAATAAGGGTCTAACGCTTGTTAAAATGCTCAAATAAAGATATGATCTTTTAATTTGGG
1 CAAATAAGGGCCTAACGCTTATCAAAATGCTCAAATAAAGATATGATCTTTTAATTTGAC
* * * * *
24205 CAAATAAGGGCCTAATGTTTATCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGAC
1 CAAATAAGGGCCTAACGCTTATCAAAATGCTCAAATAAAGATATGATCTTTTAATTTGAC
24265 CAAATAAGGGCCT
1 CAAATAAGGGCCT
24278 GGCATCGAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGCTTATCAAAATGCTCAAATAAAGATATGATCTTTTAATTTGAC
Found at i:24416 original size:60 final size:60
Alignment explanation
Indices: 24319--24479 Score: 189
Period size: 60 Copynumber: 2.7 Consensus size: 60
24309 TGACGTCAGA
* * * *
24319 CCCTTATTTGAGCATTTTTTATAACGTTAGGCCCTTATTTGGTCAAATTAAAAGATCGGG
1 CCCTTATTTAAGCATTTTTGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGG
* * **
24379 CCCTTATTTAAGCATTTTTGATAACGTTAGACTCTTATTTGGCCAAATTAAAAGATTGTA
1 CCCTTATTTAAGCATTTTTGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGG
* * * * *
24439 CCCTTATTTGAGGA-TTTTAACAAACGTTAGGCCCTTATTTG
1 CCCTTATTTAAGCATTTTTGA-TAACGTTAGACCCTTATTTG
24480 AGCAATTAAC
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
59 5 0.06
60 81 0.94
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (60 bp):
CCCTTATTTAAGCATTTTTGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGG
Found at i:27962 original size:13 final size:13
Alignment explanation
Indices: 27925--27970 Score: 69
Period size: 12 Copynumber: 3.7 Consensus size: 13
27915 TTATGCACCC
27925 AAAACATTTAT-T
1 AAAACATTTATAT
27937 AAAACATTT-TAT
1 AAAACATTTATAT
*
27949 AAAGCATTTATAT
1 AAAACATTTATAT
27962 AAAACATTT
1 AAAACATTT
27971 CCTCAACGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
11 1 0.03
12 18 0.60
13 11 0.37
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (13 bp):
AAAACATTTATAT
Found at i:28399 original size:27 final size:28
Alignment explanation
Indices: 28369--28432 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
28359 TCCGACGTTT
* *
28369 AAGGGCAAAATTGTAA-TTTAGTCAACC
1 AAGGGCAAAATGGTAATTTTAGCCAACC
* *
28396 AAGGGTAAAATGGTAATTTTAGCCGACC
1 AAGGGCAAAATGGTAATTTTAGCCAACC
28424 AAGGGCAAA
1 AAGGGCAAA
28433 TACGTAATTC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 14 0.45
28 17 0.55
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (28 bp):
AAGGGCAAAATGGTAATTTTAGCCAACC
Found at i:28433 original size:27 final size:26
Alignment explanation
Indices: 28369--28433 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
28359 TCCGACGTTT
* *
28369 AAGGGCAAAATTGTAATTTAGTCAACC
1 AAGGGC-AAATGGTAATTTAGCCAACC
* *
28396 AAGGGTAAAATGGTAATTTTAGCCGACC
1 AAGGG-CAAATGGTAA-TTTAGCCAACC
28424 AAGGGCAAAT
1 AAGGGCAAAT
28434 ACGTAATTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 17 0.55
28 14 0.45
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (26 bp):
AAGGGCAAATGGTAATTTAGCCAACC
Done.