Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019572.1 Corchorus olitorius cultivar O-4 contig19605, 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: 69434
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:13946 original size:17 final size:17
Alignment explanation
Indices: 13924--13958 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
13914 GAAAAAGTGC
13924 ATTCTTGTTGGTACATT
1 ATTCTTGTTGGTACATT
*
13941 ATTCTTGTTGGTATATT
1 ATTCTTGTTGGTACATT
13958 A
1 A
13959 ACATTATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (17 bp):
ATTCTTGTTGGTACATT
Found at i:14840 original size:21 final size:22
Alignment explanation
Indices: 14794--14855 Score: 108
Period size: 21 Copynumber: 2.8 Consensus size: 22
14784 ACTTTATTCG
14794 TTTCCAAAATCTTCTTTTTTTAT
1 TTTCCAAAATCTTC-TTTTTTAT
14817 TTTCCAAAATCTTCTTTTTT-T
1 TTTCCAAAATCTTCTTTTTTAT
14838 TTTCCAAAATCTTCTTTT
1 TTTCCAAAATCTTCTTTT
14856 GGGATATTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 19 0.49
22 6 0.15
23 14 0.36
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTCCAAAATCTTCTTTTTTAT
Found at i:18422 original size:27 final size:27
Alignment explanation
Indices: 18388--18443 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
18378 ATAATAAATG
18388 AACATGAATATGACCAAAGTAACTAAT
1 AACATGAATATGACCAAAGTAACTAAT
18415 AACATGAATATGACCAAAGTAACTAAT
1 AACATGAATATGACCAAAGTAACTAAT
18442 AA
1 AA
18444 AAACATGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.21
Consensus pattern (27 bp):
AACATGAATATGACCAAAGTAACTAAT
Found at i:18456 original size:30 final size:30
Alignment explanation
Indices: 18379--18457 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 30
18369 GTATGCCCAA
18379 TAATAAATGAACATGAATATGACCAAAGTAAC
1 TAATAAA--AACATGAATATGACCAAAGTAAC
18411 TAAT---AACATGAATATGACCAAAGTAAC
1 TAATAAAAACATGAATATGACCAAAGTAAC
*
18438 TAATAAAAACATGCATATGA
1 TAATAAAAACATGAATATGA
18458 TTGATGTAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
27 27 0.63
30 12 0.28
32 4 0.09
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.23
Consensus pattern (30 bp):
TAATAAAAACATGAATATGACCAAAGTAAC
Found at i:20117 original size:32 final size:32
Alignment explanation
Indices: 20081--20226 Score: 213
Period size: 32 Copynumber: 4.5 Consensus size: 32
20071 GTGTGAAAAG
* * *
20081 AAAACGCCCTTATTCATCGGCGTCTACACAAC
1 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
*
20113 AAAACGCCCTTATTTAGCGGCGTCTAAAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
20145 AAAACGCCCTTATTTAGCGGCGTCTGA-AGAAC
1 AAAACGCCCTTATTTAGCGGCGTCT-ACAGAAC
20177 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
1 AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
*
20209 AAAATGCCGCTATATTTA
1 AAAACGCC-CT-TATTTA
20227 ACTACTTCCA
Statistics
Matches: 105, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
31 1 0.01
32 95 0.90
33 3 0.03
34 6 0.06
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (32 bp):
AAAACGCCCTTATTTAGCGGCGTCTACAGAAC
Found at i:20376 original size:24 final size:24
Alignment explanation
Indices: 20348--20453 Score: 122
Period size: 24 Copynumber: 4.2 Consensus size: 24
20338 AAACGTGTCC
20348 AAATAGCGGCGTCTAGACGCCGTT
1 AAATAGCGGCGTCTAGACGCCGTT
*
20372 AAATAGTGGCGTCTAGACGCCGTT
1 AAATAGCGGCGTCTAGACGCCGTT
20396 AAATAGTGGCGTGGCGTCTAGACGCCGTT
1 AAATA---GC--GGCGTCTAGACGCCGTT
* ** *
20425 ACATAATGGCGTCTAGACGCCGCT
1 AAATAGCGGCGTCTAGACGCCGTT
20449 AAATA
1 AAATA
20454 TTATTTTTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
24 48 0.69
27 1 0.01
29 21 0.30
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (24 bp):
AAATAGCGGCGTCTAGACGCCGTT
Found at i:20419 original size:29 final size:28
Alignment explanation
Indices: 20355--20436 Score: 109
Period size: 29 Copynumber: 3.0 Consensus size: 28
20345 TCCAAATAGC
20355 GGCGTCTAGACGCCGTTAAATA----GT
1 GGCGTCTAGACGCCGTTAAATATGGCGT
20379 GGCGTCTAGACGCCGTTAAATAGTGGCGT
1 GGCGTCTAGACGCCGTTAAATA-TGGCGT
*
20408 GGCGTCTAGACGCCGTTACATAATGGCGT
1 GGCGTCTAGACGCCGTTAAAT-ATGGCGT
20437 CTAGACGCCG
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
24 22 0.43
29 28 0.55
30 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.32, T:0.24
Consensus pattern (28 bp):
GGCGTCTAGACGCCGTTAAATATGGCGT
Found at i:20676 original size:22 final size:21
Alignment explanation
Indices: 20646--20703 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
20636 AGCGGTGTTT
20646 AAAAACGCCGCTATATATTAA
1 AAAAACGCCGCTATATATTAA
*
20667 AATAAACGCCGCTATATGTTAA
1 AA-AAACGCCGCTATATATTAA
*
20689 AAAAAGCACCGCTAT
1 AAAAA-CGCCGCTAT
20704 CTCACTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22
Consensus pattern (21 bp):
AAAAACGCCGCTATATATTAA
Found at i:33964 original size:22 final size:20
Alignment explanation
Indices: 33934--33976 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
33924 GCTTTTCCTC
33934 TTTTTTTCTCAGGTCTTTTCT
1 TTTTTTTCTC-GGTCTTTTCT
33955 TTTTTCTTCTCGGT-TTTT-T
1 TTTTT-TTCTCGGTCTTTTCT
33974 TTT
1 TTT
33977 ATTTGTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.19
20 4 0.19
21 8 0.38
22 5 0.24
ACGTcount: A:0.02, C:0.16, G:0.09, T:0.72
Consensus pattern (20 bp):
TTTTTTTCTCGGTCTTTTCT
Found at i:34380 original size:23 final size:23
Alignment explanation
Indices: 34344--34387 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
34334 CTTTTCTTGT
34344 GTAATTTTTGTTTGCTTGGTTCG
1 GTAATTTTTGTTTGCTTGGTTCG
*
34367 GTAATGTTTT-TTTGGTTGGTT
1 GTAAT-TTTTGTTTGCTTGGTT
34388 AATTTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.09, C:0.05, G:0.27, T:0.59
Consensus pattern (23 bp):
GTAATTTTTGTTTGCTTGGTTCG
Found at i:48835 original size:56 final size:56
Alignment explanation
Indices: 48768--48882 Score: 221
Period size: 56 Copynumber: 2.1 Consensus size: 56
48758 AATAATAATA
48768 ATTGTCCTATTTGTGTATCGGACAATTTGCTGTTTGCATCTCGGACTTTTTTCCTG
1 ATTGTCCTATTTGTGTATCGGACAATTTGCTGTTTGCATCTCGGACTTTTTTCCTG
*
48824 ATTGTCCTATTTGTGTATCGGACGATTTGCTGTTTGCATCTCGGACTTTTTTCCTG
1 ATTGTCCTATTTGTGTATCGGACAATTTGCTGTTTGCATCTCGGACTTTTTTCCTG
48880 ATT
1 ATT
48883 ATTTTTTACG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (56 bp):
ATTGTCCTATTTGTGTATCGGACAATTTGCTGTTTGCATCTCGGACTTTTTTCCTG
Found at i:60955 original size:37 final size:37
Alignment explanation
Indices: 60905--60978 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
60895 ATTTTGTTGT
60905 GCGGAAATGAGGAATTAAAATGCCAAAAAACAAACGA
1 GCGGAAATGAGGAATTAAAATGCCAAAAAACAAACGA
* *
60942 GCGGAAATGAGGAATTAAAATGCGAAAAAATAAACGA
1 GCGGAAATGAGGAATTAAAATGCCAAAAAACAAACGA
60979 CTGTAAGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.54, C:0.11, G:0.23, T:0.12
Consensus pattern (37 bp):
GCGGAAATGAGGAATTAAAATGCCAAAAAACAAACGA
Found at i:64068 original size:15 final size:15
Alignment explanation
Indices: 64040--64118 Score: 59
Period size: 15 Copynumber: 5.0 Consensus size: 15
64030 TTTATTCATT
*
64040 AATATTAATAATATA
1 AATATAAATAATATA
*
64055 AATATAAATTATATA
1 AATATAAATAATATA
* * *
64070 CATTTCAAATATATTAATT
1 AATAT-AAATA-A-T-ATA
*
64089 AATATATATAATATA
1 AATATAAATAATATA
*
64104 AATATAAAAAATATA
1 AATATAAATAATATA
64119 TTTTATTTAT
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
15 31 0.65
16 5 0.10
17 2 0.04
18 5 0.10
19 5 0.10
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATAAATAATATA
Done.