Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019092.1 Corchorus olitorius cultivar O-4 contig19125, 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: 40109
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Found at i:207 original size:46 final size:46
Alignment explanation
Indices: 72--491 Score: 526
Period size: 46 Copynumber: 9.1 Consensus size: 46
62 TGGCCCGTGG
* * * *
72 CCCGCCAAGTAGCAGATGCAGAGGTAGGGGGCGATAAAAAATCAA-
1 CCCGCCAAGAAGCCGATACAGAGGTAGAGGGCGATAAAAAATCAAC
* *
117 CCCGCCAAGAAGCCGATGCAGAAGTAGAGGGCGATAAAATAATCAAC
1 CCCGCCAAGAAGCCGATACAGAGGTAGAGGGCGATAAAA-AATCAAC
** * * * *
164 CCCGCCAA-AAGGTTGATACCGAGGAATAGGGCGATAAAAAATCAAT
1 CCCGCCAAGAA-GCCGATACAGAGGTAGAGGGCGATAAAAAATCAAC
* *
210 CCCGCCAAGTAGCCGATGCAGAGGTAGAGGGCGATAAAAAATCAAC
1 CCCGCCAAGAAGCCGATACAGAGGTAGAGGGCGATAAAAAATCAAC
* *
256 CCCGCCAAGAAGCCGATGCAGAAGTAGAGGGCGATAAAATAATCAAC
1 CCCGCCAAGAAGCCGATACAGAGGTAGAGGGCGATAAAA-AATCAAC
* *
303 CCCGCCAA-AAGCCTGCTACAGAGGTAGAGGGTGATAAAAAATCAAC
1 CCCGCCAAGAAGCC-GATACAGAGGTAGAGGGCGATAAAAAATCAAC
* *
349 CCCGCCAA-AAGCCGATATAGAGGAAGAGGGCGATAAAAAATCAAC
1 CCCGCCAAGAAGCCGATACAGAGGTAGAGGGCGATAAAAAATCAAC
* * *
394 CCCGCCAAGAAGCCGATGCAGAAGTAGAGGGTGATAAAAAAAATCAAC
1 CCCGCCAAGAAGCCGATACAGAGGTAGAGGGCGAT--AAAAAATCAAC
*
442 CCCGCCAA-AAGCCGATATAGAGGTAGAGGGCGATAAAATAATCAAC
1 CCCGCCAAGAAGCCGATACAGAGGTAGAGGGCGATAAAA-AATCAAC
488 CCCG
1 CCCG
492 GCTTCGATGC
Statistics
Matches: 326, Mismatches: 39, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
45 75 0.23
46 144 0.44
47 88 0.27
48 19 0.06
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (46 bp):
CCCGCCAAGAAGCCGATACAGAGGTAGAGGGCGATAAAAAATCAAC
Found at i:230 original size:93 final size:91
Alignment explanation
Indices: 72--491 Score: 538
Period size: 93 Copynumber: 4.5 Consensus size: 91
62 TGGCCCGTGG
* * * * *
72 CCCGCCAAGTAGCAGATGCAGAGGTAGGGGGCGATAAAAAATCAA-CCCGCCAAGAAGCCGATGC
1 CCCGCCAA-AAGCCGATACAGAGGAAGAGGGCGATAAAAAATCAACCCCGCCAAGAAGCCGATGC
136 AGAAGTAGAGGGCGATAAAATAATCAAC
65 AGAAGTAGAGGGCGATAAAA-AATCAAC
** * * * *
164 CCCGCCAAAAGGTTGATACCGAGGAATAGGGCGATAAAAAATCAATCCCGCCAAGTAGCCGATGC
1 CCCGCCAAAA-GCCGATACAGAGGAAGAGGGCGATAAAAAATCAACCCCGCCAAGAAGCCGATGC
*
229 AGAGGTAGAGGGCGATAAAAAATCAAC
65 AGAAGTAGAGGGCGATAAAAAATCAAC
* * * *
256 CCCGCCAAGAAGCCGATGCAGAAGTAGAGGGCGATAAAATAATCAACCCCGCCAA-AAGCCTGCT
1 CCCGCCAA-AAGCCGATACAGAGGAAGAGGGCGATAAAA-AATCAACCCCGCCAAGAAGCC-GAT
* * *
320 ACAGAGGTAGAGGGTGATAAAAAATCAAC
63 GCAGAAGTAGAGGGCGATAAAAAATCAAC
*
349 CCCGCCAAAAGCCGATATAGAGGAAGAGGGCGATAAAAAATCAACCCCGCCAAGAAGCCGATGCA
1 CCCGCCAAAAGCCGATACAGAGGAAGAGGGCGATAAAAAATCAACCCCGCCAAGAAGCCGATGCA
*
414 GAAGTAGAGGGTGATAAAAAAAATCAAC
66 GAAGTAGAGGGCGAT--AAAAAATCAAC
* *
442 CCCGCCAAAAGCCGATATAGAGGTAGAGGGCGATAAAATAATCAACCCCG
1 CCCGCCAAAAGCCGATACAGAGGAAGAGGGCGATAAAA-AATCAACCCCG
492 GCTTCGATGC
Statistics
Matches: 289, Mismatches: 30, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
91 34 0.12
92 106 0.37
93 138 0.48
94 11 0.04
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (91 bp):
CCCGCCAAAAGCCGATACAGAGGAAGAGGGCGATAAAAAATCAACCCCGCCAAGAAGCCGATGCA
GAAGTAGAGGGCGATAAAAAATCAAC
Found at i:2676 original size:35 final size:35
Alignment explanation
Indices: 2627--2732 Score: 153
Period size: 35 Copynumber: 3.0 Consensus size: 35
2617 CAAGGCAATT
* **
2627 CAAAGTTCTTCTCCATCAAGCAAAGCAA-ATCTGCAG
1 CAAAGTTCTTCTCCATCAA-CAAAGCAACAAC-AAAG
2663 CAAAGTT-TTCTCCATCAACAAAGCAACAACAAAG
1 CAAAGTTCTTCTCCATCAACAAAGCAACAACAAAG
2697 CAAAGTTCTTCTCCATCAACAAAGCAACAACAAAG
1 CAAAGTTCTTCTCCATCAACAAAGCAACAACAAAG
2732 C
1 C
2733 CTACGAAAGT
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
34 17 0.26
35 41 0.63
36 7 0.11
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.19
Consensus pattern (35 bp):
CAAAGTTCTTCTCCATCAACAAAGCAACAACAAAG
Found at i:4021 original size:25 final size:25
Alignment explanation
Indices: 3989--4039 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
3979 ATGAATACGT
3989 TGGCAAATTTTGTATTTGGGCAAGA
1 TGGCAAATTTTGTATTTGGGCAAGA
*
4014 TGGCAAATTTTGTTTTTGGGCAAGA
1 TGGCAAATTTTGTATTTGGGCAAGA
4039 T
1 T
4040 TCCCATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.39
Consensus pattern (25 bp):
TGGCAAATTTTGTATTTGGGCAAGA
Found at i:4221 original size:13 final size:13
Alignment explanation
Indices: 4203--4228 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4193 TTCACCAATG
4203 AATAGGAATGGTT
1 AATAGGAATGGTT
4216 AATAGGAATGGTT
1 AATAGGAATGGTT
4229 GTACACCGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
AATAGGAATGGTT
Found at i:12162 original size:37 final size:37
Alignment explanation
Indices: 12121--12202 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
12111 AAAAGGGAAG
*
12121 GAGTGGATAGTGTAACATGTTAAAAGCCAAACATGGA
1 GAGTGGATAGTGTAACATGTTAAAAGCCAAAAATGGA
* * *
12158 GAGTGAAAAGTGTAACATGTTAAGAGCCAAAAATGGA
1 GAGTGGATAGTGTAACATGTTAAAAGCCAAAAATGGA
12195 GAGTGGAT
1 GAGTGGAT
12203 CCAATGGAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.41, C:0.09, G:0.29, T:0.21
Consensus pattern (37 bp):
GAGTGGATAGTGTAACATGTTAAAAGCCAAAAATGGA
Found at i:12771 original size:43 final size:43
Alignment explanation
Indices: 12716--12800 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
12706 AGTCAACCAG
12716 GCATACATAAGATTCCAAAAGGTCAATGGTTATATAAAGGCAT
1 GCATACATAAGATTCCAAAAGGTCAATGGTTATATAAAGGCAT
12759 GCATACATAAGATTCCAAAAGGTCAATGGTTATATAAAGGCA
1 GCATACATAAGATTCCAAAAGGTCAATGGTTATATAAAGGCA
12801 GACAATAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (43 bp):
GCATACATAAGATTCCAAAAGGTCAATGGTTATATAAAGGCAT
Found at i:16280 original size:2 final size:2
Alignment explanation
Indices: 16268--16321 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
16258 AATCGAATTC
* * * *
16268 TA TA CA TA TA TA TG TA TA TA TA TA TA TA TA TG TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
16310 TT TA TA TA TA TA
1 TA TA TA TA TA TA
16322 AAATAAAAGC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16294 original size:18 final size:18
Alignment explanation
Indices: 16268--16321 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
16258 AATCGAATTC
*
16268 TATACATATATATGTATA
1 TATATATATATATGTATA
16286 TATATATATATATGTATA
1 TATATATATATATGTATA
* * *
16304 TTTATATTTATATATATA
1 TATATATATATATGTATA
16322 AAATAAAAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (18 bp):
TATATATATATATGTATA
Done.