Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017800.1 Corchorus olitorius cultivar O-4 contig17833, 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: 40887
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Found at i:1266 original size:15 final size:16
Alignment explanation
Indices: 1233--1272 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1223 TTACTTTGCT
1233 TTGTTTTCTAGTATAA
1 TTGTTTTCTAGTATAA
*
1249 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTATAA
*
1264 TTGCTTTCT
1 TTGTTTTCT
1273 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTATAA
Found at i:12504 original size:31 final size:28
Alignment explanation
Indices: 12466--12526 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 28
12456 AAGAAACCAG
*
12466 AAATGGGAACTTTCCCTTCTTGTAAAACTAA
1 AAATGGGAACCTTCCCTT-TTG-AAAA-TAA
12497 AAATGGGAACCTTCCCTTTTGAAAATAA
1 AAATGGGAACCTTCCCTTTTGAAAATAA
12525 AA
1 AA
12527 CTGGTTGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 5 0.17
29 4 0.14
30 3 0.10
31 17 0.59
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (28 bp):
AAATGGGAACCTTCCCTTTTGAAAATAA
Found at i:19113 original size:31 final size:31
Alignment explanation
Indices: 19075--19239 Score: 130
Period size: 31 Copynumber: 5.5 Consensus size: 31
19065 TTTGGCTAAT
*
19075 TGCTCAAATAAGGGCCTAACGTTTATCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * **
19106 TGCTCAAATAAGGGTCTGATC-TTT-T-AATT
1 TGCTCAAATAAGGGCCT-AACGTTTGTCAAAA
*
19135 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * * **
19166 TGCTCAAATAAGAGCC---CGATTTTTTAATT
1 TGCTCAAATAAGGGCCTAACG-TTTGTCAAAA
*
19195 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
19226 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
19240 TCTGACATCG
Statistics
Matches: 101, Mismatches: 21, Indels: 24
0.69 0.14 0.16
Matches are distributed among these distances:
28 4 0.04
29 35 0.35
30 9 0.09
31 49 0.49
32 4 0.04
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
Found at i:19172 original size:60 final size:60
Alignment explanation
Indices: 19079--19244 Score: 278
Period size: 60 Copynumber: 2.8 Consensus size: 60
19069 GCTAATTGCT
**
19079 CAAATAAGGGCCTAACGTTTATCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
* * * *
19139 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGAGCCCGATTTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
19199 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGA
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGA
19245 CATCGAAAAT
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 97 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
Found at i:19322 original size:31 final size:29
Alignment explanation
Indices: 19284--19448 Score: 122
Period size: 31 Copynumber: 5.5 Consensus size: 29
19274 TTATACCAGA
19284 CCCTTATTTGAGCATTTTCGATAACGATAGG
1 CCCTTATTTGAGCATTTT-GA-AACGATAGG
** * *
19315 CCCTTATTTG-GCCAAATT-AAAAGATCGAG
1 CCCTTATTTGAG-CATTTTGAAACGATAG-G
*
19344 CCCTTATTTGAGCATTTTTGATAACGTTAGG
1 CCCTTATTTGAGCA-TTTTGA-AACGATAGG
** * *
19375 CCCTTATTTG-GCCAAATT-AAAAGATCGGG
1 CCCTTATTTGAG-CATTTTGAAACGAT-AGG
*
19404 CCCTTATTTGAGCATTTTGACAAACGTTAGG
1 CCCTTATTTGAGCATTTTG--AAACGATAGG
19435 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
19449 ATTAGCCTTT
Statistics
Matches: 103, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
28 10 0.10
29 31 0.30
30 8 0.08
31 44 0.43
32 10 0.10
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (29 bp):
CCCTTATTTGAGCATTTTGAAACGATAGG
Found at i:19352 original size:29 final size:28
Alignment explanation
Indices: 19313--19413 Score: 96
Period size: 29 Copynumber: 3.4 Consensus size: 28
19303 GATAACGATA
19313 GGCCCTTATTTGGCCAAATTAAAAGATC
1 GGCCCTTATTTGGCCAAATTAAAAGATC
** * * *
19341 GAGCCCTTATTTGAG-CATTTTTGATAACGTTA
1 G-GCCCTTATTTG-GCCA-AATT-A-AAAGATC
19373 GGCCCTTATTTGGCCAAATTAAAAGATC
1 GGCCCTTATTTGGCCAAATTAAAAGATC
19401 GGGCCCTTATTTG
1 -GGCCCTTATTTG
19414 AGCATTTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
28 5 0.09
29 26 0.46
30 6 0.11
31 14 0.25
32 5 0.09
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (28 bp):
GGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:19359 original size:60 final size:59
Alignment explanation
Indices: 19284--19444 Score: 268
Period size: 60 Copynumber: 2.7 Consensus size: 59
19274 TTATACCAGA
*
19284 CCCTTATTTGAGCATTTTCGATAACGATAGGCCCTTATTTGGCCAAATTAAAAGATCGAG
1 CCCTTATTTGAGCATTTT-GATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGAG
*
19344 CCCTTATTTGAGCATTTTTGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGAGCA-TTTTGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGAG
*
19404 CCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTTGA-TAACGTTAGGCCCTTATTTG
19445 AGCAATTAGC
Statistics
Matches: 96, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
59 6 0.06
60 86 0.90
61 4 0.04
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (59 bp):
CCCTTATTTGAGCATTTTGATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGAG
Found at i:31457 original size:21 final size:21
Alignment explanation
Indices: 31415--31459 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
31405 GCAAAATTGT
* ***
31415 CAAAAGGGGGGCGGTGTTTAG
1 CAAAAAGGGGGCGGTAAATAG
31436 CAAAAAGGGGGCGGTAAATAG
1 CAAAAAGGGGGCGGTAAATAG
31457 CAA
1 CAA
31460 CTCCCTTCTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.40, T:0.13
Consensus pattern (21 bp):
CAAAAAGGGGGCGGTAAATAG
Found at i:33768 original size:16 final size:15
Alignment explanation
Indices: 33747--33778 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
33737 GGAGGAGGAG
33747 AAAAAGAAGAAGAAAA
1 AAAAAGAAG-AGAAAA
33763 AAAAAGAAGAGAAAA
1 AAAAAGAAGAGAAAA
33778 A
1 A
33779 GGGGCCTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGAGAAAA
Found at i:33769 original size:13 final size:14
Alignment explanation
Indices: 33744--33778 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
33734 GAAGGAGGAG
*
33744 GAGAAAAAGAAGAA
1 GAGAAAAAAAAGAA
33758 GA-AAAAAAAAGAA
1 GAGAAAAAAAAGAA
33771 GAGAAAAA
1 GAGAAAAA
33779 GGGGCCTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
GAGAAAAAAAAGAA
Found at i:33863 original size:12 final size:12
Alignment explanation
Indices: 33842--33875 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
33832 AGGAAAAGAA
33842 GAAAAA-AAAAG
1 GAAAAAGAAAAG
*
33853 GAAAAGGAAAAG
1 GAAAAAGAAAAG
33865 GAAAAAGAAAA
1 GAAAAAGAAAA
33876 ATAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
GAAAAAGAAAAG
Found at i:40285 original size:31 final size:31
Alignment explanation
Indices: 40223--40290 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
40213 ATATGCAAAT
*
40223 TGAACAATTATCCAACATAAAACAACGAAAA
1 TGAACAATTATCCAACATAAAACAACAAAAA
* *
40254 TGAACAATTATCCAACA-AACACATATAAAAA
1 TGAACAATTATCCAACATAAAACA-ACAAAAA
40285 TGAACA
1 TGAACA
40291 TAGGGAAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.57, C:0.19, G:0.06, T:0.18
Consensus pattern (31 bp):
TGAACAATTATCCAACATAAAACAACAAAAA
Done.