Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016375.1 Corchorus olitorius cultivar O-4 contig16408, 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: 54642
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38 GCATAATCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1211 original size:31 final size:30
Alignment explanation
Indices: 1171--1251 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 30
1161 TTTTCCTGCT
*
1171 TTTTCGGGGCTTTTTTTATGTTGTTGAAACC
1 TTTTGGGGGCTTTTTTTATGTTGTTGAAA-C
1202 TTTTGGGGGCTTTTTTTATGTTGTTGAAAC
1 TTTTGGGGGCTTTTTTTATGTTGTTGAAAC
*
1232 TTGTTGGGGGCTTTGTTTAT
1 TT-TTGGGGGCTTTTTTTAT
1252 TGTTTTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 3 0.06
31 44 0.94
ACGTcount: A:0.11, C:0.09, G:0.27, T:0.53
Consensus pattern (30 bp):
TTTTGGGGGCTTTTTTTATGTTGTTGAAAC
Found at i:6161 original size:27 final size:27
Alignment explanation
Indices: 6131--6185 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
6121 GCATGACTAC
6131 ATTCTTCCCTTTCTGATTGTGCTTTTA
1 ATTCTTCCCTTTCTGATTGTGCTTTTA
*
6158 ATTCTTCCCTTTTTGATTGTGCTTTTA
1 ATTCTTCCCTTTCTGATTGTGCTTTTA
6185 A
1 A
6186 AAGTGGGCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.13, C:0.20, G:0.11, T:0.56
Consensus pattern (27 bp):
ATTCTTCCCTTTCTGATTGTGCTTTTA
Found at i:8444 original size:1 final size:1
Alignment explanation
Indices: 8438--8468 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
8428 TTACCCAACA
*
8438 CCCCCCCCCCCCCCCCCCCCCCTCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
8469 TTTTTCACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.97, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:25632 original size:42 final size:42
Alignment explanation
Indices: 25573--25658 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
25563 AGTACTCACA
*
25573 CTACATTGTTACTATAAATATAAGTGATATGTGGAAATGAAT
1 CTACATTGTTACTATAAATATAAGTGATATGTCGAAATGAAT
25615 CTACATTGTTACTATAAATATAAGTGATATGTCGAAATGAAT
1 CTACATTGTTACTATAAATATAAGTGATATGTCGAAATGAAT
25657 CT
1 CT
25659 TGAGATTTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (42 bp):
CTACATTGTTACTATAAATATAAGTGATATGTCGAAATGAAT
Found at i:41707 original size:2 final size:2
Alignment explanation
Indices: 41700--41732 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41690 TTCTTCTTCT
41700 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
41733 TTTTCCCACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:54394 original size:321 final size:318
Alignment explanation
Indices: 53535--54642 Score: 1424
Period size: 325 Copynumber: 3.4 Consensus size: 318
53525 TAAAATTTGC
* * * ** * *
53535 AAAACTGACCCAAAAAGCTTTTCCTCAATTTTTTTGACACAATACTCAAAAAAAAATAATAATTC
1 AAAACTGACCCGAAAGGTTTTTTGTCAA-TTTTTTGCCATAATACTCAAAAAAAAATAA-AATTC
* **
53600 AACACCAAAAA-ATTGGAAAGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTT
64 AACGCCAAAAAGATT-GACGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTT
* *
53664 ATTTCTAATTAAATCGAAATAAGATTCAGATCCTCGTAAAAACAAATCCTTAAATCCAATGT-GG
128 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAT-TCGG
* * * * * *
53728 CTGAGATTTGATTAGATGGATATAGATATCTGTTCATGGAGTCTATCTGCAAAAAATGATGCAAA
192 CTGAGATTTGATTAGATGAATATACATA--T-TTCAAGGAGTCTTTCTGCCAAAAATCATGCAAA
* * *
53793 ACTGAG-CTGGGGCCTCGACACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACATGATTTCG
254 ACTGAGTC-GGGGCCAC-A-ACGCGTTTTTAGCC-AAAAACCGTGATTGTTAGTACACGATTTCG
53857 GCTA
315 GCTA
* * *
53861 AAAACTGACCCGAAAGGTTTTTTGTAAATTTTTTGCCATAATACTCAGAAAAAATATATAATTCA
1 AAAACTGACCCGAAAGGTTTTTTGTCAATTTTTTGCCATAATACTCA-AAAAAAAATAAAATTCA
* * * * * *
53926 ATGCCAAAAAGATTGTCGGGTTTTTCATGCTTCTAATATCGTTTTTGCATTATTT-CTAATTTTA
65 ACGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAA-TTTA
53990 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATTCGGCT
129 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATTCGGCT
*
54055 GAGATTTGATTAGATGAATATACATATTTCAAAGAGTCTTTCTGCCAAAAATCATGCAAAACTGA
194 GAGATTTGATTAGATGAATATACATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGA
* * * * *
54120 GTCGCGGACACAACGCGTTTTTAGCTCAAAAACTGTGATTGTTAGTACACAATTTCGACTA
259 GTCGGGGCCACAACGCGTTTTTAGC-CAAAAACCGTGATTGTTAGTACACGATTTCGGCTA
* ** * * **
54181 AAAACTGATCCGAAAAATTTTTTGTCAATTGTTTGTCATAATACTCATAAAAAAAATAAAAACCA
1 AAAACTGACCCGAAAGGTTTTTTGTCAATTTTTTGCCATAATACTCA-AAAAAAAATAAAATTCA
*
54246 ACGCCAAAAAGATTGACGGGCTTTTT-ACGCTTCAAATATCGTTTTTCCATTTTTTTCCGAATTT
65 ACGCCAAAAAGATTGACGGG-TTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTCCGAATTT
* * * *
54310 ATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAACACAAATTCATAAATCCAATTCGGC
128 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATTCGGC
54375 TGAGATTTGATTAGATGAATATACATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTG
193 TGAGATTTGATTAGATGAATATACATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTG
*
54440 AGTCGGGGCCCAGAAACGCGTTTTTAGCACAAAAACCGTGA-TGATTAGTACACGATTTCGGCTA
258 AGTCGGGG-CCA-CAACGCGTTTTTAGC-CAAAAACCGTGATTG-TTAGTACACGATTTCGGCTA
* *
54504 AAAACTTACCCGAAAGGTTTTTTGTCAATTTTTTGCCATAATAC-C-AAGAAAAA-AAAATTCAA
1 AAAACTGACCCGAAAGGTTTTTTGTCAATTTTTTGCCATAATACTCAAAAAAAAATAAAATTCAA
* * * * * ** * *
54566 TGCCAAAAAGATTGTCGCGCTTTTCATGCACCTAATATCGTTTTTCCATTTTTTCTGATTTTATT
66 CGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTTATT
54631 TCTAATTAAATC
131 TCTAATTAAATC
Statistics
Matches: 684, Mismatches: 85, Indels: 34
0.85 0.11 0.04
Matches are distributed among these distances:
318 31 0.05
319 42 0.06
320 141 0.21
321 147 0.21
322 47 0.07
323 83 0.12
324 4 0.01
325 155 0.23
326 34 0.05
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (318 bp):
AAAACTGACCCGAAAGGTTTTTTGTCAATTTTTTGCCATAATACTCAAAAAAAAATAAAATTCAA
CGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTTATT
TCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATTCGGCTGA
GATTTGATTAGATGAATATACATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGT
CGGGGCCACAACGCGTTTTTAGCCAAAAACCGTGATTGTTAGTACACGATTTCGGCTA
Done.