Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024909.1 Corchorus olitorius cultivar O-4 contig24942, 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: 28900
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2104 original size:150 final size:153
Alignment explanation
Indices: 1940--2356 Score: 542
Period size: 154 Copynumber: 2.7 Consensus size: 153
1930 TGACTAGGAC
** * *
1940 AAAGAGAACCGGGGATCGCCGGCTTTAG-AGAGGAGA-AAAAAGTA-CTGAGGGCGCCAGAGAGG
1 AAAGAGAGTCGGGGATCGCCGGCTAT-GCAGA-GAGACAAAAAG-AGCGGAGGGCGCCAGAGAGG
* * *
2002 G-AGAGCAGA-TG-TGCT-TGTCCCACCGGGCGTGCCAAAAAGAGATGTTGGTGCAGCCGAGTGG
63 GAAGA-CAAACTGTTGCTGTGTCCCACCGAGCGTGCCAAAAAGAGATGTTGGTGCAGCCGAGTAG
2063 GCAGTCCAACGTAGCACGGAAAATTGT
127 GCAGTCCAACGTAGCACGGAAAATTGT
* * * *
2090 AAAGAGAGTCGGGGATCGCCGGCTATGCAGAGAGACAGAGAGAGGGGAGGGCGCCATAGAGGGAA
1 AAAGAGAGTCGGGGATCGCCGGCTATGCAGAGAGACAAAAAGAGCGGAGGGCGCCAGAGAGGGAA
* *
2155 GACAAACTGTTTGTTGTGTCCCACCGAGCGTGCCAAAAAGAGATGTTGGTGCGGCCGAGTAGGCA
66 GACAAACTG-TTGCTGTGTCCCACCGAGCGTGCCAAAAAGAGATGTTGGTGCAGCCGAGTAGGCA
*
2220 GTCCAACGTAGCATGGAAAATTGT
130 GTCCAACGTAGCACGGAAAATTGT
* * *
2244 AAAGAGAGTCGGGGATCGCCGGCTATGCAGAGAGACAGAGAGAGGGGAGGGCGCCAGAGAGGGAA
1 AAAGAGAGTCGGGGATCGCCGGCTATGCAGAGAGACAAAAAGAGCGGAGGGCGCCAGAGAGGGAA
* * * *
2309 GACAAACTGTTTGTTGTGTCCCACCGGGTGTGCCAAAAAGAAATGTTG
66 GACAAACTG-TTGCTGTGTCCCACCGAGCGTGCCAAAAAGAGATGTTG
2357 CGCCAAAAAT
Statistics
Matches: 241, Mismatches: 18, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
149 6 0.02
150 49 0.20
151 5 0.02
153 3 0.01
154 178 0.74
ACGTcount: A:0.30, C:0.18, G:0.37, T:0.15
Consensus pattern (153 bp):
AAAGAGAGTCGGGGATCGCCGGCTATGCAGAGAGACAAAAAGAGCGGAGGGCGCCAGAGAGGGAA
GACAAACTGTTGCTGTGTCCCACCGAGCGTGCCAAAAAGAGATGTTGGTGCAGCCGAGTAGGCAG
TCCAACGTAGCACGGAAAATTGT
Found at i:2220 original size:154 final size:154
Alignment explanation
Indices: 1986--2356 Score: 617
Period size: 154 Copynumber: 2.4 Consensus size: 154
1976 AAAAAGTACT
* *
1986 GAGGGCGCCAGAGAGGG-AGAGCAGA-TG--TGCT-TGTCCCACCGGGCGTGCCAAAAAGAGATG
1 GAGGGCGCCAGAGAGGGAAGA-CAAACTGTTTGTTGTGTCCCACCGGGCGTGCCAAAAAGAGATG
*
2046 TTGGTGCAGCCGAGTGGGCAGTCCAACGTAGCACGGAAAATTGTAAAGAGAGTCGGGGATCGCCG
65 TTGGTGCAGCCGAGTAGGCAGTCCAACGTAGCACGGAAAATTGTAAAGAGAGTCGGGGATCGCCG
2111 GCTATGCAGAGAGACAGAGAGAGGG
130 GCTATGCAGAGAGACAGAGAGAGGG
* *
2136 GAGGGCGCCATAGAGGGAAGACAAACTGTTTGTTGTGTCCCACCGAGCGTGCCAAAAAGAGATGT
1 GAGGGCGCCAGAGAGGGAAGACAAACTGTTTGTTGTGTCCCACCGGGCGTGCCAAAAAGAGATGT
* *
2201 TGGTGCGGCCGAGTAGGCAGTCCAACGTAGCATGGAAAATTGTAAAGAGAGTCGGGGATCGCCGG
66 TGGTGCAGCCGAGTAGGCAGTCCAACGTAGCACGGAAAATTGTAAAGAGAGTCGGGGATCGCCGG
2266 CTATGCAGAGAGACAGAGAGAGGG
131 CTATGCAGAGAGACAGAGAGAGGG
* *
2290 GAGGGCGCCAGAGAGGGAAGACAAACTGTTTGTTGTGTCCCACCGGGTGTGCCAAAAAGAAATGT
1 GAGGGCGCCAGAGAGGGAAGACAAACTGTTTGTTGTGTCCCACCGGGCGTGCCAAAAAGAGATGT
2355 TG
66 TG
2357 CGCCAAAAAT
Statistics
Matches: 205, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
150 19 0.09
151 5 0.02
153 3 0.01
154 178 0.87
ACGTcount: A:0.29, C:0.19, G:0.37, T:0.16
Consensus pattern (154 bp):
GAGGGCGCCAGAGAGGGAAGACAAACTGTTTGTTGTGTCCCACCGGGCGTGCCAAAAAGAGATGT
TGGTGCAGCCGAGTAGGCAGTCCAACGTAGCACGGAAAATTGTAAAGAGAGTCGGGGATCGCCGG
CTATGCAGAGAGACAGAGAGAGGG
Found at i:6445 original size:21 final size:21
Alignment explanation
Indices: 6402--6445 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6392 CTCTATTCAA
*
6402 TATTATTATTTTATATTATAT
1 TATTATTATTTTATATTACAT
*
6423 TATTTTTATTTTAT-TATACAT
1 TATTATTATTTTATAT-TACAT
6444 TA
1 TA
6446 ACTATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTATTATTTTATATTACAT
Found at i:15839 original size:50 final size:50
Alignment explanation
Indices: 15781--15877 Score: 185
Period size: 50 Copynumber: 1.9 Consensus size: 50
15771 TTTGTGATGT
*
15781 ATTGTGTAAATTACATATGTTTCTGTAAATGCTCTCAACTAATTCAACGC
1 ATTGTGTAAATTACATATGTTTCTGCAAATGCTCTCAACTAATTCAACGC
15831 ATTGTGTAAATTACATATGTTTCTGCAAATGCTCTCAACTAATTCAA
1 ATTGTGTAAATTACATATGTTTCTGCAAATGCTCTCAACTAATTCAA
15878 TTTTCCTACG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (50 bp):
ATTGTGTAAATTACATATGTTTCTGCAAATGCTCTCAACTAATTCAACGC
Found at i:16559 original size:25 final size:25
Alignment explanation
Indices: 16531--16588 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
16521 TATTTGGTAA
16531 GGACCAACCCACCACGTTAGTCATG
1 GGACCAACCCACCACGTTAGTCATG
16556 GGACCAACCCACCACGTTAGTCATG
1 GGACCAACCCACCACGTTAGTCATG
*
16581 AGACCAAC
1 GGACCAAC
16589 TATTAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.31, C:0.36, G:0.19, T:0.14
Consensus pattern (25 bp):
GGACCAACCCACCACGTTAGTCATG
Found at i:26198 original size:56 final size:57
Alignment explanation
Indices: 26111--26226 Score: 198
Period size: 56 Copynumber: 2.1 Consensus size: 57
26101 AATTATCTGT
*
26111 TTCCTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATTTCTACTTAATTA
1 TTCCTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTA
* *
26168 TTCC-TTCACACAATAAATGTTATAATAAATCCTATCCCCTTATCTCTACTTAATTA
1 TTCCTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTA
26224 TTC
1 TTC
26227 TACAAAATAA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 52 0.93
57 4 0.07
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.41
Consensus pattern (57 bp):
TTCCTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTA
Found at i:27851 original size:13 final size:13
Alignment explanation
Indices: 27833--27857 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27823 TTAGAATTCC
27833 AAATAATATTTAT
1 AAATAATATTTAT
27846 AAATAATATTTA
1 AAATAATATTTA
27858 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:28870 original size:2 final size:2
Alignment explanation
Indices: 28858--28900 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
28848 TCTCCAAATC
28858 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.