Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022798.1 Corchorus olitorius cultivar O-4 contig22831, 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: 42923
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:601 original size:27 final size:27
Alignment explanation
Indices: 511--642 Score: 126
Period size: 27 Copynumber: 4.9 Consensus size: 27
501 TTGGTTTCCA
* **
511 AAATTGGATCCTGATGGTCATGAG-AT
1 AAATTAGATCCTGATGGTCATGAGCCG
* **
537 AAATTGGATCCTGATGGTCGGGATGCC-
1 AAATTAGATCCTGATGGTCATGA-GCCG
**
564 AAGGT-GAATCCTGATGGTCATGAGCCG
1 AAATTAG-ATCCTGATGGTCATGAGCCG
*
591 AAATTAGATCCAGATGGTCATGAGCCG
1 AAATTAGATCCTGATGGTCATGAGCCG
* *
618 AAATTAGATCCCGACGGTCATGAGC
1 AAATTAGATCCTGATGGTCATGAGC
643 AATTTGGATC
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
26 25 0.28
27 63 0.71
28 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (27 bp):
AAATTAGATCCTGATGGTCATGAGCCG
Found at i:802 original size:15 final size:15
Alignment explanation
Indices: 782--811 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
772 AAAGAAATAG
782 CACACCATCAGGATA
1 CACACCATCAGGATA
797 CACACCATCAGGATA
1 CACACCATCAGGATA
812 ACTTATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.33, G:0.13, T:0.13
Consensus pattern (15 bp):
CACACCATCAGGATA
Found at i:9569 original size:14 final size:14
Alignment explanation
Indices: 9550--9578 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9540 TCCACTAAGA
9550 TTAGAGATAGAATT
1 TTAGAGATAGAATT
9564 TTAGAGATAGAATT
1 TTAGAGATAGAATT
9578 T
1 T
9579 GATGATGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (14 bp):
TTAGAGATAGAATT
Found at i:16855 original size:28 final size:29
Alignment explanation
Indices: 16823--16879 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
16813 TTTGGCAGTA
16823 AGATAATTTTCTTAGGTTA-GTTTGGTTC
1 AGATAATTTTCTTAGGTTACGTTTGGTTC
16851 AGATAATTTTCTTAGGTTACGTTTGGTTC
1 AGATAATTTTCTTAGGTTACGTTTGGTTC
16880 GTGGTATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.49
Consensus pattern (29 bp):
AGATAATTTTCTTAGGTTACGTTTGGTTC
Found at i:21927 original size:74 final size:74
Alignment explanation
Indices: 21844--21991 Score: 269
Period size: 74 Copynumber: 2.0 Consensus size: 74
21834 CTATTTTGGT
* *
21844 ATGTGGCGAACAGTAGGGATGTAATCGGGTAGGGTATCCGCGAATTTTGAGATATCCGTACCCTA
1 ATGTGGCGAACAGTAGGGATGCAACCGGGTAGGGTATCCGCGAATTTTGAGATATCCGTACCCTA
21909 ACCCTATTA
66 ACCCTATTA
*
21918 ATGTGGCGAACAGTAGGGATGCAACCGGGTAGGGTATCCGCGAATTTTGAGGTATCCGTACCCTA
1 ATGTGGCGAACAGTAGGGATGCAACCGGGTAGGGTATCCGCGAATTTTGAGATATCCGTACCCTA
21983 ACCCTATTA
66 ACCCTATTA
21992 TTTTCTAGGG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (74 bp):
ATGTGGCGAACAGTAGGGATGCAACCGGGTAGGGTATCCGCGAATTTTGAGATATCCGTACCCTA
ACCCTATTA
Found at i:22284 original size:19 final size:19
Alignment explanation
Indices: 22244--22280 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
22234 AATTTTTAAG
22244 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
22263 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
22281 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:23852 original size:10 final size:10
Alignment explanation
Indices: 23837--23866 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
23827 TGATACCGTG
23837 CACATTTTTT
1 CACATTTTTT
23847 CACATTTTTT
1 CACATTTTTT
23857 CACATTTTTT
1 CACATTTTTT
23867 TCCTGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (10 bp):
CACATTTTTT
Found at i:38494 original size:192 final size:192
Alignment explanation
Indices: 38080--38657 Score: 969
Period size: 192 Copynumber: 3.0 Consensus size: 192
38070 TCAAATTTTT
38080 AAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAAGTT
1 AAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAAGTT
*
38145 ATTTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTTGTTTTTCCAAAAATTAAGGATTA
66 ATTTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGC-TTTGTTTTTCCAAAAATTAAGGATGA
*
38210 CCCAAAGTGTCTTAACATATCATCCTTAAGTCCTCTTTAATTTAAGGAAAAAATCATAGCTTT-
130 CCCAAAGTGTCTTAACATATCATCCTTAAGTCATCTTTAATTTAAGG-AAAAATCATAGCTTTA
*
38273 AAATTCAGAACCTTAATTCCCAAATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAAGTT
1 AAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAAGTT
* *
38338 ATTTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAGATTAAGGATGAT
66 ATTTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAAATTAAGGATGAC
*
38403 CCAAAGTGTCTTAACATATCATCCTTAAGTCATCTTTAATTTAAAGAAAAATCATAGCTTTA
131 CCAAAGTGTCTTAACATATCATCCTTAAGTCATCTTTAATTTAAGGAAAAATCATAGCTTTA
* *
38465 AAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGGGATTCCCAAATTTCTTTCAAGTT
1 AAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAAGTT
* * * * *
38530 ATTTTCTAATTTGGAGAATTGGGTTTCAAACTCTAAGCTTTATTTTTCCAAATATTAAGGATGAC
66 ATTTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAAATTAAGGATGAC
* * * * *
38595 CCAAAGTGTCGTAACATGTTATCCTTAAGTGATCTTTAATTTAAGGAAAAATCAAAGCTTTA
131 CCAAAGTGTCTTAACATATCATCCTTAAGTCATCTTTAATTTAAGGAAAAATCATAGCTTTA
38657 A
1 A
38658 GTCAAAACCT
Statistics
Matches: 363, Mismatches: 21, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
191 15 0.04
192 246 0.68
193 102 0.28
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (192 bp):
AAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAAGTT
ATTTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAAATTAAGGATGAC
CCAAAGTGTCTTAACATATCATCCTTAAGTCATCTTTAATTTAAGGAAAAATCATAGCTTTA
Found at i:39942 original size:191 final size:191
Alignment explanation
Indices: 39618--40195 Score: 1014
Period size: 191 Copynumber: 3.0 Consensus size: 191
39608 AAATCAAATT
39618 TTTAAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAA
1 TTTAAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAA
39683 GTTATTTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAGATTAAGGAT
66 GTTATTTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAGATTAAGGAT
39748 GACCCAAAGTGTCTTAACATATCATCCTTAAGTCATCTTTAATTTAAGGAAAAATCATAAC
131 GACCCAAAGTGTCTTAACATATCATCCTTAAGTCATCTTTAATTTAAGGAAAAATCATAAC
* *
39809 TTTAAATTCAGAACCTTAATTCCCAGATCGAAAGTAATTTAAAGAGATTCCCCAATTACTTTCAA
1 TTTAAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAA
* *
39874 GTTATTTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTATTTTTCCAAAAATTAAGGAT
66 GTTATTTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAGATTAAGGAT
* *
39939 GACCCAAAGTGTCTTAACATATCATCCTTAAGTCCTCTTTAATTTAAGGAAAAATCATAGC
131 GACCCAAAGTGTCTTAACATATCATCCTTAAGTCATCTTTAATTTAAGGAAAAATCATAAC
* *
40000 TTTAAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGGGATTCCCAAATTTCTTTCAA
1 TTTAAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAA
*
40065 GTTATTTTCTAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAGATTAAGGAT
66 GTTATTTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAGATTAAGGAT
* * * * *
40130 GACCCAAAGTGTTTTAACATGTCATTCTTCAGTTATCTTTAATTTAAGGAAAAATCA-AAGC
131 GACCCAAAGTGTCTTAACATATCATCCTTAAGTCATCTTTAATTTAAGGAAAAATCATAA-C
40191 TTTAA
1 TTTAA
40196 GTTAAAACCT
Statistics
Matches: 366, Mismatches: 20, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
190 1 0.00
191 365 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (191 bp):
TTTAAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAA
GTTATTTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAGATTAAGGAT
GACCCAAAGTGTCTTAACATATCATCCTTAAGTCATCTTTAATTTAAGGAAAAATCATAAC
Found at i:41487 original size:191 final size:191
Alignment explanation
Indices: 41156--41507 Score: 652
Period size: 191 Copynumber: 1.8 Consensus size: 191
41146 AAATCAAATT
41156 TTTAAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAA
1 TTTAAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAA
* *
41221 GTTATTTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAAATTAAGGAT
66 GTTATGTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAAATTAAGGAC
41286 GACTCAAAGTGTCTTAACATATCATCCTTAAGTCATCTTTAATTTAAGGAAAAATCATAGC
131 GACTCAAAGTGTCTTAACATATCATCCTTAAGTCATCTTTAATTTAAGGAAAAATCATAGC
41347 TTTAAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAA
1 TTTAAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAA
*
41412 GTTATGTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAGATTAAGGAC
66 GTTATGTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAAATTAAGGAC
*
41477 GA-TCCAAAGTGTCTTAACATGTCATCCTTAA
131 GACT-CAAAGTGTCTTAACATATCATCCTTAA
41508 ATTTAAGGAA
Statistics
Matches: 156, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
190 1 0.01
191 155 0.99
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (191 bp):
TTTAAATTCAGAACCTTAATTCCCAGATCGAAAGTCATTTAAAGAGATTCCCCAATTTCTTTCAA
GTTATGTTCGAATTTGGAGAATTGGGTTTCTAACTCCAAGCTTTGTTTTTCCAAAAATTAAGGAC
GACTCAAAGTGTCTTAACATATCATCCTTAAGTCATCTTTAATTTAAGGAAAAATCATAGC
Found at i:41885 original size:22 final size:19
Alignment explanation
Indices: 41860--41900 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 19
41850 ATTTTTCCAT
41860 TTTTTTCATTTTTCCTTTCTTC
1 TTTTTT-ATTTTT--TTTCTTC
41882 TTTTTTATTTTTTTTCTTC
1 TTTTTTATTTTTTTTCTTC
41901 AACTTTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
21 6 0.32
22 6 0.32
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTTATTTTTTTTCTTC
Done.