Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021649.1 Corchorus olitorius cultivar O-4 contig21682, 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: 10833
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:82 original size:32 final size:32
Alignment explanation
Indices: 15--141 Score: 80
Period size: 32 Copynumber: 3.8 Consensus size: 32
5 CAAGATTGAA
* * * **
15 ATTAACTCAT-AATGCAATAATCCTACATCGGG
1 ATTAACTAATGAA-GCAATGATCCTAAATCAAG
*
47 ATTAACTGATGAAGCAATGATCCTAAATCAAG
1 ATTAACTAATGAAGCAATGATCCTAAATCAAG
* *
79 ATTAA--AAAGAAGCAATGATCCTCAACCAGGACTAAG
1 ATTAACTAATGAAGCAATGATCCT-AA--A--TC-AAG
* *
115 ACTAACTTATGAAGCAATGATCCTAAA
1 ATTAACTAATGAAGCAATGATCCTAAA
142 CCAGGATTGA
Statistics
Matches: 75, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
30 15 0.20
31 2 0.03
32 29 0.39
33 3 0.04
35 2 0.03
36 7 0.09
37 2 0.03
38 15 0.20
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (32 bp):
ATTAACTAATGAAGCAATGATCCTAAATCAAG
Found at i:350 original size:91 final size:90
Alignment explanation
Indices: 160--444 Score: 288
Period size: 92 Copynumber: 3.1 Consensus size: 90
150 GAAATAAAAC
*** * * *
160 AACCTTTAATCAAAGTTTAAATTTTCAAAATTAAAACTAACTTAAAGAGATTC-AATAATCTATT
1 AACCTTTAATCAAAAACTAAATTTTC-AAATTAAAATTAACTCAAAGAGATTCAAATAATC-A-A
*
224 TTTCAAGTTAATTTTAATCTAAAAATCA
63 TTTCAAGTTAATTTTAATCCAAAAATCA
**
252 AACCTTTAAATCAAAAACTAAATTTTCAAATTAAAATTAACTCAAAGAGA-TCAAATGGTCAATT
1 AACCTTT-AATCAAAAACTAAATTTTCAAATTAAAATTAACTCAAAGAGATTCAAATAATCAATT
316 TCAAAGTTAATTTTAATCCAAAAATCA
65 TC-AAGTTAATTTTAATCCAAAAATCA
* * * * * * * *
343 AACCTTTAATTAAAAGAGTTAATTTTTAAATCAAGATTAACTCCAAAAAGATTCAAA-AATCAGT
1 AACCTTTAATCAAAA-ACTAAATTTTCAAATTAAAATTAACT-CAAAGAGATTCAAATAATCA-A
* * *
407 TTTTAAGTTGATTTTAATTCAAAAATCA
63 TTTCAAGTTAATTTTAATCCAAAAATCA
*
435 ACCCTTTAAT
1 AACCTTTAAT
445 TTAAAGTTTT
Statistics
Matches: 163, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
90 11 0.07
91 54 0.33
92 74 0.45
93 24 0.15
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (90 bp):
AACCTTTAATCAAAAACTAAATTTTCAAATTAAAATTAACTCAAAGAGATTCAAATAATCAATTT
CAAGTTAATTTTAATCCAAAAATCA
Found at i:4191 original size:90 final size:87
Alignment explanation
Indices: 4035--4241 Score: 254
Period size: 90 Copynumber: 2.3 Consensus size: 87
4025 ACATGAGGGC
* * * * * * *
4035 CAAATCTCTCATCTTTCCTTAAAAAAACCTACTAGTTAACTGCATCAATATATCTTTCTTAGAAA
1 CAAATCTCTCATCTTTCCTAAAAAAAACCTACCAGTTAACTCCAGCAATATATCTCTCCTAAAAA
4100 CTATATTTGTCTCTCC-TCGGT
66 CTATATTTGTCTCTCCTTCGGT
*
4121 CAAATCTCTCATCTTTCCTAAAAAAGAAAAACCTACCGGTTAACTCCAGCAATATATCTCTCCTA
1 CAAATCTCTCATCTTTCCT---AAA-AAAAACCTACCAGTTAACTCCAGCAATATATCTCTCCTA
* *
4186 AAAACTATTTTTTTCTCTCCTTCGGT
62 AAAACTATATTTGTCTCTCCTTCGGT
*
4212 CAAATCTCTCATATTTCCTTGAAAAAAAAC
1 CAAATCTCTCATCTTTCC-T-AAAAAAAAC
4242 AACAGCAACT
Statistics
Matches: 103, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
86 19 0.18
89 8 0.08
90 53 0.51
91 22 0.21
92 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (87 bp):
CAAATCTCTCATCTTTCCTAAAAAAAACCTACCAGTTAACTCCAGCAATATATCTCTCCTAAAAA
CTATATTTGTCTCTCCTTCGGT
Found at i:5478 original size:31 final size:32
Alignment explanation
Indices: 5423--5488 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 32
5413 TAAAGGTGTT
5423 AAGTTAATAAAAAATGGAGAGGTATATTGGAG
1 AAGTTAATAAAAAATGGAGAGGTATATTGGAG
* *
5455 AAGTTAAT-AAAATTGGAGGGGTATATTGGAG
1 AAGTTAATAAAAAATGGAGAGGTATATTGGAG
5486 AAG
1 AAG
5489 ATAAATGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 24 0.75
32 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (32 bp):
AAGTTAATAAAAAATGGAGAGGTATATTGGAG
Found at i:6124 original size:30 final size:29
Alignment explanation
Indices: 6053--6128 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
6043 TTGTAGCGTC
*
6053 TGGACGTTTTGCCCCCTGAACTTCGATTT
1 TGGACGTTTTGCCCCCTGAACTTCAATTT
*
6082 TGGACATTTTGCCCCCTGAACTTCAATTT
1 TGGACGTTTTGCCCCCTGAACTTCAATTT
6111 TGGGACGTTTTGCCCCCT
1 T-GGACGTTTTGCCCCCT
6129 CGGGTTAATG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
29 28 0.65
30 15 0.35
ACGTcount: A:0.14, C:0.29, G:0.20, T:0.37
Consensus pattern (29 bp):
TGGACGTTTTGCCCCCTGAACTTCAATTT
Found at i:10668 original size:331 final size:331
Alignment explanation
Indices: 10223--10831 Score: 1182
Period size: 331 Copynumber: 1.8 Consensus size: 331
10213 AAGGTGTGTA
10223 GACATACTATAATTAGTACATTATCTAATGAGCTTTTTGATGTCTATTCTCCTTACAAAGAAGCA
1 GACATACTATAATTAGTACATTATCTAATGAGCTTTTTGATGTCTATTCTCCTTACAAAGAAGCA
10288 AAGCAAATTTGGGACTCCATGGTGACAAAGTATACCGCTGAAGATGTTGGGAAGCAAAAGTTTGT
66 AAGCAAATTTGGGACTCCATGGTGACAAAGTATACCGCTGAAGATGTTGGGAAGCAAAAGTTTGT
*
10353 GATTGGGAACTTCTATAGGTGGGAGATGTGAGAAGACAAAGACATCAAAGACCAAATTAATGAGT
131 GATTAGGAACTTCTATAGGTGGGAGATGTGAGAAGACAAAGACATCAAAGACCAAATTAATGAGT
10418 ACCATAAATTGGTGGATGATCTTAAGTCTGAAAATATCGAACTGCCAGAGGAGTTTGTTGCTGGA
196 ACCATAAATTGGTGGATGATCTTAAGTCTGAAAATATCGAACTGCCAGAGGAGTTTGTTGCTGGA
*
10483 ATTTTCATTGAAAAACTGCCTGATTCATGGAGAGACTACAAACAACAATTGAAGCACAAACAAAA
261 ATTCTCATTGAAAAACTGCCTGATTCATGGAGAGACTACAAACAACAATTGAAGCACAAACAAAA
10548 GCAGAT
326 GCAGAT
10554 GACATACTATAATTAGTACATTATCTAATGAGCTTTTTGATGTCTATTCTCCTTACAAAGAAGCA
1 GACATACTATAATTAGTACATTATCTAATGAGCTTTTTGATGTCTATTCTCCTTACAAAGAAGCA
*
10619 AAGCAAATTTGGGACTCCATGGTGACAAAGTATATCGCTGAAGATGTTGGGAAGCAAAAGTTTGT
66 AAGCAAATTTGGGACTCCATGGTGACAAAGTATACCGCTGAAGATGTTGGGAAGCAAAAGTTTGT
10684 GATTAGGAACTTCTATAGGTGGGAGATGTGAGAAGACAAAGACATCAAAGACCAAATTAATGAGT
131 GATTAGGAACTTCTATAGGTGGGAGATGTGAGAAGACAAAGACATCAAAGACCAAATTAATGAGT
*
10749 ACCATAAATTGGTGGATGATCTTAAGTTTGAAAATATCGAACTGCCAGAGGAGTTTGTTGCTGGA
196 ACCATAAATTGGTGGATGATCTTAAGTCTGAAAATATCGAACTGCCAGAGGAGTTTGTTGCTGGA
10814 ATTCTCATTGAAAAACTG
261 ATTCTCATTGAAAAACTG
10832 TC
Statistics
Matches: 274, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
331 274 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (331 bp):
GACATACTATAATTAGTACATTATCTAATGAGCTTTTTGATGTCTATTCTCCTTACAAAGAAGCA
AAGCAAATTTGGGACTCCATGGTGACAAAGTATACCGCTGAAGATGTTGGGAAGCAAAAGTTTGT
GATTAGGAACTTCTATAGGTGGGAGATGTGAGAAGACAAAGACATCAAAGACCAAATTAATGAGT
ACCATAAATTGGTGGATGATCTTAAGTCTGAAAATATCGAACTGCCAGAGGAGTTTGTTGCTGGA
ATTCTCATTGAAAAACTGCCTGATTCATGGAGAGACTACAAACAACAATTGAAGCACAAACAAAA
GCAGAT
Done.