Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024268.1 Corchorus olitorius cultivar O-4 contig24301, 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: 19711
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:7316 original size:161 final size:163
Alignment explanation
Indices: 7101--7464 Score: 572
Period size: 161 Copynumber: 2.2 Consensus size: 163
7091 TTTTCCCTGA
* * * *
7101 AAAAAAAATTCTCTCACTCCATATATTACAATTGCGGCGCTTCCTTTCCTAGACGCCACTAATTA
1 AAAAAAAA-TCTCTCCCTCCATATATTAAAATGGCGGCGTTTCCTTTCCTAGACGCCACTAATTA
* * *
7166 GCGACATCTGATGT-GAAAACGCCGGTATATATTATAGGTGTAGAGTTGGAAACTTTCTTTG-TT
65 GCGACATCTGATGTCG-AAACGCCGCTATATAATATAGGCGTAGAGTTGGAAACTTTCTTTGTTT
*
7229 TTA-GGGGAGGGAATTTTTCCCTCCAAAAAAAAGG
129 TTAGGGGGAGGGAATTTTTCACTCCAAAAAAAAGG
* *
7263 AAAAAAAATCTCTCCCTCAATATATTAAAATGGCGGCGTTTCCTTTTCTAGACGCCACTAATTAG
1 AAAAAAAATCTCTCCCTCCATATATTAAAATGGCGGCGTTTCCTTTCCTAGACGCCACTAATTAG
* *
7328 CGGCGTCTGATGTCGAAACGCCGCTATATAATATAGGCGTAGAGTTGGAAACTTTCTTTGTTTTT
66 CGACATCTGATGTCGAAACGCCGCTATATAATATAGGCGTAGAGTTGGAAACTTTCTTTGTTTTT
7393 AGGGGGAGGGAATTTTTCACTCCAAAAAAAAGG
131 AGGGGGAGGGAATTTTTCACTCCAAAAAAAAGG
*
7426 AAAAAAAATCTCTCCCTCCATATATTAATATGGCGGCGT
1 AAAAAAAATCTCTCCCTCCATATATTAAAATGGCGGCGT
7465 CTTTGTATCA
Statistics
Matches: 185, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
161 104 0.56
162 14 0.08
163 67 0.36
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (163 bp):
AAAAAAAATCTCTCCCTCCATATATTAAAATGGCGGCGTTTCCTTTCCTAGACGCCACTAATTAG
CGACATCTGATGTCGAAACGCCGCTATATAATATAGGCGTAGAGTTGGAAACTTTCTTTGTTTTT
AGGGGGAGGGAATTTTTCACTCCAAAAAAAAGG
Found at i:7485 original size:163 final size:160
Alignment explanation
Indices: 7101--7519 Score: 513
Period size: 163 Copynumber: 2.6 Consensus size: 160
7091 TTTTCCCTGA
* * * * * * *
7101 AAAAAAAATTCTCTCACTCCATATATTACAATTGCGGCGCTTCCTT-TCCTAGACGCCACTAATT
1 AAAAAAAA-TCTCTCCCTCAATATATTAAAATGGCGGCG-TTTCTTAT-CAAAACGCCACTAATT
* * * * *
7165 AGCGACATCTGATGT-GAAAACGCCGGTATATATTATAGGTGTAGAGTTGGAAACTTTCTTTGTT
63 AGCGGCGTCTGATGTCG-AAACGCCGCTATATAATATAGGCGTAGAGTTGGAAACTTTCTTTGTT
*
7229 TTAGGGGAGGGAATTTTTCCCTCCAAAAAAAAGG
127 TTAGGGGAGGGAATTTTTCACTCCAAAAAAAAGG
* * *
7263 AAAAAAAATCTCTCCCTCAATATATTAAAATGGCGGCGTTTCCTTTTCTAGACGCCACTAATTAG
1 AAAAAAAATCTCTCCCTCAATATATTAAAATGGCGGCGTTT-CTTATCAAAACGCCACTAATTAG
7328 CGGCGTCTGATGTCGAAACGCCGCTATATAATATAGGCGTAGAGTTGGAAACTTTCTTTGTTTTT
65 CGGCGTCTGATGTCGAAACGCCGCTATATAATATAGGCGTAGAGTTGGAAACTTTCTTTG-TTTT
7393 AGGGGGAGGGAATTTTTCACTCCAAAAAAAAGG
129 A-GGGGAGGGAATTTTTCACTCCAAAAAAAAGG
* * * * *
7426 AAAAAAAATCTCTCCCTCCATATATTAATATGGCGGCGTCTT-TGTATCAAAATGCCACTAAATG
1 AAAAAAAATCTCTCCCTCAATATATTAAAATGGCGGCGT-TTCT-TATCAAAACGCCACTAATTA
* *
7490 GCGGCGTCTTCATGTC-AGACGCCGCTATAT
64 GCGGCGTC-TGATGTCGAAACGCCGCTATAT
7520 TCAATTTCTG
Statistics
Matches: 228, Mismatches: 21, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
160 2 0.01
161 100 0.44
162 16 0.07
163 102 0.45
164 8 0.04
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (160 bp):
AAAAAAAATCTCTCCCTCAATATATTAAAATGGCGGCGTTTCTTATCAAAACGCCACTAATTAGC
GGCGTCTGATGTCGAAACGCCGCTATATAATATAGGCGTAGAGTTGGAAACTTTCTTTGTTTTAG
GGGAGGGAATTTTTCACTCCAAAAAAAAGG
Found at i:14752 original size:31 final size:30
Alignment explanation
Indices: 14675--14752 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
14665 GCTCAGTTTA
*
14675 CTCCACTTCAGGGACTAAATTGCATATTTT
1 CTCCACTTCAGGGACCAAATTGCATATTTT
* * * *
14705 -TTCACTTGAGGTACCAAGTTGC-TATTTT
1 CTCCACTTCAGGGACCAAATTGCATATTTT
14733 CGCTCCACTTCAGGGACCAA
1 --CTCCACTTCAGGGACCAA
14753 TTTTGTACTT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
28 6 0.16
29 17 0.46
31 14 0.38
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (30 bp):
CTCCACTTCAGGGACCAAATTGCATATTTT
Found at i:17679 original size:24 final size:24
Alignment explanation
Indices: 17635--17751 Score: 198
Period size: 24 Copynumber: 4.8 Consensus size: 24
17625 GAAAATCAAA
*
17635 CGGCCACATAGTTGGTTGTGAGATT
1 CGGCCACATAG-TGGTCGTGAGATT
17660 CGGCCACATAGTGGTCGTGAGATT
1 CGGCCACATAGTGGTCGTGAGATT
*
17684 CGGCCACATAGTTGGTCATGAGATT
1 CGGCCACATAG-TGGTCGTGAGATT
17709 CGGCCACATAGTGGTCGTGAGATT
1 CGGCCACATAGTGGTCGTGAGATT
17733 CGGCCACATAGTGGTCGTG
1 CGGCCACATAGTGGTCGTG
17752 GGAAAAGACC
Statistics
Matches: 88, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
24 54 0.61
25 34 0.39
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (24 bp):
CGGCCACATAGTGGTCGTGAGATT
Found at i:17707 original size:49 final size:49
Alignment explanation
Indices: 17635--17748 Score: 203
Period size: 49 Copynumber: 2.3 Consensus size: 49
17625 GAAAATCAAA
**
17635 CGGCCACATAGTTGGTTGTGAGATTCGGCCACATAGTGGTCGTGAGATT
1 CGGCCACATAGTTGGTCATGAGATTCGGCCACATAGTGGTCGTGAGATT
17684 CGGCCACATAGTTGGTCATGAGATTCGGCCACATAGTGGTCGTGAGATT
1 CGGCCACATAGTTGGTCATGAGATTCGGCCACATAGTGGTCGTGAGATT
17733 CGGCCACATAG-TGGTC
1 CGGCCACATAGTTGGTC
17749 GTGGGAAAAG
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
48 5 0.08
49 58 0.92
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (49 bp):
CGGCCACATAGTTGGTCATGAGATTCGGCCACATAGTGGTCGTGAGATT
Done.