Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011643.1 Corchorus olitorius cultivar O-4 contig11676, 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: 1886
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Found at i:516 original size:154 final size:154
Alignment explanation
Indices: 1--1729 Score: 2711
Period size: 154 Copynumber: 11.2 Consensus size: 154
* * *
1 CCAAATGAGCTAAAAACTTCACAATGGACTAGTCTCACCAAAATGATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
* ** *
66 AATGGAAAGAAAAGCATTGAGGGTT-ACAAATCGAAGACGATTCAAAACGTCACTAATGAGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCC
* * *
130 AATAGGCCTAAAATAAAAAGTGTT
131 GATAGGCCCAAAATAACAAGTGTT
154 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
* *
219 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACT-ATTGGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCC
*
283 GATAGGTCCAAAATAACAAGTGTT
131 GATAGGCCCAAAATAACAAGTGTT
* * *
307 CCAAATGAGCTAAAAGCTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGACATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
* * *
372 AATGGAAAGAAAATCATTTAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCC
*
437 GATAGGGCCAAAATAACAAGTGTT
131 GATAGGCCCAAAATAACAAGTGTT
* * *
461 CCAAATGAGCTAATAACTTCACAGTAGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
* *
526 AATGGAAAGAAAAGCATTGAGGGTCGCCAAATCGAAGACGATTCAAAACGAAAATAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGG-CCC
591 CGATAGGCCCAAAATAACAAGTGTT
130 CGATAGGCCCAAAATAACAAGTGTT
* *
616 CCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATATAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
* *
681 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTGAAAACAAAACTAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCC
746 GATAGGCCCAAAATAACAAGTGTT
131 GATAGGCCCAAAATAACAAGTGTT
*
770 CGAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
* * * * *
835 AATGGAAAGAAAAACATTGAGGGTTCCCAAATCGAAGACAATTCAAAACAAAACTAATTGGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCC
*
900 GATAGGTCCAAAATAACAAGTGTT
131 GATAGGCCCAAAATAACAAGTGTT
* *
924 CCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGACATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
* * * * *
989 AATAGAAA-TAAAGCATTGAGGGATGCCAAATCGAAAACGATTCAAAACGGAACTAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCC
*
1053 GATAGGCCCAAAATAACAAGCGTT
131 GATAGGCCCAAAATAACAAGTGTT
*
1077 CCAAATGAGCTATAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
* * * * *
1142 AATGGAAAGAAAAGCATTTAGAGTTGCCAAATCGAAGACAATTCAAAACAAAACTAATTGGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCC
* *
1207 GATAGGTCCAAATTAACAAGTGTT
131 GATAGGCCCAAAATAACAAGTGTT
* * * *
1231 CCAAATGAGCTAAAAACTTCATAGTGGACTAAACTCACCAAAATGATTATAGTTAGGTCATCAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
* * * *
1296 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAACAATTCAAAACAAAACTATTGGACCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAG-ACGATTCAAAACGAAACTAATGGGCCC
1361 CGATAGGCCCAAAATAACAAGTGTT
130 CGATAGGCCCAAAATAACAAGTGTT
1386 CCAAATGAGCT-AAAACTTCACAGTGGACTAATACTCACCAAAATACGATTATAGTTAGGGCGAT
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAAT-CTCACCAAAAT--GATTATAGTTAGGGC-AT
* *
1450 ATACAATGGAAAGAAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACAAAACTAATGG
62 AAACAATGGAAAG-AAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGG
*
1515 ACCCCGATAGGCCCAAAATAACAAGTGTT
126 GCCCCGATAGGCCCAAAATAACAAGTGTT
*
1544 CCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
* *
1609 AATGGAAAGAAAAGCAGTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCC
* *
1674 GATATG--C---TTAACAAGTGTT
131 GATAGGCCCAAAATAACAAGTGTT
*
1693 CAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
1730 AAATAACAAG
Statistics
Matches: 1457, Mismatches: 108, Indels: 26
0.92 0.07 0.02
Matches are distributed among these distances:
149 46 0.03
152 1 0.00
153 367 0.25
154 654 0.45
155 227 0.16
156 15 0.01
157 14 0.01
158 85 0.06
159 48 0.03
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (154 bp):
CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCC
GATAGGCCCAAAATAACAAGTGTT
Found at i:557 original size:307 final size:308
Alignment explanation
Indices: 1--1729 Score: 2751
Period size: 307 Copynumber: 5.6 Consensus size: 308
* ** *
1 CCAAATGAGCTAAAAACTTCACAATGGACTAGTCTCACCAAAATGATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGACATAAAC
* ** *
66 AATGGAAAGAAAAGCATTGAGGGTT-ACAAATCGAAGACGATTCAAAACGTCACTAATGAGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
* * *
130 AATAGGCCTAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
131 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
195 AATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA
196 AATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA
**
260 TTCAAAACGGAACT-ATTGGCCCCGATAGGTCCAAAATAACAAGTGTT
261 TTCAAAACAAAACTAATTGGCCCCGATAGGTCCAAAATAACAAGTGTT
*
307 CCAAATGAGCTAAAAGCTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGACATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGACATAAAC
* *
372 AATGGAAAGAAAATCATTTAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
* * *
437 GATAGGGCCAAAATAACAAGTGTTCCAAATGAGCTAATAACTTCACAGTAGACTAATCTCACCAA
131 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* *
502 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTCGCCAAATCGAAGACGA
196 AATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA
* *
567 TTCAAAACGAAAA-TAATGGGCCCCCGATAGGCCCAAAATAACAAGTGTT
261 TTCAAAAC-AAAACTAATTGG-CCCCGATAGGTCCAAAATAACAAGTGTT
* * * *
616 CCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATATAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGACATAAAC
* **
681 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTGAAAACAAAACTAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
*
746 GATAGGCCCAAAATAACAAGTGTTCGAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
131 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* * *
811 AATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAACATTGAGGGTTCCCAAATCGAAGACAA
196 AATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA
876 TTCAAAACAAAACTAATTGGCCCCGATAGGTCCAAAATAACAAGTGTT
261 TTCAAAACAAAACTAATTGGCCCCGATAGGTCCAAAATAACAAGTGTT
924 CCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGACATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGACATAAAC
* * * *
989 AATAGAAA-TAAAGCATTGAGGGATGCCAAATCGAAAACGATTCAAAACGGAACTAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
* *
1053 GATAGGCCCAAAATAACAAGCGTTCCAAATGAGCTATAAACTTCACAGTGGACTAATCTCACCAA
131 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* * *
1118 AATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTTAGAGTTGCCAAATCGAAGACAA
196 AATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA
*
1183 TTCAAAACAAAACTAATTGGCCCCGATAGGTCCAAATTAACAAGTGTT
261 TTCAAAACAAAACTAATTGGCCCCGATAGGTCCAAAATAACAAGTGTT
* * *
1231 CCAAATGAGCTAAAAACTTCATAGTGGACTAAACTCACCAAAATGATTATAGTTAGGTCATCAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGACATAAAC
* ** * *
1296 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAACAATTCAAAACAAAACTATTGGACCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAG-ACGATTCAAAACGGAACTAATGGGCCC
1361 CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT-AAAACTTCACAGTGGACTAATACTCACC
130 CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT-CTCACC
*
1425 AAAATACGATTATAGTTAGGGCGATATACAATGGAAAGAAAAAGCATTGAGGGTTGCCAAATCGA
194 AAAAT--GATTATAGTTAGGGC-ATAAACAATGGAAAG-AAAAGCATTGAGGGTTGCCAAATCGA
*
1490 AGACGATTCAAAACAAAACTAA-TGGACCCCGATAGGCCCAAAATAACAAGTGTT
255 AGACGATTCAAAACAAAACTAATTGG-CCCCGATAGGTCCAAAATAACAAGTGTT
* * *
1544 CCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGACATAAAC
*
1609 AATGGAAAGAAAAGCAGTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
* * *
1674 GATATG--C---TTAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
131 GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
1730 AAATAACAAG
Statistics
Matches: 1312, Mismatches: 97, Indels: 27
0.91 0.07 0.02
Matches are distributed among these distances:
306 83 0.06
307 480 0.37
308 171 0.13
309 350 0.27
310 1 0.00
311 15 0.01
312 45 0.03
313 167 0.13
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (308 bp):
CCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGACATAAAC
AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
GATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
AATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA
TTCAAAACAAAACTAATTGGCCCCGATAGGTCCAAAATAACAAGTGTT
Found at i:1742 original size:51 final size:51
Alignment explanation
Indices: 1682--1780 Score: 180
Period size: 51 Copynumber: 1.9 Consensus size: 51
1672 CCGATATGCT
1682 TAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAAAA
1 TAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAAAA
* *
1733 TAACAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGGACTAATCTCA
1 TAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
1781 CCAAAATGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.25
Consensus pattern (51 bp):
TAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAAAA
Done.