Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011710.1 Corchorus olitorius cultivar O-4 contig11743, 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: 2065
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Found at i:914 original size:154 final size:154
Alignment explanation
Indices: 507--1366 Score: 1244
Period size: 154 Copynumber: 5.7 Consensus size: 154
497 ATTCGTATCA
507 TGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
1 TGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
* * *
572 AAGTATTCCAAATGAGCTAAAAACTGCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGAC
66 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
*
637 CATAAACAATGGAAACAAAAGCAT
131 CATAAACAATGGAAAGAAAAGCAT
* **
661 TGAGGTTTGCCAAATCCAAGACGATTACAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
1 TGAGGTTTGCCAAATCGAAGACGATT-CAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAA
* * * * * *
726 CAAGTATTCCAAATGAGCTAAAAACTTCAAAGTGGACAAATCTAAACAAAATGATTATAGGTAGG
65 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* *
791 CCATAAACAATTGAAACAAAAGCAT
130 CCATAAACAATGGAAAGAAAAGCAT
* * * *
816 TGAGGCTTGCCAATTCGAAGAAGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
1 TGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
* *
881 AAGTGTTCCAAATTAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
66 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* *
946 CATAAACAATGGAATGAAAGGCAT
131 CATAAACAATGGAAAGAAAAGCAT
* ** * * * * *
970 TGAGGTCTGATAAATCGAAGACGATTCAATACGTCACTAATGGACCCCAATAAGCCCAAAATAAG
1 TGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
*
1035 AAATGTTCCAAATGAGCT-AAAACTTCACAGTGGACTAATCTCACC-AAA--A-T-TA-TT----
66 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
1089 -ATAAACAATGGAAAGAAAAGCAT
131 CATAAACAATGGAAAGAAAAGCAT
* *
1112 TGAGGTTTGCCTAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCGATAGGCCCAAAATAA
1 TGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GTCACTAATGGGCCCCGATAGGCCCAAAATAA
*
1176 CAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
65 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
1241 CCATAAACAATGGAAAGAAAAGCAT
130 CCATAAACAATGGAAAGAAAAGCAT
* *
1266 TGAGGTTTGCCAAATCGAAGAAGATT-AAGTACGTCACTAATGGGCCCCGATAGGCCCAAAATAA
1 TGAGGTTTGCCAAATCGAAGACGATTCAA-AACGTCACTAATGGGCCCCGATAGGCCCAAAATAA
* *
1330 CAGGTGTTCCAAATGAGCTAAAAATTTCACAGTGGAC
65 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
1367 GAATTCAAAA
Statistics
Matches: 629, Mismatches: 61, Indels: 32
0.87 0.08 0.04
Matches are distributed among these distances:
142 91 0.14
143 27 0.04
144 3 0.00
146 1 0.00
147 3 0.00
148 4 0.01
149 3 0.00
150 1 0.00
152 3 0.00
153 29 0.05
154 324 0.52
155 140 0.22
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (154 bp):
TGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
CATAAACAATGGAAAGAAAAGCAT
Found at i:1243 original size:296 final size:300
Alignment explanation
Indices: 507--1366 Score: 1239
Period size: 296 Copynumber: 2.8 Consensus size: 300
497 ATTCGTATCA
507 TGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
1 TGAGGTTTGCC-AATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
* * *
572 AAGTATTCCAAATGAGCTAAAAACTGCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGAC
65 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* * * **
637 CATAAACAATGGAAACAAAAGCATTGAGGTTTGCCAAATCCAAGACGATTACAAAACGGAACTAA
130 CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATT-CAATACGTCACTAA
* *
702 TGGGCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCAAAGTGGACAAAT
194 TGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAAT
*
767 CTAAACAAAATGATTATAGGTAGGCCATAAACAATTGAAACAAAAGCAT
259 CTAAACAAAA-GATTAT--GT----CATAAACAATGGAAACAAAAGCAT
* * *
816 TGAGGCTTGCCAATTCGAAGAAGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
1 TGAGGTTTGCCAA-TCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAAC
* *
881 AAGTGTTCCAAATTAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
65 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* * * **
946 CATAAACAATGGAATGAAAGGCATTGAGGTCTGATAAATCGAAGACGATTCAATACGTCACTAAT
130 CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAAT
* * * * * *
1011 GGACCCCAATAAGCCCAAAATAAGAAATGTTCCAAATGAGCT-AAAACTTCACAGTGGACTAATC
195 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAATC
* * *
1075 T-CACCAAA-ATTAT-T-ATAAACAATGGAAAGAAAAGCAT
260 TAAACAAAAGATTATGTCATAAACAATGGAAACAAAAGCAT
*
1112 TGAGGTTTGCCTAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCGATAGGCCCAAAATAA
1 TGAGGTTTGCC-AATCGAAGACGATTCAAAAC-GTCACTAATGGGCCCCGATAGGCCCAAAATAA
*
1176 CAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
64 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
*
1241 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATT-AAGTACGTCACTA
129 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA-TACGTCACTA
* *
1305 ATGGGCCCCGATAGGCCCAAAATAACAGGTGTTCCAAATGAGCTAAAAATTTCACAGTGGAC
193 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
1367 GAATTCAAAA
Statistics
Matches: 496, Mismatches: 50, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
295 2 0.00
296 231 0.47
297 19 0.04
301 1 0.00
304 5 0.01
306 5 0.01
307 21 0.04
308 50 0.10
309 162 0.33
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (300 bp):
TGAGGTTTGCCAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACA
AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
ATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATG
GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAATCT
AAACAAAAGATTATGTCATAAACAATGGAAACAAAAGCAT
Found at i:1444 original size:80 final size:80
Alignment explanation
Indices: 1301--1451 Score: 248
Period size: 80 Copynumber: 1.9 Consensus size: 80
1291 TAAGTACGTC
* * * * *
1301 ACTAATGGGCCCCGATAGGCCCAAAATAACAGGTGTTCCAAATGAGCTAAAAATTTCACAGTGGA
1 ACTAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCAAAGTGGA
1366 CGAATTCAAAACGGA
66 CGAATTCAAAACGGA
1381 ACTAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCAAAGTGGA
1 ACTAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCAAAGTGGA
*
1446 CTAATT
66 CGAATT
1452 GATACGAATC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (80 bp):
ACTAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCAAAGTGGA
CGAATTCAAAACGGA
Done.