Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009206.1 Corchorus olitorius cultivar O-4 contig09234, 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, 739
Length: 1233
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.21
Found at i:286 original size:154 final size:153
Alignment explanation
Indices: 13--1233 Score: 1637
Period size: 154 Copynumber: 8.0 Consensus size: 153
3 TCAAAACGTC
* * * *
13 ACTAATGAGTCCCAATAGGCCC-AAATAAAAAGTGTTCCAAATGAGGT-AAAACTTCACAGTGGA
1 ACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
*
76 CTAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC
66 CTAATCTCACCAAAATGATTAT-GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC
*
141 AAATTGAAGACGATTCAAAACAAA
130 AAATCGAAGACGATTCAAAACAAA
* * **
165 ACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTATA
1 ACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* * *
230 CTAATCTCACCAAAATGATTAATGTTAGGCCATAAAGAATGGAAAGAATAGAATTGAGGGTTG-C
66 CTAATCTCACCAAAATGATT-ATGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC
***
294 AAATCGAAGACGATTCAAAACGTC
130 AAATCGAAGACGATTCAAAACAAA
* * *
318 ACTAATGGGGCCCGATATG-CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGA
1 ACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* *
382 CTAAACTCACGAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTG-C
66 CTAATCTCACCAAAATGATTAT-GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC
* * ***
446 ATATCGAAGACAATTCAAAACGTT
130 AAATCGAAGACGATTCAAAACAAA
* * *
470 ACTAATGGGCCCCGATACG-CCAAAATAAAAAGTGTTCCACATCAGCTAAAAACTTCACAGTGGA
1 ACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* *
534 CTAATCTCACCAAAATGATTAT-TAACGGCCATAAACATTGGAAAGAAAAGCATTGAGGGTTG-C
66 CTAATCTCACCAAAATGATTATGTTA-GGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC
***
597 AAATCGAAGACGATTCAAAACGTC
130 AAATCGAAGACGATTCAAAACAAA
* *
621 ACTAATGAGCCCCAATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
1 ACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
*
686 CTAATCT-ACCGAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGAGTTGC
66 CTAATCTCACC-AAAATGATTA-TGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGC
*
750 CAAATCGAAGACGTTTCAAAACAAA
129 CAAATCGAAGACGATTCAAAACAAA
* * * * *
775 ATTAATGGGCCCCGATAAGCCCAAAATTACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGGA
1 ACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* * ** *
840 CTAATCTCACAAAAATGATTATTGTTAGGCAATAAACAATGGAAAGAAAAGCATTGAACGTTGCT
66 CTAATCTCACCAAAATGATTA-TGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC
**
905 AAATCGAAGACGATTCAAAACGGA
130 AAATCGAAGACGATTCAAAACAAA
* *
929 ACTAATGGGCCCCGATAGG--C---TTAACAAGTGTTCCAAATGAG-TAAAAAACTTCACAGTGG
1 ACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCT-AAAAACTTCACAGTGG
** * * * *
988 ACTAATCTCAAAAAAACGATTACAGTGT-GGGCATAAACAATGGAAAGAAAAGAATTGAGGGTTG
65 ACTAATCTCACCAAAATGATTA-TGT-TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTG
*
1052 CCAAATCGAAGACAATTCAAAACAAA
128 CCAAATCGAAGACGATTCAAAACAAA
* * * *
1078 ACTAATTGGCCCCGATAGGCGCAAAATAACAAGAGTTCCAAATGAGCTAAAAACTTCACAGTGGA
1 ACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* *
1143 CTAAACTCACCAAAATGACTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC
66 CTAATCTCACCAAAATGATTAT-GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC
*
1208 AAATCGAAGACGATTTAAAACAAA
130 AAATCGAAGACGATTCAAAACAAA
1232 AC
1 AC
Statistics
Matches: 947, Mismatches: 101, Indels: 40
0.87 0.09 0.04
Matches are distributed among these distances:
148 1 0.00
149 127 0.13
150 3 0.00
151 79 0.08
152 276 0.29
153 96 0.10
154 360 0.38
155 5 0.01
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.21
Consensus pattern (153 bp):
ACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
CTAATCTCACCAAAATGATTATGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCA
AATCGAAGACGATTCAAAACAAA
Found at i:1038 original size:303 final size:303
Alignment explanation
Indices: 1--1228 Score: 1693
Period size: 303 Copynumber: 4.0 Consensus size: 303
* * * *
1 ATTCAAAACGTCACTAATGAGTCCCAATAGGCCCAAATAAAAAGTGTTCCAAATGAGGT-AAAAC
1 ATTCAAAACGTCACTAATGGGCCCCGATAGG--C-AATAAAAAGTGTTCCAAATGAGCTAAAAAC
* *
65 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCAT
63 TTCACAGTGGACTAATCTCACGAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
* * *
130 TGAGGGTTGCCAAATTGAAGACGATTCAAAACAAAACTAATGGACCCCGATAGGCCCAAAATAAC
128 TGAGGGTTGCCAAATCGAAGACAATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAAC
* ** *
195 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTATACTAATCTCACCAAAATGATTAATGTTAGGC
193 AAGTGTTCCAAACGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATTGTTAGGC
* * *
260 CATAAAGAATGGAAAGAATAGAATTGAGGGTTGCAAATCGAAGACG
258 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCAAATCGAAGACG
* *
306 ATTCAAAACGTCACTAATGGGGCCCGATATGCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAAC
1 ATTCAAAACGTCACTAATGGGCCCCGATA-GGC--AATAAAAAGTGTTCCAAATGAGCTAAAAAC
* *
371 ATCACAGTGGACTAAACTCACGAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
63 TTCACAGTGGACTAATCTCACGAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
* *** * *
436 TGAGGGTTG-CATATCGAAGACAATTCAAAACGTTACTAATGGGCCCCGATACG-CCAAAATAAA
128 TGAGGGTTGCCAAATCGAAGACAATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAAC
* *
499 AAGTGTTCCACATC-AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA-T-TAACG
193 AAGTGTTCCA-AACGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATTGTTA-G
*
561 GCCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCAAATCGAAGACG
256 GCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCAAATCGAAGACG
* *
609 ATTCAAAACGTCACTAATGAGCCCCAATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAA
1 ATTCAAAACGTCACTAATGGGCCCCGATAGG--C--AATAAAAAGTGTTCCAAATGAGCTAAAAA
*
674 CTTCACAGTGGACTAATCT-ACCGAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGC
62 CTTCACAGTGGACTAATCTCA-CGAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* ** * * *
738 ATTGAGAGTTGCCAAATCGAAGACGTTTCAAAACAAAATTAATGGGCCCCGATAAGCCCAAAATT
126 ATTGAGGGTTGCCAAATCGAAGACAATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATA
*
803 ACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAAATGATTATTGTTAG
191 ACAAGTGTTCCAAACGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATTGTTAG
* **
868 GCAATAAACAATGGAAAGAAAAGCATTGAACGTTGCTAAATCGAAGACG
256 GCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGC-AAATCGAAGACG
** * *
917 ATTCAAAACGGAACTAATGGGCCCCGATAGGC-TTAACAAGTGTTCCAAATGAG-TAAAAAACTT
1 ATTCAAAACGTCACTAATGGGCCCCGATAGGCAATAAAAAGTGTTCCAAATGAGCT-AAAAACTT
** * * * *
980 CACAGTGGACTAATCTCAAAAAAACGATTACAGTGT-GGGCATAAACAATGGAAAGAAAAGAATT
65 CACAGTGGACTAATCTCACGAAAATGATTATAGT-TAGGCCATAAACAATGGAAAGAAAAGCATT
* *
1044 GAGGGTTGCCAAATCGAAGACAATTCAAAACAAAACTAATTGGCCCCGATAGGCGCAAAATAACA
129 GAGGGTTGCCAAATCGAAGACAATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAACA
* * * * *
1109 AGAGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGACTATAGTTAGGCC
194 AGTGTTCCAAACGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATTGTTAGGCC
1174 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACG
259 ATAAACAATGGAAAGAAAAGCATTGAGGGTTG-CAAATCGAAGACG
*
1220 ATTTAAAAC
1 ATTCAAAAC
1229 AAAAC
Statistics
Matches: 822, Mismatches: 83, Indels: 38
0.87 0.09 0.04
Matches are distributed among these distances:
302 4 0.00
303 318 0.39
304 164 0.20
305 125 0.15
306 136 0.17
307 34 0.04
308 41 0.05
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.21
Consensus pattern (303 bp):
ATTCAAAACGTCACTAATGGGCCCCGATAGGCAATAAAAAGTGTTCCAAATGAGCTAAAAACTTC
ACAGTGGACTAATCTCACGAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
GGGTTGCCAAATCGAAGACAATTCAAAACAAAACTAATGGGCCCCGATAGGCCCAAAATAACAAG
TGTTCCAAACGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATTGTTAGGCCAT
AAACAATGGAAAGAAAAGCATTGAGGGTTGCAAATCGAAGACG
Found at i:1138 original size:457 final size:453
Alignment explanation
Indices: 36--1233 Score: 1703
Period size: 457 Copynumber: 2.6 Consensus size: 453
26 AATAGGCCCA
36 AATAAAAAGTGTTCCAAATGAGGT-AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
1 AATAAAAAGTGTTCCAAATGA-GTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA-AG
*
100 TTAGGGCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATTGAAGACGATTCAAAACAAA
64 TT-GGGCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACAAA
**
165 ACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTATA
128 ACTAATGG-CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* * * *
230 CTAATCTCACCAAAATGATTAATGTTAGGCCATAAAGAATGGAAAGAATAGAATTGAGGGTTG-C
192 CTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC
* *** * *
294 AAATCGAAGACGATTCAAAACGTCACTAATGGGGCCCGATATGCCAAAATAAAAAGTGTTCCAAA
257 AAATCGAAGACGTTTCAAAACAAAACTAATGGGCCCCGATAAGCCAAAATAAAAAGTGTTCCAAA
* * *
359 TGAGCTAAAAACATCACAGTGGACTAAACTCACGAAAATGATTATAGTTAGGCCATAAACAATGG
322 CGAGCTAAAAACATCACAGTGGACTAAACTCACAAAAATGATTATAGTTAGGCAATAAACAATGG
** * **
424 AAAGAAAAGCATTGAGGGTTGCATATCGAAGACAATTCAAAACGTTACTAATGGGCCCCGATACG
387 AAAGAAAAGCATTGAACGTTGCAAATCGAAGACAATTCAAAACGGAACTAATGGGCCCCGATACG
489 CC
452 CC
* *
491 AAAATAAAAAGTGTTCCACATCAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT-A
1 --AATAAAAAGTGTTCCAAATGAG-TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAA
* *
555 -TTAACGGCCATAAACATTGGAAAGAAAAGCATTGAGGGTTG-CAAATCGAAGACGATTCAAAAC
63 GTT---GGGCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
*** * *
618 GTCACTAATGAGCCCCAATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
125 AAAACTAATG-GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
*
683 GGACTAATCT-ACCGAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGAGT
189 GGACTAATCTCACC-AAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGT
* * *
747 TGCCAAATCGAAGACGTTTCAAAACAAAATTAATGGGCCCCGATAAGCCCAAAATTACAAGTGTT
253 TGCCAAATCGAAGACGTTTCAAAACAAAACTAATGGGCCCCGATAAG-CCAAAATAAAAAGTGTT
* * *
812 CCAAACGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAAATGATTATTGTTAGGCAATAAAC
317 CCAAACGAGCTAAAAACATCACAGTGGACTAAACTCACAAAAATGATTATAGTTAGGCAATAAAC
*
877 AATGGAAAGAAAAGCATTGAACGTTGCTAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
382 AATGGAAAGAAAAGCATTGAACGTTGC-AAATCGAAGACAATTCAAAACGGAACTAATGGGCCCC
*
942 GATA-GGC
446 GATACGCC
* * ** *
949 -TTAACAAGTGTTCCAAATGAGTAAAAAACTTCACAGTGGACTAATCTCAAAAAAACGATTACAG
1 AATAAAAAGTGTTCCAAATGAGT-AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA-AG
* *
1013 TGTGGGCATAAACAATGGAAAGAAAAGAATTGAGGGTTGCCAAATCGAAGACAATTCAAAACAAA
64 T-TGGGCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACAAA
* *
1078 ACTAATTGGCCCCGATAGGCGCAAAATAACAAGAGTTCCAAATGAGCTAAAAACTTCACAGTGGA
128 ACTAA-TGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
* * *
1143 CTAAACTCACCAAAATGACTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC
192 CTAATCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCC
1208 AAATCGAAGACGATTT-AAAACAAAAC
257 AAATCGAAGACG-TTTCAAAACAAAAC
Statistics
Matches: 660, Mismatches: 63, Indels: 36
0.87 0.08 0.05
Matches are distributed among these distances:
454 1 0.00
455 56 0.08
456 169 0.26
457 250 0.38
458 146 0.22
459 38 0.06
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.21
Consensus pattern (453 bp):
AATAAAAAGTGTTCCAAATGAGTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAAGTT
GGGCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACAAAACT
AATGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
TCTCACCAAAATGATTATTGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAAT
CGAAGACGTTTCAAAACAAAACTAATGGGCCCCGATAAGCCAAAATAAAAAGTGTTCCAAACGAG
CTAAAAACATCACAGTGGACTAAACTCACAAAAATGATTATAGTTAGGCAATAAACAATGGAAAG
AAAAGCATTGAACGTTGCAAATCGAAGACAATTCAAAACGGAACTAATGGGCCCCGATACGCC
Done.