Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022974.1 Corchorus olitorius cultivar O-4 contig23007, 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, 885
Length: 1476
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Found at i:301 original size:154 final size:153
Alignment explanation
Indices: 1--1472 Score: 2093
Period size: 154 Copynumber: 9.6 Consensus size: 153
* * * * * *
1 ATTATAGTTAGGCCATAAAAAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGAATACGATTCC
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTTCCAAATCGAAGACGATTCA
* *
66 AAACGGA-ACTAAT-GGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
65 AAAC-GACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
129 ACAGTGGACTAATCTCACCAAAATG
129 ACAGTGGACTAATCTCACCAAAATG
*
154 ATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCTCAAATCGAAGACGATTCA
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTC-CAAATCGAAGACGATTCA
* *
219 AAACGACACTAATGGGCCCCGATAGGCACAAAATAACAAGTGTTCCAAATGACCTAAAAACTTCA
65 AAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
284 CAGTGGACTAATCTCACCAAAATG
130 CAGTGGACTAATCTCACCAAAATG
* * * *
308 ATTATAG-TCGGCCATAAACAATGGAAAGAAAAGCATTTAGGTTTCTAAATCGAAGACGATTCAG
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCAAATCGAAGACGATTCAA
* * *
372 AACGACACTAATGGGCCCCGATATAGACCCAAACTAACAAGTGTTCCAAATGAACTAAAAACTTC
66 AACGACACTAATGGGCCCCG--ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
437 ACAGTGGACTAATCTCACCAAAATG
129 ACAGTGGACTAATCTCACCAAAATG
* * * *
462 ATTATAGGTAGGCCATAAAGAATGGAAAGAAAAGCATTGAGGTTACCAAATCGAAGACGATTCAT
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCAAATCGAAGACGATTCAA
* *
527 AACGACACTAATGGGCCCCGATAGGGCACAAAATAACAAGTGTTCCAAATGACCTAAAAACTTCA
66 AACGACACTAATGGGCCCCGATA-GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
* *
592 CAGTGGACTAATCTTACAAAAATG
130 CAGTGGACTAATCTCACCAAAATG
* * *
616 GTTATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACTATTCA
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT-CCAAATCGAAGACGATTCA
* * *
681 GAACGACGCTAATGGGCCCCGATAGGCCCAAAATAACAATTGTTCCAAATGAGCTAAAAACTTCA
65 AAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
* *
746 CTGTGGACTAATCTCACGAAAATG
130 CAGTGGACTAATCTCACCAAAATG
*
770 ATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCTCAAATCGAAGACGATTCA
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTC-CAAATCGAAGACGATTCA
* * *
835 AAACGACACTAATGGGCCTCGATAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCA
65 AAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
*
900 CAATGGACTAATCTCACCAAAATG
130 CAGTGGACTAATCTCACCAAAATG
* ** * * * *
924 ATTATAGTTAGGCCATAAAAAATGGAAACTAAAGCATCGAGGGTTGCCAAATCGAATACGATTCC
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGTTTCCAAATCGAAGACGATTCA
* *
989 AAACGGA-ACTAAT-GGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
65 AAAC-GACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
1052 ACAGTGGACTAATCTCACCAAAATG
129 ACAGTGGACTAATCTCACCAAAATG
* * *
1077 ATTTTAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTACC-AATCGAAGACGATTCAT
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCAAATCGAAGACGATTCAA
* *
1141 AACGACACGTAATGGGCCCCGATAGGCTCAAAATAACAAGTGTTCCAAATGAGATAAAAACTTCA
66 AACGACAC-TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
*
1206 CAGTGGACTAATCTCACGAAAATG
130 CAGTGGACTAATCTCACCAAAATG
* * *
1230 ATAAGAGTTAGGACCATAAACAATGGAAAAGAAAAGCATTGAGGTTTCTACAAATCAAAGACGAT
1 ATTATAGTTAGG-CCATAAACAATGG-AAAGAAAAGCATTGAGGTTTC--CAAATCGAAGACGAT
1295 TCAAAACGACACTAATGGGCCCCGATAGGCCCAAAA-ATACAAGTGTTCCAAATGAGCTAAAAAC
62 TCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATA-ACAAGTGTTCCAAATGAGCTAAAAAC
* **
1359 TTCACA-TAAGACTTTTCTCACCAAAATG
126 TTCACAGT-GGACTAATCTCACCAAAATG
** * * * *
1387 ATTATAGTTAACCCATAAACAATGGAAACAAAAGC-TTCGAGGGCTGCCAAATCGAATACGATTC
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT-GA-GGTTTCCAAATCGAAGACGATTC
1451 AAAACGGA-ACTAAT-GGCCCCGA
64 AAAAC-GACACTAATGGGCCCCGA
1473 AAGG
Statistics
Matches: 1189, Mismatches: 106, Indels: 48
0.89 0.08 0.04
Matches are distributed among these distances:
150 2 0.00
151 19 0.02
152 54 0.05
153 293 0.25
154 549 0.46
155 151 0.13
156 19 0.02
157 79 0.07
158 23 0.02
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (153 bp):
ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCAAATCGAAGACGATTCAA
AACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
AGTGGACTAATCTCACCAAAATG
Found at i:960 original size:462 final size:461
Alignment explanation
Indices: 1--1476 Score: 2324
Period size: 462 Copynumber: 3.2 Consensus size: 461
1 ATTATAGTTAGGCCATAAAAAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGAATACGATTCC
1 ATTATAGTTAGGCCATAAAAAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGAATACGATTCC
66 AAACGGAACTAATGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
66 AAACGGAACTAATGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
*
131 AGTGGACTAATCTCACCAAAATGATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
131 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
*
196 TTTCTCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCACAAAATAACAAGTG
196 TTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCACAAAATAACAAGTG
* * * *
261 TTCCAAATGACCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG-TCGGCCATAA
261 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATAATAGTTAGGCCATAA
* *
325 ACAATGGAAAGAAAAGCATTTAGGTTTCT-AAATCGAAGACGATTCAGAACGACACTAATGGGCC
326 ACAATGGAAAGAAAAGCATTGAGGTTTCTCAAATCGAAGACGATTCAAAACGACACTAATGGGCC
* * *
389 CCGATATAGACCCAAACTAACAAGTGTTCCAAATGAACTAAAAACTTCACAGTGGACTAATCTCA
391 CCGATA-AG-CCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCA
454 CCAAAATG
454 CCAAAATG
* * * * * *
462 ATTATAGGTAGGCCATAAAGAATGGAAAGAAAAGCATTGA-GGTTACCAAATCGAAGACGATT-C
1 ATTATAGTTAGGCCATAAAAAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGAATACGATTCC
* *
525 ATAAC-GACACTAATGGGCCCCGATAGGGCAC-AAAATAACAAGTGTTCCAAATGACCTAAAAAC
66 A-AACGGA-ACTAAT-GGCCCCGA-AAGGC-CTAAAATAACAAGTGTTCCAAATGAGCTAAAAAC
* * * *
588 TTCACAGTGGACTAATCTTACAAAAATGGTTATAGGTAGGCCATAAACAATGGAAAGAAAAGCAT
126 TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
* * * *
653 TGAGGTTTCCCAAATCGAAGACTATTCAGAACGACGCTAATGGGCCCCGATAGGCCCAAAATAAC
191 TGAGGTTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCACAAAATAAC
* *
718 AATTGTTCCAAATGAGCTAAAAACTTCACTGTGGACTAATCTCACGAAAATGATAATAGTTAGGC
256 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATAATAGTTAGGC
783 CATAAACAATGGAAAGAAAAGCATTGAGGTTTCTCAAATCGAAGACGATTCAAAACGACACTAAT
321 CATAAACAATGGAAAGAAAAGCATTGAGGTTTCTCAAATCGAAGACGATTCAAAACGACACTAAT
* *
848 GGGCCTCGATAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAATGGACTAATC
386 GGGCCCCGATAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATC
913 TCACCAAAATG
451 TCACCAAAATG
*
924 ATTATAGTTAGGCCATAAAAAATGGAAACTAAAGCATCGAGGGTTGCCAAATCGAATACGATTCC
1 ATTATAGTTAGGCCATAAAAAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGAATACGATTCC
989 AAACGGAACTAATGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
66 AAACGGAACTAATGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
*
1054 AGTGGACTAATCTCACCAAAATGATTTTAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
131 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* * *
1119 -TTACC-AATCGAAGACGATTCATAACGACACGTAATGGGCCCCGATAGGCTCAAAATAACAAGT
196 TTTCCCAAATCGAAGACGATTCAAAACGACAC-TAATGGGCCCCGATAGGCACAAAATAACAAGT
* *
1182 GTTCCAAATGAGATAAAAACTTCACAGTGGACTAATCTCACGAAAATGATAAGAGTTAGGACCAT
260 GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATAATAGTTAGG-CCAT
*
1247 AAACAATGGAAAAGAAAAGCATTGAGGTTTCTACAAATCAAAGACGATTCAAAACGACACTAATG
324 AAACAATGG-AAAGAAAAGCATTGAGGTTTCT-CAAATCGAAGACGATTCAAAACGACACTAATG
* * **
1312 GGCCCCGATAGGCCCAAAA-ATACAAGTGTTCCAAATGAGCTAAAAACTTCAC-ATAAGACTTTT
387 GGCCCCGATAAGCCCAAAATA-ACAAGTGTTCCAAATGAGCTAAAAACTTCACAAT-GGACTAAT
1375 CTCACCAAAATG
450 CTCACCAAAATG
** * * * *
1387 ATTATAGTTAACCCATAAACAATGGAAACAAAAGCTTCGAGGGCTGCCAAATCGAATACGATTCA
1 ATTATAGTTAGGCCATAAAAAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGAATACGATTCC
1452 AAACGGAACTAATGGCCCCGAAAGG
66 AAACGGAACTAATGGCCCCGAAAGG
Statistics
Matches: 930, Mismatches: 68, Indels: 32
0.90 0.07 0.03
Matches are distributed among these distances:
459 26 0.03
460 121 0.13
461 157 0.17
462 336 0.36
463 247 0.27
464 43 0.05
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (461 bp):
ATTATAGTTAGGCCATAAAAAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGAATACGATTCC
AAACGGAACTAATGGCCCCGAAAGGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
TTTCCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCACAAAATAACAAGTG
TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACGAAAATGATAATAGTTAGGCCATAA
ACAATGGAAAGAAAAGCATTGAGGTTTCTCAAATCGAAGACGATTCAAAACGACACTAATGGGCC
CCGATAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATCTCACC
AAAATG
Done.