Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011614.1 Corchorus olitorius cultivar O-4 contig11647, 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, 877
Length: 1463
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Found at i:286 original size:154 final size:154
Alignment explanation
Indices: 1--1463 Score: 2176
Period size: 154 Copynumber: 9.6 Consensus size: 154
*
1 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAATCTCACCAAAATGATTATAGTTAGG
1 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* * * *
66 CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAACCGAAGACAATTCAAAACTGAACTAA
66 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
*
131 TGGGCCTCGATAGGCACAAAATAA
131 TGGGCCCCGATAGGCACAAAATAA
* *
155 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGAACTCATCTCACCAAAATGATTATAGTTAGG
1 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
** * * * *** *
220 CTTTACACAATGGAAAGAAAAGCATTGAAGTTTGCCAAATCGAAGACGATTCAAAACATCATTAA
66 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
* * *
285 TGGTCTCCGATAGGCCCAAAATAA
131 TGGGCCCCGATAGGCACAAAATAA
*
309 CAAGTGTTCCATATGAGCTAAAAACTTCACAGTGG---------------A-GATTATAGTTAGG
1 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* * * * *
358 CCATAAACAATGGAAAGAAAAGCATTGAAGTTTGCCAAACCGAAGACAATTCAAAACTGAACTAA
66 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
*
423 TGGGCCTCGATAGGCACAAAATAA
131 TGGGCCCCGATAGGCACAAAATAA
*
447 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGTTAGG
1 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
*
512 CCATAAACAATGGAAAGAAATGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
66 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
*
577 TGGGCCCCGATAGGCCCAAAATAA
131 TGGGCCCCGATAGGCACAAAATAA
601 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
1 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* * **
666 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACAATTGAAAACAAAACTAA
66 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
* *
731 TTGGCCCCGAAAGGTC-CAAAATAA
131 TGGGCCCCGATAGG-CACAAAATAA
* *
755 GAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATAATTATAGTTAGG
1 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* **
820 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTG-CAAATCAAAGACGATTCAAAACGTCACTAA
66 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
** * * *
884 TAAGCCCCAATAGGCCCAAAGTAA
131 TGGGCCCCGATAGGCACAAAATAA
* * *
908 AAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGAGTAATCTCACCAAAATGATTATAGTTAGG
1 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* *
973 GCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAATGGAACTAA
66 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
*
1038 TTGGCCCCGATAGG-ACCAAAATAA
131 TGGGCCCCGATAGGCA-CAAAATAA
* *
1062 CAAGTGTTCCAAATGAACTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGCTAGG
1 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
*
1127 GCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
66 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
*
1192 TTGGCCCCGATAGG-ACCAAAATAA
131 TGGGCCCCGATAGGCA-CAAAATAA
* *
1216 CAAGTGTTCCAAATGAACTAAAAACCTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
1 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
*
1281 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACTATTCAAAAACGGAACTA
66 CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTC-AAAACGGAACTA
*
1346 ATGGGCCCCGATAGGCCCAAAATAA
130 ATGGGCCCCGATAGGCACAAAATAA
*
1371 CAAGTGTTCCAAATGAGCTAAAAACTTCACTGTGGACTAATCTCACCAAAATGATTATAGTTAGG
1 CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
*
1436 CCGTAAACAATGGAAAG-AAAGCAATTGA
66 CCATAAACAATGGAAAGAAAAGC-ATTGA
Statistics
Matches: 1194, Mismatches: 92, Indels: 45
0.90 0.07 0.03
Matches are distributed among these distances:
138 123 0.10
139 1 0.00
152 1 0.00
153 136 0.11
154 815 0.68
155 118 0.10
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (154 bp):
CAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
CCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
TGGGCCCCGATAGGCACAAAATAA
Found at i:1062 original size:461 final size:462
Alignment explanation
Indices: 346--1463 Score: 1846
Period size: 461 Copynumber: 2.4 Consensus size: 462
336 CACAGTGGAG
* * *
346 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAAGTTTGCCAAACCGAAGACAATTCA
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACAATTCA
* *
411 AAAC-TGAACTAATGGGCCTCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
66 AAACGT-AACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
* *
475 ACAGTGGACTAAACTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAATGCATTGA
130 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA
*
540 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAG
195 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGACCAAAATAACAAG
* *
605 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
260 TGTTCCAAATGAACTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGCTAGGCCAT
*
670 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACAATTGAAAACAAAACTAATTGG
325 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACAATTCAAAACAAAACTAATTGG
* * * *
735 CCCCGAAAGGTCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
390 CCCCGAAAGGACCAAAATAACAAGTGTTCCAAATGAACTAAAAACCTCACAGTGGACTAATCTCA
800 CCAAAATA
455 CCAAAATA
* *
808 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTG-CAAATCAAAGACGATTCA
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACAATTCA
* ** * * * *
872 AAACGTCACTAATAAGCCCCAATAGGCCCAAAGTAAAAATTGTTCCAAATGAGCTAAAAACTTCA
66 AAACGTAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
* *
937 CAGTGGAGTAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTGAG
131 CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG
* *
1002 GGTTGCCAAATCGAAGACGATTCAAAATGGAACTAATTGGCCCCGATAGGACCAAAATAACAAGT
196 GGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGACCAAAATAACAAGT
*
1067 GTTCCAAATGAACTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGCTAGGGCATA
261 GTTCCAAATGAACTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGCTAGGCCATA
* **
1132 AACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATTGGC
326 AACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACAATTCAAAACAAAACTAATTGGC
*
1197 CCCGATAGGACCAAAATAACAAGTGTTCCAAATGAACTAAAAACCTCACAGTGGACTAATCTCAC
391 CCCGAAAGGACCAAAATAACAAGTGTTCCAAATGAACTAAAAACCTCACAGTGGACTAATCTCAC
*
1262 CAAAATG
456 CAAAATA
*
1269 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACTATTCA
1 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACAATTC-
*
1334 AAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
65 AAAACGTAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTC
* *
1399 ACTGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAACAATGGAAAG-AAAGCAATTG
130 ACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC-ATTG
1463 A
194 A
Statistics
Matches: 604, Mismatches: 48, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
461 427 0.71
462 65 0.11
463 112 0.19
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.20
Consensus pattern (462 bp):
ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACAATTCA
AAACGTAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
CAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAG
GGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGACCAAAATAACAAGT
GTTCCAAATGAACTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGCTAGGCCATA
AACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACAATTCAAAACAAAACTAATTGGC
CCCGAAAGGACCAAAATAACAAGTGTTCCAAATGAACTAAAAACCTCACAGTGGACTAATCTCAC
CAAAATA
Done.