Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011728.1 Corchorus olitorius cultivar O-4 contig11761, 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: 1821
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Found at i:285 original size:154 final size:154
Alignment explanation
Indices: 5--1821 Score: 2779
Period size: 154 Copynumber: 11.8 Consensus size: 154
1 ACTA
* * * *
5 AAAAACTTTACAGTGGACTAATCTAACCAAAATGATTATAGTTAGGCCATAAACAACGAAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * ** *
70 AAGCTTTGAGGTTTGCCAACTCGAAGACGATCCAAAACGTCACTAATGGCCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
* *
135 GATAACAAGTGTTCCAACTGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* * *
159 AAAAACTTCACGGTGGACTAATCTCACCAAAATGATTATACTTAGGCCATAAACAATAGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * **
224 AAGCAATGAGGTTTGCCAAATAGAAGACGATCCAAAACGTCACTAATGGGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
* *
289 AATAACAAATGTTCCAAATAAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* *
313 AAAAACTTCACAGTAGACTAATCTCACCAAAATGATTATACTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * * **
378 AAGCAATGAGGTTTGCGAAATAGAAGACGATCCAAAACGTCACTAATGGGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
*
443 AATAACAAGTGTTCCAAATAAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* *
467 GAAAACTTCACAGTAGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* ** *
532 AAGCATTGAGGTTTGTCAAATCGAAGACGATTCAAAACGTCACT-ATGGTCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
596 AAT-ACAAGTGTTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* *
619 AAAAACTTCACAGTGGACAAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAATGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* *
684 AAGCCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGACAGGCCCA
66 AAG-CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCA
749 AAATAACAAGTGTTCCAAATGAGCT
130 AAATAACAAGTGTTCCAAATGAGCT
* *
774 AAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTATGCCATAAACAATAGGAAAG-
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAAT-GGAAAGA
* *
838 AAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCA
65 AAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCA
903 AAATAACAAGTGTTCCAAATGAGCT
130 AAATAACAAGTGTTCCAAATGAGCT
* *
928 AAAAATTTCACAGTGGACTAATCTCACCAAAATGATTACAGTTAGGCCATAAACAATGG-AAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * * **
992 TAGCAATGAGGTTTGCCAAATCGAAGACGATTTAATACGTCACTAATGGGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
* *
1057 AATAACAAGTTTTCCAAATAAGCT
131 AATAACAAGTGTTCCAAATGAGCT
* * * * *
1081 AAAAATTTCACAATGGACTAATCTGACCAAATTGATTATGGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
*
1146 AAGCATTGAGGTTTGCCAAATCGAAGACGATTTAAAACGGAACTAATGGGCCCCGATAGGCCC-A
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
*
1210 AATAACAAGTATTCCAAATGAGCT
131 AATAACAAGTGTTCCAAATGAGCT
*
1234 AAAAACTTCACAGT-GACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* *
1298 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCTGATAGGGCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
*
1363 AATAACAAGTGTTCCAAATAAGCT
131 AATAACAAGTGTTCCAAATGAGCT
*
1387 AAAAACTTCACAGTAGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-A
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * *
1451 ATGCATTGAGGTTTGTCAAATCGAAGACGATTCAAAACGGAACTAATCGGCCCCGATAAGG-CCA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAT-AGGCCCA
* *
1515 AAATAACAAGGGTTCCAAATGAACT
130 AAATAACAAGTGTTCCAAATGAGCT
1540 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* *
1605 AAGCATTGAGGTTTGCCAAATTGAAGACGATTCAAAACGGAACTAATCGGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
*
1670 AATAACAAGTGTTCCAAATGAACT
131 AATAACAAGTGTTCCAAATGAGCT
* * * *
1694 AAAACCTTTACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC-ACGAAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * ** *
1758 AAGCTTTGAGGTTTGCCAACTCGAAGACGATCCAAAACGTCACTAATGGCCCCCGATAGGCCCA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCA
Statistics
Matches: 1544, Mismatches: 108, Indels: 23
0.92 0.06 0.01
Matches are distributed among these distances:
152 192 0.12
153 476 0.31
154 793 0.51
155 78 0.05
156 5 0.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (154 bp):
AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
AATAACAAGTGTTCCAAATGAGCT
Found at i:785 original size:307 final size:308
Alignment explanation
Indices: 5--1821 Score: 2781
Period size: 307 Copynumber: 5.9 Consensus size: 308
1 ACTA
* * * *
5 AAAAACTTTACAGTGGACTAATCTAACCAAAATGATTATAGTTAGGCCATAAACAACGAAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * ** *
70 AAGCTTTGAGGTTTGCCAACTCGAAGACGATCCAAAACGTCACTAATGGCCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
* * * * *
135 GATAACAAGTGTTCCAACTGAGCTAAAAACTTCACGGTGGACTAATCTCACCAAAATGATTATAC
131 AATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
* * * * **
200 TTAGGCCATAAACAATAGAAAGAAAAGCAATGAGGTTTGCCAAATAGAAGACGATCCAAAACGTC
196 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
* *
265 ACTAATGGGCCCCGATAGGCCCAAAATAACAAATGTTCCAAATAAGCT
261 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* *
313 AAAAACTTCACAGTAGACTAATCTCACCAAAATGATTATACTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * * **
378 AAGCAATGAGGTTTGCGAAATAGAAGACGATCCAAAACGTCACTAATGGGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
* *
443 AATAACAAGTGTTCCAAATAAGCTGAAAACTTCACAGTAGACTAATCTCACCAAAATGATTATAG
131 AATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
* **
508 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGTCAAATCGAAGACGATTCAAAACGTC
196 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
*
573 ACT-ATGGTCCCCGATAGGCCCAAAAT-ACAAGTGTTCCAAATGAGCT
261 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* *
619 AAAAACTTCACAGTGGACAAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAATGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* *
684 AAGCCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGACAGGCCCA
66 AAG-CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCA
* *
749 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATA
130 AAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* *
814 GTTATGCCATAAACAATAGGAAAG-AAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
195 GTTAGGCCATAAACAAT-GGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
*
878 GAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
259 GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* *
928 AAAAATTTCACAGTGGACTAATCTCACCAAAATGATTACAGTTAGGCCATAAACAATGG-AAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * * **
992 TAGCAATGAGGTTTGCCAAATCGAAGACGATTTAATACGTCACTAATGGGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
* * * * * *
1057 AATAACAAGTTTTCCAAATAAGCTAAAAATTTCACAATGGACTAATCTGACCAAATTGATTATGG
131 AATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
*
1122 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTTAAAACGGA
196 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
*
1187 ACTAATGGGCCCCGATAGGCCC-AAATAACAAGTATTCCAAATGAGCT
261 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
*
1234 AAAAACTTCACAGT-GACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* *
1298 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCTGATAGGGCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
*
1363 AATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTAGACTAATCTCACCAAAATGATTATAG
131 AATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
* *
1428 TTAGGCCATAAACAATGGAAAG-AATGCATTGAGGTTTGTCAAATCGAAGACGATTCAAAACGGA
196 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
* * *
1492 ACTAATCGGCCCCGATAAGG-CCAAAATAACAAGGGTTCCAAATGAACT
261 ACTAATGGGCCCCGAT-AGGCCCAAAATAACAAGTGTTCCAAATGAGCT
1540 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
1 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* *
1605 AAGCATTGAGGTTTGCCAAATTGAAGACGATTCAAAACGGAACTAATCGGCCCCGATAGGCCCAA
66 AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
* *
1670 AATAACAAGTGTTCCAAATGAA-CTAAAACCTTTACAGTGGACTAATCTCACCAAAATGATTATA
131 AATAACAAGTGTTCCAAAT-AAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
* * * * * *
1734 GTTAGGCCATAAAC-ACGAAAAGAAAAGCTTTGAGGTTTGCCAACTCGAAGACGATCCAAAACGT
195 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGG
* *
1798 CACTAATGGCCCCCGATAGGCCCA
260 AACTAATGGGCCCCGATAGGCCCA
Statistics
Matches: 1378, Mismatches: 119, Indels: 25
0.91 0.08 0.02
Matches are distributed among these distances:
305 98 0.07
306 315 0.23
307 615 0.45
308 274 0.20
309 76 0.06
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (308 bp):
AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
AAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
AATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
Done.