Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010964.1 Corchorus olitorius cultivar O-4 contig10996, 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: 2366
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Found at i:1387 original size:154 final size:154
Alignment explanation
Indices: 1102--1594 Score: 871
Period size: 154 Copynumber: 3.2 Consensus size: 154
1092 TGGAGATGGT
1102 TCACCAAAATGATTATATTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
1 TCACCAAAATGATTATATTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
*
1167 AAGAAGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
66 AAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* * *
1232 TAGAAACTTCAAAGTTGACTAATC
131 TAAAAACTTCACAGTGGACTAATC
* *
1256 TCACGAAAATGATTATATTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGCTTGCCAAATCG
1 TCACCAAAATGATTATATTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
1321 AAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
66 AAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
1386 TAAAAACTTCACAGTGGACTAATC
131 TAAAAACTTCACAGTGGACTAATC
*
1410 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
1 TCACCAAAATGATTATATTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
** * *
1475 AAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCTAAATGAGC
66 AAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
1540 TAAAAACTTCACAGTGGACTAATC
131 TAAAAACTTCACAGTGGACTAATC
1564 TCACCAAAATGATTAT-TGTTAGGCCATAAAC
1 TCACCAAAATGATTATAT-TTAGGCCATAAAC
1595 CATTCGAAGA
Statistics
Matches: 324, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
154 324 1.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
TCACCAAAATGATTATATTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCG
AAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGC
TAAAAACTTCACAGTGGACTAATC
Found at i:1695 original size:125 final size:126
Alignment explanation
Indices: 1472--1719 Score: 453
Period size: 125 Copynumber: 2.0 Consensus size: 126
1462 GTTTGCCAAA
*
1472 TCGAAGACGATTCAAAACGGAACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCTAAATG
1 TCGAAGACGATTCAAAACAGAACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCTAAATG
*
1537 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATTGTTAGGCCATAAACCAT
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACCAT
1598 TCGAAGACGATTCAAAACAGAACTAAT-GACCCCGATAGGCCCAAAATAACAAGTGTTCTAAATG
1 TCGAAGACGATTCAAAACAGAACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCTAAATG
* *
1662 AGCTAATAACTTCACAGTTGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
1720 AGTGGAAAGA
Statistics
Matches: 118, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
125 92 0.78
126 26 0.22
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (126 bp):
TCGAAGACGATTCAAAACAGAACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCTAAATG
AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACCAT
Found at i:1848 original size:279 final size:280
Alignment explanation
Indices: 1316--2359 Score: 1130
Period size: 308 Copynumber: 3.5 Consensus size: 280
1306 AGGCTTGCCA
** *
1316 AATCGAAGACGATTCAAAAC-GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA
1 AATCGAAGACGATTCAAAACAGAAACTAAT-GACCCCGATAGGCCCAAAATAACAAGTGTTCCAA
1380 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
65 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
*
1445 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAATGGACCCCGAT
130 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GACACTAATGGGCCCCGAT
*
1509 AGGCCCAAAATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
194 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
1574 GATTATTGTTAGGCCATAAACC
259 GATTATTGTTAGGCCATAAACC
* *
1596 ATTCGAAGACGATTCAAAACAG-AACTAATGACCCCGATAGGCCCAAAATAACAAGTGTTCTAAA
1 AATCGAAGACGATTCAAAACAGAAACTAATGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
* * *
1660 TGAGCTAATAACTTCACAGTTGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAGTGG
66 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
* * *
1725 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTTAAAACGTCACTAATGGGCCTCGATAG
131 AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAG
* * *
1790 GCCCAAAATAACAAGTGTTCCAAATGAGCTAGAAACTTCAAAGTTGACTAATCTCACCAAAATGA
196 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
1855 TTATAT-TTAGGCCATAAA-C
261 TTAT-TGTTAGGCCATAAACC
* * * ** *
1874 AATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAAT-ACGTCACTAATGGGCCC
1 AATCG-AAG---A-C---GA---TT--CAAAAC--AGAA-ACT-AATGAC--C-CCGATAGG--C
* *
1938 CGATAGGGACAAAATAACAAGTGTTCCAAATGACCTAAAAACTTCACAGTGGACTAATCTTACCA
44 C--------CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
* *
2003 AAATGATTATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACG
101 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACG
* *
2068 ATTCAGAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAATTGTTCCAAATGAGCTAAAAA
166 ATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAA
* * * *
2133 CTTCACTGTGGACTAATCTCACGAAAAATGATAATAGTTAGGCCATAAA-C
231 CTTCACAGTGGACTAATCTCAC-CAAAATGATTATTGTTAGGCCATAAACC
* *
2183 AATGGAAGAAAAACATTGAGGTTTGTCAAATCGAAGACGATTCAGAACGACACTAATGGGCCCCG
1 AATCGAAG----AC---GA------T----TC-AA-A--A--CAG-A--A-ACTAAT-GACCCCG
* *
2248 ATAGGCACAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
38 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
* * *
2313 ATGATTTTAGTTTGGCCATAAACAATGGAAAGAAAAGCATTAAGGTT
103 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTT
2360 ACCAAAT
Statistics
Matches: 649, Mismatches: 60, Indels: 82
0.82 0.08 0.10
Matches are distributed among these distances:
278 5 0.01
279 234 0.36
280 26 0.04
281 1 0.00
282 1 0.00
283 1 0.00
286 2 0.00
289 2 0.00
291 5 0.01
293 2 0.00
294 1 0.00
295 4 0.01
296 3 0.00
297 1 0.00
298 5 0.01
300 2 0.00
308 298 0.46
309 32 0.05
311 1 0.00
313 1 0.00
314 2 0.00
315 2 0.00
316 1 0.00
317 2 0.00
318 6 0.01
319 5 0.01
320 3 0.00
321 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (280 bp):
AATCGAAGACGATTCAAAACAGAAACTAATGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
AAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAG
GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
TTATTGTTAGGCCATAAACC
Found at i:1880 original size:154 final size:154
Alignment explanation
Indices: 1598--2359 Score: 1179
Period size: 154 Copynumber: 5.0 Consensus size: 154
1588 CATAAACCAT
* *
1598 TCGAAGACGATTCAAAACAGA-ACTAAT-GACCCCGATAGGCCCAAAATAACAAGTGTTCTAAAT
1 TCGAAGACGATTCAAAAC-GACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
* * *
1661 GAGCTAATAACTTCACAGTTGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAGTGGA
65 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
1726 AAGAAAAGCATTGAGGTTTGCCAAA
130 AAGAAAAGCATTGAGGTTTGCCAAA
* * *
1751 TCGAAGACGATTTAAAACGTCACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATG
1 TCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* * * *
1816 AGCTAGAAACTTCAAAGTTGACTAATCTCACCAAAATGATTATATTTAGGCCATAAACAATGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
1881 AGAAAAGCATTGAGGTTTGCCAAA
131 AGAAAAGCATTGAGGTTTGCCAAA
* * * **
1905 TCGAAGAAGATTCAATACGTCACTAATGGGCCCCGATAGGGACAAAATAACAAGTGTTCCAAATG
1 TCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* * *
1970 ACCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGATTATAGGTAGGCCATAAACAATGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
*
2035 AGAAAAGCATTGAGGTTTCCCAAA
131 AGAAAAGCATTGAGGTTTGCCAAA
* *
2059 TCGAAGACGATTCAGAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAATTGTTCCAAATG
1 TCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* * *
2124 AGCTAAAAACTTCACTGTGGACTAATCTCACGAAAAATGATAATAGTTAGGCCATAAACAATGG-
66 AGCTAAAAACTTCACAGTGGACTAATCTCAC-CAAAATGATTATAGTTAGGCCATAAACAATGGA
* *
2188 AAGAAAAACATTGAGGTTTGTCAAA
130 AAGAAAAGCATTGAGGTTTGCCAAA
* * *
2213 TCGAAGACGATTCAGAACGACACTAATGGGCCCCGATAGGCACAAAATAACAAGTGTTCAAAATG
1 TCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* *
2278 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTTTAGTTTGGCCATAAACAATGGAA
66 AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
*
2343 AGAAAAGCATTAAGGTT
131 AGAAAAGCATTGAGGTT
2360 ACCAAAT
Statistics
Matches: 555, Mismatches: 50, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
152 1 0.00
153 51 0.09
154 474 0.85
155 29 0.05
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
TCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
AGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
AGAAAAGCATTGAGGTTTGCCAAA
Done.