Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010271.1 Corchorus olitorius cultivar O-4 contig10303, 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: 1791
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Found at i:1219 original size:4 final size:4
Alignment explanation
Indices: 1207--1430 Score: 72
Period size: 4 Copynumber: 56.5 Consensus size: 4
1197 AAAAAAAAGT
* * *
1207 AATA GATA AATA AATA AATA AATA AATA GAA-A AATA AGTA AAAA TAATA
1 AATA AATA AATA AATA AATA AATA AATA -AATA AATA AATA AATA -AATA
* * ** * * **
1256 GATA AATA AAAA AGATA AATA GGTA TATA GAT- AATA AGATA AATA GTTA
1 AATA AATA AATA A-ATA AATA AATA AATA AATA AATA A-ATA AATA AATA
** * * * ** *
1305 GGTA AA-A AA-A AGTA GATA ATAGTA AATA AATA GAT- AATA GCTA AATT
1 AATA AATA AATA AATA AATA A-A-TA AATA AATA AATA AATA AATA AATA
* * * ** *
1352 AATA AATA AA-A GGATA AAT- AGTA AATA AATA GAT- AATA GTTA AATT
1 AATA AATA AATA -AATA AATA AATA AATA AATA AATA AATA AATA AATA
*
1398 AATA AATA AA-A ATATA AAT- AGTA AATA AATA AA
1 AATA AATA AATA A-ATA AATA AATA AATA AATA AA
1431 AAAAATCTTT
Statistics
Matches: 156, Mismatches: 47, Indels: 34
0.66 0.20 0.14
Matches are distributed among these distances:
3 20 0.13
4 116 0.74
5 17 0.11
6 3 0.02
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:1355 original size:19 final size:18
Alignment explanation
Indices: 1317--1406 Score: 63
Period size: 19 Copynumber: 4.4 Consensus size: 18
1307 TAAAAAAAAG
1317 TAGATAATAGTAAATAAA
1 TAGATAATAGTAAATAAA
1335 TAGATAATAGCTAAATTAATAAA
1 TAGATAATAG-T--A--AATAAA
1358 TAAAAGGATAAATAGTAAATAAA
1 T---A-GAT-AATAGTAAATAAA
*
1381 TAGATAATAGTTAAATTAA
1 TAGATAATAG-TAAATAAA
*
1400 TAAATAA
1 TAGATAA
1407 AAATATAAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 21
0.72 0.02 0.26
Matches are distributed among these distances:
18 15 0.25
19 17 0.29
20 1 0.02
21 1 0.02
23 14 0.24
25 1 0.02
26 1 0.02
27 4 0.07
28 5 0.08
ACGTcount: A:0.60, C:0.01, G:0.10, T:0.29
Consensus pattern (18 bp):
TAGATAATAGTAAATAAA
Found at i:1367 original size:27 final size:27
Alignment explanation
Indices: 1212--1430 Score: 97
Period size: 28 Copynumber: 8.3 Consensus size: 27
1202 AAAGTAATAG
* *
1212 ATAAATAAATAAATAAATAAATAGAAAA
1 ATAAATAAATAAATAGATAAATAG-TAA
* *
1240 ATAAGTAAAAATAATAGATAAATA--AA
1 ATAAATAAATA-AATAGATAAATAGTAA
** * * *
1266 A-AAGATAAATAGGTATATAGATAATAA
1 ATAA-ATAAATAAATAGATAAATAGTAA
** ** * * *
1293 GATAAATAGTTAGGTA-AAAAAAAGTAG
1 -ATAAATAAATAAATAGATAAATAGTAA
1320 ATAATAGTAAATAAATAGAT-AATAGCTAA
1 ATAA-A-TAAATAAATAGATAAATAG-TAA
*
1349 ATTAATAAATAAA-AGGATAAATAGTAA
1 ATAAATAAATAAATA-GATAAATAGTAA
* *
1376 ATAAATAGAT-AATAGTTAAAT--T-A
1 ATAAATAAATAAATAGATAAATAGTAA
1399 ATAAAT-AA-AAAT--ATAAATAGTAA
1 ATAAATAAATAAATAGATAAATAGTAA
1422 ATAAATAAA
1 ATAAATAAA
1431 AAAAATCTTT
Statistics
Matches: 144, Mismatches: 29, Indels: 40
0.68 0.14 0.19
Matches are distributed among these distances:
20 5 0.03
22 5 0.03
23 14 0.10
24 3 0.02
25 10 0.07
26 21 0.15
27 32 0.22
28 35 0.24
29 19 0.13
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (27 bp):
ATAAATAAATAAATAGATAAATAGTAA
Found at i:1373 original size:46 final size:46
Alignment explanation
Indices: 1318--1428 Score: 188
Period size: 46 Copynumber: 2.4 Consensus size: 46
1308 AAAAAAAAGT
1318 AGAT-AATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
1 AGATAAATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
* *
1363 GGATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAA
1 AGATAAATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
*
1409 ATATAAATAGTAAATAAATA
1 AGATAAATAGTAAATAAATA
1429 AAAAAAATCT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 3 0.05
46 58 0.95
ACGTcount: A:0.62, C:0.01, G:0.09, T:0.28
Consensus pattern (46 bp):
AGATAAATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
Done.