Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01005991.1 Corchorus olitorius cultivar O-4 contig06016, 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, 915
Length: 1526
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Found at i:1338 original size:27 final size:27
Alignment explanation
Indices: 1307--1500 Score: 88
Period size: 27 Copynumber: 7.4 Consensus size: 27
1297 AAAATAATAA
* *
1307 TAATATATAAATAGAT-AATAGCTAAAT
1 TAATAAATAAAAAGATAAATAG-TAAAT
1334 TAATAAATAAAAAGATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
* * * * *
1361 AAATAGATAATAA-TTAAATTAATAAA-
1 TAATAAATAAAAAGATAAA-TAGTAAAT
**
1387 TAGATAAATAGTAA-ATAAATAG-AGAA-
1 TA-ATAAATAAAAAGATAAATAGTA-AAT
* *
1413 TAGTTAAA-AATAA-ATAAATAGATAAA-
1 TA-ATAAATAAAAAGATAAATAG-TAAAT
* *
1439 TAGTAAATAAATAGAT-AATAGTTAAA-
1 TAATAAATAAAAAGATAAATAG-TAAAT
* *
1465 A-ATAAATAAATAGATAAATAGTAAAT
1 TAATAAATAAAAAGATAAATAGTAAAT
* *
1491 AAATAGATAA
1 TAATAAATAA
1501 TAGTTAAAAA
Statistics
Matches: 135, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
25 34 0.25
26 38 0.28
27 58 0.43
28 5 0.04
ACGTcount: A:0.63, C:0.01, G:0.09, T:0.28
Consensus pattern (27 bp):
TAATAAATAAAAAGATAAATAGTAAAT
Found at i:1344 original size:4 final size:4
Alignment explanation
Indices: 1329--1500 Score: 90
Period size: 4 Copynumber: 43.8 Consensus size: 4
1319 AGATAATAGC
* * * *
1329 TAAA TTAA TAAA TAAA -AAGA TAAA T-AG TAAA TAAA TAGA T-AA TAAT
1 TAAA TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * * * *
1375 TAAA TTAA TAAA TAGA TAAA T-AG TAAA TAAA TAGA GAATA GTTAA -AAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA
* * * *
1423 TAAA TAAA TAGA TAAA T-AG TAAA TAAA TAGA TAATA GTTAA -AAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA-A -TAAA TAAA TAAA
* * *
1471 TAAA TAGA TAAA T-AG TAAA TAAA TAGA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
1501 TAGTTAAAAA
Statistics
Matches: 121, Mismatches: 34, Indels: 26
0.67 0.19 0.14
Matches are distributed among these distances:
3 16 0.13
4 96 0.79
5 6 0.05
6 3 0.02
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:1444 original size:44 final size:44
Alignment explanation
Indices: 1313--1515 Score: 329
Period size: 44 Copynumber: 4.6 Consensus size: 44
1303 ATAATAATAT
* *
1313 ATAAATAGATAATAGCTAAATTAATAAATAAAAAGATAAATAGTAA
1 ATAAATAGATAATAGTTAAA--AATAAATAAATAGATAAATAGTAA
* *
1359 ATAAATAGATAATAATT--AAATTAATAAATAGATAAATAGTAA
1 ATAAATAGATAATAGTTAAAAATAAATAAATAGATAAATAGTAA
*
1401 ATAAATAGAGAATAGTTAAAAATAAATAAATAGATAAATAGTAA
1 ATAAATAGATAATAGTTAAAAATAAATAAATAGATAAATAGTAA
1445 ATAAATAGATAATAGTTAAAAATAAATAAATAGATAAATAGTAA
1 ATAAATAGATAATAGTTAAAAATAAATAAATAGATAAATAGTAA
1489 ATAAATAGATAATAGTTAAAAATAAAT
1 ATAAATAGATAATAGTTAAAAATAAAT
1516 TAAAAAAAAA
Statistics
Matches: 147, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
42 37 0.25
44 95 0.65
46 15 0.10
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (44 bp):
ATAAATAGATAATAGTTAAAAATAAATAAATAGATAAATAGTAA
Found at i:1500 original size:8 final size:8
Alignment explanation
Indices: 1230--1491 Score: 102
Period size: 8 Copynumber: 32.1 Consensus size: 8
1220 TAATAAAAAA
1230 AGATAAAT
1 AGATAAAT
* * *
1238 AGGTATAG
1 AGATAAAT
1246 AGATAAAT
1 AGATAAAT
1254 AGATAAAT
1 AGATAAAT
* *
1262 AGATACAG
1 AGATAAAT
1270 AGA-ATAAT
1 AGATA-AAT
1278 AGATAAAT
1 AGATAAAT
* **
1286 AGGTAGCT
1 AGATAAAT
* *
1294 AAAAAAAT
1 AGATAAAT
1302 A-ATAATAAT
1 AGAT-A-AAT
*
1311 ATATAAAT
1 AGATAAAT
1319 AGAT-AAT
1 AGATAAAT
*
1326 AGCTAAATT
1 AGATAAA-T
1335 A-ATAAAT
1 AGATAAAT
1342 --A-AAA-
1 AGATAAAT
1346 AGATAAAT
1 AGATAAAT
1354 AGTAAATAAAT
1 AG---ATAAAT
1365 AGAT-AAT
1 AGATAAAT
1372 A-ATTAAATT
1 AGA-TAAA-T
1381 A-ATAAAT
1 AGATAAAT
1388 AGATAAAT
1 AGATAAAT
1396 AGTAAATAAAT
1 AG---ATAAAT
*
1407 AGA-GAAT
1 AGATAAAT
*
1414 AGTTAAAAAT
1 AG--ATAAAT
*
1424 AAATAAAT
1 AGATAAAT
1432 AGATAAAT
1 AGATAAAT
1440 AGTAAATAAAT
1 AG---ATAAAT
1451 AGAT-AAT
1 AGATAAAT
*
1458 AGTTAAAAAT
1 AG--ATAAAT
*
1468 AAATAAAT
1 AGATAAAT
1476 AGATAAAT
1 AGATAAAT
1484 AG-TAAAT
1 AGATAAAT
1491 A
1 A
1492 AATAGATAAT
Statistics
Matches: 193, Mismatches: 31, Indels: 61
0.68 0.11 0.21
Matches are distributed among these distances:
5 3 0.02
6 3 0.02
7 35 0.18
8 105 0.54
9 13 0.07
10 10 0.05
11 24 0.12
ACGTcount: A:0.61, C:0.01, G:0.11, T:0.26
Consensus pattern (8 bp):
AGATAAAT
Found at i:1508 original size:19 final size:19
Alignment explanation
Indices: 1323--1504 Score: 139
Period size: 19 Copynumber: 9.7 Consensus size: 19
1313 ATAAATAGAT
* *
1323 AATAGCTAAATTAATAAATA
1 AATAGATAAA-TAGTAAATA
*
1343 AAAAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
* *
1362 AATAGATAATAATTAAATTAATA
1 AATAGAT-A-AA-T-AGTAAATA
1385 AATAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
* *
1404 AATAGA-GAATAGTTAA-A
1 AATAGATAAATAGTAAATA
*
1421 AATAAATAAATAG---ATA
1 AATAGATAAATAGTAAATA
* *
1437 AATAG-TAAATAAATAGAT-
1 AATAGATAAAT-AGTAAATA
* *
1455 AATAGTTAAA-AATAAATA
1 AATAGATAAATAGTAAATA
1473 AATAGATAAATAGTAAATA
1 AATAGATAAATAGTAAATA
1492 AATAGAT-AATAGT
1 AATAGATAAATAGT
1505 TAAAAATAAA
Statistics
Matches: 132, Mismatches: 17, Indels: 28
0.75 0.10 0.16
Matches are distributed among these distances:
15 6 0.05
16 6 0.05
17 12 0.09
18 33 0.25
19 46 0.35
20 10 0.08
21 4 0.03
22 2 0.02
23 13 0.10
ACGTcount: A:0.63, C:0.01, G:0.09, T:0.27
Consensus pattern (19 bp):
AATAGATAAATAGTAAATA
Done.