Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01000283.1 Corchorus olitorius cultivar O-4 contig00283, 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: 2048
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Found at i:1305 original size:30 final size:30
Alignment explanation
Indices: 1267--1544 Score: 155
Period size: 30 Copynumber: 9.5 Consensus size: 30
1257 TAAATATTAT
1267 TTTCTAATTATAATTTCATTACATATATAA
1 TTTCTAATTATAATTTCATTACATATATAA
* *
1297 TTGCTAATTATTATTT--TCTA-A-ATATAA
1 TTTCTAATTATAATTTCAT-TACATATATAA
* * * *
1324 TTTTTAAAAATTTTTAATTTC--TAAATAT-TAT
1 TTTCT---AA-TTATAATTTCATTACATATATAA
*
1355 TTTCTAATTATAATTTCAATACATATATAA
1 TTTCTAATTATAATTTCATTACATATATAA
*
1385 TTTCTAAATA-ATATTTCATTACATATATAA
1 TTTCTAATTATA-ATTTCATTACATATATAA
* *
1415 TTTATAA-TATAA-TTC-CTA-AT-TATAA
1 TTTCTAATTATAATTTCATTACATATATAA
* *
1440 TTTCTTCACATATATAGTTTC--TA-A-ATATCAT
1 TTTC-T-A-AT-TATAATTTCATTACATATAT-AA
*
1471 TTTCTAAATA-ATATTTCATTAC--ATATAA
1 TTTCTAATTATA-ATTTCATTACATATATAA
* *
1499 TTCCTAATTATAATTTCATTACATATATCA
1 TTTCTAATTATAATTTCATTACATATATAA
* *
1529 TTTCTAAATATTATTT
1 TTTCTAATTATAATTT
1545 TCTCATTATA
Statistics
Matches: 193, Mismatches: 27, Indels: 56
0.70 0.10 0.20
Matches are distributed among these distances:
25 8 0.04
26 4 0.02
27 27 0.14
28 28 0.15
29 20 0.10
30 82 0.42
31 22 0.11
32 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (30 bp):
TTTCTAATTATAATTTCATTACATATATAA
Found at i:1323 original size:44 final size:43
Alignment explanation
Indices: 1213--1400 Score: 191
Period size: 44 Copynumber: 4.3 Consensus size: 43
1203 CGCTATATTC
* *
1213 AAATTTTATTTTCTAAATATAATTTC-TAAATATTTTAAAATTTCT
1 AAATATTATTTTCTAAATATAATTTCTTAAATA---TATAATTTCT
* * *
1258 AAATATTATTTTCTAATTATAATTTCATTACATATATAATTGCT
1 AAATATTATTTTCTAAATATAATTTC-TTAAATATATAATTTCT
* * *
1302 AATTATTATTTTCTAAATATAATTT-TTAAAAATTTTTAATTTCT
1 AAATATTATTTTCTAAATATAATTTCTT--AAATATATAATTTCT
* * *
1346 AAATATTATTTTCTAATTATAATTTCAATACATATATAATTTCT
1 AAATATTATTTTCTAAATATAATTTC-TTAAATATATAATTTCT
*
1390 AAATAATATTT
1 AAATATTATTT
1401 CATTACATAT
Statistics
Matches: 119, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
42 2 0.02
44 87 0.73
45 24 0.20
46 1 0.01
47 5 0.04
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (43 bp):
AAATATTATTTTCTAAATATAATTTCTTAAATATATAATTTCT
Found at i:1368 original size:88 final size:89
Alignment explanation
Indices: 1214--1400 Score: 297
Period size: 88 Copynumber: 2.1 Consensus size: 89
1204 GCTATATTCA
*
1214 AATT-TTATTTTCTAAATATAATTTCTAAATATTTTAAAATTTCTAAATATTATTTTCTAATTAT
1 AATTATTATTTTCTAAATATAATTTCTAAAAATTTTAAAATTTCTAAATATTATTTTCTAATTAT
*
1278 AATTTCATTACATATATAATTGCT
66 AATTTCAATACATATATAATTGCT
* *
1302 AATTATTATTTTCTAAATATAATTTTTAAAAATTTT-TAATTTCTAAATATTATTTTCTAATTAT
1 AATTATTATTTTCTAAATATAATTTCTAAAAATTTTAAAATTTCTAAATATTATTTTCTAATTAT
*
1366 AATTTCAATACATATATAATTTCT
66 AATTTCAATACATATATAATTGCT
* *
1390 AAATAATATTT
1 AATTATTATTT
1401 CATTACATAT
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
88 62 0.68
89 29 0.32
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (89 bp):
AATTATTATTTTCTAAATATAATTTCTAAAAATTTTAAAATTTCTAAATATTATTTTCTAATTAT
AATTTCAATACATATATAATTGCT
Found at i:1385 original size:17 final size:16
Alignment explanation
Indices: 1363--1532 Score: 67
Period size: 17 Copynumber: 11.6 Consensus size: 16
1353 ATTTTCTAAT
1363 TATAATTTCAATACATA
1 TATAATTTC-ATACATA
*
1380 TATAATTTC-TAAATA
1 TATAATTTCATACATA
1395 -AT-ATTTCATTACATA
1 TATAATTTCA-TACATA
1410 TATAATTT-AT--A-A
1 TATAATTTCATACATA
*
1422 TATAA-TTCCTA-AT-
1 TATAATTTCATACATA
*
1435 TATAATTTCTTCACATA
1 TATAATTTCAT-ACATA
*
1452 TATAGTTTC-TA-A-A
1 TATAATTTCATACATA
* *
1465 TATCATTTTC-TAAATA
1 TAT-AATTTCATACATA
1481 -AT-ATTTCATTAC--A
1 TATAATTTCA-TACATA
*
1494 TATAA-TTCCTA-AT-
1 TATAATTTCATACATA
1507 TATAATTTCATTACATA
1 TATAATTTCA-TACATA
*
1524 TATCATTTC
1 TATAATTTC
1533 TAAATATTAT
Statistics
Matches: 118, Mismatches: 11, Indels: 48
0.67 0.06 0.27
Matches are distributed among these distances:
11 2 0.02
12 7 0.06
13 28 0.24
14 22 0.19
15 21 0.18
16 9 0.08
17 29 0.25
ACGTcount: A:0.40, C:0.12, G:0.01, T:0.47
Consensus pattern (16 bp):
TATAATTTCATACATA
Found at i:1440 original size:72 final size:72
Alignment explanation
Indices: 1358--1547 Score: 239
Period size: 72 Copynumber: 2.6 Consensus size: 72
1348 ATATTATTTT
* *
1358 CTAATTATAATTTCAATACATATATAATTTCTAAATAATA-TTTCATTACATATATAATTT-A-T
1 CTAATTATAATTTCATTACATATATAATTTCTAAATAATATTTTC--TAAATA-AT-ATTTCATT
1420 A-ATATAATTC
62 ACATATAATTC
*
1430 CTAATTATAATTTC-TTCACATATATAGTTTCTAAAT-ATCATTTTCTAAATAATATTTCATTAC
1 CTAATTATAATTTCATT-ACATATATAATTTCTAAATAAT-ATTTTCTAAATAATATTTCATTAC
1493 ATATAATTC
64 ATATAATTC
* *
1502 CTAATTATAATTTCATTACATATATCATTTCTAAATATTATTTTCT
1 CTAATTATAATTTCATTACATATATAATTTCTAAATAATATTTTCT
1548 CATTATAATT
Statistics
Matches: 104, Mismatches: 6, Indels: 16
0.83 0.05 0.13
Matches are distributed among these distances:
69 4 0.04
70 3 0.03
71 10 0.10
72 80 0.77
73 7 0.07
ACGTcount: A:0.39, C:0.12, G:0.01, T:0.48
Consensus pattern (72 bp):
CTAATTATAATTTCATTACATATATAATTTCTAAATAATATTTTCTAAATAATATTTCATTACAT
ATAATTC
Found at i:1443 original size:42 final size:43
Alignment explanation
Indices: 1338--1497 Score: 145
Period size: 44 Copynumber: 3.7 Consensus size: 43
1328 TAAAAATTTT
*
1338 TAATTTCTAAATATTATTT--TCTA-AT-TATAATTTCAATACATATA
1 TAATTTCTAAATAATATTTCAT-TACATATATAATTT--ATA-A-ATA
1382 TAATTTCTAAATAATATTTCATTACATATATAATTTAT-AATA
1 TAATTTCTAAATAATATTTCATTACATATATAATTTATAAATA
* * * *
1424 TAATTCCT-AATTATAATTTC-TTCACATATATAGTTTCTAAATA
1 TAATTTCTAAATAAT-ATTTCATT-ACATATATAATTTATAAATA
*
1467 TCATTTTCTAAATAATATTTCATTACATATA
1 T-AATTTCTAAATAATATTTCATTACATATA
1498 ATTCCTAATT
Statistics
Matches: 98, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
41 7 0.07
42 28 0.29
43 6 0.06
44 35 0.36
45 11 0.11
46 3 0.03
47 8 0.08
ACGTcount: A:0.41, C:0.11, G:0.01, T:0.48
Consensus pattern (43 bp):
TAATTTCTAAATAATATTTCATTACATATATAATTTATAAATA
Done.