Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005664.1 Kokia drynarioides strain JFW-HI SEQ_119837, 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: 2956
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--29 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30 TATTGTAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1338 original size:7 final size:7
Alignment explanation
Indices: 1312--1529 Score: 77
Period size: 7 Copynumber: 32.4 Consensus size: 7
1302 GTGAGTTTCG
1312 AAACCTT
1 AAACCTT
*
1319 -AACTTT
1 AAACCTT
*
1325 AAGCCTT
1 AAACCTT
1332 AAACCTT
1 AAACCTT
1339 -AACCTT
1 AAACCTT
*
1345 AAACCCT
1 AAACCTT
1352 AAACCTT
1 AAACCTT
* *
1359 ATATC-T
1 AAACCTT
1365 AAACC-T
1 AAACCTT
* *
1371 CAACTTT
1 AAACCTT
*
1378 AAACCCT
1 AAACCTT
*
1385 AAA-ATCT
1 AAACCT-T
*
1392 AATCC-T
1 AAACCTT
*
1398 AAATC-T
1 AAACCTT
1404 ATAACCTT
1 A-AACCTT
*
1412 AAACCCT
1 AAACCTT
*
1419 AATCC-T
1 AAACCTT
*
1425 AAATC-T
1 AAACCTT
1431 ATAACCTT
1 A-AACCTT
*
1439 AAA-CAT
1 AAACCTT
1445 AAACAC-T
1 AAAC-CTT
*
1452 AAACCCT
1 AAACCTT
*
1459 AAATCTT
1 AAACCTT
1466 AAACCTT
1 AAACCTT
1473 AGAACCTT
1 A-AACCTT
* *
1481 GAA-CAT
1 AAACCTT
*
1487 AAACCAT
1 AAACCTT
1494 AAACC-T
1 AAACCTT
*
1500 AAAACTT
1 AAACCTT
*
1507 AAACCCT
1 AAACCTT
*
1514 -AACCTA
1 AAACCTT
*
1520 AAACCCT
1 AAACCTT
1527 AAA
1 AAA
1530 TACTAAATTC
Statistics
Matches: 154, Mismatches: 41, Indels: 32
0.68 0.18 0.14
Matches are distributed among these distances:
6 50 0.32
7 93 0.60
8 11 0.07
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.26
Consensus pattern (7 bp):
AAACCTT
Found at i:1368 original size:33 final size:33
Alignment explanation
Indices: 1331--1508 Score: 130
Period size: 33 Copynumber: 5.3 Consensus size: 33
1321 CTTTAAGCCT
*
1331 TAAACCTTAACCTTAAACCCTAAACCTTATATC
1 TAAACCTTAACCTTAAACCCTAAACCTTAAATC
* * *
1364 TAAACCTCAACTTTAAACCCTAAA-ATCT-AATCC
1 TAAACCTTAACCTTAAACCCTAAACCT-TAAAT-C
* *
1397 TAAATCTATAACCTTAAACCCTAATCC-TAAATC
1 TAAACCT-TAACCTTAAACCCTAAACCTTAAATC
* * * *
1430 TATAACCTTAAACATAAACACTAAACCCTAAATC
1 TA-AACCTTAACCTTAAACCCTAAACCTTAAATC
* * * *
1464 TTAAACCTTAGAACCTTGAA-CATAAACCATAAACC
1 -TAAACCTT--AACCTTAAACCCTAAACCTTAAATC
*
1499 TAAAACTTAA
1 TAAACCTTAA
1509 ACCCTAACCT
Statistics
Matches: 113, Mismatches: 22, Indels: 21
0.72 0.14 0.13
Matches are distributed among these distances:
32 5 0.04
33 49 0.43
34 40 0.35
35 13 0.12
36 6 0.05
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (33 bp):
TAAACCTTAACCTTAAACCCTAAACCTTAAATC
Found at i:1369 original size:20 final size:20
Alignment explanation
Indices: 1312--1359 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1302 GTGAGTTTCG
* * *
1312 AAACCTTAACTTTAAGCCTT
1 AAACCTTAACCTTAAACCCT
1332 AAACCTTAACCTTAAACCCT
1 AAACCTTAACCTTAAACCCT
1352 AAACCTTA
1 AAACCTTA
1360 TATCTAAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.29, G:0.02, T:0.29
Consensus pattern (20 bp):
AAACCTTAACCTTAAACCCT
Found at i:1409 original size:27 final size:27
Alignment explanation
Indices: 1379--1441 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
1369 CTCAACTTTA
* *
1379 AACCCTAAAATCTAATCCTAAATCTAT
1 AACCTTAAAACCTAATCCTAAATCTAT
*
1406 AACCTTAAACCCTAATCCTAAATCTAT
1 AACCTTAAAACCTAATCCTAAATCTAT
1433 AACCTTAAA
1 AACCTTAAA
1442 CATAAACACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (27 bp):
AACCTTAAAACCTAATCCTAAATCTAT
Found at i:1442 original size:27 final size:27
Alignment explanation
Indices: 1390--1442 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1380 ACCCTAAAAT
1390 CTAATCCTAAATCTATAACCTTAAACC
1 CTAATCCTAAATCTATAACCTTAAACC
1417 CTAATCCTAAATCTATAACCTTAAAC
1 CTAATCCTAAATCTATAACCTTAAAC
1443 ATAAACACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (27 bp):
CTAATCCTAAATCTATAACCTTAAACC
Found at i:1453 original size:27 final size:27
Alignment explanation
Indices: 1395--1454 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
1385 AAAATCTAAT
* *
1395 CCTAAATCTATAACCTTAAACCCTAAT
1 CCTAAATCTATAACCTTAAACCATAAA
1422 CCTAAATCTATAACCTTAAA-CATAAA
1 CCTAAATCTATAACCTTAAACCATAAA
1448 CACTAAA
1 C-CTAAA
1455 CCCTAAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.17
27 25 0.83
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (27 bp):
CCTAAATCTATAACCTTAAACCATAAA
Found at i:1744 original size:34 final size:35
Alignment explanation
Indices: 1699--1790 Score: 93
Period size: 34 Copynumber: 2.7 Consensus size: 35
1689 AACCTTTTAT
*
1699 CATAAATCTTAAATTTATAACCCTA-AACA-TAAA
1 CATAAACCTTAAATTTATAACCCTATAACACTAAA
**
1732 CACTAAACCTTAAATCTTA-AA-TTTATAACACTAAA
1 CA-TAAACCTTAAAT-TTATAACCCTATAACACTAAA
*
1767 CATAAACCCTAAATTTATTAACCC
1 CATAAACCTTAAATTTA-TAACCC
1791 GTTATCATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
33 7 0.15
34 28 0.61
35 11 0.24
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (35 bp):
CATAAACCTTAAATTTATAACCCTATAACACTAAA
Found at i:1746 original size:41 final size:41
Alignment explanation
Indices: 1701--1779 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
1691 CCTTTTATCA
*
1701 TAAATCTTAAATTTATAACCCTAAACATAAACACTAAACCT
1 TAAATCTTAAATTTATAACACTAAACATAAACACTAAACCT
*
1742 TAAATCTTAAATTTATAACACTAAACATAAACCCTAAA
1 TAAATCTTAAATTTATAACACTAAACATAAACACTAAA
1780 TTTATTAACC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (41 bp):
TAAATCTTAAATTTATAACACTAAACATAAACACTAAACCT
Found at i:1788 original size:28 final size:28
Alignment explanation
Indices: 1717--1784 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
1707 TTAAATTTAT
** *
1717 AACCCTAAACATA-AACACTAAACCTTA
1 AACCCTAAATTTATAACACTAAACCATA
* *
1744 AATCTTAAATTTATAACACTAAA-CATA
1 AACCCTAAATTTATAACACTAAACCATA
1771 AACCCTAAATTTAT
1 AACCCTAAATTTAT
1785 TAACCCGTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
27 24 0.73
28 9 0.27
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (28 bp):
AACCCTAAATTTATAACACTAAACCATA
Done.