Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010224.1 Kokia drynarioides strain JFW-HI SEQ_125053, 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: 2987
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.32
Warning! 292 characters in sequence are not A, C, G, or T
Found at i:467 original size:18 final size:17
Alignment explanation
Indices: 437--482 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
427 TTTTTATAAT
437 AATATTATCATTATTAC
1 AATATTATCATTATTAC
454 AATATT-T-ATTATT--
1 AATATTATCATTATTAC
*
467 ATTATTATCATTATTA
1 AATATTATCATTATTA
483 ATAGCACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
13 5 0.20
14 1 0.04
15 12 0.48
16 1 0.04
17 6 0.24
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (17 bp):
AATATTATCATTATTAC
Found at i:525 original size:24 final size:24
Alignment explanation
Indices: 478--525 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
468 TTATTATCAT
*
478 TATTAATAGCACATTTATTATTAA
1 TATTAATAGCACATTTAATATTAA
*
502 TATTAATAG-ATATTTAATACTTAA
1 TATTAATAGCACATTTAATA-TTAA
526 AAAAANNNNN
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (24 bp):
TATTAATAGCACATTTAATATTAA
Found at i:775 original size:18 final size:17
Alignment explanation
Indices: 745--778 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
735 TTTTTATAAT
745 AATATTATCATTATTAC
1 AATATTATCATTATTAC
*
762 AATATTTATTATTATTA
1 AATA-TTATCATTATTA
779 TTATCATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
AATATTATCATTATTAC
Found at i:833 original size:24 final size:24
Alignment explanation
Indices: 788--833 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
778 ATTATCATTG
*
788 TTAATAGCACATTTATTATTAATA
1 TTAATAGCACATTTAATATTAATA
*
812 TTAATAG-ATATTTAATACTTAA
1 TTAATAGCACATTTAATA-TTAA
834 AAAAAATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (24 bp):
TTAATAGCACATTTAATATTAATA
Found at i:1516 original size:17 final size:17
Alignment explanation
Indices: 1478--1548 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
1468 TTTGGACTTT
* *
1478 TTTAATTTTGAAATTAAA
1 TTTAAATTT-AAAATAAA
* *
1496 TTTAAATTTAAGATTAA
1 TTTAAATTTAAAATAAA
1513 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
1530 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
1547 TT
1 TT
1549 AAAAAGGGCG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 37 0.82
18 8 0.18
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:1543 original size:7 final size:6
Alignment explanation
Indices: 1478--1541 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
1468 TTTGGACTTT
*
1478 TTTAAT TTTGAAA -TTAAA TTTAAA TTTAAGA -TT-AA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA
* *
1525 -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
1542 ATAAATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 1 0.02
5 10 0.21
6 34 0.71
7 3 0.06
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:2615 original size:67 final size:67
Alignment explanation
Indices: 2536--2696 Score: 261
Period size: 67 Copynumber: 2.4 Consensus size: 67
2526 GTTTCAATCC
* * *
2536 ACTTCTCTGTATCTCATCAGGAAGCT-GAGATTCGAAGACTTGATCACATCGATCTCAGAGTTGG
1 ACTTCTCTGTATCTCATCAGGAAGCTAG-GATTCGAAGACTTCATCACATCGAGCCCAGAGTTGG
2600 TAT
65 TAT
* *
2603 ACTTCTCTGTATCTCATCAGGAAGCTAGGATTCGAATACTTCATCACATCGAGCCCTGAGTTGGT
1 ACTTCTCTGTATCTCATCAGGAAGCTAGGATTCGAAGACTTCATCACATCGAGCCCAGAGTTGGT
2668 AT
66 AT
2670 ACTTCTCTGTATCTCATCAGGAAGCTA
1 ACTTCTCTGTATCTCATCAGGAAGCTA
2697 ACCATTTTAT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
67 87 0.99
68 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (67 bp):
ACTTCTCTGTATCTCATCAGGAAGCTAGGATTCGAAGACTTCATCACATCGAGCCCAGAGTTGGT
AT
Done.