Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009134.1 Kokia drynarioides strain JFW-HI SEQ_123838, 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: 2029
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Found at i:326 original size:19 final size:20
Alignment explanation
Indices: 296--334 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
286 AAGATGATAT
296 TTATTAAATAATTAATAATA
1 TTATTAAATAATTAATAATA
316 TTATT-AATAATTAATAATA
1 TTATTAAATAATTAATAATA
335 ATAATAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATTAAATAATTAATAATA
Found at i:330 original size:16 final size:16
Alignment explanation
Indices: 302--341 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 16
292 ATATTTATTA
302 AATAATTAATAATATTATT
1 AATAATTAATAATA--A-T
321 AATAATTAATAATAAT
1 AATAATTAATAATAAT
337 AATAA
1 AATAA
342 ACTCGAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 1 0.05
19 14 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATTAATAATAAT
Found at i:1460 original size:29 final size:28
Alignment explanation
Indices: 1388--1579 Score: 150
Period size: 29 Copynumber: 6.6 Consensus size: 28
1378 AACCGTCAAT
**
1388 AAATTCCATTTTTACCCTCGAACTTCCAA
1 AAATTCCATTTTTACCC-AAAACTTCCAA
* * *
1417 AAATCCCATTTTTTACGCCAAAATTTCTAA
1 AAATTCCA-TTTTTAC-CCAAAACTTCCAA
**
1447 AAATTCCATTTTTACCCCCGAACTTCCAA
1 AAATTCCATTTTTA-CCCAAAACTTCCAA
* * ** *
1476 AAATCCCATTTTGACCCAAATTTTCTAA
1 AAATTCCATTTTTACCCAAAACTTCCAA
* ** *
1504 AAATTTCATTTTTACCCTCGAACTCCCAA
1 AAATTCCATTTTTACCC-AAAACTTCCAA
* *
1533 AAATCCCATTTTTGACCCCAAAACTTCCTA
1 AAATTCCATTTTT-A-CCCAAAACTTCCAA
*
1563 AAATTCCCTTTTTACCC
1 AAATTCCATTTTTACCC
1580 TCGAACTCTC
Statistics
Matches: 123, Mismatches: 34, Indels: 13
0.72 0.20 0.08
Matches are distributed among these distances:
28 26 0.21
29 51 0.41
30 41 0.33
31 5 0.04
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.34
Consensus pattern (28 bp):
AAATTCCATTTTTACCCAAAACTTCCAA
Found at i:1480 original size:59 final size:58
Alignment explanation
Indices: 1388--1586 Score: 294
Period size: 59 Copynumber: 3.4 Consensus size: 58
1378 AACCGTCAAT
*
1388 AAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTTACGCCAAAATTTCTAA
1 AAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGAC-CCAAAATTTCTAA
* *
1447 AAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCA-TTTTGACCCAAATTTTCTAA
1 AAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCAAAATTTCTAA
* * *
1504 AAATTTCATTTTTACCCTCGAACTCCCAAAAATCCCATTTTTGACCCCAAAACTTCCT-A
1 AAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA-CCCAAAA-TTTCTAA
*
1563 AAATTCCCTTTTTACCCTCGAACT
1 AAATTCCATTTTTACCCTCGAACT
1587 CTCAAAATTA
Statistics
Matches: 127, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
57 46 0.36
58 12 0.09
59 65 0.51
60 4 0.03
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (58 bp):
AAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCAAAATTTCTAA
Found at i:1586 original size:29 final size:28
Alignment explanation
Indices: 1388--1633 Score: 114
Period size: 29 Copynumber: 8.5 Consensus size: 28
1378 AACCGTCAAT
*
1388 AAATTCCATTTTTACCCTCGAACTTCC-A
1 AAATTCCCTTTTTACCC-CGAACTTCCTA
* * * * *
1416 AAAATCCCATTTTTTACGCCAAAATTTCTAA
1 AAATTCCC--TTTTTACCCCGAACTTCCT-A
*
1447 AAATTCCATTTTTACCCCCGAACTTCC-A
1 AAATTCCCTTTTTA-CCCCGAACTTCCTA
* * * * *
1475 AAAATCCCATTTTGA-CCCAAATTTTCTAA
1 AAATTCCC-TTTTTACCCCGAACTTCCT-A
* * *
1504 AAATTTCATTTTTACCCTCGAAC-TCCCA
1 AAATTCCCTTTTTACCC-CGAACTTCCTA
* *
1532 AAAATCCCATTTTTGACCCCAAAACTTCCTA
1 AAATTCCC-TTTTT-ACCCC-GAACTTCCTA
1563 AAATTCCCTTTTTACCCTCGAAC-T-CTCA
1 AAATTCCCTTTTTACCC-CGAACTTCCT-A
1591 AAATTACCC-TTTTACCCCCGAA-TGT-CTA
1 AAATT-CCCTTTTTA-CCCCGAACT-TCCTA
*
1619 AGAATTCCTTTTTTA
1 A-AATTCCCTTTTTA
1634 AAACCTCAAA
Statistics
Matches: 162, Mismatches: 34, Indels: 43
0.68 0.14 0.18
Matches are distributed among these distances:
27 10 0.06
28 44 0.27
29 58 0.36
30 32 0.20
31 18 0.11
ACGTcount: A:0.31, C:0.30, G:0.04, T:0.35
Consensus pattern (28 bp):
AAATTCCCTTTTTACCCCGAACTTCCTA
Found at i:1631 original size:28 final size:27
Alignment explanation
Indices: 1560--1631 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
1550 CCAAAACTTC
* *
1560 CTAAAATTCCCTTTTTACCCTCGAACT
1 CTAAAATTACCTTTTTACCCCCGAACT
* *
1587 CTCAAAATTACCCTTTTACCCCCGAATGT
1 CT-AAAATTACCTTTTTACCCCCGAA-CT
1616 CTAAGAATT-CCTTTTT
1 CTAA-AATTACCTTTTT
1632 TAAAACCTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
27 2 0.05
28 28 0.76
29 7 0.19
ACGTcount: A:0.26, C:0.31, G:0.06, T:0.38
Consensus pattern (27 bp):
CTAAAATTACCTTTTTACCCCCGAACT
Done.