Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014069.1 Kokia drynarioides strain JFW-HI SEQ_129100, 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, 941
Length: 1569
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Found at i:293 original size:18 final size:17
Alignment explanation
Indices: 266--309 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
256 TAAACGTTTT
*
266 AATAAATAAATATAATA
1 AATAAATAAACATAATA
*
283 AATACAATAAACATAATT
1 AATA-AATAAACATAATA
301 AAT-AATAAA
1 AATAAATAAA
310 GGCAAGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.25
17 4 0.17
18 14 0.58
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAAATAAACATAATA
Found at i:449 original size:12 final size:12
Alignment explanation
Indices: 432--479 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
422 AAAAATCATT
*
432 AAACAAAATACA
1 AAACAAAATAAA
*
444 AAACAAATTAAA
1 AAACAAAATAAA
*
456 AAACAAACAAAAA
1 AAACAAA-ATAAA
*
469 AAAGAAAATAA
1 AAACAAAATAA
480 GAGAAATCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
12 20 0.69
13 9 0.31
ACGTcount: A:0.79, C:0.10, G:0.02, T:0.08
Consensus pattern (12 bp):
AAACAAAATAAA
Found at i:1339 original size:30 final size:29
Alignment explanation
Indices: 1280--1547 Score: 235
Period size: 30 Copynumber: 9.1 Consensus size: 29
1270 AGAAATAATG
* *
1280 TTTTGACCCC-AAACTTCCCAAAATCACA
1 TTTTGACCCCTAAACTTCTCAAAATTACA
*
1308 TTTTGACCCCAAAACTTCTTCAAAATTACA
1 TTTTGACCCCTAAACTTC-TCAAAATTACA
* * *
1338 TTTTGACTCCTACATTTCTCTAAAATTACA
1 TTTTGACCCCTAAACTTCTC-AAAATTACA
* *
1368 TTTTGA-CCCTAAACTTCCCAAAATAACA
1 TTTTGACCCCTAAACTTCTCAAAATTACA
* * *
1396 TTTTAACCCCAAAACATATCT-AATATTACA
1 TTTTGACCCCTAAAC-T-TCTCAAAATTACA
*
1426 TTTT-AACCCTAAAACTTCTCTAAAATTACA
1 TTTTGACCCCT-AAACTTCTC-AAAATTACA
*
1456 TTTTGACCCTTAAACTTCTCCAAAATTACA
1 TTTTGACCCCTAAACTTCT-CAAAATTACA
* **
1486 TTTT-AACTTTAAACTT-TCCTAAAATTACA
1 TTTTGACCCCTAAACTTCT-C-AAAATTACA
* *
1515 TTTT-AACCCTAAACTTTTCCAAAATTACA
1 TTTTGACCCCTAAACTTCT-CAAAATTACA
1544 TTTT
1 TTTT
1548 AACCTTGAAT
Statistics
Matches: 202, Mismatches: 25, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
28 29 0.14
29 76 0.38
30 90 0.45
31 7 0.03
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (29 bp):
TTTTGACCCCTAAACTTCTCAAAATTACA
Found at i:1397 original size:88 final size:88
Alignment explanation
Indices: 1280--1547 Score: 314
Period size: 88 Copynumber: 3.0 Consensus size: 88
1270 AGAAATAATG
* * * *
1280 TTTTGACCCCAAACTTCCCAAAATCACATTTTGACCCCAAAAC-T-TCTTCAAAATTACATTTTG
1 TTTTGACCCTAAACTTCCCAAAATAACATTTTAACCCCAAAACATATC-T-AAAATTACATTTTA
* *
1343 ACTCCT-ACATTTCTCTAAAATTACA
64 AC-CCTAAAACTTCTCTAAAATTACA
*
1368 TTTTGACCCTAAACTTCCCAAAATAACATTTTAACCCCAAAACATATCTAATATTACATTTTAAC
1 TTTTGACCCTAAACTTCCCAAAATAACATTTTAACCCCAAAACATATCTAAAATTACATTTTAAC
1433 CCTAAAACTTCTCTAAAATTACA
66 CCTAAAACTTCTCTAAAATTACA
* *** *
1456 TTTTGACCCTTAAACTTCTCCAAAATTACATTTTAA-CTTTAAAC-TTTCCTAAAATTACATTTT
1 TTTTGACCC-TAAACTTC-CCAAAATAACATTTTAACCCCAAAACATAT-CTAAAATTACATTTT
* *
1519 AACCCT-AAACTTTTCCAAAATTACA
63 AACCCTAAAACTTCTCTAAAATTACA
1544 TTTT
1 TTTT
1548 AACCTTGAAT
Statistics
Matches: 159, Mismatches: 15, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
87 3 0.02
88 103 0.65
89 35 0.22
90 18 0.11
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.37
Consensus pattern (88 bp):
TTTTGACCCTAAACTTCCCAAAATAACATTTTAACCCCAAAACATATCTAAAATTACATTTTAAC
CCTAAAACTTCTCTAAAATTACA
Found at i:1452 original size:118 final size:118
Alignment explanation
Indices: 1297--1551 Score: 318
Period size: 118 Copynumber: 2.2 Consensus size: 118
1287 CCCAAACTTC
* * * * *
1297 CCAAAATCACATTTTGACCCCAAAACTTCTTCAAAATTACATTTTGACTCC-TACATTTCTCTAA
1 CCAAAATTACATTTTAACCCCAAAACTTCTTCAAAATTACATTTTGAC-CCTTAAACTTCTCCAA
*
1361 AATTACATTTTGACCCTAAAC-TTCCCAAAATAACATTTTAACCCCAAAACATAT
65 AATTACATTTTAACCCTAAACTTTCCCAAAATAACATTTTAA-CCCAAAACATAT
* * *
1415 CTAATATTACATTTTAACCCTAAAACTTC-TCTAAAATTACATTTTGACCCTTAAACTTCTCCAA
1 CCAAAATTACATTTTAACCCCAAAACTTCTTC-AAAATTACATTTTGACCCTTAAACTTCTCCAA
** * * * * *
1479 AATTACATTTTAACTTTAAACTTTCCTAAAATTACATTTTAACCCTAAACTTTT
65 AATTACATTTTAACCCTAAACTTTCCCAAAATAACATTTTAACCCAAAACATAT
1533 CCAAAATTACATTTTAACC
1 CCAAAATTACATTTTAACC
1552 TTGAATTCCC
Statistics
Matches: 116, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
117 4 0.03
118 94 0.81
119 18 0.16
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.36
Consensus pattern (118 bp):
CCAAAATTACATTTTAACCCCAAAACTTCTTCAAAATTACATTTTGACCCTTAAACTTCTCCAAA
ATTACATTTTAACCCTAAACTTTCCCAAAATAACATTTTAACCCAAAACATAT
Done.