Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004937.1 Kokia drynarioides strain JFW-HI SEQ_118645, 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: 7617
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Found at i:756 original size:29 final size:29
Alignment explanation
Indices: 724--815 Score: 93
Period size: 29 Copynumber: 3.1 Consensus size: 29
714 TTATTAACAT
724 GATTATGTGTTGTGTGGTTGACTTAAATG
1 GATTATGTGTTGTGTGGTTGACTTAAATG
* *
753 GATT-TGAATATT-TAGTGGATTTA-TTAACAT-
1 GATTATG--TGTTGT-GTGG-TTGACTTAA-ATG
783 GATTATGTGTTGTGTGGTTGACTTAAATG
1 GATTATGTGTTGTGTGGTTGACTTAAATG
812 GATT
1 GATT
816 TGAATATTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
28 7 0.14
29 20 0.40
30 16 0.32
31 7 0.14
ACGTcount: A:0.25, C:0.03, G:0.26, T:0.46
Consensus pattern (29 bp):
GATTATGTGTTGTGTGGTTGACTTAAATG
Found at i:804 original size:59 final size:59
Alignment explanation
Indices: 712--828 Score: 234
Period size: 59 Copynumber: 2.0 Consensus size: 59
702 TAAATTATGT
712 ATTTATTAACATGATTATGTGTTGTGTGGTTGACTTAAATGGATTTGAATATTTAGTGG
1 ATTTATTAACATGATTATGTGTTGTGTGGTTGACTTAAATGGATTTGAATATTTAGTGG
771 ATTTATTAACATGATTATGTGTTGTGTGGTTGACTTAAATGGATTTGAATATTTAGTG
1 ATTTATTAACATGATTATGTGTTGTGTGGTTGACTTAAATGGATTTGAATATTTAGTG
829 AAAGTAATTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.27, C:0.03, G:0.23, T:0.46
Consensus pattern (59 bp):
ATTTATTAACATGATTATGTGTTGTGTGGTTGACTTAAATGGATTTGAATATTTAGTGG
Found at i:1975 original size:16 final size:16
Alignment explanation
Indices: 1954--1999 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
1944 TATATCTTGA
1954 TTAAACTCTTAATCAC
1 TTAAACTCTTAATCAC
* * *
1970 TTAAACT-TTATTTAA
1 TTAAACTCTTAATCAC
1985 TTAAAC-CTTAATCAC
1 TTAAACTCTTAATCAC
2000 AATTAATCAA
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (16 bp):
TTAAACTCTTAATCAC
Found at i:3364 original size:151 final size:151
Alignment explanation
Indices: 3196--3489 Score: 446
Period size: 151 Copynumber: 1.9 Consensus size: 151
3186 AACCCATTTT
3196 CACACACCTCCTTTCTTCATCCTCATCTTCTTCCCTTTTAATTCCAATATCTTTAATTACAAATC
1 CACACACCTCCTTTCTTCATCCTCATCTTCTTCCCTTTTAATTCCAATATCTTTAATTACAAATC
* * ***
3261 TGTCTCAAAGCTTAAATATTTGAAACCCATTAACCCAAAAATTTTTAACGGGAAGAAGATATTGG
66 TGTCCCAAAGCTTAAATATTTAAAACCCATTAACCCAAAAAAACTTAACGGGAAGAAGATATTGG
3326 AATCAAAGATATTGAATCTTC
131 AATCAAAGATATTGAATCTTC
* * * * *
3347 CACACACCT-CTCTTCTTCATCTTCATCTTCTTCTCTTTTGATTCCGATATCTTTAGTTACAAAT
1 CACACACCTCCT-TTCTTCATCCTCATCTTCTTCCCTTTTAATTCCAATATCTTTAATTACAAAT
* * *
3411 CTGTCCCAAAGCTTGAATCTTTAAAACTCATTAACCCAAAAAAACTTAACGGGAAGAAGATATTG
65 CTGTCCCAAAGCTTAAATATTTAAAACCCATTAACCCAAAAAAACTTAACGGGAAGAAGATATTG
*
3476 GAATCAAATATATT
130 GAATCAAAGATATT
3490 AATTTTTGGG
Statistics
Matches: 128, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
150 2 0.02
151 126 0.98
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (151 bp):
CACACACCTCCTTTCTTCATCCTCATCTTCTTCCCTTTTAATTCCAATATCTTTAATTACAAATC
TGTCCCAAAGCTTAAATATTTAAAACCCATTAACCCAAAAAAACTTAACGGGAAGAAGATATTGG
AATCAAAGATATTGAATCTTC
Found at i:5389 original size:18 final size:17
Alignment explanation
Indices: 5374--5410 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5364 ATATAAAACC
5374 TAAAA-AATAAAAAAAA
1 TAAAACAATAAAAAAAA
5390 TAAAAGCAAT-AAAAAAA
1 TAAAA-CAATAAAAAAAA
5407 TAAA
1 TAAA
5411 GCAAACAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 11 0.58
18 3 0.16
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.14
Consensus pattern (17 bp):
TAAAACAATAAAAAAAA
Found at i:5411 original size:16 final size:17
Alignment explanation
Indices: 5383--5414 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5373 CTAAAAAATA
5383 AAAAAAATAAAAGCAAT
1 AAAAAAATAAAAGCAAT
5400 AAAAAAAT-AAAGCAA
1 AAAAAAATAAAAGCAA
5415 ACAAGTGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.09
Consensus pattern (17 bp):
AAAAAAATAAAAGCAAT
Found at i:6299 original size:20 final size:21
Alignment explanation
Indices: 6267--6305 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
6257 TAATAATAAA
6267 AAAAGATATCTTTTACTTTAG
1 AAAAGATATCTTTTACTTTAG
*
6288 AAAAGA-ATCTTTTGCTTT
1 AAAAGATATCTTTTACTTT
6306 TTATTCATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (21 bp):
AAAAGATATCTTTTACTTTAG
Done.