Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000134.1 Kokia drynarioides strain JFW-HI SEQ_110784, 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: 31905
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:56 original size:39 final size:44
Alignment explanation
Indices: 1--109 Score: 120
Period size: 46 Copynumber: 2.5 Consensus size: 44
* *
1 TTACAACATCTATTCCATT-CAACCAA-ACACAA-GAA-TGCT-A
1 TTACAAC-TCTATTCCATTACAACCAACAAACAATGAATTACTGA
* *
41 TTACAACTCTATTCCATTCCAATCAACCAAACAATTGAATTACTGA
1 TTACAACTCTATTCCATTACAACCAA-CAAACAA-TGAATTACTGA
87 TTACAACTCTATTCCATTACAAC
1 TTACAACTCTATTCCATTACAAC
110 TATATTTCAT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
39 11 0.19
40 13 0.23
42 5 0.09
44 3 0.05
45 3 0.05
46 22 0.39
ACGTcount: A:0.39, C:0.28, G:0.04, T:0.29
Consensus pattern (44 bp):
TTACAACTCTATTCCATTACAACCAACAAACAATGAATTACTGA
Found at i:67 original size:44 final size:46
Alignment explanation
Indices: 12--104 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 46
2 TACAACATCT
* *
12 ATTCCATTCAACCAAACACA-AGAA-TGCT-ATTACAACTCTATTCC
1 ATTCCAATCAACCAAACA-ATAGAATTACTGATTACAACTCTATTCC
*
56 ATTCCAATCAACCAAACAATTGAATTACTGATTACAACTCTATTCC
1 ATTCCAATCAACCAAACAATAGAATTACTGATTACAACTCTATTCC
102 ATT
1 ATT
105 ACAACTATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 20 0.47
45 3 0.07
46 19 0.44
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.30
Consensus pattern (46 bp):
ATTCCAATCAACCAAACAATAGAATTACTGATTACAACTCTATTCC
Found at i:107 original size:16 final size:16
Alignment explanation
Indices: 86--139 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
76 TGAATTACTG
86 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
* *
102 ATTACAACTATATTTC
1 ATTACAACTCTATTCC
*
118 ATTACATCTCTATTCC
1 ATTACAACTCTATTCC
134 ATTACA
1 ATTACA
140 GCCCAATTCG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:14292 original size:21 final size:22
Alignment explanation
Indices: 14263--14313 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
14253 TTACGTCCCA
*
14263 CTCCATCTCACC-TCCTTATTT
1 CTCCTTCTCACCTTCCTTATTT
*
14284 CTCCTTCTCTCGCCTTCCTTATTT
1 CTCC-T-TCTCACCTTCCTTATTT
14308 CTCCTT
1 CTCCTT
14314 TAGGAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 4 0.16
22 1 0.04
23 7 0.28
24 13 0.52
ACGTcount: A:0.08, C:0.43, G:0.02, T:0.47
Consensus pattern (22 bp):
CTCCTTCTCACCTTCCTTATTT
Found at i:21504 original size:24 final size:24
Alignment explanation
Indices: 21476--21552 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 24
21466 ATTCGTAAGG
21476 ATAAATGTAAAGTGGCTGACAAGC
1 ATAAATGTAAAGTGGCTGACAAGC
* * * **
21500 GTAAACGTAAAGTGGCTCATGAGC
1 ATAAATGTAAAGTGGCTGACAAGC
*
21524 ATAAATGTAAAGTGGCTGACAAAC
1 ATAAATGTAAAGTGGCTGACAAGC
21548 ATAAA
1 ATAAA
21553 CGTACATTAG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (24 bp):
ATAAATGTAAAGTGGCTGACAAGC
Found at i:24068 original size:24 final size:24
Alignment explanation
Indices: 24029--24087 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
24019 TATCTTCTTT
* *
24029 ATCTTCACCTCGACCCTAATATTC
1 ATCTTCATCTCAACCCTAATATTC
** *
24053 ATCTTCATCTCAACCCTCGTCTTC
1 ATCTTCATCTCAACCCTAATATTC
24077 ATCTTCATCTC
1 ATCTTCATCTC
24088 CACACTCGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.39, G:0.03, T:0.37
Consensus pattern (24 bp):
ATCTTCATCTCAACCCTAATATTC
Found at i:24095 original size:24 final size:24
Alignment explanation
Indices: 24050--24110 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
24040 GACCCTAATA
*
24050 TTCATCTTCATCTCAACCCTCGTC
1 TTCATCTTCATCTCAACACTCGTC
*
24074 TTCATCTTCATCTCCACACTCGTC
1 TTCATCTTCATCTCAACACTCGTC
* *
24098 TTCGTCTCCATCT
1 TTCATCTTCATCT
24111 ACTTCTTCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.15, C:0.41, G:0.05, T:0.39
Consensus pattern (24 bp):
TTCATCTTCATCTCAACACTCGTC
Found at i:28155 original size:15 final size:15
Alignment explanation
Indices: 28107--28155 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
28097 TTTGTTTCGA
* *
28107 TTATATTCTAATTAT
1 TTATATTTTAAATAT
*
28122 TTATAATTTAAAT-T
1 TTATATTTTAAATAT
28136 GTTATATTTTAAATAT
1 -TTATATTTTAAATAT
28152 TTAT
1 TTAT
28156 TTTATAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (15 bp):
TTATATTTTAAATAT
Found at i:28309 original size:18 final size:17
Alignment explanation
Indices: 28286--28328 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
28276 TAATAGGATT
*
28286 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTAAA
*
28304 TTAATTTAAAATATTAAA
1 TTAA-TTAAAAAATTAAA
28322 TTAATTA
1 TTAATTA
28329 TACCTTGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 14 0.64
19 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATTAAAAAATTAAA
Found at i:29425 original size:15 final size:17
Alignment explanation
Indices: 29405--29438 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
29395 AATCTTTTAA
29405 AAATTA-TAAAAA-TAT
1 AAATTATTAAAAATTAT
29420 AAATTATTAAAAATTAT
1 AAATTATTAAAAATTAT
29437 AA
1 AA
29439 TTTAATTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTATTAAAAATTAT
Done.