Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000588.1 Kokia drynarioides strain JFW-HI SEQ_111518, 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: 10411
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Found at i:1202 original size:27 final size:23
Alignment explanation
Indices: 1154--1214 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 23
1144 AAAATATGTA
* *
1154 TATAAAATATAAAATCATTAAATT
1 TATAAAA-ATAAAATAATTAAAAT
1178 TATTTAAAAATAGAAATAATCTAAAAT
1 TA--TAAAAATA-AAATAAT-TAAAAT
1205 TATAAAAATA
1 TATAAAAATA
1215 CAAAAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
24 2 0.06
25 11 0.35
26 11 0.35
27 7 0.23
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (23 bp):
TATAAAAATAAAATAATTAAAAT
Found at i:3719 original size:25 final size:23
Alignment explanation
Indices: 3659--3720 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
3649 TTTTATAATT
*
3659 TTATAATTTTTATTTTTAAATAA
1 TTATAATTTTTATTTTTAAACAA
3682 -TA-AATTTTTTATTTTTAAACAA
1 TTATAA-TTTTTATTTTTAAACAA
3704 TTATATATTTATTATTT
1 TTATA-ATTT-TTATTT
3721 AGTTAATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 2 0.06
22 18 0.55
23 2 0.06
24 4 0.12
25 7 0.21
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATAATTTTTATTTTTAAACAA
Found at i:4016 original size:2 final size:2
Alignment explanation
Indices: 4003--4056 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
3993 ACCTTTCAAC
*
4003 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4045 AT AT AT AT AT AT
1 AT AT AT AT AT AT
4057 TAGTCTTTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4108 original size:16 final size:16
Alignment explanation
Indices: 4089--4121 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4079 TATTGAAATT
4089 TTATTT-TAAATATTTA
1 TTATTTATAAA-ATTTA
4105 TTATTTATAAAATTTA
1 TTATTTATAAAATTTA
4121 T
1 T
4122 CAAATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTTATAAAATTTA
Found at i:5121 original size:19 final size:19
Alignment explanation
Indices: 5097--5134 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
5087 TATTACTAAA
5097 TTTGTTATTT-TAAATATTT
1 TTTGTTATTTATAAA-ATTT
5116 TTTGTTATTTATAAAATTT
1 TTTGTTATTTATAAAATTT
5135 ATCATATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTGTTATTTATAAAATTT
Found at i:5900 original size:19 final size:18
Alignment explanation
Indices: 5862--5908 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
5852 TTCAAATAGA
*
5862 AAATTTA-AATTATTTAT
1 AAATTTATAATTATGTAT
5879 AAATTTATAATTGATGTAT
1 AAATTTATAATT-ATGTAT
5898 AAATTTTATAA
1 AAA-TTTATAA
5909 ATAATATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 7 0.27
18 4 0.15
19 8 0.31
20 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
AAATTTATAATTATGTAT
Found at i:6119 original size:26 final size:23
Alignment explanation
Indices: 6090--6141 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 23
6080 ATATTGTTAT
*
6090 ATTTTAATTATATTTATTATTTATTA
1 ATTTTAATAATA-TTATT-TTT-TTA
6116 ATTTTAATAATATTATTTTTTTA
1 ATTTTAATAATATTATTTTTTTA
6139 ATT
1 ATT
6142 ATATGTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 6 0.24
24 3 0.12
25 5 0.20
26 11 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTTAATAATATTATTTTTTTA
Found at i:7021 original size:10 final size:10
Alignment explanation
Indices: 7006--7041 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
6996 TAAAATCAAA
*
7006 ATGTATATTT
1 ATGTATATAT
7016 ATGTATATAT
1 ATGTATATAT
*
7026 ATATATATAT
1 ATGTATATAT
7036 ATGTAT
1 ATGTAT
7042 GCGTATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (10 bp):
ATGTATATAT
Found at i:8307 original size:23 final size:23
Alignment explanation
Indices: 8272--8349 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
8262 AATTTGAATC
*
8272 CAATATTTGAGTTGGATTAATTA
1 CAATATATGAGTTGGATTAATTA
* * *
8295 CAATATATAAGTTAGCATTTGAA-TC
1 CAATATATGAGTT-GGA-TT-AATTA
*
8320 CAATATTTGAGTTGGATTAATTA
1 CAATATATGAGTTGGATTAATTA
8343 CAATATA
1 CAATATA
8350 AAAATTGTCA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
22 2 0.05
23 20 0.48
24 4 0.10
25 14 0.33
26 2 0.05
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (23 bp):
CAATATATGAGTTGGATTAATTA
Found at i:8332 original size:25 final size:24
Alignment explanation
Indices: 8263--8333 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 24
8253 TCCACCATTA
*
8263 ATTTGAATCCAATATTTGAGTTGG
1 ATTTGAATCCAATATTTGAGTTGC
* * *
8287 A-TT-AATTACAATATATAAGTTAGC
1 ATTTGAA-TCCAATATTTGAGTT-GC
8311 ATTTGAATCCAATATTTGAGTTG
1 ATTTGAATCCAATATTTGAGTTG
8334 GATTAATTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
22 2 0.06
23 14 0.39
24 4 0.11
25 14 0.39
26 2 0.06
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.41
Consensus pattern (24 bp):
ATTTGAATCCAATATTTGAGTTGC
Found at i:9481 original size:13 final size:13
Alignment explanation
Indices: 9463--9488 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9453 AATTAGAGAA
9463 AACAAAAAAATCC
1 AACAAAAAAATCC
9476 AACAAAAAAATCC
1 AACAAAAAAATCC
9489 TTGGCAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.23, G:0.00, T:0.08
Consensus pattern (13 bp):
AACAAAAAAATCC
Done.