Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004045.1 Kokia drynarioides strain JFW-HI SEQ_117187, 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, 817
Length: 1363
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Found at i:34 original size:13 final size:13
Alignment explanation
Indices: 1--49 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
*
1 ATTAATAAAAATA
1 ATTAATAATAATA
14 TTATTAATAATAATA
1 --ATTAATAATAATA
*
29 ATTAATATTAATA
1 ATTAATAATAATA
*
42 ATAAATAA
1 ATTAATAA
50 AAATGAAGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 18 0.60
15 12 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATTAATAATAATA
Found at i:1211 original size:28 final size:28
Alignment explanation
Indices: 1134--1212 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 28
1124 TTTGACCCCT
1134 AAACTTTTCCAAAATTCCATTTAGACCAC
1 AAACTTTT-CAAAATTCCATTTAGACCAC
* * * *
1163 AAAGTTTTTAGAAATTACATTTA-ACCCCC
1 AAACTTTTCA-AAATTCCATTTAGA-CCAC
*
1192 GAACTTTTCAAAATTCCATTT
1 AAACTTTTCAAAATTCCATTT
1213 TTAACCTCAG
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
28 12 0.30
29 28 0.70
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (28 bp):
AAACTTTTCAAAATTCCATTTAGACCAC
Found at i:1241 original size:30 final size:30
Alignment explanation
Indices: 1201--1363 Score: 101
Period size: 29 Copynumber: 5.5 Consensus size: 30
1191 CGAACTTTTC
**
1201 AAAATT-CCATTTTTAACCTCAGTTTTCCT
1 AAAATTACCATTTTTAACCTCAAATTTCCT
*
1230 AAAATTACCA-TTTT-ACCCCTAAACTTT-CT
1 AAAATTACCATTTTTAACCTC-AAA-TTTCCT
* * * *
1259 AAAA-TACCATTTTTGACCTTAATTTCTCCA
1 AAAATTACCATTTTTAACCTCAAATT-TCCT
* *
1289 AAAATTA-CATTTTTACCCCCAAAATTTCC-
1 AAAATTACCATTTTTAACCTC-AAATTTCCT
* * *
1318 AAAA-TCCCATTTTTTACCTC-GATTTCTCT
1 AAAATTACCATTTTTAACCTCAAATTTC-CT
1347 AAAAATTACCATTTTTA
1 -AAAATTACCATTTTTA
Statistics
Matches: 101, Mismatches: 19, Indels: 26
0.69 0.13 0.18
Matches are distributed among these distances:
27 5 0.05
28 13 0.13
29 38 0.38
30 30 0.30
31 15 0.15
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (30 bp):
AAAATTACCATTTTTAACCTCAAATTTCCT
Found at i:1272 original size:29 final size:29
Alignment explanation
Indices: 1228--1363 Score: 79
Period size: 30 Copynumber: 4.6 Consensus size: 29
1218 CTCAGTTTTC
1228 CTAAAATTACCA-TTTTACCCCTAAACTTT
1 CTAAAATTACCATTTTTACCCCTAAA-TTT
*
1257 CTAAAA-TACCATTTTTGA--CCTTAATTT
1 CTAAAATTACCATTTTT-ACCCCTAAATTT
*
1284 CTCCAAAAATTA-CATTTTTACCCCCAAAATTT
1 CT---AAAATTACCATTTTTA-CCCCTAAATTT
* * * * *
1316 CCAAAA-TCCCATTTTTTACCTC-GATTTCT
1 CTAAAATTACCA-TTTTTACCCCTAAATT-T
1345 CTAAAAATTACCATTTTTA
1 CT-AAAATTACCATTTTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 27
0.69 0.08 0.22
Matches are distributed among these distances:
27 5 0.06
28 14 0.17
29 22 0.27
30 28 0.34
31 6 0.07
32 8 0.10
ACGTcount: A:0.34, C:0.25, G:0.01, T:0.40
Consensus pattern (29 bp):
CTAAAATTACCATTTTTACCCCTAAATTT
Found at i:1322 original size:59 final size:59
Alignment explanation
Indices: 1174--1361 Score: 211
Period size: 59 Copynumber: 3.2 Consensus size: 59
1164 AAGTTTTTAG
* * * * * *
1174 AAATTA-CATTTAACCCCCGAACTTTTCAAAATTCCATTTTTAACCTCAGTTT-TCCTA
1 AAATTACCATTTTACCCCCAAACTTTCCAAAATACCATTTTTAACCTCAATTTCTCCAA
* * * *
1231 AAATTACCATTTTACCCCTAAACTTTCTAAAATACCATTTTTGACCTTAATTTCTCCAA
1 AAATTACCATTTTACCCCCAAACTTTCCAAAATACCATTTTTAACCTCAATTTCTCCAA
* * * * *
1290 AAATTA-CATTTTTACCCCCAAAATTTCCAAAATCCCATTTTTTACCTCGATTTCTCTAA
1 AAATTACCA-TTTTACCCCCAAACTTTCCAAAATACCATTTTTAACCTCAATTTCTCCAA
1349 AAATTACCATTTT
1 AAATTACCATTTT
1362 TA
Statistics
Matches: 109, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
57 6 0.06
58 39 0.36
59 62 0.57
60 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (59 bp):
AAATTACCATTTTACCCCCAAACTTTCCAAAATACCATTTTTAACCTCAATTTCTCCAA
Done.