Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014331.1 Kokia drynarioides strain JFW-HI SEQ_129368, 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: 34942
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1319 original size:108 final size:108
Alignment explanation
Indices: 1197--1411 Score: 394
Period size: 108 Copynumber: 2.0 Consensus size: 108
1187 GTATGAAATG
*
1197 CCTAACATGCATGCTAAATATGGTACAAAAGAGAAAAAAAATACACAAATTTAGGGAGAAAATAG
1 CCTAACATGCATGCTAAATATGGTACAAAAGAGAAAAAAAATACAAAAATTTAGGGAGAAAATAG
1262 GTATCATTTCTAATGATATCAATGTTTAAAGTAAGTAAGAATA
66 GTATCATTTCTAATGATATCAATGTTTAAAGTAAGTAAGAATA
* *
1305 CCTAACATGCATGCTAAATATGGTACAAAAGAGACAAATAATACAAAAATTTAGGGAGAAAATAG
1 CCTAACATGCATGCTAAATATGGTACAAAAGAGAAAAAAAATACAAAAATTTAGGGAGAAAATAG
*
1370 GTATCATTTCTAATGCTATCAATGTTTAAAGTAAGTAAGAAT
66 GTATCATTTCTAATGATATCAATGTTTAAAGTAAGTAAGAAT
1412 GCCTTCCCAT
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 103 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (108 bp):
CCTAACATGCATGCTAAATATGGTACAAAAGAGAAAAAAAATACAAAAATTTAGGGAGAAAATAG
GTATCATTTCTAATGATATCAATGTTTAAAGTAAGTAAGAATA
Found at i:8385 original size:31 final size:30
Alignment explanation
Indices: 8316--8395 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
8306 ACTTTCAAAA
***
8316 GTTTTCATTTTAGGCACTCAAATTTTTTTT
1 GTTTTCATTTTAGGCACTCAAATTCCATTT
* **
8346 CTTTTCATTTTAGGCACTCCTATTACCATTT
1 GTTTTCATTTTAGGCACTCAAATT-CCATTT
*
8377 GTTTTCATTTTAGCCACTC
1 GTTTTCATTTTAGGCACTC
8396 TAAGGTATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 21 0.51
31 20 0.49
ACGTcount: A:0.19, C:0.21, G:0.09, T:0.51
Consensus pattern (30 bp):
GTTTTCATTTTAGGCACTCAAATTCCATTT
Found at i:8819 original size:25 final size:23
Alignment explanation
Indices: 8791--8842 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
8781 CTAACTGACT
8791 TAACAGCTAATT-ATCTTAACTAAGC
1 TAACAGCTAATTGA-CTTAAC-AA-C
*
8816 TAACTGCTAATTGACTTAACAAC
1 TAACAGCTAATTGACTTAACAAC
8839 TAAC
1 TAAC
8843 TATCTCTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 5 0.20
24 2 0.08
25 17 0.68
26 1 0.04
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (23 bp):
TAACAGCTAATTGACTTAACAAC
Found at i:27194 original size:6 final size:6
Alignment explanation
Indices: 27183--27254 Score: 51
Period size: 6 Copynumber: 12.0 Consensus size: 6
27173 TCCAAGGTAG
* * * *
27183 GAAAAA GAAAAA GAAGAAAA GAAAAA TGGAGAA GAAAAA G-AGAA -AAAAT
1 GAAAAA GAAAAA G-A-AAAA GAAAAA -GAAAAA GAAAAA GAAAAA GAAAAA
*
27232 GAAAAA G-AAAA TAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA
27255 AGCTGCAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
5 9 0.18
6 30 0.60
7 6 0.12
8 5 0.10
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.04
Consensus pattern (6 bp):
GAAAAA
Found at i:27237 original size:16 final size:17
Alignment explanation
Indices: 27214--27254 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
27204 AAAAATGGAG
*
27214 AAGAAAAAGAGAA-AAA
1 AAGAAAAAGAAAATAAA
*
27230 ATGAAAAAGAAAATAAA
1 AAGAAAAAGAAAATAAA
27247 AAGAAAAA
1 AAGAAAAA
27255 AGCTGCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (17 bp):
AAGAAAAAGAAAATAAA
Found at i:27242 original size:21 final size:20
Alignment explanation
Indices: 27183--27242 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 20
27173 TCCAAGGTAG
27183 GAAAAA-GAAAAAGAAGAAAA
1 GAAAAATGAAAAAGAA-AAAA
* *
27203 GAAAAATGGAGAAGAAAAAGA
1 GAAAAATGAAAAAGAAAAA-A
27224 GAAAAAATGAAAAAGAAAA
1 G-AAAAATGAAAAAGAAAA
27243 TAAAAAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 9 0.27
21 9 0.27
22 15 0.45
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (20 bp):
GAAAAATGAAAAAGAAAAAA
Found at i:28111 original size:16 final size:16
Alignment explanation
Indices: 28075--28111 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
28065 ACTTTAGAAA
28075 AAGAGAAAAATAAAAC
1 AAGAGAAAAATAAAAC
*
28091 AAGA-AAATA-AAAAC
1 AAGAGAAAAATAAAAC
28105 AAGAGAA
1 AAGAGAA
28112 TTTTTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 9 0.47
15 6 0.32
16 4 0.21
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.05
Consensus pattern (16 bp):
AAGAGAAAAATAAAAC
Done.