Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007960.1 Kokia drynarioides strain JFW-HI SEQ_122608, 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: 31620
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Found at i:934 original size:29 final size:29
Alignment explanation
Indices: 874--934 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
864 TTACAACTAG
* *
874 TAAGAAAATATTATTAATTATTATGATGT
1 TAAGAAAATATTATAAATTATTATAATGT
* *
903 TAAGAGAATATTATCAAATTATT-TAATTT
1 TAAGAAAATATTAT-AAATTATTATAATGT
932 TAA
1 TAA
935 ATAGTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (29 bp):
TAAGAAAATATTATAAATTATTATAATGT
Found at i:1452 original size:36 final size:36
Alignment explanation
Indices: 1386--1533 Score: 161
Period size: 36 Copynumber: 4.1 Consensus size: 36
1376 TGGAGGTAAG
* * * *
1386 AGACGAGGCCAAAGATCAACCGCGATGTGCACATGA
1 AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA
* * *
1422 AGACAAGGTCGAAGATCAACCCTGACGTGCACGTGA
1 AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA
* * **
1458 AGACGAGGTTAAAGATCAACCCCGACGTGCACGCGA
1 AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA
* * * *
1494 AGACAAGGCCAAAGATCAACCCCAACATGCACAAGA
1 AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA
1530 AGAC
1 AGAC
1534 GGGGCCGAAG
Statistics
Matches: 93, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 93 1.00
ACGTcount: A:0.38, C:0.27, G:0.25, T:0.10
Consensus pattern (36 bp):
AGACAAGGTCAAAGATCAACCCCGACGTGCACATGA
Found at i:1525 original size:72 final size:72
Alignment explanation
Indices: 1386--1546 Score: 187
Period size: 72 Copynumber: 2.2 Consensus size: 72
1376 TGGAGGTAAG
* * * * * ** *
1386 AGACGAGGCCAAAGATCAACCGCGATGTGCACATGAAGACAAGGTCGAAGATCAACCCTGACGTG
1 AGACGAGGCCAAAGATCAACCCCGACGTGCACACGAAGACAAGGCCAAAGATCAACCCCAACATG
**
1451 CACGTGA
66 CACAAGA
** *
1458 AGACGAGGTTAAAGATCAACCCCGACGTGCACGCGAAGACAAGGCCAAAGATCAACCCCAACATG
1 AGACGAGGCCAAAGATCAACCCCGACGTGCACACGAAGACAAGGCCAAAGATCAACCCCAACATG
1523 CACAAGA
66 CACAAGA
* *
1530 AGACGGGGCCGAAGATC
1 AGACGAGGCCAAAGATC
1547 TAGTGGAGTT
Statistics
Matches: 72, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.37, C:0.27, G:0.27, T:0.10
Consensus pattern (72 bp):
AGACGAGGCCAAAGATCAACCCCGACGTGCACACGAAGACAAGGCCAAAGATCAACCCCAACATG
CACAAGA
Found at i:12095 original size:19 final size:19
Alignment explanation
Indices: 12067--12155 Score: 76
Period size: 19 Copynumber: 4.7 Consensus size: 19
12057 TATGGCAAAG
12067 TAATATATATATAAAAATA
1 TAATATATATATAAAAATA
* *
12086 TAATACATAT-TAAATATA
1 TAATATATATATAAAAATA
* *
12104 T-ATATAAATAATAGAAATA
1 TAATATATAT-ATAAAAATA
* *
12123 T-ATATAGATAGAAAAATA
1 TAATATATATATAAAAATA
12141 CTGAATATATATATA
1 -T-AATATATATATA
12156 TATATATACT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
17 6 0.11
18 15 0.28
19 24 0.44
21 9 0.17
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
TAATATATATATAAAAATA
Found at i:12228 original size:14 final size:15
Alignment explanation
Indices: 12204--12242 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
12194 TTTTGGTGTG
*
12204 AGAAAACAAAATGC-
1 AGAAAATAAAATGCA
*
12218 AGAAATTAAAATGCA
1 AGAAAATAAAATGCA
12233 AGAAAATAAA
1 AGAAAATAAA
12243 TTGATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (15 bp):
AGAAAATAAAATGCA
Found at i:30677 original size:52 final size:52
Alignment explanation
Indices: 30602--31149 Score: 754
Period size: 52 Copynumber: 10.5 Consensus size: 52
30592 TGAAAAAGGT
* * * *
30602 CCGATGATTATGCGTCATCGTGAGTATATGAATCCTTTACGGACTATGAGGT
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGA
* * * *
30654 TCAATGACTATGTGTCATTGTGAGTATATGAATCCTTTACGGATTATGAGGT
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGA
* *
30706 CCAATGACTATGTGTCATTGTGAGTATATGAATCCTTTACGGATTATGAGGA
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGA
* *
30758 CCGATGACTATTTGTCATCGTGAGTATATGAATCCTTTTACGGATTATGAGGT
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTTACGGATTATGAGGA
* * *
30811 CCGATGACTATGTGTTATTGTGAGTATATGAATCCTTTATGGATTATGAGGA
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGA
* * *
30863 TCGATAACTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGGA
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGA
* * * ** * *
30915 CCGAGGAATATGTGTCATCGTGAGTATATGATTCCTTTATAGATTAAGAGGT
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGA
* *
30967 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGTGAA
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGA
* *
31019 CCGATGATTATGTGTCTTCGTGAGTATATGAATCCTTTACGGATTATGAGGA
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGA
* * * * * * *
31071 TCGATGACTATGTCTCATTGTGAGTATATGATTCCTTTATGGATTAAGAGGT
1 CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGA
*
31123 CCAATGACTATGTGTCATCGTGAGTAT
1 CCGATGACTATGTGTCATCGTGAGTAT
31150 TAAATGAAAC
Statistics
Matches: 436, Mismatches: 59, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
52 388 0.89
53 48 0.11
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.36
Consensus pattern (52 bp):
CCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGA
Done.