Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011860.1 Kokia drynarioides strain JFW-HI SEQ_126857, 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: 2215
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Found at i:469 original size:17 final size:18
Alignment explanation
Indices: 442--475 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
432 ATATGTTAAA
*
442 ATTTTTAATTTTTTCGTT
1 ATTTTTAATTTATTCGTT
460 ATTTTT-ATTTATTCGT
1 ATTTTTAATTTATTCGT
476 ATGTAATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (18 bp):
ATTTTTAATTTATTCGTT
Found at i:594 original size:17 final size:17
Alignment explanation
Indices: 572--651 Score: 99
Period size: 17 Copynumber: 4.6 Consensus size: 17
562 ATTTGTTTAA
572 AAATTTAAAATTATTAT
1 AAATTTAAAATTATTAT
*
589 AAATTTAAATTTAATT-T
1 AAATTTAAAATT-ATTAT
* * *
606 AAGTTTAAATTTATTTT
1 AAATTTAAAATTATTAT
623 CAAATTTAAAATTATTAT
1 -AAATTTAAAATTATTAT
641 AAATTTAAAAT
1 AAATTTAAAAT
652 AAATAAAGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
16 3 0.05
17 35 0.64
18 17 0.31
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (17 bp):
AAATTTAAAATTATTAT
Found at i:599 original size:6 final size:6
Alignment explanation
Indices: 588--649 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
578 AAAATTATTA
* * *
588 TAAATT TAAATT T-AATT TAAGTT TAAATT T-ATTT TCAAATT TAAAAT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT
635 T--ATT ATAAATT TAAA
1 TAAATT -TAAATT TAAA
650 ATAAATAAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
4 2 0.05
5 10 0.23
6 25 0.57
7 7 0.16
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:608 original size:52 final size:52
Alignment explanation
Indices: 541--649 Score: 164
Period size: 52 Copynumber: 2.1 Consensus size: 52
531 CAAACTCATC
* *
541 TTAAACTTATTTTAAGATTAAATTTGTTTAAAAATTTAAAATTATTATAAAT
1 TTAAACTTAATTTAAGATTAAATTTATTTAAAAATTTAAAATTATTATAAAT
* * **
593 TTAAATTTAATTTAAGTTTAAATTTATTTTCAAATTTAAAATTATTATAAAT
1 TTAAACTTAATTTAAGATTAAATTTATTTAAAAATTTAAAATTATTATAAAT
645 TTAAA
1 TTAAA
650 ATAAATAAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.50
Consensus pattern (52 bp):
TTAAACTTAATTTAAGATTAAATTTATTTAAAAATTTAAAATTATTATAAAT
Found at i:618 original size:12 final size:12
Alignment explanation
Indices: 588--649 Score: 51
Period size: 11 Copynumber: 5.3 Consensus size: 12
578 AAAATTATTA
588 TAAATTTAAATT
1 TAAATTTAAATT
*
600 T-AATTTAAGTT
1 TAAATTTAAATT
*
611 TAAATTT-ATTT
1 TAAATTTAAATT
*
622 TCAAATTTAAAAT
1 T-AAATTTAAATT
635 T--ATTATAAATT
1 TAAATT-TAAATT
646 TAAA
1 TAAA
650 ATAAATAAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
10 3 0.08
11 20 0.51
12 12 0.31
13 4 0.10
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (12 bp):
TAAATTTAAATT
Found at i:695 original size:14 final size:15
Alignment explanation
Indices: 663--695 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
653 AATAAAGTTT
*
663 AATTACAAAATGTCC
1 AATTACAAAATGCCC
678 AATTACAAAA-GCCC
1 AATTACAAAATGCCC
692 AATT
1 AATT
696 GGGCCCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.48, C:0.21, G:0.06, T:0.24
Consensus pattern (15 bp):
AATTACAAAATGCCC
Found at i:2105 original size:29 final size:29
Alignment explanation
Indices: 2051--2196 Score: 132
Period size: 30 Copynumber: 4.9 Consensus size: 29
2041 GCACTGGAGG
* *
2051 TCCCTAAACCTTCCAAAAATTTCATTTTTA
1 TCCCTGAA-CTTCCAAAAATTCCATTTTTA
** *
2081 TCTTTGAACTTCCAAAAATCCCATTTTT-
1 TCCCTGAACTTCCAAAAATTCCATTTTTA
* *
2109 TACCCTGAAACTTCCAAAAATTCTATTTTTT
1 T-CCCTG-AACTTCCAAAAATTCCATTTTTA
*
2140 TCCCCGAACTTCCAAAAATTCCATTTTTAA
1 TCCCTGAACTTCCAAAAATTCCATTTTT-A
* ** * *
2170 CCCCAAAACTTCCACAAATCCCATTTT
1 TCCCTGAACTTCCAAAAATTCCATTTT
2197 GACCTCAAAA
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
28 1 0.01
29 42 0.44
30 51 0.54
31 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.02, T:0.37
Consensus pattern (29 bp):
TCCCTGAACTTCCAAAAATTCCATTTTTA
Found at i:2121 original size:30 final size:30
Alignment explanation
Indices: 2087--2215 Score: 145
Period size: 29 Copynumber: 4.4 Consensus size: 30
2077 TTTATCTTTG
*
2087 AACTTCCAAAAATCCCATTTTTTACCCTGA
1 AACTTCCAAAAATCCCATTTTTTACCCCGA
* * *
2117 AACTTCCAAAAATTCTATTTTTTTCCCCG-
1 AACTTCCAAAAATCCCATTTTTTACCCCGA
* * *
2146 AACTTCCAAAAATTCCATTTTTAACCCCAA
1 AACTTCCAAAAATCCCATTTTTTACCCCGA
* * * *
2176 AACTTCCACAAATCCCA-TTTTGACCTCAA
1 AACTTCCAAAAATCCCATTTTTTACCCCGA
2205 AACTTCCAAAA
1 AACTTCCAAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
29 45 0.53
30 40 0.47
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (30 bp):
AACTTCCAAAAATCCCATTTTTTACCCCGA
Found at i:2152 original size:59 final size:58
Alignment explanation
Indices: 2052--2188 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 58
2042 CACTGGAGGT
*** *
2052 CCCTAAACCTTCCAAAAATTTCATTTTTATCTTTGAACTTCCAAAAATCCCATTTTTTA
1 CCCTAAA-CTTCCAAAAATTTCATTTTTATCCCCGAACTTCCAAAAATCCCATTTTTAA
* *
2111 CCCTGAAACTTCCAAAAA-TTCTATTTTTTTCCCCGAACTTCCAAAAATTCCATTTTTAA
1 CCCT-AAACTTCCAAAAATTTC-ATTTTTATCCCCGAACTTCCAAAAATCCCATTTTTAA
* *
2170 CCCCAAAACTTCCACAAAT
1 -CCCTAAACTTCCAAAAAT
2189 CCCATTTTGA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
58 3 0.05
59 57 0.86
60 6 0.09
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (58 bp):
CCCTAAACTTCCAAAAATTTCATTTTTATCCCCGAACTTCCAAAAATCCCATTTTTAA
Found at i:2209 original size:59 final size:59
Alignment explanation
Indices: 2087--2215 Score: 143
Period size: 59 Copynumber: 2.2 Consensus size: 59
2077 TTTATCTTTG
* ** * * ** **
2087 AACTTCCAAAAATCCCATTTTTTACCCTGAAACTTCCAAAAATTCTATTTTTTTCCCCG
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTGACCCAA
* *
2146 AACTTCCAAAAATTCCATTTTTAACCCCAAAACTTCCACAAATCCCA-TTTTGACCTCAA
1 AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTGACC-CAA
2205 AACTTCCAAAA
1 AACTTCCAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 6 0.10
59 52 0.90
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (59 bp):
AACTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATCCCATTTTTGACCCAA
Done.