Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011305.1 Kokia drynarioides strain JFW-HI SEQ_126285, 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: 13882
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:12985 original size:200 final size:200
Alignment explanation
Indices: 12637--13227 Score: 968
Period size: 200 Copynumber: 3.0 Consensus size: 200
12627 AGCGATGCAG
* * * * * *
12637 TCATTTTCCTGACGAGACACTGAGAA-GAAGACCTAAACGAGGCTCAAAACGAGCAAAATCTTCA
1 TCATCTTCCTGATGAGACGCTGA-AATGAAGACCCAAATGAGGCTCAAAACAAGCAAAATCTTCA
* * *
12701 AAACCCAACTTCCTGATGAGATACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGTTGCCAGATG
65 AAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTACCAGATG
*
12766 AGATACTGAGAAGTGAACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGCG
130 AGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGCG
12831 ATATGA
195 ATATGA
12837 TCATCTTCCTGATGAGACGCTGAAATGAAGACCCAAATGAGGCTCAAAACAAGCAAAATCTTCAA
1 TCATCTTCCTGATGAGACGCTGAAATGAAGACCCAAATGAGGCTCAAAACAAGCAAAATCTTCAA
* * *
12902 AACCCAGCTTTCTGATAAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTACCAGATGA
66 AACCCAACTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTACCAGATGA
*
12967 GATGCTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGCGA
131 GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGCGA
*
13032 TGTGA
196 TATGA
*
13037 TCATCTTCCTGATGAGACGCTGAAATGAAGACCCAAATGAGGCTCAAAACAAGCGAAATCTTCAA
1 TCATCTTCCTGATGAGACGCTGAAATGAAGACCCAAATGAGGCTCAAAACAAGCAAAATCTTCAA
* * *
13102 AACCCAACTTCCTGATGAGACATTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTTCAAGATGA
66 AACCCAACTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTACCAGATGA
* * *
13167 GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATAAGATATAGAGAAGCAGATTGAAACA
131 GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACA
13228 AGTGACGCGG
Statistics
Matches: 364, Mismatches: 26, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
199 2 0.01
200 362 0.99
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (200 bp):
TCATCTTCCTGATGAGACGCTGAAATGAAGACCCAAATGAGGCTCAAAACAAGCAAAATCTTCAA
AACCCAACTTCCTGATGAGACACTGAGAAGCAGGTGGAAGCAATAAATGGTTAGCTACCAGATGA
GATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAGCGA
TATGA
Found at i:13616 original size:6 final size:6
Alignment explanation
Indices: 13605--13683 Score: 67
Period size: 6 Copynumber: 13.7 Consensus size: 6
13595 ATTTGTTTAA
* *
13605 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * * *
13651 -ATTTT CAAATTT AAAATT -ACTAT AAATTT AAAT
1 AAATTT -AAATTT AAATTT AAATTT AAATTT AAAT
13684 AAAGTTAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
5 15 0.27
6 37 0.66
7 4 0.07
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:13616 original size:18 final size:17
Alignment explanation
Indices: 13593--13683 Score: 78
Period size: 17 Copynumber: 5.2 Consensus size: 17
13583 TTTTTTTTTA
*
13593 AAATTTGTTTAAAAATTT
1 AAATTTATTT-AAAATTT
*
13611 AAATTTATTTTAAATTT
1 AAATTTATTTAAAATTT
*
13628 AAATTTAATTT-AAGTTT
1 AAATTT-ATTTAAAATTT
*
13645 AAATTTATTTTCAAATTT
1 AAATTTA-TTTAAAATTT
* *
13663 AAAATTA-CTATAAATTT
1 AAATTTATTTA-AAATTT
13680 AAAT
1 AAAT
13684 AAAGTTAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
16 2 0.03
17 35 0.57
18 24 0.39
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
AAATTTATTTAAAATTT
Found at i:13622 original size:11 final size:11
Alignment explanation
Indices: 13608--13663 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
13598 TGTTTAAAAA
13608 TTTAAATTTAT
1 TTTAAATTTAT
*
13619 TTTAAATTTAAA
1 TTTAAATTT-AT
*
13631 TTT-AATTTAAG
1 TTTAAATTT-AT
13642 TTTAAATTTAT
1 TTTAAATTTAT
13653 TTTCAAATTTA
1 TTT-AAATTTA
13664 AAATTACTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
11 23 0.59
12 16 0.41
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:13627 original size:17 final size:17
Alignment explanation
Indices: 13605--13683 Score: 104
Period size: 17 Copynumber: 4.6 Consensus size: 17
13595 ATTTGTTTAA
13605 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
*
13622 AAATTTAAATTTAATTT
1 AAATTTAAATTTATTTT
*
13639 AAGTTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* * *
13656 CAAATTTAAAATTACTAT
1 -AAATTTAAATTTATTTT
13674 AAATTTAAAT
1 AAATTTAAAT
13684 AAAGTTAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
17 40 0.75
18 13 0.25
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.51
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Done.