Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013169.1 Kokia drynarioides strain JFW-HI SEQ_128188, 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: 17445
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 137 characters in sequence are not A, C, G, or T
Found at i:12602 original size:148 final size:144
Alignment explanation
Indices: 12444--12966 Score: 479
Period size: 148 Copynumber: 3.5 Consensus size: 144
12434 GTAAATTTTT
* * * * *
12444 TTTTTTTTTTTTTTTAAATCAGAAGTTTTCTTTTGATTAAAACAAAATCTCTACTTTACTTCAAA
1 TTTTTATTTTTTTTAAAATCA-AAGTTTTCTTTT--TT-AAAGAAAATCACTACTTTACTTAAAA
12509 ATCAAAACTTTTATTTAGAAATAGTTAAAAAATCAAAATTTTGTTTAAAAATTTAAACTTTTTTT
62 ATCAAAACTTTTATTTAGAAATAGTTAAAAAATCAAAATTTTGTTTAAAAATTTAAACTTTTTTT
* *
12574 TAAATCACTAAAAACATA
127 TAAATAACTAAAAAAATA
* * *
12592 TTTTTATTTTTTTTAAAAATCTAAGCTTT-TTTTTTAATGAAAATCACTACTTTACTTAAAAATC
1 TTTTTATTTTTTTT-AAAATCAAAGTTTTCTTTTTTAAAGAAAATCACTACTTTACTTAAAAATC
* * *
12656 GAAATTTTTA-TTATGAAATAGTTAAAAAAATAAAAATTTTGTTTAAAAATTTAAACCTTTTCTT
65 AAAACTTTTATTTA-GAAATAGTT-AAAAAATCAAAATTTTGTTTAAAAATTTAAA-CTTTT-TT
* *
12720 TAAAATGACTAAAAAAATA
126 TTAAATAACTAAAAAAATA
* * * * * *
12739 GTTTTTA--TTTTTAAAAATCTAAATTTTCTCTTTTTTAAAGAGAATCACTATTTTATTTAAGAA
1 -TTTTTATTTTTTTTAAAATC-AAAGTTT-TCTTTTTTAAAGAAAATCACTACTTTACTTAAAAA
* * * * * * *
12802 TCCAAACTTTTATTTCA-AAATAGTAAAAAAAAATCAAAACTTTATATAAAAAATTGAACTTTTT
63 TCAAAACTTTTATTT-AGAAATAGT--TAAAAAATCAAAATTTTGTTTAAAAATTTAAACTTTTT
12866 CTTTAAAATAACT--AAAAATA
125 -TTT-AAATAACTAAAAAAATA
** * * *
12886 TTTATT-TTTATTTTTAAAAAT-ATAAAATTTCTATTCTTTAAAGAAAATCACTAATTTTCATAA
1 TTT-TTATTT-TTTTT-AAAATCA-AAGTTTTCT-TT-TTTAAAGAAAATCACTACTTTACTTAA
12949 AAATCAAAACTTTTATTT
60 AAATCAAAACTTTTATTT
12967 CTAAATTGTT
Statistics
Matches: 308, Mismatches: 44, Indels: 44
0.78 0.11 0.11
Matches are distributed among these distances:
143 3 0.01
144 42 0.14
145 38 0.12
146 17 0.06
147 33 0.11
148 82 0.27
149 49 0.16
150 44 0.14
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (144 bp):
TTTTTATTTTTTTTAAAATCAAAGTTTTCTTTTTTAAAGAAAATCACTACTTTACTTAAAAATCA
AAACTTTTATTTAGAAATAGTTAAAAAATCAAAATTTTGTTTAAAAATTTAAACTTTTTTTTAAA
TAACTAAAAAAATA
Found at i:12710 original size:21 final size:21
Alignment explanation
Indices: 12677--12724 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
12667 TATGAAATAG
*
12677 TTAAAAAAATAAAAATTTTGT
1 TTAAAAAAATAAAAATTTTCT
** **
12698 TTAAAAATTTAAACCTTTTCT
1 TTAAAAAAATAAAAATTTTCT
12719 TTAAAA
1 TTAAAA
12725 TGACTAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (21 bp):
TTAAAAAAATAAAAATTTTCT
Found at i:12926 original size:150 final size:145
Alignment explanation
Indices: 12487--12994 Score: 512
Period size: 150 Copynumber: 3.4 Consensus size: 145
12477 TGATTAAAAC
* * * *
12487 AAAATCTCTACTTTACTTCAAAATCAAAACTTTTATTTAGAAATAGTT-AAAAAATCAAAATTTT
1 AAAATCACTATTTTA-TTAAAAATCAAAACTTTTATTTA-AAATAGTTAAAAAAATCAAAACTTT
*
12551 GTTTAAAAATTTAAACTTTTT-TTT-AAATCACTAAAAACATATTT-TTATTT-TTTTTAAAAAT
64 GTTTAAAAATTTAAACTTTTTCTTTAAAATAACT-AAAA-ATATTTATT-TTTATTTTTAAAAAT
** *
12612 CTAAGCTTT-TTTTTTAATG
126 CTAAAATTTCTTTTTTAAAG
* * * * * *
12631 AAAATCACTACTTTACTTAAAAATCGAAATTTTTATTATGAAATAGTTAAAAAAATAAAAATTTT
1 AAAATCACTATTTTA-TTAAAAATCAAAACTTTTATT-TAAAATAGTTAAAAAAATCAAAACTTT
* * *
12696 GTTTAAAAATTTAAACCTTTTCTTTAAAATGACTAAAAA-A-ATAGTTTTTATTTTTAAAAATCT
64 GTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAATATTTA-TTTTTATTTTTAAAAATCT
*
12759 AAATTTTCTCTTTTTTAAAG
128 AAA-ATT-TCTTTTTTAAAG
* * * *
12779 AGAATCACTATTTTATTTAAGAATCCAAACTTTTATTTCAAAATAGTAAAAAAAAATCAAAACTT
1 AAAATCACTATTTTA-TTAAAAATCAAAACTTTTATTT-AAAATAGT-TAAAAAAATCAAAACTT
* * * * *
12844 TATATAAAAAATTGAACTTTTTCTTTAAAATAACTAAAAATATTTATTTTTATTTTTAAAAATAT
63 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAATATTTATTTTTATTTTTAAAAATCT
12909 AAAATTTCTATTCTTTAAAG
128 AAAATTTCT-TT-TTTAAAG
* * *
12929 AAAATCACTAATTTTCA-TAAAAATCAAAACTTTTATTTCTAAATTGTTTAAAAAAACCAAAACT
1 AAAATCACT-ATTTT-ATTAAAAATCAAAACTTTTATTT-AAAATAG-TTAAAAAAATCAAAACT
12993 TT
62 TT
12995 TCTCAAAATC
Statistics
Matches: 307, Mismatches: 38, Indels: 32
0.81 0.10 0.08
Matches are distributed among these distances:
143 1 0.00
144 45 0.15
145 54 0.18
146 9 0.03
147 9 0.03
148 50 0.16
149 52 0.17
150 78 0.25
151 8 0.03
152 1 0.00
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (145 bp):
AAAATCACTATTTTATTAAAAATCAAAACTTTTATTTAAAATAGTTAAAAAAATCAAAACTTTGT
TTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAATATTTATTTTTATTTTTAAAAATCTAAA
ATTTCTTTTTTAAAG
Found at i:13440 original size:3 final size:3
Alignment explanation
Indices: 13434--13477 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
13424 AAAAATAATA
* *
13434 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG GTG ATG GTG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
13478 TTGGGTTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.34
Consensus pattern (3 bp):
ATG
Done.