Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011292.1 Kokia drynarioides strain JFW-HI SEQ_126272, 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: 22185
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Found at i:1508 original size:3 final size:3
Alignment explanation
Indices: 1502--1539 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1492 ATTATTATAA
1502 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1540 ATTATTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:3232 original size:150 final size:146
Alignment explanation
Indices: 2891--3539 Score: 609
Period size: 150 Copynumber: 4.4 Consensus size: 146
2881 TTTTAAAAAT
* ** * *
2891 AAAATCACTACTTTTCTTAAAAATTAAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAATTTT
1 AAAATCACTA-TTTTCTTAAAACTCCAAACTTTTATTTCGAAATAGTTAAAAAAAATAAAAATTT
* * ** *
2955 GTTTAAAAATTTAAACTTTTCTCTTTTAAAATGCCTAAAAAAACAGATTTTTA-TTTTAAAAATT
65 ATTTAAAAATTTAAACTTTT-TC-TTTAAAATGACT--AAAAA-ATTTTTTTATTTTTAAAAATC
** **
3019 TAAAC--T-TTTTTTTTAAAAA
125 TAAACTTTCTTTTTTTTTTATG
* *
3038 AAAATCACTACTTTACTTAAAAATCCAAA-TTCTTATTTCGAAATAGTTAAAAAAAATTAAAAAT
1 AAAATCACTA-TTTTCTTAAAACTCCAAACTT-TTATTTCGAAATAGTTAAAAAAAA-TAAAAAT
*
3102 TTATTTAAAAATTTAAACTTTTTCTTTAAAATGATTAAAAAAACAATTTTTTTATTTTTAAAAAT
63 TTATTTAAAAATTTAAACTTTTTCTTTAAAATGACT---AAAA-AATTTTTTTATTTTTAAAAAT
3167 CTAAA-TTTCTTTTTTTTTTATATG
124 CTAAACTTTC-TTTTTTTTT-TATG
* * *
3191 AAAATCACTA-TTT-TTAAAACTCCAAACTTTTATTTCAAAATAGTTAAAAGAAAACAAAACTTT
1 AAAATCACTATTTTCTTAAAACTCCAAACTTTTATTTCGAAATAGTTAAAA-AAAATAAAAATTT
* * *
3254 GTTTAAAAATTTAAACTTTTTCTTTAGAATGACT---AAATTTTTTTTTTTTTAAAAAAAAAATC
65 ATTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAATTTTTTTATTTTT-----AAAAATC
**
3316 TAAACTTTC-TTTTTCCTTATG
125 TAAACTTTCTTTTTTTTTTATG
* * * *
3337 AAAATTACTATTTTCTTAACACTCCAAACTTTTATTTTGAAATAGTT--AAAAAATCAAAATTTT
1 AAAATCACTATTTTCTTAAAACTCCAAACTTTTATTTCGAAATAGTTAAAAAAAAT-AAAAATTT
* * * *
3400 ATTTAAAAATTTAAACTTTTTTTTTAAAATGACTAAAAAATATATATATTTTT---AATCTAAAC
65 ATTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAATTTTTTTATTTTTAAAAATCTAAAC
3462 TTT-TTTTTTTATTTATG
130 TTTCTTTTTTT-TTTATG
* * * *
3479 AAAATCACTATTTTTCTTAAAACTCAAAATTTTTATTTCAAAATTG-TAAAAAAAATAAAAA
1 AAAATCACTA-TTTTCTTAAAACTCCAAACTTTTATTTCGAAATAGTTAAAAAAAATAAAAA
3540 CTTTTCCCAA
Statistics
Matches: 423, Mismatches: 49, Indels: 64
0.79 0.09 0.12
Matches are distributed among these distances:
141 17 0.04
142 15 0.04
143 47 0.11
144 8 0.02
145 4 0.01
146 55 0.13
147 61 0.14
148 62 0.15
149 57 0.13
150 70 0.17
151 8 0.02
152 8 0.02
153 11 0.03
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (146 bp):
AAAATCACTATTTTCTTAAAACTCCAAACTTTTATTTCGAAATAGTTAAAAAAAATAAAAATTTA
TTTAAAAATTTAAACTTTTTCTTTAAAATGACTAAAAAATTTTTTTATTTTTAAAAATCTAAACT
TTCTTTTTTTTTTATG
Found at i:3419 original size:20 final size:20
Alignment explanation
Indices: 3382--3429 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
3372 TTTGAAATAG
*
3382 TTAAAAAATCAAAATTTTAT
1 TTAAAAATTCAAAATTTTAT
* * *
3402 TTAAAAATTTAAACTTTTTT
1 TTAAAAATTCAAAATTTTAT
*
3422 TTTAAAAT
1 TTAAAAAT
3430 GACTAAAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAAAATTCAAAATTTTAT
Found at i:11642 original size:31 final size:30
Alignment explanation
Indices: 11548--11694 Score: 147
Period size: 31 Copynumber: 4.9 Consensus size: 30
11538 TTTGACCTTC
** *
11548 AAATTTTCCAAAAATTATAATTCGACCCCT
1 AAATTTTCCAAAAATTCCAATTTGACCCCT
** *
11578 AAATTTTCCAAAAAATTTGAATTCGACCCCT
1 AAATTTTCC-AAAAATTCCAATTTGACCCCT
*
11609 AAATTTTCCAAAAAATTCCAATTTGACCTCT
1 AAATTTTCC-AAAAATTCCAATTTGACCCCT
* * * *
11640 AAACTTTCTAGAACTTCCAATTTGACCCCT
1 AAATTTTCCAAAAATTCCAATTTGACCCCT
*
11670 AAA--TT-CAAAAATTCAAATTTGACCC
1 AAATTTTCCAAAAATTCCAATTTGACCC
11695 GATTTTATTT
Statistics
Matches: 101, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
27 16 0.16
28 2 0.02
30 30 0.30
31 53 0.52
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.33
Consensus pattern (30 bp):
AAATTTTCCAAAAATTCCAATTTGACCCCT
Found at i:20689 original size:50 final size:50
Alignment explanation
Indices: 20625--20751 Score: 155
Period size: 50 Copynumber: 2.5 Consensus size: 50
20615 ATCTTTTACC
* * *
20625 CCTAAAGCTATAGAGGTGCAGATTGAAACCACAAAGGCAAATCTCATACA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAACCACAAAGACAAATCTCATACA
* * *** * *
20675 CCTAAAGCTGTAGAGGGGCAGAATGAAGCTGTAATGACAAATCTCATTCA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAACCACAAAGACAAATCTCATACA
*
20725 CCTAAAGCTGTAGAGGGGCAAATTGAA
1 CCTAAAGCTGTAGAGGGGCAGATTGAA
20752 GCCATAAGGA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.20
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGGGCAGATTGAAACCACAAAGACAAATCTCATACA
Found at i:20863 original size:40 final size:40
Alignment explanation
Indices: 20806--20940 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 40
20796 AGTTACAACC
*
20806 TCCAATCTCTTACCCTAACCAGAGGGCAGATTAAAGACCA
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTAAAGACAA
* * * *
20846 TTCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAA
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTAAAGACAA
** * * *
20886 TCCAATCTCTTACCCCGACCATG-GGGCGGGTTGAA-ACAA
1 TCCAATCTCTTACCCTAACCA-GAGGGCAGATTAAAGACAA
*
20925 TCCAATCTTTTACCCT
1 TCCAATCTCTTACCCT
20941 TAAAGTTACA
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
39 18 0.22
40 61 0.76
41 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.25
Consensus pattern (40 bp):
TCCAATCTCTTACCCTAACCAGAGGGCAGATTAAAGACAA
Found at i:20989 original size:50 final size:50
Alignment explanation
Indices: 20928--21115 Score: 259
Period size: 50 Copynumber: 3.8 Consensus size: 50
20918 GAAACAATCC
* *
20928 AATCTTTTACCCTTAAAGTTACAGAGGGGCAGATTAAAGCTACAAAAGCA
1 AATCTTATACCCCTAAAGTTACAGAGGGGCAGATTAAAGCTACAAAAGCA
* * *
20978 AATCTTATACCCCTAAAGTTACAGAGGGACAGATTGAAGCTACAAAAGAA
1 AATCTTATACCCCTAAAGTTACAGAGGGGCAGATTAAAGCTACAAAAGCA
* * * *
21028 AATCTTATACCCATAAAGTTACAAAGGGGCATATTGAAGCTACAAAAGCA
1 AATCTTATACCCCTAAAGTTACAGAGGGGCAGATTAAAGCTACAAAAGCA
* * * *
21078 AATCTTATACCCCTAAAGTAATATAAGGGCAGATTAAA
1 AATCTTATACCCCTAAAGTTACAGAGGGGCAGATTAAA
21116 ACTCACAGAC
Statistics
Matches: 121, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 121 1.00
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (50 bp):
AATCTTATACCCCTAAAGTTACAGAGGGGCAGATTAAAGCTACAAAAGCA
Done.