Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013928.1 Kokia drynarioides strain JFW-HI SEQ_128958, 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: 8790
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Found at i:1263 original size:2 final size:2
Alignment explanation
Indices: 1256--1288 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1246 GATAAACCTT
1256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1289 TGACATCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1562 original size:251 final size:256
Alignment explanation
Indices: 1270--1793 Score: 674
Period size: 257 Copynumber: 2.1 Consensus size: 256
1260 TATATATATA
* ** * *
1270 TATATATATATATATATATTGACATCATCTTAGCGTTATATATATTTATATTTG-CTATTACTCA
1 TATATATATATATATATATTGAAATCATCTTAGAATTATATATATTGACATTTGCCT-TTACTCA
* ** *
1334 ATGTCAAAATGAACCTATATATA-T-TCT-CTCTT-CTC-ACTCAGATAATTTTAATTCTTCTCT
65 ATGCCAAAATGAACCTATATATATTCTCTCCTCTTCCTCTACTCAGATAAACTTAATTCTTCTCC
* * * *
1394 CATTCAAACTTATTTCTTCTCTTCTCTCATTTCATC-ATCTTTTTCTCTTTTTTAGTTTATGTTA
130 CATTAAAACTTATTTCTTCTCTTCTCCCATTTCATCTA-CTTTTTCTCTTTGTTAGTTGATGTT-
* * * * * *
1458 AG-ATGATTAAAGGAAA-AGGAAAAGTGAGT-AATGAGGTTGCTGCCAAA-CGTTCAGTTAAACC
193 AGTATGATGAAAGGAAAGA-AAAAAGTGAGTAAAT-AGGCTACT-ACAAAGCCTTCAGTTAAACC
1519 TT
255 TT
* * *
1521 TATATATATGTATATATGTTGAAATCATCTTAGAATTATATATATTGACATTTGCCTTTACTGAA
1 TATATATATATATATATATTGAAATCATCTTAGAATTATATATATTGACATTTGCCTTTACTCAA
* *
1586 TGCCAAAATGAACTTGTATATATTCTCTCCTCTTCCTCTTACTCAGATAAACTTAATTCTTCTCC
66 TGCCAAAATGAACCTATATATATTCTCTCCTCTTCCTC-TACTCAGATAAACTTAATTCTTCTCC
* *
1651 CATTAAAACTTATTTCTTCTTTTCTCCCATTTCTTCTACTTTTTCTCTTTGTTAGTTGATGTTAG
130 CATTAAAACTTATTTCTTCTCTTCTCCCATTTCATCTACTTTTTCTCTTTGTTAGTTGATGTTAG
1716 TATGATGAAAGGAAAGAAAAAAGTGAGTAAATAGGCTACTACAAAGCCTTCAGTTAAACCTT
195 TATGATGAAAGGAAAGAAAAAAGTGAGTAAATAGGCTACTACAAAGCCTTCAGTTAAACCTT
1778 TATATATATATATATA
1 TATATATATATATATA
1794 CAATACAACT
Statistics
Matches: 234, Mismatches: 27, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
251 73 0.31
252 3 0.01
253 3 0.01
254 5 0.02
255 3 0.01
256 6 0.03
257 136 0.58
258 5 0.02
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.42
Consensus pattern (256 bp):
TATATATATATATATATATTGAAATCATCTTAGAATTATATATATTGACATTTGCCTTTACTCAA
TGCCAAAATGAACCTATATATATTCTCTCCTCTTCCTCTACTCAGATAAACTTAATTCTTCTCCC
ATTAAAACTTATTTCTTCTCTTCTCCCATTTCATCTACTTTTTCTCTTTGTTAGTTGATGTTAGT
ATGATGAAAGGAAAGAAAAAAGTGAGTAAATAGGCTACTACAAAGCCTTCAGTTAAACCTT
Found at i:1913 original size:22 final size:22
Alignment explanation
Indices: 1888--1931 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1878 TGGAAAGTTG
*
1888 TAATGTAATTCAAATTTGAAAA
1 TAATGTAATTAAAATTTGAAAA
*
1910 TAATGTAATTAAAATTTTAAAA
1 TAATGTAATTAAAATTTGAAAA
1932 CTTAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (22 bp):
TAATGTAATTAAAATTTGAAAA
Found at i:1938 original size:14 final size:14
Alignment explanation
Indices: 1921--1954 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1911 AATGTAATTA
1921 AAATTTTAAAACTT
1 AAATTTTAAAACTT
1935 AAATTTTAAAACTT
1 AAATTTTAAAACTT
1949 AAATTT
1 AAATTT
1955 GAAAGTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTTTAAAACTT
Found at i:1979 original size:11 final size:11
Alignment explanation
Indices: 1963--1988 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1953 TTGAAAGTAA
1963 AAACTTTGGAG
1 AAACTTTGGAG
1974 AAACTTTGGAG
1 AAACTTTGGAG
1985 AAAC
1 AAAC
1989 AAATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (11 bp):
AAACTTTGGAG
Found at i:2231 original size:22 final size:22
Alignment explanation
Indices: 2178--2232 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2168 ATCTTGTCAA
* * *
2178 AGAATCTCAATGTTCACGTAAG
1 AGAATCTCACTCTTCACATAAG
*
2200 AGAATCTCACTCTTCACATCAG
1 AGAATCTCACTCTTCACATAAG
2222 AGAATCTCACT
1 AGAATCTCACT
2233 ATTCCTTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (22 bp):
AGAATCTCACTCTTCACATAAG
Found at i:2285 original size:93 final size:94
Alignment explanation
Indices: 2163--2334 Score: 256
Period size: 93 Copynumber: 1.8 Consensus size: 94
2153 TAAAATTATA
* *
2163 AGAGAATCTTGTCAAAGAATCTCAATGTTCACGTAAGAGAATCTCACTCTTCACATCAGAGAATC
1 AGAGAATATTGCCAAAGAATCTCAATGTTCACGTAAGAGAATCTCACTCTTCACATCAGAGAATC
2228 TCACTATTC-CTTTTGTTTTTTTTCTTTC
66 TCACTATTCACTTTTGTTTTTTTTCTTTC
* * * * * * *
2256 AGAGAATATTGCCATAGAATCTCACTGTTCATGTCAGAGAATCTTACTGTTCACATTAGAGAATC
1 AGAGAATATTGCCAAAGAATCTCAATGTTCACGTAAGAGAATCTCACTCTTCACATCAGAGAATC
2321 TCACTATTCACTTT
66 TCACTATTCACTTT
2335 GTTATTTCTT
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
93 65 0.94
94 4 0.06
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (94 bp):
AGAGAATATTGCCAAAGAATCTCAATGTTCACGTAAGAGAATCTCACTCTTCACATCAGAGAATC
TCACTATTCACTTTTGTTTTTTTTCTTTC
Found at i:2299 original size:22 final size:22
Alignment explanation
Indices: 2271--2331 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
2261 ATATTGCCAT
**
2271 AGAATCTCACTGTTCATGTCAG
1 AGAATCTCACTGTTCACATCAG
* *
2293 AGAATCTTACTGTTCACATTAG
1 AGAATCTCACTGTTCACATCAG
*
2315 AGAATCTCACTATTCAC
1 AGAATCTCACTGTTCAC
2332 TTTGTTATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (22 bp):
AGAATCTCACTGTTCACATCAG
Found at i:6592 original size:24 final size:25
Alignment explanation
Indices: 6565--6618 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
6555 GTTGCTACTG
*
6565 CATCTTGAATT-TCTCTTCCTTG-TT
1 CATCTTAAATTAT-TCTTCCTTGATT
*
6589 CATCTAAAATTATTCTTCCTTGATT
1 CATCTTAAATTATTCTTCCTTGATT
6614 -ATCTT
1 CATCTT
6619 TTTTTATTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.20, C:0.22, G:0.06, T:0.52
Consensus pattern (25 bp):
CATCTTAAATTATTCTTCCTTGATT
Found at i:8034 original size:245 final size:245
Alignment explanation
Indices: 7586--8037 Score: 640
Period size: 245 Copynumber: 1.8 Consensus size: 245
7576 ATTTTTAAAG
* * * *
7586 TTATATATATATATATATATTGACTTCATCTTAGCAATATATATATTTATATTTGTCATTACTCA
1 TTATATATATATATATATATTGACATCATCTTAGCAATATATATATTGACATTTGCCATTACTCA
* * * * * *
7651 ATGTCAAAATGAACCTGTAAATATTCTCTCTTCTCACTCAGATAAACTTAATTCTCCTCCCATTC
66 ATGCCAAAATGAACCTATAAATATTCTCTCTTCTCACTCAAATAAACTCAATCCTCCTCCCATTA
** *
7716 AATCTTATTACTTCCTTTCTCTCATTTCTTCATCTTTTTCTCTTTCTTAGTTTCTGTAAAGATGA
131 AATCTTATTACTTCCTTTCTCTCATTTCTTCATCTTTTTCTCTTTCTTAGTTGATGTAAAGACGA
*
7781 TTAAAGGAAAAGTGAGTAATTAGGTTGCTTCCAAACCTTCAGTTAAACCT
196 TGAAAGGAAAAGTGAGTAATTAGGTTGCTTCCAAACCTTCAGTTAAACCT
* * *
7831 TTATATATATGTATATATATTGACATCATCTTAG-AATTATATATATTGACATTTGCCTTTACTG
1 TTATATATATATATATATATTGACATCATCTTAGCAA-TATATATATTGACATTTGCCATTACTC
* *
7895 AATGCCAAAATGAACCTATATATATTCTCTCTTCTCACTCAAATAAACTCAATCCTTCTCCCATT
65 AATGCCAAAATGAACCTATAAATATTCTCTCTTCTCACTCAAATAAACTCAATCCTCCTCCCATT
* * * * *
7960 AAAAT-TTATTTCTT-CTGTTCTCTCATTTCTTCATCTTTTTTTCTTTGTTAGTTGATGTTAATA
130 -AAATCTTATTACTTCCT-TTCTCTCATTTCTTCATCTTTTTCTCTTTCTTAGTTGATGTAAAGA
8023 CGATGAAAGGAAAAG
193 CGATGAAAGGAAAAG
8038 AAAAAGTGAG
Statistics
Matches: 180, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
244 4 0.02
245 173 0.96
246 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.43
Consensus pattern (245 bp):
TTATATATATATATATATATTGACATCATCTTAGCAATATATATATTGACATTTGCCATTACTCA
ATGCCAAAATGAACCTATAAATATTCTCTCTTCTCACTCAAATAAACTCAATCCTCCTCCCATTA
AATCTTATTACTTCCTTTCTCTCATTTCTTCATCTTTTTCTCTTTCTTAGTTGATGTAAAGACGA
TGAAAGGAAAAGTGAGTAATTAGGTTGCTTCCAAACCTTCAGTTAAACCT
Done.