Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002944.1 Kokia drynarioides strain JFW-HI SEQ_115392, 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: 18875
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:306 original size:21 final size:21
Alignment explanation
Indices: 281--321 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
271 CTATTTTAAG
**
281 TTTTAAGTAAATGTTTTAGTC
1 TTTTAAGTAAAAATTTTAGTC
302 TTTTAAGTAAAAATTTTAGT
1 TTTTAAGTAAAAATTTTAGT
322 AATCCATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.51
Consensus pattern (21 bp):
TTTTAAGTAAAAATTTTAGTC
Found at i:399 original size:3 final size:3
Alignment explanation
Indices: 391--417 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
381 TGAGAACTCA
391 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
418 GTAATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4994 original size:20 final size:20
Alignment explanation
Indices: 4969--5007 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4959 GATGAAAGTT
4969 GTATTTCACAACGTTCTAAA
1 GTATTTCACAACGTTCTAAA
* *
4989 GTATTTCATAGCGTTCTAA
1 GTATTTCACAACGTTCTAA
5008 CCGAATGGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (20 bp):
GTATTTCACAACGTTCTAAA
Found at i:13965 original size:24 final size:24
Alignment explanation
Indices: 13938--14030 Score: 99
Period size: 24 Copynumber: 4.1 Consensus size: 24
13928 ACCCAAAAAG
13938 GACTTCTCCAATCGTTCCTCCAAT
1 GACTTCTCCAATCGTTCCTCCAAT
13962 GACTTCTCCAATCGTTCCT-CAAT
1 GACTTCTCCAATCGTTCCTCCAAT
* * ** *
13985 --C-TCTCCAGTCGAT--GGCAAG
1 GACTTCTCCAATCGTTCCTCCAAT
14004 GACTTCTCCAATCGTTCCTCCAAT
1 GACTTCTCCAATCGTTCCTCCAAT
14028 GAC
1 GAC
14031 CAATGCTAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
19 3 0.06
20 10 0.19
21 2 0.04
22 10 0.19
23 4 0.07
24 25 0.46
ACGTcount: A:0.22, C:0.35, G:0.13, T:0.30
Consensus pattern (24 bp):
GACTTCTCCAATCGTTCCTCCAAT
Found at i:15957 original size:265 final size:261
Alignment explanation
Indices: 15272--15924 Score: 863
Period size: 269 Copynumber: 2.5 Consensus size: 261
15262 TTAAGTTCCC
* *
15272 ATAGATTTTATTTTTTAGTATATTTTAAATTACATAATATATAAAAATAACATAATATAAAGTAT
1 ATAGA-TTTATTTTTTAGTATGTTTTAAATTACATAATATATAAAAATAACATAATATAAAATAT
** * * * * *
15337 TATAAACTTAAAAATAAATTGGGTGGAACT-TGAGCTCGGGCTTTAAAGGTTCAAGCCTGAACCA
65 TATAAACTTAAAAATAGGTTGGATCGAGCTATTAG-AC---C-TTAAAGGTTCAAGCCTGAACCA
* * * *
15401 CTCATACTATTTTTAATTTTTTTAAAATATTTATTTTATTTTAATATTTAATAATTTTATATCAT
125 CCCATACTATTTCTAATTTTTTTAAAATATTTATTTTATTTTAAGATTTAATAATTTTATACCAT
* * *
15466 TTTATTTATAGATTTTTTTAAATTGTTAATTTAATTTAATTTAATGTTTACATTAGAGTAGTATT
190 TTTATTTATAGATTTTTTTAAATCG----TTTAATTTAATTTAATGTTTACATTACAATAGTATT
*
15531 ATATATTTAGT
251 ATATATTTAAT
*
15542 ATAGATTTATTTTTTAGTATGTTTTAAATTACATAATATATAAAAATAACATAATATAAAGTATT
1 ATAGATTTATTTTTTAGTATGTTTTAAATTACATAATATATAAAAATAACATAATATAAAATATT
* *
15607 ATAAACTTAAAAATGGGTTGGGTCGAGCTCAAACTTAGACCTTAAAGGTTCAAGCCTGAACCACC
66 ATAAACTTAAAAATAGGTTGGATCGAGCT---A-TTAGACCTTAAAGGTTCAAGCCTGAACCACC
* *
15672 CATACTATTTTTAATTTTTTTAAAATATTTATTTTATTTTAAGATTTAATAATTTTATACCTTTT
127 CATACTATTTCTAATTTTTTTAAAATATTTATTTTATTTTAAGATTTAATAATTTTATACCATTT
15737 TATTTATAGAATTTTTTTAAATCG-TTAATTTAATTTAATGTTTACATTACAATAGTATTATATA
192 TATTTATAG-ATTTTTTTAAATCGTTTAATTTAATTTAATGTTTACATTACAATAGTATTATATA
15801 TTTAAT
256 TTTAAT
* *
15807 ATAGATTTATTTTTTAGTATGTTTTAAATTACAT-A-ATATAAAATTAATATAATATAAAATATT
1 ATAGATTTATTTTTTAGTATGTTTTAAATTACATAATATATAAAAATAACATAATATAAAATATT
* *
15870 ATAAATTTAAAAATAGGTTGGATCG-GGT-TT-GAACCTTGAAA-GTTCAAGCCTGAAC
66 ATAAACTTAAAAATAGGTTGGATCGAGCTATTAG-ACCTT-AAAGGTTCAAGCCTGAAC
15925 TCAACTCATA
Statistics
Matches: 352, Mismatches: 23, Indels: 29
0.87 0.06 0.07
Matches are distributed among these distances:
256 1 0.00
257 21 0.06
258 3 0.01
262 2 0.01
263 47 0.13
264 1 0.00
265 77 0.22
269 177 0.50
270 19 0.05
273 1 0.00
274 3 0.01
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.45
Consensus pattern (261 bp):
ATAGATTTATTTTTTAGTATGTTTTAAATTACATAATATATAAAAATAACATAATATAAAATATT
ATAAACTTAAAAATAGGTTGGATCGAGCTATTAGACCTTAAAGGTTCAAGCCTGAACCACCCATA
CTATTTCTAATTTTTTTAAAATATTTATTTTATTTTAAGATTTAATAATTTTATACCATTTTATT
TATAGATTTTTTTAAATCGTTTAATTTAATTTAATGTTTACATTACAATAGTATTATATATTTAA
T
Found at i:17312 original size:45 final size:43
Alignment explanation
Indices: 17222--17303 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
17212 CACCCACGTG
17222 CATGCCACATTAAGAAAGTTAAAAAAAAGTTAATTTTTTCATC
1 CATGCCACATTAAGAAAGTTAAAAAAAAGTTAATTTTTTCATC
*
17265 CATGCCACATT-AGAAAAGTTAAAAAAACGTTAATTTTTT
1 CATGCCACATTAAG-AAAGTTAAAAAAAAGTTAATTTTTT
17304 TTTATCCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
42 2 0.05
43 35 0.95
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (43 bp):
CATGCCACATTAAGAAAGTTAAAAAAAAGTTAATTTTTTCATC
Found at i:17670 original size:21 final size:21
Alignment explanation
Indices: 17646--17687 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17636 TAGCCAAAGC
*
17646 AAAATTAAAA-AGAGAAAAAAA
1 AAAACTAAAATAG-GAAAAAAA
17667 AAAACTAAAATAGGAAAAAAA
1 AAAACTAAAATAGGAAAAAAA
17688 TATTTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.79, C:0.02, G:0.10, T:0.10
Consensus pattern (21 bp):
AAAACTAAAATAGGAAAAAAA
Found at i:18210 original size:20 final size:22
Alignment explanation
Indices: 18185--18240 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
18175 AAATTTAAAA
*
18185 TTATATTAAATATTTT-TA-TT
1 TTATATTAAATATTTTATACAT
*
18205 TTATATCTAATTATTTTAATACAT
1 TTATAT-TAAATATTTT-ATACAT
18229 TTATATTAAATA
1 TTATATTAAATA
18241 AAATTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 6 0.21
21 9 0.31
23 7 0.24
24 7 0.24
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATATTAAATATTTTATACAT
Found at i:18570 original size:28 final size:29
Alignment explanation
Indices: 18512--18578 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
18502 ACAAATGCCC
* *
18512 TTTTCTATAATTAATTTATTCTTCACCTTA
1 TTTT-TATAATTAATTTATTCTTAACATTA
* *
18542 TTTTTATAATTAA-TTATTTTTAATATTA
1 TTTTTATAATTAATTTATTCTTAACATTA
18570 TTTTTATAA
1 TTTTTATAA
18579 AAAGAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 20 0.61
29 9 0.27
30 4 0.12
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTTTATAATTAATTTATTCTTAACATTA
Done.