Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012336.1 Kokia drynarioides strain JFW-HI SEQ_127338, 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: 20525
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Warning! 68 characters in sequence are not A, C, G, or T
Found at i:13054 original size:49 final size:49
Alignment explanation
Indices: 12993--13499 Score: 327
Period size: 49 Copynumber: 10.5 Consensus size: 49
12983 GAGATGTGAA
* ** *
12993 GGGAAAGGTTGAAGCCGTAACGGTGAACCTTGTACCTTAGAGACATAAT
1 GGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGAAATAAT
* * * * * * ** *
13042 AGGAAAGATTGAAGCCGCCACAACGAATCGTGTACCATT-GAGATTTGGA-
1 GGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACC-TTAGAGAAAT-AAT
* * * *
13091 GGGAAAGGTTGAAGCTGTAACGACGAACCTTATACCTTA-AAAAATAAT
1 GGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGAAATAAT
* ** ** * * * * *
13139 GGGAAAGATTGAAGCCGCAACGAAAAATGTAGTACCATGGAGATATGGA-
1 GGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGAAAT-AAT
* * * *
13188 GGGAACGGTTGAAGCCGCAACGGCGAACCTTATACCTTAGAAAAATAAT
1 GGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGAAATAAT
* * * * *
13237 GGGAAAGATTGAAGCCGCAAC-AGTGAATCTTGTACCAT-G-GAGATGAA-
1 GGGAAAGGTTGAAGCCGCAACGA-CGAACCTTGTACCTTAGAGAAAT-AAT
* * * *
13284 AGGAAAGGTTGAAGCCACAATGACGAACCTTATACCTTAGA-AAATAAT
1 GGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGAAATAAT
* *
13332 GGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGACATAAT
1 GGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGAAATAAT
* * * * * * * * * * ** *
13381 GGGAAAGATTGAAACTGCCACGGCAAATCGTGTACCATGGAGATTTGGA-
1 GGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGAAAT-AAT
* * * *
13430 GGGAAAGGTTAAAGCCGTAACGCCGAACCTTATACCTTAGA-AAATAAT
1 GGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGAAATAAT
* *
13478 GGGAAA-GATGAAGCCACAACGA
1 GGGAAAGGTTGAAGCCGCAACGA
13500 AAATCTAGTA
Statistics
Matches: 332, Mismatches: 110, Indels: 34
0.70 0.23 0.07
Matches are distributed among these distances:
47 46 0.14
48 86 0.26
49 195 0.59
50 5 0.02
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.19
Consensus pattern (49 bp):
GGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGAAATAAT
Found at i:13276 original size:98 final size:98
Alignment explanation
Indices: 12983--13393 Score: 456
Period size: 97 Copynumber: 4.2 Consensus size: 98
12973 TTATACCCTA
* * ** * * * *
12983 GAGATGTGAAGGGAAAGGTTGAAGCCGTAACGGTGAACCTTGTACCTTAGAGACATAATAGGAAA
1 GAGATATGAAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAAAAATAATGGGAAA
* * * *
13048 GATTGAAGCCGCCACAACGAATCGTGTACCATT
66 GATTGAAGCCGCAACAGCGAATCTTGTACCATG
* * * *
13081 GAGATTTGGAGGGAAAGGTTGAAGCTGTAACGACGAACCTTATACCTTA-AAAAATAATGGGAAA
1 GAGATATGAAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAAAAATAATGGGAAA
** * *
13145 GATTGAAGCCGCAAC-GAAAAATGTAGTACCATG
66 GATTGAAGCCGCAACAG-CGAATCTTGTACCATG
* * *
13178 GAGATATGGAGGGAACGGTTGAAGCCGCAACGGCGAACCTTATACCTTAGAAAAATAATGGGAAA
1 GAGATATGAAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAAAAATAATGGGAAA
*
13243 GATTGAAGCCGCAACAGTGAATCTTGTACCATG
66 GATTGAAGCCGCAACAGCGAATCTTGTACCATG
* * *
13276 GAG--ATGAAAGGAAAGGTTGAAGCCACAATGACGAACCTTATACCTTAG-AAAATAATGGGAAA
1 GAGATATGAAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAAAAATAATGGGAAA
* * * * *
13338 GGTTGAAGCCGCAACGGCGAACCTTGTACCTTA
66 GATTGAAGCCGCAACAGCGAATCTTGTACCATG
* *
13371 GAGACAT-AATGGGAAAGATTGAA
1 GAGATATGAA-GGGAAAGGTTGAA
13394 ACTGCCACGG
Statistics
Matches: 267, Mismatches: 40, Indels: 13
0.83 0.12 0.04
Matches are distributed among these distances:
95 44 0.16
96 41 0.15
97 93 0.35
98 88 0.33
99 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.20
Consensus pattern (98 bp):
GAGATATGAAGGGAAAGGTTGAAGCCGCAACGACGAACCTTATACCTTAGAAAAATAATGGGAAA
GATTGAAGCCGCAACAGCGAATCTTGTACCATG
Found at i:13355 original size:144 final size:145
Alignment explanation
Indices: 13188--13498 Score: 419
Period size: 144 Copynumber: 2.2 Consensus size: 145
13178 GAGATATGGA
* *
13188 GGGAACGGTTGAAGCCGCAACGGCGAACCTTATACCTTAGAAAAATAATGGGAAAGATTGAAGCC
1 GGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCTTAGAAAAATAATGGGAAAGATTGAAACC
** * * *
13253 GCAACAGTGAATCTTGTACCATGGAGA-TGAAAGGAAAGGTTGAAGCCACAATGACGAACCTTAT
66 GCAACAGCAAATCGTGTACCATGGAGATTGAAAGGAAAGGTTAAAGCCACAACGACGAACCTTAT
13317 ACCTTAGAAAATAAT
131 ACCTTAGAAAATAAT
* * * *
13332 GGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGACATAATGGGAAAGATTGAAACT
1 GGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCTTAGAAAAATAATGGGAAAGATTGAAACC
* * * * ** *
13397 GCCACGGCAAATCGTGTACCATGGAGATTTGGAGGGAAAGGTTAAAGCCGTAACGCCGAACCTTA
66 GCAACAGCAAATCGTGTACCATGGAGA-TTGAAAGGAAAGGTTAAAGCCACAACGACGAACCTTA
13462 TACCTTAGAAAATAAT
130 TACCTTAGAAAATAAT
* *
13478 GGGAAA-GATGAAGCCACAACG
1 GGGAAAGGTTGAAGCCGCAACG
13499 AAAATCTAGT
Statistics
Matches: 145, Mismatches: 20, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
144 81 0.56
145 13 0.09
146 51 0.35
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (145 bp):
GGGAAAGGTTGAAGCCGCAACGGCGAACCTTATACCTTAGAAAAATAATGGGAAAGATTGAAACC
GCAACAGCAAATCGTGTACCATGGAGATTGAAAGGAAAGGTTAAAGCCACAACGACGAACCTTAT
ACCTTAGAAAATAAT
Found at i:13552 original size:95 final size:97
Alignment explanation
Indices: 13332--13568 Score: 291
Period size: 95 Copynumber: 2.5 Consensus size: 97
13322 AGAAAATAAT
* * * *
13332 GGGAAAGGTTGAAGCCGCAACGGCGAACCTTGTACCTTAGAGACATAATGGGAAAGATTGAAACT
1 GGGAAAGGTTAAAGCCGCAACGGCGAACCTTATACCTTAGA-AAATAATGGGAAAGATTGAAACC
* * * * *
13397 GCCACGGCAAATCGTGTACCATGGAGATTTGGA
65 ACAACGGAAAATCGTGTACCATGGAGATATCGA
* * *
13430 GGGAAAGGTTAAAGCCGTAACGCCGAACCTTATACCTTAGAAAATAATGGGAAAGA-TGAAGCCA
1 GGGAAAGGTTAAAGCCGCAACGGCGAACCTTATACCTTAGAAAATAATGGGAAAGATTGAAACCA
13494 CAAC-GAAAATC-TAGTACCATGGAGATATCGA
66 CAACGGAAAATCGT-GTACCATGGAGATATCGA
* * * *
13525 GGGAAAGGTTTAAGTCGCAATGGCGAACTTTATACCTTAGAAAA
1 GGGAAAGGTTAAAGCCGCAACGGCGAACCTTATACCTTAGAAAA
13569 AGAAAAGGAA
Statistics
Matches: 120, Mismatches: 18, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
94 1 0.01
95 60 0.50
96 8 0.07
97 14 0.12
98 37 0.31
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (97 bp):
GGGAAAGGTTAAAGCCGCAACGGCGAACCTTATACCTTAGAAAATAATGGGAAAGATTGAAACCA
CAACGGAAAATCGTGTACCATGGAGATATCGA
Found at i:19924 original size:16 final size:16
Alignment explanation
Indices: 19903--19947 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
19893 TGTGGGCGCA
* *
19903 TTTTCTTGCTTCTCTT
1 TTTTCTTTCTTCTCCT
19919 TTTTCTTTCATT-TCCT
1 TTTTCTTTC-TTCTCCT
19935 TTTTCTTTCTTCT
1 TTTTCTTTCTTCT
19948 TAGGCATCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 2 0.08
16 21 0.84
17 2 0.08
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTTCTTTCTTCTCCT
Done.