Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015142.1 Kokia drynarioides strain JFW-HI SEQ_130186, 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: 23648
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:2903 original size:2 final size:2
Alignment explanation
Indices: 2896--2921 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2886 ACGACATTAG
2896 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2922 TAAGAATCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3155 original size:62 final size:62
Alignment explanation
Indices: 3071--3197 Score: 200
Period size: 62 Copynumber: 2.0 Consensus size: 62
3061 TTTTTAATAG
* *
3071 AATAAAAATATAAGTTCACATATTAAAAGAAACATTACTTTCATTTTTCTAATTTTACTGTA
1 AATAAAAATATAAGTTCACATATTAAAAAAAACATTACCTTCATTTTTCTAATTTTACTGTA
* * * *
3133 AATAAAAATATAATTTCACATATTAAAAAAAACCTTGCCTTCATTTTTTTAATTTTACTGTA
1 AATAAAAATATAAGTTCACATATTAAAAAAAACATTACCTTCATTTTTCTAATTTTACTGTA
3195 AAT
1 AAT
3198 CAAGGTAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.41
Consensus pattern (62 bp):
AATAAAAATATAAGTTCACATATTAAAAAAAACATTACCTTCATTTTTCTAATTTTACTGTA
Found at i:13229 original size:24 final size:26
Alignment explanation
Indices: 13191--13238 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
13181 TCTACATGGG
13191 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
13217 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
13239 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:16432 original size:29 final size:29
Alignment explanation
Indices: 16338--16442 Score: 97
Period size: 33 Copynumber: 3.5 Consensus size: 29
16328 ATTTAATAAA
* *
16338 TTTAGGTACCAAATTGAATCTAAAAAAA-
1 TTTAGGTACCAAATTGGATCAAAAAAAAG
* * *
16366 CTTAGGTACCAAATTAAGA-AAAAAAATGTCAAG
1 TTTAGGTACCAAATT-GGATCAAAAAA----AAG
16399 TTTAGGTACCAAATTGGATCAAAAAAAAG
1 TTTAGGTACCAAATTGGATCAAAAAAAAG
*
16428 TTTAGGTACTAAATT
1 TTTAGGTACCAAATT
16443 AGGAAAAAGC
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
28 19 0.31
29 18 0.30
32 4 0.07
33 20 0.33
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (29 bp):
TTTAGGTACCAAATTGGATCAAAAAAAAG
Found at i:16450 original size:61 final size:60
Alignment explanation
Indices: 16338--16508 Score: 188
Period size: 61 Copynumber: 2.9 Consensus size: 60
16328 ATTTAATAAA
* * * *
16338 TTTAGGTACCAAATTGAATCTAAAAAAA-CTTAGGTACCAAATTAAGAAAAAAAATGTCAAG
1 TTTAGGTACCAAATTGGATC-AAAAAAAGTTTAGGTACCAAATT-AGGAAAAAAACGTCAAG
* *
16399 TTTAGGTACCAAATTGGATCAAAAAAAAGTTTAGGTACTAAATTAGG-AAAAAGCGTCAAG
1 TTTAGGTACCAAATTGGATC-AAAAAAAGTTTAGGTACCAAATTAGGAAAAAAACGTCAAG
* * * * *
16459 TTCAGATATCATATTGGAT-AAAAAAAGTGTAGGTACCAAATTA-GAAAAAA
1 TTTAGGTACCAAATTGGATCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAA
16509 TATCAAATTC
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
57 1 0.01
58 27 0.28
60 26 0.27
61 28 0.29
62 13 0.14
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (60 bp):
TTTAGGTACCAAATTGGATCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAAACGTCAAG
Found at i:16459 original size:60 final size:59
Alignment explanation
Indices: 16338--16508 Score: 193
Period size: 58 Copynumber: 2.9 Consensus size: 59
16328 ATTTAATAAA
* * *
16338 TTTAGGTACCAAATTGAATCTAAAAAAA-CTTAGGTACCAAATTAAGAAAAAAAATGTCAAG
1 TTTAGGTACCAAATTGGATC-AAAAAAAGTTTAGGTACCAAATT-AG-AAAAAAACGTCAAG
* * *
16399 TTTAGGTACCAAATTGGATCAAAAAAAAGTTTAGGTACTAAATTAGGAAAAAGCGTCAAG
1 TTTAGGTACCAAATTGGATC-AAAAAAAGTTTAGGTACCAAATTAGAAAAAAACGTCAAG
* * * * *
16459 TTCAGATATCATATTGGAT-AAAAAAAGTGTAGGTACCAAATTAGAAAAAA
1 TTTAGGTACCAAATTGGATCAAAAAAAGTTTAGGTACCAAATTAGAAAAAA
16509 TATCAAATTC
Statistics
Matches: 95, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
58 28 0.29
60 26 0.27
61 28 0.29
62 13 0.14
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (59 bp):
TTTAGGTACCAAATTGGATCAAAAAAAGTTTAGGTACCAAATTAGAAAAAAACGTCAAG
Found at i:18837 original size:414 final size:417
Alignment explanation
Indices: 18064--18897 Score: 1347
Period size: 414 Copynumber: 2.0 Consensus size: 417
18054 AGGTTATCAA
* *
18064 TTTGAATTAAAAAGCTATCATAGTCACGATCAATTAAAAGAACCAAGCCTTCCAAAATGCCCCAC
1 TTTGAATTAAAAAGCTATCATAGCCACGATCAATTAAAAGAACCAAGCCTTCCAAAATACCCCAC
* * * *
18129 AACTCAGCATAAAAAAACGGAGCAGTTCCCCAAATATATATTTAAGCCAAAAATCTACTTCCCAA
66 AACTCAGCATAAAAAAACGAAGCAATTCCCCAAATATATATTGAAGCCAAAAATCTAATTCCCAA
*
18194 CTCGGTTTCTCGCTATTCCCCCGCCACAACAACTCCAACTTCAATCCTGTTTGATCCATCCGTAT
131 CTCGGTTTCTCGCTATTCCCCCGCCACAACAACTCCAACTTCAATCCTGATTGATCCATCCGTAT
* * *
18259 TCAAACATGCCCAATTGCCATCTAAGTGAGGATATGATGACGTACTTGGTGTGCTCACATTGAGA
196 TCAAACATGCCCAATTGCCATCCAAGTGAAGATACGATGACGTACTTGGTGTGCTCACATTGAGA
*
18324 GAGACAAATTGTCTTGCCCAATTGTACGACAACTTGATAATTTCATTAGCATTCTAGGTAATTCT
261 GAGACAAATTGTCTTGCCCAATTGTACGACAACTTGATAATTTCATTAGCATTCTAGGTAACTCT
* * *
18389 TTAAAAATAAAGAGATTACGATTTTTCATAAACACCACACAATAATCTCAAAGAAACTTTAATTC
326 CTAAAAATAAAAAGATTACGATTTTTCATAAACACCACACAATAATCCCAAAGAAACTTTAATTC
*
18454 CACGCAATTAAATTTTCCATGGCTTTT
391 CACGCAATTAAATTTTCCATGACTTTT
* * * *
18481 TTTGAATTAAAACGCTGTCATAGCCACGATCAATTAAAAGAATCAAGCCTTCCAAGATACCCCAC
1 TTTGAATTAAAAAGCTATCATAGCCACGATCAATTAAAAGAACCAAGCCTTCCAAAATACCCCAC
*
18546 AACTCAGCAT-AAAAAACGAAGCAATTCTCC-AA-ATATATTGAAGCCAAAAATCTAATTCCCAA
66 AACTCAGCATAAAAAAACGAAGCAATTCCCCAAATATATATTGAAGCCAAAAATCTAATTCCCAA
* * *
18608 CTCGGTTTCTCGCTATTCCCCTGCCACAGCAGCTCCAACTTCAATCCTGATTGA-CTCATCCGTA
131 CTCGGTTTCTCGCTATTCCCCCGCCACAACAACTCCAACTTCAATCCTGATTGATC-CATCCGTA
18672 TTCAAACATGCCCAATTGCCATCCAAGTGAAGATACGATGA-GTTACTTGGTGTGCTCACATTGA
195 TTCAAACATGCCCAATTGCCATCCAAGTGAAGATACGATGACG-TACTTGGTGTGCTCACATTGA
* *
18736 GAGAGACAAATTGTCTTGCCCAATTGTATGACAGCTTGATAATTTCATTAGCATTCTAGGTAACT
259 GAGAGACAAATTGTCTTGCCCAATTGTACGACAACTTGATAATTTCATTAGCATTCTAGGTAACT
* *
18801 C-CTGAAAATAAAAAGATTACGGTTCTTTCATAAACACCACACAATAATCCCAAAGAAACTTTAA
324 CTCTAAAAATAAAAAGATTACGATT-TTTCATAAACACCACACAATAATCCCAAAGAAACTTTAA
*
18865 TTCCCCGCAATTAAATTTTCCATGACTTTT
388 TTCCACGCAATTAAATTTTCCATGACTTTT
18895 TTT
1 TTT
18898 TAATGTTTAA
Statistics
Matches: 386, Mismatches: 28, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
413 21 0.05
414 277 0.72
415 2 0.01
416 17 0.04
417 69 0.18
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.29
Consensus pattern (417 bp):
TTTGAATTAAAAAGCTATCATAGCCACGATCAATTAAAAGAACCAAGCCTTCCAAAATACCCCAC
AACTCAGCATAAAAAAACGAAGCAATTCCCCAAATATATATTGAAGCCAAAAATCTAATTCCCAA
CTCGGTTTCTCGCTATTCCCCCGCCACAACAACTCCAACTTCAATCCTGATTGATCCATCCGTAT
TCAAACATGCCCAATTGCCATCCAAGTGAAGATACGATGACGTACTTGGTGTGCTCACATTGAGA
GAGACAAATTGTCTTGCCCAATTGTACGACAACTTGATAATTTCATTAGCATTCTAGGTAACTCT
CTAAAAATAAAAAGATTACGATTTTTCATAAACACCACACAATAATCCCAAAGAAACTTTAATTC
CACGCAATTAAATTTTCCATGACTTTT
Found at i:19000 original size:19 final size:20
Alignment explanation
Indices: 18972--19014 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
18962 TTAAACGTTT
*
18972 AAAAGATTTTCCAT-TAATTA
1 AAAAGATTTT-CATGCAATTA
18992 AAAAG-TTTTCATGCAATTA
1 AAAAGATTTTCATGCAATTA
19011 AAAA
1 AAAA
19015 TCTGTATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 13 0.62
20 5 0.24
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (20 bp):
AAAAGATTTTCATGCAATTA
Done.