Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011038.1 Kokia drynarioides strain JFW-HI SEQ_126009, 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: 27166
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Warning! 59 characters in sequence are not A, C, G, or T
Found at i:321 original size:18 final size:19
Alignment explanation
Indices: 282--325 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
272 AGAGATTAAA
* *
282 ATATATAAATATACATACT
1 ATATATAAAGATACAAACT
301 ATATATAAAGA-ACAAACT
1 ATATATAAAGATACAAACT
319 ATATATA
1 ATATATA
326 CATGCATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (19 bp):
ATATATAAAGATACAAACT
Found at i:558 original size:13 final size:13
Alignment explanation
Indices: 540--573 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
530 TTAAAATGAT
540 TAAAAAAATAAAA
1 TAAAAAAATAAAA
553 TAAAAAAATAAAA
1 TAAAAAAATAAAA
566 -AAAAAAAT
1 TAAAAAAAT
574 TTCGAATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
TAAAAAAATAAAA
Found at i:1404 original size:12 final size:12
Alignment explanation
Indices: 1387--1418 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1377 TACTTCTTTA
1387 TTTTCGTATATT
1 TTTTCGTATATT
1399 TTTTCGTATATT
1 TTTTCGTATATT
*
1411 TTCTCGTA
1 TTTTCGTA
1419 ACCTTTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.12, G:0.09, T:0.62
Consensus pattern (12 bp):
TTTTCGTATATT
Found at i:2460 original size:39 final size:39
Alignment explanation
Indices: 2294--2462 Score: 139
Period size: 39 Copynumber: 4.3 Consensus size: 39
2284 ATAGCTTTAG
* * *
2294 GGGTAAAAAATTGGATTGCTTCAATCTGCCTCATGGTC-
1 GGGTAAAAGATTGAATTGCTTCAATCTACCTCATGGTCA
* * * * *
2332 GAGGTAAGAGATCGAATAGTCTTCAATCTACCCTC-TGATTA
1 G-GGTAAAAGATTGAATTG-CTTCAATCTA-CCTCATGGTCA
*
2373 AGGTAAAAGATTGAATTGCTTCAATCTACCTCATGGTCA
1 GGGTAAAAGATTGAATTGCTTCAATCTACCTCATGGTCA
* ** **
2412 GGGTGAAAGATCTG-A-TGACTTCAATCTGTCTCATGGTTG
1 GGGTAAAAGAT-TGAATTG-CTTCAATCTACCTCATGGTCA
2451 GGGTAAAAGATT
1 GGGTAAAAGATT
2463 TGAGGTTGTA
Statistics
Matches: 103, Mismatches: 21, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
38 8 0.08
39 63 0.61
40 28 0.27
41 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (39 bp):
GGGTAAAAGATTGAATTGCTTCAATCTACCTCATGGTCA
Found at i:16356 original size:39 final size:38
Alignment explanation
Indices: 16253--16461 Score: 170
Period size: 39 Copynumber: 5.3 Consensus size: 38
16243 ATAGCTTTAG
* * * * *
16253 GGGTAAAAAATTGGATTGCTTAAATTTGCCCCATGGTCA
1 GGGTAAAAGATT-GATTGCTTCAATCTGCCTCATGGTTA
* * * *
16292 GGGTAAGAGATCGGATGGTCTTCAATCTGTCCTC-TAGTTA
1 GGGTAAAAGAT-TGATTG-CTTCAATCTG-CCTCATGGTTA
*
16332 GGGTAAAAGATTAGATTGCTTCAATCTGCCTCATGGTCA
1 GGGTAAAAGATT-GATTGCTTCAATCTGCCTCATGGTTA
* * *
16371 AGGTAAAAGATCTGA-TGACTTCAATTTGCCTCATGGTTG
1 GGGTAAAAGAT-TGATTG-CTTCAATCTGCCTCATGGTTA
* * * *
16410 GGGTAAGAGATTTGAATTACTTCAATCTACCTCATGGTTG
1 GGGTAAAAGA-TTG-ATTGCTTCAATCTGCCTCATGGTTA
16450 GGGTAAAAGATT
1 GGGTAAAAGATT
16462 TGAGGTTGTA
Statistics
Matches: 136, Mismatches: 24, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
38 6 0.04
39 69 0.51
40 57 0.42
41 4 0.03
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (38 bp):
GGGTAAAAGATTGATTGCTTCAATCTGCCTCATGGTTA
Found at i:16433 original size:79 final size:79
Alignment explanation
Indices: 16253--16447 Score: 205
Period size: 79 Copynumber: 2.5 Consensus size: 79
16243 ATAGCTTTAG
* * * * * * * * *
16253 GGGTAAAAAATTGGATTGCTTAAATTTGCCCCATGGTCAGGGTAAGAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTAGATTACTTCAATCTGCCTCATGGTCAAGGTAAAAGATCGGATGGACTTCAAT
16318 CTGTCCTCTAGTTA
66 CTGTCCTCTAGTTA
* *
16332 GGGTAAAAGATTAGATTGCTTCAATCTGCCTCATGGTCAAGGTAAAAGATCTGAT-GACTTCAAT
1 GGGTAAAAGATTAGATTACTTCAATCTGCCTCATGGTCAAGGTAAAAGATCGGATGGACTTCAAT
* * *
16396 TTG-CCTCATGGTTG
66 CTGTCCTC-TAGTTA
* * *
16410 GGGTAAGAGATTTGAATTACTTCAATCTACCTCATGGT
1 GGGTAAAAGATTAG-ATTACTTCAATCTGCCTCATGGT
16448 TGGGGTAAAA
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
77 4 0.04
78 26 0.27
79 68 0.69
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (79 bp):
GGGTAAAAGATTAGATTACTTCAATCTGCCTCATGGTCAAGGTAAAAGATCGGATGGACTTCAAT
CTGTCCTCTAGTTA
Found at i:16443 original size:40 final size:39
Alignment explanation
Indices: 16311--16464 Score: 175
Period size: 39 Copynumber: 3.9 Consensus size: 39
16301 ATCGGATGGT
* * * *
16311 CTTCAATCTGTCCTC-TAGTTAGGGTAAAAGATTAGATTG
1 CTTCAATCTG-CCTCATGGTTGGGGTAAAAGATTTGATTA
*** * *
16350 CTTCAATCTGCCTCATGGTCAAGGTAAAAGATCTGATGA
1 CTTCAATCTGCCTCATGGTTGGGGTAAAAGATTTGATTA
* *
16389 CTTCAATTTGCCTCATGGTTGGGGTAAGAGATTTGAATTA
1 CTTCAATCTGCCTCATGGTTGGGGTAAAAGATTTG-ATTA
*
16429 CTTCAATCTACCTCATGGTTGGGGTAAAAGATTTGA
1 CTTCAATCTGCCTCATGGTTGGGGTAAAAGATTTGA
16465 GGTTGTAACT
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
38 4 0.04
39 57 0.59
40 35 0.36
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (39 bp):
CTTCAATCTGCCTCATGGTTGGGGTAAAAGATTTGATTA
Found at i:16556 original size:50 final size:50
Alignment explanation
Indices: 16502--16643 Score: 160
Period size: 50 Copynumber: 2.8 Consensus size: 50
16492 CAGGAGTATA
* * * *
16502 AGATTCGTCATTGTGACTTCAATCTGCGCCTCTACAGCTTTAGGTGAATG
1 AGATTTGTCATTGCGGCTTCAATCTGCACCTCTACAGCTTTAGGTGAATG
* * * * * *
16552 AGATTTGTCATTACGGCTTCATTCTACCCCTCTACATCTTTAGGTGTATG
1 AGATTTGTCATTGCGGCTTCAATCTGCACCTCTACAGCTTTAGGTGAATG
* *
16602 AGATTTG-CAATTGCGGCTTCAATCTGCACCTCCATAGCTTTA
1 AGATTTGTC-ATTGCGGCTTCAATCTGCACCTCTACAGCTTTA
16644 AGGGTAAAAG
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
49 1 0.01
50 74 0.99
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (50 bp):
AGATTTGTCATTGCGGCTTCAATCTGCACCTCTACAGCTTTAGGTGAATG
Found at i:27007 original size:18 final size:19
Alignment explanation
Indices: 26968--27011 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
26958 AGAGATTAAA
* *
26968 ATATATAAATATACATACT
1 ATATATAAAGATACAAACT
26987 ATATATAAAGA-ACAAACT
1 ATATATAAAGATACAAACT
27005 ATATATA
1 ATATATA
27012 CATGCATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (19 bp):
ATATATAAAGATACAAACT
Done.