Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000139.1 Kokia drynarioides strain JFW-HI SEQ_110793, 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: 2348
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.36
Found at i:283 original size:30 final size:30
Alignment explanation
Indices: 232--335 Score: 97
Period size: 30 Copynumber: 3.4 Consensus size: 30
222 TATGCATATT
*
232 AAAAAACATAACAATAAAAAACATACAT-TTCAA
1 AAAAAACAT-A-AA-AAAAAACATACATAAT-AA
* *
265 ACAAAACATAAAAAAAAACCTACATAATAA
1 AAAAAACATAAAAAAAAACATACATAATAA
* * *
295 AAAAAACATAAAAATAAACATA-ACAATCA
1 AAAAAACATAAAAAAAAACATACATAATAA
324 AAAAAA-ATAAAA
1 AAAAAACATAAAA
336 GATAAAATCT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
28 6 0.10
29 11 0.18
30 33 0.53
31 3 0.05
32 1 0.02
33 8 0.13
ACGTcount: A:0.72, C:0.13, G:0.00, T:0.14
Consensus pattern (30 bp):
AAAAAACATAAAAAAAAACATACATAATAA
Found at i:303 original size:14 final size:13
Alignment explanation
Indices: 267--317 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 13
257 CATTTCAAAC
267 AAAACATAAAAAA
1 AAAACATAAAAAA
280 AAACCTACATAATAAAA
1 AAA---ACATAA-AAAA
297 AAAACAT-AAAAA
1 AAAACATAAAAAA
*
309 TAAACATAA
1 AAAACATAA
318 CAATCAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
12 10 0.31
13 5 0.16
14 4 0.12
16 6 0.19
17 7 0.22
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAACATAAAAAA
Found at i:310 original size:17 final size:18
Alignment explanation
Indices: 275--312 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
265 ACAAAACATA
* *
275 AAAAAAAACCTACATAAT
1 AAAAAAAACATACAAAAT
293 AAAAAAAACATA-AAAAT
1 AAAAAAAACATACAAAAT
310 AAA
1 AAA
313 CATAACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (18 bp):
AAAAAAAACATACAAAAT
Found at i:319 original size:17 final size:16
Alignment explanation
Indices: 263--330 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 16
253 CATACATTTC
*
263 AAACAAAACATAAAAAA
1 AAACATAACAT-AAAAA
* *
280 AAACCT-ACATAATAA
1 AAACATAACATAAAAA
295 AAA-A-AACATAAAAA
1 AAACATAACATAAAAA
309 TAAACATAACAATCAAAAA
1 -AAACATAAC-AT-AAAAA
328 AAA
1 AAA
331 TAAAAGATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
14 8 0.20
15 10 0.25
16 5 0.12
17 7 0.17
18 5 0.12
19 5 0.12
ACGTcount: A:0.75, C:0.13, G:0.00, T:0.12
Consensus pattern (16 bp):
AAACATAACATAAAAA
Found at i:408 original size:28 final size:29
Alignment explanation
Indices: 376--436 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
366 TTAACCTAAT
* *
376 TTAATAAAAAATT-CAATCAACAAAAAAA
1 TTAATAAAAAATTAAAATAAACAAAAAAA
* *
404 TTAATCAAAAATTAAAATAAACAAAATAA
1 TTAATAAAAAATTAAAATAAACAAAAAAA
433 TTAA
1 TTAA
437 ATAATTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (29 bp):
TTAATAAAAAATTAAAATAAACAAAAAAA
Found at i:426 original size:29 final size:28
Alignment explanation
Indices: 376--471 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 28
366 TTAACCTAAT
* *
376 TTAATAAAAAATTCAATCAACAAAAAAA
1 TTAATAAAAAATTAAATAAACAAAAAAA
* *
404 TTAATCAAAAATTAAAATAAACAAAATAA
1 TTAATAAAAAATT-AAATAAACAAAAAAA
*
433 TTAAATAATTAAA-TAAATCAAAATCAACAAAAA
1 TT-AATAA-AAAATTAAAT--AAA-CAA-AAAAA
466 TTAATA
1 TTAATA
472 TTTATAAATC
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
28 12 0.22
29 18 0.33
30 5 0.09
31 6 0.11
32 7 0.13
33 6 0.11
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (28 bp):
TTAATAAAAAATTAAATAAACAAAAAAA
Found at i:442 original size:26 final size:25
Alignment explanation
Indices: 400--469 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 25
390 AATCAACAAA
400 AAAATTAATCAAAAATTAAAATAAA-C
1 AAAA-TAATCAAAAATT-AAATAAATC
*
426 AAAATAATTAAATAATTAAATAAATC
1 AAAATAATCAAA-AATTAAATAAATC
452 AAAATCAA-CAAAAATTAA
1 AAAAT-AATCAAAAATTAA
470 TATTTATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 20 0.51
26 17 0.44
27 2 0.05
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAATAATCAAAAATTAAATAAATC
Found at i:462 original size:35 final size:30
Alignment explanation
Indices: 412--495 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 30
402 AATTAATCAA
*
412 AAATTAAAATAAACAAAATAATTAAATAATTAAAT
1 AAATCAAAATAAAC-AAA-AATT-AAT-ATT-AAT
* *
447 AAATCAAAATCAACAAAAATTAATATTTAT
1 AAATCAAAATAAACAAAAATTAATATTAAT
*
477 AAATCAAAATAAATAAAAA
1 AAATCAAAATAAACAAAAA
496 AACATACCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
30 19 0.43
31 3 0.07
32 3 0.07
33 4 0.09
34 3 0.07
35 12 0.27
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (30 bp):
AAATCAAAATAAACAAAAATTAATATTAAT
Done.