Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006150.1 Kokia drynarioides strain JFW-HI SEQ_120691, 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, 720
Length: 1200
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Found at i:49 original size:23 final size:22
Alignment explanation
Indices: 17--62 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
7 ATGGGACATT
*
17 ATTTAAATAAATTTAAATTTAA
1 ATTTAAATAAACTTAAATTTAA
*
39 ATTTATAATAAACTTAATTTTAA
1 ATTTA-AATAAACTTAAATTTAA
62 A
1 A
63 ATAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTTAAATAAACTTAAATTTAA
Found at i:55 original size:17 final size:17
Alignment explanation
Indices: 30--76 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
20 TAAATAAATT
*
30 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* *
47 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
64 TAAATTTAAATTT
1 TAAATTTAAATTT
77 TGTTGGGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:151 original size:10 final size:9
Alignment explanation
Indices: 136--202 Score: 50
Period size: 10 Copynumber: 7.1 Consensus size: 9
126 ATAATATATC
136 AAAAACACTT
1 AAAAACA-TT
146 AAAAACATT
1 AAAAACATT
155 AAAACAAACATT
1 --AA-AAACATT
167 AAAAA-A-T
1 AAAAACATT
*
174 AAAAAAATTT
1 AAAAACA-TT
184 AAAATACATT
1 AAAA-ACATT
194 AAAAA-ATT
1 AAAAACATT
202 A
1 A
203 TATTAAGATA
Statistics
Matches: 49, Mismatches: 1, Indels: 16
0.74 0.02 0.24
Matches are distributed among these distances:
7 6 0.12
8 6 0.12
9 6 0.12
10 20 0.41
11 4 0.08
12 7 0.14
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAAACATT
Found at i:334 original size:20 final size:21
Alignment explanation
Indices: 311--352 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
301 AAAACGCATA
*
311 AAAAATAACATCC-AAACAAC
1 AAAAATAACAACCAAAACAAC
331 AAAAATAACAACCAAAACAAC
1 AAAAATAACAACCAAAACAAC
352 A
1 A
353 GCAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.69, C:0.24, G:0.00, T:0.07
Consensus pattern (21 bp):
AAAAATAACAACCAAAACAAC
Found at i:342 original size:12 final size:12
Alignment explanation
Indices: 325--450 Score: 66
Period size: 12 Copynumber: 10.8 Consensus size: 12
315 ATAACATCCA
325 AACAACAAAAAT
1 AACAACAAAAAT
* *
337 AACAACCAAAAC
1 AACAACAAAAAT
*
349 AACAGCAAAAAT
1 AACAACAAAAAT
**
361 ---AACAGTAA-
1 AACAACAAAAAT
*
369 AACAACATTAAA-
1 AACAACA-AAAAT
381 AACAACAAAAAT
1 AACAACAAAAAT
* *
393 AGCAACAAAAAC
1 AACAACAAAAAT
** *
405 AGTAATAAAAAT
1 AACAACAAAAAT
*
417 AACAGCAAAAAT
1 AACAACAAAAAT
*
429 AAC-ACGAAAAT
1 AACAACAAAAAT
*
440 AGCAATCAAAA
1 AACAA-CAAAA
451 CAACAAAAAA
Statistics
Matches: 83, Mismatches: 24, Indels: 13
0.69 0.20 0.11
Matches are distributed among these distances:
9 5 0.06
11 15 0.18
12 59 0.71
13 4 0.05
ACGTcount: A:0.67, C:0.17, G:0.06, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:381 original size:23 final size:23
Alignment explanation
Indices: 344--387 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
334 AATAACAACC
*
344 AAAACAACAGCAAAAATAACAGT
1 AAAACAACAGCAAAAACAACAGT
**
367 AAAACAACATTAAAAACAACA
1 AAAACAACAGCAAAAACAACA
388 AAAATAGCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.09
Consensus pattern (23 bp):
AAAACAACAGCAAAAACAACAGT
Found at i:400 original size:68 final size:68
Alignment explanation
Indices: 327--459 Score: 160
Period size: 68 Copynumber: 2.0 Consensus size: 68
317 AACATCCAAA
* * *
327 CAACAAAAATAACAACCAAAACAACAGCAAAAATAACA-GTAAAACAACATTAAAAACAACAAAA
1 CAACAAAAACAACAACAAAAACAACAGCAAAAATAACACG-AAAACAACAATAAAAACAACAAAA
391 ATAG
65 ATAG
** * * * * *
395 CAACAAAAACAGTAATAAAAATAACAGCAAAAATAACACGAAAATAGCAATCAAAACAACAAAAA
1 CAACAAAAACAACAACAAAAACAACAGCAAAAATAACACGAAAACAACAATAAAAACAACAAAAA
460 AACAACTCAA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
68 53 0.98
69 1 0.02
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.09
Consensus pattern (68 bp):
CAACAAAAACAACAACAAAAACAACAGCAAAAATAACACGAAAACAACAATAAAAACAACAAAAA
TAG
Found at i:402 original size:21 final size:22
Alignment explanation
Indices: 378--481 Score: 72
Period size: 24 Copynumber: 4.6 Consensus size: 22
368 AAACAACATT
*
378 AAAAACAACAAAAATAGCAA-C
1 AAAAACAACAAAAATAACAATC
* *
399 AAAAACAGTAATAAAAATAAC-AGC
1 AAAAAC---AACAAAAATAACAATC
* *
423 AAAAATAACACGAAAATAGCAATC
1 AAAAACAACA--AAAATAACAATC
447 -AAAACAACAAAAA-AACAACTC
1 AAAAACAACAAAAATAACAA-TC
*
468 AAAAACAGCAAAAA
1 AAAAACAACAAAAA
482 AAATCAACCA
Statistics
Matches: 65, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
20 4 0.06
21 15 0.23
22 12 0.18
23 16 0.25
24 18 0.28
ACGTcount: A:0.69, C:0.17, G:0.06, T:0.08
Consensus pattern (22 bp):
AAAAACAACAAAAATAACAATC
Found at i:402 original size:44 final size:44
Alignment explanation
Indices: 311--403 Score: 100
Period size: 44 Copynumber: 2.1 Consensus size: 44
301 AAAACGCATA
* * *
311 AAAAATAACATCCAAACAACAAAAATAACAACCAAAACAACAGC
1 AAAAATAACATCAAAACAACAAAAATAACAACAAAAACAACAAC
* * *
355 AAAAATAACAGT-AAAACAACATTAAA-AACAACAAAAATAGCAAC
1 AAAAATAACA-TCAAAACAACA-AAAATAACAACAAAAACAACAAC
399 AAAAA
1 AAAAA
404 CAGTAATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
44 37 0.90
45 4 0.10
ACGTcount: A:0.69, C:0.19, G:0.03, T:0.09
Consensus pattern (44 bp):
AAAAATAACATCAAAACAACAAAAATAACAACAAAAACAACAAC
Found at i:502 original size:22 final size:23
Alignment explanation
Indices: 447--506 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
437 AATAGCAATC
*
447 AAAACAAC-AAAAAAACAACTCA
1 AAAACAGCAAAAAAAACAACTCA
469 AAAACAGCAAAAAAAATCAAC-C-
1 AAAACAGCAAAAAAAA-CAACTCA
* *
491 AAAGCAGTAAAAAAAA
1 AAAACAGCAAAAAAAA
507 GTATCAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 21 0.64
23 8 0.24
24 4 0.12
ACGTcount: A:0.72, C:0.18, G:0.05, T:0.05
Consensus pattern (23 bp):
AAAACAGCAAAAAAAACAACTCA
Done.