Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008573.1 Kokia drynarioides strain JFW-HI SEQ_123251, 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: 11867
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:591 original size:3 final size:3
Alignment explanation
Indices: 583--608 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
573 TAACTGTTAC
583 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
609 CTAATTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1293 original size:6 final size:6
Alignment explanation
Indices: 1282--1360 Score: 74
Period size: 6 Copynumber: 13.5 Consensus size: 6
1272 ATATTTATAA
* * *
1282 TAAATT TAAATT TAAATA TAAATC TAAACT TAAA-T TAAATT TAAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT
* * *
1330 TAAA-A TAAATT TAAATT CAAA-A TAAATT TAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAA
1361 TCTTAAAATA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
5 12 0.20
6 41 0.69
7 6 0.10
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (6 bp):
TAAATT
Found at i:1304 original size:18 final size:17
Alignment explanation
Indices: 1274--1375 Score: 125
Period size: 17 Copynumber: 5.9 Consensus size: 17
1264 CACTTTCAAT
*
1274 ATTTATAATAAATTTAA
1 ATTTAAAATAAATTTAA
*
1291 ATTTAAATATAAATCTAA
1 ATTTAAA-ATAAATTTAA
* *
1309 ACTTAAATTAAATTTAAA
1 ATTTAAAATAAATTT-AA
1327 ATTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
*
1344 ATTCAAAATAAATTT-A
1 ATTTAAAATAAATTTAA
1360 ATCTTAAAATAAATTT
1 AT-TTAAAATAAATTT
1376 TAAAATGGGT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
16 3 0.04
17 40 0.55
18 30 0.41
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:1379 original size:35 final size:34
Alignment explanation
Indices: 1280--1375 Score: 124
Period size: 35 Copynumber: 2.8 Consensus size: 34
1270 CAATATTTAT
*
1280 AATAAATTTAAATTTAAATATAAATCTAAACTTAA
1 AATAAATTTAAATTTAAA-ATAAATTTAAACTTAA
*
1315 ATTAAATTTAAAATTTAAAATAAATTTAAA-TTCAA
1 AATAAATTT-AAATTTAAAATAAATTTAAACTT-AA
1350 AATAAATTT-AATCTTAAAATAAATTT
1 AATAAATTTAAAT-TTAAAATAAATTT
1376 TAAAATGGGT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
33 3 0.05
34 15 0.27
35 28 0.51
36 9 0.16
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (34 bp):
AATAAATTTAAATTTAAAATAAATTTAAACTTAA
Found at i:3308 original size:16 final size:16
Alignment explanation
Indices: 3289--3347 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
3279 TCCGAATTCG
3289 AAATGACTCAAATCCA
1 AAATGACTCAAATCCA
*
3305 AAATGA-TCAAA-CTCG
1 AAATGACTCAAATC-CA
* *
3320 AAATAAGTCAAATCCAA
1 AAATGACTCAAATCC-A
3337 AAATGAC-CAAA
1 AAATGACTCAAA
3348 CCTGAAATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 1 0.03
15 11 0.32
16 16 0.47
17 6 0.18
ACGTcount: A:0.54, C:0.20, G:0.08, T:0.17
Consensus pattern (16 bp):
AAATGACTCAAATCCA
Found at i:3323 original size:31 final size:32
Alignment explanation
Indices: 3286--3358 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
3276 TGATCCGAAT
*
3286 TCGAAATGACTCAAATCC-AAAATGATCAAAC
1 TCGAAATGACTCAAATCCAAAAATGACCAAAC
* *
3317 TCGAAATAAGTCAAATCCAAAAATGACCAAAC
1 TCGAAATGACTCAAATCCAAAAATGACCAAAC
3349 -CTGAAATGAC
1 TC-GAAATGAC
3359 CCAACTCGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 17 0.49
32 18 0.51
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (32 bp):
TCGAAATGACTCAAATCCAAAAATGACCAAAC
Found at i:3355 original size:32 final size:31
Alignment explanation
Indices: 3286--3348 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
3276 TGATCCGAAT
* * *
3286 TCGAAATGACTCAAATCCAAAATGATCAAAC
1 TCGAAATAAGTCAAATCCAAAATGACCAAAC
3317 TCGAAATAAGTCAAATCCAAAAATGACCAAAC
1 TCGAAATAAGTCAAATCC-AAAATGACCAAAC
3349 CTGAAATGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.51, C:0.22, G:0.10, T:0.17
Consensus pattern (31 bp):
TCGAAATAAGTCAAATCCAAAATGACCAAAC
Found at i:6960 original size:3 final size:3
Alignment explanation
Indices: 6954--6982 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6944 TTGCTGCTGT
6954 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
6983 CTGTTTCTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Done.