Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010579.1 Kokia drynarioides strain JFW-HI SEQ_125504, 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: 4659
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Found at i:2746 original size:27 final size:27
Alignment explanation
Indices: 2695--2755 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
2685 CAATTTTCAA
*
2695 TTAATGATTGTTTCCTTTGACCCTCCCT
1 TTAAT-ATTGTTTCCTTCGACCCTCCCT
* **
2723 TTAATATTGTTTCCTTCGATCCTCTTT
1 TTAATATTGTTTCCTTCGACCCTCCCT
2750 TTAATA
1 TTAATA
2756 GAATTCTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 24 0.83
28 5 0.17
ACGTcount: A:0.18, C:0.23, G:0.08, T:0.51
Consensus pattern (27 bp):
TTAATATTGTTTCCTTCGACCCTCCCT
Found at i:3379 original size:47 final size:47
Alignment explanation
Indices: 3308--3463 Score: 172
Period size: 47 Copynumber: 3.5 Consensus size: 47
3298 TTCGAACCCC
*
3308 AGCTTCCTGATGAGACACTAAGAAGCGGGCCGTAGCAATAAAAGGTT
1 AGCTTCCTGATGAGACACTGAGAAGCGGGCCGTAGCAATAAAAGGTT
* **
3355 AGCTTCCTGATGAGATACTGAGAA-------GT-G-AACCAAA--TT
1 AGCTTCCTGATGAGACACTGAGAAGCGGGCCGTAGCAATAAAAGGTT
*
3391 CGTCTTCCTGATGAGACACTGAGAAGCGGGCCGTAGCAATAAAAGGTT
1 AG-CTTCCTGATGAGACACTGAGAAGCGGGCCGTAGCAATAAAAGGTT
*
3439 AGCTTCCTGATGAGATACTGAGAAG
1 AGCTTCCTGATGAGACACTGAGAAG
3464 TGAACCAAAT
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
36 3 0.03
37 21 0.24
38 5 0.06
39 1 0.01
40 2 0.02
44 2 0.02
45 1 0.01
46 5 0.06
47 44 0.51
48 3 0.03
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.22
Consensus pattern (47 bp):
AGCTTCCTGATGAGACACTGAGAAGCGGGCCGTAGCAATAAAAGGTT
Found at i:3451 original size:84 final size:84
Alignment explanation
Indices: 3310--3503 Score: 352
Period size: 84 Copynumber: 2.3 Consensus size: 84
3300 CGAACCCCAG
3310 CTTCCTGATGAGACACTAAGAAGCGGGCCGTAGCAATAAAAGGTTAGCTTCCTGATGAGATACTG
1 CTTCCTGATGAGACACTAAGAAGCGGGCCGTAGCAATAAAAGGTTAGCTTCCTGATGAGATACTG
3375 AGAAGTGAACCAAATTCGT
66 AGAAGTGAACCAAATTCGT
*
3394 CTTCCTGATGAGACACTGAGAAGCGGGCCGTAGCAATAAAAGGTTAGCTTCCTGATGAGATACTG
1 CTTCCTGATGAGACACTAAGAAGCGGGCCGTAGCAATAAAAGGTTAGCTTCCTGATGAGATACTG
3459 AGAAGTGAACCAAATTCGT
66 AGAAGTGAACCAAATTCGT
* * *
3478 TTTCCTGATGAGATACAAAGAAGCGG
1 CTTCCTGATGAGACACTAAGAAGCGG
3504 ATTGAAACGA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 105 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (84 bp):
CTTCCTGATGAGACACTAAGAAGCGGGCCGTAGCAATAAAAGGTTAGCTTCCTGATGAGATACTG
AGAAGTGAACCAAATTCGT
Found at i:4229 original size:17 final size:17
Alignment explanation
Indices: 4201--4273 Score: 103
Period size: 17 Copynumber: 4.4 Consensus size: 17
4191 TTGGAAATCG
4201 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
4217 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
4234 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
4251 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
4268 AATTTA
1 AATTTA
4274 GAAAGTCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
16 5 0.10
17 45 0.90
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:4249 original size:7 final size:6
Alignment explanation
Indices: 4206--4273 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
4196 AATCGAATTT
* *
4206 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
*
4252 ATTT-- ATTATAA AATTAA ATTTA
1 ATTTAA ATT-TAA ATTTAA ATTTA
4274 GAAAGTCCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 7 0.14
5 5 0.10
6 32 0.64
7 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:4293 original size:13 final size:14
Alignment explanation
Indices: 4275--4315 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
4265 TTAAATTTAG
4275 AAAGTCCAATTAA-
1 AAAGTCCAATTAAC
4288 AAAGTCCAA--AAC
1 AAAGTCCAATTAAC
4300 AAAGTCCAATT-AC
1 AAAGTCCAATTAAC
4313 AAA
1 AAA
4316 TGACCTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.08
12 9 0.36
13 14 0.56
ACGTcount: A:0.56, C:0.20, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAGTCCAATTAAC
Found at i:4327 original size:15 final size:15
Alignment explanation
Indices: 4305--4368 Score: 74
Period size: 15 Copynumber: 4.3 Consensus size: 15
4295 AAAACAAAGT
*
4305 CCAATTACAAATGAC
1 CCAAATACAAATGAC
* * * *
4320 CTAATTACAAAAGGC
1 CCAAATACAAATGAC
*
4335 CCAAATACAAATGGC
1 CCAAATACAAATGAC
4350 CCAAATACAAATGAC
1 CCAAATACAAATGAC
4365 CCAA
1 CCAA
4369 TGGCCTAAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.48, C:0.27, G:0.09, T:0.16
Consensus pattern (15 bp):
CCAAATACAAATGAC
Done.