Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013563.1 Kokia drynarioides strain JFW-HI SEQ_128589, 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: 1868
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.30
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:134 original size:29 final size:28
Alignment explanation
Indices: 101--404 Score: 265
Period size: 29 Copynumber: 10.4 Consensus size: 28
91 AAATAGGTAG
*
101 TTTTGGAAGGTTCGGAGTCAAAAAT-GGAT
1 TTTTGGAAGGTTCGGGGT--AAAATGGGAT
* **
130 TTTTGTAA-GTTCGAGGGTAAAATAGTAAT
1 TTTTGGAAGGTTCG-GGGTAAAAT-GGGAT
*
159 TTTTGAAAGGTTCGGGGTCAAAAATGGGAT
1 TTTTGGAAGGTTCGGGGT--AAAATGGGAT
* * *
189 TTTTGGAAGTTTAGGGGTAAAATGGTAAT
1 TTTTGGAAGGTTCGGGGTAAAATGG-GAT
*
218 TTTTAGAAGGTTCGGGGTCAAAAATGGGAT
1 TTTTGGAAGGTTCGGGGT--AAAATGGGAT
* * **
248 TTTTGGAAGTTTGGGGGTAAAATAGTAAT
1 TTTTGGAAGGTTCGGGGTAAAAT-GGGAT
277 TTTTGGAAGGTTCGGGGTCAAAAATGGGAT
1 TTTTGGAAGGTTCGGGGT--AAAATGGGAT
* * *
307 TTTTGGAA-GTTCGGGAGTAAAATAGTAA
1 TTTTGGAAGGTTCGGG-GTAAAATGGGAT
* *
335 TTTTGGAAGATTCGAGGTCAAAAATGGGAT
1 TTTTGGAAGGTTCGGGGT--AAAATGGGAT
*
365 TTTTGG-AGGTTCGGGGTAAAATGGTAAT
1 TTTTGGAAGGTTCGGGGTAAAATGG-GAT
393 TTTTGGAAGGTT
1 TTTTGGAAGGTT
405 TAGGGACCTC
Statistics
Matches: 222, Mismatches: 35, Indels: 36
0.76 0.12 0.12
Matches are distributed among these distances:
27 12 0.05
28 42 0.19
29 85 0.38
30 66 0.30
31 17 0.08
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (28 bp):
TTTTGGAAGGTTCGGGGTAAAATGGGAT
Found at i:217 original size:59 final size:58
Alignment explanation
Indices: 101--404 Score: 459
Period size: 59 Copynumber: 5.2 Consensus size: 58
91 AAATAGGTAG
* *
101 TTTTGGAAGGTTCGGAGTCAAAAAT-GGATTTTTGTAAGTTCGAGGGTAAAATAGTAAT
1 TTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCG-GGGTAAAATAGTAAT
* * *
159 TTTTGAAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAATGGTAAT
1 TTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGTAAAATAGTAAT
* *
218 TTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAATAGTAAT
1 TTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGTAAAATAGTAAT
277 TTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGAGTAAAATAGTAA-
1 TTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGG-GTAAAATAGTAAT
* * * *
335 TTTTGGAAGATTCGAGGTCAAAAATGGGATTTTTGGAGGTTCGGGGTAAAATGGTAAT
1 TTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGTAAAATAGTAAT
393 TTTTGGAAGGTT
1 TTTTGGAAGGTT
405 TAGGGACCTC
Statistics
Matches: 226, Mismatches: 16, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
57 11 0.05
58 81 0.36
59 131 0.58
60 3 0.01
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (58 bp):
TTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGTAAAATAGTAAT
Found at i:1483 original size:18 final size:15
Alignment explanation
Indices: 1436--1490 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 15
1426 TTTTCTATTT
1436 TTAATTATTA--ATA
1 TTAATTATTATGATA
*
1449 TTAATTATTATGTTA
1 TTAATTATTATGATA
1464 TTAATTAATGCTATGATA
1 TTAATT-AT--TATGATA
1482 TT-ATTATTA
1 TTAATTATTA
1491 ATGAGATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 10 0.29
14 2 0.06
15 8 0.23
16 4 0.11
17 3 0.09
18 8 0.23
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (15 bp):
TTAATTATTATGATA
Found at i:1488 original size:24 final size:23
Alignment explanation
Indices: 1461--1519 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
1451 AATTATTATG
1461 TTATTAATTAATGCTATGA-TATTA
1 TTATTAATTAAT--TATGACTATTA
*
1485 TTATTAATGAGATTATGACTATTA
1 TTATTAATTA-ATTATGACTATTA
1509 TTATT-ATTAAT
1 TTATTAATTAAT
1520 ACCGTTCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 2 0.06
23 8 0.26
24 19 0.61
25 2 0.06
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.51
Consensus pattern (23 bp):
TTATTAATTAATTATGACTATTA
Done.