Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006614.1 Kokia drynarioides strain JFW-HI SEQ_121204, 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: 2913
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Found at i:579 original size:64 final size:65
Alignment explanation
Indices: 460--593 Score: 148
Period size: 64 Copynumber: 2.1 Consensus size: 65
450 AAAAAATGAT
* * * * *
460 GAAAAGAAAAAAAGATCGAGATGAAAACCCGTAGAGGGCATCTTGAAACCTAAAAA-AA-AAAAA
1 GAAAAGAAAAAAAGATCAAGATGAAAACCCGCACAGGGCAACTTGAAACCAAAAAATAATAAAAA
* **
523 GAAAAG-AAAAAAGAAGTCAAGATGAAAACCTGCACAGGGCAACTTGAAATGAAAAAATAATAAA
1 GAAAAGAAAAAAAG-A-TCAAGATGAAAACCCGCACAGGGCAACTTGAAACCAAAAAATAATAAA
587 AA
64 AA
*
589 TAAAA
1 GAAAA
594 AAGGTTTTAC
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
62 7 0.12
63 7 0.12
64 33 0.57
65 2 0.03
66 9 0.16
ACGTcount: A:0.59, C:0.11, G:0.18, T:0.12
Consensus pattern (65 bp):
GAAAAGAAAAAAAGATCAAGATGAAAACCCGCACAGGGCAACTTGAAACCAAAAAATAATAAAAA
Found at i:1800 original size:21 final size:20
Alignment explanation
Indices: 1775--1906 Score: 99
Period size: 19 Copynumber: 7.0 Consensus size: 20
1765 TTCGGTGAAA
1775 AAAAAGAGAAAGAAAGAAAAG
1 AAAAAGAGAAA-AAAGAAAAG
* *
1796 AAAAAAAG-AAAAAGAAAAA
1 AAAAAGAGAAAAAAGAAAAG
* *
1815 AAAAAGAAAAAGAAAGAAGA-
1 AAAAAGAGAAA-AAAGAAAAG
*
1835 AAAAAG-GAAAAAGGAAAAAG
1 AAAAAGAGAAAAAAG-AAAAG
1855 AAAAA-AG-AAAAAG---AG
1 AAAAAGAGAAAAAAGAAAAG
1870 AAAAAGAGAAAAAA-AACAAG
1 AAAAAGAGAAAAAAGAA-AAG
1890 -AAAAG-GAAAAAA-AAAAG
1 AAAAAGAGAAAAAAGAAAAG
1907 GAGAGGTCGA
Statistics
Matches: 91, Mismatches: 9, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
15 7 0.08
16 2 0.02
17 8 0.09
18 12 0.13
19 30 0.33
20 18 0.20
21 14 0.15
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAAAGAGAAAAAAGAAAAG
Found at i:1900 original size:7 final size:6
Alignment explanation
Indices: 1775--1906 Score: 110
Period size: 7 Copynumber: 21.0 Consensus size: 6
1765 TTCGGTGAAA
* *
1775 AAAAAG AGAAAG --AAAG AAAAGAA AAAAAG AAAAAG AAAAA- AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG
1821 AAAAAG AAAGAAG AAAAAAGG AAAAAGG AAAAAG AAAAAAG AAAAAGAG
1 AAAAAG AAA-AAG -AAAAA-G AAAAA-G AAAAAG -AAAAAG -AAAA-AG
* *
1870 AAAAAG AGAAAAA AAACAAG AAAAGG AAAAA- AAAAAG
1 AAAAAG A-AAAAG AAA-AAG AAAAAG AAAAAG AAAAAG
1907 GAGAGGTCGA
Statistics
Matches: 107, Mismatches: 7, Indels: 24
0.78 0.05 0.17
Matches are distributed among these distances:
4 4 0.04
5 10 0.09
6 40 0.37
7 47 0.44
8 6 0.06
ACGTcount: A:0.80, C:0.01, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2312 original size:19 final size:19
Alignment explanation
Indices: 2274--2328 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
2264 GACCATTGTT
*
2274 TAATGTTTGCCATCTTTGAC
1 TAATGTTTGACAT-TTTGAC
2294 TAATGTTTGACATTTTGAC
1 TAATGTTTGACATTTTGAC
* *
2313 CAATGTTTGATATTTT
1 TAATGTTTGACATTTT
2329 TAATTCCTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 20 0.62
20 12 0.38
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.49
Consensus pattern (19 bp):
TAATGTTTGACATTTTGAC
Done.