Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007074.1 Kokia drynarioides strain JFW-HI SEQ_121683, 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, 697
Length: 1162
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Found at i:44 original size:18 final size:18
Alignment explanation
Indices: 20--92 Score: 78
Period size: 19 Copynumber: 4.0 Consensus size: 18
10 TTTTCTTTAA
*
20 AAAAAATGTTTAGATTTTT
1 AAAAAA-GTTTAAATTTTT
**
39 -AAAAA-TAAAAATTTTT
1 AAAAAAGTTTAAATTTTT
55 AAGAAAAGTTTAAATTTTT
1 AA-AAAAGTTTAAATTTTT
74 AAACAAAGTTTAAATTTTT
1 AAA-AAAGTTTAAATTTTT
93 TTAACTATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
16 8 0.18
17 1 0.02
18 10 0.22
19 26 0.58
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.42
Consensus pattern (18 bp):
AAAAAAGTTTAAATTTTT
Found at i:205 original size:20 final size:21
Alignment explanation
Indices: 178--227 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
168 AAGATAAAAA
*
178 TTTG-TTTTTTTAGA-AAAGT
1 TTTGATTTTTTTAAACAAAGT
197 TTTGA--TTTTTAAACAAAGT
1 TTTGATTTTTTTAAACAAAGT
216 TTTGATTTTTTT
1 TTTGATTTTTTT
228 TTAAACTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 7 0.27
19 14 0.54
21 5 0.19
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (21 bp):
TTTGATTTTTTTAAACAAAGT
Found at i:592 original size:151 final size:145
Alignment explanation
Indices: 49--607 Score: 560
Period size: 150 Copynumber: 3.8 Consensus size: 145
39 AAAAATAAAA
* * * * *
49 ATTTTTAAGAAAAGTTTAAATTTTTAAACAAAG-TTTAAATTTTTTTAACTATTTCGAAATAAAA
1 ATTTTAAAGAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTTGAAATAAAA
* * * *
113 GTTTGGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAAA-AAA-TTTAGA-TTTTTAAGATAA
66 GTTTTGATTTTTAAGT-AAATAGTGATTTTTTTTAAAAAAAGAAAGTTTAGATTTTTTAAAAAAA
*
175 AA-A--TTTGTT--T-
130 AATATGTTTTTTAGTG
** * *
185 -TTTT--AGAAAAGTTTTGATTTTTAAACAAAGTTTTGATTTTTTTTTAAACTATTTTGTAATAA
1 ATTTTAAAGAAAAGTTTAAATTTTTAAATAAAGTTTTGA-TTTTTTTT-AACTATTTTGAAATAA
* * * **
247 AA-ATTTGAATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAATAGAAAGTTTATATTTTTTTTA
64 AAGTTTTG-ATTTTTAAGT-AAATAGTGATTTTTTTTAAAAAA-AGAAAGTTTAGATTTTTTAAA
*
311 AAAAAATATGTTTTTTAGTT
126 AAAAAATATGTTTTTTAGTG
*
331 ATTTTAAAGAAAATATTTAAATTTTTAAATAAAGTTTTGA-TTTTTTTAACTATTTTGAAATAAA
1 ATTTTAAAGAAAA-GTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTTGAAATAAA
**
395 AGTTTTGATTTTTAAGT-AA-AGTGATTTTCATTAAAGAAAATAAAGAAAGTTTAGATTTTTTAA
65 AGTTTTGATTTTTAAGTAAATAGTGATTTT--TT--TTAAAA-AAAGAAAGTTTAGATTTTTT-A
458 AAATAAAAATATGTTTTTTAGTG
124 AAA-AAAAATATGTTTTTTAGTG
*
481 ATTTTAAAGAGAAAGTTTAAATTTTTAAATGAAGTTTTGATTTTTTTTAACTATTTCT-AAATAA
1 ATTTTAAAGA-AAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTT-TGAAATAA
* * * *
545 AAGTTTTGATTTTGAAGTAAAGTAGTGATTTTGTTTTAATCAAAAGAAAACTTTTGATTTTTT
64 AAGTTTTGATTTTTAAGTAAA-TAGTGATTTT-TTTTAA-AAAAAG-AAAGTTTAGATTTTTT
608 TTTTTTAAAA
Statistics
Matches: 353, Mismatches: 36, Indels: 52
0.80 0.08 0.12
Matches are distributed among these distances:
133 24 0.07
134 4 0.01
135 14 0.04
136 50 0.14
137 1 0.00
138 3 0.01
139 5 0.01
140 10 0.03
141 1 0.00
143 5 0.01
144 9 0.03
145 3 0.01
146 1 0.00
147 31 0.09
148 32 0.09
149 10 0.03
150 74 0.21
151 47 0.13
152 18 0.05
153 2 0.01
154 9 0.03
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.47
Consensus pattern (145 bp):
ATTTTAAAGAAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTTAACTATTTTGAAATAAAA
GTTTTGATTTTTAAGTAAATAGTGATTTTTTTTAAAAAAAGAAAGTTTAGATTTTTTAAAAAAAA
ATATGTTTTTTAGTG
Done.