Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012982.1 Kokia drynarioides strain JFW-HI SEQ_128000, 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: 5637
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.34
Found at i:52 original size:20 final size:21
Alignment explanation
Indices: 15--70 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
5 ATCATTAAGC
*
15 CTTAATT-AATCATTTTTA-A
1 CTTAATTAAATCATATTTACA
34 TCTTAATTAAATC-TATTTACA
1 -CTTAATTAAATCATATTTACA
*
55 CTTAATATAAACCATA
1 CTTAAT-TAAATCATA
71 CCAATCCACT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 18 0.60
21 10 0.33
22 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (21 bp):
CTTAATTAAATCATATTTACA
Found at i:706 original size:23 final size:23
Alignment explanation
Indices: 649--716 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
639 ACCATATAAA
**
649 CCAAACAGAATACGCCACAAAGG
1 CCAAACAGAATGTGCCACAAAGG
672 CCAAACTA-AATGTGCCACAAAGG
1 CCAAAC-AGAATGTGCCACAAAGG
695 CCAAACAGAATGT--CACAAAGG
1 CCAAACAGAATGTGCCACAAAGG
716 C
1 C
717 TCTATGCAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.22
22 1 0.02
23 30 0.73
24 1 0.02
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.09
Consensus pattern (23 bp):
CCAAACAGAATGTGCCACAAAGG
Found at i:4813 original size:147 final size:145
Alignment explanation
Indices: 4615--5298 Score: 656
Period size: 147 Copynumber: 4.7 Consensus size: 145
4605 TTTTTTCTTC
* * * *
4615 TTTTTTTAAAAAAAATCAAAAGTTTTCTTTTGAATAAACAAAATCACTACTTTACTTCAAAATCA
1 TTTTTTTAAAAAAAATCTAAACTTTT-TTTT-AAT---GAAAATCACTACTTTACTTAAAAATCA
*
4680 AAACTTTTATTTCGAAATAGTTAAAAAAAAATCAAAATTTTGTTTAAAAATTTAAACTTTTTTCT
61 AAACTTTTATTTCGAAATAGTT--AAAAAAATCAAAATTTTATTTAAAAATTTAAA-TTTTTTCT
*
4745 TTAAAATCACT-AAAAATAGATT
123 TTAAAATAACTAAAAAATAGATT
* * *
4767 TTTTTTTAAAAAAAATCTAAACTTTTTTTTAATGAAAATAACTACTTTACTTAAAAATCTAAACA
1 TTTTTTTAAAAAAAATCTAAACTTTTTTTTAATGAAAATCACTACTTTACTTAAAAATCAAAACT
* *
4832 TTTATTTCGAAATAATTAAAAAAATCAAAACTTTATTTAAAAATTTAAATTTTTTCTTTAAAATA
66 TTTATTTCGAAATAGTTAAAAAAATCAAAATTTTATTTAAAAATTTAAATTTTTTCTTTAAAATA
* *
4897 ACTAAAAAACAAGTTT
131 ACTAAAAAA-TAGATT
** *
4913 TTATTTTTAAAAATATAAAT-T-TTCTTTCTTTTTTAATGGAAATCACTACTTTACTTAAAAATC
1 TT-TTTTT-AAAA-A-AAATCTAAAC-TT-TTTTTTAATGAAAATCACTACTTTACTTAAAAATC
* * * * * **
4976 CAAATTTTTATTTCAAAATAATT-AAAAAATTAAAATTTTATTTAAAAATTTAAAGATTTTCTTT
60 AAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTTATTTAAAAATTTAAATTTTTTCTTT
*
5040 AAAATAACTAAAAAATAAATT
125 AAAATAACTAAAAAATAGATT
*
5061 TTTATTTTTAAAAAAA--TAAACTTTCACTTTTTTTAATGAAAATCACTACTTT-CTTAAAAATC
1 TTT-TTTTAAAAAAAATCTAAAC--T---TTTTTTTAATGAAAATCACTACTTTACTTAAAAATC
* * * * *
5123 TAAACTTTTATTTCAAAATAGTT-AAAAAATCAAAACTTTGTTTAAAAA-TTAAAATTTTTC---
60 AAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAATTTTATTTAAAAATTTAAATTTTTTCTTT
5183 ----T-A--AAAAAATAGATT
125 AAAATAACTAAAAAATAGATT
* * *
5197 TTTATTTT--TAAAAATCTAAACTCTATTTTTTAAAGAAAATCACTATTTTACTTAAAAATCAAA
1 TTT-TTTTAAAAAAAATCTAAACT-T-TTTTTTAATGAAAATCACTACTTTACTTAAAAATCAAA
* *
5260 GCTTTTAATTT-GAAATTGTTTAAAAAAATCAAAACTTTT
63 ACTTTT-ATTTCGAAATAG-TTAAAAAAATCAAAA-TTTT
5299 CCCAAAATCA
Statistics
Matches: 461, Mismatches: 49, Indels: 59
0.81 0.09 0.10
Matches are distributed among these distances:
132 2 0.00
133 22 0.05
134 28 0.06
135 6 0.01
136 36 0.08
137 3 0.01
138 1 0.00
139 1 0.00
144 19 0.04
145 39 0.08
146 19 0.04
147 104 0.23
148 37 0.08
149 57 0.12
150 59 0.13
151 4 0.01
152 24 0.05
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (145 bp):
TTTTTTTAAAAAAAATCTAAACTTTTTTTTAATGAAAATCACTACTTTACTTAAAAATCAAAACT
TTTATTTCGAAATAGTTAAAAAAATCAAAATTTTATTTAAAAATTTAAATTTTTTCTTTAAAATA
ACTAAAAAATAGATT
Found at i:5022 original size:20 final size:21
Alignment explanation
Indices: 4997--5043 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
4987 TTCAAAATAA
4997 TTAAAAAATTAAA-ATTTTAT
1 TTAAAAAATTAAAGATTTTAT
* *
5017 TTAAAAATTTAAAGATTTTCT
1 TTAAAAAATTAAAGATTTTAT
5038 TTAAAA
1 TTAAAA
5044 TAACTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TTAAAAAATTAAAGATTTTAT
Found at i:5024 original size:50 final size:49
Alignment explanation
Indices: 4962--5067 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 49
4952 AAATCACTAC
* * *
4962 TTTACTTAAAAATCCAAA-TTTTTATTTCAAAATAATTAAAAAATTAAAAT
1 TTTATTTAAAAATCCAAAGATTTTATTT-AAAATAACTAAAAAA-TAAAAT
** * *
5012 TTTATTTAAAAATTTAAAGATTTTCTTTAAAATAACTAAAAAATAAATT
1 TTTATTTAAAAATCCAAAGATTTTATTTAAAATAACTAAAAAATAAAAT
5061 TTTATTT
1 TTTATTT
5068 TTAAAAAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
49 12 0.25
50 29 0.60
51 7 0.15
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (49 bp):
TTTATTTAAAAATCCAAAGATTTTATTTAAAATAACTAAAAAATAAAAT
Found at i:5091 original size:23 final size:22
Alignment explanation
Indices: 5049--5092 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5039 TAAAATAACT
* *
5049 AAAAAATAAATTTTTATTTTTA
1 AAAAAATAAACTTTCATTTTTA
5071 AAAAAATAAACTTTCACTTTTT
1 AAAAAATAAACTTTCA-TTTTT
5093 TTAATGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAAAATAAACTTTCATTTTTA
Found at i:5186 original size:18 final size:19
Alignment explanation
Indices: 5147--5188 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5137 AAAATAGTTA
5147 AAAAATCAAAACTTTGTTT
1 AAAAATCAAAACTTTGTTT
*
5166 AAAAATTAAAA-TTT-TTCT
1 AAAAATCAAAACTTTGTT-T
5184 AAAAA
1 AAAAA
5189 AATAGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 9 0.43
19 10 0.48
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAAATCAAAACTTTGTTT
Found at i:5285 original size:134 final size:136
Alignment explanation
Indices: 5049--5297 Score: 346
Period size: 136 Copynumber: 1.8 Consensus size: 136
5039 TAAAATAACT
* *
5049 AAAAAATAAATTTTTATTTTTAAAAAAATAAACTTTCACTTTTTTTAATGAAAATCACTACTTTC
1 AAAAAATAAATTTTTATTTTTAAAAAAATAAACTCTCAC-TTTTTTAAAGAAAATCACTACTTTC
5114 TTAAAAATCTAAACTTTTATTTCAAAATAGTT-AAAAAATCAAAACTTTGTTTAAAAATTAAAAT
65 TTAAAAATCTAAACTTTTATTTCAAAATAGTTAAAAAAATCAAAACTTTGTTTAAAAATTAAAAT
5178 TTTTCTA
130 TTTTCTA
* ** *
5185 AAAAAATAGATTTTTATTTTTAAAAATCTAAACTCT-A-TTTTTTAAAGAAAATCACTATTTTAC
1 AAAAAATAAATTTTTATTTTTAAAAAAATAAACTCTCACTTTTTTAAAGAAAATCACTACTTT-C
* *
5248 TTAAAAATC-AAAGCTTTTAATTT-GAAATTGTTTAAAAAAATCAAAACTTT
65 TTAAAAATCTAAA-CTTTT-ATTTCAAAATAG-TTAAAAAAATCAAAACTTT
5298 TCCCAAAATC
Statistics
Matches: 100, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
133 25 0.25
134 20 0.20
135 7 0.07
136 48 0.48
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.41
Consensus pattern (136 bp):
AAAAAATAAATTTTTATTTTTAAAAAAATAAACTCTCACTTTTTTAAAGAAAATCACTACTTTCT
TAAAAATCTAAACTTTTATTTCAAAATAGTTAAAAAAATCAAAACTTTGTTTAAAAATTAAAATT
TTTCTA
Done.