Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005405.1 Kokia drynarioides strain JFW-HI SEQ_119414, 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: 19361
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Found at i:8400 original size:55 final size:55
Alignment explanation
Indices: 8274--8405 Score: 183
Period size: 55 Copynumber: 2.4 Consensus size: 55
8264 TGTGTAAAAG
* * *
8274 TATTTCAACATGACAATTGATTTAAATATATAAACAATCGATTCAAAAGAAGCAG
1 TATTTCAACATGACAATTGATTTAAACATAAAAACAATCGATTCAAAAGAAGCAA
* * *
8329 TATTCCAATATGACAATTGATTTAAACATAAAAACAATCGATTCAAAAGAAGTAA
1 TATTTCAACATGACAATTGATTTAAACATAAAAACAATCGATTCAAAAGAAGCAA
* * *
8384 TATTTCAGCATAACAATCGATT
1 TATTTCAACATGACAATTGATT
8406 CAATCCAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.30
Consensus pattern (55 bp):
TATTTCAACATGACAATTGATTTAAACATAAAAACAATCGATTCAAAAGAAGCAA
Found at i:9222 original size:20 final size:19
Alignment explanation
Indices: 9174--9226 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
9164 ATTTTTGTTA
* *
9174 AATAATAATTTAATATTTT
1 AATAAAAATATAATATTTT
*
9193 AATTAAAATAATAATATTTT
1 AATAAAAAT-ATAATATTTT
9213 -ATAAACAATATAAT
1 AATAAA-AATATAAT
9227 TATATATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AATAAAAATATAATATTTT
Found at i:9795 original size:16 final size:16
Alignment explanation
Indices: 9771--9856 Score: 72
Period size: 15 Copynumber: 5.4 Consensus size: 16
9761 AGGAAAGAAT
9771 ATAAATAACATAAAAA
1 ATAAATAACATAAAAA
* *
9787 ATGAATAACA-AATAA
1 ATAAATAACATAAAAA
9802 ATAAATAA-ATAAATAA
1 ATAAATAACATAAA-AA
*
9818 AT-ACTAA-ATAAAATTA
1 ATAAATAACATAAAA--A
*
9834 TATAAATAATATAAAAA
1 -ATAAATAACATAAAAA
9851 ATAAAT
1 ATAAAT
9857 GGTACCAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
14 2 0.04
15 22 0.39
16 20 0.35
17 3 0.05
18 4 0.07
19 6 0.11
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (16 bp):
ATAAATAACATAAAAA
Found at i:9799 original size:11 final size:11
Alignment explanation
Indices: 9773--9856 Score: 66
Period size: 11 Copynumber: 7.7 Consensus size: 11
9763 GAAAGAATAT
9773 AAATAACATAAA
1 AAATAA-ATAAA
* *
9785 AAATGAATAAC
1 AAATAAATAAA
9796 AAATAAATAAA
1 AAATAAATAAA
9807 TAAATAAATAAA
1 -AAATAAATAAA
* *
9819 TACTAAAT-AA
1 AAATAAATAAA
* *
9829 AATTATATAAA
1 AAATAAATAAA
*
9840 TAAT--ATAAA
1 AAATAAATAAA
9849 AAATAAAT
1 AAATAAAT
9857 GGTACCAAAT
Statistics
Matches: 56, Mismatches: 12, Indels: 9
0.73 0.16 0.12
Matches are distributed among these distances:
9 8 0.14
10 7 0.12
11 25 0.45
12 16 0.29
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:9799 original size:23 final size:23
Alignment explanation
Indices: 9773--9817 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
9763 GAAAGAATAT
*
9773 AAATAACATAAA-AAATGAATAAC
1 AAATAA-ATAAATAAATAAATAAC
9796 AAATAAATAAATAAATAAATAA
1 AAATAAATAAATAAATAAATAA
9818 ATACTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (23 bp):
AAATAAATAAATAAATAAATAAC
Found at i:9874 original size:4 final size:4
Alignment explanation
Indices: 9705--9856 Score: 93
Period size: 4 Copynumber: 37.5 Consensus size: 4
9695 TATAACTGGC
* * *
9705 ATAA A-AA ACAA ACAA ATAAA ATAA ATAA A-AA A-CA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * * *
9751 GATTAA ATAA AGGAA AGAA TATAA ATAA CATAA A-AA ATGA AT-A ACAA
1 -A-TAA ATAA A-TAA ATAA -ATAA ATAA -ATAA ATAA ATAA ATAA ATAA
* *
9798 ATAA ATAA ATAA ATAA ATAA AT-A CTAA ATAAA ATTAT ATAA ATAA TATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA A-TAA ATAA ATAA -ATAA
9848 A-AA ATAA AT
1 ATAA ATAA AT
9857 GGTACCAAAT
Statistics
Matches: 121, Mismatches: 12, Indels: 30
0.74 0.07 0.18
Matches are distributed among these distances:
3 18 0.15
4 74 0.61
5 25 0.21
6 4 0.03
ACGTcount: A:0.71, C:0.04, G:0.03, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:10023 original size:6 final size:5
Alignment explanation
Indices: 9983--10021 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
9973 TTAGAAACAG
* *
9983 AAATA AAATA AAATA AAACTA AATTC AAATA AAATA AAA
1 AAATA AAATA AAATA AAA-TA AAATA AAATA AAATA AAA
10022 ATTATAGGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:17682 original size:26 final size:26
Alignment explanation
Indices: 17652--17709 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
17642 TTTGATAATT
*
17652 AATTGTTTAATTAAGGAAAATGAGTA
1 AATTGTTTAATTAAGGAAAATAAGTA
17678 AATTGTTTAATTAAGGAAAATAAGTA
1 AATTGTTTAATTAAGGAAAATAAGTA
17704 AATTGT
1 AATTGT
17710 AAAAAAAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.36
Consensus pattern (26 bp):
AATTGTTTAATTAAGGAAAATAAGTA
Done.