Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012443.1 Kokia drynarioides strain JFW-HI SEQ_127447, 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: 59024
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:25359 original size:28 final size:28
Alignment explanation
Indices: 25323--25377 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
25313 AAATTTCACA
*
25323 TAGTATTATAATGAATTTCATATTTTCG
1 TAGTATTATAATAAATTTCATATTTTCG
*
25351 TAGTGTTATAATAAATTTCATATTTTC
1 TAGTATTATAATAAATTTCATATTTTC
25378 ATATACTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (28 bp):
TAGTATTATAATAAATTTCATATTTTCG
Found at i:30659 original size:28 final size:29
Alignment explanation
Indices: 30628--30693 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
30618 TTTCTTAAAT
**
30628 TTTAATCTTTTATTTCATTTT-CTATTTA
1 TTTAATCTTTTAAATCATTTTACTATTTA
* *
30656 TTTAATCCTTTAAATCATTTTATTATTTA
1 TTTAATCTTTTAAATCATTTTACTATTTA
30685 TTTAATCTT
1 TTTAATCTT
30694 GGTATTTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTAATCTTTTAAATCATTTTACTATTTA
Found at i:32457 original size:22 final size:22
Alignment explanation
Indices: 32432--32474 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
32422 AAAATATTTC
*
32432 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
32454 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
32475 TTGTTCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:35030 original size:20 final size:20
Alignment explanation
Indices: 34956--35031 Score: 53
Period size: 21 Copynumber: 3.7 Consensus size: 20
34946 TCATTTCTTT
* **
34956 TGTTTAGCAATTCTTTATTAA
1 TGTTT-GCAATTTTTTACCAA
*
34977 TGTTTGCTATTTTTTACCAA
1 TGTTTGCAATTTTTTACCAA
** * **
34997 CATTCTCCTTTTTTTTACCAA
1 TGTT-TGCAATTTTTTACCAA
35018 TGTTTGCAATTTTT
1 TGTTTGCAATTTTT
35032 GGCCTTTTTT
Statistics
Matches: 41, Mismatches: 13, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
20 20 0.49
21 21 0.51
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.55
Consensus pattern (20 bp):
TGTTTGCAATTTTTTACCAA
Found at i:44140 original size:17 final size:17
Alignment explanation
Indices: 44120--44153 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44110 AAATGATGAG
44120 ATGAAAAAAAAAATGCA
1 ATGAAAAAAAAAATGCA
* *
44137 ATGATAATAAAAATGCA
1 ATGAAAAAAAAAATGCA
44154 TTAAAACTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (17 bp):
ATGAAAAAAAAAATGCA
Found at i:58926 original size:23 final size:23
Alignment explanation
Indices: 58852--59024 Score: 188
Period size: 23 Copynumber: 7.5 Consensus size: 23
58842 TAAACGAAAC
* * *
58852 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
58874 AAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
58896 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
58922 AAACAGAGAGTACACAAAATGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
58945 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
58968 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
58991 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
59014 AATCAGAGAGC
1 AAACAGAGAGC
Statistics
Matches: 128, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
22 18 0.14
23 90 0.70
25 13 0.10
26 7 0.05
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Done.