Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007160.1 Kokia drynarioides strain JFW-HI SEQ_121772, 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: 8629
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:3970 original size:39 final size:39
Alignment explanation
Indices: 3908--4041 Score: 146
Period size: 39 Copynumber: 3.4 Consensus size: 39
3898 TCATCCTATT
* * * *
3908 CAATCTCTTACCCCAACCATGGGACATATTGAAGTCATC
1 CAATCTTTTACCCTAACCCTGGGACAAATTGAAGTCATC
*
3947 CAATCTTTTACCCTAACCCTGGGACAGATTGAAGTCATC
1 CAATCTTTTACCCTAACCCTGGGACAAATTGAAGTCATC
* * * *
3986 CAATCATTTACCCTAA--CTAGAGGGCAAATTAAAGACATC
1 CAATCTTTTACCCTAACCCT-G-GGACAAATTGAAGTCATC
*
4025 CAAACTTTTACCCTAAC
1 CAATCTTTTACCCTAAC
4042 TAGAGAGCAA
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
37 2 0.02
38 1 0.01
39 78 0.96
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (39 bp):
CAATCTTTTACCCTAACCCTGGGACAAATTGAAGTCATC
Found at i:4042 original size:39 final size:39
Alignment explanation
Indices: 3943--4077 Score: 141
Period size: 39 Copynumber: 3.4 Consensus size: 39
3933 ATATTGAAGT
* * * *
3943 CATCCAATCTTTTACCCTAACCCT-G-GGACAGATTGAAGT
1 CATCCAATCTTTTACCCTAA--CTAGAGGGCAAATTAAAGA
*
3982 CATCCAATCATTTACCCTAACTAGAGGGCAAATTAAAGA
1 CATCCAATCTTTTACCCTAACTAGAGGGCAAATTAAAGA
* *
4021 CATCCAAACTTTTACCCTAACTAGAGAGCAAA-TAGAAGA
1 CATCCAATCTTTTACCCTAACTAGAGGGCAAATTA-AAGA
*
4060 CCATACAATCTTTTACCC
1 -CATCCAATCTTTTACCC
4078 CTAAGTCAAG
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
37 2 0.02
38 3 0.04
39 62 0.76
40 15 0.18
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (39 bp):
CATCCAATCTTTTACCCTAACTAGAGGGCAAATTAAAGA
Found at i:4178 original size:45 final size:45
Alignment explanation
Indices: 4059--4509 Score: 573
Period size: 45 Copynumber: 10.0 Consensus size: 45
4049 CAAATAGAAG
* *
4059 ACCATACAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGTC
1 ACCATCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGCC
* * * * * *
4105 ACCATCC-ACCTTTTTCCACTAATCAAGAGAGACAGATTGAAGTC
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
*
4149 ATCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
*
4194 ACCGTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGCC
1 ACCATCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGCC
* *
4240 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGAAGATTGAAACC
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
* * *
4285 ACCATCCACTCTTTTACCTCTAATCAAGA-GGGTAGATTGAAGCC
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
* * * * * *
4329 ACCATCTAATTTTTTACCCTTAAGTTAAGAGGGGTAGGTTGAAGCC
1 ACCATCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGCC
* * * *
4375 ACCATCCAATCTTTCACCCCTAATCAAGAGTGGTAGATTGAAGCT
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
* * * *
4420 ACCATCCAATCTTTTACCCCTAACCAAAAGGGGCTGATTAAAGCC
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
* *
4465 ACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTAAAGC
1 ACCATCCAATCTTTTACCCCT-AATCAAGAGGGGCAGATTGAAGC
4510 TTCCATCTCA
Statistics
Matches: 351, Mismatches: 49, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
44 57 0.16
45 192 0.55
46 102 0.29
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (45 bp):
ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
Found at i:4968 original size:4 final size:5
Alignment explanation
Indices: 4927--4996 Score: 54
Period size: 5 Copynumber: 14.2 Consensus size: 5
4917 TAGGTGTAGT
* * * * *
4927 ACAAA ATAAA ACAAA ACCAAA ACCAA ACAAA ACTAA AC-AA ACCAA CCAAA
1 ACAAA ACAAA ACAAA A-CAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA
* *
4977 ATAAA AC-AA ATAAA ACAAA A
1 ACAAA ACAAA ACAAA ACAAA A
4997 AATATATGCA
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
4 7 0.14
5 38 0.76
6 5 0.10
ACGTcount: A:0.73, C:0.21, G:0.00, T:0.06
Consensus pattern (5 bp):
ACAAA
Found at i:4970 original size:19 final size:19
Alignment explanation
Indices: 4946--4996 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
4936 AACAAAACCA
4946 AAACCAAACAAAACT-AAAC
1 AAACCAAACAAAA-TAAAAC
*
4965 AAACCAACCAAAATAAAAC
1 AAACCAAACAAAATAAAAC
**
4984 AAATAAAACAAAA
1 AAACCAAACAAAA
4997 AATATATGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 1 0.04
19 26 0.96
ACGTcount: A:0.73, C:0.22, G:0.00, T:0.06
Consensus pattern (19 bp):
AAACCAAACAAAATAAAAC
Found at i:6544 original size:30 final size:30
Alignment explanation
Indices: 6492--6548 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
6482 CCCTCAAAAT
* **
6492 TTTTCTTTTAAATTTTGCCCTTTTATTCTG
1 TTTTCTTTTAAACTAAGCCCTTTTATTCTG
*
6522 TTTTCTTTTAAACTAAGTCCTTTTATT
1 TTTTCTTTTAAACTAAGCCCTTTTATT
6549 TTTATTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.18, C:0.16, G:0.05, T:0.61
Consensus pattern (30 bp):
TTTTCTTTTAAACTAAGCCCTTTTATTCTG
Found at i:6553 original size:6 final size:6
Alignment explanation
Indices: 6542--6585 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
6532 AACTAAGTCC
*
6542 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA- TTTTAT TTTCAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
6586 AAATTTAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:6565 original size:18 final size:17
Alignment explanation
Indices: 6542--6585 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
6532 AACTAAGTCC
6542 TTTTATTTTTATTTTTAT
1 TTTTATTTTTA-TTTTAT
6560 TTTTATTTTTATTTTAT
1 TTTTATTTTTATTTTAT
*
6577 TTTCATTTT
1 TTTTATTTT
6586 AAATTTAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTATTTTTATTTTAT
Done.