Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007159.1 Kokia drynarioides strain JFW-HI SEQ_121771, 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: 8617
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:3960 original size:39 final size:38
Alignment explanation
Indices: 3906--4078 Score: 157
Period size: 39 Copynumber: 4.4 Consensus size: 38
3896 ACATCATCCT
* * *
3906 ATCCAATCTCTTACCCCAACCATGGGACATATTGAAGTC
1 ATCCAATCTTTTACCCTAACCA-GGGACAAATTGAAGTC
* *
3945 ATCCAATCTTTTACCCTAACCCTGGGACAGATTGAAGTC
1 ATCCAATCTTTTACCCTAA-CCAGGGACAAATTGAAGTC
** * * * *
3984 ATCCAATCACTTACCCTAACTAGAGGGCAAATTAAAGAC
1 ATCCAATCTTTTACCCTAACCAG-GGACAAATTGAAGTC
* * * *
4023 ATCCAAACTTTTACCCTAACCAGAGAGCAAATAGAAGACC
1 ATCCAATCTTTTACCCTAACCAGGGA-CAAATTGAAG-TC
*
4063 ATACAATCTTTTACCC
1 ATCCAATCTTTTACCC
4079 CTAAGTCAAG
Statistics
Matches: 107, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
38 3 0.03
39 87 0.81
40 17 0.16
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.24
Consensus pattern (38 bp):
ATCCAATCTTTTACCCTAACCAGGGACAAATTGAAGTC
Found at i:4179 original size:45 final size:45
Alignment explanation
Indices: 4060--4517 Score: 587
Period size: 45 Copynumber: 10.1 Consensus size: 45
4050 CAAATAGAAG
* *
4060 ACCATACAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGTC
1 ACCATCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGCC
* * * * * *
4106 ACCATCC-ACCTTTTTCCACTAATCAAGAGAGACAGATTGAAGTC
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
*
4150 ATCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
*
4195 ACCGTCCAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGCC
1 ACCATCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGCC
* *
4241 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGAAGATTGAAACC
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
* * *
4286 ACCATCCACTCTTTTACCTCTAATCAAGA-GGGTAGATTGAAGCC
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
* * * * * *
4330 ACCATCTAATTTTTTACCCTTAAGTTAAGAGGGGTAGGTTGAAGCC
1 ACCATCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGCC
* * *
4376 ACCATCCAATCTTTCACCCCTAATCAAGAGTGGTAGATTGAAGCC
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
* * * *
4421 ACCATCCAATCTTTTACCCCTAACCAAAAGGGGCTGATTAAAGCC
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
* * *
4466 ACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTAAAGCT
1 ACCATCCAATCTTTTACCCCT-AATCAAGAGGGGCAGATTGAAGCC
4512 ACCATC
1 ACCATC
4518 TCACAGAAGT
Statistics
Matches: 359, Mismatches: 48, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
44 57 0.16
45 194 0.54
46 108 0.30
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (45 bp):
ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCC
Found at i:4247 original size:91 final size:90
Alignment explanation
Indices: 4060--4517 Score: 587
Period size: 91 Copynumber: 5.1 Consensus size: 90
4050 CAAATAGAAG
* * * * *
4060 ACCATACAATCTTTTACCCCTAAGTCAAGAGGGGCAGATTGAAGTCACCATCC-ACCTTTTTCCA
1 ACCATCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCC
* * *
4124 CTAATCAAGAGAGACAGATTGAAGTC
65 CTAATCAAGAGGGGCAGATTGAAGCC
* *
4150 ATCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCGTCCAATCTTTTACCCC
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCC
4215 TAAGTCAAGAGGGGCAGATTGAAGCC
66 TAA-TCAAGAGGGGCAGATTGAAGCC
* * * *
4241 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGAAGATTGAAACCACCATCCACTCTTTTACCTC
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCC
*
4306 TAATCAAGA-GGGTAGATTGAAGCC
66 TAATCAAGAGGGGCAGATTGAAGCC
* * * * * * *
4330 ACCATCTAATTTTTTACCCTTAAGTTAAGAGGGGTAGGTTGAAGCCACCATCCAATCTTTCACCC
1 ACCATCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCC
* *
4395 CTAATCAAGAGTGGTAGATTGAAGCC
65 CTAATCAAGAGGGGCAGATTGAAGCC
* * * *
4421 ACCATCCAATCTTTTACCCCTAACCAAAAGGGGCTGATTAAAGCCACCATCCAATCTTTTACCCC
1 ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCC
* * *
4486 TAAATCCAGAGGGGCAGATTAAAGCT
66 T-AATCAAGAGGGGCAGATTGAAGCC
4512 ACCATC
1 ACCATC
4518 TCACAGAAGT
Statistics
Matches: 319, Mismatches: 44, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
89 61 0.19
90 118 0.37
91 140 0.44
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (90 bp):
ACCATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCC
TAATCAAGAGGGGCAGATTGAAGCC
Found at i:4969 original size:4 final size:5
Alignment explanation
Indices: 4928--4997 Score: 54
Period size: 5 Copynumber: 14.2 Consensus size: 5
4918 TAGGTGTAGT
* * * * *
4928 ACAAA ATAAA ACAAA ACCAAA ACCAA ACAAA ACTAA AC-AA ACCAA CCAAA
1 ACAAA ACAAA ACAAA A-CAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA
* *
4978 ATAAA AC-AA ATAAA ACAAA A
1 ACAAA ACAAA ACAAA ACAAA A
4998 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:4971 original size:19 final size:19
Alignment explanation
Indices: 4947--4997 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
4937 AACAAAACCA
4947 AAACCAAACAAAACT-AAAC
1 AAACCAAACAAAA-TAAAAC
*
4966 AAACCAACCAAAATAAAAC
1 AAACCAAACAAAATAAAAC
**
4985 AAATAAAACAAAA
1 AAACCAAACAAAA
4998 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:6545 original size:30 final size:30
Alignment explanation
Indices: 6493--6549 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
6483 CCCTCAAAAT
* **
6493 TTTTCTTTTAAATTTTGCCCTTTTATTCTG
1 TTTTCTTTTAAACTAAGCCCTTTTATTCTG
*
6523 TTTTCTTTTAAACTAAGTCCTTTTATT
1 TTTTCTTTTAAACTAAGCCCTTTTATT
6550 TTATTTTTAT
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:6559 original size:11 final size:11
Alignment explanation
Indices: 6543--6574 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
6533 AACTAAGTCC
6543 TTTTATTTTAT
1 TTTTATTTTAT
6554 TTTTATTTTAT
1 TTTTATTTTAT
*
6565 TTTCATTTTA
1 TTTTATTTTA
6575 AATTTAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:6559 original size:41 final size:42
Alignment explanation
Indices: 6513--6607 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
6503 AATTTTGCCC
*
6513 TTTTATTCTGTTTTC-TTTTAAA-CTAAGTCCTTTTATTTTAT
1 TTTTATTCTATTTTCATTTTAAATCTAA-TCCTTTTATTTTAT
* * *
6554 TTTTATTTTATTTTCATTTTAAATTTAATCCTTTTATTTTGT
1 TTTTATTCTATTTTCATTTTAAATCTAATCCTTTTATTTTAT
*
6596 TGTTA-TCTATTT
1 TTTTATTCTATTT
6608 AATCCTTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 19 0.41
42 24 0.52
43 3 0.07
ACGTcount: A:0.20, C:0.09, G:0.04, T:0.66
Consensus pattern (42 bp):
TTTTATTCTATTTTCATTTTAAATCTAATCCTTTTATTTTAT
Done.