Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011997.1 Kokia drynarioides strain JFW-HI SEQ_126995, 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: 23986
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.28
Warning! 4240 characters in sequence are not A, C, G, or T
Found at i:949 original size:22 final size:22
Alignment explanation
Indices: 923--975 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
913 ACTTTAGAAG
* *
923 AGATTCAAGTACCTGAAACT-AA
1 AGATTCAAATA-CTGAAAATAAA
*
945 AGATTAAAATACTGAAAATAAA
1 AGATTCAAATACTGAAAATAAA
967 AGATCTCAA
1 AGAT-TCAA
976 TAAGTTATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 7 0.28
22 15 0.60
23 3 0.12
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.23
Consensus pattern (22 bp):
AGATTCAAATACTGAAAATAAA
Found at i:7137 original size:41 final size:41
Alignment explanation
Indices: 7075--7374 Score: 397
Period size: 41 Copynumber: 7.3 Consensus size: 41
7065 ACTTGACGTA
*
7075 TAAATGGAAGACTCTTGTCTCGAGATGAGCATGAGATTATAT
1 TAAA-GGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
*
7117 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGATATTATAT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
* * * *
7158 TAAAGGAAGACTCGTGACACGAAATGAGCATGAAATTATAT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
* * * *
7199 TGAAGG-GGACTCGTGACTCGAAATGAGCATGAGATTATAT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
* *
7239 TAAAGGAAGACTCGTGTCTCGTGGTGAGCATGAGATTATAT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
* * * *
7280 TAAAGGAATACTCATGTCTC-AGGGTAAGCATGAGATTATAT
1 TAAAGGAAGACTCGTGTCTCGA-GATGAGCATGAGATTATAT
* *
7321 TAAAGGAAGACTCGTGACTCGGGATGAGCATGAGATTATATT
1 TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATA-T
7363 TAAAGGAAGACT
1 TAAAGGAAGACT
7375 TATGACTCGG
Statistics
Matches: 228, Mismatches: 26, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
40 36 0.16
41 175 0.77
42 17 0.07
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (41 bp):
TAAAGGAAGACTCGTGTCTCGAGATGAGCATGAGATTATAT
Found at i:7310 original size:122 final size:123
Alignment explanation
Indices: 7075--7374 Score: 406
Period size: 122 Copynumber: 2.4 Consensus size: 123
7065 ACTTGACGTA
* *
7075 TAAATGGAAGACTCTTGTCTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCGTGTCTCGAG
1 TAAA-GGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCGTGTCTCGAG
* * *
7140 ATGAGCATGATATTATATTAAAGGAAGACTCGTGACACGAAATGAGCATGAAATTATAT
65 ATGAGCATGAGATTATATTAAAGGAAGACTCATGACACGAAATAAGCATGAAATTATAT
* * * * *
7199 TGAAGG-GGACTCGTGACTCGAAATGAGCATGAGATTATATTAAAGGAAGACTCGTGTCTCGTGG
1 TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCGTGTCTCGAGA
* * * ** *
7263 TGAGCATGAGATTATATTAAAGGAATACTCATGTCTC-AGGGTAAGCATGAGATTATAT
66 TGAGCATGAGATTATATTAAAGGAAGACTCATGACACGA-AATAAGCATGAAATTATAT
*
7321 TAAAGGAAGACTCGTGACTCGGGATGAGCATGAGATTATATTTAAAGGAAGACT
1 TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATA-TTAAAGGAAGACT
7375 TATGACTCGG
Statistics
Matches: 153, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
121 1 0.01
122 104 0.68
123 32 0.21
124 16 0.10
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (123 bp):
TAAAGGAAGACTCGTGACTCGAGATGAGCATGAGATTATATTAAAGGAAGACTCGTGTCTCGAGA
TGAGCATGAGATTATATTAAAGGAAGACTCATGACACGAAATAAGCATGAAATTATAT
Found at i:9220 original size:18 final size:18
Alignment explanation
Indices: 9197--9231 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
9187 CATTTTATAA
9197 AAAGGACTAAATTGTGTT
1 AAAGGACTAAATTGTGTT
9215 AAAGGACTAAATTGTGT
1 AAAGGACTAAATTGTGT
9232 GATTTAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (18 bp):
AAAGGACTAAATTGTGTT
Found at i:9556 original size:52 final size:52
Alignment explanation
Indices: 9468--9713 Score: 235
Period size: 52 Copynumber: 4.6 Consensus size: 52
9458 AAATGGTAAA
* *
9468 AGGTTCGATGACTATGTGTCATCGTGAGTATCTGAATTCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTATG
* * * * ** *
9520 AGGTTCGATGACTATGTGTCATCATGAATATATGAATCCTTTACAAAATATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTATG
* * * * **
9572 AGGTCCGATGACTATGTGTCATCGTGAGTATAT-AAATCCTAATGGATTAAA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTATG
*
9623 AGGTCCGATGACTATGTGTCATCGTGAGTATTAAATGAAATGAATCTCATTACGGATTA-A
1 AGGTCCGATGACTATGTGTCATCGTGAGTA-T--ATG-AAT---TCT--TTACGGATTATG
* *
9683 AGGTCCGATGACTTTGTGTCATTGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
9714 CGAATGCAAA
Statistics
Matches: 158, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
51 38 0.24
52 76 0.48
54 2 0.01
56 2 0.01
59 3 0.02
60 29 0.18
61 8 0.05
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATTCTTTACGGATTATG
Found at i:14839 original size:25 final size:25
Alignment explanation
Indices: 14794--14846 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
14784 TTTAATTAGT
*
14794 AAATATATTTATTTTTAAAATTTATA
1 AAATATATTTATTTATAAAATTT-TA
14820 AAATATA-TTATTTA-ATAAATTTTA
1 AAATATATTTATTTATA-AAATTTTA
14844 AAA
1 AAA
14847 AATAAACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 6 0.24
25 12 0.48
26 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAATATATTTATTTATAAAATTTTA
Found at i:14847 original size:25 final size:26
Alignment explanation
Indices: 14794--14850 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
14784 TTTAATTAGT
*
14794 AAATATATTTATTTTTAAAATTTATA
1 AAATATATTTATTTATAAAATTTATA
* *
14820 AAATATA-TTATTTAATAAATTTTAAA
1 AAATATATTTATTT-ATAAAATTTATA
14846 AAATA
1 AAATA
14851 AACATATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AAATATATTTATTTATAAAATTTATA
Found at i:15482 original size:19 final size:19
Alignment explanation
Indices: 15460--15504 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
15450 TTTTATTAGG
15460 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
15479 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
15498 ATTTAAT
1 ATTTAAT
15505 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Done.