Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001715.1 Kokia drynarioides strain JFW-HI SEQ_113412, 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: 74714
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 36 characters in sequence are not A, C, G, or T
Found at i:2372 original size:22 final size:23
Alignment explanation
Indices: 2330--2373 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
2320 GAAAAAAATC
*
2330 ATTTATTTAAATTTTCGTTATTA
1 ATTTATTTAAATTTTCATTATTA
2353 ATTT-TTTAAATTTAT-ATTATT
1 ATTTATTTAAATTT-TCATTATT
2374 TATTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTTATTTAAATTTTCATTATTA
Found at i:12086 original size:2 final size:2
Alignment explanation
Indices: 12079--12112 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12069 ATAAAATAAG
12079 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12113 TTGTTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14214 original size:2 final size:2
Alignment explanation
Indices: 14207--14232 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14197 ATTAAATTTA
14207 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
14233 TTCCTGTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:15500 original size:6 final size:6
Alignment explanation
Indices: 15489--15528 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
15479 CAGTGAGGCC
* *
15489 GAAGTG GAAGTG GAAGTG GAAGTG GAAATG GAAATG GAAG
1 GAAGTG GAAGTG GAAGTG GAAGTG GAAGTG GAAGTG GAAG
15529 AGGCCAGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.45, T:0.15
Consensus pattern (6 bp):
GAAGTG
Found at i:27310 original size:176 final size:173
Alignment explanation
Indices: 26984--27313 Score: 475
Period size: 176 Copynumber: 1.9 Consensus size: 173
26974 CATCTTCCCC
* *
26984 TACCATCGCTCCTCTTCTCTCCCTCGTCTCTGCAAATCAGTTTTTTTTCTTCTCATCTCAGTTCT
1 TACCATCGCCCCTCTTCTCTCCCTCGTCTCTACAAATCAGTTTTTTTTCTTCTCATCTCAGTTCT
* * * * *
27049 TGCCCACCGCCGTCTCCACTGATTTTTTCCGGATCTGACCCGTATTCCGTTTCGGATCGTGTTGA
66 CGCCCACCGACG-CTCCACTGATTTTTGCCGGATCTGACCCGTATCCCGTTTCGGATCGTGTCGA
*
27114 CACAGGTACTGCACCCCAAATTGCCGAGTCAGGGTAAGGAAGCT
130 CACAAGTACTGCACCCCAAATTGCCGAGTCAGGGTAAGGAAGCT
*
27158 TACCATCGCCCCTCTTCTCTCTCTCGTCTCTACAAATCAGGTTTTTTCATTCTCTTCTCATCTCA
1 TACCATCGCCCCTCTTCTCTCCCTCGTCTCTACAAATCA-G-TTTTT--TT-TCTTCTCATCTCA
* * *
27223 GTTCTCGCCCACC-AC-CTCCGCTGGTTTTTGCCGGATCTGATCCGTATCCCGTTTCGGATCGTG
61 GTTCTCGCCCACCGACGCTCCACTGATTTTTGCCGGATCTGACCCGTATCCCGTTTCGGATCGTG
*
27286 TCGACACAAGTACTGCATCCCAAATTGC
126 TCGACACAAGTACTGCACCCCAAATTGC
27314 TCCGGGTCCG
Statistics
Matches: 138, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
174 36 0.26
175 1 0.01
176 73 0.53
178 3 0.02
179 25 0.18
ACGTcount: A:0.16, C:0.34, G:0.16, T:0.34
Consensus pattern (173 bp):
TACCATCGCCCCTCTTCTCTCCCTCGTCTCTACAAATCAGTTTTTTTTCTTCTCATCTCAGTTCT
CGCCCACCGACGCTCCACTGATTTTTGCCGGATCTGACCCGTATCCCGTTTCGGATCGTGTCGAC
ACAAGTACTGCACCCCAAATTGCCGAGTCAGGGTAAGGAAGCT
Found at i:38146 original size:22 final size:23
Alignment explanation
Indices: 38103--38148 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
38093 ACTTGAAGAG
*
38103 ATAAATAATTTTATCTTATATAA
1 ATAAATAATTTTATCTAATATAA
38126 ATAAA-AATTTTAT-TAATTATAA
1 ATAAATAATTTTATCTAA-TATAA
38148 A
1 A
38149 GTAGTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 14 0.67
23 5 0.24
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
ATAAATAATTTTATCTAATATAA
Found at i:39826 original size:23 final size:23
Alignment explanation
Indices: 39795--39849 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
39785 GATCACCCAA
*
39795 AACCCAAAATCTCCAAATTCAAC
1 AACCTAAAATCTCCAAATTCAAC
*
39818 AACCTAAAATCTCCAAATTCAAT
1 AACCTAAAATCTCCAAATTCAAC
39841 AACCATAAA
1 AACC-TAAA
39850 CAATTCATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 25 0.86
24 4 0.14
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (23 bp):
AACCTAAAATCTCCAAATTCAAC
Found at i:40331 original size:18 final size:18
Alignment explanation
Indices: 40284--40333 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
40274 AATTAGGGTG
*
40284 TTTTAAAGATTTTTTTTAA
1 TTTTAAA-ATATTTTTTAA
*
40303 TTTT-AATTATTTTTTAA
1 TTTTAAAATATTTTTTAA
40320 TTTTAAAATATTTT
1 TTTTAAAATATTTT
40334 GTCGACGTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 13 0.48
18 10 0.37
19 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTAAAATATTTTTTAA
Found at i:52781 original size:67 final size:64
Alignment explanation
Indices: 52710--52850 Score: 176
Period size: 67 Copynumber: 2.1 Consensus size: 64
52700 TATTATTCTT
*
52710 ATAAATA-TAAAATAATATTAATTTTATTTTATTATTTATTTTTTTATTATTGTATGAATATAAA
1 ATAAATAGTAAAATAATACTAATTTTATTTTATTATTTA----TTTATTATTGTATGAATATAAA
52774 TAA
62 TAA
* * *
52777 ATAAATAAATGTAAAATGATACTAATTTTGTTTTATTATTTATTTATTATTTTATGAATATAAAT
1 ATAAAT--A-GTAAAATAATACTAATTTTATTTTATTATTTATTTATTATTGTATGAATATAAAT
52842 AA
63 AA
52844 ATAAATA
1 ATAAATA
52851 ACAAACCAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
65 1 0.02
67 36 0.55
69 1 0.02
71 28 0.42
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (64 bp):
ATAAATAGTAAAATAATACTAATTTTATTTTATTATTTATTTATTATTGTATGAATATAAATAA
Found at i:52803 original size:71 final size:67
Alignment explanation
Indices: 52710--52851 Score: 203
Period size: 71 Copynumber: 2.1 Consensus size: 67
52700 TATTATTCTT
*
52710 ATAAATATAAAATAATATTAATTTTATTTTATTATTTATTTTTTTATTATTGTATGAATATAAAT
1 ATAAATATAAAATAATACTAATTTTATTTTATTATTTA----TTTATTATTGTATGAATATAAAT
52775 AAATAA
62 AAATAA
* * * *
52781 ATAAATGTAAAATGATACTAATTTTGTTTTATTATTTATTTATTATTTTATGAATATAAATAAAT
1 ATAAATATAAAATAATACTAATTTTATTTTATTATTTATTTATTATTGTATGAATATAAATAAAT
52846 AA
66 AA
52848 ATAA
1 ATAA
52852 CAAACCAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
67 32 0.48
71 34 0.52
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (67 bp):
ATAAATATAAAATAATACTAATTTTATTTTATTATTTATTTATTATTGTATGAATATAAATAAAT
AA
Found at i:72147 original size:28 final size:28
Alignment explanation
Indices: 72095--72166 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
72085 TTTTTTATAT
*
72095 TTTTATAATTTTTAAAAAGTTAAAT-TAAA
1 TTTTAT-ATTTTTAAAAAGTAAAATGT-AA
**
72124 TTTTATATTTTTAAAGGGTAAAATGTAA
1 TTTTATATTTTTAAAAAGTAAAATGTAA
*
72152 TTTTATCTTTATTAA
1 TTTTATATTT-TTAA
72167 TTTAAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 26 0.70
29 11 0.30
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.51
Consensus pattern (28 bp):
TTTTATATTTTTAAAAAGTAAAATGTAA
Found at i:72870 original size:16 final size:17
Alignment explanation
Indices: 72840--72881 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
72830 ACAAAGGCTG
72840 ATAAAAACTAAAAAAAA
1 ATAAAAACTAAAAAAAA
*
72857 ATAAAAA-TATAAAAAA
1 ATAAAAACTAAAAAAAA
72873 ATAAAAACT
1 ATAAAAACT
72882 GAATATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (17 bp):
ATAAAAACTAAAAAAAA
Found at i:73286 original size:24 final size:23
Alignment explanation
Indices: 73232--73297 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 23
73222 CAAAAAATAA
*
73232 AAATAATAAC-TATTTTCTAAAAAT
1 AAATAA-AACATATTTT-TAAAAAC
73256 AAA-AAAACATATTTTTAGAAAAC
1 AAATAAAACATATTTTTA-AAAAC
73279 AAATAAAACCATTATTTTT
1 AAATAAAA-CA-TATTTTT
73298 CCTTGAAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 5 0.14
23 15 0.42
24 7 0.19
25 2 0.06
26 7 0.19
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.35
Consensus pattern (23 bp):
AAATAAAACATATTTTTAAAAAC
Done.