Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011430.1 Kokia drynarioides strain JFW-HI SEQ_126414, 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: 57258
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Warning! 49 characters in sequence are not A, C, G, or T
Found at i:451 original size:27 final size:27
Alignment explanation
Indices: 421--475 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
411 AAAAAGAGAA
421 GGGATGATTTCCTTACCCTCAACATAT
1 GGGATGATTTCCTTACCCTCAACATAT
448 GGGATGATTTCCTTACCCTCAACATAT
1 GGGATGATTTCCTTACCCTCAACATAT
475 G
1 G
476 CCTTAACTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (27 bp):
GGGATGATTTCCTTACCCTCAACATAT
Found at i:15095 original size:3 final size:3
Alignment explanation
Indices: 15089--15114 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
15079 AAAAAAAAAA
15089 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
15115 ACCTCCCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17477 original size:18 final size:18
Alignment explanation
Indices: 17454--17492 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
17444 AGGAAAAAAT
17454 AAAGAAAAAGAAAGAAAG
1 AAAGAAAAAGAAAGAAAG
* * *
17472 AAAGAAGAAGGAAGAAGG
1 AAAGAAAAAGAAAGAAAG
17490 AAA
1 AAA
17493 AGGAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAGAAAGAAAG
Found at i:17657 original size:12 final size:12
Alignment explanation
Indices: 17640--17664 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17630 TTAAATATGG
17640 TTAATTTTAAAA
1 TTAATTTTAAAA
17652 TTAATTTTAAAA
1 TTAATTTTAAAA
17664 T
1 T
17665 ATTTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATTTTAAAA
Found at i:17861 original size:20 final size:21
Alignment explanation
Indices: 17822--17864 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
17812 TAATTTACTT
*
17822 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTGGTTAGTTAG
*
17843 TAATTTTATTTGGTT-GTTAG
1 TAATTTAATTTGGTTAGTTAG
17863 TA
1 TA
17865 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (21 bp):
TAATTTAATTTGGTTAGTTAG
Found at i:20253 original size:45 final size:45
Alignment explanation
Indices: 20130--20266 Score: 166
Period size: 45 Copynumber: 3.0 Consensus size: 45
20120 GCATAGCTCA
* * *
20130 TCAAGCCAAGGATATCAGCCTCAATTTCACGAGTCACCGCAATAC
1 TCAAGCGAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
* *
20175 TCAAGCTAAGGATATCAGCCTCAATTTGGCGAGCCACCGCAATAC
1 TCAAGCGAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
* ** * * * *
20220 TCAAGGGAAGGATATCAGGTTGAGTTTGACGAGCCACTGCGATAC
1 TCAAGCGAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
20265 TC
1 TC
20267 TATTCCTCCC
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (45 bp):
TCAAGCGAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
Found at i:20555 original size:21 final size:19
Alignment explanation
Indices: 20509--20577 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 19
20499 TTTCATAACA
*
20509 TTAAACCCTAAAACTTAAAT
1 TTAAACCCT-AAACTTAAAC
20529 TATAAACCCTAAACTTGAAACC
1 T-TAAACCCTAAACTT-AAA-C
* *
20551 TTAAACCATAAACATTAGAC
1 TTAAACCCTAAAC-TTAAAC
20571 TTCAAAC
1 TT-AAAC
20578 TCTATACCGT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
20 10 0.24
21 28 0.68
22 3 0.07
ACGTcount: A:0.48, C:0.23, G:0.03, T:0.26
Consensus pattern (19 bp):
TTAAACCCTAAACTTAAAC
Found at i:27611 original size:76 final size:76
Alignment explanation
Indices: 27482--27633 Score: 243
Period size: 76 Copynumber: 2.0 Consensus size: 76
27472 TCTCAATAAA
* * * *
27482 ATTAACCTTTAATGACTAAATTGACAAATTGGCTAATGAAAGTACTTAGTTTAC-AATATTGCTA
1 ATTAACATTTAATGACTAAACTGACAAATTGACTAATGAAAGTACTTAATTTACGAA-ATTGCTA
27546 TATTGAGAACTC
65 TATTGAGAACTC
27558 ATTAACATTTAATGACTAAACTGACAAATTGACTAATGAAAGTACTTAATTTACGAAATTGCTAT
1 ATTAACATTTAATGACTAAACTGACAAATTGACTAATGAAAGTACTTAATTTACGAAATTGCTAT
*
27623 CTTGAGAACTC
66 ATTGAGAACTC
27634 GATAAAACGT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
76 68 0.97
77 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (76 bp):
ATTAACATTTAATGACTAAACTGACAAATTGACTAATGAAAGTACTTAATTTACGAAATTGCTAT
ATTGAGAACTC
Found at i:31358 original size:5 final size:6
Alignment explanation
Indices: 31341--31368 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
31331 GTGAAACCTT
31341 GTGGGG GTGGGG GTGGGG GTGGGG GTGG
1 GTGGGG GTGGGG GTGGGG GTGGGG GTGG
31369 TGGATGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.82, T:0.18
Consensus pattern (6 bp):
GTGGGG
Found at i:33083 original size:18 final size:17
Alignment explanation
Indices: 33056--33090 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
33046 GTTTTCAAAC
*
33056 ATAAACAATAAAATAAAT
1 ATAAAAAATAAAA-AAAT
33074 ATAAAAAATAAAAAAAT
1 ATAAAAAATAAAAAAAT
33091 TATCTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (17 bp):
ATAAAAAATAAAAAAAT
Found at i:36143 original size:10 final size:10
Alignment explanation
Indices: 36128--36152 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
36118 ACAAAGCAAA
36128 AAAAAAAACT
1 AAAAAAAACT
36138 AAAAAAAACT
1 AAAAAAAACT
36148 AAAAA
1 AAAAA
36153 CAAAAAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAAACT
Found at i:54117 original size:19 final size:19
Alignment explanation
Indices: 54089--54133 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
54079 CTTCGAATGC
*
54089 TCACACGGTCTGGGCTATT
1 TCACACGGTCTGGGCTATG
* *
54108 TCACATGGTCTTGGCTATG
1 TCACACGGTCTGGGCTATG
54127 TCACACG
1 TCACACG
54134 ACTTGTTACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.31
Consensus pattern (19 bp):
TCACACGGTCTGGGCTATG
Found at i:57223 original size:6 final size:7
Alignment explanation
Indices: 57206--57232 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
57196 TATATTCTTT
57206 AAAAAAG
1 AAAAAAG
57213 AAAAAAG
1 AAAAAAG
57220 AAAAAAG
1 AAAAAAG
57227 AAAAAA
1 AAAAAA
57233 AACAAAGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Done.