Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011953.1 Kokia drynarioides strain JFW-HI SEQ_126951, 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: 7230
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Warning! 73 characters in sequence are not A, C, G, or T
Found at i:78 original size:17 final size:16
Alignment explanation
Indices: 49--83 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
39 CTTAATTTTC
*
49 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
65 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
82 AA
1 AA
84 TACACAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:620 original size:115 final size:114
Alignment explanation
Indices: 418--648 Score: 444
Period size: 115 Copynumber: 2.0 Consensus size: 114
408 TACACCTCGT
418 CTATGAATTGTTCAACATTTAAATTTGCAGTCGCACACGCTGCATGAACATGCACACATGAATAT
1 CTATGAATTGTTCAACATTTAAATTTGCAGTCGCACACGCTGCATGAACATGCACACATGAATAT
483 CGGAGAGCTTGAAATCTACAGCACTCGCATCGCCTGTTTGCCAGATCAA
66 CGGAGAGCTTGAAATCTACAGCACTCGCATCGCCTGTTTGCCAGATCAA
*
532 NCTATGAATTGTTCAACATTTAAATTTGCAGTCGCACACGCTGCATGAACATGCACACATTAATA
1 -CTATGAATTGTTCAACATTTAAATTTGCAGTCGCACACGCTGCATGAACATGCACACATGAATA
597 TCGGAGAGCTTGAAATCTACAGCACTCGCATCGCCTGTTTGCCAGATCAA
65 TCGGAGAGCTTGAAATCTACAGCACTCGCATCGCCTGTTTGCCAGATCAA
647 CT
1 CT
649 GCGTACGACC
Statistics
Matches: 115, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
114 2 0.02
115 113 0.98
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (114 bp):
CTATGAATTGTTCAACATTTAAATTTGCAGTCGCACACGCTGCATGAACATGCACACATGAATAT
CGGAGAGCTTGAAATCTACAGCACTCGCATCGCCTGTTTGCCAGATCAA
Found at i:4055 original size:60 final size:60
Alignment explanation
Indices: 3972--4307 Score: 299
Period size: 60 Copynumber: 5.5 Consensus size: 60
3962 AGAGAAAGTT
* * * *
3972 GGTGTC-AGCCATTGCATGACCAACACTAAAAAATTTGATTTTTTTTATCAGATAAATAAG
1 GGTGTCGA-CCATGGCATGGCCAACACAAAAAAATTTGAATTTTTTTATCAGATAAATAAG
** ** *
4032 GGTGTCGGTCATGGCATGGCCAACACCCAAAAATTT-AATTTTTTTATTCAGATAAAAAAAGG
1 GGTGTCGACCATGGCATGGCCAACACAAAAAAATTTGAATTTTTTTA-TCAGAT-AAATAA-G
* * * **
4094 GGTGTCGATCATGGCATGGCTAACACAAAAAAAATTTGAAAATTTTTTATTTGATAAAT-AG
1 GGTGTCGACCATGGCATGGCCAACAC-AAAAAAATTTG-AATTTTTTTATCAGATAAATAAG
* * * * * *
4155 GGTTGTTGACCACGGCATGGTCAACACCAAAAAAA-TTGAA-TTTTTTATCTGACAAAAAAGG
1 GG-TGTCGACCATGGCATGGCCAACA-CAAAAAAATTTGAATTTTTTTATCAGATAAATAA-G
* * * * *
4216 GGTGTC-AGCCATTGCATAGACAACACAAAAAAATTTGATTTTTTTTATCA-ATAAATAGG
1 GGTGTCGA-CCATGGCATGGCCAACACAAAAAAATTTGAATTTTTTTATCAGATAAATAAG
*
4275 GGTGTCGACCATCGCATGGCCAACACAAAAAAA
1 GGTGTCGACCATGGCATGGCCAACACAAAAAAA
4308 ATTAAAATTT
Statistics
Matches: 224, Mismatches: 37, Indels: 31
0.77 0.13 0.11
Matches are distributed among these distances:
59 61 0.27
60 64 0.29
61 23 0.10
62 51 0.23
63 12 0.05
64 4 0.02
65 9 0.04
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (60 bp):
GGTGTCGACCATGGCATGGCCAACACAAAAAAATTTGAATTTTTTTATCAGATAAATAAG
Found at i:4246 original size:59 final size:60
Alignment explanation
Indices: 3992--4339 Score: 228
Period size: 59 Copynumber: 5.8 Consensus size: 60
3982 ATTGCATGAC
* * * * * * ** *
3992 CAACACTAAAAAATTTGATTTTTTTTATCAGATAAATAA-GGGTGTCGGTCATGGCATGGC
1 CAACACAAAAAAAATTGA-ATTTTTTATCTGACAAAAAAGGGGTGTCGACCATGGCATGGA
** * * * *
4052 CAACAC-CCAAAAATTTAATTTTTTTATTCAGATAAAAAAAGGGGTGTCGATCATGGCATGG-
1 CAACACAAAAAAAATTGAA-TTTTTTA-TCTGA-CAAAAAAGGGGTGTCGACCATGGCATGGA
* * * * * * *
4113 CTAACACAAAAAAAATTTGAAAATTTTTTATTTGA-TAAATAGGGTTGTTGACCACGGCATGGT
1 C-AACACAAAAAAAA-TTG--AATTTTTTATCTGACAAAAAAGGGGTGTCGACCATGGCATGGA
* * *
4176 CAACACCAAAAAAATTGAATTTTTTATCTGACAAAAAAGGGGTGTC-AGCCATTGCATAGA
1 CAACACAAAAAAAATTGAATTTTTTATCTGACAAAAAAGGGGTGTCGA-CCATGGCATGGA
* * *
4236 CAACACAAAAAAATTTG-ATTTTTT-T-T-ATCAATAAATAGGGGTGTCGACCATCGCATGGC
1 CAACACAAAAAAAATTGAATTTTTTATCTGA-CAA-AAA-AGGGGTGTCGACCATGGCATGGA
* * * * *
4295 CAACACAAAAAAAATTAAAATTTTCATCTGACAAATAGGGGGTGT
1 CAACACAAAAAAAATTGAATTTTTTATCTGACAAAAAAGGGGTGT
4340 TGGCAATGAC
Statistics
Matches: 228, Mismatches: 40, Indels: 40
0.74 0.13 0.13
Matches are distributed among these distances:
56 1 0.00
57 4 0.02
58 4 0.02
59 68 0.30
60 57 0.25
61 12 0.05
62 61 0.27
63 7 0.03
64 5 0.02
65 7 0.03
66 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (60 bp):
CAACACAAAAAAAATTGAATTTTTTATCTGACAAAAAAGGGGTGTCGACCATGGCATGGA
Found at i:4970 original size:24 final size:24
Alignment explanation
Indices: 4943--4989 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
4933 GAGTTAATGT
*
4943 GTTAAA-AATATTAATTAAAAAAAA
1 GTTAAACAATA-TAAATAAAAAAAA
4967 GTTAAAGCAATATAAATAAAAAA
1 GTTAAA-CAATATAAATAAAAAA
4990 TAAAAAAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 10 0.50
26 4 0.20
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (24 bp):
GTTAAACAATATAAATAAAAAAAA
Found at i:5268 original size:29 final size:29
Alignment explanation
Indices: 5204--5268 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
5194 TTTAGCTAAA
*
5204 ATTAAAATCGACATAATCTGATAAATTTT
1 ATTAAAATCGACATAATCTGATAAATTTG
** **
5233 AAAAAAATCGATTTAATCTGAT-AATTATG
1 ATTAAAATCGACATAATCTGATAAATT-TG
5262 ATTAAAA
1 ATTAAAA
5269 ATCAACATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (29 bp):
ATTAAAATCGACATAATCTGATAAATTTG
Done.