Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003040.1 Kokia drynarioides strain JFW-HI SEQ_115566, 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: 75666
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:990 original size:52 final size:52
Alignment explanation
Indices: 886--1068 Score: 239
Period size: 52 Copynumber: 3.6 Consensus size: 52
876 TAAATGAAAA
* * *
886 AGGTCCGATAACTATGTGTCATCGT-A-TGT-TG-ATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG
* * *
934 AGGTCCGATGACTTTGTGTCATCGTGAGTATATGAATCCTTTATGGATTACG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG
* * * *
986 AGGTCTGATGACTATGTGTAATCATGAGTATATGAATCCTTTACGGAATAAG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG
*
1038 AGGTCCGATGACTATGTGTCATCTTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
1069 TAAATGAAAT
Statistics
Matches: 116, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
48 23 0.20
49 1 0.01
50 2 0.02
51 2 0.02
52 88 0.76
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAG
Found at i:9371 original size:52 final size:52
Alignment explanation
Indices: 9283--9410 Score: 186
Period size: 52 Copynumber: 2.5 Consensus size: 52
9273 AAAAGGTCCA
* *
9283 ATGACTATGTGTCATCGTGAGTATATGGATCATTTACGAATTATGAGGTTTG
1 ATGACTATGTGTCATCGTGAGTATATGAATCATTTACGAATTATGAGGTCTG
* * * *
9335 ATGACTTTGTGTCATCGTGAGTATA-GAAATCCTTTACGGATTATGATGTCTG
1 ATGACTATGTGTCATCGTGAGTATATG-AATCATTTACGAATTATGAGGTCTG
9387 ATGACTATGTGTCATCGTGAGTAT
1 ATGACTATGTGTCATCGTGAGTAT
9411 TAAATGAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 1 0.01
52 67 0.99
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (52 bp):
ATGACTATGTGTCATCGTGAGTATATGAATCATTTACGAATTATGAGGTCTG
Found at i:13193 original size:83 final size:83
Alignment explanation
Indices: 13092--13245 Score: 283
Period size: 83 Copynumber: 1.9 Consensus size: 83
13082 TCTGGGATCG
13092 ATACTTTACTTATCACTGTATTACTTGTGTTATGTACACTTGCACATTT-ACGATTGCAATATTA
1 ATACTTTACTTATCACTGTATTACTTGTGTTATGTACACTTGCACATTTGA-GATTGCAATATTA
13156 TTTTACAAGCGATAGTACA
65 TTTTACAAGCGATAGTACA
*
13175 ATACTTTACTTATCACTGTATTACTTGTGTTGTGTACACTTGCACATTTGAGATTGCAATATTAT
1 ATACTTTACTTATCACTGTATTACTTGTGTTATGTACACTTGCACATTTGAGATTGCAATATTAT
13240 TTTACA
66 TTTACA
13246 CGTGACAATT
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
83 68 0.99
84 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (83 bp):
ATACTTTACTTATCACTGTATTACTTGTGTTATGTACACTTGCACATTTGAGATTGCAATATTAT
TTTACAAGCGATAGTACA
Found at i:16335 original size:10 final size:10
Alignment explanation
Indices: 16320--16345 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
16310 TATACATTAT
16320 TTTTTTATTC
1 TTTTTTATTC
16330 TTTTTTATTC
1 TTTTTTATTC
16340 TTTTTT
1 TTTTTT
16346 TTATTTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTATTC
Found at i:24128 original size:21 final size:21
Alignment explanation
Indices: 24104--24143 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24094 AAATCGAGTA
* *
24104 TCACTGAGTTAGAAAATGCAG
1 TCACTAAGTTAAAAAATGCAG
24125 TCACTAAGTTAAAAAATGC
1 TCACTAAGTTAAAAAATGC
24144 TAAAAATGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
TCACTAAGTTAAAAAATGCAG
Found at i:27429 original size:34 final size:34
Alignment explanation
Indices: 27390--27459 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
27380 GTAGTTGTAA
* * *
27390 TTTAATTTTCACCAGATTTCCTTTGTCATTGCAT
1 TTTAATTGTCACCAGATCTCCATTGTCATTGCAT
** *
27424 TTTAATTGTCACTGGATCTGCATTGTCATTGCAT
1 TTTAATTGTCACCAGATCTCCATTGTCATTGCAT
27458 TT
1 TT
27460 CCATGTGTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.49
Consensus pattern (34 bp):
TTTAATTGTCACCAGATCTCCATTGTCATTGCAT
Found at i:27432 original size:17 final size:17
Alignment explanation
Indices: 27412--27459 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
27402 CAGATTTCCT
*
27412 TTGTCATTGCATTTTAA
1 TTGTCATTGCATTTGAA
* * * *
27429 TTGTCACTGGATCTGCA
1 TTGTCATTGCATTTGAA
27446 TTGTCATTGCATTT
1 TTGTCATTGCATTT
27460 CCATGTGTCA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (17 bp):
TTGTCATTGCATTTGAA
Found at i:32679 original size:83 final size:83
Alignment explanation
Indices: 32540--32700 Score: 286
Period size: 83 Copynumber: 1.9 Consensus size: 83
32530 TGGCTAATTG
* *
32540 TCACGTGTAAAATAATATTGCAATCGCAAATGTGCAAGTGTACACAACACAAGTAATAGAGTGAT
1 TCACGTGTAAAATAATATTGCAATCGCAAATATGCAAGTGTACACAACACAAGTAATACAGTGAT
32605 AAGTAAAGTATCGTACTA
66 AAGTAAAGTATCGTACTA
* *
32623 TCACGTGTAAAATAATATTGCAATCGCAATTATGCAAGTGTACACAACGCAAGTAATACAGTGAT
1 TCACGTGTAAAATAATATTGCAATCGCAAATATGCAAGTGTACACAACACAAGTAATACAGTGAT
32688 AAGTAAAGTATCG
66 AAGTAAAGTATCG
32701 ATCCCACAGA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 74 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (83 bp):
TCACGTGTAAAATAATATTGCAATCGCAAATATGCAAGTGTACACAACACAAGTAATACAGTGAT
AAGTAAAGTATCGTACTA
Found at i:58109 original size:14 final size:15
Alignment explanation
Indices: 58090--58119 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
58080 AAGGAGAAAA
58090 AGAAGGACC-TGAAG
1 AGAAGGACCTTGAAG
58104 AGAAGGACCTTGAAG
1 AGAAGGACCTTGAAG
58119 A
1 A
58120 AGAGAAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.13, G:0.33, T:0.10
Consensus pattern (15 bp):
AGAAGGACCTTGAAG
Found at i:74108 original size:19 final size:19
Alignment explanation
Indices: 74086--74123 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
74076 ATCAAAAAGT
74086 CGAGAAAAA-AAGAAAAATA
1 CGAGAAAAATAA-AAAAATA
74105 CGAGAAAAATAAAAAAATA
1 CGAGAAAAATAAAAAAATA
74124 AAAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (19 bp):
CGAGAAAAATAAAAAAATA
Done.