Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008980.1 Kokia drynarioides strain JFW-HI SEQ_123677, 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: 29077
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 110 characters in sequence are not A, C, G, or T
Found at i:3523 original size:17 final size:17
Alignment explanation
Indices: 3503--3542 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3493 ATTAAGATTG
*
3503 AAATTTTAAAATTAAAA
1 AAATTTAAAAATTAAAA
*
3520 AAATATAAAAATTAAAA
1 AAATTTAAAAATTAAAA
3537 ATAATT
1 A-AATT
3543 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATTTAAAAATTAAAA
Found at i:7139 original size:12 final size:12
Alignment explanation
Indices: 7122--7153 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
7112 CACACAATGA
7122 CTTCTCCTCCTC
1 CTTCTCCTCCTC
7134 CTTCTCCTCCTC
1 CTTCTCCTCCTC
*
7146 CTCCTCCT
1 CTTCTCCT
7154 TTAGAGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (12 bp):
CTTCTCCTCCTC
Found at i:8867 original size:25 final size:24
Alignment explanation
Indices: 8839--8894 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
8829 TTTACATGTT
8839 TAATTTTTA-AATTTATTAAATAATA
1 TAATTTTTATAATTT-TTAAA-AATA
8864 TAA-TTTTATAATTTTTAAAAATA
1 TAATTTTTATAATTTTTAAAAATA
*
8887 TATTTTTT
1 TAATTTTT
8895 CTAGTTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 6 0.21
24 14 0.50
25 8 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TAATTTTTATAATTTTTAAAAATA
Found at i:9359 original size:7 final size:7
Alignment explanation
Indices: 9347--9378 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
9337 GCAAGACAAA
9347 TGTTTTT
1 TGTTTTT
9354 TGTTTTT
1 TGTTTTT
9361 TGTTTTT
1 TGTTTTT
9368 T-TTTTT
1 TGTTTTT
9374 T-TTTT
1 TGTTTT
9379 AACCACTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 10 0.40
7 15 0.60
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (7 bp):
TGTTTTT
Found at i:13348 original size:41 final size:39
Alignment explanation
Indices: 13303--13382 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 39
13293 AGGGTAATTA
*
13303 CATCAAAACATTAATTAAAAATAAAAATAATTCAAAAATAT
1 CATCAAAACATTAATTAAAAATAAAAA-AA-TAAAAAATAT
*
13344 CATCAAAGCATTAATTAAAAATAAAAAAATAAAAAATAT
1 CATCAAAACATTAATTAAAAATAAAAAAATAAAAAATAT
13383 GAAATAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 9 0.24
40 2 0.05
41 26 0.70
ACGTcount: A:0.65, C:0.09, G:0.01, T:0.25
Consensus pattern (39 bp):
CATCAAAACATTAATTAAAAATAAAAAAATAAAAAATAT
Found at i:20841 original size:57 final size:57
Alignment explanation
Indices: 20764--20877 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
20754 ACTTTTTATC
20764 CAACGTTACAATATTGTTACAATATTTAATCTCATTGTTATCGTTATTTTTACAACT
1 CAACGTTACAATATTGTTACAATATTTAATCTCATTGTTATCGTTATTTTTACAACT
20821 CAACGTTACAATATTGTTACAATATTTAATCTCATTGTTATCGTTATTTTTACAACT
1 CAACGTTACAATATTGTTACAATATTTAATCTCATTGTTATCGTTATTTTTACAACT
20878 TATCCTAAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.46
Consensus pattern (57 bp):
CAACGTTACAATATTGTTACAATATTTAATCTCATTGTTATCGTTATTTTTACAACT
Done.