Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013282.1 Kokia drynarioides strain JFW-HI SEQ_128303, 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: 308372
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 53 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:300487 original size:51 final size:51
Alignment explanation
Indices: 300417--300648 Score: 349
Period size: 51 Copynumber: 4.5 Consensus size: 51
300407 TAGACGAAAG
* *
300417 GGTCCGATGACAAACTGTCATCGTGAGTAAATGAATCCTATATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTATATGGATTAAA
* * *
300468 GGTCCGATGACTAAGTGTCATCGTGAGTGAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTATATGGATTAAA
* *
300519 GATCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCTATATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTATATGGATTAAA
* * *
300570 GGTCCGATGACTAAGTGTCATCGTCAGTGAATGAATCCTTTATGGATTAATA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTATATGGATTAA-A
*
300622 -GTCCGATGACTAAGTGTCATTGTGAGT
1 GGTCCGATGACTAAGTGTCATCGTGAGT
300649 TTATAGATTA
Statistics
Matches: 163, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
51 162 0.99
52 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTATATGGATTAAA
Found at i:300599 original size:102 final size:102
Alignment explanation
Indices: 300418--300648 Score: 392
Period size: 102 Copynumber: 2.3 Consensus size: 102
300408 AGACGAAAGG
* * *
300418 GTCCGATGACAAACTGTCATCGTGAGTAAATGAATCCTATATGGATTAAAGGTCCGATGACTAAG
1 GTCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCTATATGGATTAAAGGTCCGATGACTAAG
*
300483 TGTCATCGTGAGTGAATGAATCCTTTATGGATTAAT-
66 TGTCATCGTCAGTGAATGAATCCTTTATGGATTAATA
300519 GATCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCTATATGGATTAAAGGTCCGATGACTAA
1 G-TCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCTATATGGATTAAAGGTCCGATGACTAA
300584 GTGTCATCGTCAGTGAATGAATCCTTTATGGATTAATA
65 GTGTCATCGTCAGTGAATGAATCCTTTATGGATTAATA
* *
300622 GTCCGATGACTAAGTGTCATTGTGAGT
1 GTCCAATGACTAAGTGTCATCGTGAGT
300649 TTATAGATTA
Statistics
Matches: 122, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
101 1 0.01
102 120 0.98
103 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (102 bp):
GTCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCTATATGGATTAAAGGTCCGATGACTAAG
TGTCATCGTCAGTGAATGAATCCTTTATGGATTAATA
Found at i:301446 original size:21 final size:22
Alignment explanation
Indices: 301421--301478 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
301411 GATGCATGAC
301421 ATGTATCGGTAGAAATTA-TACT
1 ATGTATCGGTAGAAATTAGTA-T
*
301443 -TGTATCGGTA-AAACTAGTAT
1 ATGTATCGGTAGAAATTAGTAT
*
301463 AGGTATCGGTAGAAAT
1 ATGTATCGGTAGAAAT
301479 CTGCACTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 6 0.20
21 21 0.70
22 3 0.10
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (22 bp):
ATGTATCGGTAGAAATTAGTAT
Found at i:307524 original size:47 final size:47
Alignment explanation
Indices: 307474--307641 Score: 176
Period size: 51 Copynumber: 3.4 Consensus size: 47
307464 GAAAGGGTTC
*
307474 GATGACAAACTGTCATCGTAAATGAATCCTATATGGATTAAAGGT-T
1 GATGACTAACTGTCATCGTAAATGAATCCTATATGGATTAAAGGTCT
* * * * *
307520 CGATGACTAAGTGTTATTGTGAGTGAATGAATCCTTTATGGATTAATGGTCT
1 -GATGACTAACTGTCATCGT-A---AATGAATCCTATATGGATTAAAGGTCT
*
307572 GATGACTAACTGTCATCGTGAGTAAATGAATCCTGTATGGATTAAAGGTCT
1 GATGACTAACTGTCATC----GTAAATGAATCCTATATGGATTAAAGGTCT
*
307623 GATGACTAAGTGTCATCGT
1 GATGACTAACTGTCATCGT
307642 GAGTTTATAG
Statistics
Matches: 100, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
47 17 0.17
48 1 0.01
51 78 0.78
52 1 0.01
54 1 0.01
55 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.33
Consensus pattern (47 bp):
GATGACTAACTGTCATCGTAAATGAATCCTATATGGATTAAAGGTCT
Found at i:307561 original size:51 final size:51
Alignment explanation
Indices: 307491--307664 Score: 233
Period size: 51 Copynumber: 3.4 Consensus size: 51
307481 AACTGTCATC
* *
307491 GTAAATGAATCCTATATGGATTAAAGGT-TCGATGACTAAGTGTTATTGTGA
1 GTAAATGAATCCTATATGGATTAAAGGTCT-GATGACTAAGTGTCATCGTGA
* * * *
307542 GTGAATGAATCCTTTATGGATTAATGGTCTGATGACTAACTGTCATCGTGA
1 GTAAATGAATCCTATATGGATTAAAGGTCTGATGACTAAGTGTCATCGTGA
*
307593 GTAAATGAATCCTGTATGGATTAAAGGTCTGATGACTAAGTGTCATCGTGA
1 GTAAATGAATCCTATATGGATTAAAGGTCTGATGACTAAGTGTCATCGTGA
** *
307644 GTTTATAGATTCCTATATGGA
1 GTAAAT-GAATCCTATATGGA
307665 ACGAGAGGTT
Statistics
Matches: 107, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
51 94 0.88
52 13 0.12
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (51 bp):
GTAAATGAATCCTATATGGATTAAAGGTCTGATGACTAAGTGTCATCGTGA
Done.