Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009823.1 Kokia drynarioides strain JFW-HI SEQ_124544, 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: 6426
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1023 original size:3 final size:3
Alignment explanation
Indices: 1008--1116 Score: 83
Period size: 3 Copynumber: 34.0 Consensus size: 3
998 GGTTATATAT
* * * *
1008 TAA TAA TAT TAA TAA TAT TAA TAA TGA TAAA TAA TAAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA T-AA TAA TAA TAA
* * *
1055 TAAA TACA TTAA TAA TTAT TAA TAA AAA TAT TAA TAA TAA TAA TAA TTAA
1 T-AA TA-A -TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
*
1105 TAT TAA TAA TAA
1 TAA TAA TAA TAA
1117 ATAAAAATGA
Statistics
Matches: 83, Mismatches: 16, Indels: 14
0.73 0.14 0.12
Matches are distributed among these distances:
3 66 0.80
4 15 0.18
5 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1115 original size:22 final size:22
Alignment explanation
Indices: 1011--1116 Score: 92
Period size: 22 Copynumber: 4.7 Consensus size: 22
1001 TATATATTAA
*
1011 TAATATTAATAATATTAATAAT
1 TAATATTAATAATAATAATAAT
*
1033 GATAA-A-TAATAAATAATGATAAT
1 --TAATATTAAT-AATAATAATAAT
* *
1056 AAATACATTAATAATTATTAATAA-
1 TAAT--ATTAATAA-TAATAATAAT
*
1080 AAATATTAATAATAATAATAAT
1 TAATATTAATAATAATAATAAT
1102 TAATATTAATAATAA
1 TAATATTAATAATAA
1117 ATAAAAATGA
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
21 10 0.15
22 26 0.38
23 11 0.16
24 10 0.15
25 11 0.16
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (22 bp):
TAATATTAATAATAATAATAAT
Found at i:2257 original size:29 final size:29
Alignment explanation
Indices: 2123--2433 Score: 180
Period size: 29 Copynumber: 10.7 Consensus size: 29
2113 CCATTAAACT
* *
2123 TTTCCAAAATTCCATTTTCAACC-CGAAC
1 TTTCCAAAATTCCATTTTTACCCTCGAAC
* * * *
2151 TTTCTAAAAATTACATTTTTCCCCT-AAAC
1 TTTC-CAAAATTCCATTTTTACCCTCGAAC
* * **
2180 TTTTCAAAAATCCATTTTTAACCCT-GATTT
1 TTTCCAAAATTCCATTTTT-ACCCTCGA-AC
**
2210 TTTTTAAAATTACCA-TTTTACCCTCGAAC
1 TTTCCAAAATT-CCATTTTTACCCTCGAAC
*
2239 TTTCCAAAATTCCATTTTTGA-CCTCG-AT
1 TTTCCAAAATTCCATTTTT-ACCCTCGAAC
*
2267 TTCTCCAAAAATTACCA-TTTTACTCTCGAAC
1 TT-TCC-AAAATT-CCATTTTTACCCTCGAAC
** * **
2298 -TTCCAGTATTCCATTTGTAACCC-CGATG
1 TTTCCAAAATTCCATTT-TTACCCTCGAAC
* * **
2326 TCTCAAAAATTAAATTTTTACCCTCGAAC
1 TTTCCAAAATTCCATTTTTACCCTCGAAC
*
2355 TTTCCAAAATCCCATTTTTTACCC-CG-A-
1 TTTCCAAAATTCCA-TTTTTACCCTCGAAC
*
2382 TTTCTCAAAAAATTACCATTTTTTCCCTCGAAC
1 TTTC-C--AAAATT-CCATTTTTACCCTCGAAC
2415 -TTCCAAAATTCCATTTTTA
1 TTTCCAAAATTCCATTTTTA
2434 ACCTTAATTT
Statistics
Matches: 212, Mismatches: 46, Indels: 50
0.69 0.15 0.16
Matches are distributed among these distances:
27 7 0.03
28 46 0.22
29 89 0.42
30 53 0.25
31 13 0.06
32 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.39
Consensus pattern (29 bp):
TTTCCAAAATTCCATTTTTACCCTCGAAC
Found at i:2509 original size:29 final size:28
Alignment explanation
Indices: 2122--2525 Score: 115
Period size: 29 Copynumber: 13.9 Consensus size: 28
2112 ACCATTAAAC
* * * *
2122 TTTTCCAAAATTCCATTTTCAACCCGAA
1 TTTTCAAAAATTCCATTTTTACCCCGAT
* * * *
2150 CTTTCTAAAAATTACATTTTT-CCCCTAAAC
1 TTTTC-AAAAATTCCATTTTTACCCC--GAT
*
2180 TTTTCAAAAA-TCCATTTTTAACCCTGATT
1 TTTTCAAAAATTCCATTTTT-ACCCCGA-T
** *
2209 TTTTTTAAAATTACCA-TTTTACCCTCGAA
1 TTTTCAAAAATT-CCATTTTTACCC-CGAT
* * *
2238 CTTTCCAAAATTCCATTTTTGACCTCGAT
1 TTTTCAAAAATTCCATTTTT-ACCCCGAT
* *
2267 TTCTCCAAAAATTACCA-TTTTACTCTCGA-
1 TT-TTCAAAAATT-CCATTTTTAC-CCCGAT
** * ** *
2296 ACTTCCAGTATTCCATTTGTAACCCCGAT
1 TTTTCAAAAATTCCATTT-TTACCCCGAT
* * ** *
2325 GTCTCAAAAATTAAATTTTTACCCTCGAA
1 TTTTCAAAAATTCCATTTTTACCC-CGAT
* * *
2354 CTTTCCAAAATCCCATTTTTTACCCCGAT
1 TTTTCAAAAATTCCA-TTTTTACCCCGAT
* *
2383 TTCTCAAAAAATTACCATTTTTTCCCTCGA-
1 TTTTC-AAAAATT-CCATTTTTACCC-CGAT
** * ***
2413 ACTTCCAAAATTCCATTTTTAACCTTAAT
1 TTTTCAAAAATTCCATTTTT-ACCCCGAT
* * * *
2442 TTCTCCAAAAATT--ATTATTTTACTCTGAA
1 TT-TTCAAAAATTCCA-T-TTTTACCCCGAT
**
2471 ACTTCAAAAAATTCCATTTTTAACCCCGAT
1 TTTTC-AAAAATTCCATTTTT-ACCCCGAT
2501 TTTTCAAAAAATTACCA-TTTTACCC
1 TTTTC-AAAAATT-CCATTTTTACCC
2526 TTGGATGTCT
Statistics
Matches: 266, Mismatches: 78, Indels: 63
0.65 0.19 0.15
Matches are distributed among these distances:
27 3 0.01
28 48 0.18
29 107 0.40
30 92 0.35
31 16 0.06
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (28 bp):
TTTTCAAAAATTCCATTTTTACCCCGAT
Found at i:2542 original size:59 final size:58
Alignment explanation
Indices: 2124--2526 Score: 381
Period size: 59 Copynumber: 6.9 Consensus size: 58
2114 CATTAAACTT
* * *
2124 TTCCAAAATTCCATTTTCAA-CCCGAACTTTCT--AAAAATTA-CATTTTTCCC-CTAAAC
1 TTCCAAAATTCCATTTTTAACCCCG-A-TTTCTCAAAAAATTACCATTTTACCCTC-GAAC
* * * * ***
2180 TTTTCAAAAATCCATTTTTAACCCTGATTTTTTTTAAAATTACCATTTTACCCTCGAAC
1 -TTCCAAAATTCCATTTTTAACCCCGATTTCTCAAAAAATTACCATTTTACCCTCGAAC
* * * *
2239 TTTCCAAAATTCCATTTTTGACCTCGATTTCTCCAAAAATTACCATTTTACTCTCGAAC
1 -TTCCAAAATTCCATTTTTAACCCCGATTTCTCAAAAAATTACCATTTTACCCTCGAAC
** * * *
2298 TTCCAGTATTCCATTTGTAACCCCGATGTCTC-AAAAATTA-AATTTTTACCCTCGAAC
1 TTCCAAAATTCCATTTTTAACCCCGATTTCTCAAAAAATTACCA-TTTTACCCTCGAAC
* * *
2355 TTTCCAAAATCCCATTTTTTACCCCGATTTCTCAAAAAATTACCATTTTTTCCCTCGAAC
1 -TTCCAAAATTCCATTTTTAACCCCGATTTCTCAAAAAATTACCA-TTTTACCCTCGAAC
*** * ** *
2415 TTCCAAAATTCCATTTTTAACCTTAATTTCTCCAAAAATTATTATTTTACTCT-GAAAC
1 TTCCAAAATTCCATTTTTAACCCCGATTTCTCAAAAAATTACCATTTTACCCTCG-AAC
* *
2473 TTCAAAAAATTCCATTTTTAACCCCGATTTTTCAAAAAATTACCATTTTACCCT
1 TTC-CAAAATTCCATTTTTAACCCCGATTTCTCAAAAAATTACCATTTTACCCT
2527 TGGATGTCTA
Statistics
Matches: 282, Mismatches: 53, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
56 5 0.02
57 40 0.14
58 75 0.27
59 146 0.52
60 16 0.06
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.39
Consensus pattern (58 bp):
TTCCAAAATTCCATTTTTAACCCCGATTTCTCAAAAAATTACCATTTTACCCTCGAAC
Done.