Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011206.1 Kokia drynarioides strain JFW-HI SEQ_126183, 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: 6452
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Found at i:2080 original size:39 final size:38
Alignment explanation
Indices: 2037--2222 Score: 153
Period size: 39 Copynumber: 4.8 Consensus size: 38
2027 ACTACCTATG
* **
2037 CAGTATAGCATTACTGTGTTTACAGTGTCATAATCATTT
1 CAGTATAGTATTAC-GTGTTTACAGTGTCACCATCATTT
* *
2076 CAGTA-AGGTATTACGGTGTTTACAGTGTCACCATAATCT
1 CAGTATA-GTATTAC-GTGTTTACAGTGTCACCATCATTT
* * *
2115 CAATATAGTATTACGATGTTTAAAGTGTCACCGTCATTT
1 CAGTATAGTATTACG-TGTTTACAGTGTCACCATCATTT
* ** * **
2154 CAGTATATTATCT-CGGTGTTTGTAATGTCACTGTCATTT
1 CAGTATAGTAT-TAC-GTGTTTACAGTGTCACCATCATTT
2193 CAGTATAGTATTGTA-GTGTTTACAGTGTCA
1 CAGTATAGTA-T-TACGTGTTTACAGTGTCA
2223 TTGCCGATTC
Statistics
Matches: 118, Mismatches: 22, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
38 2 0.02
39 111 0.94
40 5 0.04
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (38 bp):
CAGTATAGTATTACGTGTTTACAGTGTCACCATCATTT
Found at i:4384 original size:60 final size:59
Alignment explanation
Indices: 4319--4669 Score: 333
Period size: 60 Copynumber: 5.8 Consensus size: 59
4309 AATATTTAAC
* * *
4319 GTTAAAATATATGATATGAAAAAAAAACTAAAAAAATAAATATTTATTTAAAGTTAAGAA
1 GTTAAAATATATAATATGAAAAAAAAA-TAAAAAAATAAATATTTATTTAAAATTAAAAA
* * * **
4379 GTTAAAATATATGATATGGAAAAAAAAAGAAATAAAT-AAT-TTTATTATATAAATATTTAAA
1 GTTAAAATATATAATAT-GAAAAAAAAATAAAAAAATAAATATTTATT-TA-AAAT-TAAAAA
* **
4440 GTTAAAATATATGATATGAAAAAAAAA-AAAAGGAT--ATATTTATTTAAAATTAAAAA
1 GTTAAAATATATAATATGAAAAAAAAATAAAAAAATAAATATTTATTTAAAATTAAAAA
* * **
4496 GTTAAAATATATAATATGAAAAAAAAATAAAGAAAGAAATAATTTTATTATATAAA-TACTTGAA
1 GTTAAAATATATAATATGAAAAAAAAATAAAAAAATAAAT-A-TTTATT-TA-AAATTA--AAAA
*
4560 GTTAAAATATATAATATGAAAAAAAAATTAAAAAGA-AAATATTTATTTAAAATTAAAAAA
1 GTTAAAATATATAATATGAAAAAAAAA-TAAAAAAATAAATATTTATTTAAAATT-AAAAA
* * *
4620 GTTAAAATATATAATATGAATAAAATAAAGAAAGAAA-GAAT-TTTATTTAA
1 GTTAAAATATATAATATGAA-AAAA-AAATAAAAAAATAAATATTTATTTAA
4670 TGTTCAAAGT
Statistics
Matches: 246, Mismatches: 26, Indels: 38
0.79 0.08 0.12
Matches are distributed among these distances:
56 30 0.12
57 8 0.03
58 10 0.04
59 18 0.07
60 72 0.29
61 51 0.21
62 14 0.06
63 4 0.02
64 33 0.13
65 6 0.02
ACGTcount: A:0.60, C:0.01, G:0.08, T:0.31
Consensus pattern (59 bp):
GTTAAAATATATAATATGAAAAAAAAATAAAAAAATAAATATTTATTTAAAATTAAAAA
Found at i:4504 original size:117 final size:118
Alignment explanation
Indices: 4300--4666 Score: 504
Period size: 121 Copynumber: 3.0 Consensus size: 118
4290 AGTTGAAATA
* *
4300 TATTATATAAATATTTAACGTTAAAATATATGATATGAAAAAAAAACTAAAAAAATAAATATTTA
1 TATTATATAAATATTTAAAGTTAAAATATATGATATGAAAAAAAAA--AAAAGAAT--ATATTTA
* * * *
4365 TTTAAAGTTAAGAAGTTAAAATATATGATATGGAAAAAA-AAAGAAATAAATAATTT
62 TTTAAAATTAAAAAGTTAAAATATATAATATGGAAAAAATAAAGAAAGAAATAATTT
*
4421 TATTATATAAATATTTAAAGTTAAAATATATGATATGAAAAAAAAAAAAAGGATATATTTATTTA
1 TATTATATAAATATTTAAAGTTAAAATATATGATATGAAAAAAAAAAAAAGAATATATTTATTTA
*
4486 AAATTAAAAAGTTAAAATATATAATATGAAAAAAAAATAAAGAAAGAAATAATTT
66 AAATTAAAAAGTTAAAATATATAATATG--GAAAAAATAAAGAAAGAAATAATTT
* * * *
4541 TATTATATAAATACTTGAAGTTAAAATATATAATATGAAAAAAAAATTAAAAAGAAAATATTTAT
1 TATTATATAAATATTTAAAGTTAAAATATATGATATG-AAAAAAAA--AAAAAGAATATATTTAT
*
4606 TTAAAATTAAAAAAGTTAAAATATATAATAT-GAATAAAATAAAGAAAGAAAGAATTT
63 TTAAAATT-AAAAAGTTAAAATATATAATATGGAA-AAAATAAAGAAAGAAATAATTT
4663 TATT
1 TATT
4667 TAATGTTCAA
Statistics
Matches: 223, Mismatches: 15, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
117 36 0.16
119 12 0.05
120 50 0.22
121 55 0.25
122 25 0.11
123 23 0.10
124 22 0.10
ACGTcount: A:0.59, C:0.01, G:0.08, T:0.32
Consensus pattern (118 bp):
TATTATATAAATATTTAAAGTTAAAATATATGATATGAAAAAAAAAAAAAGAATATATTTATTTA
AAATTAAAAAGTTAAAATATATAATATGGAAAAAATAAAGAAAGAAATAATTT
Done.