Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012181.1 Kokia drynarioides strain JFW-HI SEQ_127182, 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: 15443
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:2159 original size:21 final size:22
Alignment explanation
Indices: 2113--2159 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
2103 CGATCTAAGG
2113 AAAAATAAAATAAACA-A-AATT
1 AAAAATAAAATAAA-ATAGAATT
2134 AAAAATAAAATAAAATAGAATT
1 AAAAATAAAATAAAATAGAATT
2156 AAAA
1 AAAA
2160 GAAATAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 1 0.04
21 15 0.62
22 8 0.33
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (22 bp):
AAAAATAAAATAAAATAGAATT
Found at i:10146 original size:21 final size:21
Alignment explanation
Indices: 10103--10156 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
10093 GGAGTTTTTA
* *
10103 GTATTGGTAGAAGCATGATTT
1 GTATCGGTAGAAGCATGACTT
* * *
10124 GTTTCGGTAGAAGCTTTACTT
1 GTATCGGTAGAAGCATGACTT
*
10145 GTATCTGTAGAA
1 GTATCGGTAGAA
10157 CTATCATAGG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (21 bp):
GTATCGGTAGAAGCATGACTT
Found at i:10898 original size:23 final size:23
Alignment explanation
Indices: 10868--10914 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
10858 CATCGTAAGG
10868 ATGTAGTTTTTGGAGATTCTCCA
1 ATGTAGTTTTTGGAGATTCTCCA
10891 ATGTAGTTTTTGGAGATTCTCCA
1 ATGTAGTTTTTGGAGATTCTCCA
10914 A
1 A
10915 ATTATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.43
Consensus pattern (23 bp):
ATGTAGTTTTTGGAGATTCTCCA
Found at i:14611 original size:878 final size:878
Alignment explanation
Indices: 12917--14672 Score: 3251
Period size: 878 Copynumber: 2.0 Consensus size: 878
12907 GCCCCTAGCA
12917 ATCTAGGCCATAATATAGGGCTCACCCAAACAATCTACCATCATCGCACTCCAAACGCTTAATAG
1 ATCTAGGCCATAATATAGGGCTCACCCAAACAATCTACCATCATCGCACTCCAAACGCTTAATAG
12982 AGTTAAAACTCCGCCACTAGGTTTCACACTTATGAAAGAACGTCGTATTCCTATCCCCACTTTTC
66 AGTTAAAACTCCGCCACTAGGTTTCACACTTATGAAAGAACGTCGTATTCCTATCCCCACTTTTC
*
13047 AACCAATTTACCCTGGCCTTCTACTCCCAATAAACTTCCTCTTTATTAACTTCCCAATTCAAATT
131 AACCAATTTACCCTGGCCTTCTACTCCCAATAAACTTCCTCTTTATTAACTTCCCAATTCAAATG
13112 GAGTTTCATATCAACAATTGCAATTATATTCTCATCATCCCTATCCACATCTAACAACTCATTCA
196 GAGTTTCATATCAACAATTGCAATTATATTCTCATCATCCCTATCCACATCTAACAACTCATTCA
* *
13177 ACTTTTCGGTTAACTCCTCCTGTAAACCAACTCTATCATTCTTCTGATGTTTTGCCCAATCATTT
261 ACTTTTCGGTTAACTCCTCCCGTAAACCAACTCTATCATTCTTCCGATGTTTTGCCCAATCATTT
*
13242 AAACGGCATCGAAGACACTCTAATTTCATCCCAATATCCTCATTAGTTTGCTCTCATATACTCTG
326 AAACGGCATCGAAGACACTCTAATTTCATCCCAATATCCCCATTAGTTTGCTCTCATATACTCTG
*
13307 AACCACCTCCTCAAATGACGGCTCAAGGATCTACCAAGCTTCAAACTTGGAAGGTTGATGTACCA
391 AACCACCTCCTCAAATGACGGCTCAAGAATCTACCAAGCTTCAAACTTGGAAGGTTGATGTACCA
*
13372 CTTGATTCACCACTGCACTAGCCTGAATTAGCAAGGGACAATAGTCAGAGTAAGAATGCGAAAGA
456 CTCGATTCACCACTGCACTAGCCTGAATTAGCAAGGGACAATAGTCAGAGTAAGAATGCGAAAGA
* * *
13437 TGTCTTAGCGACGCATTCGAAAAACCAACCAACTAGGCATCATTTGCCACAGCTCTATCCAATCT
521 TGTCTTACCGACACATTCAAAAAACCAACCAACTAGGCATCATTTGCCACAGCTCTATCCAATCT
13502 TTCCTTAATATTTATTGCAAGGGAATTACCCATTTCCCAAGTATGATAGAGCCACAATCAACTAA
586 TTCCTTAATATTTATTGCAAGGGAATTACCCATTTCCCAAGTATGATAGAGCCACAATCAACTAA
*
13567 TCCACATTCCTGCAAAACATCACGAAAGACTTTCATGCACCATTCATCCCGGGGAAACCCACCTT
651 TCCACATTCCTACAAAACATCACGAAAGACTTTCATGCACCATTCATCCCGGGGAAACCCACCTT
*
13632 CCTTCTCATGGATATACATAATTTCATTAAAATCACCACAAACAAGCCACGGACTCTCCTTATCC
716 CCTTCTCATGGACATACATAATTTCATTAAAATCACCACAAACAAGCCACGGACTCTCCTTATCC
13697 ATACCCAACATTCGAAGCTCATCCCAAGATTCCATTCTACTATAATAAAAAGGGGACTAATGGTA
781 ATACCCAACATTCGAAGCTCATCCCAAGATTCCATTCTACTATAATAAAAAGGGGACTAATGGTA
*
13762 TTACAAATGACATAAATTTTCGTCCTAATTTAG
846 TTACAAATGACATAAATTTTCGTCCCAATTTAG
13795 ATCTAGGCCATAATATAGGGCTCACCCAAACAATCTACCATCATCGCACTCCAAACGCTTAATAG
1 ATCTAGGCCATAATATAGGGCTCACCCAAACAATCTACCATCATCGCACTCCAAACGCTTAATAG
*
13860 AGTTAAAACTCCGCCACTAGGTTTCATACTTATGAAAGAACGTCGTATTCCTATCCCCACTTTTC
66 AGTTAAAACTCCGCCACTAGGTTTCACACTTATGAAAGAACGTCGTATTCCTATCCCCACTTTTC
13925 AACCAATTTACCCTGGCCTTCTACTCCCAATAAACTTCCTCTTTATTAACTTCCCAATTCAAATG
131 AACCAATTTACCCTGGCCTTCTACTCCCAATAAACTTCCTCTTTATTAACTTCCCAATTCAAATG
*
13990 GAGTTTCATATCAACAATTGCAATTATATTCTCATCATCCCTGTCCACATCTAACAACTCATTCA
196 GAGTTTCATATCAACAATTGCAATTATATTCTCATCATCCCTATCCACATCTAACAACTCATTCA
* *
14055 GCTTTTCGGTTAACTCCTCCCGTAAACCAGCTCTATCATTCTTCCGATGTTTTGCCCAATCATTT
261 ACTTTTCGGTTAACTCCTCCCGTAAACCAACTCTATCATTCTTCCGATGTTTTGCCCAATCATTT
*
14120 AAACGGCATCGAAGACACTTTAATTTCATCCCAATATCCCCATTAGTTTGCTCTCATATACTCTG
326 AAACGGCATCGAAGACACTCTAATTTCATCCCAATATCCCCATTAGTTTGCTCTCATATACTCTG
14185 AACCACCTCCTCAAATGACGGCTCAAGAATCTACCAAGCTTCAAACTTGGAAGGTTGATGTACCA
391 AACCACCTCCTCAAATGACGGCTCAAGAATCTACCAAGCTTCAAACTTGGAAGGTTGATGTACCA
* * *
14250 CTCGATTCACCACTGTACTAGTCTGAATTAGCAAGGGACAATGGTCAGAGTAAGAATGCGAAAGA
456 CTCGATTCACCACTGCACTAGCCTGAATTAGCAAGGGACAATAGTCAGAGTAAGAATGCGAAAGA
14315 TGTCTTACCGACACATTCAAAAAACCAACCAACTAGGCATCATTTGCCACAGCTCTATCCAATCT
521 TGTCTTACCGACACATTCAAAAAACCAACCAACTAGGCATCATTTGCCACAGCTCTATCCAATCT
* *
14380 TTCCTTAATATTTGTTGCAAGGGAATTATCCATTTCCCAAGTATGATAGAGCCACAATCAACTAA
586 TTCCTTAATATTTATTGCAAGGGAATTACCCATTTCCCAAGTATGATAGAGCCACAATCAACTAA
* *
14445 TCCACATTCCTACAAAACATCACGAAAGACTTTCATGCACCGTTCATCCCGGGGAAGCCCACCTT
651 TCCACATTCCTACAAAACATCACGAAAGACTTTCATGCACCATTCATCCCGGGGAAACCCACCTT
* * *
14510 CTTTCTCATGGACGTACGTAATTTCATTAAAATCACCACAAACAAGCCACGGACTCTCCTTATCC
716 CCTTCTCATGGACATACATAATTTCATTAAAATCACCACAAACAAGCCACGGACTCTCCTTATCC
* *
14575 ATACCCAACTTTCGAAGCTCATCCCAAGATTCCATTCTACTATAATAAAAAGGGGACTGATGGTA
781 ATACCCAACATTCGAAGCTCATCCCAAGATTCCATTCTACTATAATAAAAAGGGGACTAATGGTA
14640 TTACAAATGACATAAATTTTCGTCCCAATTTAG
846 TTACAAATGACATAAATTTTCGTCCCAATTTAG
14673 TCTTTAAATT
Statistics
Matches: 849, Mismatches: 29, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
878 849 1.00
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.29
Consensus pattern (878 bp):
ATCTAGGCCATAATATAGGGCTCACCCAAACAATCTACCATCATCGCACTCCAAACGCTTAATAG
AGTTAAAACTCCGCCACTAGGTTTCACACTTATGAAAGAACGTCGTATTCCTATCCCCACTTTTC
AACCAATTTACCCTGGCCTTCTACTCCCAATAAACTTCCTCTTTATTAACTTCCCAATTCAAATG
GAGTTTCATATCAACAATTGCAATTATATTCTCATCATCCCTATCCACATCTAACAACTCATTCA
ACTTTTCGGTTAACTCCTCCCGTAAACCAACTCTATCATTCTTCCGATGTTTTGCCCAATCATTT
AAACGGCATCGAAGACACTCTAATTTCATCCCAATATCCCCATTAGTTTGCTCTCATATACTCTG
AACCACCTCCTCAAATGACGGCTCAAGAATCTACCAAGCTTCAAACTTGGAAGGTTGATGTACCA
CTCGATTCACCACTGCACTAGCCTGAATTAGCAAGGGACAATAGTCAGAGTAAGAATGCGAAAGA
TGTCTTACCGACACATTCAAAAAACCAACCAACTAGGCATCATTTGCCACAGCTCTATCCAATCT
TTCCTTAATATTTATTGCAAGGGAATTACCCATTTCCCAAGTATGATAGAGCCACAATCAACTAA
TCCACATTCCTACAAAACATCACGAAAGACTTTCATGCACCATTCATCCCGGGGAAACCCACCTT
CCTTCTCATGGACATACATAATTTCATTAAAATCACCACAAACAAGCCACGGACTCTCCTTATCC
ATACCCAACATTCGAAGCTCATCCCAAGATTCCATTCTACTATAATAAAAAGGGGACTAATGGTA
TTACAAATGACATAAATTTTCGTCCCAATTTAG
Done.