Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014515.1 Kokia drynarioides strain JFW-HI SEQ_129554, 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: 207493
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 161 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:203557 original size:31 final size:31
Alignment explanation
Indices: 203517--203654 Score: 117
Period size: 31 Copynumber: 4.6 Consensus size: 31
203507 TTAATATAAT
* *
203517 ATTTTATATTTAAATTTTATATTTTTTCTTA
1 ATTTGATATTTAAATTTTACATTTTTTCTTA
*
203548 ATTTGATA-TTAAATTTT---TTTTTAT-TCA
1 ATTTGATATTTAAATTTTACATTTTT-TCTTA
* * *
203575 ATTTGATACTTAAATTTAACACTTTTTCTTA
1 ATTTGATATTTAAATTTTACATTTTTTCTTA
* * * *
203606 ATTTGATATTTAAGTTTGACA-CTTTTATTA
1 ATTTGATATTTAAATTTTACATTTTTTCTTA
*
203636 AGTTGATATTTAAACTTTT
1 ATTTGATATTTAAA-TTTT
203655 TAGGAATACA
Statistics
Matches: 87, Mismatches: 13, Indels: 14
0.76 0.11 0.12
Matches are distributed among these distances:
27 15 0.17
28 9 0.10
30 29 0.33
31 34 0.39
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (31 bp):
ATTTGATATTTAAATTTTACATTTTTTCTTA
Found at i:203577 original size:27 final size:27
Alignment explanation
Indices: 203538--203591 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
203528 AAATTTTATA
*
203538 TTTTTTCTTAATTTGATA-TTAAATTT
1 TTTTTTATTAATTTGATACTTAAATTT
203564 TTTTTTATTCAATTTGATACTTAAATTT
1 TTTTTTATT-AATTTGATACTTAAATTT
203592 AACACTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 8 0.32
27 9 0.36
28 8 0.32
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.63
Consensus pattern (27 bp):
TTTTTTATTAATTTGATACTTAAATTT
Found at i:203644 original size:30 final size:31
Alignment explanation
Indices: 203517--203649 Score: 116
Period size: 30 Copynumber: 4.5 Consensus size: 31
203507 TTAATATAAT
* * * * *
203517 ATTTTATATTTAAATTTTATATTTTTTCTTA
1 ATTTGATATTTAAATTTAACACTTTTTATTA
*
203548 ATTTGATA-TTAAATTT----TTTTTTATTCA
1 ATTTGATATTTAAATTTAACACTTTTTATT-A
* *
203575 ATTTGATACTTAAATTTAACACTTTTTCTTA
1 ATTTGATATTTAAATTTAACACTTTTTATTA
* *
203606 ATTTGATATTTAAGTTTGACAC-TTTTATTA
1 ATTTGATATTTAAATTTAACACTTTTTATTA
*
203636 AGTTGATATTTAAA
1 ATTTGATATTTAAA
203650 CTTTTTAGGA
Statistics
Matches: 86, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
26 8 0.09
27 9 0.10
28 8 0.09
30 27 0.31
31 27 0.31
32 7 0.08
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.57
Consensus pattern (31 bp):
ATTTGATATTTAAATTTAACACTTTTTATTA
Found at i:203978 original size:59 final size:59
Alignment explanation
Indices: 203891--204034 Score: 179
Period size: 60 Copynumber: 2.5 Consensus size: 59
203881 CAAATTAAGA
* * ** * *
203891 AAAAAAAATATCAAATTTAAGTATCAAATT-GGGTTCAAAAAAATTTAAATACCAAATT
1 AAAAAAAATATCAAATTTAAATACCAAATTAAAGTTAAAAAAAAATTAAATACCAAATT
* *
203949 AAAAAAAATTATCAAATTTAAATACCAAATTAAATTTAAAAAAAAATTAAATACGAAATT
1 AAAAAAAA-TATCAAATTTAAATACCAAATTAAAGTTAAAAAAAAATTAAATACCAAATT
204009 --AAAAAA-ATCAAATTTAAATACCAAAT
1 AAAAAAAATATCAAATTTAAATACCAAAT
204035 AATATATTAA
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
56 20 0.26
58 14 0.18
59 20 0.26
60 22 0.29
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.28
Consensus pattern (59 bp):
AAAAAAAATATCAAATTTAAATACCAAATTAAAGTTAAAAAAAAATTAAATACCAAATT
Found at i:204190 original size:25 final size:26
Alignment explanation
Indices: 204142--204193 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
204132 GTATAAATTT
*
204142 AAACTCTAAATTAAAAATATTAATAA
1 AAACTCTAAATTAAAAATAGTAATAA
204168 AAACTCT-AA-TAAAAATAAGTAATAA
1 AAACTCTAAATTAAAAAT-AGTAATAA
204193 A
1 A
204194 TAAAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 10 0.42
26 7 0.29
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (26 bp):
AAACTCTAAATTAAAAATAGTAATAA
Found at i:205971 original size:96 final size:96
Alignment explanation
Indices: 205797--205978 Score: 233
Period size: 96 Copynumber: 1.9 Consensus size: 96
205787 AAGGATAATT
** * * * ** *
205797 GATTATCTCGATTTGAAGAAAGGTTGCACCTAGTGAGTTAAGGCGCAATATTTCGGAATCTGAGA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAATATTTCGAAACCCAAAA
*
205862 TAAGGAAACATTGCCTCGATTAAGGGTATTC
66 TAAAGAAACATTGCCTCGATTAAGGGTATTC
*
205893 GATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAA-AGTTTCGAAACCCAAA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAATA-TTTCGAAACCCAAA
*
205957 ATAAA-AGAATATTGCCTCGATT
65 ATAAAGA-AACATTGCCTCGATT
205979 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
95 2 0.03
96 71 0.97
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAATATTTCGAAACCCAAAA
TAAAGAAACATTGCCTCGATTAAGGGTATTC
Found at i:206373 original size:59 final size:59
Alignment explanation
Indices: 206282--206710 Score: 564
Period size: 59 Copynumber: 7.3 Consensus size: 59
206272 GTTCGGATCA
* * * *
206282 AAAATGG-GATTTTTGG-AAGTTCGGGGTAAAAAATGGAATTTATGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
206339 AAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
** * * * * *
206398 AAAATTATATTTTTTAGAAGGTTCGAGGTTAAAAATGGGATTTTTGCG-AGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTG-GAAGTTCGGGGGT
*** * *
206457 AAAATGGTAATTTTTGGAAAGTTTAAGGTCAAAAATGGGATTTTTGGAAGTTTGAGGGT
1 AAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * * *
206516 AAAATGGTAAATTTTAGAAGGTTCGGGGTTAAAAATGGGATTTTTGGGAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
206575 AAAATGGTAATTTTT-GAAAGGTTCGGGGTCAAAAATAGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAA-GTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
206634 AAAATGGTAATTTTTGG-AAGATTC-GGGTAAAAAATGGGATTTTTGGAAGCTCGGGGGT
1 AAAATGGTAATTTTTGGAAAG-TTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
206692 AAAATGGTAATTTTTGGAA
1 AAAATGGTAATTTTTGGAA
206711 GGTTTAGGGA
Statistics
Matches: 323, Mismatches: 41, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
57 7 0.02
58 60 0.19
59 254 0.79
60 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:206394 original size:29 final size:28
Alignment explanation
Indices: 206194--206711 Score: 376
Period size: 29 Copynumber: 17.7 Consensus size: 28
206184 AAGGGGGGGC
* * **
206194 AAAATGGTAGTTTTGGAAGGTTCGGAATCA
1 AAAATGGAATTTTTGGAA-GTTCGGGGT-A
206224 AAAAT-GAGATTTTTGGAAGTTCGAGGGT-
1 AAAATGGA-ATTTTTGGAAGTTCG-GGGTA
* * *
206252 AAAATGGTAATTTTCGAAAGGTTC-GGATCA
1 AAAATGG-AATTTTTGGAA-GTTCGGGGT-A
*
206282 AAAATGGGATTTTTGGAAGTTCGGGGTAA
1 AAAATGGAATTTTTGGAAGTTCGGGGT-A
*
206311 AAAATGGAATTTATGGAAGTTCGGGGGT-
1 AAAATGGAATTTTTGGAAGTTC-GGGGTA
206339 AAAATGGTAATTTTTGGAAAGTTCGGGGTCA
1 AAAATGG-AATTTTTGG-AAGTTCGGGGT-A
*
206370 AAAATGGGATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTC-GGGGTA
* ** * * *
206399 AAATTATATTTTTTAGAAGGTTCGAGGTTA
1 AAAATGGAATTTTTGGAA-GTTCG-GGGTA
*
206429 AAAATGGGATTTTTGCG-AGTTCGGGGGT-
1 AAAATGGAATTTTTG-GAAGTTC-GGGGTA
***
206457 AAAATGGTAATTTTTGGAAAGTTTAAGGTCA
1 AAAATGG-AATTTTTGG-AAGTTCGGGGT-A
* *
206488 AAAATGGGATTTTTGGAAGTTTGAGGGT-
1 AAAATGGAATTTTTGGAAGTTCG-GGGTA
* *
206516 AAAATGGTAAATTTTAGAAGGTTCGGGGTTA
1 AAAATGG-AATTTTTGGAA-GTTCGGGG-TA
* *
206547 AAAATGGGATTTTTGGGAGTTCGGGGGT-
1 AAAATGGAATTTTTGGAAGTTC-GGGGTA
*
206575 AAAATGGTAATTTTTGAAAGGTTCGGGGTCA
1 AAAATGG-AATTTTTGGAA-GTTCGGGGT-A
206606 AAAATAGG-ATTTTTGGAAGTTCGAGGGT-
1 AAAAT-GGAATTTTTGGAAGTTCG-GGGTA
206634 AAAATGGTAATTTTTGGAAGATTC-GGGTAA
1 AAAATGG-AATTTTTGGAAG-TTCGGGGT-A
* *
206664 AAAATGGGATTTTTGGAAGCTCGGGGGT-
1 AAAATGGAATTTTTGGAAGTTC-GGGGTA
206692 AAAATGGTAATTTTTGGAAG
1 AAAATGG-AATTTTTGGAAG
206712 GTTTAGGGAC
Statistics
Matches: 393, Mismatches: 52, Indels: 87
0.74 0.10 0.16
Matches are distributed among these distances:
27 2 0.01
28 59 0.15
29 170 0.43
30 133 0.34
31 27 0.07
32 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGGGGTA
Done.