Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009959.1 Kokia drynarioides strain JFW-HI SEQ_124707, 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: 28530
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1479 original size:35 final size:33
Alignment explanation
Indices: 1412--1480 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 33
1402 CTTAAAATAC
* *
1412 ATAAAAATTTAAAATTATTTTTTCATATTTTAA
1 ATAAAAATTTAAAATTATTTTTTCAAAATTTAA
1445 ATAAAAATTTTAAAAATTATATTTTT-AAAATTTAA
1 ATAAAAA-TTT-AAAATTAT-TTTTTCAAAATTTAA
1480 A
1 A
1481 ATACAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 7 0.23
34 3 0.10
35 16 0.52
36 5 0.16
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (33 bp):
ATAAAAATTTAAAATTATTTTTTCAAAATTTAA
Found at i:1514 original size:16 final size:16
Alignment explanation
Indices: 1471--1524 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
1461 TTATATTTTT
1471 AAAATTTAAAATACAA
1 AAAATTTAAAATACAA
*
1487 AAAACTTAAAAATA-AA
1 AAAA-TTTAAAATACAA
* *
1503 ATAATTTGAAAATATAA
1 AAAATTT-AAAATACAA
1520 AAAAT
1 AAAAT
1525 CCAAAATTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 2 0.06
16 15 0.48
17 14 0.45
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.26
Consensus pattern (16 bp):
AAAATTTAAAATACAA
Found at i:10872 original size:18 final size:17
Alignment explanation
Indices: 10849--10886 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
10839 GCATCTAATA
10849 TTGTTCCTTGTAATTATT
1 TTGTTCCTTGTAATT-TT
10867 TTGTTCCTTGTAATTTT
1 TTGTTCCTTGTAATTTT
10884 TTG
1 TTG
10887 GCAATTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.13, C:0.11, G:0.13, T:0.63
Consensus pattern (17 bp):
TTGTTCCTTGTAATTTT
Found at i:11418 original size:49 final size:48
Alignment explanation
Indices: 11365--11847 Score: 229
Period size: 49 Copynumber: 9.9 Consensus size: 48
11355 CCTCAGAAGC
*
11365 ATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAATACCATAAAGAT
1 ATGAAGGGAAAGATTTAAGCCGCAAC-GCGAATCCAGTACCATAAAGAT
* * * * *
11414 ATGAAAGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTGTACC-TCAGAAG-C
1 ATGAAGGGAAAGATTTAAGCCGCAAC-GCGAATCC-AGTACCAT-A-AAGAT
* * *
11463 ATGAAGGGAAATATTTAAGCCGCAACGACAAATCCAGTACCATGAAGAT
1 ATGAAGGGAAAGATTTAAGCCGCAACG-CGAATCCAGTACCATAAAGAT
* * * *
11512 ATGAAGGGAAAGGTTTAAGTCGCAACGAC-AAACCTTGTACC-TCAGAAGCAT
1 ATGAAGGGAAAGATTTAAGCCGCAACG-CGAATCC-AGTACCAT-A-AAG-AT
* * * *
11563 A--AAGGGAAAGATTTAAGTCGCAACGGCAAATCTAGTACCATGAAGAT
1 ATGAAGGGAAAGATTTAAGCCGCAAC-GCGAATCCAGTACCATAAAGAT
** * * ** *
11610 ACAAAGGGAAAGGTTTAAGTCGCAACGACGAA-CTTTGTACC-TCAAA-AGC
1 ATGAAGGGAAAGATTTAAGCCGCAACG-CGAATC-CAGTACCAT-AAAGA-T
* ** * * **
11659 ACGAAGGGAAAGATTTAAGCATCAATGTCGAATCTAGTACCACGAAGAT
1 ATGAAGGGAAAGATTTAAGCCGCAACG-CGAATCCAGTACCATAAAGAT
* * * ** ** *
11708 ATAAAGGAAAAGGTTTAAATCGCAACGGCGAA-CCTTTTACC-TCAGAAG-C
1 ATGAAGGGAAAGATTTAAGCCGCAAC-GCGAATCC-AGTACCAT-A-AAGAT
* * * *
11757 ACGAAGGGAAAGACTTAAGCCGCAACGGCGAATCTAGTACCATGAAG-T
1 ATGAAGGGAAAGATTTAAGCCGCAAC-GCGAATCCAGTACCATAAAGAT
* * * *
11805 CATGAAGGGAAAAATTTAAGTCGTAACGGCGAATCTAGTACCA
1 -ATGAAGGGAAAGATTTAAGCCGCAAC-GCGAATCCAGTACCA
11848 CGTAGACATT
Statistics
Matches: 330, Mismatches: 74, Indels: 60
0.71 0.16 0.13
Matches are distributed among these distances:
47 3 0.01
48 23 0.07
49 279 0.85
50 22 0.07
51 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.19
Consensus pattern (48 bp):
ATGAAGGGAAAGATTTAAGCCGCAACGCGAATCCAGTACCATAAAGAT
Found at i:11497 original size:98 final size:98
Alignment explanation
Indices: 11322--11846 Score: 662
Period size: 98 Copynumber: 5.4 Consensus size: 98
11312 AGGTTTGGAG
* *
11322 GGAAAGGTTTAAGTCGTAACGTCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCG
1 GGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCG
* * *
11387 CAAC-AGCGAATCCAATACCATAAAGATATGAAA
66 CAACGA-CGAATCTAGTACCATGAAGATATGAAA
*
11420 GGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAATATTTAAGCCG
1 GGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCG
* * *
11485 CAACGACAAATCCAGTACCATGAAGATATGAAG
66 CAACGACGAATCTAGTACCATGAAGATATGAAA
* * * *
11518 GGAAAGGTTTAAGTCGCAACGACAAACCTTGTACCTCAGAAGCATAAAGGGAAAGATTTAAGTCG
1 GGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCG
* * *
11583 CAACGGCAAATCTAGTACCATGAAGATA-CAAA
66 CAACGACGAATCTAGTACCATGAAGATATGAAA
* * * * *
11615 GGGAAAGGTTTAAGTCGCAACGACGAACTTTGTACCTCAAAAGCACGAAGGGAAAGATTTAAGCA
1 -GGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCC
* * * *
11680 TCAATGTCGAATCTAGTACCACGAAGATAT-AAA
65 GCAACGACGAATCTAGTACCATGAAGATATGAAA
* * * *
11713 GGAAAAGGTTTAAATCGCAACGGCGAACCTTTTACCTCAGAAGCACGAAGGGAAAGACTTAAGCC
1 GG-AAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCC
* *
11778 GCAACGGCGAATCTAGTACCATGAAG-TCATGAAG
65 GCAACGACGAATCTAGTACCATGAAGAT-ATGAAA
** * * *
11812 GGAAAAATTTAAGTCGTAACGGCGAATCTAGTACC
1 GGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACC
11847 ACGTAGACAT
Statistics
Matches: 374, Mismatches: 47, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
97 5 0.01
98 364 0.97
99 5 0.01
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (98 bp):
GGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCG
CAACGACGAATCTAGTACCATGAAGATATGAAA
Found at i:16446 original size:33 final size:33
Alignment explanation
Indices: 16409--16473 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
16399 TATTATATTT
* *
16409 TTAAAAATAAGATCTGTTT-AAAATACAAAAAAC
1 TTAAAAATAAAATAT-TTTGAAAATACAAAAAAC
*
16442 TTAAAAATAAAATATTTTGAAAATATAAAAAA
1 TTAAAAATAAAATATTTTGAAAATACAAAAAA
16474 TCCAAAATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (33 bp):
TTAAAAATAAAATATTTTGAAAATACAAAAAAC
Found at i:18381 original size:49 final size:49
Alignment explanation
Indices: 18305--18505 Score: 244
Period size: 49 Copynumber: 4.1 Consensus size: 49
18295 TCAAAAGCAC
* *
18305 GAAGGGAAAGATTTAAGCCGTAACGGCGAATCTAGTACCACGAAGATAT
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACAT
* * * ** * * * *
18354 AAAAGGAAAGGTTTAAATCGTAACGGCGAACCTTGTACCTCAGAAG-CAT
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAC-GAAGACAT
18403 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACAT
1 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACAT
* *
18452 GAAGGGAAA-ATTTTAAGCCGCAAAGACGAATCTAGTACCACGAAGACATT
1 GAAGGGAAAGA-TTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACA-T
18502 GAAG
1 GAAG
18506 CCGCAATGGC
Statistics
Matches: 128, Mismatches: 20, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
48 5 0.04
49 114 0.89
50 9 0.07
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (49 bp):
GAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGACAT
Found at i:26496 original size:98 final size:98
Alignment explanation
Indices: 26327--26810 Score: 614
Period size: 98 Copynumber: 4.9 Consensus size: 98
26317 ACAGGTTTAG
* *
26327 AGGGAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCTCA-AATGCATGAAGGAAAAGATTTAAG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA-GCATGAAGGGAAAGATTTAAG
* * * *
26391 TCGCAACGGCGAATCCAGTAACATGATGATATGA
65 CCGCAACGGCGAATCTAGTAACATGAAGATATAA
* *
26425 AGGGAAAGGTTTAAGTTGCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * *
26490 CGCAACGGCGAATCCAGTACCATGAAGATATGA
66 CGCAACGGCGAATCTAGTAACATGAAGATATAA
*
26523 AGGGAAAGG-TTAAGTCGCAACGGCGAATCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
*** *
26587 CGCAACGATAAATCTAGT-ACAATGAAGATACAA
66 CGCAACGGCGAATCTAGTAAC-ATGAAGATATAA
* * * * * *
26620 AAGGAAAGGTTTAAGTCGTAACAGCGAACCTTGTACCTCAAAAGCACGAAGGGAAGGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * *
26685 TGCAACGGCGAATCTAGTACCACGAAGATATAA
66 CGCAACGGCGAATCTAGTAACATGAAGATATAA
* * * * * *
26718 AGGGAAAGGTTTAAATCGCAACGGCGAACCTTGTACCTCAGAAACACGAAGGAAAATATTTAAGT
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
* * * *
26783 CGTAACAGCGAATCTAGTACCACGAAGA
66 CGCAACGGCGAATCTAGTAACATGAAGA
26811 CATTGAAGTG
Statistics
Matches: 338, Mismatches: 44, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
96 1 0.00
97 84 0.25
98 250 0.74
99 3 0.01
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (98 bp):
AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
CGCAACGGCGAATCTAGTAACATGAAGATATAA
Found at i:26673 original size:195 final size:196
Alignment explanation
Indices: 26327--26781 Score: 628
Period size: 195 Copynumber: 2.3 Consensus size: 196
26317 ACAGGTTTAG
*
26327 AGGGAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCTCA-AATGCATGAAGGAAAAGATTTAAG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA-GCATGAAGGAAAAGATTTAAG
* * * * ** * * **
26391 TCGCAACGGCGAATCCAGTAACATGATGATATGAAGGGAAAGGTTTAAGTTGCAATGGCGAACCT
65 CCGCAACGACAAATCCAGTAACATGAAGATACAAAAGGAAAGGTTTAAGTCGCAACAGCGAACCT
* * *
26456 TGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCATGAAGATAT
130 TGTACCTCAAAAGCACGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAT
*
26521 GA
195 AA
* *
26523 AGGGAAAGG-TTAAGTCGCAACGGCGAATCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGAAAAGATTTAAGC
* * *
26587 CGCAACGATAAATCTAGT-ACAATGAAGATACAAAAGGAAAGGTTTAAGTCGTAACAGCGAACCT
66 CGCAACGACAAATCCAGTAAC-ATGAAGATACAAAAGGAAAGGTTTAAGTCGCAACAGCGAACCT
* * *
26651 TGTACCTCAAAAGCACGAAGGGAAGGATTTAAGCTGCAACGGCGAATCTAGTACCACGAAGATAT
130 TGTACCTCAAAAGCACGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATAT
26716 AA
195 AA
* * * *
26718 AGGGAAAGGTTTAAATCGCAACGGCGAACCTTGTACCTCAGAAACACGAAGGAAAATATTTAAG
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGAAAAGATTTAAG
26782 TCGTAACAGC
Statistics
Matches: 227, Mismatches: 29, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
194 2 0.01
195 166 0.73
196 59 0.26
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (196 bp):
AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGAAGGAAAAGATTTAAGC
CGCAACGACAAATCCAGTAACATGAAGATACAAAAGGAAAGGTTTAAGTCGCAACAGCGAACCTT
GTACCTCAAAAGCACGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATA
A
Found at i:26754 original size:49 final size:49
Alignment explanation
Indices: 26327--26810 Score: 342
Period size: 49 Copynumber: 9.9 Consensus size: 49
26317 ACAGGTTTAG
* *
26327 AGGGAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCTC-AA-ATGCATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCACGAAGAT--ATGA
* * * * * *
26376 AGGAAAAGATTTAAGTCGCAACGGCGAATCC-AGTAACATGATGATATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTGTACCACGAAGATATGA
* * * *
26425 AGGGAAAGGTTTAAGTTGCAATGGCGAACCTTGTACCTCAGAAG-CATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCAC-GAAGATATGA
* * * *
26474 AGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCATGAAGATATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTGTACCACGAAGATATGA
* * *
26523 AGGGAAAGG-TTAAGTCGCAACGGCGAATCTTGTACCTCAGAAG-CATGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCAC-GAAGATATGA
* * *** * * * * **
26571 AGGGAAAGATTTAAGCCGCAACGATAAATCTAGTACAATGAAGATACAA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCACGAAGATATGA
* * * * * * *
26620 AAGGAAAGGTTTAAGTCGTAACAGCGAACCTTGTACCTC-AAAAGCACGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCACGAAGA-TATGA
* * *
26669 AGGG-AAGGATTTAAG-CTGCAACGGCGAATCTAGTACCACGAAGATATAA
1 AGGGAAAGG-TTTAAGTC-GCAACGGCGAACCTTGTACCACGAAGATATGA
* * * *
26718 AGGGAAAGGTTTAAATCGCAACGGCGAACCTTGTACCTCAGAA-ACACGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCAC-GAAGATATGA
* ** * * * *
26767 AGGAAAATATTTAAGTCGTAACAGCGAATCTAGTACCACGAAGA
1 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCACGAAGA
26811 CATTGAAGTG
Statistics
Matches: 329, Mismatches: 87, Indels: 38
0.72 0.19 0.08
Matches are distributed among these distances:
47 1 0.00
48 55 0.17
49 252 0.77
50 19 0.06
51 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (49 bp):
AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCACGAAGATATGA
Done.