Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006502.1 Kokia drynarioides strain JFW-HI SEQ_121086, 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: 13256
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Found at i:3180 original size:86 final size:89
Alignment explanation
Indices: 3049--3232 Score: 248
Period size: 86 Copynumber: 2.1 Consensus size: 89
3039 ATAAACTATT
* * *
3049 AATTTAAAACTTAAAAAATCAACAACAAAAAAAGTAAGGATCCAGTCGGATTGCTAAGAAATTAC
1 AATTCAAAACTTAAAAAATCAACAACAAAAAAAG-AACGATCCAGTCGGATGGCTAAGAAATTAC
* *
3114 ACAAAAATAT-CAGAAATACGATTA
65 ACAAAAATATAAAAAAATACGATTA
* * * *
3138 AATTCAAAACTTTAAAGATCAACAA-AAGAAAAG-ACGATCCAGTCGGATGGCTTAGAAATTACA
1 AATTCAAAACTTAAAAAATCAACAACAAAAAAAGAACGATCCAGTCGGATGGCTAAGAAATTACA
3201 CAAAAATATAAAAAAAATACGATTA
66 CAAAAATAT-AAAAAAATACGATTA
3226 AATTCAA
1 AATTCAA
3233 GGATAAACTA
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
86 36 0.43
88 26 0.31
89 22 0.26
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.21
Consensus pattern (89 bp):
AATTCAAAACTTAAAAAATCAACAACAAAAAAAGAACGATCCAGTCGGATGGCTAAGAAATTACA
CAAAAATATAAAAAAATACGATTA
Found at i:3499 original size:108 final size:108
Alignment explanation
Indices: 3310--3505 Score: 311
Period size: 108 Copynumber: 1.8 Consensus size: 108
3300 GTTCAATGAC
* * * * * *
3310 GATCCAGTCGGATTGCTAAGAAATCACACAAATATATCTGAAATACGATTAAATTCAAGAATAAC
1 GATCCAGTCGGATTACTAAGAAATCACACAAAAATACCAGAAATACGATTAAATTCAAGAACAAA
3375 CTACTAATTTAAAACTTAAAAAATCAACAGAAAAAAAAGTACG
66 CTACTAATTTAAAACTTAAAAAATCAACAGAAAAAAAAGTACG
* *
3418 GATCCAGTCGGATTACTAAGAAATTACACAAAAATACCAGAAATACGATTCAATTCAAGAACAAA
1 GATCCAGTCGGATTACTAAGAAATCACACAAAAATACCAGAAATACGATTAAATTCAAGAACAAA
*
3483 CTATTAATTTAAAACTTAAAAAA
66 CTACTAATTTAAAACTTAAAAAA
3506 GACGATCCAG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 79 1.00
ACGTcount: A:0.51, C:0.16, G:0.10, T:0.23
Consensus pattern (108 bp):
GATCCAGTCGGATTACTAAGAAATCACACAAAAATACCAGAAATACGATTAAATTCAAGAACAAA
CTACTAATTTAAAACTTAAAAAATCAACAGAAAAAAAAGTACG
Found at i:3519 original size:91 final size:87
Alignment explanation
Indices: 3407--3589 Score: 237
Period size: 91 Copynumber: 2.1 Consensus size: 87
3397 ATCAACAGAA
*
3407 AAAAAAGTACGGATCCAGTCGGATTACTAAGAAATTACACAAAAATACCAGAAATACGATTCAAT
1 AAAAAAGTACGGATCCAGTCGGATTACTAAAAAATTACACAAAAAT------AATACGATTCAAT
3472 TCAAGAACA-AACTATTAATTTAAAACTT
60 TCAAGAACAGAACTATTAATTTAAAAC-T
* *
3500 AAAAAAG-AC-GATCCAGTCGGATTGCTAAAAAATTACACAAAAATAATACGATTTAATTCAAGA
1 AAAAAAGTACGGATCCAGTCGGATTACTAAAAAATTACACAAAAATAATACGATTCAATTCAAGA
* *
3563 ACAGAACTATTACTTTTAAACT
66 ACAGAACTATTAATTTAAAACT
3585 AAAAA
1 AAAAA
3590 CAAAAAAGGC
Statistics
Matches: 84, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
85 27 0.32
86 15 0.18
91 33 0.39
92 2 0.02
93 7 0.08
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.24
Consensus pattern (87 bp):
AAAAAAGTACGGATCCAGTCGGATTACTAAAAAATTACACAAAAATAATACGATTCAATTCAAGA
ACAGAACTATTAATTTAAAACT
Found at i:5497 original size:28 final size:28
Alignment explanation
Indices: 5466--5533 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
5456 TTCATATTAA
* *
5466 TTTTGAATTTTTATAAACTTTTTATAATT
1 TTTTAAATTTTT-GAAACTTTTTATAATT
** **
5495 TTTTTTATTTTTGAATTTTTTTATAA-T
1 TTTTAAATTTTTGAAACTTTTTATAATT
5522 TTTTAAATTTTT
1 TTTTAAATTTTT
5534 TGTTGATCGT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
27 11 0.34
28 11 0.34
29 10 0.31
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTTAAATTTTTGAAACTTTTTATAATT
Found at i:5506 original size:19 final size:18
Alignment explanation
Indices: 5484--5534 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
5474 TTTTATAAAC
5484 TTTTTATAATTTTTTT-TA
1 TTTTTA-AATTTTTTTATA
*
5502 TTTTTGAATTTTTTTATAA
1 TTTTTAAATTTTTTTAT-A
5521 TTTTTAAATTTTTT
1 TTTTTAAATTTTTT
5535 GTTGATCGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 9 0.31
18 6 0.21
19 14 0.48
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTTAAATTTTTTTATA
Found at i:5933 original size:3 final size:3
Alignment explanation
Indices: 5925--5961 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5915 GGACATTTAA
5925 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5962 CGGACTGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:10450 original size:29 final size:30
Alignment explanation
Indices: 10408--10466 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
10398 TACAGTTTAA
*
10408 TGTGTAATTGTATACATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* *
10437 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
10467 GATCCAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:10475 original size:30 final size:29
Alignment explanation
Indices: 10413--10477 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
10403 TTTAATGTGT
* *
10413 AATTGTATACATGAACTTTGATTTTGTGC
1 AATTTTATACATGAACTTTGATTTTGTCC
*
10442 AATTTTATACATGAAATTTTGA-TTTGATCC
1 AATTTTATACATG-AACTTTGATTTTG-TCC
10472 AATTTT
1 AATTTT
10478 TGTAAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (29 bp):
AATTTTATACATGAACTTTGATTTTGTCC
Done.