Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015219.1 Kokia drynarioides strain JFW-HI SEQ_130263, 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: 403163
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 256 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:371830 original size:27 final size:27
Alignment explanation
Indices: 371791--371876 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
371781 TAACACCAAC
* * *
371791 AAATTTAACAATT-GAACTTAAATTTTT
1 AAATATAAAAATTAGAAC-TAAATTCTT
*
371818 AAATATAAAAATTAGGACTAAATTCTT
1 AAATATAAAAATTAGAACTAAATTCTT
* * *
371845 AAAAATAAAAGTATAGAGACTAAAAT-TT
1 AAATATAAAAAT-TAGA-ACTAAATTCTT
371873 AAAT
1 AAAT
371877 TTATGAAGAG
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
27 29 0.62
28 11 0.23
29 7 0.15
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.34
Consensus pattern (27 bp):
AAATATAAAAATTAGAACTAAATTCTT
Found at i:371865 original size:29 final size:27
Alignment explanation
Indices: 371809--371868 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
371799 CAATTGAACT
* *
371809 TAAATTTTTAAATATAAAAATTAGGAC
1 TAAATTCTTAAAAATAAAAATTAGGAC
*
371836 TAAATTCTTAAAAATAAAAGTATAGAGAC
1 TAAATTCTTAAAAATAAAAAT-TAG-GAC
371865 TAAA
1 TAAA
371869 ATTTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 18 0.64
28 3 0.11
29 7 0.25
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (27 bp):
TAAATTCTTAAAAATAAAAATTAGGAC
Found at i:382097 original size:29 final size:29
Alignment explanation
Indices: 382064--382122 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
382054 AGGTATTTGA
382064 CTCTATTTTTCTAGGTT-ATTTTTCATCAT
1 CTCTATTTTTCTAGGTTAATTTTT-ATCAT
* *
382093 CTCTATTTTTTTGGGTTAATTTTTATCAT
1 CTCTATTTTTCTAGGTTAATTTTTATCAT
382122 C
1 C
382123 GGATTAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.17, C:0.15, G:0.08, T:0.59
Consensus pattern (29 bp):
CTCTATTTTTCTAGGTTAATTTTTATCAT
Found at i:382274 original size:30 final size:30
Alignment explanation
Indices: 382239--382312 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
382229 TGTTTTTGTA
* *
382239 CGTATTATATTTGACTTCCAATTTTTATTT
1 CGTATTATATTTAACTTCCAATTTTTAATT
* * ** *
382269 TGTATTATATCTAACTTTTATTTTTTAATT
1 CGTATTATATTTAACTTCCAATTTTTAATT
382299 CGTATTATATTTAA
1 CGTATTATATTTAA
382313 ATTTTATTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.58
Consensus pattern (30 bp):
CGTATTATATTTAACTTCCAATTTTTAATT
Found at i:382318 original size:30 final size:30
Alignment explanation
Indices: 382260--382324 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
382250 TGACTTCCAA
* * *
382260 TTTTTATTTTGTATTATATCTAACTTTTAT
1 TTTTTAATTCGTATTATATCTAAATTTTAT
*
382290 TTTTTAATTCGTATTATATTTAAATTTTAT
1 TTTTTAATTCGTATTATATCTAAATTTTAT
382320 TTTTT
1 TTTTT
382325 GTTTTTGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (30 bp):
TTTTTAATTCGTATTATATCTAAATTTTAT
Found at i:382531 original size:18 final size:18
Alignment explanation
Indices: 382496--382605 Score: 93
Period size: 18 Copynumber: 6.2 Consensus size: 18
382486 TACGTACTGT
**
382496 TATGTTATGTATGCTATG
1 TATGTTATGTATATTATG
*
382514 TATATTATGTATATTATG
1 TATGTTATGTATATTATG
* * * *
382532 TACGTTATATTTACTAT-
1 TATGTTATGTATATTATG
382549 TATGTT-TGTATATT-TG
1 TATGTTATGTATATTATG
*
382565 TATG-TATGTTATGTTATG
1 TATGTTATG-TATATTATG
*
382583 TACTGTTTTGTATATTATG
1 TA-TGTTATGTATATTATG
382602 TATG
1 TATG
382606 ATTAATTGTA
Statistics
Matches: 71, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
15 2 0.03
16 11 0.15
17 10 0.14
18 33 0.46
19 12 0.17
20 3 0.04
ACGTcount: A:0.25, C:0.04, G:0.16, T:0.55
Consensus pattern (18 bp):
TATGTTATGTATATTATG
Found at i:382589 original size:10 final size:9
Alignment explanation
Indices: 382449--382619 Score: 84
Period size: 9 Copynumber: 18.4 Consensus size: 9
382439 GTTTTTAAAT
382449 TGTTATGTA
1 TGTTATGTA
*
382458 TATTATGTA
1 TGTTATGTA
382467 TGTATAATTGTA
1 TGT-T-A-TGTA
382479 TGTCTAT-TA
1 TGT-TATGTA
*
382488 CG-TACTGTTA
1 TGTTA-TG-TA
382498 TGTTATGTA
1 TGTTATGTA
*
382507 TGCTATGTA
1 TGTTATGTA
*
382516 TATTATGTA
1 TGTTATGTA
*
382525 TATTATGTA
1 TGTTATGTA
* * *
382534 CGTTATATT
1 TGTTATGTA
**
382543 TACTAT-TA
1 TGTTATGTA
382551 TGTT-TGTA
1 TGTTATGTA
*
382559 TATT-TGTA
1 TGTTATGTA
382567 TG-TATGTTA
1 TGTTATG-TA
382576 TGTTATGTA
1 TGTTATGTA
*
382585 CTGTTTTGTA
1 -TGTTATGTA
*
382595 TATTATGTA
1 TGTTATGTA
382604 TGATTAATTGTA
1 TG-TT-A-TGTA
382616 TGTT
1 TGTT
382620 TGTTATGTGT
Statistics
Matches: 123, Mismatches: 24, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
7 4 0.03
8 16 0.13
9 61 0.50
10 21 0.17
11 7 0.06
12 14 0.11
ACGTcount: A:0.25, C:0.04, G:0.16, T:0.54
Consensus pattern (9 bp):
TGTTATGTA
Found at i:382657 original size:17 final size:18
Alignment explanation
Indices: 382611--382657 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
382601 GTATGATTAA
*
382611 TTGTATGTTTGTTATGTG
1 TTGTATGATTGTTATGTG
* *
382629 TTGT-TTACTGTTATGT-
1 TTGTATGATTGTTATGTG
382645 TTGTATGATTGTT
1 TTGTATGATTGTT
382658 TATTAATGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
16 4 0.17
17 15 0.65
18 4 0.17
ACGTcount: A:0.13, C:0.02, G:0.23, T:0.62
Consensus pattern (18 bp):
TTGTATGATTGTTATGTG
Found at i:390588 original size:101 final size:101
Alignment explanation
Indices: 390432--390692 Score: 380
Period size: 101 Copynumber: 2.6 Consensus size: 101
390422 TATAGTTAGA
* *
390432 CTATGACATTTTGATGATAAGATCATAATCGGGTTATGAG-ACTATGAACATAAGACCATGGTTG
1 CTATGACATTCTGATGATAAGATCATAATCGGGTTATG-GCACTATGAACGTAAGACCATGGTTG
* *
390496 GACCATGGCAGTGTATATATGTAAGACCATAGCTGAG
65 GACCATGACAGTGTATATATGTAAGACCATAACTGAG
* * * * *
390533 CTATGGCATTCTGATGATAAGGTCATAATTGGGTTATGGCATTATGAACGCAAGACCATGGTTGG
1 CTATGACATTCTGATGATAAGATCATAATCGGGTTATGGCACTATGAACGTAAGACCATGGTTGG
* *
390598 ACCATGACAGTGTATATATGTAAGACCATAATTGGG
66 ACCATGACAGTGTATATATGTAAGACCATAACTGAG
* * *
390634 CTATGACATTCTGATGATAAGACCATAACCGGGTCATGGCACTATGAACGTAAGACCAT
1 CTATGACATTCTGATGATAAGATCATAATCGGGTTATGGCACTATGAACGTAAGACCAT
390693 AGTAAGGCAA
Statistics
Matches: 140, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
100 1 0.01
101 139 0.99
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (101 bp):
CTATGACATTCTGATGATAAGATCATAATCGGGTTATGGCACTATGAACGTAAGACCATGGTTGG
ACCATGACAGTGTATATATGTAAGACCATAACTGAG
Found at i:392957 original size:2 final size:2
Alignment explanation
Indices: 392950--392990 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
392940 TTTTTGCAAG
392950 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
392991 GTTTTGAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:396037 original size:39 final size:39
Alignment explanation
Indices: 395994--396075 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
395984 TTCAGGTTTT
395994 TTAAAAGGATTTCAGAAACATCTTGGCTGTTTCATGGTG
1 TTAAAAGGATTTCAGAAACATCTTGGCTGTTTCATGGTG
396033 TTAAAAGGATTTCAGAAACATCTTGGCTGTTTCATGGTG
1 TTAAAAGGATTTCAGAAACATCTTGGCTGTTTCATGGTG
396072 TTAA
1 TTAA
396076 GTGGGTTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (39 bp):
TTAAAAGGATTTCAGAAACATCTTGGCTGTTTCATGGTG
Found at i:396480 original size:46 final size:44
Alignment explanation
Indices: 396395--396483 Score: 115
Period size: 46 Copynumber: 2.0 Consensus size: 44
396385 AACATCCTTC
396395 CATTCAATCAAATATAAAAATATTATTATAAATATATTTTATTT
1 CATTCAATCAAATATAAAAATATTATTATAAATATATTTTATTT
* * * * *
396439 CATTCAATTAAATAATTAAATTATTGATTATAATTTTATTTTATT
1 CATTCAATCAAAT-ATAAAAATATT-ATTATAAATATATTTTATT
396484 AAAGTGAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 12 0.32
45 9 0.24
46 17 0.45
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (44 bp):
CATTCAATCAAATATAAAAATATTATTATAAATATATTTTATTT
Done.