Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008136.1 Kokia drynarioides strain JFW-HI SEQ_122794, 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: 28952
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:8542 original size:22 final size:22
Alignment explanation
Indices: 8517--8585 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
8507 AACCTACCGT
8517 ATCAATTATAATCAATCTTCTC
1 ATCAATTATAATCAATCTTCTC
* *
8539 ATCAAACTTACTAA-C-ATATTGT-
1 ATC-AA-TTA-TAATCAATCTTCTC
* *
8561 ATCAATTATAGTCAATCTTCCC
1 ATCAATTATAATCAATCTTCTC
8583 ATC
1 ATC
8586 CAATCAGCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
19 2 0.06
20 4 0.11
21 6 0.17
22 9 0.26
23 7 0.20
24 4 0.11
25 3 0.09
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (22 bp):
ATCAATTATAATCAATCTTCTC
Found at i:9127 original size:120 final size:117
Alignment explanation
Indices: 8885--9207 Score: 388
Period size: 120 Copynumber: 2.8 Consensus size: 117
8875 TTCGAAATTG
* * * *
8885 CCTCAACCTAAGATATCATAATCGAAAAGCACTCAATAATTAATTAAGCTCAAACTTAAGTAC-T
1 CCTCAACCTAAGATATTATAATCGAAAAGCACTGAATAACTAATTAAACTCAAACTTAAGTACTT
* * * * *
8949 -TT-ACTTTTTAATAATAATTTGTATGGCAAACTTAATATTGTTCAAAACTG
66 ATTCACTTTTTAATAATAATTTTTAAGCCAAACTTAACATTGTTCAAAACTA
* * * *
8999 CCTTAACCTAAGATATTATAAGCGAAAAACACTGGATAACTAATTAAACTCAAACTTAAGTACTT
1 CCTCAACCTAAGATATTATAATCGAAAAGCACTGAATAACTAATTAAACTCAAACTTAAGTACTT
9064 CGAATTCACTTTTTAATAATAATTTTTAAGCCAAACTTAACATTGTTCAAAACTA
66 ---ATTCACTTTTTAATAATAATTTTTAAGCCAAACTTAACATTGTTCAAAACTA
* * * * * * * *
9119 TCTCAACCTAAGATACTATAATCGAAAAGCATTGTATAACTAATTGAATTCAAACATAATTA--T
1 CCTCAACCTAAGATATTATAATCGAAAAGCACTGAATAACTAATTAAACTCAAACTTAAGTACTT
9182 -TTCACTTTTTAATAATAATTTTTAAG
66 ATTCACTTTTTAATAATAATTTTTAAG
9208 GTATAACGAC
Statistics
Matches: 179, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
114 81 0.45
115 1 0.01
118 1 0.01
119 2 0.01
120 94 0.53
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (117 bp):
CCTCAACCTAAGATATTATAATCGAAAAGCACTGAATAACTAATTAAACTCAAACTTAAGTACTT
ATTCACTTTTTAATAATAATTTTTAAGCCAAACTTAACATTGTTCAAAACTA
Found at i:9449 original size:20 final size:19
Alignment explanation
Indices: 9426--9494 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 19
9416 TTTTTATATA
9426 TTAAAATATTTTTTAATTTT
1 TTAAAAT-TTTTTTAATTTT
*
9446 TTAAATTTTTTTTATAATTTT
1 TTAAA-ATTTTTT-TAATTTT
*
9467 TTATAATTTTTTTAAATTTT
1 TTAAAATTTTTTT-AATTTT
9487 TTAAAATT
1 TTAAAATT
9495 AATTAATTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
19 1 0.02
20 29 0.69
21 12 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTAAAATTTTTTTAATTTT
Found at i:9452 original size:9 final size:9
Alignment explanation
Indices: 9433--9491 Score: 66
Period size: 11 Copynumber: 6.1 Consensus size: 9
9423 ATATTAAAAT
9433 ATTTTTT-A
1 ATTTTTTAA
9441 ATTTTTTAA
1 ATTTTTTAA
9450 ATTTTTTTTATA
1 A--TTTTTTA-A
9462 ATTTTTTATA
1 ATTTTTTA-A
9472 ATTTTTTTAA
1 A-TTTTTTAA
9482 ATTTTTTAA
1 ATTTTTTAA
9491 A
1 A
9492 ATTAATTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
8 7 0.15
9 11 0.24
10 12 0.26
11 14 0.30
12 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:9458 original size:21 final size:19
Alignment explanation
Indices: 9429--9491 Score: 81
Period size: 21 Copynumber: 3.2 Consensus size: 19
9419 TTATATATTA
*
9429 AAATATTTTTTAATTTTTT
1 AAATTTTTTTTAATTTTTT
9448 AAATTTTTTTTATAATTTTTT
1 AAA-TTTTTTT-TAATTTTTT
*
9469 ATAATTTTTTTAAATTTTTT
1 A-AATTTTTTTTAATTTTTT
9489 AAA
1 AAA
9492 ATTAATTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 5 0.13
20 15 0.38
21 17 0.44
22 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
AAATTTTTTTTAATTTTTT
Found at i:9493 original size:10 final size:10
Alignment explanation
Indices: 9426--9494 Score: 68
Period size: 10 Copynumber: 6.8 Consensus size: 10
9416 TTTTTATATA
9426 TTAAAATATTT
1 TTAAAAT-TTT
*
9437 TT-TAATTTT
1 TTAAAATTTT
*
9446 TTAAATTTTTT
1 TTAAA-ATTTT
*
9457 TTATAATTTT
1 TTAAAATTTT
*
9467 TTATAATTTT
1 TTAAAATTTT
*
9477 TTTAAATTTT
1 TTAAAATTTT
9487 TTAAAATT
1 TTAAAATT
9495 AATTAATTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
9 5 0.10
10 33 0.69
11 10 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTAAAATTTT
Found at i:12044 original size:17 final size:17
Alignment explanation
Indices: 12022--12067 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 17
12012 GACCCAATAG
12022 AATTTAAATTTATTGA-A
1 AATTTAAATTTATT-ATA
12039 AATTTAAATTTATTATA
1 AATTTAAATTTATTATA
12056 AATTTAAATTTA
1 AATTTAAATTTA
12068 AGATTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 1 0.04
17 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:12064 original size:23 final size:23
Alignment explanation
Indices: 12038--12081 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
12028 AATTTATTGA
12038 AAATTTAA-ATTTATTATAAATTT
1 AAATTTAAGATTTATT-TAAATTT
12061 AAATTTAAGATTTATTTAAAT
1 AAATTTAAGATTTATTTAAAT
12082 AATGTCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AAATTTAAGATTTATTTAAATTT
Found at i:12077 original size:11 final size:10
Alignment explanation
Indices: 12023--12081 Score: 52
Period size: 11 Copynumber: 5.8 Consensus size: 10
12013 ACCCAATAGA
12023 ATTTAAATTT
1 ATTTAAATTT
*
12033 ATTGAAA---
1 ATTTAAATTT
12040 ATTTAAATTT
1 ATTTAAATTT
12050 ATTATAAATTT
1 ATT-TAAATTT
12061 AAATTTAAGATTT
1 --ATTTAA-ATTT
12074 ATTTAAAT
1 ATTTAAAT
12082 AATGTCTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
7 6 0.15
10 11 0.28
11 13 0.32
12 3 0.08
13 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:12773 original size:10 final size:10
Alignment explanation
Indices: 12758--12865 Score: 50
Period size: 10 Copynumber: 11.3 Consensus size: 10
12748 GCATTAAATA
*
12758 AATTAATAGT
1 AATTAATAAT
12768 AATTAATAAT
1 AATTAATAAT
12778 AA-TAATAAT
1 AATTAATAAT
*
12787 -GTTAATAAT
1 AATTAATAAT
* *
12796 AAATAGA-AGT
1 AATTA-ATAAT
* *
12806 AATAAAT-AG
1 AATTAATAAT
*
12815 CATTAATAA-
1 AATTAATAAT
12824 ATATTAATAA-
1 A-ATTAATAAT
* *
12834 AAATATTAAT
1 AATTAATAAT
*
12844 AA-TATTAAT
1 AATTAATAAT
*
12853 AATTAATATT
1 AATTAATAAT
12863 AAT
1 AAT
12866 ATTAAATAAA
Statistics
Matches: 74, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
9 35 0.47
10 38 0.51
11 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (10 bp):
AATTAATAAT
Found at i:12810 original size:13 final size:13
Alignment explanation
Indices: 12792--12826 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
12782 ATAATGTTAA
12792 TAATAAATAGAAG
1 TAATAAATAGAAG
* *
12805 TAATAAATAGCAT
1 TAATAAATAGAAG
12818 TAATAAATA
1 TAATAAATA
12827 TTAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.29
Consensus pattern (13 bp):
TAATAAATAGAAG
Found at i:12839 original size:12 final size:12
Alignment explanation
Indices: 12822--12866 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
12812 TAGCATTAAT
12822 AAATATTAATAA
1 AAATATTAATAA
12834 AAATATTAAT--
1 AAATATTAATAA
12844 -AATATTAATAA
1 AAATATTAATAA
*
12855 TTAATATTAATA
1 -AAATATTAATA
12867 TTAAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 9 0.31
12 10 0.34
13 10 0.34
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATATTAATAA
Found at i:12841 original size:22 final size:23
Alignment explanation
Indices: 12816--12866 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
12806 AATAAATAGC
12816 ATTAATAAATATTAATAA-AAAT
1 ATTAATAAATATTAATAATAAAT
*
12838 ATTAAT-AATATTAATAATTAAT
1 ATTAATAAATATTAATAATAAAT
12860 ATTAATA
1 ATTAATA
12867 TTAAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTAATAAATATTAATAATAAAT
Found at i:13399 original size:41 final size:41
Alignment explanation
Indices: 13353--13446 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
13343 AAAGGGGCTA
13353 CCTCTGCTACCTTGCAACAACTTCTTCCATATCAATCCATT
1 CCTCTGCTACCTTGCAACAACTTCTTCCATATCAATCCATT
13394 CCTCTGCTACCTTGCAACAACTTCTTCCATATCAATCCATT
1 CCTCTGCTACCTTGCAACAACTTCTTCCATATCAATCCATT
13435 CCTCTGCTACCT
1 CCTCTGCTACCT
13447 CTGCTGAACA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.22, C:0.38, G:0.05, T:0.34
Consensus pattern (41 bp):
CCTCTGCTACCTTGCAACAACTTCTTCCATATCAATCCATT
Done.