Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002800.1 Kokia drynarioides strain JFW-HI SEQ_115143, 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: 88569
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 76 characters in sequence are not A, C, G, or T
Found at i:3907 original size:16 final size:16
Alignment explanation
Indices: 3886--3917 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3876 AATCAATTTA
3886 AATTAAATAATTTTCT
1 AATTAAATAATTTTCT
3902 AATTAAATAATTTTCT
1 AATTAAATAATTTTCT
3918 CAACCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTAAATAATTTTCT
Found at i:17525 original size:30 final size:30
Alignment explanation
Indices: 17489--17549 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
17479 ACCCAACCCT
*
17489 TTACAATTTCAATCTAGTTTACACCACAAG
1 TTACAATTTCAACCTAGTTTACACCACAAG
17519 TTACAATTTCAACCTAGTTTACACCACAAG
1 TTACAATTTCAACCTAGTTTACACCACAAG
17549 T
1 T
17550 CACCAAGGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.33
Consensus pattern (30 bp):
TTACAATTTCAACCTAGTTTACACCACAAG
Found at i:24868 original size:94 final size:95
Alignment explanation
Indices: 24695--24887 Score: 325
Period size: 94 Copynumber: 2.0 Consensus size: 95
24685 CAAATAAACC
*
24695 TATTGATAGCATTAGAAAAGACCATTAATTTCTCCTTATTTAAAGTATAATTTGTTCCCATTATA
1 TATTGATAGCATTAGAAAAGACCATTAATTTCTCCTGATTTAAAGTATAATTTGTTCCCATTATA
*
24760 TCATGTTTAACATGCATTTTTAGCATTTTA
66 CCATGTTTAACATGCATTTTTAGCATTTTA
* * *
24790 TATTGATAGCATTAGAAAAGACCATTAATTTC-CCTGATTTAGAGTATAATTTGTTCCCTTTGTA
1 TATTGATAGCATTAGAAAAGACCATTAATTTCTCCTGATTTAAAGTATAATTTGTTCCCATTATA
*
24854 CCATGTTTAGCATGCATTTTTAGCATTTTA
66 CCATGTTTAACATGCATTTTTAGCATTTTA
24884 TATT
1 TATT
24888 TAGTAATTGC
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
94 60 0.65
95 32 0.35
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (95 bp):
TATTGATAGCATTAGAAAAGACCATTAATTTCTCCTGATTTAAAGTATAATTTGTTCCCATTATA
CCATGTTTAACATGCATTTTTAGCATTTTA
Found at i:33991 original size:61 final size:61
Alignment explanation
Indices: 33921--34039 Score: 211
Period size: 61 Copynumber: 2.0 Consensus size: 61
33911 TGAGAATTTT
33921 TTTCGTATTACGATTTGACCATGTAATACCAAGTAGTATTAGTTAAATGTTAGATAAACAA
1 TTTCGTATTACGATTTGACCATGTAATACCAAGTAGTATTAGTTAAATGTTAGATAAACAA
* * *
33982 TTTCGTATTACGATTTGACCATGTAATATCGATTAGTATTAGTTAAATGTTAGATAAA
1 TTTCGTATTACGATTTGACCATGTAATACCAAGTAGTATTAGTTAAATGTTAGATAAA
34040 AAATGAGCCA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (61 bp):
TTTCGTATTACGATTTGACCATGTAATACCAAGTAGTATTAGTTAAATGTTAGATAAACAA
Found at i:34404 original size:85 final size:86
Alignment explanation
Indices: 34299--34464 Score: 221
Period size: 85 Copynumber: 1.9 Consensus size: 86
34289 TGCTCCACAT
* * * *
34299 ATTTGTGTTGTTGCAGGTATGTCACAAT-ATCA-TCTGAAATTGGATTCTGACCATATCTTTGAT
1 ATTTGTGTTGTTGCAGGTATGTCAC-ATGATCATTC-AAAATCGGATTCTAACCATATCTTTGAC
* *
34362 ATTATCTTACTTATGGTGTAATA
64 ATTACCTTACCTATGGTGTAATA
*
34385 ATTT-TGTTGTTGCAGGTATGTCACATGATCATTCAAAATCGGATTCTAACCTTATCTTTGACAT
1 ATTTGTGTTGTTGCAGGTATGTCACATGATCATTCAAAATCGGATTCTAACCATATCTTTGACAT
*
34449 TGCCTTACCTATGGTG
66 TACCTTACCTATGGTG
34465 AAAGTGAATC
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
84 2 0.03
85 62 0.89
86 6 0.09
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (86 bp):
ATTTGTGTTGTTGCAGGTATGTCACATGATCATTCAAAATCGGATTCTAACCATATCTTTGACAT
TACCTTACCTATGGTGTAATA
Found at i:36047 original size:17 final size:17
Alignment explanation
Indices: 36021--36054 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
36011 TCTTCAAAAC
*
36021 TTCCCTCATTTTGAAGG
1 TTCCCCCATTTTGAAGG
36038 TTCCCCCATTTTGAAGG
1 TTCCCCCATTTTGAAGG
36055 GTTTGGTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (17 bp):
TTCCCCCATTTTGAAGG
Found at i:39038 original size:7 final size:7
Alignment explanation
Indices: 39026--39050 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39016 TCTAATTTCC
39026 TGTCATG
1 TGTCATG
39033 TGTCATG
1 TGTCATG
39040 TGTCATG
1 TGTCATG
39047 TGTC
1 TGTC
39051 GTGAGCAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.28, T:0.44
Consensus pattern (7 bp):
TGTCATG
Found at i:39701 original size:17 final size:17
Alignment explanation
Indices: 39666--39698 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39656 TTAAGATAAG
*
39666 TATTAAATTTAATTTAA
1 TATTAAATTTAATTAAA
39683 TATTAAATTT-ATTAAA
1 TATTAAATTTAATTAAA
39699 ATAATATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAAATTTAATTAAA
Found at i:40931 original size:15 final size:15
Alignment explanation
Indices: 40911--40940 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40901 CTATGCATGC
40911 AAAATAAGAAAGACA
1 AAAATAAGAAAGACA
*
40926 AAAATACGAAAGACA
1 AAAATAAGAAAGACA
40941 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.10, G:0.13, T:0.07
Consensus pattern (15 bp):
AAAATAAGAAAGACA
Found at i:47760 original size:20 final size:19
Alignment explanation
Indices: 47737--47784 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
47727 AGAGACATAA
47737 AAAGTAAATAAGTA-AAAAT
1 AAAGTAAATAA-TATAAAAT
*
47756 GAAAGGAAATAATATAAAAT
1 -AAAGTAAATAATATAAAAT
*
47776 AAAATAAAT
1 AAAGTAAAT
47785 GAAAACAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (19 bp):
AAAGTAAATAATATAAAAT
Found at i:49745 original size:99 final size:94
Alignment explanation
Indices: 49571--49824 Score: 214
Period size: 99 Copynumber: 2.6 Consensus size: 94
49561 GGTGATGTAA
* *
49571 CTTCACTCCATTCCACTTTAACCTCAGGGACATTGAGAT-T-CGTTACTTGTTTTAATCCACTTC
1 CTTCACTCCATTCCA-TTTAACCTCAGGGACATTGAGATCTAC-TTACTTATTTTAATCCACTCC
* * * * *
49634 ATTGCATCTTCAGGAAGATAGAATTTATTGTTGAAG
64 ACTGCATATTCAGG--GATA-AA-TGATTCTAG-AG
*
49670 CTTCACTCCATTCCATTATAACCTCAGGGACATTGAGATCTACTT-CGTTATTTTCATCCGAC-C
1 CTTCACTCCATTCCATT-TAACCTCAGGGACATTGAGATCTACTTAC-TTATTTTAATCC-ACTC
* * * *
49733 CACTGTA-ATTCAGGGGTATATGATTCTAGTG
63 CACTGCATATTCAGGGATAAATGATTCTAGAG
* * * * *
49764 CTTCACTCCAATCCATTGTAACCTCAGGGACCTTGAGATCTAC-TACCTGTTTTAACCCACT
1 CTTCACTCCATTCCATT-TAACCTCAGGGACATTGAGATCTACTTACTTATTTTAATCCACT
49825 TCTCTTTACC
Statistics
Matches: 129, Mismatches: 19, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
92 2 0.02
93 9 0.07
94 42 0.33
95 6 0.05
96 1 0.01
97 3 0.02
98 2 0.02
99 43 0.33
100 18 0.14
101 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (94 bp):
CTTCACTCCATTCCATTTAACCTCAGGGACATTGAGATCTACTTACTTATTTTAATCCACTCCAC
TGCATATTCAGGGATAAATGATTCTAGAG
Found at i:49949 original size:189 final size:190
Alignment explanation
Indices: 49664--50088 Score: 539
Period size: 189 Copynumber: 2.2 Consensus size: 190
49654 GAATTTATTG
* * * * *
49664 TTGAAGCTTCACTCCATTCCATTATAACCTCAGGGACATTGAGATCTACTTCGTTATTTTCATCC
1 TTGAAGATTCAATCCACTCCACTATAACCTCAGGGACATTGAGATCTACTTCATTATTTTCATCC
* ** * * * *
49729 GACCCACTGTAATTCAGGGGTATATGATTCTAGTGCTTCACTCCAATCCATTGTAACCTCAGGGA
66 GACCCACTGCAACCCAAGGGTATAGGATTCTACTGCTTCACTCCAATCCACTGTAACCTCAGGGA
* * *
49794 CCTTGAGATCTACTACCTGTTTTAACCCACTTCTCTTTACCTCACCAA-GAATATGGGA-T
131 CCTTGAGATCTACTACCTATTTTAACCCACTTCTCTATACCTCA-CAAGGAAGATGGGATT
* * * * * *
49853 TTGAAGATTCAATCCACTCCACTGTCACCTCAGAGACATTGAGCTTTGCTTCATTATTTTCATCC
1 TTGAAGATTCAATCCACTCCACTATAACCTCAGGGACATTGAGATCTACTTCATTATTTTCATCC
* *
49918 GACCCACTGCAACCCAAGGGTATAGGATTCTACTGCTTCACTCCACTCTACTGTAACCTCAGGGA
66 GACCCACTGCAACCCAAGGGTATAGGATTCTACTGCTTCACTCCAATCCACTGTAACCTCAGGGA
** * *
49983 TGTTGAGATCTGCTATCTATTTTAACCCACTTCTCTATACCTCACAAGGAAGATGGGATT
131 CCTTGAGATCTACTACCTATTTTAACCCACTTCTCTATACCTCACAAGGAAGATGGGATT
** * * *
50043 TTGGCGCTTCACTCCACTCCACTATAACCTCAGGGACGTTGAGATC
1 TTGAAGATTCAATCCACTCCACTATAACCTCAGGGACATTGAGATC
50089 CATTTTGTTA
Statistics
Matches: 197, Mismatches: 37, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
188 3 0.02
189 157 0.80
190 37 0.19
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.32
Consensus pattern (190 bp):
TTGAAGATTCAATCCACTCCACTATAACCTCAGGGACATTGAGATCTACTTCATTATTTTCATCC
GACCCACTGCAACCCAAGGGTATAGGATTCTACTGCTTCACTCCAATCCACTGTAACCTCAGGGA
CCTTGAGATCTACTACCTATTTTAACCCACTTCTCTATACCTCACAAGGAAGATGGGATT
Found at i:50297 original size:49 final size:49
Alignment explanation
Indices: 50251--51185 Score: 855
Period size: 49 Copynumber: 19.1 Consensus size: 49
50241 CCTCATCTTC
** * *
50251 AGGGTATAAGATTCACCATTGTGGCTTCAATCTTTCCCTTCACATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * * * * *
50300 AAGGTATAAGGTTCATTGTTGCGGCTTCAACCTTTTCCTTCACATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * * * * *
50349 AGGGTATAAGGTTTGTCGTTGCAGCTTCAACCTTTCCCTCCATATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * ** *
50398 AGGGTACAAGATTCG-CTGTTACGAATTCAATCTTTCCCATCACATCTCT
1 AGGGTATAAGATTCGTC-GTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * * * **
50447 AAGGTATAAGGTTCGTCATTGCAGCTTCAGCCTTT-CCTTCCACATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTT-CACATCTCT
* * * * * *
50496 ATGGTATAAGATTTGTCGTTACAGCTTCAAT-TTTTCCAT--CATCT-T
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * *
50541 CAGAGTATAAGATTCGTCGTTACGGCTTCAATCTTTCCCTTCACATCTTT
1 -AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * * * * *
50591 AGGGTATAAGGTTCGTCGTTACGGCTTCAACCTTTCCCTCCATATTTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
** * * *
50640 AGGGTATAAGATTCACCGTTACTGCTTCAATCTTTCCCTTTACATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
*** * * *
50689 AGGGTATAAGATTCG-CTGTTTATGCTTCAACCTTTCCCTCCGCATCTCT
1 AGGGTATAAGATTCGTC-GTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * * * *
50738 AGGGTATAAGGTTTGTCGTTGCGGCTTCAACCTTTCCCTCCATATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * * ** * *
50787 AGAGTATAAGATTCGTCATTACTTCTTCAATCTTTCCCTTCACAACTTT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* ** * * * *
50836 AGGGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTTAATATTTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
***
50885 AGGGTATAAGATTTACCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * *
50934 AGGGTATAAGGTTCGTCGTTGCGGCTTCAACCTTTCCCTTTACATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* ** * * *
50983 AGGGTATAAGGTTCACCGTTGCAGCTTCAA-CATTTCCCTCCATATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATC-TTTCCCTTCACATCTCT
* *
51032 AAGGTATAAGATTTGTCGTTGCGGCTTCAATCTTTCCC-TCTACATCTCT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTC-ACATCTCT
* * *
51081 AGGGTATTAAGATTCGTCGTTGCGACCTCAATCTTTCCTTTCACATCTCT
1 AGGGTA-TAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
* * * * * * * *
51131 AAGGTATAAGGTTCGTTGTTACGGCTT-TATCCTTTCCCTCCACGTCTTT
1 AGGGTATAAGATTCGTCGTTGCGGCTTCAAT-CTTTCCCTTCACATCTCT
51180 AGGGTA
1 AGGGTA
51186 CACGATTCAA
Statistics
Matches: 718, Mismatches: 151, Indels: 34
0.80 0.17 0.04
Matches are distributed among these distances:
45 1 0.00
46 32 0.04
47 6 0.01
48 12 0.02
49 620 0.86
50 45 0.06
51 2 0.00
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (49 bp):
AGGGTATAAGATTCGTCGTTGCGGCTTCAATCTTTCCCTTCACATCTCT
Found at i:51822 original size:112 final size:112
Alignment explanation
Indices: 51622--51837 Score: 324
Period size: 112 Copynumber: 1.9 Consensus size: 112
51612 ATCGTTAGAT
* * *
51622 CACTAACCATCATTTCAATGCAAAAAAGCTTGAATAGGGTTGTAAAGTGGATAAAATTGAATTTT
1 CACTAACCATCATTTCAATGCAAAAAAGCTTGAACAAGATTGTAAAGTGGATAAAATTGAATTTT
* *
51687 ATTAGAGGAAAAGCTCGCGTGAATGAAAAGATTAAAAATCATTAGTC
66 ATTAGAGGAAAAGCTCACATGAATGAAAAGATTAAAAATCATTAGTC
* *** *
51734 CACTAACCATTATTTCAATGCAAATTTGCTTGAACAAGATTGTAAGGTGGATAAAATTGAATTTT
1 CACTAACCATCATTTCAATGCAAAAAAGCTTGAACAAGATTGTAAAGTGGATAAAATTGAATTTT
* *
51799 ATTATAGGCAAAGCTCACATGAATGAAAAGATTAAAAAT
66 ATTAGAGGAAAAGCTCACATGAATGAAAAGATTAAAAAT
51838 GAAAAACATT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
112 92 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (112 bp):
CACTAACCATCATTTCAATGCAAAAAAGCTTGAACAAGATTGTAAAGTGGATAAAATTGAATTTT
ATTAGAGGAAAAGCTCACATGAATGAAAAGATTAAAAATCATTAGTC
Found at i:52161 original size:7 final size:7
Alignment explanation
Indices: 52149--52214 Score: 84
Period size: 7 Copynumber: 9.7 Consensus size: 7
52139 CGACCTCTCC
52149 TTTTTCT
1 TTTTTCT
52156 TTTTTCT
1 TTTTTCT
52163 TTTTTCT
1 TTTTTCT
*
52170 TCTCTTCT
1 T-TTTTCT
*
52178 CTTTTCT
1 TTTTTCT
52185 TTTTTC-
1 TTTTTCT
52191 TTTTTC-
1 TTTTTCT
52197 TTTTT-T
1 TTTTTCT
52203 TTTTTCT
1 TTTTTCT
52210 TTTTT
1 TTTTT
52215 TTGGGTGAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
6 16 0.31
7 31 0.60
8 5 0.10
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:52177 original size:22 final size:20
Alignment explanation
Indices: 52148--52213 Score: 91
Period size: 22 Copynumber: 3.3 Consensus size: 20
52138 TCGACCTCTC
52148 CTTTTTCTTTTTTCTTTTTT
1 CTTTTTCTTTTTTCTTTTTT
*
52168 CTTCTCTTCTCTTTTCTTTTTT
1 CTT-T-TTCTTTTTTCTTTTTT
52190 CTTTTTC-TTTTT-TTTTTT
1 CTTTTTCTTTTTTCTTTTTT
52208 CTTTTT
1 CTTTTT
52214 TTTGGGTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
18 12 0.29
19 4 0.10
20 6 0.14
21 2 0.05
22 18 0.43
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
CTTTTTCTTTTTTCTTTTTT
Found at i:52215 original size:12 final size:12
Alignment explanation
Indices: 52149--52216 Score: 73
Period size: 12 Copynumber: 5.2 Consensus size: 12
52139 CGACCTCTCC
52149 TTTTTCTTTTTTCT
1 TTTTTC-TTTTT-T
52163 TTTTTCTTCTCTTCT
1 TTTTTCTT-T-TT-T
*
52178 CTTTTCTTTTTT
1 TTTTTCTTTTTT
52190 CTTTTTCTTTTTT
1 -TTTTTCTTTTTT
52203 TTTTTCTTTTTT
1 TTTTTCTTTTTT
52215 TT
1 TT
52217 GGGTGAAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
12 15 0.31
13 15 0.31
14 8 0.16
15 11 0.22
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:54955 original size:14 final size:14
Alignment explanation
Indices: 54916--54969 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
54906 AATACATTTG
54916 TTTTTTCTTGTTGTC
1 TTTTTTCTT-TTGTC
* **
54931 TTGTTGATTTTGTC
1 TTTTTTCTTTTGTC
*
54945 TTTTTTCTTTTGTTA
1 TTTTTTCTTTTG-TC
54960 TTTTTTCTTT
1 TTTTTTCTTT
54970 GTTTTTGCAG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 14 0.45
15 17 0.55
ACGTcount: A:0.04, C:0.09, G:0.11, T:0.76
Consensus pattern (14 bp):
TTTTTTCTTTTGTC
Found at i:58428 original size:40 final size:40
Alignment explanation
Indices: 58373--58455 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
58363 CCAATATATG
58373 CATGGCATGCTATGTCAATTTTATAATATTGACATTCATT
1 CATGGCATGCTATGTCAATTTTATAATATTGACATTCATT
58413 CATGGCATGCTATGTCAATTTTATAATATTGACATTCATT
1 CATGGCATGCTATGTCAATTTTATAATATTGACATTCATT
58453 CAT
1 CAT
58456 ACACAATAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (40 bp):
CATGGCATGCTATGTCAATTTTATAATATTGACATTCATT
Found at i:59448 original size:11 final size:11
Alignment explanation
Indices: 59432--59508 Score: 54
Period size: 11 Copynumber: 6.8 Consensus size: 11
59422 GATAATCACT
59432 TTAATATTAAA
1 TTAATATTAAA
59443 TTAATA--AAA
1 TTAATATTAAA
59452 -TAATATTAAGA
1 TTAATATTAA-A
*
59463 TAAATATTAAA
1 TTAATATTAAA
59474 TTTAAT-TTAATA
1 -TTAATATTAA-A
59486 TTAAATATATTAAA
1 TT--A-ATATTAAA
*
59500 ATAATATTA
1 TTAATATTA
59509 TTTTTGTAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 20
0.70 0.04 0.26
Matches are distributed among these distances:
8 5 0.09
9 3 0.06
10 2 0.04
11 20 0.38
12 14 0.26
13 1 0.02
14 4 0.08
15 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:68050 original size:23 final size:23
Alignment explanation
Indices: 68027--68355 Score: 401
Period size: 23 Copynumber: 14.3 Consensus size: 23
68017 TTAAATGTGT
* *
68027 TTAAATGTTAATATGATTTATGT
1 TTAAATGTTAATGTGATTTATGC
** *
68050 TTAAAACTTAATGTGATTTATAC
1 TTAAATGTTAATGTGATTTATGC
*
68073 TTAAAAGTTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
* *
68096 TTAAATGTTAATATGATTTATAC
1 TTAAATGTTAATGTGATTTATGC
*
68119 TTAAATGTTAATATGATTTATAG-
1 TTAAATGTTAATGTGATTTAT-GC
*
68142 TTAAATGTTAATGTGATTTGTGC
1 TTAAATGTTAATGTGATTTATGC
* * *
68165 TTAAAAGTTAATGCGATTTGTGC
1 TTAAATGTTAATGTGATTTATGC
* *
68188 TTAAATATTAATGTGATTTGTGC
1 TTAAATGTTAATGTGATTTATGC
* *
68211 TTAAATATTAATGTGATTTGTGC
1 TTAAATGTTAATGTGATTTATGC
*
68234 TTAAATATTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
* * *
68257 TTACATATTAATGTGATTTGTGC
1 TTAAATGTTAATGTGATTTATGC
* *
68280 TTAAATGTTAATATAATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
68303 TTAAATATTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
68326 TTAAATATTAATGTGATTTATG-
1 TTAAATGTTAATGTGATTTATGC
68348 TGTAAATG
1 T-TAAATG
68356 GACCCATGAA
Statistics
Matches: 273, Mismatches: 30, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
22 2 0.01
23 271 0.99
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (23 bp):
TTAAATGTTAATGTGATTTATGC
Found at i:71775 original size:106 final size:106
Alignment explanation
Indices: 71589--71779 Score: 264
Period size: 106 Copynumber: 1.8 Consensus size: 106
71579 CAGGTCATTG
* * * *
71589 TTGTCGGGCAATCCAGGGTGGTAAGTCATCATCGCCGGACAATTCGGGGTGGCAAGTCACCATTT
1 TTGTCAGGCAATCCAGGATGGTAAGCCATCATCGCAGGACAATTCGGGGTGGCAAGTCACCATTT
**
71654 TCGGACAATTTGGGATGACATAAAAGAATTAAAAACCATCA
66 TCGGACAATCCGGGATGACATAAAAGAATTAAAAACCATCA
71695 TTGTCAGGCAATCC-GAGATGGTAAGCCATCATCGCTAGGA-AATTCGGGGTGGCAAGTCATCC-
1 TTGTCAGGCAATCCAG-GATGGTAAGCCATCATCGC-AGGACAATTCGGGGTGGCAAGTCA-CCA
71757 TTTTCAGG-CAATCCGGGATGACA
63 TTTTC-GGACAATCCGGGATGACA
71780 GATTGAAAGG
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
105 1 0.01
106 67 0.89
107 7 0.09
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.24
Consensus pattern (106 bp):
TTGTCAGGCAATCCAGGATGGTAAGCCATCATCGCAGGACAATTCGGGGTGGCAAGTCACCATTT
TCGGACAATCCGGGATGACATAAAAGAATTAAAAACCATCA
Found at i:75808 original size:19 final size:19
Alignment explanation
Indices: 75784--75820 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
75774 TAGATCATTG
*
75784 TATGCATAATAGCTCACTA
1 TATGCATAATAGCCCACTA
75803 TATGCATAATAGCCCACT
1 TATGCATAATAGCCCACT
75821 TCGTTGTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (19 bp):
TATGCATAATAGCCCACTA
Found at i:83508 original size:6 final size:6
Alignment explanation
Indices: 83491--83525 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
83481 GGTTTCGGGA
* *
83491 TAGGGT TGGGGT TTGGGT TAGGGT TAGGGT TAGGG
1 TAGGGT TAGGGT TAGGGT TAGGGT TAGGGT TAGGG
83526 ATTGCGGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.11, C:0.00, G:0.54, T:0.34
Consensus pattern (6 bp):
TAGGGT
Found at i:83514 original size:18 final size:19
Alignment explanation
Indices: 83479--83521 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
83469 GCGGAAGGTA
83479 AGGGTTTCGGGATAGGGTT
1 AGGGTTTCGGGATAGGGTT
* *
83498 GGGGTTT-GGGTTAGGGTT
1 AGGGTTTCGGGATAGGGTT
83516 AGGGTT
1 AGGGTT
83522 AGGGATTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.12, C:0.02, G:0.51, T:0.35
Consensus pattern (19 bp):
AGGGTTTCGGGATAGGGTT
Found at i:84108 original size:37 final size:34
Alignment explanation
Indices: 84061--84158 Score: 89
Period size: 30 Copynumber: 2.9 Consensus size: 34
84051 TTAAAATTTT
*
84061 AAATTAATAAAAATAAAATTATATTTTATCTCTCTTAA
1 AAATT-ATAAAAATAAAATTA-ATTTAAT-T-TCTTAA
*
84099 AAATTATAAAAAT----TTAATTTAATTTTTTAA
1 AAATTATAAAAATAAAATTAATTTAATTTCTTAA
*
84129 AAATTATAAAAATAAAAACT-ATTTAATTTC
1 AAATTATAAAAAT-AAAATTAATTTAATTTC
84159 AACCCTCTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
30 18 0.35
31 1 0.02
32 6 0.12
33 3 0.06
34 9 0.18
35 1 0.02
37 8 0.16
38 5 0.10
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (34 bp):
AAATTATAAAAATAAAATTAATTTAATTTCTTAA
Found at i:84453 original size:20 final size:19
Alignment explanation
Indices: 84430--84478 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 19
84420 AATTTGTCAC
84430 TATACTTTTTTATTTACCTT
1 TATA-TTTTTTATTTACCTT
84450 TATATTTTTTTTATTTACCTT
1 TATA--TTTTTTATTTACCTT
84471 TATATTTT
1 TATATTTT
84479 GAAATTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 4 0.15
21 19 0.70
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.69
Consensus pattern (19 bp):
TATATTTTTTATTTACCTT
Found at i:84461 original size:21 final size:21
Alignment explanation
Indices: 84435--84478 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
84425 GTCACTATAC
84435 TTTTTTATTTACCTTTATATT
1 TTTTTTATTTACCTTTATATT
84456 TTTTTTATTTACCTTTATATT
1 TTTTTTATTTACCTTTATATT
84477 TT
1 TT
84479 GAAATTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTTATTTACCTTTATATT
Found at i:87157 original size:42 final size:47
Alignment explanation
Indices: 87045--87158 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 47
87035 AAACATTCTT
* * **
87045 AATATTAT-TCAAAATTTATTA-ATAATTTTATTTATTTTTCATTCA
1 AATATAATATCAAAATTTATTATATATTTTTATCCATTTTTCATTCA
* *
87090 AATATAATATCAAATTTTATAATATATTTTTA-CCA-TTTT-ATT-A
1 AATATAATATCAAAATTTATTATATATTTTTATCCATTTTTCATTCA
87133 AAT-TAATATCAAAATTTATTATATAT
1 AATATAATATCAAAATTTATTATATAT
87159 ATATTTACAA
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
42 21 0.36
43 4 0.07
44 3 0.05
45 11 0.19
46 12 0.20
47 8 0.14
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (47 bp):
AATATAATATCAAAATTTATTATATATTTTTATCCATTTTTCATTCA
Done.