Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003182.1 Kokia drynarioides strain JFW-HI SEQ_115790, 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: 147936
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 87 characters in sequence are not A, C, G, or T
Found at i:43 original size:2 final size:2
Alignment explanation
Indices: 36--73 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
26 ATTTAACATA
36 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
74 TTACAATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4353 original size:30 final size:31
Alignment explanation
Indices: 4297--4364 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
4287 AAAACTTAAC
* *
4297 TCAATTATTTAAATAAAAACTTTTGAATAGT
1 TCAATGATTTAAATAAAAACTTTTGAATAAT
*
4328 TCAATGATTTAAATGAAAA-TTTTGAATAAT
1 TCAATGATTTAAATAAAAACTTTTGAATAAT
4358 TCAATGA
1 TCAATGA
4365 CCATTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 17 0.50
31 17 0.50
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (31 bp):
TCAATGATTTAAATAAAAACTTTTGAATAAT
Found at i:10105 original size:29 final size:29
Alignment explanation
Indices: 10063--10130 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
10053 AATGCCCATA
10063 ATTACACTCTAATTGCTGCCTGAAAGAAT
1 ATTACACTCTAATTGCTGCCTGAAAGAAT
10092 ATTACACTCTAATTGCTGCCTGAAAGAAT
1 ATTACACTCTAATTGCTGCCTGAAAGAAT
10121 ATTACACTCT
1 ATTACACTCT
10131 TTTGCTTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (29 bp):
ATTACACTCTAATTGCTGCCTGAAAGAAT
Found at i:14517 original size:83 final size:83
Alignment explanation
Indices: 14360--14520 Score: 207
Period size: 83 Copynumber: 1.9 Consensus size: 83
14350 GAGGAATTGA
* * * *
14360 CTAAGGTGTGAGGTTTCGTCCTCCTTATGCCCTTGAAAACTAAGACGAGAGGTCTCATCTCCCTT
1 CTAAGGTGTAAGGTCTCGTCCACCTTATGCCCTTGAAAACTAAGACGAAAGGTCTCATCTCCCTT
*
14425 AATAGAATCAATCAAAGG
66 AATAAAATCAATCAAAGG
* * * * *
14443 CTAAGGTGTAAGGTCTCGTCCACTTTATGCCTTTGAAGACTAAGGCGAAAGGTCTCCTC-CCTCT
1 CTAAGGTGTAAGGTCTCGTCCACCTTATGCCCTTGAAAACTAAGACGAAAGGTCTCATCTCC-CT
*
14507 TGATAAAATCAATC
65 TAATAAAATCAATC
14521 GAAGATCAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
82 2 0.03
83 64 0.97
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (83 bp):
CTAAGGTGTAAGGTCTCGTCCACCTTATGCCCTTGAAAACTAAGACGAAAGGTCTCATCTCCCTT
AATAAAATCAATCAAAGG
Found at i:16866 original size:24 final size:24
Alignment explanation
Indices: 16839--16891 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
16829 TGCCACTTTC
*
16839 TGTTTAGCCTTATTATAATATTTT
1 TGTTTAGCCTTAATATAATATTTT
*
16863 TGTTTAGGCTTAATATAATATTTT
1 TGTTTAGCCTTAATATAATATTTT
16887 T-TTTA
1 TGTTTA
16892 TCCAATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.58
Consensus pattern (24 bp):
TGTTTAGCCTTAATATAATATTTT
Found at i:17197 original size:16 final size:17
Alignment explanation
Indices: 17176--17214 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
17166 CAAATTGAAA
17176 AAAATAAATGAA-ATTT
1 AAAATAAATGAACATTT
*
17192 AAAATAATTGAACATTT
1 AAAATAAATGAACATTT
17209 AAAATA
1 AAAATA
17215 CAAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (17 bp):
AAAATAAATGAACATTT
Found at i:17465 original size:29 final size:30
Alignment explanation
Indices: 17402--17467 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
17392 AATAATCTAT
*
17402 ATTTTATAATATTTAAAAGATTAAATCAAA
1 ATTTTATAATATTTAAAAGATAAAATCAAA
* * * *
17432 ATTTTATTATTTTTAAAAGCTAAAAT-ACA
1 ATTTTATAATATTTAAAAGATAAAATCAAA
17461 ATTTTAT
1 ATTTTAT
17468 CTTTATTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (30 bp):
ATTTTATAATATTTAAAAGATAAAATCAAA
Found at i:18786 original size:15 final size:14
Alignment explanation
Indices: 18748--18792 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
18738 ATAAAATACT
18748 AACATAAATAATTA
1 AACATAAATAATTA
*
18762 AA-ATATAATATTTCA
1 AACATA-AATAATT-A
18777 AACATAAATAATTA
1 AACATAAATAATTA
18791 AA
1 AA
18793 ATGTAACATG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.12
14 11 0.42
15 9 0.35
16 3 0.12
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (14 bp):
AACATAAATAATTA
Found at i:39985 original size:13 final size:14
Alignment explanation
Indices: 39963--39991 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39953 AATGTTGCCC
39963 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
39977 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
39991 T
1 T
39992 CTGGTGGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTTCTTTTTTTTT
Found at i:40326 original size:6 final size:6
Alignment explanation
Indices: 40315--40349 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
40305 GGATTATTAT
40315 TGTGGA TGTGGA TGTGGA TGTGGA TGTGGA TGTGG
1 TGTGGA TGTGGA TGTGGA TGTGGA TGTGGA TGTGG
40350 GGATTATACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.51, T:0.34
Consensus pattern (6 bp):
TGTGGA
Found at i:45878 original size:6 final size:6
Alignment explanation
Indices: 45867--45922 Score: 76
Period size: 6 Copynumber: 8.7 Consensus size: 6
45857 GTTCCAATTT
45867 CTTTTA CTTTTA CTTTTA CTTTTATA CTTTTA CTTTTATA CTTTTA CTTTTA
1 CTTTTA CTTTTA CTTTTA C-TTT-TA CTTTTA C-TTT-TA CTTTTA CTTTTA
45919 CTTT
1 CTTT
45923 CACCTTTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
6 28 0.61
7 12 0.26
8 6 0.13
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (6 bp):
CTTTTA
Found at i:45896 original size:14 final size:14
Alignment explanation
Indices: 45867--45918 Score: 90
Period size: 14 Copynumber: 3.9 Consensus size: 14
45857 GTTCCAATTT
45867 CTTTTAC-TTT-TA
1 CTTTTACTTTTATA
45879 CTTTTACTTTTATA
1 CTTTTACTTTTATA
45893 CTTTTACTTTTATA
1 CTTTTACTTTTATA
45907 CTTTTACTTTTA
1 CTTTTACTTTTA
45919 CTTTCACCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.18
13 3 0.08
14 28 0.74
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.65
Consensus pattern (14 bp):
CTTTTACTTTTATA
Found at i:45931 original size:20 final size:19
Alignment explanation
Indices: 45867--45922 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 19
45857 GTTCCAATTT
45867 CTTTTACTTTTAC-TTTTA
1 CTTTTACTTTTACTTTTTA
45885 CTTTTATACTTTTACTTTTATA
1 C-TTT-TACTTTTACTTTT-TA
45907 CTTTTACTTTTACTTT
1 CTTTTACTTTTACTTT
45923 CACCTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.03
19 3 0.09
20 21 0.62
21 6 0.18
22 3 0.09
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (19 bp):
CTTTTACTTTTACTTTTTA
Found at i:46490 original size:31 final size:30
Alignment explanation
Indices: 46431--46490 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 30
46421 CCGTTTCAAA
46431 AATAATTATATTTAGAACAACCATTGTTTGG
1 AATAATTATATTTAGAACAA-CATTGTTTGG
*
46462 AATAATTTGTATTTAGAACAA-ATATGTTT
1 AATAA-TTATATTTAGAACAACAT-TGTTT
46491 TTTTTTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 2 0.08
31 10 0.38
32 14 0.54
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (30 bp):
AATAATTATATTTAGAACAACATTGTTTGG
Found at i:56511 original size:21 final size:22
Alignment explanation
Indices: 56471--56511 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
56461 TTTAAAATCG
56471 AAATTAAAATAATATAAAATTA
1 AAATTAAAATAATATAAAATTA
*
56493 AAATTAAAAT-ATCTAAAAT
1 AAATTAAAATAATATAAAAT
56512 CGATAATCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATTAAAATAATATAAAATTA
Found at i:56989 original size:18 final size:18
Alignment explanation
Indices: 56963--56997 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56953 AAACTATTTT
56963 CTTAAAATTAGAATTATG
1 CTTAAAATTAGAATTATG
* *
56981 CTTATAATTATAATTAT
1 CTTAAAATTAGAATTAT
56998 TATATGTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (18 bp):
CTTAAAATTAGAATTATG
Found at i:58747 original size:3 final size:3
Alignment explanation
Indices: 58741--58771 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
58731 CTAACAACAA
*
58741 AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
58772 GGAGAAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:60701 original size:16 final size:16
Alignment explanation
Indices: 60680--60710 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60670 CATGTTAGAG
60680 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
60696 CATATATATTTGAAA
1 CATATAAATTTGAAA
60711 ACATTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:60895 original size:19 final size:20
Alignment explanation
Indices: 60871--60915 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
60861 TAAATTTTAA
60871 AATTTTTATAAA-TATTTTG-
1 AATTTTTA-AAATTATTTTGT
60890 AA-TTTTAAAATTATTTTGT
1 AATTTTTAAAATTATTTTGT
60909 AATTTTT
1 AATTTTT
60916 TTTGAGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
19 4 0.17
20 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
AATTTTTAAAATTATTTTGT
Found at i:63065 original size:2 final size:2
Alignment explanation
Indices: 63058--63082 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63048 AAGCCCCTTC
63058 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
63083 ATTCATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:64542 original size:2 final size:2
Alignment explanation
Indices: 64535--64560 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
64525 TTTAGCTGAA
64535 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
64561 GATGGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85048 original size:19 final size:20
Alignment explanation
Indices: 85021--85075 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
85011 AAAATAATTA
85021 AAATCTTATTTAAAAAT-TTT
1 AAAT-TTATTTAAAAATGTTT
*
85041 AAATTTA-TTAAAAGTGTTT
1 AAATTTATTTAAAAATGTTT
*
85060 AAATTT-TTTGAAAATG
1 AAATTTATTTAAAAATG
85076 CAAAAAACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 7 0.23
19 19 0.63
20 4 0.13
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (20 bp):
AAATTTATTTAAAAATGTTT
Found at i:90865 original size:20 final size:21
Alignment explanation
Indices: 90840--90878 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
90830 ACAGTTATTA
*
90840 TCTTTCTAT-TTTTCACTTAT
1 TCTTTCCATCTTTTCACTTAT
90860 TCTTTCCATCTTTTCACTT
1 TCTTTCCATCTTTTCACTT
90879 TTTCACTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (21 bp):
TCTTTCCATCTTTTCACTTAT
Found at i:96668 original size:2 final size:2
Alignment explanation
Indices: 96661--96689 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
96651 GCATGCGAAA
96661 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
96690 CTCAGACGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:98512 original size:6 final size:6
Alignment explanation
Indices: 98474--98511 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
98464 AGATTCCGAT
* *
98474 GGTGGT GGTGGC GGTGGC GGTGGC GGTGGC GGCGGC GG
1 GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GGTGGC GG
98512 CCAATATTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.16, G:0.68, T:0.16
Consensus pattern (6 bp):
GGTGGC
Found at i:100011 original size:78 final size:79
Alignment explanation
Indices: 99911--100063 Score: 272
Period size: 78 Copynumber: 1.9 Consensus size: 79
99901 GAAAATTCAA
*
99911 ATTGAGCTTGTATAAAATATTATGAATCAAGATACAAAACTATCAG-CCATTAAGAAGTTTAAAG
1 ATTGAGCTTGTATAAAATATTATGAATCAAGATACAAAACTATCAGACCATGAAGAAGTTTAAAG
99975 GAAACCCAAATCAG
66 GAAACCCAAATCAG
* *
99989 ATTGGGCTTGTATAGAATATTATGAATCAAGATACAAAACTATCAGACCATGAAGAAGTTTAAAG
1 ATTGAGCTTGTATAAAATATTATGAATCAAGATACAAAACTATCAGACCATGAAGAAGTTTAAAG
100054 GAAACCCAAA
66 GAAACCCAAA
100064 AAGAAAAATA
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 44 0.62
79 27 0.38
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.25
Consensus pattern (79 bp):
ATTGAGCTTGTATAAAATATTATGAATCAAGATACAAAACTATCAGACCATGAAGAAGTTTAAAG
GAAACCCAAATCAG
Found at i:106490 original size:16 final size:17
Alignment explanation
Indices: 106456--106493 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
106446 ATACGCATAC
**
106456 AAAAATATTTTAATAAT
1 AAAAATATTAAAATAAT
106473 AAAAATATTAAAAT-AT
1 AAAAATATTAAAATAAT
106489 AAAAA
1 AAAAA
106494 GCATGATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAAATATTAAAATAAT
Found at i:112166 original size:31 final size:31
Alignment explanation
Indices: 112131--112189 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
112121 GTGTAATTCA
*
112131 TATTCGAGTTAAACCGAAA-AACTTAATTTTT
1 TATTCAAGTTAAACC-AAATAACTTAATTTTT
* *
112162 TATTCAAGTTTATCCAAATAACTTAATT
1 TATTCAAGTTAAACCAAATAACTTAATT
112190 AACTCAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 21 0.88
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.41
Consensus pattern (31 bp):
TATTCAAGTTAAACCAAATAACTTAATTTTT
Found at i:123562 original size:11 final size:11
Alignment explanation
Indices: 123548--123573 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
123538 ACTAAAAGCA
123548 ATATATCAAAT
1 ATATATCAAAT
123559 ATATATCAAAT
1 ATATATCAAAT
123570 ATAT
1 ATAT
123574 TTACTTGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATATCAAAT
Found at i:123961 original size:4 final size:4
Alignment explanation
Indices: 123952--123977 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
123942 TAATTTTAAG
123952 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
123978 ACTATCGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:130665 original size:2 final size:2
Alignment explanation
Indices: 130658--130691 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
130648 CAATGTTTTC
*
130658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
130692 CGATAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:135780 original size:2 final size:2
Alignment explanation
Indices: 135773--135810 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
135763 ATGAAAATGT
135773 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
135811 CTTGGTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:143361 original size:78 final size:79
Alignment explanation
Indices: 143223--143370 Score: 226
Period size: 78 Copynumber: 1.9 Consensus size: 79
143213 TAAAAAATTA
*
143223 AAAATTAAAATTTTTTTAGCATAATACACAACTTCAAACCAATGCCTTTGACCATAGAGACAAAG
1 AAAATTAAAA-TTTATTAGCATAATACACAACTTCAAACCAATGCCTTTGACCATAGAGACAAAG
143288 GGGTTAGAATTTTTG
65 GGGTTAGAATTTTTG
** * * *
143303 AAAATTAAAA-TTATTAGCATAATGGACAACTTCAAACCAGTGCCTTTGACTATGGAGACAAAGG
1 AAAATTAAAATTTATTAGCATAATACACAACTTCAAACCAATGCCTTTGACCATAGAGACAAAGG
143367 GGTT
66 GGTT
143371 GGTTTTTAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
78 52 0.84
80 10 0.16
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (79 bp):
AAAATTAAAATTTATTAGCATAATACACAACTTCAAACCAATGCCTTTGACCATAGAGACAAAGG
GGTTAGAATTTTTG
Found at i:146235 original size:14 final size:14
Alignment explanation
Indices: 146216--146242 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
146206 AAGTGCTAAA
146216 TGTTTTTTTTTTTT
1 TGTTTTTTTTTTTT
146230 TGTTTTTTTTTTT
1 TGTTTTTTTTTTT
146243 GGTGGATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (14 bp):
TGTTTTTTTTTTTT
Done.