Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold295
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: 644316
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 33643 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:4357 original size:19 final size:19
Alignment explanation
Indices: 4333--4381 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
4323 AATAATTTTT
*
4333 ATTTTTAAAAAATTACTTA
1 ATTTTTAAAAAATTAATTA
4352 ATTTTTTTAAAAAATTAATTA
1 A--TTTTTAAAAAATTAATTA
*
4373 ATTGTTAAA
1 ATTTTTAAA
4382 CACATGTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 8 0.31
21 18 0.69
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTTTTAAAAAATTAATTA
Found at i:4360 original size:21 final size:21
Alignment explanation
Indices: 4334--4375 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4324 ATAATTTTTA
*
4334 TTTTTAAAAAATTACTTAATT
1 TTTTTAAAAAATTAATTAATT
4355 TTTTTAAAAAATTAATTAATT
1 TTTTTAAAAAATTAATTAATT
4376 GTTAAACACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTTAAAAAATTAATTAATT
Found at i:7364 original size:20 final size:20
Alignment explanation
Indices: 7339--7378 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
7329 CTAGTTGTAT
7339 CAATACAAGTCCACTTCTAC
1 CAATACAAGTCCACTTCTAC
*
7359 CAATACAAGTCTACTTCTAC
1 CAATACAAGTCCACTTCTAC
7379 TCAAGATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.33, G:0.05, T:0.28
Consensus pattern (20 bp):
CAATACAAGTCCACTTCTAC
Found at i:9060 original size:16 final size:16
Alignment explanation
Indices: 9039--9070 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9029 ATTTAAATTA
*
9039 AATTAACTAATTTTTT
1 AATTAAATAATTTTTT
9055 AATTAAATAATTTTTT
1 AATTAAATAATTTTTT
9071 CAACCCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTAAATAATTTTTT
Found at i:9995 original size:20 final size:19
Alignment explanation
Indices: 9962--10005 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
9952 CCTCGATAGC
9962 CCCCTTTTCACTCCTATGAT
1 CCCCTTTTCACTCCT-TGAT
** *
9982 CCCCTTTTTGCTCCTTTAT
1 CCCCTTTTCACTCCTTGAT
10001 CCCCT
1 CCCCT
10006 CTACATGCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.09, C:0.43, G:0.05, T:0.43
Consensus pattern (19 bp):
CCCCTTTTCACTCCTTGAT
Found at i:24339 original size:25 final size:25
Alignment explanation
Indices: 24305--24354 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
24295 ATGAATGATA
24305 GTAAAATTATCAATTTGTTACAATT
1 GTAAAATTATCAATTTGTTACAATT
24330 GTAAAATTATCAATTTGTTACAATT
1 GTAAAATTATCAATTTGTTACAATT
24355 TAGTACAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (25 bp):
GTAAAATTATCAATTTGTTACAATT
Found at i:29827 original size:2 final size:2
Alignment explanation
Indices: 29820--29851 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
29810 TTTCCACATT
29820 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29852 TACAAGGTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:31331 original size:44 final size:46
Alignment explanation
Indices: 31281--31370 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
31271 AGCTATTCCC
**
31281 TTCAACCAAACACAAT-AAT-ACT-ATTACAGTTCTATTCCATTACA
1 TTCAACCAAACA-AATGAATCACTGATTACAACTCTATTCCATTACA
*
31325 TTCAACCAAACAATTGAATCACTGATTACAACTCTATTCCATTACA
1 TTCAACCAAACAAATGAATCACTGATTACAACTCTATTCCATTACA
31371 GCCCTATTCC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
43 2 0.05
44 15 0.38
45 3 0.08
46 20 0.50
ACGTcount: A:0.40, C:0.26, G:0.03, T:0.31
Consensus pattern (46 bp):
TTCAACCAAACAAATGAATCACTGATTACAACTCTATTCCATTACA
Found at i:31370 original size:16 final size:16
Alignment explanation
Indices: 31349--31399 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
31339 TGAATCACTG
*
31349 ATTACAACTCTATTCC
1 ATTACAACACTATTCC
* *
31365 ATTACAGCCCTATTCC
1 ATTACAACACTATTCC
*
31381 ATTACAACAGTATTCC
1 ATTACAACACTATTCC
31397 ATT
1 ATT
31400 CCAATGAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.35
Consensus pattern (16 bp):
ATTACAACACTATTCC
Found at i:31687 original size:16 final size:16
Alignment explanation
Indices: 31668--31702 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31658 TACAGTTTTG
* *
31668 TTCCATTATAGCCCTA
1 TTCCATTACAACCCTA
31684 TTCCATTACAACCCTA
1 TTCCATTACAACCCTA
31700 TTC
1 TTC
31703 TATTCCAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.03, T:0.37
Consensus pattern (16 bp):
TTCCATTACAACCCTA
Found at i:31780 original size:27 final size:25
Alignment explanation
Indices: 31734--31799 Score: 62
Period size: 26 Copynumber: 2.4 Consensus size: 25
31724 CTGTAATTAT
31734 AAATAAATTTATTTTATAATTATTTG
1 AAATAAATTTATTTTATAA-TATTTG
*
31760 AAATAATTATTATATTT-TAATATTTATG
1 AAATAAAT-TTAT-TTTATAATA-TT-TG
31788 AAAATAAATTTA
1 -AAATAAATTTA
31800 AACATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
26 9 0.27
27 9 0.27
28 8 0.24
29 7 0.21
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (25 bp):
AAATAAATTTATTTTATAATATTTG
Found at i:33149 original size:88 final size:89
Alignment explanation
Indices: 33041--33226 Score: 347
Period size: 88 Copynumber: 2.1 Consensus size: 89
33031 ACTTGAAACT
33041 TAAAAAATATATATAAATTATTTTTTATAAAATAACCGGTTTATTAAGTTTGAAATTATATTGTT
1 TAAAAAATATATATAAATTATTTTTTATAAAATAACCGGTTTATTAAGTTTGAAATTATATTGTT
33106 TTACTTATTGATGTTAAATATAAA
66 TTACTTATTGATGTTAAATATAAA
33130 TAAAAAATAT-TATAAATTATTTTTTATAAAATAACCGGTTTATTAAGTTTGAAATTATATTGTT
1 TAAAAAATATATATAAATTATTTTTTATAAAATAACCGGTTTATTAAGTTTGAAATTATATTGTT
33194 TTACTTATTGATGTTAAATATAAA
66 TTACTTATTGATGTTAAATATAAA
* *
33218 GAGAAAATA
1 TAAAAAATA
33227 AAAAAGTATT
Statistics
Matches: 95, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
88 85 0.89
89 10 0.11
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (89 bp):
TAAAAAATATATATAAATTATTTTTTATAAAATAACCGGTTTATTAAGTTTGAAATTATATTGTT
TTACTTATTGATGTTAAATATAAA
Found at i:34201 original size:5 final size:5
Alignment explanation
Indices: 34191--34226 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
34181 TGAGTATTCG
* *
34191 ATCGA ATCGA ATTGA ATCGA ATTGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
34227 AATTTTCGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (5 bp):
ATCGA
Found at i:35151 original size:9 final size:9
Alignment explanation
Indices: 35134--35164 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
35124 TTGAGTTGAT
35134 TCGAATAAC
1 TCGAATAAC
*
35143 TCGATTAAC
1 TCGAATAAC
35152 TCGAATAAC
1 TCGAATAAC
35161 TCGA
1 TCGA
35165 TTCATTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:43129 original size:24 final size:24
Alignment explanation
Indices: 43102--43163 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
43092 TGGCTTTTCG
*
43102 GAGCTACCCGTTATTGGCTCGCAT
1 GAGCTTCCCGTTATTGGCTCGCAT
* **
43126 GAGCTTCCTGATTA-TGGCTCTTAT
1 GAGCTTCCCG-TTATTGGCTCGCAT
43150 GAGCTTCCCGTTAT
1 GAGCTTCCCGTTAT
43164 ACAACCTGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 3 0.10
24 25 0.81
25 3 0.10
ACGTcount: A:0.16, C:0.26, G:0.23, T:0.35
Consensus pattern (24 bp):
GAGCTTCCCGTTATTGGCTCGCAT
Found at i:46949 original size:44 final size:42
Alignment explanation
Indices: 46885--47126 Score: 215
Period size: 43 Copynumber: 5.7 Consensus size: 42
46875 TAACCGTTAC
**
46885 ACGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTCATAATC-AAGGAT
* * *
46928 CCCGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
1 -ACGGTGGAATCAGCACTTAGCAACCACCTCATAATCAAGGAT
* * *
46971 ACGG-GGAATCAGCACATAACAACC-CCTTTCACAATCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACC--TCATAATCAAGGAT
* *
47013 ACGGTGGAATCAGCACTTAGCAACCACCT-TTATATTAAGTGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTCATA-ATCAAG-GAT
* * * * **
47056 ACGG-GAAATCAACACTTAGCAACC-CCATTCACAATAAAAAAT
1 ACGGTGGAATCAGCACTTAGCAACCACC--TCATAATCAAGGAT
* *
47098 ACGGTGGGATCAACACTTAGCAACCACCT
1 ACGGTGGAATCAGCACTTAGCAACCACCT
47127 TTAGAGTCAA
Statistics
Matches: 162, Mismatches: 25, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
40 2 0.01
41 21 0.13
42 49 0.30
43 53 0.33
44 37 0.23
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (42 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTCATAATCAAGGAT
Found at i:46994 original size:41 final size:41
Alignment explanation
Indices: 46885--47169 Score: 220
Period size: 42 Copynumber: 6.7 Consensus size: 41
46875 TAACCGTTAC
* ** *
46885 ACGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGAT
1 ACGG-GGAATCAGCACTTAGCAACCACCTTATAATC-AATGAT
*
46928 CCCGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
1 -ACGG-GGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
* * * *
46971 ACGGGGAATCAGCACATAACAACC-CCTTTCACAATCAAGGAT
1 ACGGGGAATCAGCACTTAGCAACCACC-TT-ATAATCAATGAT
*
47013 ACGGTGGAATCAGCACTTAGCAACCACCTT-TATATTAAGTGAT
1 ACGG-GGAATCAGCACTTAGCAACCACCTTATA-ATCAA-TGAT
* * * * **
47056 ACGGGAAATCAACACTTAGCAACC-CCATTCACAATAAAAAAT
1 ACGGGGAATCAGCACTTAGCAACCACC-TT-ATAATCAATGAT
* * *
47098 ACGGTGGGATCAACACTTAGCAACCACCTT-TAGAGTCAATAAT
1 ACGG-GGAATCAGCACTTAGCAACCACCTTATA-A-TCAATGAT
**
47141 TTGGGGAATCAGCACTTAGCAACC-CCTTA
1 ACGGGGAATCAGCACTTAGCAACCACCTTA
47170 CATTCAAAGA
Statistics
Matches: 197, Mismatches: 30, Indels: 30
0.77 0.12 0.12
Matches are distributed among these distances:
40 2 0.01
41 28 0.14
42 66 0.34
43 64 0.32
44 37 0.19
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (41 bp):
ACGGGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
Found at i:47122 original size:128 final size:128
Alignment explanation
Indices: 46885--47168 Score: 287
Period size: 128 Copynumber: 2.2 Consensus size: 128
46875 TAACCGTTAC
* * * *
46885 ACGGTGGAATCAGCACTTAGCAACCACC-TCATGTTCAAAGGATCCCGGTGGAATCAGCACTTAG
1 ACGGTGGAATCAGCACTTAGCAACCACCTTCATATT-AAAGGATCACGGTGAAATCAACACTTAG
* * ** * *
46949 CAACCACCTTATAATCAATGATACGGGGAATCAGCACATAACAACC-CCTTTCACAATCAAGGAT
65 CAACCACCTTACAATAAAAAATACGGGGAATCAACACATAACAACCACCTTT-ACAATCAAGAAT
*
47013 ACGGTGGAATCAGCACTTAGCAACCACCTTTATATT-AAGTGAT-ACGG-GAAATCAACACTTAG
1 ACGGTGGAATCAGCACTTAGCAACCACCTTCATATTAAAG-GATCACGGTGAAATCAACACTTAG
* * * * * *
47075 CAACC-CCATTCACAATAAAAAATACGGTGGGATCAACACTTAGCAACCACCTTTAGAGTCAATA
65 CAACCACC-TT-ACAATAAAAAATACGG-GGAATCAACACATAACAACCACCTTTACAATCAAGA
47139 AT
127 AT
**
47141 TTGG-GGAATCAGCACTTAGCAACC-CCTT
1 ACGGTGGAATCAGCACTTAGCAACCACCTT
47169 ACATTCAAAG
Statistics
Matches: 131, Mismatches: 19, Indels: 14
0.80 0.12 0.09
Matches are distributed among these distances:
125 2 0.02
126 24 0.18
127 38 0.29
128 57 0.44
129 10 0.08
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (128 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTCATATTAAAGGATCACGGTGAAATCAACACTTAGC
AACCACCTTACAATAAAAAATACGGGGAATCAACACATAACAACCACCTTTACAATCAAGAAT
Found at i:47151 original size:85 final size:83
Alignment explanation
Indices: 46930--47166 Score: 303
Period size: 85 Copynumber: 2.8 Consensus size: 83
46920 CAAAGGATCC
* *
46930 CGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAACAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTT-TAATCAATGATACGGGGAATCAGCACTTAGCAACC
* * **
46995 CCTTTCACAATCAAGGATA
65 CCATTCACAATAAAAAATA
* * *
47014 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTAAGTGATACGGGAAATCAACACTTAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTA-ATCAA-TGATACGGGGAATCAGCACTTAGCAAC
47079 CCCATTCACAATAAAAAATA
64 CCCATTCACAATAAAAAATA
* * * **
47099 CGGTGGGATCAACACTTAGCAACCACCTTTAGAGTCAATAATTTGGGGAATCAGCACTTAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTA-A-TCAATGATACGGGGAATCAGCACTTAGCAAC
47164 CCC
64 CCC
47167 TTACATTCAA
Statistics
Matches: 132, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
83 2 0.02
84 33 0.25
85 94 0.71
86 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (83 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTAATCAATGATACGGGGAATCAGCACTTAGCAACCC
CATTCACAATAAAAAATA
Found at i:54917 original size:108 final size:107
Alignment explanation
Indices: 54722--54951 Score: 397
Period size: 108 Copynumber: 2.1 Consensus size: 107
54712 CCTCCACCTT
54722 GACTTGTATTTTCTCAACGCCTTCTTTGCCAATACCTGTCATGGCCTAACTTGTTCTTTACAGGA
1 GACTTGTATTTTCTCAACGCCTTCTTTGCCAATACCTGTCATGGCCTAACTTGTTCTTTACAGGA
*
54787 TACTAACCGAGTCTAAATAGTGCTTGAACCTTGAAACTGGAA
66 TACTAACCGAGTCTAAATAGTGCTTGAACCTTAAAACTGGAA
*
54829 GACTTGTATTTTCTCAACGTCTTCTTTGCCAATACCTGTCATGGACCTAACTTGTTCTTTACAGG
1 GACTTGTATTTTCTCAACGCCTTCTTTGCCAATACCTGTCATGG-CCTAACTTGTTCTTTACAGG
* *
54894 ATATTAACCGAGTCTAAATAGTGCTTGAACTTTAAAACTGGAA
65 ATACTAACCGAGTCTAAATAGTGCTTGAACCTTAAAACTGGAA
*
54937 GACTTTTAGTTTTCT
1 GACTTGTA-TTTTCT
54952 AAATTGCCAA
Statistics
Matches: 116, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
107 43 0.37
108 67 0.58
109 6 0.05
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (107 bp):
GACTTGTATTTTCTCAACGCCTTCTTTGCCAATACCTGTCATGGCCTAACTTGTTCTTTACAGGA
TACTAACCGAGTCTAAATAGTGCTTGAACCTTAAAACTGGAA
Found at i:56726 original size:24 final size:25
Alignment explanation
Indices: 56689--56738 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
56679 TATCCCTAGA
*
56689 ATAATTAGACTTTAATTGAGAAAAG
1 ATAATTAGACTTTAACTGAGAAAAG
*
56714 ATAA-TAGAGTTTAACTGAGAAAAG
1 ATAATTAGACTTTAACTGAGAAAAG
56738 A
1 A
56739 AACTCGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.50, C:0.04, G:0.18, T:0.28
Consensus pattern (25 bp):
ATAATTAGACTTTAACTGAGAAAAG
Found at i:63934 original size:1 final size:1
Alignment explanation
Indices: 63928--63992 Score: 130
Period size: 1 Copynumber: 65.0 Consensus size: 1
63918 AATGTTTGAG
63928 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
63993 ACCGCTGAAC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:64952 original size:38 final size:40
Alignment explanation
Indices: 64865--64958 Score: 101
Period size: 37 Copynumber: 2.5 Consensus size: 40
64855 AAAGTATATG
*
64865 TAAAAATTTTATAAATA-ATTAGAAAAATTAAAAAACTCA
1 TAAAAATTATATAAATATATTAGAAAAATTAAAAAACTCA
* *
64904 -AAAAA-TATATAAATATATTA-CAAATTTAAAAAA-T-A
1 TAAAAATTATATAAATATATTAGAAAAATTAAAAAACTCA
*
64939 TAAAAATTGATATATATATA
1 TAAAAATT-ATATAAATATA
64959 CACATTAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
35 1 0.02
36 6 0.13
37 21 0.45
38 19 0.40
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (40 bp):
TAAAAATTATATAAATATATTAGAAAAATTAAAAAACTCA
Found at i:66191 original size:7 final size:7
Alignment explanation
Indices: 66179--66214 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
66169 GTCTTCCTCA
*
66179 ACCTTTG
1 ACCTTTC
*
66186 ACCTTTG
1 ACCTTTC
66193 ACCTTTC
1 ACCTTTC
66200 ACCTTTC
1 ACCTTTC
66207 ACCTTTC
1 ACCTTTC
66214 A
1 A
66215 TCTCCTTGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.17, C:0.36, G:0.06, T:0.42
Consensus pattern (7 bp):
ACCTTTC
Found at i:82366 original size:40 final size:40
Alignment explanation
Indices: 82311--82386 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
82301 ATATTTTATA
* * *
82311 TTCCACCATAATGCACTTAGATGAATTATCAAGTATAATG
1 TTCCAACATAATGCACTAAGATGAATCATCAAGTATAATG
*
82351 TTCCAACATAATGCACTAAGATTAATCATCAAGTAT
1 TTCCAACATAATGCACTAAGATGAATCATCAAGTAT
82387 GAAGTTGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (40 bp):
TTCCAACATAATGCACTAAGATGAATCATCAAGTATAATG
Found at i:83643 original size:14 final size:14
Alignment explanation
Indices: 83624--83651 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
83614 TAAAGAATTG
83624 TTATTGAGTATCCA
1 TTATTGAGTATCCA
83638 TTATTGAGTATCCA
1 TTATTGAGTATCCA
83652 ATAGTGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
TTATTGAGTATCCA
Found at i:92719 original size:16 final size:17
Alignment explanation
Indices: 92691--92724 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
92681 CCAGTCGAAG
92691 AGAAGACAAAAAAGAAA
1 AGAAGACAAAAAAGAAA
*
92708 AGAAGA-AAAAAATAAA
1 AGAAGACAAAAAAGAAA
92724 A
1 A
92725 AGAAAGACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (17 bp):
AGAAGACAAAAAAGAAA
Found at i:92725 original size:17 final size:17
Alignment explanation
Indices: 92691--92728 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
92681 CCAGTCGAAG
*
92691 AGAAGACAAAAAAGAAA
1 AGAAGACAAAAAAAAAA
92708 AGAAGA-AAAAAATAAAA
1 AGAAGACAAAAAA-AAAA
92725 AGAA
1 AGAA
92729 AGACTACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (17 bp):
AGAAGACAAAAAAAAAA
Found at i:96842 original size:18 final size:19
Alignment explanation
Indices: 96802--96842 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
96792 GATAATATAT
*
96802 AATAGTAATATAAGAAGGA
1 AATAGTAATACAAGAAGGA
*
96821 AATAGTAATACAA-AATGA
1 AATAGTAATACAAGAAGGA
96839 AATA
1 AATA
96843 AAATCCTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.61, C:0.02, G:0.15, T:0.22
Consensus pattern (19 bp):
AATAGTAATACAAGAAGGA
Found at i:102510 original size:3 final size:3
Alignment explanation
Indices: 102502--102534 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
102492 TGGTAAAAAT
102502 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
102535 GTGCAAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:109093 original size:29 final size:27
Alignment explanation
Indices: 109023--109191 Score: 121
Period size: 29 Copynumber: 6.0 Consensus size: 27
109013 CTTTATTATA
* *
109023 TATACTATATATACATGCATGGG-TTTGT
1 TATA-TATAAATATATG-ATGGGTTTTGT
**
109051 TATGCATAATATATATGTATGGGTTTTGT
1 TATATATAA-ATATATG-ATGGGTTTTGT
109080 TATATATTAAATATATGCATGGGTTTTGT
1 TATATA-TAAATATATG-ATGGGTTTTGT
* *
109109 TATCTAT-AATATATGAGTGAGTTTTGT
1 TATATATAAATATATGA-TGGGTTTTGT
* *
109136 TATATA-ATATATAT-ATGGGTCTTGTTT
1 TATATATAAATATATGATGGGT-TT-TGT
* *
109163 TATAATATATATATATGGATGAGTTTTGT
1 TAT-ATATAAATATAT-GATGGGTTTTGT
109192 AATGTTTGCG
Statistics
Matches: 114, Mismatches: 16, Indels: 21
0.75 0.11 0.14
Matches are distributed among these distances:
25 4 0.04
26 4 0.04
27 36 0.32
28 18 0.16
29 42 0.37
30 5 0.04
31 5 0.04
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.48
Consensus pattern (27 bp):
TATATATAAATATATGATGGGTTTTGT
Found at i:109138 original size:56 final size:56
Alignment explanation
Indices: 109037--109152 Score: 148
Period size: 56 Copynumber: 2.1 Consensus size: 56
109027 CTATATATAC
* *
109037 ATGCATGGGTTTGTTATGCATAATATATATGTATGGGTTTTGTTATATATTAAATAT
1 ATGCATGGGTTTGTTATGCATAATATATATG-ATGAGTTTTGTTATATAATAAATAT
*
109094 ATGCATGGGTTTTGTTAT-C-T-ATAATATATGAGTGAGTTTTGTTATATAATATATAT
1 ATGCATGGG-TTTGTTATGCATAAT-ATATATGA-TGAGTTTTGTTATATAATAAATAT
109150 ATG
1 ATG
109153 GGTCTTGTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
55 3 0.06
56 32 0.60
57 10 0.19
58 8 0.15
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.47
Consensus pattern (56 bp):
ATGCATGGGTTTGTTATGCATAATATATATGATGAGTTTTGTTATATAATAAATAT
Found at i:109160 original size:25 final size:25
Alignment explanation
Indices: 109041--109176 Score: 114
Period size: 25 Copynumber: 5.1 Consensus size: 25
109031 ATATACATGC
109041 ATGGG-TTTGTTATGCATAATATATATGT
1 ATGGGTTTTGTTAT--ATAATATATA--T
*
109069 ATGGGTTTTGTTATATATTAAATATAT
1 ATGGGTTTTGTTATATA--ATATATAT
109096 GCATGGGTTTTGTTATCTATAATATATGA-
1 --ATGGGTTTTGTTA--TATAATATAT-AT
* *
109125 GTGAGTTTTGTTATATAATATATAT
1 ATGGGTTTTGTTATATAATATATAT
* *
109150 ATGGGTCTTGTTTTATAATATATAT
1 ATGGGTTTTGTTATATAATATATAT
109175 AT
1 AT
109177 ATGGATGAGT
Statistics
Matches: 91, Mismatches: 8, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
24 1 0.01
25 33 0.36
27 15 0.16
28 5 0.05
29 32 0.35
30 1 0.01
31 4 0.04
ACGTcount: A:0.30, C:0.03, G:0.18, T:0.49
Consensus pattern (25 bp):
ATGGGTTTTGTTATATAATATATAT
Found at i:109173 original size:27 final size:27
Alignment explanation
Indices: 109041--109180 Score: 128
Period size: 27 Copynumber: 5.1 Consensus size: 27
109031 ATATACATGC
*
109041 ATGGG-TTTGTTATGCATAATATATATGT
1 ATGGGTTTTGTTAT--ATAATATATATAT
* *
109069 ATGGGTTTTGTTATATATTAAATATAT
1 ATGGGTTTTGTTATATAATATATATAT
*
109096 GCATGGGTTTTGTTATCT-ATA-ATATAT
1 --ATGGGTTTTGTTATATAATATATATAT
*
109123 GAGTGAGTTTTGTTATAT-A-ATATATAT
1 -A-TGGGTTTTGTTATATAATATATATAT
* *
109150 ATGGGTCTTGTTTTATAATATATATAT
1 ATGGGTTTTGTTATATAATATATATAT
109177 ATGG
1 ATGG
109181 ATGAGTTTTG
Statistics
Matches: 94, Mismatches: 11, Indels: 15
0.78 0.09 0.12
Matches are distributed among these distances:
25 12 0.13
26 4 0.04
27 48 0.51
28 7 0.07
29 23 0.24
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.49
Consensus pattern (27 bp):
ATGGGTTTTGTTATATAATATATATAT
Found at i:109476 original size:36 final size:36
Alignment explanation
Indices: 109418--109487 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
109408 TTGTGAACCA
*
109418 TGTTAACTTGGCGAATTATATTATTATGGCGAACTG
1 TGTTAACTTGGCGAATTATATTAATATGGCGAACTG
* * * *
109454 TGTTAATTTGGTGATTTGTATTAATATGGCGAAC
1 TGTTAACTTGGCGAATTATATTAATATGGCGAAC
109488 GATATTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (36 bp):
TGTTAACTTGGCGAATTATATTAATATGGCGAACTG
Found at i:110162 original size:17 final size:17
Alignment explanation
Indices: 110140--110251 Score: 82
Period size: 17 Copynumber: 6.5 Consensus size: 17
110130 TTATGATAGA
110140 GTATGAACTGTTATTTT
1 GTATGAACTGTTATTTT
* **
110157 GCATGAA-TAGTTATTCG
1 GTATGAACT-GTTATTTT
* *
110174 GTATGAACTGATATTTC
1 GTATGAACTGTTATTTT
* * *
110191 ATATAAACTATTATTTT
1 GTATGAACTGTTATTTT
* * *
110208 GCATGAGCTGTCATTTGGT
1 GTATGAACTGTTATTT--T
110227 GTATGAACTGTTATTTT
1 GTATGAACTGTTATTTT
*
110244 ATATGAAC
1 GTATGAAC
110252 AGATGTTTGA
Statistics
Matches: 69, Mismatches: 22, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
16 1 0.01
17 53 0.77
18 1 0.01
19 14 0.20
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.44
Consensus pattern (17 bp):
GTATGAACTGTTATTTT
Found at i:115453 original size:21 final size:21
Alignment explanation
Indices: 115429--115468 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
115419 TAAAATCCTT
*
115429 GGAACAAATGAAA-GAACTTGG
1 GGAAAAAAT-AAATGAACTTGG
115450 GGAAAAAATAAATGAACTT
1 GGAAAAAATAAATGAACTT
115469 AGCTACATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.53, C:0.07, G:0.23, T:0.17
Consensus pattern (21 bp):
GGAAAAAATAAATGAACTTGG
Found at i:116682 original size:3 final size:3
Alignment explanation
Indices: 116668--116710 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
116658 ATTGACCATT
*
116668 ATC ATT ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
116711 ATGTCTTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.30, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:128348 original size:13 final size:13
Alignment explanation
Indices: 128330--128354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
128320 CAATTTAATT
128330 TTAAATAAATAAA
1 TTAAATAAATAAA
128343 TTAAATAAATAA
1 TTAAATAAATAA
128355 TATTTTTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAATAAATAAA
Found at i:135365 original size:35 final size:36
Alignment explanation
Indices: 135302--135401 Score: 84
Period size: 37 Copynumber: 2.8 Consensus size: 36
135292 TGAGTCCCTT
* *
135302 TACAATA-AACCAA-TTCA-ATATTCGAATCTGTACAA
1 TACAATACAAACAATTTCACATA-TC-AATCTATACAA
* *
135337 T--AATATCAAACAATTTCACATATCAATCTATTCAC
1 TACAATA-CAAACAATTTCACATATCAATCTATACAA
*
135372 TACAATGACAAACAGTTTCACATATCAATC
1 TACAAT-ACAAACAATTTCACATATCAATC
135402 AATTTAACAT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
33 4 0.08
35 15 0.28
36 6 0.11
37 27 0.51
38 1 0.02
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.30
Consensus pattern (36 bp):
TACAATACAAACAATTTCACATATCAATCTATACAA
Found at i:135420 original size:37 final size:36
Alignment explanation
Indices: 135338--135443 Score: 115
Period size: 37 Copynumber: 2.9 Consensus size: 36
135328 TCTGTACAAT
* * *
135338 AATATCAAACAATTTCACATATCAATCTATTCACTAC
1 AATAACAAACAGTTTCACATATCAATCAATTCAC-AC
* *
135375 AATGACAAACAGTTTCACATATCAATCAATTTA-AC
1 AATAACAAACAGTTTCACATATCAATCAATTCACAC
**
135410 ATGATAACAAATGGTTTCACATATCAATCAATTC
1 A--ATAACAAACAGTTTCACATATCAATCAATTC
135444 CATATGGTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
35 3 0.05
37 55 0.95
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (36 bp):
AATAACAAACAGTTTCACATATCAATCAATTCACAC
Found at i:136034 original size:16 final size:15
Alignment explanation
Indices: 136013--136042 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
136003 ATACAAATGC
136013 AATGCAATGCAATCAT
1 AATGCAAT-CAATCAT
136029 AATGCAATCAATCA
1 AATGCAATCAATCA
136043 ATATCATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.23
Consensus pattern (15 bp):
AATGCAATCAATCAT
Found at i:136241 original size:59 final size:59
Alignment explanation
Indices: 136150--136261 Score: 143
Period size: 59 Copynumber: 1.9 Consensus size: 59
136140 TAAATAAATA
* ** *
136150 TATATAATAATTCACAAATTTAAACAAACAATCATAAGTGATTATATCATAAAAGCAAT
1 TATAAAATAATTCACAAATTTAAACAAACAATCATAAGCAATTAAATCATAAAAGCAAT
* * * * *
136209 TATAAAATCATTCACAGATTTATACCATCAATCATAAGCAATTAAATCATAAA
1 TATAAAATAATTCACAAATTTAAACAAACAATCATAAGCAATTAAATCATAAA
136262 TTCTTGTATT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 44 1.00
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.30
Consensus pattern (59 bp):
TATAAAATAATTCACAAATTTAAACAAACAATCATAAGCAATTAAATCATAAAAGCAAT
Found at i:136822 original size:7 final size:7
Alignment explanation
Indices: 136787--136811 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
136777 ACAAATGGGG
136787 AATAATA
1 AATAATA
136794 AATAATA
1 AATAATA
136801 AATAATA
1 AATAATA
136808 AATA
1 AATA
136812 GAAATAAGAA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAATA
Found at i:142799 original size:62 final size:63
Alignment explanation
Indices: 142295--142808 Score: 501
Period size: 63 Copynumber: 8.2 Consensus size: 63
142285 CGTGTGTGTC
* * * * ***
142295 ACACGGTCGTGTG-CCAGGCCGTGTAACTTACTGTTTGTGATTTAAAATCACACGGGCCAGGG
1 ACACGGGCGTGTGTCCAGGCTGTGTAACTCACTATTTGTGATTTAGGGTCACACGGGCCAGGG
** * ** *
142357 ACACGGGTATGTGTCCAGGCTGTGTAACTCGCTATTTGTGATTTAAAGTCACACGGGCCAAGG
1 ACACGGGCGTGTGTCCAGGCTGTGTAACTCACTATTTGTGATTTAGGGTCACACGGGCCAGGG
* * ** * *
142420 ACACGGGTGTGTGTCCAGGCCGTGTAACTCGTTATTTATGATTTAGAGTCACACGGGCCAGGG
1 ACACGGGCGTGTGTCCAGGCTGTGTAACTCACTATTTGTGATTTAGGGTCACACGGGCCAGGG
* * * * * * * ** *
142483 ACACAGGTGTGTGACCAGGCCGTGTAACTCGCTATTTGTGATTTAGAGTCGCATAGGACAGGG
1 ACACGGGCGTGTGTCCAGGCTGTGTAACTCACTATTTGTGATTTAGGGTCACACGGGCCAGGG
* * * *
142546 ACACAGGTGTGTGACCAGGCTGTGTAACTCTCTATTTGTGATTTAGGGTCACACGGGCCAGGG
1 ACACGGGCGTGTGTCCAGGCTGTGTAACTCACTATTTGTGATTTAGGGTCACACGGGCCAGGG
* * * * *
142609 ACACAGGCCTGTGTCCAGGCTATGTAACTCACTATTTGTGATTTACGGTCACACGGGCTAGGG
1 ACACGGGCGTGTGTCCAGGCTGTGTAACTCACTATTTGTGATTTAGGGTCACACGGGCCAGGG
* * * * * * * ** *
142672 ACATGGGCTTCTGTCCAGGCTCTGTAACTCACTGTTTGTGATTTAGGGTTACATGAACTAGGG
1 ACACGGGCGTGTGTCCAGGCTGTGTAACTCACTATTTGTGATTTAGGGTCACACGGGCCAGGG
* * * * * * * *
142735 ACGCGGACGTGTGTCTAGACTGTGTAACTCAC-ATTTGTTATTTAAGGTCACATGGGCCAAGG
1 ACACGGGCGTGTGTCCAGGCTGTGTAACTCACTATTTGTGATTTAGGGTCACACGGGCCAGGG
*
142797 ACGCGGGCGTGT
1 ACACGGGCGTGT
142809 ATCGACGCCA
Statistics
Matches: 386, Mismatches: 65, Indels: 2
0.85 0.14 0.00
Matches are distributed among these distances:
62 43 0.11
63 343 0.89
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (63 bp):
ACACGGGCGTGTGTCCAGGCTGTGTAACTCACTATTTGTGATTTAGGGTCACACGGGCCAGGG
Found at i:143473 original size:22 final size:22
Alignment explanation
Indices: 143445--143512 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
143435 AGGAAACTGT
143445 ATCTGTATCTGATCTGTTCTAC
1 ATCTGTATCTGATCTGTTCTAC
* *
143467 ATCTGTATC-GAATCTGTTTTGC
1 ATCTGTATCTG-ATCTGTTCTAC
* * *
143489 ATCTATAACTGATATGTTCTAC
1 ATCTGTATCTGATCTGTTCTAC
143511 AT
1 AT
143513 ATTACCTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 1 0.03
22 35 0.95
23 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (22 bp):
ATCTGTATCTGATCTGTTCTAC
Found at i:149323 original size:50 final size:50
Alignment explanation
Indices: 149269--149376 Score: 162
Period size: 50 Copynumber: 2.2 Consensus size: 50
149259 CATGCCAGGG
* *
149269 ACACGGGTGTGTGTCCAGGTCATGTAACTCACTATTTGTGATTTAGAGTC
1 ACACGGGCGTGTGTCCAGGCCATGTAACTCACTATTTGTGATTTAGAGTC
* * * *
149319 ACACGGGCGTGTGTCCAGGCCGTGTGACTCACTATTTGTGGTTTAGGGTC
1 ACACGGGCGTGTGTCCAGGCCATGTAACTCACTATTTGTGATTTAGAGTC
149369 ACACGGGC
1 ACACGGGC
149377 TAAGGACGCG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.30
Consensus pattern (50 bp):
ACACGGGCGTGTGTCCAGGCCATGTAACTCACTATTTGTGATTTAGAGTC
Found at i:149402 original size:63 final size:63
Alignment explanation
Indices: 149325--149446 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
149315 AGTCACACGG
* * * * *
149325 GCGTGTGTCCAGGCCGTGTGACTCACTATTTGTGGTTTAGGGTCACACGGGCTAAGGACGCGA
1 GCGTGCGTACAGGCCGTGTAACTCACTATTTGTGATTTAGGGTAACACGGGCTAAGGACGCGA
* * * * *
149388 GCGTGCGTACAGGCCGTGTAACTCATTATTTTTTATTTAGGGTAACATGGGTTAAGGAC
1 GCGTGCGTACAGGCCGTGTAACTCACTATTTGTGATTTAGGGTAACACGGGCTAAGGAC
149447 ATGGTTGTGT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (63 bp):
GCGTGCGTACAGGCCGTGTAACTCACTATTTGTGATTTAGGGTAACACGGGCTAAGGACGCGA
Found at i:150082 original size:22 final size:22
Alignment explanation
Indices: 150049--150143 Score: 129
Period size: 22 Copynumber: 4.3 Consensus size: 22
150039 GGTAGGAAAT
150049 TGCATCTGTATTTGATCTGTTC
1 TGCATCTGTATTTGATCTGTTC
* * *
150071 TTCATCTTTATTTGATTTGTTC
1 TGCATCTGTATTTGATCTGTTC
*
150093 TGCATCTGTA-TCGAATCTGTTC
1 TGCATCTGTATTTG-ATCTGTTC
*
150115 TGCATCTGTATATGATCTGTTC
1 TGCATCTGTATTTGATCTGTTC
150137 TGCATCT
1 TGCATCT
150144 TATCTGAATG
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
21 2 0.03
22 59 0.95
23 1 0.02
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.49
Consensus pattern (22 bp):
TGCATCTGTATTTGATCTGTTC
Found at i:150143 original size:11 final size:12
Alignment explanation
Indices: 150049--150149 Score: 76
Period size: 11 Copynumber: 9.2 Consensus size: 12
150039 GGTAGGAAAT
*
150049 TGCATCTGTATT
1 TGCATCTGTATC
150061 TG-ATCTGT-TC
1 TGCATCTGTATC
* * *
150071 TTCATCTTTATT
1 TGCATCTGTATC
*
150083 TG-ATTTGT-TC
1 TGCATCTGTATC
150093 TGCATCTGTATC
1 TGCATCTGTATC
*
150105 -GAATCTGT-TC
1 TGCATCTGTATC
*
150115 TGCATCTGTATA
1 TGCATCTGTATC
150127 TG-ATCTGT-TC
1 TGCATCTGTATC
150137 TGCATCT-TATC
1 TGCATCTGTATC
150148 TG
1 TG
150150 AATGGTTACG
Statistics
Matches: 68, Mismatches: 13, Indels: 17
0.69 0.13 0.17
Matches are distributed among these distances:
10 11 0.16
11 48 0.71
12 9 0.13
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (12 bp):
TGCATCTGTATC
Found at i:154538 original size:19 final size:19
Alignment explanation
Indices: 154514--154550 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
154504 ATGGTAAGTC
154514 TGCATCTATAGCTAATGTT
1 TGCATCTATAGCTAATGTT
154533 TGCATCTATAGCTAATGT
1 TGCATCTATAGCTAATGT
154551 AGACTCTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (19 bp):
TGCATCTATAGCTAATGTT
Found at i:155875 original size:21 final size:21
Alignment explanation
Indices: 155849--155888 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
155839 CATCTCCTAT
155849 GGCACACTCCTCAGTCCCACC
1 GGCACACTCCTCAGTCCCACC
155870 GGCACACTCCTCAGTCCCA
1 GGCACACTCCTCAGTCCCA
155889 TCTCATCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.50, G:0.15, T:0.15
Consensus pattern (21 bp):
GGCACACTCCTCAGTCCCACC
Found at i:158674 original size:38 final size:39
Alignment explanation
Indices: 158623--158711 Score: 126
Period size: 38 Copynumber: 2.3 Consensus size: 39
158613 TTAAGTATTA
* *
158623 AATTATGTCATAATTTGAACATCATTAATATGAG-TTTT
1 AATTATGTCATAATCTGAACATCATTAATAAGAGTTTTT
* * *
158661 AATTATGCCATAATCTGAACATCTTTAATAAGGGTTTTT
1 AATTATGTCATAATCTGAACATCATTAATAAGAGTTTTT
158700 AATTATGTCATA
1 AATTATGTCATA
158712 GTTTAGGACA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
38 29 0.66
39 15 0.34
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.43
Consensus pattern (39 bp):
AATTATGTCATAATCTGAACATCATTAATAAGAGTTTTT
Found at i:158769 original size:38 final size:40
Alignment explanation
Indices: 158694--158773 Score: 119
Period size: 38 Copynumber: 2.0 Consensus size: 40
158684 TTTAATAAGG
*
158694 GTTTTTAATTATGTCATAGTTTAGGACATCTTAAATACAT
1 GTTTTGAATTATGTCATAGTTTAGGACATCTTAAATACAT
* *
158734 GTTTTGAA-TATGTCCTAGTTTA-GACATCTTCAATACAT
1 GTTTTGAATTATGTCATAGTTTAGGACATCTTAAATACAT
158772 GT
1 GT
158774 CTTTAGTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 17 0.46
39 13 0.35
40 7 0.19
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (40 bp):
GTTTTGAATTATGTCATAGTTTAGGACATCTTAAATACAT
Found at i:160023 original size:44 final size:43
Alignment explanation
Indices: 159961--160048 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 43
159951 TATTCTTTTG
*
159961 GTTTTTATAGCATTCAATATGGAGGACTTTTGGAAACTTCCAT
1 GTTTTTATAGCATTCAATATGAAGGACTTTTGGAAACTTCCAT
*
160004 GTTTTTATAGGCATTCAATATGAAGGACTTTTGGAAATTTCCAT
1 GTTTTTATA-GCATTCAATATGAAGGACTTTTGGAAACTTCCAT
160048 G
1 G
160049 AATAAAGATA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 9 0.21
44 33 0.79
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (43 bp):
GTTTTTATAGCATTCAATATGAAGGACTTTTGGAAACTTCCAT
Found at i:162654 original size:14 final size:14
Alignment explanation
Indices: 162635--162661 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
162625 TATTCAATAA
162635 CTCGTGAAGTTATG
1 CTCGTGAAGTTATG
162649 CTCGTGAAGTTAT
1 CTCGTGAAGTTAT
162662 ATTCAATAAC
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:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (14 bp):
CTCGTGAAGTTATG
Found at i:163599 original size:25 final size:25
Alignment explanation
Indices: 163571--163643 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 25
163561 GAAAATCTTT
*
163571 TGAGCCATATAACGGGAAGCTCATG
1 TGAGCCATATAACGAGAAGCTCATG
** **
163596 TGAGCTGTATAACGAGAAGCTCCGG
1 TGAGCCATATAACGAGAAGCTCATG
* *
163621 AGAGCCAT-TAACGTGAAGCTCAT
1 TGAGCCATATAACGAGAAGCTCAT
163644 ACGCGCCAAT
Statistics
Matches: 37, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
24 12 0.32
25 25 0.68
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.21
Consensus pattern (25 bp):
TGAGCCATATAACGAGAAGCTCATG
Found at i:163662 original size:24 final size:24
Alignment explanation
Indices: 163635--163689 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
163625 CCATTAACGT
*
163635 GAAGCTCATA-CGCGCCAATATCAG
1 GAAGCTCA-AGCGAGCCAATATCAG
* *
163659 GAAGTTCAAGCGAGCCAATATCGG
1 GAAGCTCAAGCGAGCCAATATCAG
163683 GAAGCTC
1 GAAGCTC
163690 TAGAGGGCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.16
Consensus pattern (24 bp):
GAAGCTCAAGCGAGCCAATATCAG
Found at i:163699 original size:24 final size:24
Alignment explanation
Indices: 163648--163715 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
163638 GCTCATACGC
* *
163648 GCCAATATCAGGAAGTTCAAGCGA
1 GCCAATATCAGGAAGCTCAAGAGA
* * *
163672 GCCAATATCGGGAAGCTCTAGAGG
1 GCCAATATCAGGAAGCTCAAGAGA
* *
163696 GCCATATTTCAAGAAGCTCA
1 GCCA-ATATCAGGAAGCTCA
163716 TGAAAGAGCC
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
24 23 0.68
25 11 0.32
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (24 bp):
GCCAATATCAGGAAGCTCAAGAGA
Found at i:164729 original size:19 final size:18
Alignment explanation
Indices: 164705--164744 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
164695 CTTCATCTCC
164705 TTCTTTCTCGCTTTTCTTT
1 TTCTTTCTCGC-TTTCTTT
**
164724 TTCTTTCTTTCTTTCTTT
1 TTCTTTCTCGCTTTCTTT
164742 TTC
1 TTC
164745 CTTTTGTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (18 bp):
TTCTTTCTCGCTTTCTTT
Found at i:164765 original size:24 final size:24
Alignment explanation
Indices: 164705--164774 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 24
164695 CTTCATCTCC
* *
164705 TTCTTTCTCGC-TTTTCTTTTTCT
1 TTCTTTCTTGCTTTTTCCTTTTCT
* *
164728 TTCTTTCTTTCTTTTTCCTTTTGT
1 TTCTTTCTTGCTTTTTCCTTTTCT
*
164752 TTCGTTT-TTGCTTTGTTTCTTTT
1 TTC-TTTCTTGCTTT-TTCCTTTT
164775 TAATTCTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
23 9 0.24
24 19 0.50
25 10 0.26
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.73
Consensus pattern (24 bp):
TTCTTTCTTGCTTTTTCCTTTTCT
Found at i:166895 original size:38 final size:38
Alignment explanation
Indices: 166844--166918 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
166834 GTGGTAGGGC
*
166844 AGTGTTAGAGTGATTTTAGGAGGGAAATATGGGATTGG
1 AGTGTTAGAGTGATTTTAGGAGGAAAATATGGGATTGG
*
166882 AGTGTTGGAGTGATTTTAGGAGGAAAATATGGGATTG
1 AGTGTTAGAGTGATTTTAGGAGGAAAATATGGGATTG
166919 TGGAGTTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.29, C:0.00, G:0.39, T:0.32
Consensus pattern (38 bp):
AGTGTTAGAGTGATTTTAGGAGGAAAATATGGGATTGG
Found at i:174042 original size:48 final size:50
Alignment explanation
Indices: 173893--174045 Score: 136
Period size: 49 Copynumber: 3.1 Consensus size: 50
173883 ACACGTTAAC
** * * * * * *
173893 AAATAAATATAAATATTTATATTAAATACA--AGATCTGAACAAATAATAT
1 AAATAAATATCTATATTTATGTAAAAAACACTAGATCTAAAAAAACAAT-T
*
173942 AAATAAATATTTATATTTATGTAAAAAACACTAGATCTAAGAAAAACAAATT
1 AAATAAATATCTATATTTATGTAAAAAACACTAGATCTAA-AAAAAC-AATT
* *
173994 AAATAAATATCTATATTTATTTAAAAGA-A-TCAGATCT-AAAAAACAATT
1 AAATAAATATCTATATTTATGTAAAAAACACT-AGATCTAAAAAAACAATT
174042 AAAT
1 AAAT
174046 GAACAAAATC
Statistics
Matches: 88, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
48 8 0.09
49 31 0.35
50 2 0.02
51 14 0.16
52 30 0.34
53 3 0.03
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.32
Consensus pattern (50 bp):
AAATAAATATCTATATTTATGTAAAAAACACTAGATCTAAAAAAACAATT
Found at i:176531 original size:20 final size:20
Alignment explanation
Indices: 176506--176545 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
176496 CGTAAAATGA
*
176506 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
176526 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
176546 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:176535 original size:34 final size:35
Alignment explanation
Indices: 176491--176557 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
176481 CAGTAAAATA
*
176491 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
176525 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
176558 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:176561 original size:14 final size:15
Alignment explanation
Indices: 176485--176561 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
176475 GATTGCCAGT
* *
176485 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
176499 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
176513 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
176533 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
176548 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
176562 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:178615 original size:148 final size:149
Alignment explanation
Indices: 178433--178730 Score: 535
Period size: 148 Copynumber: 2.0 Consensus size: 149
178423 TTTATAAGCT
*
178433 ATAGTAAGACTTAATTAAATGCGTATTTAAATGGTCCAAAATTCCAACAGCAAATTAATTAGCTG
1 ATAGTAAGACTTAATTAAATGCATATTTAAATGGTCCAAAATTCCAACAGCAAATTAATTAGCTG
*
178498 GGACGAAATTCAGCTTCCAACAAGTTGAAAATATTCAGCTCGTTTTTAAACTCCTTGCTATCATT
66 GAACGAAATTCAGCTTCCAACAAGTTGAAAATATTCAGCTCGTTTTTAAACTCCTTGCTATCATT
178563 TTCCCAAGTTCGTCCCAAC
131 TTCCCAAGTTCGTCCCAAC
*
178582 ATAGTAAGAC-TAATTAAATGCATATTTAAATGGTCCAAAATTCCAGCAGCAAATTAATTAGCTG
1 ATAGTAAGACTTAATTAAATGCATATTTAAATGGTCCAAAATTCCAACAGCAAATTAATTAGCTG
* * *
178646 GAATGAAATTCAGCTTCCAACATGTTGAAAATATTCAGCTCGTTTTTAAACTTCTTGCTATCATT
66 GAACGAAATTCAGCTTCCAACAAGTTGAAAATATTCAGCTCGTTTTTAAACTCCTTGCTATCATT
178711 TTCCCAAGTTCGTCCCAAC
131 TTCCCAAGTTCGTCCCAAC
178730 A
1 A
178731 ATGCTGAAAT
Statistics
Matches: 143, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
148 133 0.93
149 10 0.07
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (149 bp):
ATAGTAAGACTTAATTAAATGCATATTTAAATGGTCCAAAATTCCAACAGCAAATTAATTAGCTG
GAACGAAATTCAGCTTCCAACAAGTTGAAAATATTCAGCTCGTTTTTAAACTCCTTGCTATCATT
TTCCCAAGTTCGTCCCAAC
Found at i:183856 original size:23 final size:24
Alignment explanation
Indices: 183830--183874 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
183820 CAAAATTCTT
*
183830 TTTTTATAATATA-ATTTTTTTAA
1 TTTTCATAATATATATTTTTTTAA
*
183853 TTTTCGTAATATATATTTTTTT
1 TTTTCATAATATATATTTTTTT
183875 TTTCGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTCATAATATATATTTTTTTAA
Found at i:183894 original size:10 final size:12
Alignment explanation
Indices: 183870--183903 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
183860 AATATATATT
183870 TTTTTTTTCGAA
1 TTTTTTTTCGAA
183882 TTTTTTTT-G-A
1 TTTTTTTTCGAA
183892 TTTTTTTTCGAA
1 TTTTTTTTCGAA
183904 ACTACAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.45
11 2 0.10
12 9 0.45
ACGTcount: A:0.15, C:0.06, G:0.09, T:0.71
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:185843 original size:31 final size:31
Alignment explanation
Indices: 185805--185869 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
185795 AAGTGTTTTC
**
185805 AAGCAAGCTCCCTATGTGAGCTCTCTGTGAT
1 AAGCAAGCTCCCTATGCAAGCTCTCTGTGAT
* *
185836 AAGCAAGCTCTCTATGCAAGCTCTTTGTGAT
1 AAGCAAGCTCCCTATGCAAGCTCTCTGTGAT
185867 AAG
1 AAG
185870 TCTTTATGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (31 bp):
AAGCAAGCTCCCTATGCAAGCTCTCTGTGAT
Found at i:186872 original size:18 final size:18
Alignment explanation
Indices: 186849--186890 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
186839 TGAATTGTGC
186849 GAACCCATATATGTATGT
1 GAACCCATATATGTATGT
* *
186867 GAACCCATGTATTTATGT
1 GAACCCATATATGTATGT
186885 GAACCC
1 GAACCC
186891 TATGAAAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (18 bp):
GAACCCATATATGTATGT
Found at i:189221 original size:15 final size:17
Alignment explanation
Indices: 189203--189237 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
189193 TTTAACCAAA
189203 ATAATTTT-TT-TAAAT
1 ATAATTTTATTATAAAT
189218 ATAATTTTATTATAAAT
1 ATAATTTTATTATAAAT
189235 ATA
1 ATA
189238 TCTATTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 2 0.11
17 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATAATTTTATTATAAAT
Found at i:191313 original size:6 final size:6
Alignment explanation
Indices: 191302--191354 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
191292 CATAATATAA
191302 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
191350 TTAAT
1 TTAAT
191355 CCAATTTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTAATT
Found at i:198944 original size:20 final size:20
Alignment explanation
Indices: 198919--198958 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
198909 AAATGAAATC
*
198919 TTTAGGATAAATCAATGAAA
1 TTTAGGAGAAATCAATGAAA
*
198939 TTTAGGAGGAATCAATGAAA
1 TTTAGGAGAAATCAATGAAA
198959 GGACATCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (20 bp):
TTTAGGAGAAATCAATGAAA
Found at i:201123 original size:18 final size:18
Alignment explanation
Indices: 201100--201135 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
201090 ATCAAGTTTC
201100 AATTTTGCAGAGTGACTA
1 AATTTTGCAGAGTGACTA
201118 AATTTTGCAGAGTGACTA
1 AATTTTGCAGAGTGACTA
201136 CCGGCAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (18 bp):
AATTTTGCAGAGTGACTA
Found at i:205606 original size:20 final size:20
Alignment explanation
Indices: 205569--205642 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
205559 GAAAATTTTG
205569 AAATAATTTTAAAATCAAGTTA
1 AAATAATTTT--AATCAAGTTA
*
205591 AAATAATTTTAATCAAGTCA
1 AAATAATTTTAATCAAGTTA
* * *
205611 AAATGATTTCAACCAAGTTA
1 AAATAATTTTAATCAAGTTA
*
205631 AAATCATTTTAA
1 AAATAATTTTAA
205643 CACATCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 35 0.78
22 10 0.22
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.35
Consensus pattern (20 bp):
AAATAATTTTAATCAAGTTA
Found at i:205628 original size:40 final size:40
Alignment explanation
Indices: 205569--205668 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 40
205559 GAAAATTTTG
* *
205569 AAATAATTTTAAAATCAAGTTAAAATAATTTTAATCA-AGTCA
1 AAATGATTTTCAAA-CAAGTTAAAATAATTTTAA-CACA-TCA
* *
205611 AAATGA-TTTCAACCAAGTTAAAATCATTTTAACACATCA
1 AAATGATTTTCAAACAAGTTAAAATAATTTTAACACATCA
*
205650 AAATTATTTTCAAACAAGT
1 AAATGATTTTCAAACAAGT
205669 CGGAATTGCT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
39 10 0.20
40 30 0.60
41 5 0.10
42 5 0.10
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (40 bp):
AAATGATTTTCAAACAAGTTAAAATAATTTTAACACATCA
Found at i:214203 original size:20 final size:20
Alignment explanation
Indices: 214128--214203 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
214118 AAGTTTATGC
*
214128 TAAGTAAATGGAATGGAAAG
1 TAAGTAAATGGAATGGTAAG
* * *
214148 TAAGTAAATGAAATAG-AAC
1 TAAGTAAATGGAATGGTAAG
214167 TAAGTAAATGGAATGGTAAG
1 TAAGTAAATGGAATGGTAAG
*
214187 TAAGTAAATGGAGTGGT
1 TAAGTAAATGGAATGGT
214204 TCATAGTCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.33
20 32 0.67
ACGTcount: A:0.47, C:0.01, G:0.28, T:0.24
Consensus pattern (20 bp):
TAAGTAAATGGAATGGTAAG
Found at i:218260 original size:78 final size:78
Alignment explanation
Indices: 218159--218316 Score: 291
Period size: 78 Copynumber: 2.0 Consensus size: 78
218149 CAGCAAAATT
218159 TAATTAGAATCAATTAGATCTGGAAACTAAAAATCCCAAAATCAATAAAGAACAACCAAGAATCA
1 TAATTAGAATCAATTAGATCTGGAAACTAAAAATCCCAAAATCAATAAAGAACAACCAAGAATCA
218224 AAACACTTATGAA
66 AAACACTTATGAA
*
218237 TAATTAGAAATCAATTAGA-CTGGAAACTAAAAATCCCCAAATCAATAAAGAACAACCAAGAATC
1 TAATTAG-AATCAATTAGATCTGGAAACTAAAAATCCCAAAATCAATAAAGAACAACCAAGAATC
218301 AAAACACTTATGAA
65 AAAACACTTATGAA
218315 TA
1 TA
218317 GATGTTCTTA
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
78 67 0.86
79 11 0.14
ACGTcount: A:0.54, C:0.17, G:0.09, T:0.20
Consensus pattern (78 bp):
TAATTAGAATCAATTAGATCTGGAAACTAAAAATCCCAAAATCAATAAAGAACAACCAAGAATCA
AAACACTTATGAA
Found at i:218625 original size:44 final size:45
Alignment explanation
Indices: 218559--218649 Score: 166
Period size: 44 Copynumber: 2.0 Consensus size: 45
218549 AACAAGAACA
218559 ATTAAATCCCAAATTATTCAACAAAACGGCACAAGCAGAATTTAAT
1 ATTAAATCCC-AATTATTCAACAAAACGGCACAAGCAGAATTTAAT
218605 ATTAAATCCC-ATTATTCAACAAAACGGCACAAGCAGAATTTAAT
1 ATTAAATCCCAATTATTCAACAAAACGGCACAAGCAGAATTTAAT
218649 A
1 A
218650 AAGAAGAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 35 0.78
46 10 0.22
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (45 bp):
ATTAAATCCCAATTATTCAACAAAACGGCACAAGCAGAATTTAAT
Found at i:239290 original size:25 final size:26
Alignment explanation
Indices: 239241--239292 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
239231 ATTCGCGTAA
239241 TTATTCTTGTAATTGCCATTACATTT
1 TTATTCTTGTAATTGCCATTACATTT
*
239267 TTATTCTTGT-TTTGCC-TTATCATTT
1 TTATTCTTGTAATTGCCATTA-CATTT
239292 T
1 T
239293 CTAATATTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 3 0.12
25 11 0.46
26 10 0.42
ACGTcount: A:0.17, C:0.15, G:0.08, T:0.60
Consensus pattern (26 bp):
TTATTCTTGTAATTGCCATTACATTT
Found at i:240869 original size:18 final size:18
Alignment explanation
Indices: 240846--240881 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
240836 GTTTTAGAAT
240846 TTAATTCAAAAT-TATTTA
1 TTAATT-AAAATATATTTA
240864 TTAATTAAAATATATTTA
1 TTAATTAAAATATATTTA
240882 ATTGATGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATTAAAATATATTTA
Found at i:241344 original size:31 final size:31
Alignment explanation
Indices: 241306--241372 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
241296 ATTTTACTTG
* *
241306 TTTTATTTTTTAAAATTAATATTT-TATTTTA
1 TTTTATTTTATAAAATTAA-ATTTGTATGTTA
* *
241337 TTTTATTTTATAGATTTAAATTTGTATGTTA
1 TTTTATTTTATAAAATTAAATTTGTATGTTA
241368 TTTTA
1 TTTTA
241373 AAAATAAGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (31 bp):
TTTTATTTTATAAAATTAAATTTGTATGTTA
Found at i:248187 original size:42 final size:41
Alignment explanation
Indices: 248121--248226 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 41
248111 GTGATTTCCA
* * * * *
248121 TATAAGACCATATCTGAGATATGGCATCGGCGTGCAATC-TCG
1 TATAAGACCATGTCTGGGACATGGCATCGACAT-CAATCAT-G
*
248163 TATAAGACCATGTCTGGGACATGGCATCGACATCGATCATG
1 TATAAGACCATGTCTGGGACATGGCATCGACATCAATCATG
248204 --TAAGACCATGTCTGGGACATGGC
1 TATAAGACCATGTCTGGGACATGGC
248227 GTTGGCACCG
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
39 23 0.40
41 5 0.09
42 29 0.51
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (41 bp):
TATAAGACCATGTCTGGGACATGGCATCGACATCAATCATG
Found at i:248262 original size:50 final size:50
Alignment explanation
Indices: 248203--248333 Score: 181
Period size: 50 Copynumber: 2.6 Consensus size: 50
248193 CATCGATCAT
* ** *
248203 GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCAC
* * *
248253 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCAC
* *
248303 GTAAGACCATATCTGGGATATGGCATTGGCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA
248334 GTACAGGAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.21
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACTCCCAC
Found at i:248367 original size:49 final size:49
Alignment explanation
Indices: 248201--248372 Score: 150
Period size: 50 Copynumber: 3.5 Consensus size: 49
248191 GACATCGATC
* * * * ** *
248201 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATGGGCA-CGACAGGAGAACTCCA
** * * *
248251 CCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATGGGCA-CGACAGGAGAACTCCA
* * *
248301 ATGTAAGACCATATCTGGGATATGGCATTGGCA-GTACAGGA-AACATCCA
1 ATGTAAGACCATGTCTGGGACATGGCATGGGCACG-ACAGGAGAAC-TCCA
*
248350 ATGTAAGACTATGTCTGGGACAT
1 ATGTAAGACCATGTCTGGGACAT
248373 AGCTTTGGCA
Statistics
Matches: 102, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
48 4 0.04
49 27 0.26
50 71 0.70
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (49 bp):
ATGTAAGACCATGTCTGGGACATGGCATGGGCACGACAGGAGAACTCCA
Found at i:256267 original size:71 final size:71
Alignment explanation
Indices: 256156--256297 Score: 232
Period size: 71 Copynumber: 2.0 Consensus size: 71
256146 GATTCAAGCT
*
256156 CATCAAACATACTTATTTCATTCACAAGCTACATACAAGCATTTGTTTCAA-GAAAAAACATAAT
1 CATCAAACATACTTATTTCATTCACAAGCTAAATACAAGCATTTGTTTCAAGGAAAAAA-ATAAT
256220 TCAAAAG
65 TCAAAAG
* * *
256227 CATCAAACATACTTATTTCATTCACAAGCTAAATATAAGCATTTGTTTCAAGGCAAAAAATGATT
1 CATCAAACATACTTATTTCATTCACAAGCTAAATACAAGCATTTGTTTCAAGGAAAAAAATAATT
256292 CAAAAG
66 CAAAAG
256298 TTTACATGGC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
71 60 0.91
72 6 0.09
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.29
Consensus pattern (71 bp):
CATCAAACATACTTATTTCATTCACAAGCTAAATACAAGCATTTGTTTCAAGGAAAAAAATAATT
CAAAAG
Found at i:265177 original size:146 final size:143
Alignment explanation
Indices: 264927--265251 Score: 438
Period size: 146 Copynumber: 2.2 Consensus size: 143
264917 TTTTTTTAAA
*
264927 AAAAGAGAAAGTTTAGATTTTTAAAATAAAAATCTATTTTTTTTAGTCATATTAAAGGAAAAGTT
1 AAAAGAGAAAG-TTAGATTTTTAAAATAAAAAT-T-TGTTTTTTAGTCATATTAAAGGAAAAGTT
* ** *** *
264992 TAAAATTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTTGAAATATTTTTTTTATTTTTAAGA
63 TAAAATTTTAAAACAAAATTTTGATCTTTTTCAACTATTTCAAAATAAAGTTTTGATTTTTAA-A
*
265057 AAAATAGTTATTTTTTT
127 AAAATAGTGATTTTTTT
* *
265074 AAAAGAGAAAGTATAGATTTTTAAAATAAAAATTTGTTTTTTAGTCATTTTAAAGGAAAATTTTA
1 AAAAGAGAAAGT-TAGATTTTTAAAATAAAAATTTGTTTTTTAGTCATATTAAAGGAAAAGTTT-
* *
265139 AAAATTTTAAAATAAAATTTTGATCTTTTTCAATTATTTCAAAATAAAGTTTTGATTTTTAAAAA
64 AAAATTTTAAAACAAAATTTTGATCTTTTTCAACTATTTCAAAATAAAGTTTTGATTTTTAAAAA
265204 AATAGTGATTTTTTT
129 AATAGTGATTTTTTT
* *
265219 AAAAGA-AAAATTAGATTTTGTAATA-AAAAATTT
1 AAAAGAGAAAGTTAGATTTT-TAAAATAAAAATTT
265252 CCGACCACCG
Statistics
Matches: 160, Mismatches: 15, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
143 16 0.10
144 8 0.05
145 50 0.31
146 55 0.34
147 31 0.19
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (143 bp):
AAAAGAGAAAGTTAGATTTTTAAAATAAAAATTTGTTTTTTAGTCATATTAAAGGAAAAGTTTAA
AATTTTAAAACAAAATTTTGATCTTTTTCAACTATTTCAAAATAAAGTTTTGATTTTTAAAAAAA
TAGTGATTTTTTT
Found at i:267839 original size:59 final size:58
Alignment explanation
Indices: 267771--267919 Score: 163
Period size: 59 Copynumber: 2.5 Consensus size: 58
267761 TTTGTACTTG
* * * *
267771 GTTACAAATTTTGATATCCATTAGAAATTTTGATATTTGATTAAAAAATGTGGTATTT
1 GTTACAAATTTTGATATCCGTTAGAAATTTTCATATATGATTAAAAAATGTGGTATGT
* * * * * *
267829 GTTACAAAATTTTGATATCTGTTAGAAGATTTTCATATATGGTTAGATATTTTGGTATGT
1 GTTAC-AAATTTTGATATCCGTTAGAA-ATTTTCATATATGATTAAAAAATGTGGTATGT
* * *
267889 GTTAGAAATTTCGATATTCGTTAGAAATTTT
1 GTTACAAATTTTGATATCCGTTAGAAATTTT
267920 AGTATTGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
58 10 0.13
59 37 0.49
60 28 0.37
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (58 bp):
GTTACAAATTTTGATATCCGTTAGAAATTTTCATATATGATTAAAAAATGTGGTATGT
Found at i:267851 original size:20 final size:19
Alignment explanation
Indices: 267771--267919 Score: 75
Period size: 20 Copynumber: 7.6 Consensus size: 19
267761 TTTGTACTTG
* *
267771 GTTACAAATTTTGATATCC
1 GTTAAAAATTTTGATATCT
* * *
267790 ATTAGAAATTTTGATATTT
1 GTTAAAAATTTTGATATCT
* * * *
267809 GATTAAAAAATGTGGTATTT
1 G-TTAAAAATTTTGATATCT
267829 GTTACAAAATTTTGATATCT
1 GTTA-AAAATTTTGATATCT
* * *
267849 GTTAGAAGATTTTCATATAT
1 GTTA-AAAATTTTGATATCT
* * * *
267869 GGTTAGATATTTTGGTATGT
1 -GTTAAAAATTTTGATATCT
* *
267889 GTTAGAAATTTCGATAT-T
1 GTTAAAAATTTTGATATCT
*
267907 CGTTAGAAATTTT
1 -GTTAAAAATTTT
267920 AGTATTGGTC
Statistics
Matches: 100, Mismatches: 26, Indels: 8
0.75 0.19 0.06
Matches are distributed among these distances:
18 1 0.01
19 43 0.43
20 52 0.52
21 4 0.04
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (19 bp):
GTTAAAAATTTTGATATCT
Found at i:267925 original size:19 final size:18
Alignment explanation
Indices: 267835--267926 Score: 55
Period size: 19 Copynumber: 4.8 Consensus size: 18
267825 ATTTGTTACA
267835 AAATTTT-GATATCTGTTAG
1 AAATTTTAG-TAT-TGTTAG
267854 AAGATTTTCA-TATATGGTTAG
1 AA-ATTTT-AGTAT-T-GTTAG
* *
267875 ATATTTTGGTATGTGTTAG
1 AAATTTTAGTAT-TGTTAG
*
267894 AAA-TTTCGATATTCGTTAG
1 AAATTTTAG-TATT-GTTAG
267913 AAATTTTAGTATTG
1 AAATTTTAGTATTG
267927 GTCCCTACAC
Statistics
Matches: 58, Mismatches: 7, Indels: 17
0.71 0.09 0.21
Matches are distributed among these distances:
18 6 0.10
19 24 0.41
20 22 0.38
21 6 0.10
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.47
Consensus pattern (18 bp):
AAATTTTAGTATTGTTAG
Found at i:268332 original size:20 final size:20
Alignment explanation
Indices: 268307--268346 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
268297 ATGAAAGGGT
* *
268307 AATTTAGTGATATTTTTAAG
1 AATTTAGTAAAATTTTTAAG
*
268327 AATTTATTAAAATTTTTAAG
1 AATTTAGTAAAATTTTTAAG
268347 GCTTTACCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (20 bp):
AATTTAGTAAAATTTTTAAG
Found at i:268358 original size:20 final size:20
Alignment explanation
Indices: 268321--268418 Score: 83
Period size: 20 Copynumber: 4.9 Consensus size: 20
268311 TAGTGATATT
* ** *
268321 TTTAAGAATTTATTAAAATT
1 TTTAAGGATTTACCAAAATA
*
268341 TTTAAGGCTTTACCAAAATA
1 TTTAAGGATTTACCAAAATA
* * *
268361 TCTAAGAATTTAACAAAA-A
1 TTTAAGGATTTACCAAAATA
*
268380 TTTTAAAG-TTATACCAAAATA
1 -TTTAAGGATT-TACCAAAATA
268401 TTTAAGGATTTACCAAAA
1 TTTAAGGATTTACCAAAA
268419 CTTCTTTCTT
Statistics
Matches: 60, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
19 3 0.05
20 54 0.90
21 3 0.05
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (20 bp):
TTTAAGGATTTACCAAAATA
Found at i:268367 original size:40 final size:40
Alignment explanation
Indices: 268323--268418 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
268313 GTGATATTTT
** * *
268323 TAAGAATTTATTAAAATTTTTAAGGCTT-TACCAAAATATC
1 TAAGAATTTAACAAAAATTTTAAAG-TTATACCAAAATATC
*
268363 TAAGAATTTAACAAAAATTTTAAAGTTATACCAAAATATT
1 TAAGAATTTAACAAAAATTTTAAAGTTATACCAAAATATC
* *
268403 TAAGGATTTACCAAAA
1 TAAGAATTTAACAAAA
268419 CTTCTTTCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 2 0.04
40 46 0.96
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.35
Consensus pattern (40 bp):
TAAGAATTTAACAAAAATTTTAAAGTTATACCAAAATATC
Found at i:268707 original size:20 final size:20
Alignment explanation
Indices: 268682--268769 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
268672 ATATTATTCC
268682 TTACCAAAATATCTAAGAAT
1 TTACCAAAATATCTAAGAAT
* *
268702 TTACCAAAATTTCTAATGTTAT
1 TTACCAAAATATCTAA-G-AAT
* ** * *
268724 ATAAAAAAAAATCTAACAAT
1 TTACCAAAATATCTAAGAAT
* *
268744 TTACCAATATTTCTAAGAAT
1 TTACCAAAATATCTAAGAAT
268764 TTACCA
1 TTACCA
268770 TTGCTTCTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
20 36 0.72
21 1 0.02
22 13 0.26
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (20 bp):
TTACCAAAATATCTAAGAAT
Found at i:268777 original size:20 final size:20
Alignment explanation
Indices: 268735--268799 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
268725 TAAAAAAAAA
*
268735 TCTAACAATTTACCAATATT
1 TCTAACAATTTACCAATACT
* * *
268755 TCTAAGAATTTACCATTGCT
1 TCTAACAATTTACCAATACT
* *
268775 TCTAA-AGATTTAGCAATATT
1 TCTAACA-ATTTACCAATACT
268795 TCTAA
1 TCTAA
268800 AGATTTCCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
19 1 0.03
20 35 0.97
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (20 bp):
TCTAACAATTTACCAATACT
Found at i:268800 original size:20 final size:20
Alignment explanation
Indices: 268742--268805 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
268732 AAATCTAACA
268742 ATTTACCAATATTTCT-AAG
1 ATTTACCAATATTTCTAAAG
* **
268761 AATTTACCATTGCTTCTAAAG
1 -ATTTACCAATATTTCTAAAG
*
268782 ATTTAGCAATATTTCTAAAG
1 ATTTACCAATATTTCTAAAG
268802 ATTT
1 ATTT
268806 CCTTAATACC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 33 0.92
21 3 0.08
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (20 bp):
ATTTACCAATATTTCTAAAG
Found at i:269239 original size:22 final size:22
Alignment explanation
Indices: 269196--269240 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
269186 TATTTTAATG
*
269196 TTTACCAAAAATTTTAAGGATT
1 TTTACCAAAAATTTTAAAGATT
*
269218 TTTACC-AATATTTCTAAAGATT
1 TTTACCAAAAATTT-TAAAGATT
269240 T
1 T
269241 CCTTAATGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (22 bp):
TTTACCAAAAATTTTAAAGATT
Found at i:281945 original size:14 final size:14
Alignment explanation
Indices: 281926--281961 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
281916 GAGGCAGAAG
281926 AAAGAAAAACGTAA
1 AAAGAAAAACGTAA
*
281940 AAAGAAAAAGGTAA
1 AAAGAAAAACGTAA
281954 AAAGAAAA
1 AAAGAAAA
281962 TGCTGTGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.06
Consensus pattern (14 bp):
AAAGAAAAACGTAA
Found at i:286233 original size:42 final size:42
Alignment explanation
Indices: 286169--286249 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
286159 TATGAAAGTG
286169 ATTAGACGTGATATTTCATTATGTTTGTTATATAAGTCATAA
1 ATTAGACGTGATATTTCATTATGTTTGTTATATAAGTCATAA
* * * * *
286211 ATTAGATGTGATGTTTCGTTATGTTTTTTATATGAGTCA
1 ATTAGACGTGATATTTCATTATGTTTGTTATATAAGTCA
286250 AGAAAGTAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.48
Consensus pattern (42 bp):
ATTAGACGTGATATTTCATTATGTTTGTTATATAAGTCATAA
Found at i:287860 original size:21 final size:20
Alignment explanation
Indices: 287816--287883 Score: 84
Period size: 20 Copynumber: 3.2 Consensus size: 20
287806 GTTGACGTAC
*
287816 AATGAATAAATTTTAACCATAA
1 AATGAATAAATTTTTA--ATAA
287838 AATGAATGAAATTTTTAATAA
1 AATGAAT-AAATTTTTAATAA
287859 AATG-ATCAAATTTTTAATAA
1 AATGAAT-AAATTTTTAATAA
287879 AATGA
1 AATGA
287884 TCAGTTCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
20 19 0.45
21 8 0.19
22 7 0.17
23 8 0.19
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.35
Consensus pattern (20 bp):
AATGAATAAATTTTTAATAA
Found at i:287871 original size:20 final size:20
Alignment explanation
Indices: 287834--287886 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
287824 AATTTTAACC
*
287834 ATAAAATGAATGAAATTTTTA
1 ATAAAATG-ATCAAATTTTTA
287855 ATAAAATGATCAAATTTTTA
1 ATAAAATGATCAAATTTTTA
287875 ATAAAATGATCA
1 ATAAAATGATCA
287887 GTTCATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 23 0.74
21 8 0.26
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.36
Consensus pattern (20 bp):
ATAAAATGATCAAATTTTTA
Found at i:295768 original size:20 final size:21
Alignment explanation
Indices: 295745--295791 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
295735 TTTCATATCA
* *
295745 ATTTAATAT-TAAAGAATATT
1 ATTTAATATCAAAAGAATAAT
**
295765 ATTTTCTATCAAAAGAATAAT
1 ATTTAATATCAAAAGAATAAT
295786 ATTTAA
1 ATTTAA
295792 ATATAAATAT
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (21 bp):
ATTTAATATCAAAAGAATAAT
Found at i:297978 original size:42 final size:41
Alignment explanation
Indices: 297929--298033 Score: 149
Period size: 42 Copynumber: 2.6 Consensus size: 41
297919 GAAATAAAAC
* **
297929 TTGCATGTTAAGCATGCCGACTATGTTGACTATAAATTTGA
1 TTGCATGTTAAGCATGCCGACTATATTGACTATAAATCCGA
*
297970 TTCGCATGTTAAGCATGCCGACTATATTGATTATAAATCCGA
1 TT-GCATGTTAAGCATGCCGACTATATTGACTATAAATCCGA
*
298012 TTGCATGTTCAGCATGCC-ACTA
1 TTGCATGTTAAGCATGCCGACTA
298034 AAAATATTGT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
40 4 0.07
41 17 0.29
42 37 0.64
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (41 bp):
TTGCATGTTAAGCATGCCGACTATATTGACTATAAATCCGA
Found at i:298645 original size:38 final size:39
Alignment explanation
Indices: 298548--298658 Score: 188
Period size: 39 Copynumber: 2.9 Consensus size: 39
298538 TTAATAAATA
*
298548 AAATTATCCAACCCAATAAAACTAAAACTAAAGTCTACC
1 AAATTACCCAACCCAATAAAACTAAAACTAAAGTCTACC
298587 AAATTACCCAACCCAATAAAACTAAAACTAAAGTCTACC
1 AAATTACCCAACCCAATAAAACTAAAACTAAAGTCTACC
* *
298626 CAATTA-CCAACCCAATAAAAATAAAACTAAAGT
1 AAATTACCCAACCCAATAAAACTAAAACTAAAGT
298659 TTAACTCTTA
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
38 26 0.38
39 43 0.62
ACGTcount: A:0.53, C:0.25, G:0.03, T:0.19
Consensus pattern (39 bp):
AAATTACCCAACCCAATAAAACTAAAACTAAAGTCTACC
Found at i:298816 original size:37 final size:37
Alignment explanation
Indices: 298789--298861 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
298779 TGTTAATTTC
* * *
298789 AAGAATTATTTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
* *
298826 AAGATTTATGTAATATTTTTAATTATGTAGTGATTC
1 AAGAATTATGTAATATTTTTAATTATGTAGTAATTC
298862 CGATATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTAATTCA
Found at i:298867 original size:26 final size:26
Alignment explanation
Indices: 298838--298887 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
298828 GATTTATGTA
298838 ATATTTTTAATTATGTAGTGATTCCG
1 ATATTTTTAATTATGTAGTGATTCCG
*
298864 ATATTTTTAATTATGTAGTTATTC
1 ATATTTTTAATTATGTAGTGATTC
298888 AATTCGGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.54
Consensus pattern (26 bp):
ATATTTTTAATTATGTAGTGATTCCG
Found at i:298902 original size:9 final size:9
Alignment explanation
Indices: 298888--298918 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
298878 GTAGTTATTC
*
298888 AATTCGGGT
1 AATTCGGTT
298897 AATTCGGTT
1 AATTCGGTT
298906 AATTCGGTT
1 AATTCGGTT
298915 AATT
1 AATT
298919 TTTAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:302010 original size:16 final size:16
Alignment explanation
Indices: 301989--302019 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
301979 TTAGTAGAAC
*
301989 CTTAATTTTTTATAAT
1 CTTAATTTTTAATAAT
302005 CTTAATTTTTAATAA
1 CTTAATTTTTAATAA
302020 ATATTTAGAA
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:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
CTTAATTTTTAATAAT
Found at i:302217 original size:20 final size:20
Alignment explanation
Indices: 302177--302213 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
302167 ACTTCAAAAT
*
302177 TTTTATTTTTTTAATGTTAA
1 TTTTATTTGTTTAATGTTAA
302197 TTTTATTTGTTT-ATGTT
1 TTTTATTTGTTTAATGTT
302214 TAATAAGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (20 bp):
TTTTATTTGTTTAATGTTAA
Found at i:304539 original size:33 final size:33
Alignment explanation
Indices: 304497--304562 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
304487 GTGGTGGTTG
*
304497 ATAGTGTGAACGCTCTTCGACGTCTTCAAGATC
1 ATAGTGTGAACGCTCTCCGACGTCTTCAAGATC
304530 ATAGTGTGAACGCTCTCCGACGTCTTCAAGATC
1 ATAGTGTGAACGCTCTCCGACGTCTTCAAGATC
304563 CCGACTATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (33 bp):
ATAGTGTGAACGCTCTCCGACGTCTTCAAGATC
Found at i:308052 original size:25 final size:25
Alignment explanation
Indices: 308013--308072 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
308003 GAATGTTCTA
*
308013 TATGACT-TTGAAATTCATGCATAC
1 TATGACTCATGAAATTCATGCATAC
308037 TATGACTCATGAAATTCATGCATAC
1 TATGACTCATGAAATTCATGCATAC
308062 TATGACTCATG
1 TATGACTCATG
308073 TTGACAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 7 0.21
25 27 0.79
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.35
Consensus pattern (25 bp):
TATGACTCATGAAATTCATGCATAC
Found at i:317797 original size:27 final size:26
Alignment explanation
Indices: 317756--317928 Score: 145
Period size: 27 Copynumber: 6.4 Consensus size: 26
317746 GTGAGGTCAA
**
317756 TAAAATGACCAAAATAGCCCCATAGGG
1 TAAAATGACTGAAATA-CCCCATAGGG
*
317783 TAAAATGACTGAAATACCTCCGTAGGG
1 TAAAATGACTGAAATACC-CCATAGGG
* ** *
317810 CAAAAT-AGCTGAAATACCCCCGCAAGG
1 TAAAATGA-CTGAAATA-CCCCATAGGG
317837 TAAAATGA-TCGAAATACCCCCATAGGG
1 TAAAATGACT-GAAATA-CCCCATAGGG
*
317864 TAAAATGATTGAAATACCCCTATAGGG
1 TAAAATGACTGAAATACCCC-ATAGGG
**
317891 TAAAATGACTGTCATACCCC-TAGGAG
1 TAAAATGACTGAAATACCCCATAGG-G
*
317917 ATGAAATGACTG
1 -TAAAATGACTG
317929 TTATGGGGTT
Statistics
Matches: 123, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
25 4 0.03
26 9 0.07
27 106 0.86
28 4 0.03
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.20
Consensus pattern (26 bp):
TAAAATGACTGAAATACCCCATAGGG
Found at i:347758 original size:18 final size:18
Alignment explanation
Indices: 347735--347776 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
347725 AGTGGAAACA
**
347735 TATGTTATTATGTGAACC
1 TATGTTATTATACGAACC
*
347753 TATGTTTTTATACGAACC
1 TATGTTATTATACGAACC
347771 TATGTT
1 TATGTT
347777 GTATGAAGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (18 bp):
TATGTTATTATACGAACC
Found at i:348595 original size:20 final size:20
Alignment explanation
Indices: 348570--348631 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
348560 GCTTTTATGA
348570 GTTTGCACTTCGGTGCCTCT
1 GTTTGCACTTCGGTGCCTCT
*
348590 GTTTGCACTTTGGTGCCTCT
1 GTTTGCACTTCGGTGCCTCT
* * *
348610 ATTTGCACTACGATGCCTCT
1 GTTTGCACTTCGGTGCCTCT
348630 GT
1 GT
348632 ATAGCATTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.10, C:0.27, G:0.23, T:0.40
Consensus pattern (20 bp):
GTTTGCACTTCGGTGCCTCT
Found at i:349976 original size:30 final size:30
Alignment explanation
Indices: 349941--350006 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
349931 CCTGCAGGGG
**
349941 ACACACAATCGTGTTGCATGGCCGTGTGTC
1 ACACACAATCGTGTCACATGGCCGTGTGTC
** * *
349971 ACACACGGTTGTGTCACATGGTCGTGTGTC
1 ACACACAATCGTGTCACATGGCCGTGTGTC
350001 ACACAC
1 ACACAC
350007 GACTGAGACA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.21, C:0.27, G:0.26, T:0.26
Consensus pattern (30 bp):
ACACACAATCGTGTCACATGGCCGTGTGTC
Found at i:350019 original size:30 final size:30
Alignment explanation
Indices: 349957--350027 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
349947 AATCGTGTTG
** * *
349957 CATGGCCGTGTGTCACACACGGTTGTGTCA
1 CATGGCCGTGTGTCACACACGACTGAGACA
*
349987 CATGGTCGTGTGTCACACACGACTGAGACA
1 CATGGCCGTGTGTCACACACGACTGAGACA
*
350017 CATGCCCGTGT
1 CATGGCCGTGT
350028 CTTAGGTAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.24
Consensus pattern (30 bp):
CATGGCCGTGTGTCACACACGACTGAGACA
Found at i:353070 original size:45 final size:45
Alignment explanation
Indices: 353006--353093 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
352996 ACAGATACTC
* *
353006 GGTGGATTCAGCACATAGCAACCACCTTATTAATCCATGATGTCT
1 GGTGGATTCAGCACATAGCAACCACCTTACTAATCAATGATGTCT
353051 GGTGGAATT-AGCACATAGCAACCACCTTACTAATCAATGATGT
1 GGTGG-ATTCAGCACATAGCAACCACCTTACTAATCAATGATGT
353094 TCGGTTCACA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 37 0.93
46 3 0.08
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (45 bp):
GGTGGATTCAGCACATAGCAACCACCTTACTAATCAATGATGTCT
Found at i:353162 original size:51 final size:50
Alignment explanation
Indices: 353095--353290 Score: 225
Period size: 51 Copynumber: 3.9 Consensus size: 50
353085 CAATGATGTT
* * * *
353095 CGGTTCACATAGTAGCCTGCACATAGTACTAAACATGTGGCCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATTA-CATC
* * * *
353146 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA-AACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATTAC-ATC
* * * *
353197 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATTA-TTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACC-ATTACATC
*
353247 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCAT
353291 CACTTTCACT
Statistics
Matches: 121, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
49 2 0.02
50 42 0.35
51 74 0.61
52 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATTACATC
Found at i:353278 original size:101 final size:101
Alignment explanation
Indices: 353102--353286 Score: 300
Period size: 101 Copynumber: 1.8 Consensus size: 101
353092 GTTCGGTTCA
* *
353102 CATAGTAGCCTGCACATAGTACTAAACATGTGGCCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTAAACATGCGACCATTA-CATCCGATACACGTAGTAGCCTGCA
353167 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * *
353204 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATTA-TTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTAAACATGCGACC-ATTACATCCGATACACGTAGTAGCCTGCA
353268 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
353287 CCATCACTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 41 0.53
102 32 0.42
103 4 0.05
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTAAACATGCGACCATTACATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Done.