Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 14 of 185
Found at i:3767775 original size:7 final size:6
Alignment explanation
Indices: 3767751--3767813 Score: 65
Period size: 6 Copynumber: 10.2 Consensus size: 6
3767741 TATTGTTGAT
* * *
3767751 AATGGG AATGGG AATGGG AAATGGG AAATGGG AATGGG TAT-TG CATGGG
1 AATGGG AATGGG AATGGG -AATGGG -AATGGG AATGGG AATGGG AATGGG
3767800 AATGGG AAATGGG A
1 AATGGG -AATGGG A
3767814 GGAGGGCACG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
5 3 0.06
6 27 0.55
7 19 0.39
ACGTcount: A:0.35, C:0.02, G:0.44, T:0.19
Consensus pattern (6 bp):
AATGGG
Found at i:3767861 original size:60 final size:59
Alignment explanation
Indices: 3767795--3767987 Score: 232
Period size: 60 Copynumber: 3.3 Consensus size: 59
3767785 TGGGTATTGC
3767795 ATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAATCGATGGAAGAGGGGAG
1 ATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAAT-GATGGAAGAGGGGAG
* * * * *
3767855 ATGGGAATGGGAAATGGGAGGATGGCACGGTGGAA-TGGGAAAT--TGGAA-TGGGTATTG
1 ATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAATGATGGAAGAGGGGA--G
* * * *
3767912 CATGGGAATAGGAAATGGGAGGAGGGTACGGTGGAAGAGGGGAATGAGGGAAGATGGGAG
1 -ATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAATGATGGAAGAGGGGAG
3767972 ATGGGAATGGAGAAAT
1 ATGGGAATGG-GAAAT
3767988 TGCATTGTAT
Statistics
Matches: 110, Mismatches: 15, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
55 4 0.04
56 5 0.05
57 1 0.01
58 32 0.29
59 21 0.19
60 40 0.36
61 4 0.04
62 3 0.03
ACGTcount: A:0.33, C:0.04, G:0.49, T:0.15
Consensus pattern (59 bp):
ATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAATGATGGAAGAGGGGAG
Found at i:3767890 original size:28 final size:28
Alignment explanation
Indices: 3767798--3767897 Score: 94
Period size: 28 Copynumber: 3.4 Consensus size: 28
3767788 GTATTGCATG
3767798 GGAATGGGAAATGGGAGGAGGGCACGGT
1 GGAATGGGAAATGGGAGGAGGGCACGGT
* * * * *
3767826 GGAAGAGGGGAATCGATGGAAGAGGGGA-GAT
1 GGAA-TGGGAAAT-G--GGAGGAGGGCACGGT
*
3767857 GGGAATGGGAAATGGGAGGATGGCACGGT
1 -GGAATGGGAAATGGGAGGAGGGCACGGT
3767886 GGAATGGGAAAT
1 GGAATGGGAAAT
3767898 TGGAATGGGT
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 24 0.44
29 8 0.15
30 2 0.04
31 8 0.15
32 13 0.24
ACGTcount: A:0.32, C:0.05, G:0.51, T:0.12
Consensus pattern (28 bp):
GGAATGGGAAATGGGAGGAGGGCACGGT
Found at i:3767987 original size:118 final size:118
Alignment explanation
Indices: 3767770--3767987 Score: 375
Period size: 118 Copynumber: 1.8 Consensus size: 118
3767760 GGGAATGGGA
*
3767770 AATGGGAAATGGGAATGGGTATTGCATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGG
1 AATGGGAAATGGGAATGGGTATTGCATGGGAATAGGAAATGGGAGGAGGGCACGGTGGAAGAGGG
*
3767835 GAATCGATGGAAGAGGGGAGATGGGAATGGGAAATGGGAGGATGGCACGGTGG
66 GAATCGAGGGAAGAGGGGAGATGGGAATGGGAAATGGGAGGATGGCACGGTGG
* *
3767888 AATGGGAAATTGGAATGGGTATTGCATGGGAATAGGAAATGGGAGGAGGGTACGGTGGAAGAGGG
1 AATGGGAAATGGGAATGGGTATTGCATGGGAATAGGAAATGGGAGGAGGGCACGGTGGAAGAGGG
*
3767953 GAAT-GAGGGAAGATGGGAGATGGGAATGGAGAAAT
66 GAATCGAGGGAAGAGGGGAGATGGGAATGG-GAAAT
3767988 TGCATTGTAT
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
117 23 0.24
118 71 0.76
ACGTcount: A:0.33, C:0.04, G:0.48, T:0.16
Consensus pattern (118 bp):
AATGGGAAATGGGAATGGGTATTGCATGGGAATAGGAAATGGGAGGAGGGCACGGTGGAAGAGGG
GAATCGAGGGAAGAGGGGAGATGGGAATGGGAAATGGGAGGATGGCACGGTGG
Found at i:3768048 original size:29 final size:29
Alignment explanation
Indices: 3768003--3768317 Score: 392
Period size: 31 Copynumber: 10.8 Consensus size: 29
3767993 TGTATTTAAA
* **
3768003 ATTTTAGAAATTAAAAAATACGTGTAGTGT
1 ATTTTA-AAAATAAAAAATATATGTAGTGT
3768033 ATTTTAAAAATAAAAAAAATATATGTAGTGT
1 ATTTTAAAAAT--AAAAAATATATGTAGTGT
* *
3768064 ATTTTAAAAATAAAAAAATATATGTACTAT
1 ATTTTAAAAAT-AAAAAATATATGTAGTGT
3768094 ATTTTAAAAATAAAAAATATATATGTAGTGT
1 ATTTTAAAAAT-AAAAA-ATATATGTAGTGT
* *
3768125 ATTTT-AAAAT-ATATATATATGTAGTGT
1 ATTTTAAAAATAAAAAATATATGTAGTGT
* *
3768152 ATTTTAAAAGTAAAAAAAATATGTAGTGT
1 ATTTTAAAAATAAAAAATATATGTAGTGT
3768181 ATTTTAAAAATAAAAAATATATATGTAGTGT
1 ATTTTAAAAAT-AAAAA-ATATATGTAGTGT
*
3768212 ATTTT--AAAT---ATATATATGTAGTGT
1 ATTTTAAAAATAAAAAATATATGTAGTGT
*
3768236 ATTTTAAAAGTAAAAAAAATATATGTAGTGT
1 ATTTTAAAA--ATAAAAAATATATGTAGTGT
3768267 ATTTTAAAAATAAAAAATATATGTAGTGT
1 ATTTTAAAAATAAAAAATATATGTAGTGT
3768296 ATTTTAAAAATAAAAAATATAT
1 ATTTTAAAAATAAAAAATATAT
3768318 AAAGTAGTCA
Statistics
Matches: 252, Mismatches: 19, Indels: 29
0.84 0.06 0.10
Matches are distributed among these distances:
24 18 0.07
25 1 0.00
26 2 0.01
27 18 0.07
28 7 0.03
29 73 0.29
30 50 0.20
31 83 0.33
ACGTcount: A:0.50, C:0.01, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTTTAAAAATAAAAAATATATGTAGTGT
Found at i:3768135 original size:60 final size:60
Alignment explanation
Indices: 3768003--3768318 Score: 411
Period size: 60 Copynumber: 5.4 Consensus size: 60
3767993 TGTATTTAAA
* * **
3768003 ATTTTAGAAATTAAAAAATACGTGTAGTGTATTTTAAAAATAAAAAAAATATATGTAGTGT
1 ATTTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAAT-AAAAAAATATATGTAGTGT
* *
3768064 ATTTTAAAAATAAAAAAATATATGTACTATATTTTAAAAATAAAAAATATATATGTAGTGT
1 ATTTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAA-ATATATGTAGTGT
* * *
3768125 ATTTT-AAAAT--ATATATATATGTAGTGTATTTTAAAAGTAAAAAAA-ATATGTAGTGT
1 ATTTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAAATATATGTAGTGT
*
3768181 ATTTTAAAAATAAAAAATATATATGTAGTGTATTTT--AAAT----ATATATATGTAGTGT
1 ATTTTAAAAATAAAAAA-ATATATGTAGTGTATTTTAAAAATAAAAAAATATATGTAGTGT
*
3768236 ATTTTAAAAGTAAAAAAAATATATGTAGTGTATTTTAAAAAT-AAAAAATATATGTAGTGT
1 ATTTTAAAAAT-AAAAAAATATATGTAGTGTATTTTAAAAATAAAAAAATATATGTAGTGT
3768296 ATTTTAAAAATAAAAAATATATA
1 ATTTTAAAAATAAAAAA-ATATA
3768319 AAGTAGTCAA
Statistics
Matches: 224, Mismatches: 18, Indels: 27
0.83 0.07 0.10
Matches are distributed among these distances:
54 2 0.01
55 39 0.17
56 22 0.10
57 10 0.04
58 32 0.14
59 8 0.04
60 58 0.26
61 53 0.24
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.39
Consensus pattern (60 bp):
ATTTTAAAAATAAAAAAATATATGTAGTGTATTTTAAAAATAAAAAAATATATGTAGTGT
Found at i:3768223 original size:22 final size:23
Alignment explanation
Indices: 3768194--3768244 Score: 93
Period size: 24 Copynumber: 2.2 Consensus size: 23
3768184 TTAAAAATAA
3768194 AAAATATATATGTAGTGTATTTT
1 AAAATATATATGTAGTGTATTTT
3768217 AAATATATATATGTAGTGTATTTT
1 AAA-ATATATATGTAGTGTATTTT
3768241 AAAA
1 AAAA
3768245 GTAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (23 bp):
AAAATATATATGTAGTGTATTTT
Found at i:3768307 original size:86 final size:87
Alignment explanation
Indices: 3768043--3768307 Score: 434
Period size: 84 Copynumber: 3.1 Consensus size: 87
3768033 ATTTTAAAAA
* * * *
3768043 TAAAAA-AAATATATGTAGTGTATTTTAAAAATAAAAAAATATATGTACTATATTTTAAAAATAA
1 TAAAAATATATATATGTAGTGTATTTTAAAAGTAAAAAAATATATGTAGTGTATTTTAAAAATAA
3768107 AAAATATATATGTAGTGTATTT
66 AAAATATATATGTAGTGTATTT
3768129 TAAAATATATATATATGTAGTGTATTTTAAAAGTAAAAAAA-ATATGTAGTGTATTTTAAAAATA
1 TAAAA-ATATATATATGTAGTGTATTTTAAAAGTAAAAAAATATATGTAGTGTATTTTAAAAATA
3768193 AAAAATATATATGTAGTGTATTT
65 AAAAATATATATGTAGTGTATTT
3768216 T--AAATATATATATGTAGTGTATTTTAAAAGTAAAAAAAATATATGTAGTGTATTTTAAAAAT-
1 TAAAAATATATATATGTAGTGTATTTTAAAAGT-AAAAAAATATATGTAGTGTATTTTAAAAATA
3768278 AAAAA-ATATATGTAGTGTATTT
65 AAAAATATATATGTAGTGTATTT
3768300 TAAAAATA
1 TAAAAATA
3768308 AAAAATATAT
Statistics
Matches: 169, Mismatches: 4, Indels: 12
0.91 0.02 0.06
Matches are distributed among these distances:
84 46 0.27
85 14 0.08
86 32 0.19
87 46 0.27
88 31 0.18
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.39
Consensus pattern (87 bp):
TAAAAATATATATATGTAGTGTATTTTAAAAGTAAAAAAATATATGTAGTGTATTTTAAAAATAA
AAAATATATATGTAGTGTATTT
Found at i:3772186 original size:21 final size:21
Alignment explanation
Indices: 3772162--3772214 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3772152 CATTATTTCT
* *
3772162 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAATAACC
*
3772183 AATCTCACCGCTACAATAACT
1 AATCTCACCGCTACAATAACC
3772204 AATCTCACCGC
1 AATCTCACCGC
3772215 CACCACTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.40, G:0.08, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:3776142 original size:30 final size:32
Alignment explanation
Indices: 3776082--3776143 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
3776072 AAAACAAATA
*
3776082 TATATATAATTGTATATCTTAATTATTCTATT
1 TATATATAATTGTATATCTAAATTATTCTATT
*
3776114 TATATATATTTGT-TA-CTAAAGTTA-TCTATT
1 TATATATAATTGTATATCTAAA-TTATTCTATT
3776144 GCTACTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 10 0.37
31 5 0.19
32 12 0.44
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (32 bp):
TATATATAATTGTATATCTAAATTATTCTATT
Found at i:3777845 original size:42 final size:42
Alignment explanation
Indices: 3777795--3777894 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
3777785 TTATATGAAC
3777795 GGCACTAAGTGTGCGAAACTAAAAT-GACGAGGTTGAATAAAG
1 GGCACTAAGTGTGCGAAACTAAAATAGA-GAGGTTGAATAAAG
* * *
3777837 GGCACTAAGTGTGCGAAATTAAAATAGAGATGTTGAATAATG
1 GGCACTAAGTGTGCGAAACTAAAATAGAGAGGTTGAATAAAG
3777879 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
3777895 TACCGAGAGC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
42 52 0.96
43 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.29, T:0.22
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAACTAAAATAGAGAGGTTGAATAAAG
Found at i:3781128 original size:29 final size:30
Alignment explanation
Indices: 3781095--3781165 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
3781085 AAATCAAAAT
3781095 TTCATGTATAAAATT-ACATAAAATTAAAG
1 TTCATGTATAAAATTAACATAAAATTAAAG
* * * * *
3781124 TTCATATGTACAATTACACATTAAATTACAG
1 TTCATGTATAAAATTA-ACATAAAATTAAAG
3781155 TTCATGTATAA
1 TTCATGTATAA
3781166 TTTTGAGATT
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
29 12 0.38
31 20 0.62
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.37
Consensus pattern (30 bp):
TTCATGTATAAAATTAACATAAAATTAAAG
Found at i:3784355 original size:3 final size:3
Alignment explanation
Indices: 3784349--3784373 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3784339 CCTCCTACTC
3784349 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
3784374 ATGAATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:3796920 original size:18 final size:17
Alignment explanation
Indices: 3796879--3796945 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
3796869 AGCATGTTTC
3796879 GAACTTAAAGAAA-TTTT
1 GAACTT-AAGAAATTTTT
**
3796896 GGGCTTAAGCAAATTTTT
1 GAACTTAAG-AAATTTTT
*
3796914 GAACTTAA-ATATGTTTT
1 GAACTTAAGAAAT-TTTT
3796931 GAACTTAAGTAAATT
1 GAACTTAAG-AAATT
3796946 CTGAACTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
16 6 0.15
17 19 0.49
18 11 0.28
19 3 0.08
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (17 bp):
GAACTTAAGAAATTTTT
Found at i:3799122 original size:13 final size:13
Alignment explanation
Indices: 3799104--3799128 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3799094 TGTAAATCCG
3799104 AATTCATTTTAAA
1 AATTCATTTTAAA
3799117 AATTCATTTTAA
1 AATTCATTTTAA
3799129 CCAAATTATT
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTCATTTTAAA
Found at i:3802095 original size:48 final size:48
Alignment explanation
Indices: 3802007--3802098 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
3801997 CCAAGTTTGC
* * * *
3802007 TTCTTTTCTCATTTCTATCTCGAATCCATTGACCCGTTTTATATTTAT
1 TTCTTTTCTCATTTCTATCTCAAATCCACTAACCCATTTTATATTTAT
* **
3802055 TTCTTTTCTCATTTCTATTTCAAATCCACTAATTCATTTTATAT
1 TTCTTTTCTCATTTCTATCTCAAATCCACTAACCCATTTTATAT
3802099 CCATATCAGC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.22, C:0.22, G:0.03, T:0.53
Consensus pattern (48 bp):
TTCTTTTCTCATTTCTATCTCAAATCCACTAACCCATTTTATATTTAT
Found at i:3802319 original size:28 final size:31
Alignment explanation
Indices: 3802270--3802330 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 31
3802260 ACATTTTTGT
3802270 TTGATCAATTTTAGCCTTTATACTTTT-AAA
1 TTGATCAATTTTAGCCTTTATACTTTTCAAA
3802300 TTGATC-A-TTTAGTCC-TTATACTTTTCAAA
1 TTGATCAATTTTAG-CCTTTATACTTTTCAAA
3802329 TT
1 TT
3802331 TTAAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 15 0.52
29 8 0.28
30 6 0.21
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.51
Consensus pattern (31 bp):
TTGATCAATTTTAGCCTTTATACTTTTCAAA
Found at i:3811229 original size:9 final size:9
Alignment explanation
Indices: 3811204--3811244 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
3811194 TTATTTATCG
3811204 AATTAATTA
1 AATTAATTA
* *
3811213 AATAAATTT
1 AATTAATTA
3811222 AATTAATTA
1 AATTAATTA
*
3811231 ACTTAATTA
1 AATTAATTA
3811240 AATTA
1 AATTA
3811245 TATTCTCAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTAATTA
Found at i:3823107 original size:17 final size:18
Alignment explanation
Indices: 3823059--3823095 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3823049 CTCGCCTCAC
3823059 TCGAAAAAATTAAATTGT
1 TCGAAAAAATTAAATTGT
3823077 TCGAAAAAATTAAATTGT
1 TCGAAAAAATTAAATTGT
3823095 T
1 T
3823096 TTAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (18 bp):
TCGAAAAAATTAAATTGT
Found at i:3823433 original size:29 final size:30
Alignment explanation
Indices: 3823346--3823434 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 30
3823336 AACGGCTCAG
* * *
3823346 TGACTAAAATGTTACAACGTGATAACGTAAA
1 TGACTAAAATGTAAC-ATGTGATAACATAAA
* * *
3823377 TGACTAAAACGTAACATTTCA-AACATAAA
1 TGACTAAAATGTAACATGTGATAACATAAA
*
3823406 TGACTAAAATGTAACATGAGATAA-ATAAA
1 TGACTAAAATGTAACATGTGATAACATAAA
3823435 AATGACTTTG
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
29 29 0.62
30 5 0.11
31 13 0.28
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (30 bp):
TGACTAAAATGTAACATGTGATAACATAAA
Found at i:3823620 original size:21 final size:21
Alignment explanation
Indices: 3823596--3823636 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3823586 AAAATTTAAG
3823596 ATTCA-AAAAATTATAAAAAAA
1 ATTCATAAAAATT-TAAAAAAA
3823617 ATTCATAAAAATTTAAAAAA
1 ATTCATAAAAATTTAAAAAA
3823637 CAGCATGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (21 bp):
ATTCATAAAAATTTAAAAAAA
Found at i:3824300 original size:21 final size:20
Alignment explanation
Indices: 3824278--3824356 Score: 61
Period size: 21 Copynumber: 3.9 Consensus size: 20
3824268 AAATCTTAGA
3824278 ATTTTATGAATTTTTTTAAG
1 ATTTTATGAATTTTTTTAAG
** *
3824298 AATTTTA-GGGTATTTTTGAAG
1 -ATTTTATGAAT-TTTTTTAAG
* * *
3824319 ATTTCAATGATTTTTTTTATG
1 ATTT-TATGAATTTTTTTAAG
*
3824340 TTTTTATGAATTTTTTT
1 ATTTTATGAATTTTTTT
3824357 TATATTTTCT
Statistics
Matches: 44, Mismatches: 11, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
20 17 0.39
21 25 0.57
22 2 0.05
ACGTcount: A:0.25, C:0.01, G:0.13, T:0.61
Consensus pattern (20 bp):
ATTTTATGAATTTTTTTAAG
Found at i:3828492 original size:41 final size:41
Alignment explanation
Indices: 3828447--3828644 Score: 238
Period size: 41 Copynumber: 4.8 Consensus size: 41
3828437 AAATTGTTCA
3828447 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
*
3828488 GACTATACGTCCAGCAGGCTAAGTGCCGGTGAATTGAATCG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
* * * *
3828529 GATTATATGTCCAGCAGGCTAAGTGCCGGTGAACTGAATCAG
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATC-G
* * ** **
3828571 GA-TATAGGCCTAGCAGGCTAAGTGCCGGTGAACGGAATTA
1 GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
* * *
3828611 GACTATAAGTCTATCAGG-TGAAGTGCCAGTGAAT
1 GACTATACGTCTAGCAGGCT-AAGTGCCGGTGAAT
3828645 CTGTTTAAAT
Statistics
Matches: 139, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
40 3 0.02
41 133 0.96
42 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (41 bp):
GACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAATCG
Found at i:3834693 original size:25 final size:25
Alignment explanation
Indices: 3834631--3834739 Score: 101
Period size: 25 Copynumber: 4.4 Consensus size: 25
3834621 CGCTCTTATG
* *
3834631 AGCTTCCCGATATTTAACTCACATG
1 AGCTTCCCGATATTTAGCTCACATA
* * **
3834656 AGATTTCTAATATTTAGCTCACATA
1 AGCTTCCCGATATTTAGCTCACATA
*
3834681 AGCTTCCCGATATTTAGCTCATATA
1 AGCTTCCCGATATTTAGCTCACATA
** * * *
3834706 AGCTTTTCGATACTTAGCTCGCATG
1 AGCTTCCCGATATTTAGCTCACATA
*
3834731 AGTTTCCCG
1 AGCTTCCCG
3834740 TTATACAACT
Statistics
Matches: 64, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 64 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (25 bp):
AGCTTCCCGATATTTAGCTCACATA
Found at i:3834723 original size:50 final size:50
Alignment explanation
Indices: 3834631--3834739 Score: 121
Period size: 50 Copynumber: 2.2 Consensus size: 50
3834621 CGCTCTTATG
* *
3834631 AGCTTCCCGATATTTAACTCACATGAGATTTCTAATATTTAGCTCACATA
1 AGCTTCCCGATATTTAACTCACATAAGATTTCTAATACTTAGCTCACATA
* * * * * *
3834681 AGCTTCCCGATATTTAGCTCATATAAGCTTT-TCGATACTTAGCTCGCATG
1 AGCTTCCCGATATTTAACTCACATAAGATTTCT-AATACTTAGCTCACATA
*
3834731 AGTTTCCCG
1 AGCTTCCCG
3834740 TTATACAACT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 1 0.02
50 48 0.98
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.36
Consensus pattern (50 bp):
AGCTTCCCGATATTTAACTCACATAAGATTTCTAATACTTAGCTCACATA
Found at i:3837561 original size:23 final size:22
Alignment explanation
Indices: 3837518--3837561 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
3837508 TTTCAAGTCA
3837518 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
3837541 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
3837562 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:3839965 original size:18 final size:18
Alignment explanation
Indices: 3839944--3839982 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3839934 TTTCTTCAAC
* *
3839944 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
3839962 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
3839980 TTC
1 TTC
3839983 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:3846591 original size:20 final size:20
Alignment explanation
Indices: 3846566--3846611 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
3846556 TATTTATTAA
3846566 GAAAGAATCACTAGACTTGT
1 GAAAGAATCACTAGACTTGT
3846586 GAAAGAATCACTAGACTTGT
1 GAAAGAATCACTAGACTTGT
3846606 GAAAGA
1 GAAAGA
3846612 TGACGCTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (20 bp):
GAAAGAATCACTAGACTTGT
Found at i:3848352 original size:19 final size:21
Alignment explanation
Indices: 3848314--3848354 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
3848304 TTTCCCAATA
*
3848314 CCTCAAACATTTTTATTTCTC
1 CCTCAAACATTTTTACTTCTC
3848335 CCTCAAA-A-TTTTACTTCTC
1 CCTCAAACATTTTTACTTCTC
3848354 C
1 C
3848355 AAAACCCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 1 0.05
21 7 0.37
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (21 bp):
CCTCAAACATTTTTACTTCTC
Found at i:3848418 original size:71 final size:72
Alignment explanation
Indices: 3848315--3848475 Score: 163
Period size: 72 Copynumber: 2.2 Consensus size: 72
3848305 TTCCCAATAC
* *
3848315 CTCAAACATTTTTATTT-CTCCCTCAAAATTTTACTTCTCCAAAACC-CTAAA-ATTTTTTTCCT
1 CTCAAA-ACTTTTATTTCCTCCCTCAAAATTTTAC--CTCCAAAACCTCAAAACATTTTTTTCCT
*
3848377 TT-CATTCTTA
63 TTAC-TTCCTA
* * *
3848387 TTCAAAACTTTTATTTCCT-CC-CAAATATTTTACCTCCCAAACCTTCAAAACATTTTTTTTCTT
1 CTCAAAACTTTTATTTCCTCCCTCAAA-ATTTTACCTCCAAAACC-TCAAAACATTTTTTTCCTT
*
3848450 TACTTCCTC
64 TACTTCCTA
3848459 CTCAAAACTTTTATTTC
1 CTCAAAACTTTTATTTC
3848476 TTCAAACCTC
Statistics
Matches: 75, Mismatches: 8, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
69 9 0.12
70 4 0.05
71 22 0.29
72 39 0.52
73 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.45
Consensus pattern (72 bp):
CTCAAAACTTTTATTTCCTCCCTCAAAATTTTACCTCCAAAACCTCAAAACATTTTTTTCCTTTA
CTTCCTA
Found at i:3850979 original size:21 final size:21
Alignment explanation
Indices: 3850925--3850984 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
3850915 ATCAGTATAT
3850925 GACACATAAGTGCCTG-TAAC
1 GACACATAAGTGCCTGATAAC
* *
3850945 GACACACGAGGTGCCTGAT-AC
1 GACACA-TAAGTGCCTGATAAC
3850966 GACACATAAAGTGCCTGAT
1 GACACAT-AAGTGCCTGAT
3850985 CGGCAAAGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 6 0.18
21 26 0.79
22 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.18
Consensus pattern (21 bp):
GACACATAAGTGCCTGATAAC
Found at i:3852188 original size:15 final size:16
Alignment explanation
Indices: 3852170--3852201 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3852160 TTAATTAATA
3852170 TAATTT-ATAATATTT
1 TAATTTAATAATATTT
3852185 TAATTTAATAATATTT
1 TAATTTAATAATATTT
3852201 T
1 T
3852202 TATAGTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTAATAATATTT
Found at i:3852828 original size:19 final size:21
Alignment explanation
Indices: 3852789--3852830 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3852779 CTCGTGCTTT
*
3852789 TATATATATTATAAATTAAAA
1 TATATATATTATAAATAAAAA
*
3852810 TATATAT-TTATAAAAAAAAA
1 TATATATATTATAAATAAAAA
3852830 T
1 T
3852831 TTAAAACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATATATATTATAAATAAAAA
Found at i:3856710 original size:17 final size:15
Alignment explanation
Indices: 3856670--3856713 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
3856660 ATTATTGATT
*
3856670 AATTAATATTTTTAA
1 AATTAAAATTTTTAA
3856685 AATTTAAAATTTTATAGA
1 AA-TTAAAATTTT-TA-A
3856703 AATTAAAATTT
1 AATTAAAATTT
3856714 CTGGTCTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 2 0.08
16 9 0.36
17 11 0.44
18 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
AATTAAAATTTTTAA
Found at i:3871877 original size:13 final size:13
Alignment explanation
Indices: 3871859--3871884 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3871849 CTCTAAAGAA
3871859 GGTTCACAAATAT
1 GGTTCACAAATAT
3871872 GGTTCACAAATAT
1 GGTTCACAAATAT
3871885 ATATAAACGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
GGTTCACAAATAT
Found at i:3884344 original size:97 final size:97
Alignment explanation
Indices: 3884178--3884373 Score: 365
Period size: 97 Copynumber: 2.0 Consensus size: 97
3884168 TTTCTTAAAA
* *
3884178 TATAACAGATTTTGTAGTAAGCTTTTGAGGGTAAACTACAAAAATAGTCACTTTTGTTTGCCTCA
1 TATAACAGATTTTGTAGTAAACTTTTAAGGGTAAACTACAAAAATAGTCACTTTTGTTTGCCTCA
3884243 GATTACATTTTAGTCACTTATGTTTGAAATGT
66 GATTACATTTTAGTCACTTATGTTTGAAATGT
*
3884275 TATAACAGATTTTGTAGTAAACTTTTAAGGGTAAACTACAAAAATAGTTACTTTTGTTTGCCTCA
1 TATAACAGATTTTGTAGTAAACTTTTAAGGGTAAACTACAAAAATAGTCACTTTTGTTTGCCTCA
3884340 GATTACATTTTAGTCACTTATGTTTGAAATGT
66 GATTACATTTTAGTCACTTATGTTTGAAATGT
3884372 TA
1 TA
3884374 GGTTTTAGTC
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
97 96 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (97 bp):
TATAACAGATTTTGTAGTAAACTTTTAAGGGTAAACTACAAAAATAGTCACTTTTGTTTGCCTCA
GATTACATTTTAGTCACTTATGTTTGAAATGT
Found at i:3884787 original size:23 final size:23
Alignment explanation
Indices: 3884753--3884796 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3884743 TTTATCCAAT
*
3884753 TTTTAATAAATAAATTTAATATA
1 TTTTAATAAATAAATATAATATA
* *
3884776 TTTTAATTAATATATATAATA
1 TTTTAATAAATAAATATAATA
3884797 CAAATAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTAATAAATAAATATAATATA
Found at i:3887150 original size:73 final size:73
Alignment explanation
Indices: 3886932--3887250 Score: 487
Period size: 73 Copynumber: 4.4 Consensus size: 73
3886922 AAAATAATCA
* ** ***
3886932 TTAGCGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCCCAACGACATCGTTTCCCGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
* *
3886996 TCGGGGAA
66 TCAGGGAT
* * *
3887004 TTAGCGGCGTTTCTGAGAAAGCGCCACAAAAAAACCATAAGCCCAACGACGCCGTTTTGTGAGCT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACC-TAAGCCCAACGACGCCGTTTTGTGAGCT
*
3887069 TTCGGGGAT
65 TTCAGGGAT
3887078 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
*
3887143 TTAGGGAT
66 TCAGGGAT
* *
3887151 TTAGCGGCGTTTTTAAGGAAGCGCCGCAAAAAAACCTAAGGCCAACGACGCCGTTTTGTGAGCTT
1 TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
3887216 TCAGGGAT
66 TCAGGGAT
3887224 TTAGCGGCGTTTTTAAGAAAGCGCCGC
1 TTAGCGGCGTTTTTAAGAAAGCGCCGC
3887251 TAATGCTTTG
Statistics
Matches: 228, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
72 25 0.11
73 139 0.61
74 64 0.28
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (73 bp):
TTAGCGGCGTTTTTAAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTGTGAGCTT
TCAGGGAT
Found at i:3887292 original size:114 final size:114
Alignment explanation
Indices: 3887145--3887458 Score: 474
Period size: 114 Copynumber: 2.8 Consensus size: 114
3887135 GTGAGCTTTT
* * * *
3887145 AGGGATTTAGCGGCGTTTTTAAGG-AAGCGCCGCAAAAAAACCTAAGGCCAACGACGCCGTTTTG
1 AGGGCTTTAGCGGCGTTTTT-GGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTC
*
3887209 TGAGCTTTCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTT-
65 TGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATG-TTC
*
3887259 TGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCT
1 AGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCT
* *
3887324 GAGCTTTCGGGGATTTAACGACGTTTTTAAGAAAGCGCCGCTAATGTTC
66 GAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGTTC
* * *
3887373 AGGGCTTTAGCGGCGTTTTTGAGAAAGCGCTGCAAAAATTA--TAAGCCCAACGACGCCGTTTTC
1 AGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAA-AACCTAAGCCCAACGACGCCGTTTTC
3887436 TGAGCTTTCGGGGATTTAGCGGC
65 TGAGCTTTCGGGGATTTAGCGGC
3887459 CAAAAATGCT
Statistics
Matches: 183, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
113 47 0.26
114 135 0.74
115 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (114 bp):
AGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCT
GAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGTTC
Found at i:3887797 original size:14 final size:14
Alignment explanation
Indices: 3887778--3887809 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3887768 AAGTATGGGT
3887778 TTAGGGATTATGGA
1 TTAGGGATTATGGA
3887792 TTAGGGATTATGGA
1 TTAGGGATTATGGA
3887806 TTAG
1 TTAG
3887810 AGGTTGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:3887837 original size:7 final size:7
Alignment explanation
Indices: 3887827--3887875 Score: 53
Period size: 7 Copynumber: 6.4 Consensus size: 7
3887817 GATTTAAGGT
3887827 TTAGGGG
1 TTAGGGG
3887834 TTAGAGGG
1 TTAG-GGG
3887842 TTAGGGG
1 TTAGGGG
3887849 TTTAGGGG
1 -TTAGGGG
*
3887857 TTAGACGTG
1 TTAG--GGG
3887866 TTAGGGG
1 TTAGGGG
3887873 TTA
1 TTA
3887876 AAAGTTAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
7 16 0.44
8 14 0.39
9 6 0.17
ACGTcount: A:0.18, C:0.02, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:3887847 original size:15 final size:15
Alignment explanation
Indices: 3887827--3887875 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
3887817 GATTTAAGGT
3887827 TTAGGGG-TTAGAGGG
1 TTAGGGGTTTAG-GGG
3887842 TTAGGGGTTTAGGGG
1 TTAGGGGTTTAGGGG
**
3887857 TTAGACGTGTTAGGGG
1 TTAGGGGT-TTAGGGG
3887873 TTA
1 TTA
3887876 AAAGTTAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 16 0.53
16 14 0.47
ACGTcount: A:0.18, C:0.02, G:0.47, T:0.33
Consensus pattern (15 bp):
TTAGGGGTTTAGGGG
Found at i:3887851 original size:23 final size:24
Alignment explanation
Indices: 3887824--3887874 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
3887814 TGGGATTTAA
3887824 GGTTTAGGGGTTAGA-GGGTTAGG
1 GGTTTAGGGGTTAGACGGGTTAGG
*
3887847 GGTTTAGGGGTTAGACGTGTTAGG
1 GGTTTAGGGGTTAGACGGGTTAGG
3887871 GGTT
1 GGTT
3887875 AAAAGTTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.16, C:0.02, G:0.49, T:0.33
Consensus pattern (24 bp):
GGTTTAGGGGTTAGACGGGTTAGG
Found at i:3888132 original size:21 final size:22
Alignment explanation
Indices: 3888102--3888142 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3888092 AGGGATTATG
*
3888102 GTTTAAGGGTTGGGA-TTTAAT
1 GTTTAAGGGTTAGGAGTTTAAT
*
3888123 GTTTAGGGGTTAGGAGTTTA
1 GTTTAAGGGTTAGGAGTTTA
3888143 GGGGTTAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (22 bp):
GTTTAAGGGTTAGGAGTTTAAT
Found at i:3888159 original size:14 final size:13
Alignment explanation
Indices: 3888125--3888173 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
3888115 GATTTAATGT
3888125 TTAGGGGTTAGGAG
1 TTAGGGGTTA-GAG
3888139 TTTAGGGGTTAGATG
1 -TTAGGGGTTAGA-G
3888154 TTAGGGGTTAAGAG
1 TTAGGGGTT-AGAG
3888168 TTAGGG
1 TTAGGG
3888174 ATTTAAGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 18 0.56
15 14 0.44
ACGTcount: A:0.22, C:0.00, G:0.45, T:0.33
Consensus pattern (13 bp):
TTAGGGGTTAGAG
Found at i:3888283 original size:303 final size:299
Alignment explanation
Indices: 3887674--3888287 Score: 959
Period size: 303 Copynumber: 2.0 Consensus size: 299
3887664 AGAGATAATA
* *
3887674 ATAATAATAAATTTGTTTAGGGTTTTTGGTTTAGGGTATATGATTTATTTAAGATTTAAGGCCGA
1 ATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCGA
* * *
3887739 TTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGGTTTAGGGATTATGGATTAGGGATTATG
66 TTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGATTTAGGAATTATGAATTAGGGATTATG
*
3887804 GATTAGAGGTTGGGATTTAAGGTTTAGGGGTTAGAGGGTTAGGGGTTTAGGGGTTAGACGTGTTA
131 GATTAGAGGTTGGGATTTAAGGTTTAGGGGTTAGAGGGTTAGGGGTTTAGGGGTTAGACGAGTTA
* * *
3887869 GGGGTTAAAAGTTAGGGATTCAGGGGTCGAGTTAGGGTTTTGGGTTTAGATTAATTATTTTTTAA
196 GGGATTAAAAGTTAGGGATTCAGGGGTCGAGTTAAGGTTTTGAGTTTAGATTAATTATTTTTTAA
3887934 TTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAG
261 TTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAG
*
3887973 ATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCGG
1 ATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCGA
3888038 TTTAGGAGTTCATATTTTAAGGTTTAGGG-AGTATGGATTTAGGAATTATGAATTAGGGATTATG
66 TTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGATTTAGGAATTATGAATTAGGGATTATG
* * *
3888102 GTTTA-AGGGTTGGGATTTAATGTTTAGGGGTTAG-GAGTTTAGGGGTTAGATGTTAGGGGTTA-
131 GATTAGA-GGTTGGGATTTAAGGTTTAGGGGTTAGAG-GGTTA-GGG---G-T-TTAGGGGTTAG
* *
3888164 A-GAGTTAGGGATTTAAGGTTTAGGGATTCAGGGGTCGAGTTAAGGTTTTGAGTTTAGATTAATT
188 ACGAGTTAGGGATTAAAAG-TTAGGGATTCAGGGGTCGAGTTAAGGTTTTGAGTTTAGATTAATT
*
3888228 ATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAATAG
252 ATTTTTTAATTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAG
*
3888276 GTAATAATAAAT
1 ATAATAATAAAT
3888288 CAAATATATT
Statistics
Matches: 289, Mismatches: 17, Indels: 14
0.90 0.05 0.04
Matches are distributed among these distances:
297 2 0.01
298 66 0.23
299 94 0.33
302 14 0.05
303 103 0.36
304 10 0.03
ACGTcount: A:0.29, C:0.02, G:0.28, T:0.41
Consensus pattern (299 bp):
ATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATATGATTAATTTAAGATTTAAGGCCGA
TTTAGGAGTTCATATTTTAAGGTTTAGGGAAGTATGGATTTAGGAATTATGAATTAGGGATTATG
GATTAGAGGTTGGGATTTAAGGTTTAGGGGTTAGAGGGTTAGGGGTTTAGGGGTTAGACGAGTTA
GGGATTAAAAGTTAGGGATTCAGGGGTCGAGTTAAGGTTTTGAGTTTAGATTAATTATTTTTTAA
TTTATATTTTAAATATGTTCTTATATAATTGTAAAAGAG
Found at i:3888491 original size:107 final size:106
Alignment explanation
Indices: 3888300--3888498 Score: 317
Period size: 106 Copynumber: 1.9 Consensus size: 106
3888290 AATATATTGA
* * *
3888300 TTTATAAAAAACGCCACAAAAAATTAATCAATTTATAAAAAAATAAAATAAAAATTTTTAGCATA
1 TTTATAAAAAACGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTAGCAGA
** *
3888365 GCAAAACGGCGTCATTTTGTTGAAAATTAAATAGCGGCATT
66 GCAAAACAACGTCATTTTGTTCAAAATTAAATAGCGGCATT
* *
3888406 TTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAATTAAAAAAATTTTAGCAG
1 TTTATAAAAAACGCCACAAAAAATAAATCAATTTATAAAAAAATAAAAT-AAAAAATTTTAGCAG
3888471 AGCAAAACAACGTCATTTTGTTCAAAAT
65 AGCAAAACAACGTCATTTTGTTCAAAAT
3888499 GAAAAAAAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
106 46 0.55
107 38 0.45
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (106 bp):
TTTATAAAAAACGCCACAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTAGCAGA
GCAAAACAACGTCATTTTGTTCAAAATTAAATAGCGGCATT
Found at i:3888680 original size:108 final size:104
Alignment explanation
Indices: 3888551--3888760 Score: 305
Period size: 103 Copynumber: 2.0 Consensus size: 104
3888541 GTAAGCAATA
*
3888551 GCGGCGTTTTTTTATAAAAACGCCGTAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAAA
1 GCGGCGTTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTAT---A-AAAT-AAATAAAAAA
* * *
3888616 AATTTAGCATAACAAAACGGCGTCATTTTGCTGAAAATGAAATT
61 AATTTAGCAGAACAAAACGACGTCATTTTGCTCAAAATGAAATT
*
3888660 GCGGCG-TTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAATAAATAAAAAAATTTT
1 GCGGCGTTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAATAAATAAAAAAAATTT
* *
3888724 AGCAGAGCAAAACGACGTCATTTTGTTCAAAATGAAA
66 AGCAGAACAAAACGACGTCATTTTGCTCAAAATGAAA
3888761 AAATTTTTGC
Statistics
Matches: 94, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
103 46 0.49
104 4 0.04
105 1 0.01
108 37 0.39
109 6 0.06
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (104 bp):
GCGGCGTTTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAATAAATAAAAAAAATTT
AGCAGAACAAAACGACGTCATTTTGCTCAAAATGAAATT
Found at i:3888867 original size:241 final size:245
Alignment explanation
Indices: 3888300--3888957 Score: 927
Period size: 241 Copynumber: 2.6 Consensus size: 245
3888290 AATATATTGA
* *
3888300 TTTATAAAAAACGCCACAAAAAATTAATCAATTTATAAAA-AAATAAAATAAAAATTTTTAGCAT
1 TTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAATTTTTAGCAT
* *
3888364 AGCAAAACGGCGTCATTTTGTTGAAAATTAAATAGCGGC-ATTTTTATAAAAAACGCCGCAAAAA
66 AGCAAAACGGCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTTTAT-AAAAACGCCGCAAAAA
3888428 ATAAATCAATTTATAAAAAAATAAATTAAAAAAATTTTAGCAGAGCAAAACAACGTCATTTTGTT
130 ATAAATCAATTTAT---AAAATAAA-TAAAAAAATTTTAGCAGAGCAAAACAACGTCATTTTGTT
3888493 CAAAATGAAAAAAAATTTGCGGCGTTTTTATGAAAAACGCCGCTAAAGGTAAGCAATAGCGGCGT
191 CAAAATGAAAAAAAATTTGCGGCGTTTTTAT----AA-----CT--AGGTAAGCAATAGCGGCGT
3888558 T
245 T
* * **
3888559 TTTTTATAAAAACGCCGTAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAAAAATTTAGC
1 TTTATA-AAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAAT-AAAAATTTTTAGC
* * *
3888624 ATAACAAAACGGCGTCATTTTGCTGAAAATGAAATTGCGGCGTTTTTTATAAAAACGCCGCAAAA
64 ATAGCAAAACGGCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTTTATAAAAACGCCGCAAAA
*
3888689 AATAAATCAATTTATAAAATAAATAAAAAAATTTTAGCAGAGCAAAACGACGTCATTTTGTTCAA
129 AATAAATCAATTTATAAAATAAATAAAAAAATTTTAGCAGAGCAAAACAACGTCATTTTGTTCAA
**
3888754 AATGAAAAAATTTTTGCGGCG-TTTT-T-A-T-GGTAAGCAATAGCGGCGTT
194 AATGAAAAAAAATTTGCGGCGTTTTTATAACTAGGTAAGCAATAGCGGCGTT
*
3888801 TTTATAAAAAACACCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAATTTTTTAGCA
1 TTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAA-TTTTTAGCA
* *
3888866 TAGCAAAACAGCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTTATAAAAAAACGCCGCAAAA
65 TAGCAAAACGGCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTT-TATAAAAACGCCGCAAAA
3888931 AATAAATCAATTTATAAAA-AAATAAAA
129 AATAAATCAATTTATAAAATAAATAAAA
3888958 TATAAAATTT
Statistics
Matches: 369, Mismatches: 24, Indels: 30
0.87 0.06 0.07
Matches are distributed among these distances:
240 5 0.01
241 99 0.27
242 60 0.16
245 1 0.00
251 1 0.00
256 1 0.00
257 4 0.01
258 60 0.16
259 13 0.04
260 31 0.08
261 9 0.02
262 78 0.21
263 7 0.02
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (245 bp):
TTTATAAAAAACGCCGCAAAAAATAAATCAATTTATAAAACAAATAAAATAAAAATTTTTAGCAT
AGCAAAACGGCGTCATTTTGTTGAAAATGAAATAGCGGCGTTTTTTATAAAAACGCCGCAAAAAA
TAAATCAATTTATAAAATAAATAAAAAAATTTTAGCAGAGCAAAACAACGTCATTTTGTTCAAAA
TGAAAAAAAATTTGCGGCGTTTTTATAACTAGGTAAGCAATAGCGGCGTT
Found at i:3890233 original size:30 final size:31
Alignment explanation
Indices: 3890172--3890236 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
3890162 ATCTCCAAAC
* *
3890172 TATATATGAACTTTGATTTTATGTATAATTT
1 TATATAGGAACTTTGATTTTATGAATAATTT
*
3890203 TATATAGGAAC-TTGATTTTGTGCAAT-ATTT
1 TATATAGGAACTTTGATTTTATG-AATAATTT
3890233 TATA
1 TATA
3890237 CTTGAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 18 0.60
31 12 0.40
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (31 bp):
TATATAGGAACTTTGATTTTATGAATAATTT
Found at i:3890409 original size:31 final size:31
Alignment explanation
Indices: 3890373--3890433 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
3890363 ATTTTTTTAA
*
3890373 ATGTATATAATTGAA-TCAAAATTAAAGTTTT
1 ATGTATACAATTGAACT-AAAATTAAAGTTTT
* *
3890404 ATGTATACATTTGAACTACAATTAAAGTTT
1 ATGTATACAATTGAACTAAAATTAAAGTTT
3890434 CACGTGTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.41
Consensus pattern (31 bp):
ATGTATACAATTGAACTAAAATTAAAGTTTT
Found at i:3909282 original size:20 final size:21
Alignment explanation
Indices: 3909259--3909302 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
3909249 AAAAATTACA
3909259 AAAAAATT-AAAATAATTTTC
1 AAAAAATTCAAAATAATTTTC
*
3909279 -AAAAATTCAAAATAATTTTT
1 AAAAAATTCAAAATAATTTTC
3909299 AAAA
1 AAAA
3909303 TTGAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 11 0.52
21 3 0.14
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAAATTCAAAATAATTTTC
Found at i:3909284 original size:19 final size:19
Alignment explanation
Indices: 3909260--3909330 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
3909250 AAAATTACAA
3909260 AAAAATT-AAAATAATTTT
1 AAAAATTCAAAATAATTTT
3909278 CAAAAATTCAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
* *
3909298 TAAAATTGAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
3909317 AAAAATTCTAAAAT
1 AAAAATTC-AAAAT
3909331 TAAAGAAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
18 4 0.09
19 25 0.56
20 16 0.36
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:3909393 original size:9 final size:9
Alignment explanation
Indices: 3909381--3909410 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3909371 TTTTTTGAAT
3909381 TTAAATAAG
1 TTAAATAAG
3909390 TT-AATAAG
1 TTAAATAAG
3909398 TTAAATAAG
1 TTAAATAAG
3909407 TTAA
1 TTAA
3909411 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (9 bp):
TTAAATAAG
Found at i:3912849 original size:20 final size:19
Alignment explanation
Indices: 3912826--3912893 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 19
3912816 TTACAAATAG
3912826 AATTTAAAATAATTTTCAAA
1 AATTTAAAATAATTTT-AAA
* *
3912846 AATTCAAAATAATTTTTAA
1 AATTTAAAATAATTTTAAA
*
3912865 AATTGAAAAT-ATTTGTAAA
1 AATTTAAAATAATTT-TAAA
3912884 AATTCTAAAA
1 AATT-TAAAA
3912894 ATTCTAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 4 0.10
19 18 0.44
20 19 0.46
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.38
Consensus pattern (19 bp):
AATTTAAAATAATTTTAAA
Found at i:3912885 original size:19 final size:19
Alignment explanation
Indices: 3912826--3912903 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
3912816 TTACAAATAG
*
3912826 AATTTAAAATAATTTTCAAA
1 AATTCAAAATAATTTT-AAA
*
3912846 AATTCAAAATAATTTTTAA
1 AATTCAAAATAATTTTAAA
*
3912865 AATTGAAAAT-ATTTGTAAA
1 AATTCAAAATAATTT-TAAA
* *
3912884 AATTCTAAA-AATTCTAAA
1 AATTCAAAATAATTTTAAA
3912902 AA
1 AA
3912904 AAAAAGAAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
18 10 0.20
19 24 0.49
20 15 0.31
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:3916347 original size:40 final size:40
Alignment explanation
Indices: 3916296--3916376 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
3916286 AATTAGTAAA
3916296 TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
1 TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
3916336 TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
1 TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
3916376 T
1 T
3916377 CGAGAAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (40 bp):
TTGAATGAAATATTAATTTAGATCAAGATTGGGTGGAAAT
Found at i:3916387 original size:40 final size:40
Alignment explanation
Indices: 3916293--3916387 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
3916283 TTAAATTAGT
*
3916293 AAATT-GAATGAAATATTAATTTAGATCAAGATTGGGTGG
1 AAATTCGAATAAAATATTAATTTAGATCAAGATTGGGTGG
* *
3916332 AAATTTGAATGAAATATTAATTTAGATCAAGATTGGGTGG
1 AAATTCGAATAAAATATTAATTTAGATCAAGATTGGGTGG
3916372 AAATTCGAGA-AAAATA
1 AAATTCGA-ATAAAATA
3916388 GAAATTTTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
39 5 0.10
40 46 0.88
41 1 0.02
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.32
Consensus pattern (40 bp):
AAATTCGAATAAAATATTAATTTAGATCAAGATTGGGTGG
Found at i:3930037 original size:6 final size:6
Alignment explanation
Indices: 3930026--3930136 Score: 156
Period size: 6 Copynumber: 19.0 Consensus size: 6
3930016 AAGATTACAC
*
3930026 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA A-TTTA TTTTTA ATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
* *
3930073 ATTTTT A-TAT- ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
* *
3930119 ATTTTT ATTTTT ATTTTA
1 ATTTTA ATTTTA ATTTTA
3930137 CATGTAGACA
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
4 1 0.01
5 8 0.08
6 86 0.91
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
ATTTTA
Found at i:3930093 original size:45 final size:46
Alignment explanation
Indices: 3930038--3930126 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
3930028 TTTAATTTTA
*
3930038 ATTTTAATTTTAATTTTAA-TTTATTTTTAATTTTAATTTTTATAT
1 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTATAT
3930083 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTAT
1 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTAT
3930127 TTTTATTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
45 19 0.45
46 23 0.55
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (46 bp):
ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTATAT
Found at i:3930098 original size:51 final size:52
Alignment explanation
Indices: 3930032--3930132 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 52
3930022 ACACATTTTA
*
3930032 ATTTTAATTTTAATTTTAATTTTAA-TTTATTTTTAATTTTAATTTTTATAT
1 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTATAT
*
3930083 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTATTTTTAT
1 ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTAT
3930133 TTTACATGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 25 0.53
52 22 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (52 bp):
ATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTAATTTTTATAT
Found at i:3939534 original size:47 final size:47
Alignment explanation
Indices: 3939475--3939781 Score: 474
Period size: 47 Copynumber: 6.6 Consensus size: 47
3939465 ATTCATGAAT
* ** **
3939475 TTGGTCAGCATATATAAAACAGTTTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
3939522 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
* * *
3939569 TTGGACAGCAT-TATGTAACAAATTGGGCAGCTTTTATGCATCACAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
*
3939615 TTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
*
3939662 TTGGACAGCAT-TATGTAACAAATTGGGCAGCATTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
* * *
3939708 TTGGACAGCATAAATGTAATAAATTGGGCAGCATTTATGCATCAAAA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
*
3939755 TTGGACAGCATATATGTAATAAATTGG
1 TTGGACAGCATATATGTAACAAATTGG
3939782 TTCAACTCAT
Statistics
Matches: 241, Mismatches: 17, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
46 87 0.36
47 154 0.64
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (47 bp):
TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAA
Found at i:3939657 original size:93 final size:93
Alignment explanation
Indices: 3939498--3939781 Score: 496
Period size: 93 Copynumber: 3.0 Consensus size: 93
3939488 ATAAAACAGT
* *
3939498 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
3939563 TCAAAATTGGACAGCATTATGTAACAAA
66 TCAAAATTGGACAGCATTATGTAACAAA
* *
3939591 TTGGGCAGCTTTTATGCATCACAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
3939656 TCAAAATTGGACAGCATTATGTAACAAA
66 TCAAAATTGGACAGCATTATGTAACAAA
* *
3939684 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATAAATGTAATAAATTGGGCAGCATTTATGCA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
*
3939749 TCAAAATTGGACAGCATATATGTAATAAA
66 TCAAAATTGGACAGCAT-TATGTAACAAA
3939778 TTGG
1 TTGG
3939782 TTCAACTCAT
Statistics
Matches: 181, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
93 167 0.92
94 14 0.08
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (93 bp):
TTGGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCA
TCAAAATTGGACAGCATTATGTAACAAA
Found at i:3939732 original size:140 final size:140
Alignment explanation
Indices: 3939498--3939781 Score: 507
Period size: 140 Copynumber: 2.0 Consensus size: 140
3939488 ATAAAACAGT
3939498 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
1 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
* * *
3939563 TCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCTTTTATGCATCACAATTGGACAGCATAT
66 TCAAAATTGGACAGCATAATGTAACAAATTGGGCAGCATTTATGCATCAAAATTGGACAGCATAT
3939628 ATGTAATAAA
131 ATGTAATAAA
*
3939638 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCAT-TATGTAACAAATTGGGCAGCATTTATGCA
1 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
*
3939702 TCAAAATTGGACAGCATAAATGTAATAAATTGGGCAGCATTTATGCATCAAAATTGGACAGCATA
66 TCAAAATTGGACAGCAT-AATGTAACAAATTGGGCAGCATTTATGCATCAAAATTGGACAGCATA
3939767 TATGTAATAAA
130 TATGTAATAAA
3939778 TTGG
1 TTGG
3939782 TTCAACTCAT
Statistics
Matches: 138, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
139 45 0.33
140 93 0.67
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (140 bp):
TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
TCAAAATTGGACAGCATAATGTAACAAATTGGGCAGCATTTATGCATCAAAATTGGACAGCATAT
ATGTAATAAA
Found at i:3940731 original size:43 final size:43
Alignment explanation
Indices: 3940622--3940737 Score: 141
Period size: 43 Copynumber: 2.7 Consensus size: 43
3940612 AACTCGTACA
*
3940622 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
*
3940665 ATGCC-ACTGTCCCAGACAG-GGTCTTAGACGTTAA-CACA-AGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACG-TAATCACATA-TCG
*
3940708 ATGCCAACGTCCCAAACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
3940738 ATGATTAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
42 4 0.06
43 53 0.84
44 6 0.10
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:3945799 original size:15 final size:16
Alignment explanation
Indices: 3945767--3945799 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3945757 AGTGGGAGAA
3945767 TATTATGGGATTTATTT
1 TATTATGGGA-TTATTT
3945784 TATTATGGGA-TATTT
1 TATTATGGGATTATTT
3945799 T
1 T
3945800 TTTCCTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TATTATGGGATTATTT
Found at i:3966252 original size:16 final size:17
Alignment explanation
Indices: 3966213--3966265 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
3966203 TTTTTAAAAA
* *
3966213 AATATTTTAAAAAATAT
1 AATATTTTTACAAATAT
3966230 AATATTTTTACAAATAT
1 AATATTTTTACAAATAT
*
3966247 -ATATTTTTACAAAGAT
1 AATATTTTTACAAATAT
3966263 AAT
1 AAT
3966266 GAATTTTGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 15 0.47
17 17 0.53
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
AATATTTTTACAAATAT
Found at i:3966254 original size:17 final size:16
Alignment explanation
Indices: 3966224--3966264 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3966214 ATATTTTAAA
3966224 AAATATAATATTTTTAC
1 AAATATAA-ATTTTTAC
*
3966241 AAATATATATTTTTAC
1 AAATATAAATTTTTAC
*
3966257 AAAGATAA
1 AAATATAA
3966265 TGAATTTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (16 bp):
AAATATAAATTTTTAC
Found at i:3966319 original size:3 final size:3
Alignment explanation
Indices: 3966311--3966336 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3966301 CCCCTTTAAA
3966311 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
3966337 TATTTATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3968751 original size:18 final size:17
Alignment explanation
Indices: 3968725--3968762 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
3968715 CACTCTAGAC
*
3968725 ATATTTTTTAATATTTTT
1 ATATATTTTAA-ATTTTT
3968743 ATATATTTTAAATTTTT
1 ATATATTTTAAATTTTT
3968760 ATA
1 ATA
3968763 ACATATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATATTTTAAATTTTT
Found at i:3969027 original size:9 final size:9
Alignment explanation
Indices: 3969015--3969052 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
3969005 GTGTTATACG
3969015 TTTTATATA
1 TTTTATATA
*
3969024 TTTT-TAGA
1 TTTTATATA
*
3969032 TTTTATTTA
1 TTTTATATA
3969041 TTTTATATA
1 TTTTATATA
3969050 TTT
1 TTT
3969053 GGACAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (9 bp):
TTTTATATA
Found at i:3971386 original size:30 final size:32
Alignment explanation
Indices: 3971345--3971432 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 32
3971335 TAGAAACAGT
3971345 ACATA-AA-TCTTAAAAGTTAACAATGAC-A-
1 ACATAGAAGTCTTAAAAGTTAACAATGACAAC
**
3971373 ACATAGAAGTCTTAAAAGTTTAA-AAAAACAAC
1 ACATAGAAGTCTTAAAAG-TTAACAATGACAAC
* *
3971405 ACAAAGTAAGTCTTGAAAGTTAACAATG
1 ACATAG-AAGTCTTAAAAGTTAACAATG
3971433 GTAGAACATA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
28 5 0.11
29 2 0.04
30 13 0.28
31 5 0.11
32 9 0.19
33 13 0.28
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.24
Consensus pattern (32 bp):
ACATAGAAGTCTTAAAAGTTAACAATGACAAC
Found at i:3972661 original size:23 final size:22
Alignment explanation
Indices: 3972633--3972696 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
3972623 AACATGAAAT
* *
3972633 TTTGTGAAACCTTTGTGGCGTAA
1 TTTGTGAAGCCTTTGTGGCAT-A
* *
3972656 TTTGTGACGCCTTTGTAGCATA
1 TTTGTGAAGCCTTTGTGGCATA
3972678 TTCTGTGAAGCCTTTGTGG
1 TT-TGTGAAGCCTTTGTGG
3972697 TCTGGTTAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.41
Consensus pattern (22 bp):
TTTGTGAAGCCTTTGTGGCATA
Found at i:3975263 original size:89 final size:89
Alignment explanation
Indices: 3975112--3975289 Score: 356
Period size: 89 Copynumber: 2.0 Consensus size: 89
3975102 CTCCAACATG
3975112 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
1 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
3975177 CATTTAACAACCTAACCATTCCAA
66 CATTTAACAACCTAACCATTCCAA
3975201 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
1 AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
3975266 CATTTAACAACCTAACCATTCCAA
66 CATTTAACAACCTAACCATTCCAA
3975290 CTATCATAAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.29
Consensus pattern (89 bp):
AAGCACACAAAACATGCATTCAATTACATCTCATACTTATCATTCAAGTATACCATTTCTCAAGT
CATTTAACAACCTAACCATTCCAA
Found at i:3980948 original size:74 final size:74
Alignment explanation
Indices: 3980821--3980958 Score: 190
Period size: 74 Copynumber: 1.9 Consensus size: 74
3980811 ACCAGTTTTA
* * *
3980821 TTTTACTTTAATATTTTGACCGAAAGGTGAAGATTAGGGCTAAAAGTGGAAATGAAAGTCTTCTT
1 TTTTACTTTAATAATTCGACCGAAAGGTGAAGATTAGGGCTAAAAGTGGAAATG-AAGGCTTCTT
3980886 CCATCGTGTT
65 CCATCGTGTT
** *
3980896 TTTTA-TTTAATAATTCGACCGAAAGGT-ATCTATTAGGGGTAAAAGTGGAAATGAAGGCTTCTT
1 TTTTACTTTAATAATTCGACCGAAAGGTGA-AGATTAGGGCTAAAAGTGGAAATGAAGGCTTCTT
3980959 ATAGATGACG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
73 10 0.18
74 41 0.73
75 5 0.09
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.36
Consensus pattern (74 bp):
TTTTACTTTAATAATTCGACCGAAAGGTGAAGATTAGGGCTAAAAGTGGAAATGAAGGCTTCTTC
CATCGTGTT
Found at i:3981103 original size:9 final size:8
Alignment explanation
Indices: 3981076--3981116 Score: 66
Period size: 8 Copynumber: 5.1 Consensus size: 8
3981066 GTTTCGTAAA
3981076 TTTAAA-T
1 TTTAAATT
3981083 TTTAAATT
1 TTTAAATT
3981091 TTTAAATTT
1 TTTAAA-TT
3981100 TTTAAATT
1 TTTAAATT
3981108 TTTAAATT
1 TTTAAATT
3981116 T
1 T
3981117 AAGTTTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 6 0.19
8 18 0.56
9 8 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTAAATT
Found at i:3981104 original size:17 final size:17
Alignment explanation
Indices: 3981082--3981116 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3981072 TAAATTTAAA
3981082 TTTTAAATTTTTAAATT
1 TTTTAAATTTTTAAATT
3981099 TTTTAAATTTTTAAATT
1 TTTTAAATTTTTAAATT
3981116 T
1 T
3981117 AAGTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTAAATTTTTAAATT
Found at i:3983782 original size:68 final size:71
Alignment explanation
Indices: 3983652--3983784 Score: 182
Period size: 68 Copynumber: 1.9 Consensus size: 71
3983642 CATGGTTAAA
* * *
3983652 GTTCGAATGTATGATACAAGTTTATTGAGCTGAACTTAATATTATGAATTTCATATATATATATG
1 GTTCGAATATATGATACAAGTTTATTGAGCTGAACTTAATAGTATGAATTTCATATACATATATG
3983717 TGTGTG
66 TGTGTG
* * * *
3983723 GTTCGAATATAT-ATTCAAG-TTCTTGAGCTGAATTTAAT-GTATGAATTTTATATACATATATG
1 GTTCGAATATATGATACAAGTTTATTGAGCTGAACTTAATAGTATGAATTTCATATACATATATG
3983785 GTTCGAATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
68 21 0.38
69 17 0.31
70 6 0.11
71 11 0.20
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.43
Consensus pattern (71 bp):
GTTCGAATATATGATACAAGTTTATTGAGCTGAACTTAATAGTATGAATTTCATATACATATATG
TGTGTG
Found at i:3984028 original size:41 final size:40
Alignment explanation
Indices: 3983971--3984084 Score: 174
Period size: 41 Copynumber: 2.8 Consensus size: 40
3983961 TGAGATTTTT
3983971 AGACTTTACGTCTAGCATGCTTAATGCCGGTGAAATATTTC
1 AGACTTTACGTCTAGCA-GCTTAATGCCGGTGAAATATTTC
3984012 AGACTTTACGTCTAGCAGACTTAATGCCGGTGAAATATTTC
1 AGACTTTACGTCTAGCAG-CTTAATGCCGGTGAAATATTTC
* * *
3984053 AGACCTTAAGTCTAGCAGGTTTAATGCCGGTG
1 AGACTTTACGTCTAGCA-GCTTAATGCCGGTG
3984085 TATTGAATCA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
40 1 0.01
41 66 0.97
42 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (40 bp):
AGACTTTACGTCTAGCAGCTTAATGCCGGTGAAATATTTC
Found at i:3988800 original size:41 final size:42
Alignment explanation
Indices: 3988685--3988800 Score: 182
Period size: 41 Copynumber: 2.8 Consensus size: 42
3988675 ACTGGCACTT
* * *
3988685 AGCCTGCTAGACATAAAGTTTGAAATGTTTCA-CTGGCGTCA
1 AGCCTGCTAGACATAAAGTCTAAAATGTTTCACCTGGCATCA
3988726 AGCCTGCTAGACATAAAGTCTAAAATGTTTCACCT-GCATCA
1 AGCCTGCTAGACATAAAGTCTAAAATGTTTCACCTGGCATCA
*
3988767 AGCCTGCTAGACTTAAAGTCTAAAATGTTTCACC
1 AGCCTGCTAGACATAAAGTCTAAAATGTTTCACC
3988801 GACAATAAAC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 68 0.97
42 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (42 bp):
AGCCTGCTAGACATAAAGTCTAAAATGTTTCACCTGGCATCA
Found at i:3989883 original size:16 final size:16
Alignment explanation
Indices: 3989864--3989901 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
3989854 AACATTTACA
3989864 CTTTTTACAATTTAAT
1 CTTTTTACAATTTAAT
3989880 CTTTTTACAATTTAAT
1 CTTTTTACAATTTAAT
3989896 CTTTTT
1 CTTTTT
3989902 TGCTCAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (16 bp):
CTTTTTACAATTTAAT
Found at i:3990402 original size:19 final size:20
Alignment explanation
Indices: 3990365--3990408 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
3990355 CTTTTGTTTT
3990365 ATTTAGTTATCATTATACTA
1 ATTTAGTTATCATTATACTA
* *
3990385 ATTTA-TTATTATTTTACTA
1 ATTTAGTTATCATTATACTA
3990404 ATTTA
1 ATTTA
3990409 ACCTTTACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTAGTTATCATTATACTA
Found at i:3990646 original size:14 final size:15
Alignment explanation
Indices: 3990627--3990655 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3990617 TCACAAAACT
3990627 TTCACACAT-ATAAA
1 TTCACACATAATAAA
3990641 TTCACACATAATAAA
1 TTCACACATAATAAA
3990656 CATAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:3992803 original size:2 final size:2
Alignment explanation
Indices: 3992796--3992841 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3992786 ACAAACAAGG
3992796 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3992838 GA GA
1 GA GA
3992842 ATTCCATTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4000384 original size:13 final size:13
Alignment explanation
Indices: 4000362--4000394 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
4000352 CCCCATATAC
*
4000362 AGATAAATATAAT
1 AGATACATATAAT
4000375 AGATACATATAAT
1 AGATACATATAAT
4000388 AGATACA
1 AGATACA
4000395 AATATACAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (13 bp):
AGATACATATAAT
Found at i:4007872 original size:27 final size:26
Alignment explanation
Indices: 4007842--4007898 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
4007832 AATTTCGAGG
*
4007842 TTTACAATTTT-TAATTTTTATTAATT
1 TTTAC-ATTTTCTAACTTTTATTAATT
*
4007868 ATTTACATTTTCTCACTTTTATTAATT
1 -TTTACATTTTCTAACTTTTATTAATT
4007895 TTTA
1 TTTA
4007899 TTATTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTACATTTTCTAACTTTTATTAATT
Found at i:4008054 original size:22 final size:23
Alignment explanation
Indices: 4008015--4008057 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
4008005 TTTAAAAAAT
*
4008015 AAAACATAATATAATATTTATCA
1 AAAAAATAATATAATATTTATCA
*
4008038 AAAAAATAA-ATATTATTTAT
1 AAAAAATAATATAATATTTAT
4008058 TTGATTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAAAATAATATAATATTTATCA
Found at i:4008208 original size:86 final size:84
Alignment explanation
Indices: 4008090--4008311 Score: 192
Period size: 86 Copynumber: 2.6 Consensus size: 84
4008080 ATGATATGTT
* * * * * * *
4008090 TTTAGCGGCATTTTTGCGAGAAGCGTCGCTAAAGGTTTGTTCTATAGCGACATTTGTGATAAAAA
1 TTTAGCGGCATTTGTG-GAAAAGCGCCACTAAAGGTATGGTCTATAGCGACATTTGTG-GAAAAA
4008155 ACGCCGCTAAAGATCATGGTC
64 ACGCCGCTAAAGATCATGGTC
** * * * *
4008176 TTTAGCGGCATTTGTGGTAAAAGCGCCACTAAAGAACATGGTCTTTAGCGGCGTTTGTGGGAAAA
1 TTTAGCGGCATTTGTGG-AAAAGCGCCACTAAAG-GTATGGTCTATAGCGACATTTGTGGAAAAA
*** * *
4008241 GTTCCGCTAAAGGTCGTGGTC
64 ACGCCGCTAAAGATCATGGTC
* * * *
4008262 TATAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGGTCCTGGTCTTTAGCG
1 TTTAGCGGCATTTGTGG-AAAAGCGCCACTAAAGGT-ATGGTCTATAGCG
4008312 GCGTTTATTT
Statistics
Matches: 109, Mismatches: 24, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
85 1 0.01
86 91 0.83
87 17 0.16
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (84 bp):
TTTAGCGGCATTTGTGGAAAAGCGCCACTAAAGGTATGGTCTATAGCGACATTTGTGGAAAAAAC
GCCGCTAAAGATCATGGTC
Found at i:4008312 original size:86 final size:86
Alignment explanation
Indices: 4008158--4008317 Score: 248
Period size: 86 Copynumber: 1.9 Consensus size: 86
4008148 ATAAAAAACG
* *
4008158 CCGCTAAAGATCATGGTCTTTAGCGGCATTTGTGGTAAAAGCGCCACTAAAGAACATGGTCTTTA
1 CCGCTAAAGATCATGGTCTATAGCGGCATTTGTGGAAAAAGCGCCACTAAAGAACATGGTCTTTA
4008223 GCGGCGTTTGTGGGAAAAGTT
66 GCGGCGTTTGTGGGAAAAGTT
* * * ** *
4008244 CCGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGGTCCTGGTCTTTA
1 CCGCTAAAGATCATGGTCTATAGCGGCATTTGTGGAAAAAGCGCCACTAAAGAACATGGTCTTTA
4008309 GCGGCGTTT
66 GCGGCGTTT
4008318 ATTTCCAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 66 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (86 bp):
CCGCTAAAGATCATGGTCTATAGCGGCATTTGTGGAAAAAGCGCCACTAAAGAACATGGTCTTTA
GCGGCGTTTGTGGGAAAAGTT
Found at i:4008314 original size:43 final size:43
Alignment explanation
Indices: 4008150--4008317 Score: 210
Period size: 43 Copynumber: 3.9 Consensus size: 43
4008140 CATTTGTGAT
* * *
4008150 AAAAAACGCCGCTAAAGATCATGGTCTTTAGCGGCATTTGTGG
1 AAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGG
* *
4008193 TAAAAGCGCCACTAAAGAACATGGTCTTTAGCGGCGTTTGTGG
1 AAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGG
* ** * * * *
4008236 GAAAAGTTCCGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTGG
1 AAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGG
* *
4008279 AAAAAGCGCCACTAAAGGTCCTGGTCTTTAGCGGCGTTT
1 AAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTT
4008318 ATTTCCAAAA
Statistics
Matches: 106, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 106 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (43 bp):
AAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGG
Found at i:4008636 original size:18 final size:20
Alignment explanation
Indices: 4008608--4008645 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
4008598 TTAATTAAGA
4008608 AATTAAATAAAT-ATATTTT
1 AATTAAATAAATAATATTTT
4008627 AATT-AATAAATAATATTTT
1 AATTAAATAAATAATATTTT
4008646 TTTAGAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTAAATAAATAATATTTT
Found at i:4011856 original size:22 final size:22
Alignment explanation
Indices: 4011826--4011867 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4011816 TGCAGTTCTT
*
4011826 ATTTTTATACGTGTATATATGA
1 ATTTGTATACGTGTATATATGA
* *
4011848 ATTTGTATATGTGTGTATAT
1 ATTTGTATACGTGTATATAT
4011868 AAATAATGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (22 bp):
ATTTGTATACGTGTATATATGA
Found at i:4015036 original size:26 final size:26
Alignment explanation
Indices: 4015000--4015054 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
4014990 TCTTCAATGA
4015000 TTAATTTCTAACCGGTTTTTTGGTGG
1 TTAATTTCTAACCGGTTTTTTGGTGG
*
4015026 TTAATTTCTAACCGGTTTTTTTGTGG
1 TTAATTTCTAACCGGTTTTTTGGTGG
4015052 TTA
1 TTA
4015055 TTAGTGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.53
Consensus pattern (26 bp):
TTAATTTCTAACCGGTTTTTTGGTGG
Found at i:4018864 original size:54 final size:54
Alignment explanation
Indices: 4018800--4018906 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 54
4018790 TTTGAACAGT
* *
4018800 AGTCTCCCCCT-AAGCAGTAGCTT-CCCTTCGAACAATGGTGTTTTCTGGAATAAC
1 AGTCTCCCCCTGAA-CAATAACTTCCCCTT-GAACAATGGTGTTTTCTGGAATAAC
*
4018854 AGTCTTCCCCTGAACAATAACTTCCCCTTGAACAATGGTGTTTTCTGGAATAA
1 AGTCTCCCCCTGAACAATAACTTCCCCTTGAACAATGGTGTTTTCTGGAATAA
4018907 AGTTTTCAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
54 41 0.85
55 7 0.15
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (54 bp):
AGTCTCCCCCTGAACAATAACTTCCCCTTGAACAATGGTGTTTTCTGGAATAAC
Found at i:4041901 original size:23 final size:23
Alignment explanation
Indices: 4041886--4041931 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4041876 GTTTGCGAAT
* *
4041886 GTTAAATGAACATGTTCGTAAAC
1 GTTAAATGAAAATGTTCGCAAAC
*
4041909 GTTAAATGAAAATGTTCACAAAC
1 GTTAAATGAAAATGTTCGCAAAC
4041932 AATAAACCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (23 bp):
GTTAAATGAAAATGTTCGCAAAC
Found at i:4041937 original size:23 final size:23
Alignment explanation
Indices: 4041888--4041937 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
4041878 TTGCGAATGT
* ** **
4041888 TAAATGAACATGTTCGTAAACGT
1 TAAATGAAAATGTTCACAAACAA
4041911 TAAATGAAAATGTTCACAAACAA
1 TAAATGAAAATGTTCACAAACAA
4041934 TAAA
1 TAAA
4041938 CCAACCAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (23 bp):
TAAATGAAAATGTTCACAAACAA
Found at i:4048459 original size:16 final size:18
Alignment explanation
Indices: 4048436--4048475 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
4048426 TTTTTATTTT
4048436 TATTTTGAT-AATTTAAA
1 TATTTTGATGAATTTAAA
*
4048453 T-TTTTGATGATTTTAAA
1 TATTTTGATGAATTTAAA
4048470 TATTTT
1 TATTTT
4048476 TTATAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 7 0.35
17 9 0.45
18 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (18 bp):
TATTTTGATGAATTTAAA
Found at i:4048469 original size:17 final size:17
Alignment explanation
Indices: 4048436--4048489 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
4048426 TTTTTATTTT
4048436 TATTTTGATAATTTAAA
1 TATTTTGATAATTTAAA
*
4048453 T-TTTTGATGATTTTAAA
1 TATTTTGAT-AATTTAAA
* *
4048470 TATTTTTTATAATTTTAA
1 TA-TTTTGATAATTTAAA
4048488 TA
1 TA
4048490 AAAATTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.23
17 9 0.30
18 8 0.27
19 6 0.20
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TATTTTGATAATTTAAA
Found at i:4063055 original size:25 final size:23
Alignment explanation
Indices: 4063011--4063071 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
4063001 ATTTTAATTC
*
4063011 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
4063035 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
4063059 ATATAAATTATAT
1 AT-TTAATTATAT
4063072 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:4063060 original size:35 final size:33
Alignment explanation
Indices: 4063019--4063102 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 33
4063009 TCATTTAATA
* *
4063019 ATATAATATCATTATAATTTAATTATCATAAATT
1 ATATAATATAATTAT-ATTTAAATATCATAAATT
*
4063053 CATATAATATAAATTATATTTAAATATCATTAATT
1 -ATATAATAT-AATTATATTTAAATATCATAAATT
4063088 ATATATATATAATTA
1 ATATA-ATATAATTA
4063103 AACAAATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
34 10 0.23
35 29 0.66
36 5 0.11
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (33 bp):
ATATAATATAATTATATTTAAATATCATAAATT
Found at i:4067392 original size:43 final size:43
Alignment explanation
Indices: 4067307--4067392 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 43
4067297 AATCATGACA
* * * *
4067307 ACTTTACGTAAAAGTATTTATGATAAAATATATTTAATTTTTT
1 ACTTTACATAAAAGTATCTATAAGAAAATATATTTAATTTTTT
4067350 ACTTTACCATAAAAGTATCTATAAGAAAATATATTTAATTTTT
1 ACTTTA-CATAAAAGTATCTATAAGAAAATATATTTAATTTTT
4067393 CTACATTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
43 6 0.16
44 32 0.84
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (43 bp):
ACTTTACATAAAAGTATCTATAAGAAAATATATTTAATTTTTT
Found at i:4068567 original size:34 final size:34
Alignment explanation
Indices: 4068524--4068645 Score: 111
Period size: 34 Copynumber: 3.6 Consensus size: 34
4068514 CAATATGGCG
*
4068524 TGCTTATAACATATCAATATGGTAGCAATTGATA
1 TGCTTATAACATATCAATATGGTAGCAATTAATA
* * *
4068558 TGCTCATAACAGT-TCCATATGGTAGCAAATAATA
1 TGCTTATAACA-TATCAATATGGTAGCAATTAATA
*** * * *
4068592 TGCTTATAATGGATTAATACGGTGGCAATTAATA
1 TGCTTATAACATATCAATATGGTAGCAATTAATA
* * *
4068626 TACTGATAACAAATCAATAT
1 TGCTTATAACATATCAATAT
4068646 CCTAGTAAAA
Statistics
Matches: 66, Mismatches: 20, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
34 65 0.98
35 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (34 bp):
TGCTTATAACATATCAATATGGTAGCAATTAATA
Found at i:4071981 original size:19 final size:20
Alignment explanation
Indices: 4071957--4072002 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
4071947 ACATATTGCC
4071957 TTAGATTACGTCAAAGGCA-
1 TTAGATTACGTCAAAGGCAT
*
4071976 TTAGATTATGTCAAAGGCAT
1 TTAGATTACGTCAAAGGCAT
4071996 TTAGATT
1 TTAGATT
4072003 GGGTTCAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (20 bp):
TTAGATTACGTCAAAGGCAT
Found at i:4074546 original size:18 final size:18
Alignment explanation
Indices: 4074525--4074580 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
4074515 AAATTGTGAT
*
4074525 AAAATTAAAATTTATTAA
1 AAAATTAAAATATATTAA
4074543 AAAATTACAAA-ATACTTAA
1 AAAATTA-AAATATA-TTAA
*
4074562 AAAATAAAAATATATTAA
1 AAAATTAAAATATATTAA
4074580 A
1 A
4074581 GTTATTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 17 0.52
19 16 0.48
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATTAAAATATATTAA
Found at i:4075089 original size:24 final size:24
Alignment explanation
Indices: 4075061--4075109 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
4075051 ATATGAGTAC
4075061 AATATATTA--TAT-AAATTATATA
1 AATATATTATTTATGAAATT-TATA
4075083 AATATATTATTTATGAAATTTATA
1 AATATATTATTTATGAAATTTATA
4075107 AAT
1 AAT
4075110 GATCTATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.38
24 10 0.42
25 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
AATATATTATTTATGAAATTTATA
Found at i:4076902 original size:22 final size:22
Alignment explanation
Indices: 4076877--4076921 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4076867 TGTTATAACT
4076877 TTTTTTTATTTACCAAAATATA
1 TTTTTTTATTTACCAAAATATA
4076899 TTTTTTTATTTACCAAAATATA
1 TTTTTTTATTTACCAAAATATA
4076921 T
1 T
4076922 CAAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTTTTATTTACCAAAATATA
Found at i:4077105 original size:18 final size:19
Alignment explanation
Indices: 4077060--4077137 Score: 104
Period size: 19 Copynumber: 4.2 Consensus size: 19
4077050 TATTCTCCTT
* *
4077060 TAACTCTTTTTTTATTTAA
1 TAACTCTATTTTAATTTAA
4077079 TAACTCTATTTTAATTTAA
1 TAACTCTATTTTAATTTAA
* * *
4077098 TAA-GCTATTCTCATTTAA
1 TAACTCTATTTTAATTTAA
4077116 TAACTCTATTTTAATTTAA
1 TAACTCTATTTTAATTTAA
4077135 TAA
1 TAA
4077138 ACTATTAAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
18 15 0.30
19 35 0.70
ACGTcount: A:0.35, C:0.12, G:0.01, T:0.53
Consensus pattern (19 bp):
TAACTCTATTTTAATTTAA
Found at i:4077117 original size:37 final size:37
Alignment explanation
Indices: 4077073--4077143 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
4077063 CTCTTTTTTT
*
4077073 ATTTAATAACTCTATTTTAATTTAATAAGCTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
4077110 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
4077144 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:4077398 original size:18 final size:18
Alignment explanation
Indices: 4077361--4077429 Score: 84
Period size: 19 Copynumber: 3.7 Consensus size: 18
4077351 TCAACTCAAT
* *
4077361 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAA-ACTA
4077380 TTTTAATTTAATAAACTA
1 TTTTAATTTAATAAACTA
* *
4077398 TTCTCATTTAATAAATCTA
1 TTTTAATTTAATAAA-CTA
4077417 TTTTAATTTAATA
1 TTTTAATTTAATA
4077430 TAATATTAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
18 16 0.37
19 27 0.63
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTAATTTAATAAACTA
Found at i:4077742 original size:37 final size:37
Alignment explanation
Indices: 4077695--4077765 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
4077685 AGTATTACTT
*
4077695 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGCTTATTAAATTAAAATAGAGTTATTAAATGAG
4077732 AATAGCTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGCTTATTAAATTAAAATAGAGTTATTAAAT
4077766 AATAAAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.38
Consensus pattern (37 bp):
AATAGCTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:4077743 original size:18 final size:19
Alignment explanation
Indices: 4077701--4077765 Score: 96
Period size: 19 Copynumber: 3.5 Consensus size: 19
4077691 ACTTAATAGT
4077701 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
4077720 TTATTAAATGAGAATAG-C
1 TTATTAAATTAAAATAGAG
4077738 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
4077757 TTATTAAAT
1 TTATTAAAT
4077766 AATAAAAAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.38
19 24 0.62
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:4077892 original size:27 final size:27
Alignment explanation
Indices: 4077843--4077920 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 27
4077833 ACTTTTTTTC
4077843 CTTTGGCACCA-TGGTGCCGCCAATGA
1 CTTTGGCACCATTGGTGCCGCCAATGA
* *
4077869 CTTTGGCACCATTGGTGCCACCAATTTA
1 CTTTGGCACCATTGGTGCCGCCAA-TGA
*
4077897 -TTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
4077921 TTAATTGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.26
27 32 0.70
28 2 0.04
ACGTcount: A:0.18, C:0.29, G:0.23, T:0.29
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATGA
Found at i:4077921 original size:27 final size:26
Alignment explanation
Indices: 4077844--4077929 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 26
4077834 CTTTTTTTCC
* *
4077844 TTTGGCACCATGGTGCCGCCAA-TGA
1 TTTGGCACCTTGGTGCCGCCAATTTA
*
4077869 CTTTGGCACCATTGGTGCCACCAATTTA
1 -TTTGGCACC-TTGGTGCCGCCAATTTA
4077897 TTTGGCACCTTTGGTGCCGCCAATTTA
1 TTTGGCACC-TTGGTGCCGCCAATTTA
*
4077924 ATTGGC
1 TTTGGC
4077930 CTGATCAGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 9 0.17
27 41 0.79
28 2 0.04
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (26 bp):
TTTGGCACCTTGGTGCCGCCAATTTA
Found at i:4078000 original size:24 final size:24
Alignment explanation
Indices: 4077967--4078014 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
4077957 TTTGTTTTTT
4077967 TATATATTTTGGTAAATAAAAAAA
1 TATATATTTTGGTAAATAAAAAAA
*
4077991 TATATTTTTTGGTAAATAAAAAAA
1 TATATATTTTGGTAAATAAAAAAA
4078015 AGTTATAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (24 bp):
TATATATTTTGGTAAATAAAAAAA
Found at i:4088741 original size:16 final size:17
Alignment explanation
Indices: 4088702--4088741 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
4088692 TTTTATAACA
4088702 TAAT-AAATTATTATTT
1 TAATAAAATTATTATTT
4088718 TAATAAAATT-TTATTT
1 TAATAAAATTATTATTT
4088734 TAATAAAA
1 TAATAAAA
4088742 AAATTTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAATAAAATTATTATTT
Found at i:4088967 original size:16 final size:18
Alignment explanation
Indices: 4088944--4088984 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4088934 ATTATGTCTA
4088944 TATAAAATA-T-AATTAT
1 TATAAAATATTAAATTAT
*
4088960 TTTAAAATATTAAATTAT
1 TATAAAATATTAAATTAT
4088978 TATAAAA
1 TATAAAA
4088985 AATATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 8 0.38
17 1 0.05
18 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAAATATTAAATTAT
Found at i:4088977 original size:18 final size:16
Alignment explanation
Indices: 4088944--4088997 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 16
4088934 ATTATGTCTA
4088944 TATAAAATATAATTAT
1 TATAAAATATAATTAT
*
4088960 TTTAAAATATTAAATTAT
1 TATAAAATA-T-AATTAT
* *
4088978 TATAAAAAAT-ATTTT
1 TATAAAATATAATTAT
4088993 TATAA
1 TATAA
4088998 TATTTTACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 9 0.28
16 8 0.25
17 2 0.06
18 13 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATAAAATATAATTAT
Found at i:4089547 original size:2 final size:2
Alignment explanation
Indices: 4089540--4089564 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4089530 TGGTAAGCCC
4089540 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
4089565 ACATCACCTT
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:4094462 original size:20 final size:21
Alignment explanation
Indices: 4094425--4094463 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4094415 ACATAAAATC
*
4094425 GTTAAATGGTATCTATACTAG
1 GTTAAATGGTATCGATACTAG
4094446 GTTAAAT-GTATCGATACT
1 GTTAAATGGTATCGATACT
4094464 TTAAGCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (21 bp):
GTTAAATGGTATCGATACTAG
Found at i:4100617 original size:72 final size:70
Alignment explanation
Indices: 4100499--4100642 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 70
4100489 TAGAAAAGAA
* *
4100499 AGAAACATATGAAACGAAACAGAGAAGGAAAAAGGGGGAAAGAAAAAGAGAAAGAAAAAAAGAGA
1 AGAAACATATGAAACGAAACAGAGAAGGAAAAAGGGAGAAACAAAAAGAG--AGAAAAAAAGAGA
*
4100564 GAAGCTT
64 AAAGCTT
*
4100571 AGAAACATATGAAACGGAACAGAGAAGGAAAAAGGGAGAAACAAAAAGAGAGAAAAAAAGAGAAA
1 AGAAACATATGAAACGAAACAGAGAAGGAAAAAGGGAGAAACAAAAAGAGAGAAAAAAAGAGAAA
*
4100636 AGGTT
66 AGCTT
4100641 AG
1 AG
4100643 GGTTTTAAGG
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
70 20 0.30
72 47 0.70
ACGTcount: A:0.61, C:0.06, G:0.28, T:0.06
Consensus pattern (70 bp):
AGAAACATATGAAACGAAACAGAGAAGGAAAAAGGGAGAAACAAAAAGAGAGAAAAAAAGAGAAA
AGCTT
Done.