Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 131 of 208
Found at i:40164577 original size:19 final size:17
Alignment explanation
Indices: 40164530--40164576 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
40164520 TAAAATGAAA
* *
40164530 TTAAAATGAAATTATAT
1 TTAAAAAGAAAATATAT
*
40164547 TTAAAATGAAAATATAT
1 TTAAAAAGAAAATATAT
40164564 TTAAAAAAGAAAA
1 TT-AAAAAGAAAA
40164577 AAAATATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (17 bp):
TTAAAAAGAAAATATAT
Found at i:40164744 original size:33 final size:33
Alignment explanation
Indices: 40164706--40164819 Score: 113
Period size: 33 Copynumber: 3.3 Consensus size: 33
40164696 TTTAATTAAA
40164706 AGAAAAAAAGTAAAATGAAATTCAAATAAAATG
1 AGAAAAAAAGTAAAATGAAATTCAAATAAAATG
* * * * *
40164739 AGAAAAAAATGAAATTCAAATGAAGTTTTAATTAAAA-A
1 AGAAAAAAA-G----TAAAATGAA-ATTCAAATAAAATG
40164777 AGAAAAAAAAGTAAAATGAAATTCAAATAAAATG
1 AG-AAAAAAAGTAAAATGAAATTCAAATAAAATG
40164811 AGAAAAAAA
1 AGAAAAAAA
40164820 AGAAATTCAA
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
33 25 0.40
34 11 0.17
38 11 0.17
39 16 0.25
ACGTcount: A:0.67, C:0.03, G:0.11, T:0.19
Consensus pattern (33 bp):
AGAAAAAAAGTAAAATGAAATTCAAATAAAATG
Found at i:40164810 original size:72 final size:69
Alignment explanation
Indices: 40164688--40164834 Score: 258
Period size: 72 Copynumber: 2.1 Consensus size: 69
40164678 ATGAATTTTT
*
40164688 AATGAAGTTTTAATTAAAAGAAAAAAAGTAAAATGAAATTCAAATAAAATGAGAAAAAAATGAAA
1 AATGAAGTTTTAATTAAAAGAAAAAAAGTAAAATGAAATTCAAATAAAATGAGAAAAAAAAGAAA
40164753 TTCA
66 TTCA
40164757 AATGAAGTTTTAATTAAAAAAGAAAAAAAAGTAAAATGAAATTCAAATAAAATGAGAAAAAAAAG
1 AATGAAGTTTTAATT--AAAAG-AAAAAAAGTAAAATGAAATTCAAATAAAATGAGAAAAAAAAG
40164822 AAATTCA
63 AAATTCA
40164829 AATGAA
1 AATGAA
40164835 ATTTAAAAAG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
69 15 0.20
71 5 0.07
72 54 0.73
ACGTcount: A:0.64, C:0.03, G:0.12, T:0.22
Consensus pattern (69 bp):
AATGAAGTTTTAATTAAAAGAAAAAAAGTAAAATGAAATTCAAATAAAATGAGAAAAAAAAGAAA
TTCA
Found at i:40164815 original size:34 final size:34
Alignment explanation
Indices: 40164708--40164821 Score: 122
Period size: 34 Copynumber: 3.2 Consensus size: 34
40164698 TAATTAAAAG
40164708 AAAAAAAGTAAAATGAAATTCAAATAAAATGAGAAA
1 AAAAAAAGTAAAATGAAATTCAAATAAAATGAG--A
* * * * * *
40164744 AAAATGAAATTCAAATGAAGTTTTAATTAAAA-AAGA
1 AAAA--AAAGTAAAATGAA-ATTCAAATAAAATGAGA
40164780 AAAAAAAGTAAAATGAAATTCAAATAAAATGAGA
1 AAAAAAAGTAAAATGAAATTCAAATAAAATGAGA
40164814 AAAAAAAG
1 AAAAAAAG
40164822 AAATTCAAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
33 9 0.15
34 22 0.35
36 9 0.15
38 13 0.21
39 9 0.15
ACGTcount: A:0.67, C:0.03, G:0.11, T:0.19
Consensus pattern (34 bp):
AAAAAAAGTAAAATGAAATTCAAATAAAATGAGA
Found at i:40164842 original size:34 final size:34
Alignment explanation
Indices: 40164732--40164842 Score: 98
Period size: 34 Copynumber: 3.1 Consensus size: 34
40164722 GAAATTCAAA
* *
40164732 TAAAATGAGAAAAAAATGAAATTCAAATGAAGTT
1 TAAAATGAGAAAAAAAAGAAATTCAAATGAAATT
* * * * * *
40164766 T-TAATTAAAAAAGAAAAAAAAGTAAAATGAAATT
1 TAAAATGAGAAAA-AAAAGAAATTCAAATGAAATT
40164800 CAAATAAAATGAGAAAAAAAAGAAATTCAAATGAAATT
1 ----TAAAATGAGAAAAAAAAGAAATTCAAATGAAATT
40164838 TAAAA
1 TAAAA
40164843 AGAAATTGAA
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
33 8 0.14
34 22 0.39
38 19 0.33
39 8 0.14
ACGTcount: A:0.65, C:0.03, G:0.11, T:0.22
Consensus pattern (34 bp):
TAAAATGAGAAAAAAAAGAAATTCAAATGAAATT
Found at i:40164928 original size:17 final size:17
Alignment explanation
Indices: 40164908--40164941 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40164898 AAAAATAAGT
40164908 GAAATGAAATTCAAATA
1 GAAATGAAATTCAAATA
*
40164925 GAAATGAAGTTCAAATA
1 GAAATGAAATTCAAATA
40164942 ACATGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (17 bp):
GAAATGAAATTCAAATA
Found at i:40164994 original size:124 final size:121
Alignment explanation
Indices: 40164734--40165173 Score: 398
Period size: 124 Copynumber: 3.5 Consensus size: 121
40164724 AATTCAAATA
* * *
40164734 AAATGAGAAAAAAA-TGAAAT-TCAAATGAAGTTTTAATTAAAAAAGAAAAAAAAGTAAAATGAA
1 AAATGA-AAAAAAATTGACATCACAAATGAAGTTTTAATT--AAAAGAAAAAAAAGTGAAATGAA
** *
40164797 ATTCAAATA-AAATG-AG---AAAAAAAAGAAATTCAAATGAAATTTAAAAAGAAATTG
63 ATTCAAATAGAAATGAAGTTCAAAAAAAAGAAATAAAAATGAAATCTAAAAAGAAATTG
*
40164851 AAATGAAAAAAAATTGACATCACAAAATGATA-TTTTAATTGAAAAGGAAAAATAAGTGAAATGA
1 AAATGAAAAAAAATTGACATCAC-AAATGA-AGTTTTAATT-AAAA-GAAAAAAAAGTGAAATGA
* *
40164915 AATTCAAATAGAAATGAAGTTCAAATAACATGAAA-AAAAATGAAATCTAAAAAGAAATTG
62 AATTCAAATAGAAATGAAGTTCAAA-AAAAAGAAATAAAAATGAAATCTAAAAAGAAATTG
* *
40164975 AAATGAAAAAAGATTGACATGACAAATGAAGTTTTTAATTAAAA-AATAAAAAAGTGAAATGAAA
1 AAATGAAAAAAAATTGACATCACAAATGAAG-TTTTAATTAAAAGAA-AAAAAAGTGAAATGAAA
* * * * ** * * *
40165039 TTTAAATTGAAATGAAATTCATGAGAAAAAAATTAAATTCAAATGAATTTTAAAAAGAAATTAA
64 TTCAAATAGAAATGAAGTTC---A-AAAAAAA-GAAATAAAAATGAAATCTAAAAAGAAATT-G
* * *
40165103 AATTATAAAAAAAAATT-ACATGACAAATGAAGTTTTTAATTGAAAAAGAAAAAAAAGGTAAAAT
1 AA--ATGAAAAAAAATTGACATCACAAATGAAG-TTTTAATT--AAAAGAAAAAAAA-GTGAAAT
40165167 GAAATTC
60 GAAATTC
40165174 TGAAATTCAA
Statistics
Matches: 268, Mismatches: 28, Indels: 39
0.80 0.08 0.12
Matches are distributed among these distances:
116 7 0.03
117 11 0.04
118 5 0.02
119 40 0.15
120 6 0.02
121 4 0.01
122 34 0.13
123 10 0.04
124 54 0.20
125 11 0.04
126 5 0.02
127 20 0.07
128 2 0.01
129 24 0.09
130 11 0.04
131 10 0.04
132 14 0.05
ACGTcount: A:0.60, C:0.04, G:0.12, T:0.24
Consensus pattern (121 bp):
AAATGAAAAAAAATTGACATCACAAATGAAGTTTTAATTAAAAGAAAAAAAAGTGAAATGAAATT
CAAATAGAAATGAAGTTCAAAAAAAAGAAATAAAAATGAAATCTAAAAAGAAATTG
Found at i:40165091 original size:48 final size:48
Alignment explanation
Indices: 40165031--40165147 Score: 121
Period size: 48 Copynumber: 2.4 Consensus size: 48
40165021 TAAAAAAGTG
* * * *
40165031 AAATGAAATTTAAATTGAAA-TGAAATTCATGAGAAAAAAATTAAAT-TC
1 AAATGAATTTTAAATTGAAATTAAAATT-AT-AAAAAAAAATTAAATGAC
** *
40165079 AAATGAATTTTAAAAAGAAATTAAAATTATAAAAAAAAATTACATGAC
1 AAATGAATTTTAAATTGAAATTAAAATTATAAAAAAAAATTAAATGAC
*
40165127 AAATGAAGTTTTTAATTGAAA
1 AAATGAA-TTTTAAATTGAAA
40165148 AAGAAAAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
47 13 0.23
48 27 0.48
49 16 0.29
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.30
Consensus pattern (48 bp):
AAATGAATTTTAAATTGAAATTAAAATTATAAAAAAAAATTAAATGAC
Found at i:40165111 original size:19 final size:19
Alignment explanation
Indices: 40165084--40165120 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40165074 AATTCAAATG
* *
40165084 AATTTTAAAAAGAAATTAA
1 AATTATAAAAAAAAATTAA
40165103 AATTATAAAAAAAAATTA
1 AATTATAAAAAAAAATTA
40165121 CATGACAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
AATTATAAAAAAAAATTAA
Found at i:40166601 original size:89 final size:88
Alignment explanation
Indices: 40166465--40166708 Score: 276
Period size: 88 Copynumber: 2.7 Consensus size: 88
40166455 TAAAAAAAAT
* * ** *
40166465 AAATATATAATTCGAAAAATTAATAATAC-GCAAC-AAATTAAATTTACAGATACAAGAAGATAC
1 AAATATAAAATTCGAACAACAAATAATACAG--ACTAAATTAAATTTACAGATACAA-AAAATAC
* * * *
40166528 AAATATTCTAGAATATTAATACAAGG
63 AAACATTCTAAAAAATTAATACAAGA
40166554 AAATATAAAATTCGAACAACAAATAATACAGACTAAATTAAATTTACAGATACAAAAAATACAAA
1 AAATATAAAATTCGAACAACAAATAATACAGACTAAATTAAATTTACAGATACAAAAAATACAAA
*
40166619 CATTCTAAAAAATTAATACACGA
66 CATTCTAAAAAATTAATACAAGA
* * * * ** *
40166642 AAATATAAAATTTGAACAACAAATAATAAATATTAAATTTGATTTATAGATACAAAAATAATACA
1 AAATATAAAATTCGAACAACAAATAATACAGACTAAATTAAATTTACAGATAC-AAAA-AATACA
40166707 AA
64 AA
40166709 AATTTTGAAT
Statistics
Matches: 134, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
88 75 0.56
89 50 0.37
90 9 0.07
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.26
Consensus pattern (88 bp):
AAATATAAAATTCGAACAACAAATAATACAGACTAAATTAAATTTACAGATACAAAAAATACAAA
CATTCTAAAAAATTAATACAAGA
Found at i:40167301 original size:52 final size:52
Alignment explanation
Indices: 40167220--40167325 Score: 158
Period size: 52 Copynumber: 2.0 Consensus size: 52
40167210 AAAATATTTT
* * *
40167220 AAAATCTGATAAAGTTGGTGCGGGCCATCAGTGTCCCAAAACCAAAAAAAAA
1 AAAATCTGAAAAAGTTGGTACGGGCCATCAGTATCCCAAAACCAAAAAAAAA
* * *
40167272 AAAATCTGAAAAAGTTGGTACTGGTCATCAGTATCCCAAAACTAAAAAAAAA
1 AAAATCTGAAAAAGTTGGTACGGGCCATCAGTATCCCAAAACCAAAAAAAAA
40167324 AA
1 AA
40167326 TTCGGGACCC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.19
Consensus pattern (52 bp):
AAAATCTGAAAAAGTTGGTACGGGCCATCAGTATCCCAAAACCAAAAAAAAA
Found at i:40170082 original size:11 final size:11
Alignment explanation
Indices: 40170068--40170105 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
40170058 TTTTTTTTAA
40170068 TTTTAAAATAT
1 TTTTAAAATAT
40170079 TTTTAAAATACTT
1 TTTTAAAATA--T
40170092 TTTTAAAA-AT
1 TTTTAAAATAT
40170102 TTTT
1 TTTT
40170106 TATTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.20
11 10 0.40
12 1 0.04
13 9 0.36
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:40175839 original size:20 final size:20
Alignment explanation
Indices: 40175814--40175854 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
40175804 TTGAAATGCT
40175814 AACAGAGGCACCAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
40175834 AACAGAGGCACCAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
40175854 A
1 A
40175855 TCCCATACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.24, T:0.05
Consensus pattern (20 bp):
AACAGAGGCACCAAAGTGCA
Found at i:40178540 original size:31 final size:31
Alignment explanation
Indices: 40178502--40178563 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
40178492 ATACTATAAA
40178502 ATCGTATTAGTAGCCGTTTAGACTTAATTGT
1 ATCGTATTAGTAGCCGTTTAGACTTAATTGT
40178533 ATCGTATTAGTAGCCGTTTAGACTTAATTGT
1 ATCGTATTAGTAGCCGTTTAGACTTAATTGT
40178564 GTATATTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (31 bp):
ATCGTATTAGTAGCCGTTTAGACTTAATTGT
Found at i:40191170 original size:25 final size:25
Alignment explanation
Indices: 40191100--40191156 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
40191090 ATTTTTAGAT
* *
40191100 TGACAGTTCATTAT-AGAATCAAAA
1 TGACATTTCATTTTCAGAATCAAAA
*
40191124 TGACATATCATTTTCAGAATCAAAA
1 TGACATTTCATTTTCAGAATCAAAA
40191149 TGACATTT
1 TGACATTT
40191157 GATTATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 11 0.39
25 17 0.61
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (25 bp):
TGACATTTCATTTTCAGAATCAAAA
Found at i:40191380 original size:23 final size:23
Alignment explanation
Indices: 40191342--40191391 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
40191332 CACTCCACAA
*
40191342 AATGAATCGCATCAAAGTGCTAG
1 AATGAATCGCACCAAAGTGCTAG
* *
40191365 AATGAATTGCACCAAATTGCTAG
1 AATGAATCGCACCAAAGTGCTAG
40191388 AATG
1 AATG
40191392 TACCACACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (23 bp):
AATGAATCGCACCAAAGTGCTAG
Found at i:40197093 original size:25 final size:25
Alignment explanation
Indices: 40197043--40197094 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
40197033 CTCATAGTCG
* **
40197043 TTTTTCTATTTTGGTATTTAATTTT
1 TTTTTCAATTTTGGTATCGAATTTT
40197068 TTTTTCAATTTTGGTATCCGAATTTT
1 TTTTTCAATTTTGGTAT-CGAATTTT
40197094 T
1 T
40197095 ATTAGTTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.17, C:0.08, G:0.10, T:0.65
Consensus pattern (25 bp):
TTTTTCAATTTTGGTATCGAATTTT
Found at i:40197288 original size:18 final size:17
Alignment explanation
Indices: 40197265--40197299 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40197255 TTGTTTATTG
40197265 ATTAAAAAATTTGTAAAA
1 ATTAAAAAATTT-TAAAA
*
40197283 ATTAAAAAGTTTTAAAA
1 ATTAAAAAATTTTAAAA
40197300 TGGTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
ATTAAAAAATTTTAAAA
Found at i:40197357 original size:39 final size:40
Alignment explanation
Indices: 40197279--40197400 Score: 112
Period size: 39 Copynumber: 3.1 Consensus size: 40
40197269 AAAAATTTGT
** *
40197279 AAAAAT-TAAAAAGTT-TTAAA-ATGGTAAAAAAATAT-AA
1 AAAAATATAAAAA-TTCTTAAAGATCTTAAAAATATATAAA
* * * *
40197316 AAAATTATAAAAGTTGTTAAATG-TCTTAAAAAT-TGTAAA
1 AAAAATATAAAAATTCTTAAA-GATCTTAAAAATATATAAA
*
40197355 AAAAATATAAAAATTCTTAAAGATTTTAAAAATATATAAA
1 AAAAATATAAAAATTCTTAAAGATCTTAAAAATATATAAA
40197395 AAAAAT
1 AAAAAT
40197401 TTGGAGTATA
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
37 7 0.10
38 13 0.19
39 36 0.54
40 11 0.16
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.31
Consensus pattern (40 bp):
AAAAATATAAAAATTCTTAAAGATCTTAAAAATATATAAA
Found at i:40197397 original size:30 final size:31
Alignment explanation
Indices: 40197334--40197396 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
40197324 AAAAGTTGTT
40197334 AAATGTCTTAAAAATTGTAAAAAAAATATAA
1 AAATGTCTTAAAAATTGTAAAAAAAATATAA
* * *
40197365 AAAT-TCTTAAAGATT-TTAAAAATATATAA
1 AAATGTCTTAAAAATTGTAAAAAAAATATAA
40197394 AAA
1 AAA
40197397 AAATTTGGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.52
30 10 0.34
31 4 0.14
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (31 bp):
AAATGTCTTAAAAATTGTAAAAAAAATATAA
Found at i:40198046 original size:13 final size:13
Alignment explanation
Indices: 40198028--40198060 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
40198018 AGTCCGCCCG
40198028 TATTAATTTTTTA
1 TATTAATTTTTTA
40198041 TATTAA-TTTTTA
1 TATTAATTTTTTA
40198053 TA-TAATTT
1 TATTAATTT
40198061 CTTGTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.16
12 10 0.53
13 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTAATTTTTTA
Found at i:40198562 original size:19 final size:18
Alignment explanation
Indices: 40198538--40198585 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 18
40198528 ACTGAACTGC
40198538 TTAAATATTGTTATAATTT
1 TTAAATATT-TTATAATTT
40198557 TTAAATATTTTAT-ATTT
1 TTAAATATTTTATAATTT
*
40198574 TAAAATAATTTT
1 TTAAAT-ATTTT
40198586 TACAATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.33
18 9 0.33
19 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TTAAATATTTTATAATTT
Found at i:40198576 original size:16 final size:19
Alignment explanation
Indices: 40198538--40198594 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
40198528 ACTGAACTGC
40198538 TTAAATATTGTTATAATTT
1 TTAAATATTGTTATAATTT
40198557 TTAAATATT-TTAT-ATTT
1 TTAAATATTGTTATAATTT
* * *
40198574 TAAAATAATTTTTACAATTT
1 TTAAAT-ATTGTTATAATTT
40198594 T
1 T
40198595 AAGAATTCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 9 0.27
18 7 0.21
19 12 0.36
20 5 0.15
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTAAATATTGTTATAATTT
Found at i:40198706 original size:18 final size:19
Alignment explanation
Indices: 40198675--40198721 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
40198665 TACTATTTTT
* *
40198675 ATAATTTTTAATATTTTAAA
1 ATAATTTAT-ATATTGTAAA
40198695 ATATATTTATATATTGTAAA
1 ATA-ATTTATATATTGTAAA
40198715 ATAATTT
1 ATAATTT
40198722 TTAAATGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.17
20 15 0.62
21 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
ATAATTTATATATTGTAAA
Found at i:40202825 original size:2 final size:2
Alignment explanation
Indices: 40202818--40202843 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40202808 TATTTAAACC
40202818 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
40202844 GAGCATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40205298 original size:43 final size:43
Alignment explanation
Indices: 40205251--40205801 Score: 628
Period size: 43 Copynumber: 12.9 Consensus size: 43
40205241 ACGCAATTAA
* * *
40205251 ACTGGCACACACAGTGCATCATCGAATAATACCAAAGCAACAT
1 ACTGGCACACATAGTGCATCATCGGATAATACCGAAGCAACAT
* * * *
40205294 ACTGGCACACATAGTGCATTATTGGATAAAACCGAATCAACAT
1 ACTGGCACACATAGTGCATCATCGGATAATACCGAAGCAACAT
* *
40205337 ACTGGCACATATAGTGCATCATTGGATAATACCGAAGCAACAT
1 ACTGGCACACATAGTGCATCATCGGATAATACCGAAGCAACAT
* * *
40205380 ATTGGCACACACAATGCATCATCAGG-TAATACCGAAGCAACAT
1 ACTGGCACACATAGTGCATCATC-GGATAATACCGAAGCAACAT
* * * *
40205423 ACTGGCGCACACAGTGCATCATCAGG-TAATACCGAAGTAAGAT
1 ACTGGCACACATAGTGCATCATC-GGATAATACCGAAGCAACAT
* *
40205466 ACCGGCACACACAGTGCATCATCAGG-TAATACCGAAGCAACAT
1 ACTGGCACACATAGTGCATCATC-GGATAATACCGAAGCAACAT
* ** * *
40205509 ACTAGCACACATAGTGCATCAT-TAAGCAATACCGAAGAAACAT
1 ACTGGCACACATAGTGCATCATCGGA-TAATACCGAAGCAACAT
* * *
40205552 ACTAGCACACATAGTGCATTATCGGTTAATACCGAAGCAACAT
1 ACTGGCACACATAGTGCATCATCGGATAATACCGAAGCAACAT
* * *
40205595 ACTAGCACACATAGTGCATTATCGGTTAATACCGAAGCAACAT
1 ACTGGCACACATAGTGCATCATCGGATAATACCGAAGCAACAT
* * *
40205638 ACTGGCACACATAGTGTATCATTGGGTAATACCGAAGCAACAT
1 ACTGGCACACATAGTGCATCATCGGATAATACCGAAGCAACAT
* * * *
40205681 ATTGGCACACACAGTGCATCATTGGATAATATCGAAGCAACAT
1 ACTGGCACACATAGTGCATCATCGGATAATACCGAAGCAACAT
* *
40205724 ACTGGCACACATAGTGCATCATTGGATAATATCGAAG-AAC-T
1 ACTGGCACACATAGTGCATCATCGGATAATACCGAAGCAACAT
* * * * * *
40205765 ACTGACACATACAATGAATCATCAGATAATACCGAAG
1 ACTGGCACACATAGTGCATCATCGGATAATACCGAAG
40205802 TATAACCTGC
Statistics
Matches: 446, Mismatches: 58, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
41 30 0.07
42 3 0.01
43 411 0.92
44 2 0.00
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (43 bp):
ACTGGCACACATAGTGCATCATCGGATAATACCGAAGCAACAT
Found at i:40219605 original size:25 final size:25
Alignment explanation
Indices: 40219543--40219621 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
40219533 GTCATTAAGG
* * *
40219543 TTACCAAT-TTCAGCTCGTATGAGT
1 TTACCGATATTCAGCTCGAATGAGC
** *
40219567 TTACCGATGCTCAGCTCGCATGAGC
1 TTACCGATATTCAGCTCGAATGAGC
* *
40219592 TTACCGTTATTCAGCTCGAAGGAGC
1 TTACCGATATTCAGCTCGAATGAGC
40219617 TTACC
1 TTACC
40219622 TTTTATAGCT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 7 0.16
25 38 0.84
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (25 bp):
TTACCGATATTCAGCTCGAATGAGC
Found at i:40225540 original size:2 final size:2
Alignment explanation
Indices: 40225533--40225560 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40225523 ACCATGCTAC
40225533 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40225561 TTACAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40230947 original size:25 final size:25
Alignment explanation
Indices: 40230903--40230956 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
40230893 CAAAATTTAG
40230903 AAATAAAATTATTTTGTAAT-TAATT
1 AAATAAAATTATTTTGTAATCT-ATT
*
40230928 AAATAGAATTATTTAT-TAATCTATT
1 AAATAAAATTATTT-TGTAATCTATT
40230953 AAAT
1 AAAT
40230957 TGGTTATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
AAATAAAATTATTTTGTAATCTATT
Found at i:40232370 original size:22 final size:21
Alignment explanation
Indices: 40232327--40232366 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
40232317 TTTCAACAAC
40232327 CAAAACACATGGCAACATTAGT
1 CAAAACACATGGC-ACATTAGT
40232349 CAAAACACATGGC-CATTA
1 CAAAACACATGGCACATTA
40232367 TAGTGTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.45, C:0.25, G:0.12, T:0.17
Consensus pattern (21 bp):
CAAAACACATGGCACATTAGT
Found at i:40232870 original size:23 final size:23
Alignment explanation
Indices: 40232844--40232897 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
40232834 CCATTAAATC
40232844 CTGTACAT-GTATGCTCACACGAG
1 CTGTA-ATCGTATGCTCACACGAG
*
40232867 CTGTGAATCGGTATGCTCACACTAG
1 CTGT-AATC-GTATGCTCACACGAG
40232892 CTGTAA
1 CTGTAA
40232898 AATGGGCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 6 0.22
24 3 0.11
25 18 0.67
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (23 bp):
CTGTAATCGTATGCTCACACGAG
Found at i:40256436 original size:19 final size:19
Alignment explanation
Indices: 40256400--40256450 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
40256390 ATTTTTGCGA
* *
40256400 AAATTAATTTTGATCAAAT
1 AAATTAATATTAATCAAAT
40256419 AAAATT-ATATTAATCAAAT
1 -AAATTAATATTAATCAAAT
*
40256438 TAATTAATATTAA
1 AAATTAATATTAA
40256451 CGTGATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.15
19 18 0.67
20 5 0.19
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (19 bp):
AAATTAATATTAATCAAAT
Found at i:40259103 original size:71 final size:73
Alignment explanation
Indices: 40259019--40259157 Score: 219
Period size: 73 Copynumber: 1.9 Consensus size: 73
40259009 ACAAAGATAA
* * *
40259019 TAATTAGTGAATCTTTATT-TTTTTC-ATTCAAATATGTCTCATACTCCTCTTATTAGCATTCTT
1 TAATTAGTAAATCTTTATTATTTTTCAATTCAAATATGTCTCACACTCCTCTTATTAGCATACTT
40259082 ACTAAGAC
66 ACTAAGAC
* *
40259090 TAATTAGTAAATCTTTATTATTTTTCAATTTAAATATGTCTCCCACTCCTCTTATTAGCATACTT
1 TAATTAGTAAATCTTTATTATTTTTCAATTCAAATATGTCTCACACTCCTCTTATTAGCATACTT
40259155 ACT
66 ACT
40259158 GAGAATAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
71 18 0.30
72 6 0.10
73 37 0.61
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.47
Consensus pattern (73 bp):
TAATTAGTAAATCTTTATTATTTTTCAATTCAAATATGTCTCACACTCCTCTTATTAGCATACTT
ACTAAGAC
Found at i:40260189 original size:18 final size:17
Alignment explanation
Indices: 40260165--40260199 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
40260155 CTTAAGGAAG
40260165 ATTTTTTTAAAGAACGT
1 ATTTTTTTAAAGAACGT
40260182 ATTTTTTTAAAGAACGT
1 ATTTTTTTAAAGAACGT
40260199 A
1 A
40260200 CATTTTGATA
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:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (17 bp):
ATTTTTTTAAAGAACGT
Found at i:40260205 original size:17 final size:17
Alignment explanation
Indices: 40260168--40260205 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
40260158 AAGGAAGATT
**
40260168 TTTTTAAAGAACGTATT
1 TTTTTAAAGAACGTACA
40260185 TTTTTAAAGAACGTACA
1 TTTTTAAAGAACGTACA
40260202 TTTT
1 TTTT
40260206 GATAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (17 bp):
TTTTTAAAGAACGTACA
Found at i:40262554 original size:12 final size:11
Alignment explanation
Indices: 40262528--40262561 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
40262518 TAGACCCAGG
40262528 ATGAATTAATT
1 ATGAATTAATT
*
40262539 ATGAATTCATTT
1 ATGAATT-AATT
40262551 ATGAATTAATT
1 ATGAATTAATT
40262562 CACTTGTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (11 bp):
ATGAATTAATT
Found at i:40263850 original size:12 final size:12
Alignment explanation
Indices: 40263835--40263874 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
40263825 TAAGTATTGA
40263835 ATTAAATTTAAT
1 ATTAAATTTAAT
*
40263847 ATTAAAGTTAAT
1 ATTAAATTTAAT
40263859 ATTAAATTTAAT
1 ATTAAATTTAAT
40263871 -TTAA
1 ATTAA
40263875 TGCTTATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 4 0.15
12 22 0.85
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (12 bp):
ATTAAATTTAAT
Found at i:40263851 original size:29 final size:29
Alignment explanation
Indices: 40263794--40263875 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
40263784 TTTAATAGAT
** * *
40263794 TTAATATTAAATTAATAAAATACTATTAATG
1 TTAATATTAAATT-A-AATTTAATATTAAAG
*
40263825 -TAAGTATTGAATTAAATTTAATATTAAAG
1 TTAA-TATTAAATTAAATTTAATATTAAAG
*
40263854 TTAATATTAAATTTAATTTAAT
1 TTAATATTAAATTAAATTTAAT
40263876 GCTTATCTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
29 27 0.64
30 7 0.17
31 8 0.19
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (29 bp):
TTAATATTAAATTAAATTTAATATTAAAG
Found at i:40273615 original size:72 final size:71
Alignment explanation
Indices: 40273445--40274043 Score: 466
Period size: 72 Copynumber: 8.4 Consensus size: 71
40273435 TCAACGAAAA
* * ** * * *
40273445 CCCAAATAGTTAGCGAGAGTTAAAAGCTCTCAACTGTCATTATTAAGGCTCACAAGTTCAATACC
1 CCCAAATAGTTAGCGAGAGTTAAAAGCTCCCAGCTGTCATTATTAAGGCTCGTAGGTTTAAAACC
*
40273510 AGAACC
66 ACAACC
* * ** * *
40273516 CCCAAATAATTAGCGAGACTTAAAAGCTCCCATTTGTTATCATTAAGGCTCGTAGGTTTAAAACC
1 CCCAAATAGTTAGCGAGAGTTAAAAGCTCCCAGCTGTCATTATTAAGGCTCGTAGGTTTAAAACC
40273581 ACAACC
66 ACAACC
* * * * * *
40273587 CCTTAAATAGTTAGCGAGAGATAAAAGCTCCTAGCTATCATAATTAAGGCTCGTAGGTTTAAAAT
1 CC-CAAATAGTTAGCGAGAGTTAAAAGCTCCCAGCTGTCATTATTAAGGCTCGTAGGTTTAAAAC
*** *
40273652 TGTAGCC
65 CACAACC
* * * *
40273659 CACCAAACAGTTAGCGAGAGTTAAAAGCTTCCAGCTGTCATCATTAAGGCTCGTAGGTTTCAAAC
1 C-CCAAATAGTTAGCGAGAGTTAAAAGCTCCCAGCTGTCATTATTAAGGCTCGTAGGTTTAAAAC
*
40273724 CACAGCC
65 CACAACC
* * * *
40273731 CCCAAAATAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTTGCAGGATTAAAAC
1 CCC-AAATAGTTAGCGAGAGTTAAAAGCTCCCAGCTGTCATTATTAAGGCTCGTAGGTTTAAAAC
*
40273796 TACAACC
65 CACAACC
* * * ** * * *
40273803 CCCAAATAGTTAACAAGATTTAAAAGCTTTCAGTTGTCATTATTAAGGCTCGTAAGTTTAAAACT
1 CCCAAATAGTTAGCGAGAGTTAAAAGCTCCCAGCTGTCATTATTAAGGCTCGTAGGTTTAAAACC
* * *
40273868 GCAGTCT
66 ACA-ACC
* * * * * * * * * **
40273875 CCTAAACAGTTAGCGAGAGTTAAAAGCTCTCAGTTGTC-TTATTAAAGCTTGCAAGTTCATTACC
1 CCCAAATAGTTAGCGAGAGTTAAAAGCTCCCAGCTGTCATTATTAAGGCTCGTAGGTTTAAAACC
*
40273939 ACAGCCCC
66 ACA--ACC
* * * ** * * * * *
40273947 CCCAAACAGTT-G-GAAAATTTTAAAAGCTCCCAAATATTATTATTAAGACTCATAGGTTTAGAA
1 CCCAAATAGTTAGCG-AGA-GTTAAAAGCTCCCAGCTGTCATTATTAAGGCTCGTAGGTTTAAAA
*
40274010 CCACAGCTC
64 CCACAAC-C
* *
40274019 CCCAAACAGTCAGCGAGAGTTAAAA
1 CCCAAATAGTTAGCGAGAGTTAAAA
40274044 ACTCTCAGAT
Statistics
Matches: 415, Mismatches: 102, Indels: 21
0.77 0.19 0.04
Matches are distributed among these distances:
70 1 0.00
71 140 0.34
72 249 0.60
73 24 0.06
74 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (71 bp):
CCCAAATAGTTAGCGAGAGTTAAAAGCTCCCAGCTGTCATTATTAAGGCTCGTAGGTTTAAAACC
ACAACC
Found at i:40273709 original size:144 final size:142
Alignment explanation
Indices: 40273448--40273903 Score: 482
Period size: 143 Copynumber: 3.2 Consensus size: 142
40273438 ACGAAAACCC
* * * * * * * *
40273448 AAATAGTTAGCGAGAGTTAAAAGCTCTCAACTGTCATTATTAAGGCTCACAAG-TTCAATACCAG
1 AAATAGTTAGCGAGAGTTAAAAGCTCCCAACTATCATAATTAAGGCTCGCAGGATT-AAAACTAC
* * * * *
40273512 AACCCCCAAATAATTAGCGAGACTTAAAAGCTCCCATTTGTTATCATTAAGGCTCGTAGGTTTAA
65 AACCCCCAAACAGTTAGCGAGACTTAAAAGCTTCCAGTTGTCATCATTAAGGCTCGTAGGTTTAA
40273577 AACCACAACCCCTT
130 AACCACAACCCC-T
* * * * * * **
40273591 AAATAGTTAGCGAGAGATAAAAGCTCCTAGCTATCATAATTAAGGCTCGTAGGTTTAAAATTGTA
1 AAATAGTTAGCGAGAGTTAAAAGCTCCCAACTATCATAATTAAGGCTCGCAGGATTAAAACTACA
* * * *
40273656 GCCCACCAAACAGTTAGCGAGAGTTAAAAGCTTCCAGCTGTCATCATTAAGGCTCGTAGGTTTCA
66 ACCC-CCAAACAGTTAGCGAGACTTAAAAGCTTCCAGTTGTCATCATTAAGGCTCGTAGGTTTAA
* *
40273721 AACCACAGCCCCCA
130 AACCACA-ACCCCT
* * *
40273735 AAATAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTTGCAGGATTAAAACTACA
1 AAATAGTTAGCGAGAGTTAAAAGCTCCCAACTATCATAATTAAGGCTCGCAGGATTAAAACTACA
* * * * * * *
40273800 ACCCCCAAATAGTTAACAAGATTTAAAAGCTTTCAGTTGTCATTATTAAGGCTCGTAAGTTTAAA
66 ACCCCCAAACAGTTAGCGAGACTTAAAAGCTTCCAGTTGTCATCATTAAGGCTCGTAGGTTTAAA
** * *
40273865 ACTGCAGTCTCCT
131 ACCACA-ACCCCT
*
40273878 AAACAGTTAGCGAGAGTTAAAAGCTC
1 AAATAGTTAGCGAGAGTTAAAAGCTC
40273904 TCAGTTGTCT
Statistics
Matches: 258, Mismatches: 52, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
143 136 0.53
144 118 0.46
145 4 0.02
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (142 bp):
AAATAGTTAGCGAGAGTTAAAAGCTCCCAACTATCATAATTAAGGCTCGCAGGATTAAAACTACA
ACCCCCAAACAGTTAGCGAGACTTAAAAGCTTCCAGTTGTCATCATTAAGGCTCGTAGGTTTAAA
ACCACAACCCCT
Found at i:40273972 original size:215 final size:215
Alignment explanation
Indices: 40273446--40273993 Score: 581
Period size: 215 Copynumber: 2.5 Consensus size: 215
40273436 CAACGAAAAC
* * *
40273446 CCAAATAGTTAGCGAGAGTTAAAAGCTCTCAACTGTCATTATTAAGGCTCACAAGTTCAATACCA
1 CCAAACAGTTAGCGAGAGTTAAAAGCTCTCAGCTGTCATTATTAAGGCTCGCAAGTTC-ATACCA
* * * ** * * *
40273511 GA-ACCCCCAAATAATTAGCGAGACTTAAAAGCTCCCATTTGTTATCATTAAGGCTCGTAGGTTT
65 CAGCCCCCCAAATAGTTAGCGAGACTTAAAAGCTCCCAAATGTTATTATTAAGGCTCGCAGGATT
* * *
40273575 AAAACCACAACCCCTTAAATAGTTAGCGAGAGATAAAAGCTCCTAGCTATCATAATTAAGGCTCG
130 AAAACCACAACCCCTCAAATAGTTAACAAGAGATAAAAGCTCCTAGCTATCATAATTAAGGCTCG
* * *
40273640 TAGGTTTAAAATTGTAGCCCA
195 TAAGTTTAAAACTGCAGCCCA
* * * *
40273661 CCAAACAGTTAGCGAGAGTTAAAAGCT-TCCAGCTGTCATCATTAAGGCTCGTAGGTTTCAAACC
1 CCAAACAGTTAGCGAGAGTTAAAAGCTCT-CAGCTGTCATTATTAAGGCTCGCAAG-TTCATACC
* * * * *
40273725 ACAGCCCCCAAAATAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTTGCAGGAT
64 ACAGCCCCCCAAATAGTTAGCGAGACTTAAAAGCTCCCAAATGTTATTATTAAGGCTCGCAGGAT
* ** * * * *
40273790 TAAAACTACAACCCC-CAAATAGTTAACAAGATTTAAAAGCT-TTCAGTTGTCATTATTAAGGCT
129 TAAAACCACAACCCCTCAAATAGTTAACAAGAGATAAAAGCTCCT-AGCTATCATAATTAAGGCT
*
40273853 CGTAAGTTTAAAACTGCAGTCTC-
193 CGTAAGTTTAAAACTGCAG-CCCA
* * * *
40273876 CTAAACAGTTAGCGAGAGTTAAAAGCTCTCAGTTGTC-TTATTAAAGCTTGCAAGTTCATTACCA
1 CCAAACAGTTAGCGAGAGTTAAAAGCTCTCAGCTGTCATTATTAAGGCTCGCAAGTTCA-TACCA
* * * *
40273940 CAGCCCCCCCAAACAGTT-G-GAAAATTTTAAAAGCTCCCAAATATTATTATTAAG
65 CAG-CCCCCCAAATAGTTAGCG-AGA-CTTAAAAGCTCCCAAATGTTATTATTAAG
40273994 ACTCATAGGT
Statistics
Matches: 275, Mismatches: 48, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
213 5 0.02
214 24 0.09
215 176 0.64
216 70 0.25
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (215 bp):
CCAAACAGTTAGCGAGAGTTAAAAGCTCTCAGCTGTCATTATTAAGGCTCGCAAGTTCATACCAC
AGCCCCCCAAATAGTTAGCGAGACTTAAAAGCTCCCAAATGTTATTATTAAGGCTCGCAGGATTA
AAACCACAACCCCTCAAATAGTTAACAAGAGATAAAAGCTCCTAGCTATCATAATTAAGGCTCGT
AAGTTTAAAACTGCAGCCCA
Found at i:40273972 original size:287 final size:287
Alignment explanation
Indices: 40273445--40274043 Score: 620
Period size: 287 Copynumber: 2.1 Consensus size: 287
40273435 TCAACGAAAA
* *
40273445 CCCAAATAGTTAGCGAGAGTTAAAAGCTCTCAACTGTCATTATTAAGGCTCACAAGTTCAATACC
1 CCCAAATAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCACAAGTTCAAAACC
* * * * * *
40273510 AGAACCCCCAAATAATTAGCGAGACTTAAAAGCTCCCATTTGTTATCATTAAGGCTCGTAGGTTT
66 ACAACCCCCAAATAATTAACAAGACTTAAAAGCTCCCAGTTGTCATCATTAAGGCTCGTAAGTTT
* *
40273575 AAAACCACAACCCCTTAAATAGTTAGCGAGAGATAAAAGCTCCTAGCTATCATAATTAAGGCTCG
131 AAAACCACAACCCCTTAAACAGTTAGCGAGAGATAAAAGCTCCTAGCTATCATAATTAAAGCTCG
* * * **** * * ** *
40273640 TAGGTTTAAAATTGTAGCCCACCAAACAGTTAGCGAGAGTTAAAAGCTTCCAGCTGTCATCATTA
196 CAAGTTCAAAACCACAGCCCACCAAACAGTTAGCGAAAGTTAAAAGCTCCCAAATATCATCATTA
* *
40273705 AGGCTCGTAGGTTTCA-AACCACAGC-C
261 AGACTCATAGGTTT-AGAACCACAGCTC
** *
40273731 CCCAAAATAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTTGCAGGATT-AAAA
1 CCC-AAATAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCACAAG-TTCAAAA
* * * ** *
40273795 CTACAACCCCCAAATAGTTAACAAGATTTAAAAGCTTTCAGTTGTCATTATTAAGGCTCGTAAGT
64 CCACAACCCCCAAATAATTAACAAGACTTAAAAGCTCCCAGTTGTCATCATTAAGGCTCGTAAGT
** * * * * * *
40273860 TTAAAACTGCAGTCTCC-TAAACAGTTAGCGAGAGTTAAAAGCT-CTCAGTTGTC-TTATTAAAG
129 TTAAAACCACA-ACCCCTTAAACAGTTAGCGAGAGATAAAAGCTCCT-AGCTATCATAATTAAAG
* ** * * *
40273922 CTTGCAAGTTCATTACCACAGCCCCCCCAAACAGTT-G-GAAAATTTTAAAAGCTCCCAAATATT
192 CTCGCAAGTTCAAAACCACAG-CCCACCAAACAGTTAGCG-AAA-GTTAAAAGCTCCCAAATATC
*
40273985 ATTATTAAGACTCATAGGTTTAGAACCACAGCTC
254 ATCATTAAGACTCATAGGTTTAGAACCACAGCTC
* *
40274019 CCCAAACAGTCAGCGAGAGTTAAAA
1 CCCAAATAGTTAGCGAGAGTTAAAA
40274044 ACTCTCAGAT
Statistics
Matches: 254, Mismatches: 50, Indels: 17
0.79 0.16 0.05
Matches are distributed among these distances:
285 1 0.00
286 27 0.11
287 217 0.85
288 9 0.04
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (287 bp):
CCCAAATAGTTAGCGAGAGTTAAAAGCTCCCAACTGTCATTATTAAGGCTCACAAGTTCAAAACC
ACAACCCCCAAATAATTAACAAGACTTAAAAGCTCCCAGTTGTCATCATTAAGGCTCGTAAGTTT
AAAACCACAACCCCTTAAACAGTTAGCGAGAGATAAAAGCTCCTAGCTATCATAATTAAAGCTCG
CAAGTTCAAAACCACAGCCCACCAAACAGTTAGCGAAAGTTAAAAGCTCCCAAATATCATCATTA
AGACTCATAGGTTTAGAACCACAGCTC
Found at i:40274505 original size:27 final size:27
Alignment explanation
Indices: 40274426--40274508 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 27
40274416 TTCTTTTTCC
* *
40274426 CAGTAGGAAGAGTCACATTATCATTCT
1 CAGTAGGAGGAGTCACATTGTCATTCT
* * * *
40274453 CAGTAGGAGGGGCCACACTGTTATTCT
1 CAGTAGGAGGAGTCACATTGTCATTCT
*
40274480 C-GATAGGAGGAGTCACGTTGTCATTCT
1 CAG-TAGGAGGAGTCACATTGTCATTCT
40274507 CA
1 CA
40274509 ACTAGGTCCT
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
26 1 0.02
27 42 0.98
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (27 bp):
CAGTAGGAGGAGTCACATTGTCATTCT
Found at i:40280167 original size:18 final size:19
Alignment explanation
Indices: 40280141--40280183 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
40280131 TTTCCCAAAA
40280141 TAAATATT-ATTTACTAAAT
1 TAAATATTAATTTACT-AAT
*
40280160 TAAA-ATTAATTTTCTAAT
1 TAAATATTAATTTACTAAT
40280178 TAAATA
1 TAAATA
40280184 ATTTTCTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAATATTAATTTACTAAT
Found at i:40281953 original size:24 final size:25
Alignment explanation
Indices: 40281904--40281953 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
40281894 TATGAAAATT
*
40281904 CTTGAGAAAATGCTTGTTAATGTATA
1 CTTGAGAAAAT-CTAGTTAATGTATA
*
40281930 CTTGAGAAAAT-TAGTTAATTTATA
1 CTTGAGAAAATCTAGTTAATGTATA
40281954 TACTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
26 11 0.50
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (25 bp):
CTTGAGAAAATCTAGTTAATGTATA
Found at i:40283523 original size:21 final size:21
Alignment explanation
Indices: 40283477--40283549 Score: 55
Period size: 21 Copynumber: 3.7 Consensus size: 21
40283467 ATTAAAATAT
* * *
40283477 AAAA-ATCAAAAAAATTTTAT
1 AAAATATCATAAAAATTATAA
*
40283497 AGAATATCATAAAAATTATAA
1 AAAATATCATAAAAATTATAA
** *
40283518 AAAATATTTTTAAAA--ATAA
1 AAAATATCATAAAAATTATAA
40283537 AAAATAT-ATAAAA
1 AAAATATCATAAAA
40283550 GTAAAAATAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
18 4 0.10
19 11 0.26
20 3 0.07
21 24 0.57
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (21 bp):
AAAATATCATAAAAATTATAA
Found at i:40283596 original size:25 final size:25
Alignment explanation
Indices: 40283568--40283620 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
40283558 AATAGGAAAT
* * *
40283568 TATAAAATTCTTATAAATGAAAAAA
1 TATAAAATTATAAGAAATGAAAAAA
*
40283593 TAT-AAATTATAAGAAATGGAAAAA
1 TATAAAATTATAAGAAATGAAAAAA
40283617 TATA
1 TATA
40283621 TTAATAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (25 bp):
TATAAAATTATAAGAAATGAAAAAA
Found at i:40283691 original size:20 final size:20
Alignment explanation
Indices: 40283664--40283709 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
40283654 TGATATAAAC
40283664 TATG-AAAAAA-TAAAAAGTT
1 TATGAAAAAAATTAAAAA-TT
40283683 TATGAAAAAAATTAAAAATT
1 TATGAAAAAAATTAAAAATT
40283703 TA-GAAAA
1 TATGAAAA
40283710 TTATTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.36
20 10 0.40
21 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (20 bp):
TATGAAAAAAATTAAAAATT
Found at i:40284204 original size:28 final size:27
Alignment explanation
Indices: 40284165--40284262 Score: 85
Period size: 28 Copynumber: 3.5 Consensus size: 27
40284155 CTTTTAATAA
40284165 TTTTTATAATTTTTATATTTTTATACAAT
1 TTTTTAT-ATTTTTATATTTTTATA-AAT
* *
40284194 TTTTTATATTTTTCATA-ATTTATATAT
1 TTTTTATATTTTT-ATATTTTTATAAAT
*
40284221 TTTTTATA-ATTTATATTTATTTATAATAT
1 TTTTTATATTTTTATA-TT-TTTATAA-AT
40284250 TTTTGTA-ATTTTT
1 TTTT-TATATTTTT
40284263 TAATAAAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
25 3 0.05
26 3 0.05
27 10 0.18
28 18 0.32
29 17 0.30
30 5 0.09
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (27 bp):
TTTTTATATTTTTATATTTTTATAAAT
Found at i:40284217 original size:16 final size:17
Alignment explanation
Indices: 40284164--40284238 Score: 66
Period size: 17 Copynumber: 4.2 Consensus size: 17
40284154 ACTTTTAATA
40284164 ATTTTT-ATAATTTTTAT
1 ATTTTTCATAA-TTTTAT
40284181 ATTTTT-ATACAATTTTTTAT
1 ATTTTTCAT--AA--TTTTAT
40284201 ATTTTTCATAATTTATAT
1 ATTTTTCATAATTT-TAT
*
40284219 ATTTTTTATAA-TTTAT
1 ATTTTTCATAATTTTAT
40284235 ATTT
1 ATTT
40284239 ATTTATAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
16 7 0.13
17 13 0.25
18 13 0.25
19 4 0.08
20 13 0.25
21 2 0.04
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTTCATAATTTTAT
Found at i:40284354 original size:9 final size:9
Alignment explanation
Indices: 40284096--40284336 Score: 118
Period size: 9 Copynumber: 25.7 Consensus size: 9
40284086 TTTTCCAAAT
40284096 ATTTTTA-A
1 ATTTTTATA
*
40284104 ATATTTTATG
1 AT-TTTTATA
* *
40284114 CTTTTTATG
1 ATTTTTATA
*
40284123 TTTTTTATA
1 ATTTTTATA
*
40284132 ATATTTTGTTA
1 AT-TTTT-ATA
*
40284143 ATTTTATTAAA
1 A-TTT-TTATA
*
40284154 ACTTTTAATA
1 A-TTTTTATA
40284164 ATTTTTATA
1 ATTTTTATA
40284173 ATTTTTAT-
1 ATTTTTATA
40284181 ATTTTTATACA
1 ATTTTTAT--A
40284192 ATTTTT-TA
1 ATTTTTATA
40284200 TATTTTTCATA
1 -ATTTTT-ATA
*
40284211 ATTTATATA
1 ATTTTTATA
*
40284220 TTTTTTATA
1 ATTTTTATA
40284229 A--TTTATA
1 ATTTTTATA
*
40284236 TTTATTTATAA
1 ATT-TTTAT-A
*
40284247 TATTTTTGTA
1 -ATTTTTATA
40284257 ATTTTTTAATA
1 A-TTTTT-ATA
**
40284268 AAATTTATA
1 ATTTTTATA
*
40284277 ATTTATATA
1 ATTTTTATA
40284286 ATTTTT-TCA
1 ATTTTTAT-A
* *
40284295 ATTATAATA
1 ATTTTTATA
* *
40284304 AATTTTACA
1 ATTTTTATA
40284313 ATTTTCTAT-
1 ATTTT-TATA
40284322 ATTTTTATA
1 ATTTTTATA
40284331 ATTTTT
1 ATTTTT
40284337 GCACTTTATA
Statistics
Matches: 176, Mismatches: 34, Indels: 45
0.69 0.13 0.18
Matches are distributed among these distances:
7 6 0.03
8 15 0.09
9 92 0.52
10 32 0.18
11 26 0.15
12 5 0.03
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (9 bp):
ATTTTTATA
Found at i:40284517 original size:38 final size:38
Alignment explanation
Indices: 40284474--40284548 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
40284464 TGACTATTAG
40284474 CTTTAATGGTAAAAGGGCTTAATTGATT-AAAGTGTTAA
1 CTTTAATGGTAAAAGGGCTTAATTGATTGAAA-TGTTAA
40284512 CTTTAATGGTAAAAGGGCTTAATTGATTGAAATGTTA
1 CTTTAATGGTAAAAGGGCTTAATTGATTGAAATGTTA
40284549 TCATTCGAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 33 0.92
39 3 0.08
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.37
Consensus pattern (38 bp):
CTTTAATGGTAAAAGGGCTTAATTGATTGAAATGTTAA
Found at i:40289189 original size:2 final size:2
Alignment explanation
Indices: 40289182--40289206 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40289172 GTTCACTAAC
40289182 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
40289207 TATTTATTGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40302006 original size:47 final size:47
Alignment explanation
Indices: 40301948--40302128 Score: 177
Period size: 47 Copynumber: 3.9 Consensus size: 47
40301938 GGCAGAGTAT
* * *
40301948 CTGCTCGACCAGTGGTTTATCCACAATGTATTTTAGGCGGCAGTCAC
1 CTGCTCAACCAGTGGTTTATCCACAATGTATTTTAGTCAGCAGTCAC
* * * * * * *
40301995 CTGCTTAACCAGTAGTTTATCCACAATGTATCTTAGTTAACAGTTAT
1 CTGCTCAACCAGTGGTTTATCCACAATGTATTTTAGTCAGCAGTCAC
* *
40302042 CTGCTCGACCAGTGGTTTATCCATAATGTATTTTAGTCAGCAGTCAC
1 CTGCTCAACCAGTGGTTTATCCACAATGTATTTTAGTCAGCAGTCAC
* * * * **
40302089 TTGCTCGACTAAT-GTTATATCCACAACATATTTTAG-CAGC
1 CTGCTCAACCAGTGGTT-TATCCACAATGTATTTTAGTCAGC
40302129 TTTTATCTGC
Statistics
Matches: 108, Mismatches: 25, Indels: 3
0.79 0.18 0.02
Matches are distributed among these distances:
46 7 0.06
47 101 0.94
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (47 bp):
CTGCTCAACCAGTGGTTTATCCACAATGTATTTTAGTCAGCAGTCAC
Found at i:40303497 original size:21 final size:21
Alignment explanation
Indices: 40303460--40303502 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
40303450 CGTCTATCTT
40303460 TTTTATTTTCTTCTTTA-TTA
1 TTTTATTTTCTTCTTTACTTA
40303480 TTTTATTGTTCTAT-TTTACTTA
1 TTTTATT-TTCT-TCTTTACTTA
40303502 T
1 T
40303503 CTTAGTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 7 0.35
21 8 0.40
22 5 0.25
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTATTTTCTTCTTTACTTA
Found at i:40306781 original size:16 final size:18
Alignment explanation
Indices: 40306755--40306791 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
40306745 TGTTTTCTAT
40306755 ATATATTTTTAATTTT-A
1 ATATATTTTTAATTTTGA
40306772 ATAT-TTTTTAATTTTGA
1 ATATATTTTTAATTTTGA
40306789 ATA
1 ATA
40306792 AACATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
ATATATTTTTAATTTTGA
Found at i:40307098 original size:23 final size:22
Alignment explanation
Indices: 40307068--40307115 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
40307058 TATTATCAAT
40307068 TATTTTTTTAAATCTATAAAAAA
1 TATTTTTTTAAATC-ATAAAAAA
* *
40307091 TA-TTTTTTAATTCCTAAAAAA
1 TATTTTTTTAAATCATAAAAAA
40307112 TATT
1 TATT
40307116 AAGGGTACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 9 0.41
22 11 0.50
23 2 0.09
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTTTTTTAAATCATAAAAAA
Found at i:40307099 original size:22 final size:21
Alignment explanation
Indices: 40307071--40307115 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40307061 TATCAATTAT
40307071 TTTTTTAAATCTATAAAAAATA
1 TTTTTTAAATC-ATAAAAAATA
* *
40307093 TTTTTTAATTCCTAAAAAATA
1 TTTTTTAAATCATAAAAAATA
40307114 TT
1 TT
40307116 AAGGGTACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTTTAAATCATAAAAAATA
Found at i:40316766 original size:19 final size:19
Alignment explanation
Indices: 40316739--40316783 Score: 81
Period size: 19 Copynumber: 2.3 Consensus size: 19
40316729 ATAAAGGTTC
40316739 TTACTACAACTCATTTCCAA
1 TTAC-ACAACTCATTTCCAA
40316759 TTACACAACTCATTTCCAA
1 TTACACAACTCATTTCCAA
40316778 TTACAC
1 TTACAC
40316784 TTATGTGCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (19 bp):
TTACACAACTCATTTCCAA
Found at i:40321141 original size:53 final size:53
Alignment explanation
Indices: 40321078--40321185 Score: 137
Period size: 53 Copynumber: 2.0 Consensus size: 53
40321068 AGTAGCACAT
* * * * *
40321078 ATCACGCCGATGCCATATCCCAAATATGGTCTTATA-TGAAAACTCATAATCAC
1 ATCACACCGATGCCATAGCCCAAATATCGTCTTATACGGAAAACACAT-ATCAC
**
40321131 ATCACACCGATGCCATAGCCCAGCTATCGTCTTATACGGAAAACACATATCAC
1 ATCACACCGATGCCATAGCCCAAATATCGTCTTATACGGAAAACACATATCAC
40321184 AT
1 AT
40321186 GTTGCCATGG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 38 0.81
54 9 0.19
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (53 bp):
ATCACACCGATGCCATAGCCCAAATATCGTCTTATACGGAAAACACATATCAC
Found at i:40328029 original size:45 final size:43
Alignment explanation
Indices: 40327907--40328354 Score: 166
Period size: 44 Copynumber: 10.3 Consensus size: 43
40327897 TTGCAGCTTC
* * *
40327907 AGAGAGATAAGATCTATGGTTTT-AATCCGCTCCACTGCAACATC
1 AGAGAGATAAGA-CT-TGGTTTTAAATCCGCTCCACTACAACTTT
* * *** *
40327951 AGGGAGATAA-A-ATGGTTTCTTCTGTCTGCTCCACTACAACTTT
1 AGAGAGATAAGACTTGG-TT-TTAAATCCGCTCCACTACAACTTT
*
40327994 AGAGAGATAAGACCTGTGGTTTTAAATCCGCTCCACTACAACTTC
1 AGAGAGATAAGA-CT-TGGTTTTAAATCCGCTCCACTACAACTTT
* * *** * *
40328039 AAAGAGATAGGA-TTGGCTTCTTCTGTCTGCTCCACTGCAACTTT
1 AGAGAGATAAGACTTGG-TT-TTAAATCCGCTCCACTACAACTTT
* * *** * * *
40328083 AGGGAGATAAGAC-TGG-ATGCGATCTGCTCTACTACAACTTC
1 AGAGAGATAAGACTTGGTTTTAAATCCGCTCCACTACAACTTT
* *
40328124 AGAGAGATAAGATCTATGGTTTTAAATCCGCTCTACTGCAACTTT
1 AGAGAGATAAGA-CT-TGGTTTTAAATCCGCTCCACTACAACTTT
* *** * ** *
40328169 A-AGGAGATAGGA-TTGGCTTCTTCTGTCTGCTCCAC--CGCCTTC
1 AGA-GAGATAAGACTTGG-TT-TTAAATCCGCTCCACTACAACTTT
* * *** * * *
40328211 AGGGAGATAAGA-TTGG-ATGCGATCTGCTCTACTGCAACTTT
1 AGAGAGATAAGACTTGGTTTTAAATCCGCTCCACTACAACTTT
* *
40328252 AGAGAGATAAGATCAGTGGTTTTAAATCCGCTCCACTGCAACTTT
1 AGAGAGATAAGA-C-TTGGTTTTAAATCCGCTCCACTACAACTTT
* * ** * ** *
40328297 AGGGAGATAGGA-TTGGATTCTTCTATCTGCTCCACTGGAACTTC
1 AGAGAGATAAGACTTGG-TT-TTAAATCCGCTCCACTACAACTTT
*
40328341 AGGGAGATAAGACT
1 AGAGAGATAAGACT
40328355 AGATGCGATC
Statistics
Matches: 300, Mismatches: 77, Indels: 53
0.70 0.18 0.12
Matches are distributed among these distances:
39 11 0.04
40 3 0.01
41 46 0.15
42 29 0.10
43 33 0.11
44 87 0.29
45 86 0.29
46 2 0.01
47 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (43 bp):
AGAGAGATAAGACTTGGTTTTAAATCCGCTCCACTACAACTTT
Found at i:40328071 original size:89 final size:87
Alignment explanation
Indices: 40327907--40328095 Score: 261
Period size: 89 Copynumber: 2.1 Consensus size: 87
40327897 TTGCAGCTTC
* * ** *
40327907 AGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACATCAGGGAGATAAAATGGTTTCTT
1 AGAGAGATAAGACCTATGGTTTTAATCCGCTCCACTACAACATCAAAGAGATAAAATGGCTTCTT
40327972 CTGTCTGCTCCACTACAACTTT
66 CTGTCTGCTCCACTACAACTTT
* * * *
40327994 AGAGAGATAAGACCTGTGGTTTTAAATCCGCTCCACTACAACTTCAAAGAGATAGGATTGGCTTC
1 AGAGAGATAAGACCTATGGTTTT-AATCCGCTCCACTACAACATCAAAGAGATA-AAATGGCTTC
*
40328059 TTCTGTCTGCTCCACTGCAACTTT
64 TTCTGTCTGCTCCACTACAACTTT
*
40328083 AGGGAGATAAGAC
1 AGAGAGATAAGAC
40328096 TGGATGCGAT
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
87 21 0.24
88 26 0.29
89 42 0.47
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (87 bp):
AGAGAGATAAGACCTATGGTTTTAATCCGCTCCACTACAACATCAAAGAGATAAAATGGCTTCTT
CTGTCTGCTCCACTACAACTTT
Found at i:40328150 original size:130 final size:130
Alignment explanation
Indices: 40327975--40328395 Score: 641
Period size: 130 Copynumber: 3.3 Consensus size: 130
40327965 GTTTCTTCTG
* * * * * *
40327975 TCTGCTCCACTACAACTTTAGAGAGATAAGACCTGTGGTTTTAAATCCGCTCCACTACAACTTCA
1 TCTGCTCTACTACAACTTCAGAGAGATAAGATCTATGGTTTTAAATCCGCTCCACTGCAACTTTA
* *
40328040 AAGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTGGATGCGA
66 AGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGA
*
40328105 TCTGCTCTACTACAACTTCAGAGAGATAAGATCTATGGTTTTAAATCCGCTCTACTGCAACTTTA
1 TCTGCTCTACTACAACTTCAGAGAGATAAGATCTATGGTTTTAAATCCGCTCCACTGCAACTTTA
* *
40328170 AGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACCGC--CTTCAGGGAGATAAGATTGGATGCGA
66 AGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGA
* *
40328233 TCTGCTCTACTGCAACTTTAGAGAGATAAGATC-AGTGGTTTTAAATCCGCTCCACTGCAACTTT
1 TCTGCTCTACTACAACTTCAGAGAGATAAGATCTA-TGGTTTTAAATCCGCTCCACTGCAACTTT
* * * * *
40328297 AGGGAGATAGGATTGGATTCTTCTATCTGCTCCACTGGAACTTCAGGGAGATAAGACTAGATGCG
65 AAGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCG
40328362 A
130 A
*
40328363 TCTGCTCTACTGCAACTTCAGAGAGATAAGATC
1 TCTGCTCTACTACAACTTCAGAGAGATAAGATC
40328396 NNNNNNNNNN
Statistics
Matches: 266, Mismatches: 22, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
127 1 0.00
128 116 0.44
130 149 0.56
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (130 bp):
TCTGCTCTACTACAACTTCAGAGAGATAAGATCTATGGTTTTAAATCCGCTCCACTGCAACTTTA
AGGAGATAGGATTGGCTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGA
Found at i:40328622 original size:41 final size:41
Alignment explanation
Indices: 40328577--40328982 Score: 150
Period size: 44 Copynumber: 9.4 Consensus size: 41
40328567 GCTCCACTGG
* *
40328577 AACTTCAGGGAGATAAGACTGGATGTGATCTGCTTTACTAC
1 AACTTCAGGGAGATAAGACTGGATGTAATCTGCTCTACTAC
* * * * * *
40328618 AACTTTAGAGAGATAAGATCTGTGGTTTTAAAT-TCGCTCCACTGC
1 AACTTCAGGGAGATAAGA-C--TGGATGT-AATCT-GCTCTACTAC
* * * * * ** *
40328663 AACTTTAGGGAGATAGGATTGGCTTCTTCTTTCTGCTCTACTGC
1 AACTTCAGGGAGATAAGACTGG-AT-GT-AATCTGCTCTACTAC
* ** *
40328707 AACTTCAGGGAGATAAGACTAGATGCGATCTGCTATACTGA-
1 AACTTCAGGGAGATAAGACTGGATGTAATCTGCTCTACT-AC
** * * * *
40328748 AACTTCAGAAAGATAAGATCTGTGGTTTTAAATCTGCTCCACTGC
1 AACTTCAGGGAGATAAGA-C--TGGATGT-AATCTGCTCTACTAC
* * * ** * * *
40328793 AACTTCAGGGAGATAGGATTGGCTGCTTCTGTTTGCTCCACTAT
1 AACTTCAGGGAGATAAGACTGGATG--T-AATCTGCTCTACTAC
* *
40328837 AACTTCAGGGAGATAAGACTAGATGCAATCTGCTCTACTAC
1 AACTTCAGGGAGATAAGACTGGATGTAATCTGCTCTACTAC
* * * * *
40328878 AACTTCAGAGAGATAAGATCTATGGTTTTAAATCGGCTCCACTAC
1 AACTTCAGGGAGATAAGA-C--TGGATGT-AATCTGCTCTACTAC
* * * * * * *
40328923 AACTTTAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGC
1 AACTTCAGGGAGATA--A-GACTGGATGTAATCTGCTCTACTAC
*
40328967 AATTTCAGGGAGATAA
1 AACTTCAGGGAGATAA
40328983 AATTCGCCAT
Statistics
Matches: 268, Mismatches: 74, Indels: 45
0.69 0.19 0.12
Matches are distributed among these distances:
41 69 0.26
42 11 0.04
43 3 0.01
44 100 0.37
45 83 0.31
47 1 0.00
48 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (41 bp):
AACTTCAGGGAGATAAGACTGGATGTAATCTGCTCTACTAC
Found at i:40328717 original size:44 final size:43
Alignment explanation
Indices: 40328524--40329072 Score: 224
Period size: 45 Copynumber: 12.6 Consensus size: 43
40328514 TTTAAATCCA
* * * * *
40328524 CTCCACTGCAACTTCAGTGAAATAGGATTGACTTCTTCTGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGGCTT-TTCTATCTG
* * * * *
40328568 CTCCACTGGAACTTCAGGGAGATAAGACTGG-ATGT-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGGCTTTTCTATCTG
** * * * * **
40328609 CTTTACTACAACTTTAGAGAGATAAGATCTGTGGTTTTAAAT-TCG
1 CTCCACTGCAACTTCAGGGAGATAAGAT-TG-GCTTTTCTATCT-G
* * *
40328654 CTCCACTGCAACTTTAGGGAGATAGGATTGGCTTCTTCTTTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGGCTT-TTCTATCTG
* * * * * *
40328698 CTCTACTGCAACTTCAGGGAGATAAGACTAG--ATGCGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGGCTTTTCTATCTG
** * ** * **
40328739 CTATACTGAAACTTCAGAAAGATAAGATCTGTGGTTTTAAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGAT-TG-GCTTTTCTATCTG
* * * *
40328784 CTCCACTGCAACTTCAGGGAGATAGGATTGGCTGCTTCTGTTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGGCT-TTTCTATCTG
** * * * * *
40328828 CTCCACTATAACTTCAGGGAGATAAGACTAG--ATGCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGGCTTTTCTATCTG
* * * ** *
40328869 CTCTACTACAACTTCAGAGAGATAAGATCTATGG-TTTTAAATCGG
1 CTCCACTGCAACTTCAGGGAGATAAGA--T-TGGCTTTTCTATCTG
* * * *
40328914 CTCCACTACAACTTTAGGGAGATAGGATTATTGGC-TTT-AATCTG
1 CTCCACTGCAACTTCAGGGAGATA--A-GATTGGCTTTTCTATCTG
* * * *
40328958 CTCCACTGCAATTTCAGGGAGATAAAATTCGCCATATTC-AGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATT-GGC-TTTTCTA-TCTG
* * * **
40329003 CCCCACTGCAACTTCAAGGG-GATAAAACTT-GCTATTTTCAATCCA
1 CTCCACTGCAACTTC-AGGGAGATAAGA-TTGGC--TTTTCTATCTG
*
40329048 CTCCACTGCAACTTTAGGGAGATAA
1 CTCCACTGCAACTTCAGGGAGATAA
40329073 TATTTGCAGT
Statistics
Matches: 377, Mismatches: 98, Indels: 59
0.71 0.18 0.11
Matches are distributed among these distances:
41 86 0.23
42 7 0.02
43 8 0.02
44 129 0.34
45 137 0.36
46 8 0.02
47 1 0.00
48 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTGGCTTTTCTATCTG
Found at i:40328737 original size:130 final size:130
Alignment explanation
Indices: 40328496--40328982 Score: 635
Period size: 130 Copynumber: 3.7 Consensus size: 130
40328486 NNNNNNNNNN
* ** * * *
40328496 AGAGATAAGATTTGTGGTTTTAAATCCACTCCACTGCAACTTCAGTGAAATAGGATTGACTTCTT
1 AGAGATAAGATCTGTGGTTTTAAATCGGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTTCTT
* * * * * *
40328561 CTGTCTGCTCCACTGGAACTTCAGGGAGATAAGACTGGATGTGATCTGCTTTACTACAACTTTAG
66 CTTTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTATACTACAACTTCAG
*
40328626 AGAGATAAGATCTGTGGTTTTAAATTC-GCTCCACTGCAACTTTAGGGAGATAGGATTGGCTTCT
1 AGAGATAAGATCTGTGGTTTTAAA-TCGGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTTCT
*
40328690 TCTTTCTGCTCTACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTATACTGA-AACTTC
65 TCTTTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTATACT-ACAACTTC
40328754 AG
129 AG
* * *
40328756 AAAGATAAGATCTGTGGTTTTAAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTGCTT
1 AGAGATAAGATCTGTGGTTTTAAATCGGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTTCTT
** * *
40328821 CTGTT-TGCTCCACTATAACTTCAGGGAGATAAGACTAGATGCAATCTGCTCTACTACAACTTCA
66 CT-TTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTATACTACAACTTCA
40328885 G
130 G
* * *
40328886 AGAGATAAGATCTATGGTTTTAAATCGGCTCCACTACAACTTTAGGGAGATAGGATTATTGGC-T
1 AGAGATAAGATCTGTGGTTTTAAATCGGCTCCACTGCAACTTCAGGGAGATAGG---ATTGGCTT
** *
40328950 -TT-AATCTGCTCCACTGCAATTTCAGGGAGATAA
63 CTTCTTTCTGCTCCACTGCAACTTCAGGGAGATAA
40328983 AATTCGCCAT
Statistics
Matches: 316, Mismatches: 32, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
129 4 0.01
130 299 0.95
131 7 0.02
133 6 0.02
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.31
Consensus pattern (130 bp):
AGAGATAAGATCTGTGGTTTTAAATCGGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTTCTT
CTTTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTATACTACAACTTCAG
Found at i:40328960 original size:260 final size:260
Alignment explanation
Indices: 40328498--40328982 Score: 717
Period size: 260 Copynumber: 1.9 Consensus size: 260
40328488 NNNNNNNNAG
* * *
40328498 AGATAAGATTTGTGGTTTTAAATCCACTCCACTGCAACTTCAGTGAAATAGGATTGACTTCTTCT
1 AGATAAGATCTGTGGTTTTAAATCCACTCCACTGCAACTTCAGGGAAATAGGATTGACTGCTTCT
* * ** * *
40328563 GTCTGCTCCACTGGAACTTCAGGGAGATAAGACTGGATGTGATCTGCTTTACTACAACTTTAGAG
66 GTCTGCTCCACTAGAACTTCAGGGAGATAAGACTAGATGCAATCTGCTCTACTACAACTTCAGAG
* * *
40328628 AGATAAGATCTGTGGTTTTAAATTCGCTCCACTGCAACTTTAGGGAGATAGGATTGGCTTCTTCT
131 AGATAAGATCTATGGTTTTAAATTCGCTCCACTACAACTTTAGGGAGATAGGATTGGCTTCTTCA
* *
40328693 TTCTGCTCTACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTATACTGAAACTTCAGAA
196 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTATACTGAAACTTCAGAA
** * *
40328758 AGATAAGATCTGTGGTTTTAAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGGCTGCTTCT
1 AGATAAGATCTGTGGTTTTAAATCCACTCCACTGCAACTTCAGGGAAATAGGATTGACTGCTTCT
* *
40328823 GTTTGCTCCACTATAACTTCAGGGAGATAAGACTAGATGCAATCTGCTCTACTACAACTTCAGAG
66 GTCTGCTCCACTAGAACTTCAGGGAGATAAGACTAGATGCAATCTGCTCTACTACAACTTCAGAG
40328888 AGATAAGATCTATGGTTTTAAA-TCGGCTCCACTACAACTTTAGGGAGATAGGATTATTGGC-T-
131 AGATAAGATCTATGGTTTTAAATTC-GCTCCACTACAACTTTAGGGAGATAGG---ATTGGCTTC
*
40328950 TT-AATCTGCTCCACTGCAATTTCAGGGAGATAA
192 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
40328983 AATTCGCCAT
Statistics
Matches: 200, Mismatches: 21, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
259 2 0.01
260 189 0.94
261 2 0.01
262 1 0.00
263 6 0.03
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.31
Consensus pattern (260 bp):
AGATAAGATCTGTGGTTTTAAATCCACTCCACTGCAACTTCAGGGAAATAGGATTGACTGCTTCT
GTCTGCTCCACTAGAACTTCAGGGAGATAAGACTAGATGCAATCTGCTCTACTACAACTTCAGAG
AGATAAGATCTATGGTTTTAAATTCGCTCCACTACAACTTTAGGGAGATAGGATTGGCTTCTTCA
ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTATACTGAAACTTCAGAA
Found at i:40331370 original size:18 final size:18
Alignment explanation
Indices: 40331339--40331380 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
40331329 TGATTTGGAA
40331339 GAAA-AATCTAAAAGAAT
1 GAAAGAATCTAAAAGAAT
*
40331356 GAAAGAATCTTAAAGAAT
1 GAAAGAATCTAAAAGAAT
40331374 GAAAGAA
1 GAAAGAA
40331381 CATTAGCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.62, C:0.05, G:0.17, T:0.17
Consensus pattern (18 bp):
GAAAGAATCTAAAAGAAT
Found at i:40333509 original size:16 final size:16
Alignment explanation
Indices: 40333475--40333509 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40333465 TTCTATAATG
*
40333475 AAATGCCATGCAGTCA
1 AAATGCCATGCAGTAA
*
40333491 AAATGTCATGCAGTAA
1 AAATGCCATGCAGTAA
40333507 AAA
1 AAA
40333510 AAACACAACA
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:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (16 bp):
AAATGCCATGCAGTAA
Found at i:40338129 original size:25 final size:25
Alignment explanation
Indices: 40338101--40338162 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
40338091 TTACAGTTCT
40338101 TATGAGCTTCCCGATATACAACTCA
1 TATGAGCTTCCCGATATACAACTCA
* *
40338126 TATGAGCTTCCCGTTATACAGCTCA
1 TATGAGCTTCCCGATATACAACTCA
* *
40338151 GAAGAGCTTCCC
1 TATGAGCTTCCC
40338163 ATTTACATGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (25 bp):
TATGAGCTTCCCGATATACAACTCA
Found at i:40345638 original size:25 final size:25
Alignment explanation
Indices: 40345610--40345665 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
40345600 AATGGCCCAC
40345610 ATGAGCTTCCCGATCTACA-GCTCGT
1 ATGAGCTTCCCG-TCTACATGCTCGT
*
40345635 ATGAGCTTCCCGTTTACATGCTCGT
1 ATGAGCTTCCCGTCTACATGCTCGT
40345660 ATGAGC
1 ATGAGC
40345666 ATACATGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.20, C:0.29, G:0.21, T:0.30
Consensus pattern (25 bp):
ATGAGCTTCCCGTCTACATGCTCGT
Found at i:40352883 original size:25 final size:24
Alignment explanation
Indices: 40352855--40352909 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
40352845 TTCTTGTTTT
40352855 TTTTTCAAATTTCAG-CTTCTCATAC
1 TTTTTCAAATTTCAGCCTT-TC-TAC
* *
40352880 TTTTCCCAAATTTCGGCCTTTCTAC
1 TTTT-TCAAATTTCAGCCTTTCTAC
40352905 TTTTT
1 TTTTT
40352910 TTTGACATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
25 11 0.44
26 11 0.44
27 3 0.12
ACGTcount: A:0.18, C:0.25, G:0.05, T:0.51
Consensus pattern (24 bp):
TTTTTCAAATTTCAGCCTTTCTAC
Found at i:40352883 original size:26 final size:25
Alignment explanation
Indices: 40352854--40352910 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
40352844 TTTCTTGTTT
40352854 TTTTTTCAAATTTCAG-CTTCTCATAC
1 TTTTTTCAAATTTCAGCCTT-TC-TAC
** *
40352880 TTTTCCCAAATTTCGGCCTTTCTAC
1 TTTTTTCAAATTTCAGCCTTTCTAC
40352905 TTTTTT
1 TTTTTT
40352911 TTGACATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
25 7 0.28
26 15 0.60
27 3 0.12
ACGTcount: A:0.18, C:0.25, G:0.05, T:0.53
Consensus pattern (25 bp):
TTTTTTCAAATTTCAGCCTTTCTAC
Found at i:40354731 original size:18 final size:18
Alignment explanation
Indices: 40354710--40354771 Score: 72
Period size: 18 Copynumber: 3.2 Consensus size: 18
40354700 GTATATACAC
40354710 AAAATTACACATATATAA
1 AAAATTACACATATATAA
40354728 AAAATTATCA-ATGTATATACA
1 AAAATTA-CACA--TATATA-A
40354749 CAAAATTACACATATATAA
1 -AAAATTACACATATATAA
40354768 AAAA
1 AAAA
40354772 ATTAAAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
18 12 0.32
19 3 0.08
20 12 0.32
21 3 0.08
22 8 0.21
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAATTACACATATATAA
Found at i:40354745 original size:40 final size:40
Alignment explanation
Indices: 40354690--40354771 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
40354680 AGAAATTGGG
40354690 AATTATCAATGTATATACACAAAATTACACATATATAAAA
1 AATTATCAATGTATATACACAAAATTACACATATATAAAA
40354730 AATTATCAATGTATATACACAAAATTACACATATATAAAA
1 AATTATCAATGTATATACACAAAATTACACATATATAAAA
40354770 AA
1 AA
40354772 ATTAAAAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.29
Consensus pattern (40 bp):
AATTATCAATGTATATACACAAAATTACACATATATAAAA
Found at i:40355322 original size:23 final size:24
Alignment explanation
Indices: 40355276--40355352 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 24
40355266 AGATATATAA
* **
40355276 AATAATACATAATAAA-TTTCAAT
1 AATAATACATGATAAACTTAAAAT
40355299 AATAATACATGA-AAACTTAAAAT
1 AATAATACATGATAAACTTAAAAT
* * **
40355322 AATTATATATGATAATTTTAAAAT
1 AATAATACATGATAAACTTAAAAT
40355346 AATAATA
1 AATAATA
40355353 TGCAATAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 3 0.07
23 26 0.59
24 15 0.34
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (24 bp):
AATAATACATGATAAACTTAAAAT
Found at i:40355360 original size:24 final size:24
Alignment explanation
Indices: 40355287--40355367 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
40355277 ATAATACATA
* * *
40355287 ATAAATTT-CAATAATAATACATG
1 ATAAATTTAAAATAATTATATATG
*
40355310 A-AAACTTAAAATAATTATATATG
1 ATAAATTTAAAATAATTATATATG
*
40355333 ATAATTTTAAAATAA-TA-ATATG
1 ATAAATTTAAAATAATTATATATG
40355355 CAATAAATTTAAA
1 --ATAAATTTAAA
40355368 CAATATTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
22 10 0.21
23 16 0.34
24 21 0.45
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.36
Consensus pattern (24 bp):
ATAAATTTAAAATAATTATATATG
Found at i:40357337 original size:134 final size:131
Alignment explanation
Indices: 40357111--40357359 Score: 338
Period size: 134 Copynumber: 1.9 Consensus size: 131
40357101 CACTATCATT
* *
40357111 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTCACTTCAATCCGCTCCACTGCAACTTCAG
1 AGTCTGCCCCAATGCAACTTCAGGGAGATAAGACTTCACTTCAATCCGCTCCACTGCAACTTCAG
* *
40357176 GGAGATAGAATTATTGGTTTTAATCTGCTCCACTACAAATTTAGGGAGATCAAATTTGCCATCTT
66 GGAGATAGAATTATTAGTTTTAATCTGCTCCACTACAAATTCAGGGAGATCAAATTTGCCATCTT
40357241 C
131 C
* * * *
40357242 AGTCTGCCCCAATGCAACTTTAGGGGGATAAGACTTGCTCTCTTCAATCTGCTCCACTGCAACTT
1 AGTCTGCCCCAATGCAACTTCAGGGAGATAAGAC-T--TCACTTCAATCCGCTCCACTGCAACTT
* * * * *
40357307 CAGGGTGATAAGACTTGTTAG-TTTAATCTGCTCCACTGCAACTTCAGGGAGAT
63 CAGGGAGAT-AGAATTATTAGTTTTAATCTGCTCCACTACAAATTCAGGGAGAT
40357360 AGGATTATTG
Statistics
Matches: 101, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
131 30 0.30
132 1 0.01
134 62 0.61
135 8 0.08
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (131 bp):
AGTCTGCCCCAATGCAACTTCAGGGAGATAAGACTTCACTTCAATCCGCTCCACTGCAACTTCAG
GGAGATAGAATTATTAGTTTTAATCTGCTCCACTACAAATTCAGGGAGATCAAATTTGCCATCTT
C
Found at i:40357617 original size:178 final size:178
Alignment explanation
Indices: 40356882--40358030 Score: 752
Period size: 178 Copynumber: 6.5 Consensus size: 178
40356872 GTATTCATCG
* * * *
40356882 TTTTAATCC-GCTCCACTGCAACTTCAGGGAGATAGGATTAGTAGCTTCAATCTGCTCCACTGCA
1 TTTTAATCCTGCCCCACTGCAACTTCAGGGAGATAAGATTACTCGCTTCAATCTGCTCCACTGCA
* * * * *
40356946 ACTTCAAGGAGATAAGA-TTGGTATCTTCAACCTGCTCCATTGCAACTTCAAGGAGATAAGG--T
66 ACTTCAGGGAGATAAGACTT-GTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGAT-AGGACT
* * * * * *
40357008 -TT-GATAT-GATCTTCTCTACTGCAACTTCAGAGAGATAAGATCTACAATTTATAGC
129 ATTGGCTTTAG-TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT----TGTA-A-C
* *** * ** * * ** *
40357063 -TTCAA-CCTATTCCACCGCAGTTTTAGGGAAATAAGATTCACTATCATT-AGTCTGCTCCACTG
1 TTTTAATCCTGCCCCACTGCAACTTCAGGGAGATAAGATT-ACTCGC-TTCAATCTGCTCCACTG
* * * *
40357125 CAACTTCAGGGAGATAAGAC-T-TCACTTCAATCCGCTCCACTGCAACTTCAGGGAGATAGAATT
64 CAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGACT
* * * * * * **
40357188 ATTGGTTTTAATCTGCTCCACTACAAATTTAGGGAGATCAA-ATTTGCCA-
129 ATTGGCTTTAGTCTGCTCCACTGCAACTTCAGGGAGAT-AAGACTTGTAAC
* * * * * * *
40357237 TCTTCAGT-CTGCCCCAATGCAACTTTAGGGGGATAAGACTTGCTCTCTTCAATCTGCTCCACTG
1 T-TTTAATCCTGCCCCACTGCAACTTCAGGGAGATAAGA-TTACTCGCTTCAATCTGCTCCACTG
* * * * *
40357301 CAACTTCAGGGTGATAAGACTTGTTAGTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATT
64 CAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGACT
* * * * * **
40357366 ATTGGCTTTAATCTGCTACACTACAACTTCAGGGTGATAAGATTTGCCA-
129 ATTGGCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAAC
* * * * * *
40357415 TATTCAGTCC-GCCCCACTGCAACTTCA-GGAGGATAAGACTTGCTCTCTTCAGTCTGCTCCATT
1 T-TTTAATCCTGCCCCACTGCAACTTCAGGGA-GATAAGA-TTACTCGCTTCAATCTGCTCCACT
* *
40357478 GCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCAACTTCAAGGAGATAGGAC
63 GCAACTTCAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGAC
*
40357543 TATTGGCTTTAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTAAC
128 TATTGGCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAAC
* * * * * * * * *
40357594 TTTTAATCCT-CTCCACCGCAACTTCAGGGAGATAGGATTATTGGCTTTAACCTACTCCATTGCA
1 TTTTAATCCTGCCCCACTGCAACTTCAGGGAGATAAGATTACTCGCTTCAATCTGCTCCACTGCA
* * * * * * * * *
40357658 ATTTCAGGGAGATAAGA-TTCGCCATCTTGAGTCTACCCCACTGCAACTTCAGGGGGATAAGACT
66 ACTTCAGGGAGATAAGACTT-G-TAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGACT
** * * * * *
40357722 -TGCTTTCTTCAGTCTGTTACACTGTAACTTTAGGGAGATAAGACTTGTAAC
129 AT--TGGCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAAC
* * * * * * * *
40357773 -TTTAAT-CTGCTCCACTGTAACTTTAGGGAGATAGGATTATTGGCTTTAATCTACTCCACTGCA
1 TTTTAATCCTGCCCCACTGCAACTTCAGGGAGATAAGATTACTCGCTTCAATCTGCTCCACTGCA
* *** * * * * *
40357836 ACTTCAGGGAGATAAGAATCACCATCTTCAGTCTGCCCCACTGCAACTTCAAAGG-GATAAGACT
66 ACTTCAGGGAGATAAGACT-TGTAACTTCAATCTGCTCCACTGCAACTTC-AGGGAGATAGGACT
** * *
40357900 -TGCTTTCTTCAGTCTGCTCC-CTTGCAACTTCAGGAAGATAAGACTTGTAAC
129 AT--TGGCTTTAGTCTGCTCCAC-TGCAACTTCAGGGAGATAAGACTTGTAAC
* * * * * * * * **
40357951 -TTTAATCC-GCTCTACTGTAACTTCAAGGAGATAGGATTATTGGCTTTAATCTATTCCACTGCA
1 TTTTAATCCTGCCCCACTGCAACTTCAGGGAGATAAGATTACTCGCTTCAATCTGCTCCACTGCA
40358014 ACTTCAGGGAGATAAGA
66 ACTTCAGGGAGATAAGA
40358031 TTCATCATCT
Statistics
Matches: 808, Mismatches: 127, Indels: 69
0.80 0.13 0.07
Matches are distributed among these distances:
175 2 0.00
176 64 0.08
177 48 0.06
178 517 0.64
179 82 0.10
180 27 0.03
181 39 0.05
182 27 0.03
183 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (178 bp):
TTTTAATCCTGCCCCACTGCAACTTCAGGGAGATAAGATTACTCGCTTCAATCTGCTCCACTGCA
ACTTCAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAGGACTAT
TGGCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAAC
Found at i:40357617 original size:445 final size:442
Alignment explanation
Indices: 40357109--40358030 Score: 1346
Period size: 445 Copynumber: 2.1 Consensus size: 442
40357099 TTCACTATCA
* *
40357109 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTCACTTCAATCCGCTCCACTGCAACTTC
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTAACTTCAATCCGCTCCACCGCAACTTC
* * * *
40357174 AGGGAGATAGAATTATTGGTTTTAATCTGCTCCACTACAAATTT-AGGGAGATCAA-ATTTGCCA
66 AGGGAGATAGAATTATTGGCTTTAACCTACTCCACTAC-AATTTCAGGGAGAT-AAGATTCGCCA
* * *
40357237 TCTTCAGTCTGCCCCAATGCAACTTTAGGGGGATAAGACTTGCTCTCTTCAATCTGCTCCACTGC
129 TCTTCAGTCTACCCCAATGCAACTTCAGGGGGATAAGACTTGCTCTCTTCAATCTGCTACACTGC
* * *
40357302 AACTTCAGGGTGATAAGACTTGTTAGTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTA
194 AACTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTA
* * * **
40357367 TTGGCTTTAATCTGCTACACTACAACTTCAGGGTGATAAGATTTGCCATATTCAGTCCGCCCCAC
259 TTGGCTTTAATCTACTACACTACAACTTCAGGGAGATAAGAATCACCATATTCAGTCCGCCCCAC
* *
40357432 TGCAACTTC-AGGAGGATAAGACTTGCTCTCTTCAGTCTGCTCCATTGCAACTTCAGGGAGATAA
324 TGCAACTTCAAAG-GGATAAGACTTGCTCTCTTCAGTCTGCTCCATTGCAACTTCAGGAAGATAA
*
40357496 GACTTGTAACTTTAATCTGCTCCACTGCAACTTCAAGGAGATAGGACTATTGGCT
388 GACTTGTAACTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGACTATTGGCT
* * *
40357551 TTAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTAACTTTTAATCCTCTCCACCGCAAC
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC-T-TAAC-TTCAATCCGCTCCACCGCAAC
* * *
40357616 TTCAGGGAGATAGGATTATTGGCTTTAACCTACTCCATTGCAATTTCAGGGAGATAAGATTCGCC
63 TTCAGGGAGATAGAATTATTGGCTTTAACCTACTCCACTACAATTTCAGGGAGATAAGATTCGCC
* * * * *
40357681 ATCTTGAGTCTACCCCACTGCAACTTCAGGGGGATAAGACTTGCTTTCTTCAGTCTGTTACACTG
128 ATCTTCAGTCTACCCCAATGCAACTTCAGGGGGATAAGACTTGCTCTCTTCAATCTGCTACACTG
* * * *
40357746 TAACTTTAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGTAACTTTAGGGAGATAGGATT
193 CAACTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATT
* * * *
40357811 ATTGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGAATCACCATCTTCAGTCTGCCCCA
258 ATTGGCTTTAATCTACTACACTACAACTTCAGGGAGATAAGAATCACCATATTCAGTCCGCCCCA
* *
40357876 CTGCAACTTCAAAGGGATAAGACTTGCTTTCTTCAGTCTGCTCCCTTGCAACTTCAGGAAGATAA
323 CTGCAACTTCAAAGGGATAAGACTTGCTCTCTTCAGTCTGCTCCATTGCAACTTCAGGAAGATAA
* * *
40357941 GACTTGTAACTTTAATCCGCTCTACTGTAACTTCAAGGAGATAGGATTATTGGCT
388 GACTTGTAACTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGACTATTGGCT
* **
40357996 TTAATCTATTCCACTGCAACTTCAGGGAGATAAGA
1 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
40358031 TTCATCATCT
Statistics
Matches: 426, Mismatches: 48, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
442 35 0.08
443 1 0.00
444 10 0.02
445 378 0.89
446 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (442 bp):
TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTAACTTCAATCCGCTCCACCGCAACTTC
AGGGAGATAGAATTATTGGCTTTAACCTACTCCACTACAATTTCAGGGAGATAAGATTCGCCATC
TTCAGTCTACCCCAATGCAACTTCAGGGGGATAAGACTTGCTCTCTTCAATCTGCTACACTGCAA
CTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTATT
GGCTTTAATCTACTACACTACAACTTCAGGGAGATAAGAATCACCATATTCAGTCCGCCCCACTG
CAACTTCAAAGGGATAAGACTTGCTCTCTTCAGTCTGCTCCATTGCAACTTCAGGAAGATAAGAC
TTGTAACTTTAATCCGCTCCACTGCAACTTCAAGGAGATAGGACTATTGGCT
Found at i:40357733 original size:267 final size:266
Alignment explanation
Indices: 40357287--40357852 Score: 837
Period size: 267 Copynumber: 2.1 Consensus size: 266
40357277 TGCTCTCTTC
* * *
40357287 AATCTGCTCCACTGCAACTTCAGGGTGATAAGACTTGTTAGTTTAATCTGCTCCACTGCAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAAGTTTAATCTGCTCCACCGCAACTTC
* * * *
40357352 AGGGAGATAGGATTATTGGCTTTAATCTGCTACACTACAACTTCAGGGTGATAAGATTTGCCATA
66 AGGGAGATAGGATTATTGGCTTTAACCTACTACACTACAACTTCAGGGAGATAAGATTCGCCATA
* * *
40357417 TTCAGTCCGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTCTCTTCAGTCTGCTCCATTGCAA
131 TTCAGTCCACCCCACTGCAACTTCAGGAGGATAAGACTTGCTCTCTTCAGTCTGCTACACTGCAA
40357482 CTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCAACTTCAAGGAGATAGGACTATT
196 CTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCAACTTCAAGGAGATAGGACTATT
40357547 GGCTTT
261 GGCTTT
* * *
40357553 AGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTAACTTTTAATCCT-CTCCACCGCAACT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAA-GTTTAAT-CTGCTCCACCGCAACT
* * * *
40357617 TCAGGGAGATAGGATTATTGGCTTTAACCTACTCCATTGCAATTTCAGGGAGATAAGATTCGCCA
64 TCAGGGAGATAGGATTATTGGCTTTAACCTACTACACTACAACTTCAGGGAGATAAGATTCGCCA
* * * * * * *
40357682 TCTTGAGTCTACCCCACTGCAACTTCAGGGGGATAAGACTTGCTTTCTTCAGTCTGTTACACTGT
129 TATTCAGTCCACCCCACTGCAACTTCAGGAGGATAAGACTTGCTCTCTTCAGTCTGCTACACTGC
* * * * *
40357747 AACTTTAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGTAACTTTAGGGAGATAGGATTA
194 AACTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCAACTTCAAGGAGATAGGACTA
40357812 TTGGCTTT
259 TTGGCTTT
*
40357820 AATCTACTCCACTGCAACTTCAGGGAGATAAGA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA
40357853 ATCACCATCT
Statistics
Matches: 266, Mismatches: 32, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
266 36 0.14
267 228 0.86
268 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (266 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAAGTTTAATCTGCTCCACCGCAACTTC
AGGGAGATAGGATTATTGGCTTTAACCTACTACACTACAACTTCAGGGAGATAAGATTCGCCATA
TTCAGTCCACCCCACTGCAACTTCAGGAGGATAAGACTTGCTCTCTTCAGTCTGCTACACTGCAA
CTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCAACTTCAAGGAGATAGGACTATT
GGCTTT
Found at i:40357975 original size:267 final size:267
Alignment explanation
Indices: 40357287--40357942 Score: 662
Period size: 267 Copynumber: 2.5 Consensus size: 267
40357277 TGCTCTCTTC
* * * * ** * * *
40357287 AATCTGCTCCACTGCAACTTCAGGGTGATAAGACTTGTTAGTTT-AAT-CTGCTCCACTGCAACT
1 AATCTACTCCACTGCAACTTCAGAGAGATAAGACATGCAACTTTCAATCCT-CCCCACCGCAACT
* * * * * * * * ** *
40357350 TCAGGGAGATAGGATTATTGGCTTTAATCTGCTACACTACAACTTCAGGGTGATAAGATTTGCCA
65 TCAAGGAGATAAGATTATTGGCTTCAACCTACTCCATTGCAACTTCAGGAAGATAAGATTCGCCA
* * * * *
40357415 TA-TTCAGTCCGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTCTCTTCAGTCTGCTCCATTG
130 -ACTTGAATCCACCCCACTGCAACTTCAGGAGGATAAGACTTGCTCTCTTCAGTCTGCTACACTG
40357479 CAACTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCAACTTCAAGGAGATAGGACT
194 CAACTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCAACTTCAAGGAGATAGGACT
40357544 ATTGGCTTT
259 ATTGGCTTT
* * * * * *
40357553 AGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTAACTTTTAATCCTCTCCACCGCAACTT
1 AATCTACTCCACTGCAACTTCAGAGAGATAAGACATGCAACTTTCAATCCTCCCCACCGCAACTT
* * * * * *
40357618 CAGGGAGATAGGATTATTGGCTTTAACCTACTCCATTGCAATTTCAGGGAGATAAGATTCGCCAT
66 CAAGGAGATAAGATTATTGGCTTCAACCTACTCCATTGCAACTTCAGGAAGATAAGATTCGCCAA
* * * * * *
40357683 CTTGAGTCTACCCCACTGCAACTTCAGGGGGATAAGACTTGCTTTCTTCAGTCTGTTACACTGTA
131 CTTGAATCCACCCCACTGCAACTTCAGGAGGATAAGACTTGCTCTCTTCAGTCTGCTACACTGCA
* * * * *
40357748 ACTTTAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGTAACTTTAGGGAGATAGGATTAT
196 ACTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCAACTTCAAGGAGATAGGACTAT
40357813 TGGCTTT
261 TGGCTTT
* * * *
40357820 AATCTACTCCACTGCAACTTCAGGGAGATAAGA-AT-CACCATCTTCAGT-CTGCCCCACTGCAA
1 AATCTACTCCACTGCAACTTCAGAGAGATAAGACATGCAAC-T-TTCAATCCT-CCCCACCGCAA
* * ** * *
40357882 CTTCAAAGG-GATAAGACTTGCTT-TCTTCAGTCTGCTCCCTTGCAACTTCAGGAAGATAAGA
63 CTTC-AAGGAGATAAGA-TT-ATTGGCTTCAACCTACTCCATTGCAACTTCAGGAAGATAAGA
40357943 CTTGTAACTT
Statistics
Matches: 331, Mismatches: 50, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
265 2 0.01
266 43 0.13
267 247 0.75
268 37 0.11
269 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (267 bp):
AATCTACTCCACTGCAACTTCAGAGAGATAAGACATGCAACTTTCAATCCTCCCCACCGCAACTT
CAAGGAGATAAGATTATTGGCTTCAACCTACTCCATTGCAACTTCAGGAAGATAAGATTCGCCAA
CTTGAATCCACCCCACTGCAACTTCAGGAGGATAAGACTTGCTCTCTTCAGTCTGCTACACTGCA
ACTTCAGGGAGATAAGACTTGTAACTTTAATCTGCTCCACTGCAACTTCAAGGAGATAGGACTAT
TGGCTTT
Found at i:40360208 original size:11 final size:11
Alignment explanation
Indices: 40360194--40360236 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
40360184 GGCCTCTCCT
40360194 TTTTCTTTTCC
1 TTTTCTTTTCC
40360205 TTTTCTTTTTCC
1 TTTTC-TTTTCC
*
40360217 TTCTCTTTTCC
1 TTTTCTTTTCC
40360228 TTTTCTTTT
1 TTTTCTTTT
40360237 TTCATCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTCTTTTCC
Found at i:40360237 original size:6 final size:6
Alignment explanation
Indices: 40360190--40360236 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
40360180 CTTTGGCCTC
* * *
40360190 TCCTTT TTCTTT TCCTTT TCTTTT TCCTTC T-CTTT TCCTTT T-CTTT
1 TCCTTT TCCTTT TCCTTT TCCTTT TCCTTT TCCTTT TCCTTT TCCTTT
40360236 T
1 T
40360237 TTCATCATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
5 9 0.26
6 25 0.74
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (6 bp):
TCCTTT
Found at i:40360250 original size:6 final size:6
Alignment explanation
Indices: 40360241--40360265 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40360231 TCTTTTTTCA
40360241 TCATTT TCATTT TCATTT TCATTT T
1 TCATTT TCATTT TCATTT TCATTT T
40360266 TTTAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TCATTT
Found at i:40360280 original size:27 final size:27
Alignment explanation
Indices: 40360250--40360306 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
40360240 ATCATTTTCA
*
40360250 TTTTCATTTTCAT-TTTTTTAAAATAT
1 TTTTTATTTTCATATTTTTTAAAATAT
**
40360276 TTTTTATTTTTTTATTTTTTAAAATAT
1 TTTTTATTTTCATATTTTTTAAAATAT
40360303 TTTT
1 TTTT
40360307 GATTGAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTTATTTTCATATTTTTTAAAATAT
Found at i:40366045 original size:20 final size:21
Alignment explanation
Indices: 40365994--40366045 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
40365984 TAAAGATATA
*
40365994 TAAAATAATACATAATAAATT
1 TAAAATAATACATAATAAACT
*
40366015 TGAATAATAATACATGA-AAACT
1 T-AA-AATAATACATAATAAACT
40366037 TAAAATAAT
1 TAAAATAAT
40366046 TATATATGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 6 0.22
21 3 0.11
22 7 0.26
23 11 0.41
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.31
Consensus pattern (21 bp):
TAAAATAATACATAATAAACT
Found at i:40366068 original size:24 final size:23
Alignment explanation
Indices: 40365994--40366088 Score: 81
Period size: 24 Copynumber: 4.2 Consensus size: 23
40365984 TAAAGATATA
40365994 TAAAATAATACATA-AT--AAATT
1 TAAAATAATA-ATATATGAAAATT
* * *
40366015 T-GAATAATAATACATGAAAACT
1 TAAAATAATAATATATGAAAATT
*
40366037 TAAAATAATTATATATGACAAATT
1 TAAAATAATAATATATGA-AAATT
**
40366061 TAAAATAATAATATGCGATAAATT
1 TAAAATAATAATATATGA-AAATT
40366085 TAAA
1 TAAA
40366089 CAATATTAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
19 3 0.05
20 9 0.15
21 1 0.02
22 5 0.08
23 13 0.22
24 28 0.47
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (23 bp):
TAAAATAATAATATATGAAAATT
Found at i:40375106 original size:12 final size:13
Alignment explanation
Indices: 40375089--40375117 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40375079 TTACTCGTCG
40375089 TTTTTTATTTT-A
1 TTTTTTATTTTCA
40375101 TTTTTTATTTTCA
1 TTTTTTATTTTCA
40375114 TTTT
1 TTTT
40375118 GTTTTTCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTATTTTCA
Found at i:40376000 original size:10 final size:9
Alignment explanation
Indices: 40375974--40376015 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
40375964 CAAGCTTACA
40375974 TTATTTT-T
1 TTATTTTAT
40375982 TTA-TTTAT
1 TTATTTTAT
40375990 TTCATTTTATT
1 TT-ATTTTA-T
40376001 TTATTTTAT
1 TTATTTTAT
40376010 TTATTT
1 TTATTT
40376016 GCTTATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 3 0.10
8 6 0.20
9 8 0.27
10 10 0.33
11 3 0.10
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (9 bp):
TTATTTTAT
Found at i:40376533 original size:107 final size:107
Alignment explanation
Indices: 40376404--40376846 Score: 615
Period size: 107 Copynumber: 4.1 Consensus size: 107
40376394 TTTATCCAAA
* *
40376404 TAAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAGTTCGAGAAAACGTGCCCTATCGTGCT
1 TAAAA-TTTCAAAATAAGGCAATATTTTACGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCT
40376469 GGGTTTCGATTTTTCGTTCGACCAAATACCTAAAATATCCTTT
65 GGGTTTCGATTTTTCGTTCGACCAAATACCTAAAATATCCTTT
* * **
40376512 TAAAATTTCAAAATAAAGCAATATTTTACGTTTGGAAGTTCGAGAAAACGTACCCTAATATGCTG
1 TAAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCTG
* * * *
40376577 GGTTTCAATTTTTTGTTCGACAAAATAGCTAAAAATATCCTTT
66 GGTTTCGATTTTTCGTTCGACCAAATACCT-AAAATATCCTTT
* *
40376620 TAAAATTTCAAAATAAGGCAATATTTCACGTTTGGAAGTTCGAGAAAATGTGCCCTAACGTGCTG
1 TAAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCTG
* *
40376685 GGTTTCGATTTTTTTTTCGTTCGACCAAATAGCTAAAATATCCTTC
66 GGTTTCGA----TTTTTCGTTCGACCAAATACCTAAAATATCCTTT
* *
40376731 TAAAATTTCAGAATAAGGCAATATTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
1 TAAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCTG
* * *
40376796 GGTTTCGATTTCTCGTT-GAACCATATAGCC--AAATATCCTCT
66 GGTTTCGATTTTTCGTTCG-ACCAAATA-CCTAAAATATCCTTT
40376837 T-AAATTTCAA
1 TAAAATTTCAA
40376847 TCCATGTCAT
Statistics
Matches: 298, Mismatches: 30, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
105 8 0.03
106 11 0.04
107 95 0.32
108 84 0.28
111 80 0.27
112 20 0.07
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Consensus pattern (107 bp):
TAAAATTTCAAAATAAGGCAATATTTTACGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCTG
GGTTTCGATTTTTCGTTCGACCAAATACCTAAAATATCCTTT
Found at i:40376797 original size:219 final size:216
Alignment explanation
Indices: 40376404--40376806 Score: 646
Period size: 219 Copynumber: 1.9 Consensus size: 216
40376394 TTTATCCAAA
** *
40376404 TAAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAGTTCGAGAAAACGTGCCCTATCGTGCT
1 TAAAATTTTCAAAATAAGGCAATATTTCACGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCT
*
40376469 GGGTTTCGATTTTTCGTTCGACCAAATACCTAAAATATCCTTTTAAAATTTCAAAATAAAGCAAT
66 GGGTTTCGATTTTTCGTTCGACCAAATACCTAAAATATCCTTCTAAAATTTCAAAATAAAGCAAT
* *
40376534 ATTTTACGTTTGGAAGTTCGAGAAAACGTACCCTAATATGCTGGGTTTCAATTTTTTGTTCGACA
131 ATTTTACGTTTGGAAATTCGAGAAAACGTACCCTAACATGCTGGGTTTCAATTTTTTGTTCGACA
40376599 AAATAGCTAAAAATATCCTTT
196 AAATAGCTAAAAATATCCTTT
*
40376620 TAAAA-TTTCAAAATAAGGCAATATTTCACGTTTGGAAGTTCGAGAAAATGTGCCCTAACGTGCT
1 TAAAATTTTCAAAATAAGGCAATATTTCACGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCT
* * *
40376684 GGGTTTCGATTTTTTTTTCGTTCGACCAAATAGCTAAAATATCCTTCTAAAATTTCAGAATAAGG
66 GGGTTTCGA----TTTTTCGTTCGACCAAATACCTAAAATATCCTTCTAAAATTTCAAAATAAAG
* * *
40376749 CAATATTTTACGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATTT
127 CAATATTTTACGTTTGGAAATTCGAGAAAACGTACCCTAACATGCTGGGTTTCAATTT
40376807 CTCGTTGAAC
Statistics
Matches: 170, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
215 64 0.38
216 5 0.03
219 101 0.59
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (216 bp):
TAAAATTTTCAAAATAAGGCAATATTTCACGTTTGGAAGTTCGAGAAAACGTGCCCTAACGTGCT
GGGTTTCGATTTTTCGTTCGACCAAATACCTAAAATATCCTTCTAAAATTTCAAAATAAAGCAAT
ATTTTACGTTTGGAAATTCGAGAAAACGTACCCTAACATGCTGGGTTTCAATTTTTTGTTCGACA
AAATAGCTAAAAATATCCTTT
Found at i:40377474 original size:19 final size:17
Alignment explanation
Indices: 40377397--40377461 Score: 103
Period size: 17 Copynumber: 3.8 Consensus size: 17
40377387 TGAACTGGGC
*
40377397 CGTGTGGGCCACACGGG
1 CGTGTGGGCCCCACGGG
40377414 CGTGTGGGCCCCACGGG
1 CGTGTGGGCCCCACGGG
*
40377431 TGTGTGGGCCCCACGGG
1 CGTGTGGGCCCCACGGG
*
40377448 TGTGTGGGCCCCAC
1 CGTGTGGGCCCCAC
40377462 ATGAGCGTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.08, C:0.32, G:0.45, T:0.15
Consensus pattern (17 bp):
CGTGTGGGCCCCACGGG
Found at i:40378777 original size:42 final size:42
Alignment explanation
Indices: 40378730--40378904 Score: 183
Period size: 42 Copynumber: 4.2 Consensus size: 42
40378720 AAAGCCCGAA
** **
40378730 GGTTGAATAGAAGCTCATGAGAGCTAAACGGAAACCCATAAG
1 GGTTGAATAGAAGCTCAAAAGAGCTAAACAAAAACCCATAAG
* ** * *
40378772 GGTTGAACAGAAGCTCGTAAGAGCTGAACGAAAACCCATAAG
1 GGTTGAATAGAAGCTCAAAAGAGCTAAACAAAAACCCATAAG
*
40378814 GGTTG-ATCTGAAGCTCAAAAGAGCTAAACAAAAACCCATAAG
1 GGTTGAAT-AGAAGCTCAAAAGAGCTAAACAAAAACCCATAAG
* * * * *
40378856 AGTTAAACT-GAAGCTCAAAAGAGCTGAACAGAAACCCATTAG
1 GGTTGAA-TAGAAGCTCAAAAGAGCTAAACAAAAACCCATAAG
40378898 GGTTGAA
1 GGTTGAA
40378905 CGGAAACTCA
Statistics
Matches: 112, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
41 1 0.01
42 109 0.97
43 1 0.01
44 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (42 bp):
GGTTGAATAGAAGCTCAAAAGAGCTAAACAAAAACCCATAAG
Found at i:40378813 original size:21 final size:21
Alignment explanation
Indices: 40378749--40378857 Score: 51
Period size: 21 Copynumber: 5.2 Consensus size: 21
40378739 GAAGCTCATG
* *
40378749 AGAGCTAAACGGAAACCCATA
1 AGAGCTGAACGAAAACCCATA
* * * * *
40378770 AGGGTTGAAC-AGAAGCTCGTA
1 AGAGCTGAACGA-AAACCCATA
40378791 AGAGCTGAACGAAAACCCATA
1 AGAGCTGAACGAAAACCCATA
* * * * * *
40378812 AGGGTTGATCTG-AAGCTCAAA
1 AGAGCTGAAC-GAAAACCCATA
* *
40378833 AGAGCTAAACAAAAACCCATA
1 AGAGCTGAACGAAAACCCATA
40378854 AGAG
1 AGAG
40378858 TTAAACTGAA
Statistics
Matches: 58, Mismatches: 26, Indels: 8
0.63 0.28 0.09
Matches are distributed among these distances:
21 56 0.97
22 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (21 bp):
AGAGCTGAACGAAAACCCATA
Found at i:40378871 original size:84 final size:84
Alignment explanation
Indices: 40378739--40378903 Score: 224
Period size: 84 Copynumber: 2.0 Consensus size: 84
40378729 AGGTTGAATA
** ** * * **
40378739 GAAGCTCATGAGAGCTAAACGGAAACCCATAAGGGTTGAACAGAAGCTCGTAAGAGCTGAAC-GA
1 GAAGCTCAAAAGAGCTAAACAAAAACCCATAAGAGTTAAACAGAAGCTCAAAAGAGCTGAACAG-
40378803 AAACCCATAAGGGTTGATCT
65 AAACCCATAAGGGTTGATCT
*
40378823 GAAGCTCAAAAGAGCTAAACAAAAACCCATAAGAGTTAAACTGAAGCTCAAAAGAGCTGAACAGA
1 GAAGCTCAAAAGAGCTAAACAAAAACCCATAAGAGTTAAACAGAAGCTCAAAAGAGCTGAACAGA
*
40378888 AACCCATTAGGGTTGA
66 AACCCATAAGGGTTGA
40378904 ACGGAAACTC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
84 69 0.99
85 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (84 bp):
GAAGCTCAAAAGAGCTAAACAAAAACCCATAAGAGTTAAACAGAAGCTCAAAAGAGCTGAACAGA
AACCCATAAGGGTTGATCT
Found at i:40378877 original size:21 final size:21
Alignment explanation
Indices: 40378821--40378880 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
40378811 AAGGGTTGAT
40378821 CTGAAGCTCAAAAGAGCTAAA
1 CTGAAGCTCAAAAGAGCTAAA
** * * * *
40378842 CAAAAACCCATAAGAGTTAAA
1 CTGAAGCTCAAAAGAGCTAAA
40378863 CTGAAGCTCAAAAGAGCT
1 CTGAAGCTCAAAAGAGCT
40378881 GAACAGAAAC
Statistics
Matches: 27, Mismatches: 12, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.20, G:0.17, T:0.15
Consensus pattern (21 bp):
CTGAAGCTCAAAAGAGCTAAA
Found at i:40381008 original size:4 final size:4
Alignment explanation
Indices: 40380999--40381028 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
40380989 AATAAACTAA
40380999 TATT TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TATT TA
40381029 ATCTAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:40384244 original size:20 final size:20
Alignment explanation
Indices: 40384219--40384258 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40384209 AATATTTTCC
*
40384219 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
40384239 AGTAAAACATTTTTCAGAAA
1 AGTAAAACATTTTACAGAAA
40384259 TCATTTTACG
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:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:40384260 original size:34 final size:35
Alignment explanation
Indices: 40384207--40384273 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
40384197 CAAACACCAG
*
40384207 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
40384242 AAAACATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
40384274 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:40386390 original size:21 final size:21
Alignment explanation
Indices: 40386345--40386390 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
40386335 TCATGATATC
****
40386345 AAAACTATGGGAAATTATTGT
1 AAAACTATGGGAAATTAAAAA
40386366 AAAACTATGGGAAATTAAAAA
1 AAAACTATGGGAAATTAAAAA
40386387 AAAA
1 AAAA
40386391 AATGTAAGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.04, G:0.15, T:0.24
Consensus pattern (21 bp):
AAAACTATGGGAAATTAAAAA
Found at i:40392264 original size:18 final size:18
Alignment explanation
Indices: 40392241--40392276 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40392231 ACGATACTCG
40392241 AAAAGCAAGACTCGCTCT
1 AAAAGCAAGACTCGCTCT
40392259 AAAAGCAAGACTCGCTCT
1 AAAAGCAAGACTCGCTCT
40392277 TTCTTTGTTT
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:0.39, C:0.28, G:0.17, T:0.17
Consensus pattern (18 bp):
AAAAGCAAGACTCGCTCT
Found at i:40392368 original size:5 final size:5
Alignment explanation
Indices: 40392358--40392397 Score: 80
Period size: 5 Copynumber: 8.0 Consensus size: 5
40392348 AAAAGAACCA
40392358 GGGAT GGGAT GGGAT GGGAT GGGAT GGGAT GGGAT GGGAT
1 GGGAT GGGAT GGGAT GGGAT GGGAT GGGAT GGGAT GGGAT
40392398 AGGAGGGAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.20, C:0.00, G:0.60, T:0.20
Consensus pattern (5 bp):
GGGAT
Found at i:40396793 original size:3 final size:3
Alignment explanation
Indices: 40396787--40396837 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
40396777 TCTCCTCCTA
* * * *
40396787 TTC TTC TTA TT- TTC TTC TTC TTC TTC TTT TTC TTT TTC TTC -TC TGC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
40396833 TTC TT
1 TTC TT
40396838 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:40396835 original size:26 final size:24
Alignment explanation
Indices: 40396787--40396848 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 24
40396777 TCTCCTCCTA
*
40396787 TTCTTCTTA-TTTTCTTCTTCTTC
1 TTCTTTTTATTTTTCTTCTTCTTC
*
40396810 TTCTTTTTCTTTTTCTTCTCTGCTTC
1 TTCTTTTTATTTTTCTTCT-T-CTTC
*
40396836 TTTTTTTTATTTT
1 TTCTTTTTATTTT
40396849 ACTGCCTAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 7 0.22
24 9 0.28
25 1 0.03
26 15 0.47
ACGTcount: A:0.03, C:0.21, G:0.02, T:0.74
Consensus pattern (24 bp):
TTCTTTTTATTTTTCTTCTTCTTC
Found at i:40397182 original size:2 final size:2
Alignment explanation
Indices: 40397175--40397200 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40397165 TTAGAAGCTT
40397175 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
40397201 GATGTGTGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40401606 original size:18 final size:18
Alignment explanation
Indices: 40401583--40401654 Score: 74
Period size: 18 Copynumber: 3.7 Consensus size: 18
40401573 GAAATGGCTA
40401583 AGATGAGAAATGAATATG
1 AGATGAGAAATGAATATG
40401601 AGATGAGAAATATTGAAT-TGG
1 AGATGAG-AA-A-TGAATAT-G
40401622 CAAAGATGAGAAATGAATATG
1 ---AGATGAGAAATGAATATG
40401643 AGATGAGAAATG
1 AGATGAGAAATG
40401655 TGATATGTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
18 19 0.41
19 2 0.04
20 2 0.04
21 12 0.26
22 2 0.04
23 2 0.04
24 7 0.15
ACGTcount: A:0.49, C:0.01, G:0.28, T:0.22
Consensus pattern (18 bp):
AGATGAGAAATGAATATG
Found at i:40401628 original size:42 final size:42
Alignment explanation
Indices: 40401568--40401653 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
40401558 TATGTGATTG
*
40401568 ATATTGAAATGGCTAAGATGAGAAATGAATATGAGATGAGAA
1 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAA
*
40401610 ATATTGAATTGGCAAAGATGAGAAATGAATATGAGATGAGAA
1 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAA
40401652 AT
1 AT
40401654 GTGATATGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.48, C:0.02, G:0.26, T:0.24
Consensus pattern (42 bp):
ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAA
Found at i:40401638 original size:21 final size:20
Alignment explanation
Indices: 40401572--40401639 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 20
40401562 TGATTGATAT
*
40401572 TGAAATGGCTAAGATGAGAAA
1 TGAATTGGC-AAGATGAGAAA
40401593 TGAATAT-G--AGATGAGAAATA
1 TGAAT-TGGCAAGATGAG-AA-A
40401613 TTGAATTGGCAAAGATGAGAAA
1 -TGAATTGGC-AAGATGAGAAA
40401635 TGAAT
1 TGAAT
40401640 ATGAGATGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 16
0.69 0.02 0.29
Matches are distributed among these distances:
18 7 0.18
19 2 0.05
20 2 0.05
21 16 0.42
22 2 0.05
23 2 0.05
24 7 0.18
ACGTcount: A:0.47, C:0.03, G:0.26, T:0.24
Consensus pattern (20 bp):
TGAATTGGCAAGATGAGAAA
Found at i:40402195 original size:25 final size:22
Alignment explanation
Indices: 40402161--40402205 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 22
40402151 TAGTTGAGGC
40402161 AATGTTGGTATGGTAGCTTAGCAT
1 AATGTTGGTAT-GT-GCTTAGCAT
40402185 AATGCTTGGTATGTGCTTAGC
1 AATG-TTGGTATGTGCTTAGC
40402206 TTCAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 6 0.30
25 7 0.35
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.38
Consensus pattern (22 bp):
AATGTTGGTATGTGCTTAGCAT
Found at i:40406938 original size:20 final size:21
Alignment explanation
Indices: 40406901--40406940 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
40406891 TCTTCCTTGG
*
40406901 AAGGTGGATATCATGATACCC
1 AAGGTGGATATCACGATACCC
*
40406922 AAGG-GGATATCGCGATACC
1 AAGGTGGATATCACGATACC
40406941 ACTGAAAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (21 bp):
AAGGTGGATATCACGATACCC
Found at i:40408563 original size:45 final size:45
Alignment explanation
Indices: 40408514--40408684 Score: 220
Period size: 45 Copynumber: 3.8 Consensus size: 45
40408504 ATACCAGAAA
*
40408514 CGAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGACATCACGATTCTAT
* * *
40408559 CGAGTAAGACCATGACTGAAAGATGTTATGGCATCATGATT-TCAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGACATCACGATTCT-AT
* * * *
40408604 TGAGTAAAACCATGAATGAAAGACGTTATGACATCACAATTCTAT
1 CGAGTAAGACCATGACTGAAAGACGTTATGACATCACGATTCTAT
* *
40408649 CAAGTAAGACCAT-AGCTGAAAGACGTCATGACATCA
1 CGAGTAAGACCATGA-CTGAAAGACGTTATGACATCA
40408685 TGAATCAAAG
Statistics
Matches: 109, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
44 2 0.02
45 106 0.97
46 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (45 bp):
CGAGTAAGACCATGACTGAAAGACGTTATGACATCACGATTCTAT
Found at i:40408626 original size:90 final size:90
Alignment explanation
Indices: 40408515--40408687 Score: 258
Period size: 90 Copynumber: 1.9 Consensus size: 90
40408505 TACCAGAAAC
* * * * *
40408515 GAGTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGAGTAAGACCAT-GACTGAA
1 GAGTAAAACCATGAATGAAAGACGTTATGACATCACAATTCTATCAAGTAAGACCATAG-CTGAA
* * *
40408579 AGATGTTATGGCATCATGATTTCATT
65 AGACGTCATGACATCATGATTTCATT
40408605 GAGTAAAACCATGAATGAAAGACGTTATGACATCACAATTCTATCAAGTAAGACCATAGCTGAAA
1 GAGTAAAACCATGAATGAAAGACGTTATGACATCACAATTCTATCAAGTAAGACCATAGCTGAAA
40408670 GACGTCATGACATCATGA
66 GACGTCATGACATCATGA
40408688 ATCAAAGAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 73 0.99
91 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (90 bp):
GAGTAAAACCATGAATGAAAGACGTTATGACATCACAATTCTATCAAGTAAGACCATAGCTGAAA
GACGTCATGACATCATGATTTCATT
Found at i:40408706 original size:90 final size:90
Alignment explanation
Indices: 40408518--40408706 Score: 238
Period size: 90 Copynumber: 2.1 Consensus size: 90
40408508 CAGAAACGAG
* * * * *
40408518 TAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGAGTAAGACCATGACTGAAAGAT
1 TAAGACCATGAATGAAAGACGTTATGACATCACAATTCTATCAAGTAAGACCATGACTGAAAGAC
* * * ** *
40408583 GTTATGGCATCATGATTTCATTGAG
66 GTCATGACATCATGATATCAAAGAA
*
40408608 TAAAACCATGAATGAAAGACGTTATGACATCACAATTCTATCAAGTAAGACCAT-AGCTGAAAGA
1 TAAGACCATGAATGAAAGACGTTATGACATCACAATTCTATCAAGTAAGACCATGA-CTGAAAGA
40408672 CGTCATGACATCATGA-ATCAAAGAAA
65 CGTCATGACATCATGATATCAAAG-AA
40408698 TAAGACCAT
1 TAAGACCAT
40408707 AGTTGAAAGA
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
89 5 0.06
90 79 0.94
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (90 bp):
TAAGACCATGAATGAAAGACGTTATGACATCACAATTCTATCAAGTAAGACCATGACTGAAAGAC
GTCATGACATCATGATATCAAAGAA
Found at i:40408862 original size:45 final size:45
Alignment explanation
Indices: 40408695--40408863 Score: 203
Period size: 45 Copynumber: 3.7 Consensus size: 45
40408685 TGAATCAAAG
* * * *
40408695 AAATAAGACCATAGTTGAAAGACACTATGGCAACACGACGAAAAAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCATCAAGACG--AGAAT
* * * * *
40408742 GAATAAGAACATGGTTGAAAGATACTATGGAATCAAGACAAGAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCATCAAGACGAGAAT
* * *
40408787 GAATAAAACCATGGTTGAAAGGCACTATGGCATCAAGACGAGAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCATCAAGACGAGAAT
*
40408832 AAATAAGACCATGGTTGAAAGACACCATGGCA
1 AAATAAGACCATGGTTGAAAGACACTATGGCA
40408864 CACTCCTATC
Statistics
Matches: 103, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
45 71 0.69
47 32 0.31
ACGTcount: A:0.47, C:0.15, G:0.21, T:0.17
Consensus pattern (45 bp):
AAATAAGACCATGGTTGAAAGACACTATGGCATCAAGACGAGAAT
Found at i:40411824 original size:24 final size:24
Alignment explanation
Indices: 40411791--40411844 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
40411781 GGGGTGTGAC
40411791 ATGAAATGTGGCACTTCAATGCAA
1 ATGAAATGTGGCACTTCAATGCAA
* *
40411815 TTGAAATGTGGCACTTCAGTGCAA
1 ATGAAATGTGGCACTTCAATGCAA
40411839 ATGAAA
1 ATGAAA
40411845 ATGGAACTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (24 bp):
ATGAAATGTGGCACTTCAATGCAA
Found at i:40412852 original size:29 final size:29
Alignment explanation
Indices: 40412820--40412881 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
40412810 CTTTGGTACC
*
40412820 TGTACTATT-TTTATTATCAGTTTGACCTT
1 TGTACT-TTATTTATTATCAGTTTGACATT
* * *
40412849 TGTAGTTTATTTTTTATTAGTTTGACATT
1 TGTACTTTATTTATTATCAGTTTGACATT
40412878 TGTA
1 TGTA
40412882 TTTTCATTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.21, C:0.08, G:0.13, T:0.58
Consensus pattern (29 bp):
TGTACTTTATTTATTATCAGTTTGACATT
Found at i:40413456 original size:20 final size:20
Alignment explanation
Indices: 40413433--40413470 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40413423 TTTGGGACTT
40413433 TTTTTCGAATTTTTTTATGG
1 TTTTTCGAATTTTTTTATGG
* *
40413453 TTTTTGGGATTTTTTTAT
1 TTTTTCGAATTTTTTTAT
40413471 ATTTTAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.03, G:0.16, T:0.68
Consensus pattern (20 bp):
TTTTTCGAATTTTTTTATGG
Found at i:40415092 original size:37 final size:37
Alignment explanation
Indices: 40415050--40415120 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
40415040 ATAGTCAGTG
40415050 ATCGAGTTTTAGGTCATCATTTGCGTTATGCTTAGTA
1 ATCGAGTTTTAGGTCATCATTTGCGTTATGCTTAGTA
40415087 ATCGAGTTTTAGGTCATCATTTGCGTTATGCTTA
1 ATCGAGTTTTAGGTCATCATTTGCGTTATGCTTA
40415121 CCATGTGACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.44
Consensus pattern (37 bp):
ATCGAGTTTTAGGTCATCATTTGCGTTATGCTTAGTA
Found at i:40419204 original size:20 final size:20
Alignment explanation
Indices: 40419181--40419220 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
40419171 AGTTGATTAG
*
40419181 AAATATTTTAAATTTAAATT
1 AAATAATTTAAATTTAAATT
**
40419201 AAATAATTTGTATTTAAATT
1 AAATAATTTAAATTTAAATT
40419221 TATTTATTAA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
AAATAATTTAAATTTAAATT
Done.