Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 88 of 91
Found at i:19940101 original size:19 final size:19
Alignment explanation
Indices: 19940079--19940226 Score: 251
Period size: 19 Copynumber: 7.7 Consensus size: 19
19940069 GCGACCAGAC
19940079 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
19940098 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
19940118 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
19940137 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
19940156 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
19940176 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
19940195 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
19940214 AATCGCAATGCGA
1 AATCGCAACGCGA
19940227 TTTTGGTTTC
Statistics
Matches: 122, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
19 86 0.70
20 36 0.30
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:19940122 original size:39 final size:38
Alignment explanation
Indices: 19939984--19940226 Score: 263
Period size: 39 Copynumber: 6.6 Consensus size: 38
19939974 TCTTTTGGTT
* *
19939984 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** * *
19940023 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGA
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** * *
19940057 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
19940090 GAAATGAAAATCGCAACCGCGAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCGCAACGC
19940129 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAA-CGC
*
19940168 GAAATAAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
19940206 GAAATGAAAATCGCAATGCGA
1 GAAATGAAAATCGCAACGCGA
19940227 TTTTGGTTTC
Statistics
Matches: 179, Mismatches: 16, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
33 41 0.23
34 15 0.08
35 2 0.01
38 42 0.23
39 65 0.36
40 14 0.08
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:19940142 original size:58 final size:58
Alignment explanation
Indices: 19940079--19940221 Score: 286
Period size: 58 Copynumber: 2.5 Consensus size: 58
19940069 GCGACCAGAC
19940079 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAAAATCGCAACGCGAAATGAA
19940137 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAAAATCGCAACGCGAAATGAA
19940195 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
19940222 TGCGATTTTG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 85 1.00
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.10
Consensus pattern (58 bp):
AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAAAATCGCAACGCGAAATGAA
Found at i:19940826 original size:20 final size:20
Alignment explanation
Indices: 19940801--19940853 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
19940791 GCGCTATGTA
19940801 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
19940821 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
19940841 TATCTCGTTGCGA
1 AATCGCGTTGCGA
19940854 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:19940913 original size:21 final size:21
Alignment explanation
Indices: 19940884--19940976 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
19940874 ATAGTAAGTA
19940884 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
19940905 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
19940925 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
19940946 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
19940966 TCGCATTGCGA
1 TCGCATTGCGA
19940977 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:19940914 original size:41 final size:41
Alignment explanation
Indices: 19940823--19940957 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
19940813 AAAGTCAGAA
* * * * ** *
19940823 TCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
19940863 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
19940905 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
19940946 TCGCGTTGCGAT
1 TCGCGTTGCGAT
19940958 TTACTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:19940958 original size:41 final size:41
Alignment explanation
Indices: 19940884--19940976 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
19940874 ATAGTAAGTA
19940884 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
19940925 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
19940966 TCGCATTGCGA
1 TCGCATTGCGA
19940977 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:19941546 original size:3 final size:3
Alignment explanation
Indices: 19941540--19941590 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
19941530 TTTATTGTTG
**
19941540 TTA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA AAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
19941585 TTA TTA
1 TTA TTA
19941591 CAAACATGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:19941556 original size:21 final size:21
Alignment explanation
Indices: 19941531--19941575 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
19941521 ACCCATTTTT
19941531 TTATTGTT-GTTATTATTATTA
1 TTATT-TTAGTTATTATTATTA
*
19941552 TTATTTTATTTATTATTATTA
1 TTATTTTAGTTATTATTATTA
19941573 TTA
1 TTA
19941576 AAATTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (21 bp):
TTATTTTAGTTATTATTATTA
Found at i:19941564 original size:15 final size:15
Alignment explanation
Indices: 19941525--19941571 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
19941515 TTTTTTACCC
*
19941525 ATTTT-TTTATTGTT
1 ATTTTATTTATTATT
*
19941539 GTTATTA-TTATTATT
1 ATT-TTATTTATTATT
19941554 ATTTTATTTATTATT
1 ATTTTATTTATTATT
19941569 ATT
1 ATT
19941572 ATTAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (15 bp):
ATTTTATTTATTATT
Found at i:19943200 original size:112 final size:112
Alignment explanation
Indices: 19943076--19943283 Score: 308
Period size: 112 Copynumber: 1.9 Consensus size: 112
19943066 ACATACTACA
** * *
19943076 TATTTATTTATTTATTAATATTGAAGGAAAGAGTTGTCTTAAAGCAACTAGAAACGCTTTTCTAA
1 TATTTATTTATTTATTAATATCAAAAGAAAGAGCTGTCTTAAAGCAACTAGAAACGCTTTTCTAA
*
19943141 TATTTTTAAATAAATAAATATCTTACTATATTAAAATAATTTTTTAT
66 TATTTCTAAATAAATAAATATCTTACTATATTAAAATAATTTTTTAT
* * * *
19943188 TATTTATTTATTTTTTAATATCAAAAGAAAGAGCTGTCTTAAAGCACCTAGAAACTCTTTTCTTA
1 TATTTATTTATTTATTAATATCAAAAGAAAGAGCTGTCTTAAAGCAACTAGAAACGCTTTTCTAA
* * *
19943253 TATTTCTAAATAAATAATTATGTTATTATAT
66 TATTTCTAAATAAATAAATATCTTACTATAT
19943284 ATATATATAT
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
112 84 1.00
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.45
Consensus pattern (112 bp):
TATTTATTTATTTATTAATATCAAAAGAAAGAGCTGTCTTAAAGCAACTAGAAACGCTTTTCTAA
TATTTCTAAATAAATAAATATCTTACTATATTAAAATAATTTTTTAT
Found at i:19943832 original size:26 final size:27
Alignment explanation
Indices: 19943780--19943837 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
19943770 TAATTCTTTC
*
19943780 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
19943808 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
19943834 TTTT
1 TTTT
19943838 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:19949145 original size:7 final size:7
Alignment explanation
Indices: 19949125--19949218 Score: 77
Period size: 7 Copynumber: 13.3 Consensus size: 7
19949115 TCCAGCAAAG
*
19949125 AAAGAAG
1 AAAGAAA
*
19949132 AAGGAAA
1 AAAGAAA
19949139 AAAGAAA
1 AAAGAAA
19949146 ATAA-AAA
1 A-AAGAAA
* *
19949153 AGATAAA
1 AAAGAAA
19949160 AAAGGAAA
1 AAA-GAAA
19949168 AATGAGAAA
1 AA--AGAAA
19949177 AAAGAAA
1 AAAGAAA
19949184 AAAGAAA
1 AAAGAAA
19949191 AAAG--A
1 AAAGAAA
19949196 AAAGAAA
1 AAAGAAA
*
19949203 AATGAAA
1 AAAGAAA
*
19949210 AATGAAA
1 AAAGAAA
19949217 AA
1 AA
19949219 TGGAGAAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
5 5 0.07
6 1 0.01
7 53 0.73
8 7 0.10
9 6 0.08
10 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (7 bp):
AAAGAAA
Found at i:19949177 original size:26 final size:25
Alignment explanation
Indices: 19949148--19949226 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 25
19949138 AAAAGAAAAT
19949148 AAAAAAGATAAAAAAGGAAAAATGAG
1 AAAAAAGATAAAAAA-GAAAAATGAG
*
19949174 AAAAAAG--AAAAAAGAAAAAAGA-
1 AAAAAAGATAAAAAAGAAAAATGAG
* *
19949196 AAAGAAAAATGAAAAATGAAAAATGGAG
1 AAA-AAAGAT-AAAAAAGAAAAAT-GAG
19949224 AAA
1 AAA
19949227 TTGAATCAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 3 0.07
23 11 0.26
24 6 0.14
26 18 0.42
27 2 0.05
28 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (25 bp):
AAAAAAGATAAAAAAGAAAAATGAG
Found at i:19949216 original size:19 final size:19
Alignment explanation
Indices: 19949121--19949217 Score: 72
Period size: 19 Copynumber: 4.8 Consensus size: 19
19949111 TTCATCCAGC
* *
19949121 AAAGAAAGAAG-AAGGAAA
1 AAAGAAAAAAGAAAAGAAA
19949139 AAAGAAAATAA-AAAAGATAAA
1 AAAGAAAA-AAGAAAAG--AAA
19949160 AAAGGAAAAATGAGAAAAAAGAAA
1 AAA-GAAAAA--AG--AAAAGAAA
19949184 AAAGAAAAAAGAAAAGAAA
1 AAAGAAAAAAGAAAAGAAA
* *
19949203 AATGAAAAATGAAAA
1 AAAGAAAAAAGAAAA
19949218 ATGGAGAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
18 7 0.11
19 26 0.40
21 9 0.14
22 5 0.08
23 7 0.11
24 6 0.09
26 5 0.08
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (19 bp):
AAAGAAAAAAGAAAAGAAA
Found at i:19952452 original size:76 final size:75
Alignment explanation
Indices: 19952326--19952505 Score: 220
Period size: 76 Copynumber: 2.4 Consensus size: 75
19952316 TTAACATCTG
* * * * * *
19952326 TATCAACAAATGTTGAGGCATGATGAAAAGCCCTTTTCAATCAGAATCAGGAATGTTGATGTATC
1 TATCAGCAAATGATGGGGCATGCTG-AAAGCCCCTTTCAATCAGAATCAGGAATATTGATGTATC
* *
19952391 CTGAATATTTA
65 CTGAACATTCA
*
19952402 TATCAGCAAAATGATGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATATTGATGTATT
1 TATCAGC-AAATGATGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATATTGATGTATC
* *
19952467 TTGAACGTTCA
65 CTGAACATTCA
19952478 TATCAGCAAAT-ACTGGGGCATGCT-AAAG
1 TATCAGCAAATGA-TGGGGCATGCTGAAAG
19952506 GCCCATATCA
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
74 5 0.05
75 15 0.16
76 56 0.62
77 15 0.16
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (75 bp):
TATCAGCAAATGATGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAGGAATATTGATGTATCC
TGAACATTCA
Found at i:19954454 original size:113 final size:113
Alignment explanation
Indices: 19954242--19954690 Score: 733
Period size: 113 Copynumber: 4.0 Consensus size: 113
19954232 TAGCAAAGAT
*
19954242 TCAAATCCATCAC--AATGGATCAACATTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTG
*
19954304 AAGAAGGAAGAAGAAGTTCATAATGAGAATAGCTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
*
19954353 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
19954418 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* *
19954466 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* ** *
19954531 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
** * * *
19954579 TTGAATTCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCTTCTGA
1 TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
19954644 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTG
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTG
19954691 AATGACTCTA
Statistics
Matches: 316, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
111 13 0.04
113 301 0.95
114 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
Found at i:19955046 original size:3 final size:3
Alignment explanation
Indices: 19955040--19955099 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
19955030 TTTATTGTTT
19955040 TTA TTA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
**
19955085 AAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
19955100 CAAATAGGCA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:19955066 original size:24 final size:24
Alignment explanation
Indices: 19955031--19955099 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
19955021 ACCCATTTTT
19955031 TTATTGTT-TTTATTATTATTATTA
1 TTATT-TTATTTATTATTATTATTA
19955055 TTATTTTATTTATTATTATTATTA
1 TTATTTTATTTATTATTATTATTA
** *
19955079 TTATTAAAATTATTATTATTA
1 TTATTTTATTTATTATTATTA
19955100 CAAATAGGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 2 0.05
24 39 0.95
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (24 bp):
TTATTTTATTTATTATTATTATTA
Found at i:19956420 original size:25 final size:24
Alignment explanation
Indices: 19956375--19956421 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
19956365 TTAATCATTA
**
19956375 TTTATTTATTATTTTGTTATTACT
1 TTTATTTATTATTTTCATATTACT
19956399 TTTATATTATTATTTTCATATTA
1 TTTAT-TTATTATTTTCATATTA
19956422 GTCACATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTATTTATTATTTTCATATTACT
Found at i:19956730 original size:112 final size:112
Alignment explanation
Indices: 19956602--19956807 Score: 322
Period size: 112 Copynumber: 1.8 Consensus size: 112
19956592 TATTTTAATA
** * *
19956602 TTTATTTATTTATTAATATTGAAGGAAAGAGTTGTCTTAAAGCAACTAGAAACCCTTTTCTAATA
1 TTTATTTATTTATTAATATCAAAAGAAAGAGCTGTCTTAAAGCAACTAGAAACCCTTTTCTAATA
*
19956667 TTTTTAAATAAATAAATATCTTACTATATTAAAATAATTTTTTATTT
66 TTTCTAAATAAATAAATATCTTACTATATTAAAATAATTTTTTATTT
* * *
19956714 TTTATTTATTTTTTAATATCAAAAGAAAGAGCTGTCTTAAAGCACCTAGAAACCCTTTTCTGATA
1 TTTATTTATTTATTAATATCAAAAGAAAGAGCTGTCTTAAAGCAACTAGAAACCCTTTTCTAATA
* *
19956779 TTTCTAAATAAATAAATATGTTATTATAT
66 TTTCTAAATAAATAAATATCTTACTATAT
19956808 ATATATATTT
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
112 84 1.00
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.44
Consensus pattern (112 bp):
TTTATTTATTTATTAATATCAAAAGAAAGAGCTGTCTTAAAGCAACTAGAAACCCTTTTCTAATA
TTTCTAAATAAATAAATATCTTACTATATTAAAATAATTTTTTATTT
Found at i:19957665 original size:14 final size:14
Alignment explanation
Indices: 19957646--19957686 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
19957636 AAATTTATAA
19957646 AATAATAATATTTT
1 AATAATAATATTTT
19957660 AATAATAATATTTT
1 AATAATAATATTTT
*
19957674 GATAAATAATATT
1 AAT-AATAATATT
19957687 AAATAAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
AATAATAATATTTT
Found at i:19957692 original size:14 final size:14
Alignment explanation
Indices: 19957645--19957692 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
19957635 TAAATTTATA
19957645 AAATAATAATATTT
1 AAATAATAATATTT
*
19957659 TAATAATAATATTT
1 AAATAATAATATTT
**
19957673 TGATAAATAATA-TT
1 AAAT-AATAATATTT
19957687 AAATAA
1 AAATAA
19957693 GTTATTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 2 0.07
14 20 0.69
15 7 0.24
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
AAATAATAATATTT
Found at i:19961389 original size:21 final size:21
Alignment explanation
Indices: 19961364--19961414 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
19961354 TAATTTGAAT
19961364 AAATATAATTAAAAAAAAG-AA
1 AAATATAA-TAAAAAAAAGCAA
*
19961385 AAATAGTAA-AAAAAAAGGCAA
1 AAATA-TAATAAAAAAAAGCAA
19961406 AAAT-TAATA
1 AAATATAATA
19961415 GAAATGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 3 0.12
20 9 0.35
21 11 0.42
22 3 0.12
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.18
Consensus pattern (21 bp):
AAATATAATAAAAAAAAGCAA
Found at i:19962609 original size:40 final size:40
Alignment explanation
Indices: 19962565--19962703 Score: 181
Period size: 40 Copynumber: 3.5 Consensus size: 40
19962555 ATGGTTGTCT
* *
19962565 CGTAGTTAAACGGTGTCAGATTAACAATTAATCGTCACAA
1 CGTAGTTAAACGGTGTCAGATCAACAATTAACCGTCACAA
* **
19962605 CGTAGTTAAACGGTGTCAGGTCAACGGTTAACCGTCACAA
1 CGTAGTTAAACGGTGTCAGATCAACAATTAACCGTCACAA
* * *
19962645 CGTAGTTAAACGGTGTCA-AGCAACAATTAACCCGCCACAT
1 CGTAGTTAAACGGTGTCAGATCAACAATTAA-CCGTCACAA
*
19962685 CGTAGTTAAATGGTGTCAG
1 CGTAGTTAAACGGTGTCAG
19962704 GTTAATAGTT
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 8 0.09
40 77 0.91
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (40 bp):
CGTAGTTAAACGGTGTCAGATCAACAATTAACCGTCACAA
Found at i:19962622 original size:21 final size:21
Alignment explanation
Indices: 19962598--19962662 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
19962588 ACAATTAATC
19962598 GTCACAACGTAGTTAAACGGT
1 GTCACAACGTAGTTAAACGGT
*
19962619 GTCAGGTCAACG--GTT-AAC--C
1 GTCA---CAACGTAGTTAAACGGT
19962638 GTCACAACGTAGTTAAACGGT
1 GTCACAACGTAGTTAAACGGT
19962659 GTCA
1 GTCA
19962663 AGCAACAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
16 5 0.15
18 3 0.09
19 7 0.21
21 11 0.32
22 3 0.09
24 5 0.15
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.23
Consensus pattern (21 bp):
GTCACAACGTAGTTAAACGGT
Found at i:19962715 original size:80 final size:80
Alignment explanation
Indices: 19962565--19962717 Score: 209
Period size: 80 Copynumber: 1.9 Consensus size: 80
19962555 ATGGTTGTCT
** * *
19962565 CGTAGTTAAACGGTGTCAGATTAACAATTAATCGTCACAACGTAGTTAAACGGTGTCAGGTCAAC
1 CGTAGTTAAACGGTGTCAGAGCAACAATTAACCGCCACAACGTAGTTAAACGGTGTCAGGTCAAC
*
19962630 GGTTAACCGTCACAA
66 AGTTAACCGTCACAA
* * *
19962645 CGTAGTTAAACGGTGTCA-AGCAACAATTAACCCGCCACATCGTAGTTAAATGGTGTCAGGTTAA
1 CGTAGTTAAACGGTGTCAGAGCAACAATTAA-CCGCCACAACGTAGTTAAACGGTGTCAGGTCAA
*
19962709 TAGTTAACC
65 CAGTTAACC
19962718 CGCGATATCT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 10 0.16
80 53 0.84
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.25
Consensus pattern (80 bp):
CGTAGTTAAACGGTGTCAGAGCAACAATTAACCGCCACAACGTAGTTAAACGGTGTCAGGTCAAC
AGTTAACCGTCACAA
Found at i:19964714 original size:37 final size:36
Alignment explanation
Indices: 19964673--19964757 Score: 82
Period size: 37 Copynumber: 2.3 Consensus size: 36
19964663 ATATATGTAC
*
19964673 AAAGAATAAAGAAAATAAACAAACGA-AACAAAGATAA
1 AAAGAATAAAG-AAATAAACAAAAGATAA-AAAGATAA
* * *
19964710 AAAGAGATCAAGATATAAATAAAAGATAAAAAGATAA
1 AAAGA-ATAAAGAAATAAACAAAAGATAAAAAGATAA
*
19964747 AATAAAATAAA
1 AA-AGAATAAA
19964758 ATAAAGGTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
37 30 0.77
38 9 0.23
ACGTcount: A:0.72, C:0.05, G:0.11, T:0.13
Consensus pattern (36 bp):
AAAGAATAAAGAAATAAACAAAAGATAAAAAGATAA
Found at i:19964735 original size:21 final size:20
Alignment explanation
Indices: 19964709--19964753 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
19964699 AACAAAGATA
**
19964709 AAAAGAGATCAAGATATAAAT
1 AAAAGAGAAAAAGATA-AAAT
*
19964730 AAAAGATAAAAAGATAAAAT
1 AAAAGAGAAAAAGATAAAAT
19964750 AAAA
1 AAAA
19964754 TAAAATAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.16
Consensus pattern (20 bp):
AAAAGAGAAAAAGATAAAAT
Found at i:19964763 original size:21 final size:21
Alignment explanation
Indices: 19964719--19964763 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
19964709 AAAAGAGATC
*
19964719 AAGATATAAATAAAAGATAAA
1 AAGATATAAATAAAAGAAAAA
*
19964740 AAGATA-AAATAAAATAAAATA
1 AAGATATAAATAAAAGAAAA-A
19964761 AAG
1 AAG
19964764 GTAATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (21 bp):
AAGATATAAATAAAAGAAAAA
Found at i:19964779 original size:16 final size:17
Alignment explanation
Indices: 19964755--19964789 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
19964745 AAAATAAAAT
*
19964755 AAAATAAAGGT-AATAA
1 AAAAGAAAGGTAAATAA
19964771 AAAAGAAAGGTAAATAA
1 AAAAGAAAGGTAAATAA
19964788 AA
1 AA
19964790 TAAGCACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (17 bp):
AAAAGAAAGGTAAATAA
Found at i:19964849 original size:19 final size:18
Alignment explanation
Indices: 19964809--19964853 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
19964799 TATAAGTAGA
* *
19964809 AAACAAAATAATTAAAAT
1 AAACAAAATAAGTAAAAC
*
19964827 AAACTAAAATAAGTAAACC
1 AAAC-AAAATAAGTAAAAC
19964846 AAACAAAA
1 AAACAAAA
19964854 GATATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.71, C:0.11, G:0.02, T:0.16
Consensus pattern (18 bp):
AAACAAAATAAGTAAAAC
Found at i:19966801 original size:65 final size:65
Alignment explanation
Indices: 19966730--19966981 Score: 220
Period size: 65 Copynumber: 3.7 Consensus size: 65
19966720 GTTTTTTTGT
* **
19966730 GTTTCAAGAGAAACTGTCTCGAGAGAGATGAAATTTGTTTAAAGGAAAATATATTCAAAGATTTC
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGGAAAATATATTCAAAGATTTC
* * * * * *
19966795 GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGT-CTCAAGAGA-G
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT-AAAGGAAAATATATTCAA-AGATT
*
19966858 AC
64 TC
* * * * *
19966860 AAAGCTTAGTTCTAAAAGAAACTGTCTCGAGAGGGACGAAATTTGTTTAAAGGAAAATAGATTCA
1 ---G--T--TTC-AAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGGAAAATATATTCA
*
19966925 AAGATTTT
58 AAGATTTC
* * *
19966933 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTGATTAAAGAGAAA
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAG-GAAA
19966982 CTGTCTCAAG
Statistics
Matches: 144, Mismatches: 30, Indels: 25
0.72 0.15 0.13
Matches are distributed among these distances:
65 73 0.51
66 19 0.13
68 2 0.01
70 2 0.01
72 14 0.10
73 34 0.24
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (65 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGGAAAATATATTCAAAGATTTC
Found at i:19966842 original size:36 final size:36
Alignment explanation
Indices: 19966785--19967220 Score: 314
Period size: 36 Copynumber: 12.3 Consensus size: 36
19966775 AAAATATATT
*
19966785 CAAAGATTTCGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAA-ATTT-GTTTCAAGAGAAACTGTCTCAAGAGAGA
*
19966823 CAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
* * * * *
19966859 CAAAGCTTAG-TTCTAAAAGAAACTGTCTCGAGAGGGA
1 CAAA-ATTTGTTTC-AAGAGAAACTGTCTCAAGAGAGA
* * *
19966896 CGAAATTTGTTTAAAG-GAAAATAGAT-TC-A-A-AG-
1 CAAAATTTGTTTCAAGAGAAACT-G-TCTCAAGAGAGA
* * *
19966928 ---ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
1 CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
* *
19966961 CAAAATTTGATTAAAGAGAAACTGTCTCAAGAGAGA
1 CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
* ** * *
19966997 CAAAATTTGTTTCAAAAGAATTTGTCTAAAGAGAGC
1 CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
** * * *
19967033 CAAAACTAAGTTCCAAAAGAAACTGTCTCAAGGGAGA
1 CAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
** * *
19967070 TGAAATTTGTTTCAAG-GAAAACAGAT-T-TA-A-AG-
1 CAAAATTTGTTTCAAGAG-AAACTG-TCTCAAGAGAGA
*** *
19967102 --TTTTTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
* *
19967136 CAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGA
1 CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
* * *
19967172 CAAAAATTATTTTAAGAGAAACTGTCTCAAGAGAGA
1 CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
19967208 CAAAACTTTGTTT
1 CAAAA-TTTGTTT
19967221 TGAGTAAATT
Statistics
Matches: 310, Mismatches: 62, Indels: 53
0.73 0.15 0.12
Matches are distributed among these distances:
28 1 0.00
29 14 0.05
30 23 0.07
31 3 0.01
32 3 0.01
33 5 0.02
34 1 0.00
35 8 0.03
36 184 0.59
37 64 0.21
38 4 0.01
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (36 bp):
CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
Found at i:19966986 original size:138 final size:138
Alignment explanation
Indices: 19966738--19967000 Score: 454
Period size: 138 Copynumber: 1.9 Consensus size: 138
19966728 GTGTTTCAAG
* *
19966738 AGAAACTGTCTCGAGAGAGATGAAATTTGTTTAAAGGAAAATATATTCAAAGATTTCGTTTCAAG
1 AGAAACTGTCTCGAGAGAGACGAAATTTGTTTAAAGGAAAATAGATTCAAAGATTTCGTTTCAAG
* * * *
19966803 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGCTTA
66 GGAAACTATCTCAAGAGAGACAAAATTTGATTAAAGAGAAACTGTCTCAAGAGAGACAAAGCTTA
19966868 GTTCTAAA
131 GTTCTAAA
* *
19966876 AGAAACTGTCTCGAGAGGGACGAAATTTGTTTAAAGGAAAATAGATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCGAGAGAGACGAAATTTGTTTAAAGGAAAATAGATTCAAAGATTTCGTTTCAAG
19966941 GGAAACTATCTCAAGAGAGACAAAATTTGATTAAAGAGAAACTGTCTCAAGAGAGACAAA
66 GGAAACTATCTCAAGAGAGACAAAATTTGATTAAAGAGAAACTGTCTCAAGAGAGACAAA
19967001 ATTTGTTTCA
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 117 1.00
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.25
Consensus pattern (138 bp):
AGAAACTGTCTCGAGAGAGACGAAATTTGTTTAAAGGAAAATAGATTCAAAGATTTCGTTTCAAG
GGAAACTATCTCAAGAGAGACAAAATTTGATTAAAGAGAAACTGTCTCAAGAGAGACAAAGCTTA
GTTCTAAA
Found at i:19968742 original size:95 final size:94
Alignment explanation
Indices: 19968543--19968805 Score: 294
Period size: 95 Copynumber: 2.7 Consensus size: 94
19968533 GGCTAGCTGA
* * * *
19968543 ATCCATAAAGCCAGGGTGTTTAACCAATTGCTCTAGAGGGACAAATTAATATCATTGTATAG-AT
1 ATCCATAAAGCC-GGGCGTTTAACCAATTGCTCTAGAGGGAC-AACTAA-AGC-TT-TATTGTAT
** *
19968607 ATTATAATCGTCTTTATCAGGCTAGCTGAATTTT
61 ATTATAATCACCTTTATCAGGCTAGCTGAATCTT
* *
19968641 ATCCATAAAGCCGCTGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCG-GGCGTTTAACCAATTGCTCTAGAGGGACAACTAAAGCTTTATTGTATATTA
*
19968706 TAATCACCTTTATCAGGTTAGCTGAATCTT
65 TAATCACCTTTATCAGGCTAGCTGAATCTT
* * * * * * *
19968736 ATCCATAAAGTCGGGGCATTTAACCAATTGATTTAGAGGGATAGCTTAAGCTTTATTGTATATAT
1 ATCCATAAAG-CCGGGCGTTTAACCAATTGCTCTAGAGGGACAACTAAAGCTTTATTGTATAT-T
19968801 ATAAT
64 ATAAT
19968806 ATTATAATGT
Statistics
Matches: 143, Mismatches: 18, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
94 4 0.03
95 86 0.60
96 10 0.07
97 5 0.03
98 38 0.27
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (94 bp):
ATCCATAAAGCCGGGCGTTTAACCAATTGCTCTAGAGGGACAACTAAAGCTTTATTGTATATTAT
AATCACCTTTATCAGGCTAGCTGAATCTT
Found at i:19972947 original size:19 final size:19
Alignment explanation
Indices: 19972920--19972956 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19972910 ATATAAATAG
*
19972920 AAAACAAAATAATTAAAAT
1 AAAACAAAATAAGTAAAAT
*
19972939 AAAATAAAATAAGTAAAA
1 AAAACAAAATAAGTAAAA
19972957 CAAATGAAAG
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:0.76, C:0.03, G:0.03, T:0.19
Consensus pattern (19 bp):
AAAACAAAATAAGTAAAAT
Found at i:19973065 original size:51 final size:50
Alignment explanation
Indices: 19972936--19973051 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 50
19972926 AAATAATTAA
* *
19972936 AATAA-AATAAAATAAGTAAAAC-AAATGAAAG--ATATATATATAATGAT
1 AATAATAATAAAA-AAGGAAAACAAAATAAAAGTAATATATATATAATGAT
19972983 AATAATAATAAAAAAGGGAAAACAAAATAAAAGTAATATATATATATAT-AT
1 AATAATAATAAAAAA-GGAAAACAAAATAAAAGTAATATATATATA-ATGAT
*
19973034 AAATAATGATGAAAAAAG
1 -AATAATAAT-AAAAAAG
19973052 AAATAATAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
47 7 0.12
48 13 0.22
49 8 0.14
51 13 0.22
52 11 0.19
53 6 0.10
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (50 bp):
AATAATAATAAAAAAGGAAAACAAAATAAAAGTAATATATATATAATGAT
Found at i:19981434 original size:11 final size:11
Alignment explanation
Indices: 19981418--19981447 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
19981408 CCGTAACTGC
19981418 TGTTAAAATTT
1 TGTTAAAATTT
19981429 TGTTAAAATTT
1 TGTTAAAATTT
19981440 TGTTAAAA
1 TGTTAAAA
19981448 GACACATGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (11 bp):
TGTTAAAATTT
Found at i:19981976 original size:26 final size:27
Alignment explanation
Indices: 19981930--19981980 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
19981920 AGATTTTCAA
19981930 TTTTTTTTAAAAAATATAATTTTAAGT
1 TTTTTTTTAAAAAATATAATTTTAAGT
*
19981957 TTTTATTTTAAATAA-A-AATTTTAA
1 TTTT-TTTTAAAAAATATAATTTTAA
19981981 AAGTACTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 5 0.23
28 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
TTTTTTTTAAAAAATATAATTTTAAGT
Found at i:19982203 original size:2 final size:2
Alignment explanation
Indices: 19982192--19982227 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
19982182 GAAGGACACC
19982192 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19982228 ATAGGATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:19985633 original size:20 final size:20
Alignment explanation
Indices: 19985605--19985674 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
19985595 AAATTTGTGC
19985605 ACCGATGCACACCCTAGTGT
1 ACCGATGCACACCCTAGTGT
*
19985625 ACCGGTGCACACCCTAGTGT
1 ACCGATGCACACCCTAGTGT
19985645 ACCGATGCACACCCTAGTGT
1 ACCGATGCACACCCTAGTGT
19985665 ACCGATGCAC
1 ACCGATGCAC
19985675 TAAGTCTTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (20 bp):
ACCGATGCACACCCTAGTGT
Found at i:19986372 original size:16 final size:16
Alignment explanation
Indices: 19986351--19986388 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
19986341 TCATAGGACT
19986351 AAAATAAAATG-AATA
1 AAAATAAAATGAAATA
*
19986366 GAAAATAAAGTGAAATA
1 -AAAATAAAATGAAATA
19986383 AAAATA
1 AAAATA
19986389 TTGCAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (16 bp):
AAAATAAAATGAAATA
Found at i:19986491 original size:15 final size:15
Alignment explanation
Indices: 19986449--19986491 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
19986439 TAAATGCTAT
19986449 AATATAAATAATAAAG
1 AATA-AAATAATAAAG
*
19986465 AATAAAAAAATAAA-
1 AATAAAATAATAAAG
19986479 AATAAAATTAATA
1 AATAAAA-TAATA
19986492 CTTGAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 13 0.54
16 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (15 bp):
AATAAAATAATAAAG
Found at i:19987639 original size:37 final size:37
Alignment explanation
Indices: 19987589--19987673 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
19987579 TTGATGTTGA
* *
19987589 TCTATATCCTTTCTCTCTATTAAAAATATTGAGCTGC
1 TCTATCTCCTTTCTCTATATTAAAAATATTGAGCTGC
* * *
19987626 TCTATCTCCTTTCTTTATGTTAAAAATGTTGAGCTGC
1 TCTATCTCCTTTCTCTATATTAAAAATATTGAGCTGC
19987663 TCTATCTCCTT
1 TCTATCTCCTT
19987674 CTACGATAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.46
Consensus pattern (37 bp):
TCTATCTCCTTTCTCTATATTAAAAATATTGAGCTGC
Found at i:19988038 original size:120 final size:122
Alignment explanation
Indices: 19987690--19988254 Score: 814
Period size: 123 Copynumber: 4.6 Consensus size: 122
19987680 TAGAGTCAAA
** * * *
19987690 TGAATAAGTTCTTCAGATTATGAACTTCTGATTTCTCTTCGGATGAGTTCTTCTTATTACGAACT
1 TGAATAAGTTCTTCAGATTATGAACTT-TTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAACT
* * *
19987755 TGTTCTGAAAATGACGATGA-TGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGT
65 TCTTCTGGAAATGACGAT-ACTACTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGT
* * *
19987813 TGAATAAGTTCTTCAAATTATGAACTTTT-TTCCTCTTCAGACGAGTTCTTTTTATTATGAACTT
1 TGAATAAGTTCTTCAGATTATGAACTTTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAACTT
* * * * *
19987877 CTTATGGAAATGACGATGCTGCTCTATCTCCTTCTGTGATAGAGTCAAGAAAAAGGT
66 CTTCTGGAAATGACGATACTACTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGT
*
19987934 TGAATAAGTTCTTCAGATTATGAAC-TTT-TTCCACTTCAGACGAGTTCTTCTTATTACGAACTT
1 TGAATAAGTTCTTCAGATTATGAACTTTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAACTT
* * *
19987997 CTTCTGGAAATGACGATACTACTCTATCTCCTTATTCGATAGAGTCAAGTAAAAGGT
66 CTTCTGGAAATGACGATACTACTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGT
* *
19988054 TGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTATTATTACGAACT
1 TGAATAAGTTCTTCAGATTATGAAC-TTTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAACT
* * *
19988119 TCTTCTGGAAATGATGATGCTACTCTATCTCCTTCTGCGATAAAGTCAAGCAAAAGGT
65 TCTTCTGGAAATGACGATACTACTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGT
*
19988177 TGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGACGAGTTCTTCTTATTATGAACT
1 TGAATAAGTTCTTCAGATTATGAAC-TTTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAACT
* *
19988242 TCTTGTGAAAATG
65 TCTTCTGGAAATG
19988255 TTAATCCATC
Statistics
Matches: 400, Mismatches: 38, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
120 110 0.28
121 104 0.26
122 4 0.01
123 182 0.46
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (122 bp):
TGAATAAGTTCTTCAGATTATGAACTTTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAACTT
CTTCTGGAAATGACGATACTACTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGT
Found at i:19989013 original size:15 final size:15
Alignment explanation
Indices: 19988995--19989030 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
19988985 TAATTTCCAG
*
19988995 ATGCCTAATATCAAC
1 ATGCATAATATCAAC
19989010 ATGCATAATATCAAC
1 ATGCATAATATCAAC
19989025 ATGCAT
1 ATGCAT
19989031 TTAAGCTGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (15 bp):
ATGCATAATATCAAC
Found at i:19989125 original size:8 final size:7
Alignment explanation
Indices: 19989112--19989178 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 7
19989102 CTTGACCCTC
19989112 CTTTTTAT
1 CTTTTT-T
19989120 CTTTTTT
1 CTTTTTT
19989127 CTTTTCTT
1 CTTTT-TT
19989135 -TTCTTTT
1 CTT-TTTT
*
19989142 CTCTTTT
1 CTTTTTT
*
19989149 CTTTACTT
1 CTTT-TTT
19989157 -TTTTTT
1 CTTTTTT
19989163 CTTTTTT
1 CTTTTTT
*
19989170 -TTTCTT
1 CTTTTTT
19989176 CTT
1 CTT
19989179 AAAGCACAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
6 7 0.15
7 28 0.58
8 13 0.27
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (7 bp):
CTTTTTT
Found at i:19989133 original size:5 final size:5
Alignment explanation
Indices: 19989123--19989175 Score: 63
Period size: 5 Copynumber: 10.4 Consensus size: 5
19989113 TTTTTATCTT
* *
19989123 TTTTC TTTTC TTTTC TTTTCTC TTTTC TTTAC TTTT- TTTTC TTTTT TTTTC
1 TTTTC TTTTC TTTTC -TTT-TC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
19989174 TT
1 TT
19989176 CTTAAAGCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 4 0.10
5 29 0.71
6 6 0.15
7 2 0.05
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:19996429 original size:15 final size:15
Alignment explanation
Indices: 19996409--19996467 Score: 91
Period size: 15 Copynumber: 3.9 Consensus size: 15
19996399 CTTAATGAAT
19996409 AATGTATGAAAAATG
1 AATGTATGAAAAATG
*
19996424 AATGTATGCAAAATG
1 AATGTATGAAAAATG
*
19996439 AATGTATGCAAAATG
1 AATGTATGAAAAATG
19996454 AATGTATGCAAAAA
1 AATGTATG-AAAAA
19996468 GGTGTTGATA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 37 0.90
16 4 0.10
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGTATGAAAAATG
Found at i:19996445 original size:30 final size:30
Alignment explanation
Indices: 19996409--19996466 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
19996399 CTTAATGAAT
19996409 AATGTATGAAAAATGAATGTATGCAAAATG
1 AATGTATGAAAAATGAATGTATGCAAAATG
*
19996439 AATGTATGCAAAATGAATGTATGCAAAA
1 AATGTATGAAAAATGAATGTATGCAAAA
19996467 AGGTGTTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.26
Consensus pattern (30 bp):
AATGTATGAAAAATGAATGTATGCAAAATG
Found at i:20002960 original size:21 final size:21
Alignment explanation
Indices: 20002936--20002975 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
20002926 AAGACTTTAT
20002936 TTTCAAAATAT-AAAAATGATA
1 TTTCAAAAT-TGAAAAATGATA
20002957 TTTCAAAATTGAAAAATGA
1 TTTCAAAATTGAAAAATGA
20002976 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTGAAAAATGATA
Found at i:20003724 original size:27 final size:27
Alignment explanation
Indices: 20003686--20003744 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
20003676 AGGATTCAAT
20003686 GTCATGTTTGAAACTAATGGTTGTAAA
1 GTCATGTTTGAAACTAATGGTTGTAAA
20003713 GTCATGTTTGAAACTAATGGTTGTAAA
1 GTCATGTTTGAAACTAATGGTTGTAAA
20003740 GTCAT
1 GTCAT
20003745 TGACATTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.37
Consensus pattern (27 bp):
GTCATGTTTGAAACTAATGGTTGTAAA
Found at i:20006850 original size:23 final size:22
Alignment explanation
Indices: 20006820--20006900 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
20006810 ACACTAGTTA
*
20006820 GTGCATCGAAGCATCCCTTGAAT
1 GTGCATCGATGCA-CCCTTGAAT
* * *
20006843 GTGCATCGATTCA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
20006864 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
20006887 GTGCATCGATGCAC
1 GTGCATCGATGCAC
20006901 TCTGTTGTGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.36
23 30 0.64
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:20015963 original size:2 final size:2
Alignment explanation
Indices: 20015956--20016136 Score: 124
Period size: 2 Copynumber: 95.5 Consensus size: 2
20015946 CGAGACTTTC
*
20015956 TA TA TA TA TA TA TA TA TA TA T- TA TA T- TG TA T- TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
20015994 TA GTT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
20016036 TA GTA TC TA T- TA TA TA T- TA TA TA TA -A TA TA GTA -A T- TA TGG
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA T-A
* * *
20016076 TA TA TA T- TA TA -A TA TGG GA TT TA TA T- TA TA TA T- TA TA -A
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
*
20016114 TA TT TA TA CTA TA -A TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA T
20016137 TAAATATAAC
Statistics
Matches: 142, Mismatches: 15, Indels: 44
0.71 0.07 0.22
Matches are distributed among these distances:
1 16 0.11
2 118 0.83
3 8 0.06
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20016351 original size:20 final size:19
Alignment explanation
Indices: 20016313--20016352 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20016303 AAAATGTTTT
**
20016313 TATGAATAGTATTATACTG
1 TATGAATAGTACGATACTG
20016332 TATGAATAGTACCGATACTG
1 TATGAATAGTA-CGATACTG
20016352 T
1 T
20016353 GCAAATAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (19 bp):
TATGAATAGTACGATACTG
Found at i:20016359 original size:20 final size:20
Alignment explanation
Indices: 20016336--20016389 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
20016326 ATACTGTATG
*
20016336 AATAGTACCGATACTGTGCA
1 AATAGTACCGATACTATGCA
* *
20016356 AATAGTATCAATACTATGCA
1 AATAGTACCGATACTATGCA
20016376 AATAGTACCGATAC
1 AATAGTACCGATAC
20016390 AATGTGAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (20 bp):
AATAGTACCGATACTATGCA
Found at i:20017413 original size:23 final size:23
Alignment explanation
Indices: 20017382--20017425 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
20017372 AATACATATA
20017382 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCGAAGGACCACGTAGAAT
*
20017405 TGTCTCGAAGGACCACGTAGA
1 TGTCCCGAAGGACCACGTAGA
20017426 CCCTCGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACGTAGAAT
Found at i:20019384 original size:19 final size:21
Alignment explanation
Indices: 20019343--20019398 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 21
20019333 TATAATATAT
20019343 ATATAATATAGTATATTTAAAA
1 ATAT-ATATAGTATATTTAAAA
*
20019365 ATATATATAGT-T-TTTGAAA
1 ATATATATAGTATATTTAAAA
*
20019384 ATATATGTAGTATAT
1 ATATATATAGTATAT
20019399 ATATATTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 16 0.53
20 2 0.07
21 8 0.27
22 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (21 bp):
ATATATATAGTATATTTAAAA
Found at i:20019423 original size:26 final size:25
Alignment explanation
Indices: 20019394--20019461 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
20019384 ATATATGTAG
* *
20019394 TATATATATATTATATAGTTTTCAAT
1 TATATATATATTATATAGTATGC-AT
* *
20019420 TATATACATAATATATAGTATGCAT
1 TATATATATATTATATAGTATGCAT
20019445 TATATATATATATATAT
1 TATATATATAT-TATAT
20019462 TCAAAGACCC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 11 0.31
26 24 0.69
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (25 bp):
TATATATATATTATATAGTATGCAT
Found at i:20019988 original size:23 final size:23
Alignment explanation
Indices: 20019961--20020026 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
20019951 CAAATTAAGT
*
20019961 CTCAATCAAAACAAAAAAGGAAA
1 CTCAATCAAAACAAAAAAAGAAA
*
20019984 CTCAA--AAAA-AAAAAAATACAA
1 CTCAATCAAAACAAAAAAAGA-AA
* *
20020005 C-GAATCAAAACAAAAAATGAAA
1 CTCAATCAAAACAAAAAAAGAAA
20020027 AGATGTCTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
20 9 0.26
21 7 0.21
22 6 0.18
23 12 0.35
ACGTcount: A:0.70, C:0.15, G:0.06, T:0.09
Consensus pattern (23 bp):
CTCAATCAAAACAAAAAAAGAAA
Found at i:20022305 original size:18 final size:19
Alignment explanation
Indices: 20022282--20022323 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
20022272 TTTTGGTATT
20022282 GATACTCAT-GGT-ATTATC
1 GATACT-ATAGGTAATTATC
20022300 GATACTATAGGTAGATTATC
1 GATACTATAGGTA-ATTATC
20022320 GATA
1 GATA
20022324 TTTCCAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 2 0.10
18 9 0.43
20 10 0.48
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (19 bp):
GATACTATAGGTAATTATC
Found at i:20031274 original size:18 final size:18
Alignment explanation
Indices: 20031251--20031299 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
20031241 CCATTTTTGA
20031251 TATCAACACTTATGG-GAG
1 TATCAACACTTA-GGAGAG
*
20031269 TATCAATACTGTAGGTAGAG
1 TATCAACACT-TAGG-AGAG
20031289 TATCAACACTT
1 TATCAACACTT
20031300 CCGGTAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 11 0.42
19 3 0.12
20 12 0.46
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (18 bp):
TATCAACACTTAGGAGAG
Found at i:20031405 original size:20 final size:20
Alignment explanation
Indices: 20031380--20031423 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
20031370 TAGTATTGAT
20031380 ATAATCCTA-TTAAAGTATCG
1 ATAAT-CTAGTTAAAGTATCG
*
20031400 ATAATCTAGGTTAGAGTATCG
1 ATAATCTA-GTTAAAGTATCG
20031421 ATA
1 ATA
20031424 CTAAGTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 5 0.24
21 13 0.62
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (20 bp):
ATAATCTAGTTAAAGTATCG
Found at i:20032636 original size:136 final size:138
Alignment explanation
Indices: 20032385--20032639 Score: 417
Period size: 136 Copynumber: 1.9 Consensus size: 138
20032375 CAATTTTCCA
*
20032385 AACTCATGTTTATTTTATGGATTTGATTTTATCATATTAAATACCATTTTTTAAAAGAAAAAAAA
1 AACTCATGTTTATTTTATGGATTTGATTTAATCATATTAAATACCA-TTTTTAAAAGAAAAAAAA
*
20032450 TTGGGTTAGCCACTTCGGTGGTCTTGTGTGACATTCTAATCAATTGATTTTCGGGTTAGATCGAA
65 TTGGGTTAGCCACTTCGGTGGTCTCGTGTGACATTCTAATCAATTGATTTTCGGGTTAGATCGAA
20032515 TTAGGGTGT
130 TTAGGGTGT
* *
20032524 AACTCATGTTTATTTTATGGATTTGATTTAATCATGTTAAATATCA-TTTTAAAA-ATAAAAAAA
1 AACTCATGTTTATTTTATGGATTTGATTTAATCATATTAAATACCATTTTTAAAAGA-AAAAAAA
* *
20032587 -TGGGTTATCCACTTCGGTGGTCTCGTGTGACGTTCTAATCAATTGATTTTCGG
65 TTGGGTTAGCCACTTCGGTGGTCTCGTGTGACATTCTAATCAATTGATTTTCGG
20032640 ATCGGACCAA
Statistics
Matches: 109, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
136 51 0.47
137 15 0.14
139 43 0.39
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (138 bp):
AACTCATGTTTATTTTATGGATTTGATTTAATCATATTAAATACCATTTTTAAAAGAAAAAAAAT
TGGGTTAGCCACTTCGGTGGTCTCGTGTGACATTCTAATCAATTGATTTTCGGGTTAGATCGAAT
TAGGGTGT
Found at i:20035212 original size:136 final size:137
Alignment explanation
Indices: 20034994--20035266 Score: 424
Period size: 136 Copynumber: 2.0 Consensus size: 137
20034984 CAATTGTCCA
* *
20034994 AACTCATATTTATTTTATGGATTTGTTTTATCATGTTAAATACCATTTTTTAAAAGAAAAAAATT
1 AACTCATATTTATTTTATGGATTTGTTTAATCATGTTAAATACCATTTTTAAAAAGAAAAAAATT
* * * *
20035059 GGGTTAGCCACTTCGGTGGTCTTGTGTGACATTCTAATCAATTGATTTTCGGGTTGGACCGAATT
66 GGGTTAGCCACTTCGGTGGTCTCGTGTGACATTCTAATCAATTGATTTTCGGATCGGACCAAATT
20035124 AGGGTGT
131 AGGGTGT
* * *
20035131 AACTCATGTTTATTTTATGGATTTGATTTAATCATGTTAAATATCA-TTTTAAAAATAAAAAAA-
1 AACTCATATTTATTTTATGGATTTG-TTTAATCATGTTAAATACCATTTTTAAAAAGAAAAAAAT
* *
20035194 TGGGTTATCCACTTCGGTGGTCTCGTGTGACGTTCTAATCAATTGATTTTCGGATCGGACCAAAT
65 TGGGTTAGCCACTTCGGTGGTCTCGTGTGACATTCTAATCAATTGATTTTCGGATCGGACCAAAT
20035259 TAGGGTGT
130 TAGGGTGT
20035267 CACAGATTGT
Statistics
Matches: 124, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
136 67 0.54
137 39 0.31
138 18 0.15
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (137 bp):
AACTCATATTTATTTTATGGATTTGTTTAATCATGTTAAATACCATTTTTAAAAAGAAAAAAATT
GGGTTAGCCACTTCGGTGGTCTCGTGTGACATTCTAATCAATTGATTTTCGGATCGGACCAAATT
AGGGTGT
Found at i:20039057 original size:374 final size:375
Alignment explanation
Indices: 20038471--20039162 Score: 899
Period size: 374 Copynumber: 1.8 Consensus size: 375
20038461 CTTCGAAATA
* * *
20038471 AAGGATATTGGACTAGATGAAGACCCAAGATCGACTGCGATTTAACTTAACTCAACGACAAGGAG
1 AAGGATATTAGACTAGAAGAAGACCCAAGATCGACTACGATTTAACTTAACTCAACGACAAGGAG
* * * *
20038536 ATATTTCCCAACCCAGATTTCAAGCAAGATTTCAACTTCACAGCGAAATATATCATGCTCAAGTC
66 ATACTTCCCAACCCAGATTTCAAGCAAGATTTCAACTTCACAACGAAAGATATCAAGCTCAAGTC
* * * * *
20038601 ATACAAGATCGACTTAAATCGAAATGGAGGAGTCCTCTACAACCAGCTTAACTCAACAATAAGAA
131 ATACAAGATCGACTTAAATCGAAATGGACGACTCATCTACAACCAGCTTAAATAAACAATAAGAA
*
20038666 TCTATTTTCCCAACTATTTATGAGTCAAG-TTTCAACTCCATGAAGGAGGATATCC-AGCTTGAA
196 TCTATTTTCCCAACTATTTATGAGT-AAGATTTCAACTCCACGAAGGAGGATATCCGA-CTTGAA
* * * * * *
20038729 GAACATTTTATTTTGACTTAACTCACAATGAATGAATCATCCAAAACATAGTTTAACTCAGCAAG
259 GAACATTTCATTTTGACCTAACTCACAATGAAGGAAGCACCCAAAACATAGCTTAACTCAGCAAG
20038794 GAGGAGCTATTTTCCAATCAAGGTCTTTAAATCGAATTTCAACATCGCAACG
324 GAGGAGCTATTTTCCAATCAAGGTCTTTAAATCGAATTTCAACATCGCAACG
* * * **
20038846 AAGGATATTAGACTAGAAGAAGACCCAAGATTGACTACGATTTAGCTTAACTCAATGATGAGGAG
1 AAGGATATTAGACTAGAAGAAGACCCAAGATCGACTACGATTTAACTTAACTCAACGACAAGGAG
* * * * * *
20038911 CTACTT-CCAGCCCATATTTCGAGCAAGATTTCAATTTCACAATGAAAGATATCAAGCTCAAGTC
66 ATACTTCCCAACCCAGATTTCAAGCAAGATTTCAACTTCACAACGAAAGATATCAAGCTCAAGTC
* * * * * * *
20038975 GTACAAGGTCGACTTAACTCGTAATGGACGACTCATCTAGAACATAGCTTAAATAAACAATGATG
131 ATACAAGATCGACTTAAATCGAAATGGACGACTCATCTACAAC-CAGCTTAAATAAACAAT-AAG
* * * * *
20039040 AGT-TATTTT-CCAACTATTTATGAGTTAGATTTCAACTCTACGATGGATGATATCCGACTTGAA
194 AATCTATTTTCCCAACTATTTATGAGTAAGATTTCAACTCCACGAAGGAGGATATCCGACTTGAA
* * * *
20039103 GTACATTTCATTTTGACCTAACTCTCAATGAAGGAAGCACCCATATCATAGCTTAACTCA
259 GAACATTTCATTTTGACCTAACTCACAATGAAGGAAGCACCCAAAACATAGCTTAACTCA
20039163 ACAACAAGGA
Statistics
Matches: 267, Mismatches: 46, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
373 2 0.01
374 179 0.67
375 82 0.31
376 4 0.01
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (375 bp):
AAGGATATTAGACTAGAAGAAGACCCAAGATCGACTACGATTTAACTTAACTCAACGACAAGGAG
ATACTTCCCAACCCAGATTTCAAGCAAGATTTCAACTTCACAACGAAAGATATCAAGCTCAAGTC
ATACAAGATCGACTTAAATCGAAATGGACGACTCATCTACAACCAGCTTAAATAAACAATAAGAA
TCTATTTTCCCAACTATTTATGAGTAAGATTTCAACTCCACGAAGGAGGATATCCGACTTGAAGA
ACATTTCATTTTGACCTAACTCACAATGAAGGAAGCACCCAAAACATAGCTTAACTCAGCAAGGA
GGAGCTATTTTCCAATCAAGGTCTTTAAATCGAATTTCAACATCGCAACG
Found at i:20039711 original size:2 final size:2
Alignment explanation
Indices: 20039698--20039813 Score: 63
Period size: 2 Copynumber: 61.5 Consensus size: 2
20039688 GAGAATTATG
*
20039698 TA TA TG TA TA TA TA TA TA -A TA TA GTA T- TCA TA T- TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T-A TA TA TA TA TA TA
* * * * * *
20039738 TA TA T- TT TA -A AA TA TA TA CA -A TT TT TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
20039777 TA TA TA TA TA TA T- TA TA CA TA GTA T- TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T
20039814 TATGGTTTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
1 10 0.11
2 75 0.83
3 5 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20039753 original size:19 final size:20
Alignment explanation
Indices: 20039731--20039781 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
20039721 GTATTCATAT
20039731 TATATATTATATTTTAAA-A
1 TATATATTATATTTTAAATA
**
20039750 TATATACAAT-TTTTAAATA
1 TATATATTATATTTTAAATA
20039769 TATATATATATAT
1 TATATAT-TATAT
20039782 ATATATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.28
19 15 0.60
20 2 0.08
21 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATATTATATTTTAAATA
Found at i:20041741 original size:3 final size:3
Alignment explanation
Indices: 20041733--20041764 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20041723 TATTTATTTG
20041733 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
20041765 TTACAAATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:20042107 original size:36 final size:36
Alignment explanation
Indices: 20042032--20042216 Score: 228
Period size: 36 Copynumber: 5.1 Consensus size: 36
20042022 AAACTTGATC
* * **
20042032 TTGATTTGCTTCACTACTATTTTTGTGAAGGCTTGGA
1 TTGATTTGCTTCACTACT-CTTCTGTGAAGGCTAAGA
* * *
20042069 TTGATTTGCTTTATTACTCTTATGTGAAGGCTAAGA
1 TTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAGA
20042105 TTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAGA
1 TTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAGA
* * *
20042141 TTGATTTGCTTCACTATTATTTTGTGAAGGCTGAA-A
1 TTGATTTGCTTCACTACTCTTCTGTGAAGGCT-AAGA
* * *
20042177 TTGGTTTGCTTCACTACTCCTCTATGAAGGCTAAGA
1 TTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAGA
20042213 TTGA
1 TTGA
20042217 AGTTAATTTG
Statistics
Matches: 127, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
35 2 0.02
36 107 0.84
37 18 0.14
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (36 bp):
TTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAGA
Found at i:20042432 original size:89 final size:89
Alignment explanation
Indices: 20042222--20042434 Score: 284
Period size: 89 Copynumber: 2.4 Consensus size: 89
20042212 ATTGAAGTTA
* * *
20042222 ATTTGATTCACTGCTTTGCCAGGAAGACCAAAGTTTCAATGAAAAGAATCTATTCCACTACTCTT
1 ATTTGATTCACTACTTTGCCAGGAAGACCAAATTTTCAATGAAAAGAATATATTCCACTACTCTT
* *
20042287 CCATGGAGATCATACTCAAGTTTT
66 CCATGGAGATCAGACTCAAGTTTG
* * * * * *
20042311 ATTTGATTCATTATTTTTCCAGGAAGACCAAATTTTCAATGAGAATAATATGTTCCACTACTCTT
1 ATTTGATTCACTACTTTGCCAGGAAGACCAAATTTTCAATGAAAAGAATATATTCCACTACTCTT
* *
20042376 TCGTGGAGATCAGACTCAACG-TTG
66 CCATGGAGATCAGACTCAA-GTTTG
*
20042400 ATTTGATTCGCTACTTTGCCAGGAAGACCAAATTT
1 ATTTGATTCACTACTTTGCCAGGAAGACCAAATTT
20042435 GTAATATTGA
Statistics
Matches: 106, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
89 105 0.99
90 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (89 bp):
ATTTGATTCACTACTTTGCCAGGAAGACCAAATTTTCAATGAAAAGAATATATTCCACTACTCTT
CCATGGAGATCAGACTCAAGTTTG
Found at i:20042654 original size:62 final size:62
Alignment explanation
Indices: 20042585--20042715 Score: 149
Period size: 62 Copynumber: 2.1 Consensus size: 62
20042575 GATATCAATA
* *
20042585 ATTGACT-CTACTAGGGAGTCAAG-AATAAAAAAAGTTGACTTCACTTTACGAGAAAATCAAGG
1 ATTGACTCCT-CT-GGGAGTCAAGAAATAAAAAAAGTTGACTTCACTTAACGAGAAAATCAAAG
* * * * * * *
20042647 ATTGACTCCTCTGGGAGTCAGGAAATAACAAAGGTTGACTTCTCTTAATGAGGAAATCAAAT
1 ATTGACTCCTCTGGGAGTCAAGAAATAAAAAAAGTTGACTTCACTTAACGAGAAAATCAAAG
20042709 ATTGACT
1 ATTGACT
20042716 ATATTGGGAA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
61 9 0.16
62 47 0.81
63 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (62 bp):
ATTGACTCCTCTGGGAGTCAAGAAATAAAAAAAGTTGACTTCACTTAACGAGAAAATCAAAG
Found at i:20042724 original size:62 final size:61
Alignment explanation
Indices: 20042440--20042849 Score: 245
Period size: 66 Copynumber: 6.6 Consensus size: 61
20042430 AATTTGTAAT
* * * *
20042440 ATTGACTTCTCTTCATGAGGAAGTCAAGGATTGACTCTACTGGGGAGTCA-GAAATAACACAA
1 ATTGACTTCTCTTAATGAGGAAATCAAAGATTGACTCTA-TTGGGAGTCAGGAAATAACA-AA
* * * *
20042502 ATTGACTT-TCTTAATGAGAAAATCAAAGATTGGCAC-CTCTTCGGAGTTAGG-AAT-A-AAA
1 ATTGACTTCTCTTAATGAGGAAATCAAAGATT-G-ACTCTATTGGGAGTCAGGAAATAACAAA
* * * * *
20042560 TTTGACTTCTC----TGAGGATATCAATA-ATTGACTCTACTAGGGAGTCAAG-AATAAAAAA
1 ATTGACTTCTCTTAATGAGGAAATCAA-AGATTGACTCTA-TTGGGAGTCAGGAAATAACAAA
* * * * * *
20042617 AGTTGACTTCACTTTACGAGAAAATCAAGGATTGACTCCT-CTGGGAGTCAGGAAATAACAAA
1 A-TTGACTTCTCTTAATGAGGAAATCAAAGATTGACT-CTATTGGGAGTCAGGAAATAACAAA
* * * *
20042679 GGTTGACTTCTCTTAATGAGGAAATCAAATATTGACTATATTGGGAAGTGAGTCAGAAATAACAA
1 -ATTGACTTCTCTTAATGAGGAAATCAAAGATTGACTCTATTGGG-AGTCAG---GAAATAACAA
20042744 A
61 A
* * * * * *
20042745 GATTTACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTGTTGGGGAGAGAGTCA-TAAATAACA
1 -ATTGACTTCTCTTAATGAGGAAATCAAAGATTGACTCTATT---G-G-GAGTCAGGAAATAAC-
20042809 AAA
59 AAA
* * * *
20042812 ATTGACTTCTCTTTACGAGGAAGTCAAGGATTGACTCT
1 ATTGACTTCTCTTAATGAGGAAATCAAAGATTGACTCT
20042850 TAGGAAACAA
Statistics
Matches: 271, Mismatches: 48, Indels: 54
0.73 0.13 0.14
Matches are distributed among these distances:
53 2 0.01
54 3 0.01
55 24 0.09
56 2 0.01
57 3 0.01
58 18 0.07
59 3 0.01
60 1 0.00
61 39 0.14
62 69 0.25
63 9 0.03
66 88 0.32
67 3 0.01
69 1 0.00
70 5 0.02
71 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (61 bp):
ATTGACTTCTCTTAATGAGGAAATCAAAGATTGACTCTATTGGGAGTCAGGAAATAACAAA
Found at i:20042756 original size:66 final size:66
Alignment explanation
Indices: 20042661--20042847 Score: 248
Period size: 66 Copynumber: 2.8 Consensus size: 66
20042651 ACTCCTCTGG
* * * * *
20042661 GAGTCAGGAAATAACAAAGGTTGACTTCTCTTAATGAGGAAATCAAATATTGACTATATTGGGAA
1 GAGTCA-GAAATAACAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTATATTGGGAA
*
20042726 GT
65 GA
* * * *
20042728 GAGTCAGAAATAACAAAGATTTACTTCTCTTTACGAGGAAGTCAAAGATTGACTCTGTTGGGGAG
1 GAGTCAGAAATAACAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTATATTGGGAAG
20042793 A
66 A
* * *
20042794 GAGTCATAAATAACAAAAATTGACTTCTCTTTACGAGGAAGTCAAGGATTGACT
1 GAGTCAGAAATAACAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACT
20042848 CTTAGGAAAC
Statistics
Matches: 106, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
66 100 0.94
67 6 0.06
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (66 bp):
GAGTCAGAAATAACAAAGATTGACTTCTCTTTACGAGGAAGTCAAAGATTGACTATATTGGGAAG
A
Found at i:20045305 original size:100 final size:100
Alignment explanation
Indices: 20045126--20045326 Score: 269
Period size: 100 Copynumber: 2.0 Consensus size: 100
20045116 ATCTTTATTG
* * **
20045126 TAATCACCTTTATTAGGCTAGCTCAATATGATCCATAAAGTCGGGTTGTTTAACCAATTGCATTA
1 TAATCACCTTTATCAGGCTAGCTAAATATGATCCATAAAGTCGGGGAGTTTAACCAATTGCATTA
** *
20045191 AAGGGATGGTTCAAGCTTTATTGTAT-ATATAATA
66 AAGGGAAAGCTCAAGCTTTATTGTATAATATAATA
* * *
20045225 TAATCACCTTTATCAGGCTAGCTGAAATCTTATCCATAAAGTCGGGGAGTTTAACCAATTGCTTT
1 TAATCACCTTTATCAGGCTAGCT-AAATATGATCCATAAAGTCGGGGAGTTTAACCAATTGCATT
**
20045290 AGCGGGAAAGCTCAAGCTTTATTGTATACATATAATA
65 AAAGGGAAAGCTCAAGCTTTATTGTATA-ATATAATA
20045327 ATATGATCTG
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
99 22 0.25
100 57 0.66
102 8 0.09
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (100 bp):
TAATCACCTTTATCAGGCTAGCTAAATATGATCCATAAAGTCGGGGAGTTTAACCAATTGCATTA
AAGGGAAAGCTCAAGCTTTATTGTATAATATAATA
Found at i:20049987 original size:15 final size:14
Alignment explanation
Indices: 20049967--20049996 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
20049957 TACCTTTTAA
20049967 AATAATTTTAATAAT
1 AATAATTTTAA-AAT
20049982 AATAATTTTAAAAT
1 AATAATTTTAAAAT
20049996 A
1 A
20049997 TAAAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATAATTTTAAAAT
Found at i:20053354 original size:17 final size:17
Alignment explanation
Indices: 20053332--20053367 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
20053322 CATTGGAAAT
*
20053332 GAGATAGAGTTACTATG
1 GAGATAGAGTGACTATG
20053349 GAGATAGAGTGACTATG
1 GAGATAGAGTGACTATG
20053366 GA
1 GA
20053368 CTTTGTGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.25
Consensus pattern (17 bp):
GAGATAGAGTGACTATG
Found at i:20056939 original size:30 final size:30
Alignment explanation
Indices: 20056903--20056963 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
20056893 AACACTACGC
20056903 TACGCATACTTAAATACTAATTTGCTAGGT
1 TACGCATACTTAAATACTAATTTGCTAGGT
20056933 TACGCATACTTAAATACTAATTTGCTAGGT
1 TACGCATACTTAAATACTAATTTGCTAGGT
20056963 T
1 T
20056964 TCCATGTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (30 bp):
TACGCATACTTAAATACTAATTTGCTAGGT
Found at i:20061082 original size:21 final size:21
Alignment explanation
Indices: 20061056--20061113 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
20061046 TTATCCAATG
*
20061056 AACTTGACATCCATAACAAGA
1 AACTTGAAATCCATAACAAGA
*
20061077 AACTTGAAATTCATAACAAGA
1 AACTTGAAATCCATAACAAGA
20061098 AACTTGAAATCCATAA
1 AACTTGAAATCCATAA
20061114 AAATAAATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.50, C:0.19, G:0.09, T:0.22
Consensus pattern (21 bp):
AACTTGAAATCCATAACAAGA
Found at i:20063715 original size:11 final size:11
Alignment explanation
Indices: 20063657--20063722 Score: 55
Period size: 11 Copynumber: 6.1 Consensus size: 11
20063647 GTCCCATTTT
*
20063657 TATTTTTATTA
1 TATTATTATTA
*
20063668 TTTTATTATTA
1 TATTATTATTA
20063679 TA--ATTATTA
1 TATTATTATTA
***
20063688 TAATTATTGCAA
1 T-ATTATTATTA
*
20063700 AATTATTATTA
1 TATTATTATTA
20063711 TATTATTATTA
1 TATTATTATTA
20063722 T
1 T
20063723 TAAATAATTT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
9 8 0.20
10 1 0.02
11 28 0.68
12 4 0.10
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (11 bp):
TATTATTATTA
Found at i:20063718 original size:14 final size:14
Alignment explanation
Indices: 20063656--20063741 Score: 66
Period size: 14 Copynumber: 6.1 Consensus size: 14
20063646 TGTCCCATTT
* *
20063656 TTATTTTTATTATT
1 TTATTATTATTATA
*
20063670 TTATTATTATAATTA
1 TTATTATTATTA-TA
* **
20063685 TTATAATTATTGCA
1 TTATTATTATTATA
**
20063699 AAATTATTATTATA
1 TTATTATTATTATA
*
20063713 TTATTATTATTAAA
1 TTATTATTATTATA
*
20063727 TAATT-TTATTATA
1 TTATTATTATTATA
20063740 TT
1 TT
20063742 TCAGGCCCAA
Statistics
Matches: 53, Mismatches: 18, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
13 8 0.15
14 35 0.66
15 10 0.19
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:20063738 original size:3 final size:3
Alignment explanation
Indices: 20063656--20063724 Score: 61
Period size: 3 Copynumber: 23.0 Consensus size: 3
20063646 TGTCCCATTT
* * * **
20063656 TTA TTT TTA TTA TT- TTA TTA TTA TAA TTA TTA TAA TTA TTGCA AAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT--A TTA
20063702 TTA TTA TTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
20063725 AATAATTTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
2 4 0.08
3 47 0.90
5 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:20065001 original size:21 final size:20
Alignment explanation
Indices: 20064977--20065021 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
20064967 ATTATTGTCC
20064977 TTTAGTT-TTCAATATATTTAT
1 TTTAGTTCTTCAAT-TA-TTAT
*
20064998 TTTAGTTCTTTAATTATTAT
1 TTTAGTTCTTCAATTATTAT
20065018 TTTA
1 TTTA
20065022 TTATTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTAGTTCTTCAATTATTAT
Found at i:20065425 original size:18 final size:20
Alignment explanation
Indices: 20065388--20065427 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
20065378 CAAATTATTT
20065388 TTTATATATTCTTATTAATA
1 TTTATATATTCTTATTAATA
*
20065408 TTTATTTATT-TT-TTAATA
1 TTTATATATTCTTATTAATA
20065426 TT
1 TT
20065428 GAAGAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTATATATTCTTATTAATA
Found at i:20073532 original size:24 final size:23
Alignment explanation
Indices: 20073505--20073552 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 23
20073495 AATTTTCCAA
20073505 AAAAAAAT-TTAAATTTTCGAAATT
1 AAAAAAATGTT-AATTTTC-AAATT
20073529 AAAAAAATGTTAATTTTCAAATT
1 AAAAAAATGTTAATTTTCAAATT
20073552 A
1 A
20073553 TTGTGTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.26
24 15 0.65
25 2 0.09
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (23 bp):
AAAAAAATGTTAATTTTCAAATT
Found at i:20080080 original size:7 final size:7
Alignment explanation
Indices: 20080070--20080171 Score: 52
Period size: 7 Copynumber: 14.9 Consensus size: 7
20080060 ATCCATCATG
*
20080070 AAAATAA
1 AAAAGAA
20080077 AAAAG-A
1 AAAAGAA
*
20080083 AAAAGAG
1 AAAAGAA
* *
20080090 AGATGAA
1 AAAAGAA
20080097 AAAA-AA
1 AAAAGAA
*
20080103 AGAA-AA
1 AAAAGAA
*
20080109 AAAAGAG
1 AAAAGAA
* *
20080116 ATATG-A
1 AAAAGAA
20080122 AAAAGAAA
1 AAAAG-AA
20080130 AAAAGAA
1 AAAAGAA
20080137 AAAA-AGA
1 AAAAGA-A
20080144 AAAAGAA
1 AAAAGAA
*
20080151 AATAGAAA
1 AAAAG-AA
20080159 AAAAGAA
1 AAAAGAA
*
20080166 GAAAGA
1 AAAAGA
20080172 TCAAAGATGG
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
6 20 0.29
7 37 0.53
8 13 0.19
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (7 bp):
AAAAGAA
Found at i:20080124 original size:24 final size:24
Alignment explanation
Indices: 20080067--20080133 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 24
20080057 CTCATCCATC
20080067 ATGAAAATAAA-AAAGAAAAAGAGAG
1 ATGAAAA-AAAGAAA-AAAAAGAGAG
*
20080092 ATGAAAAAAAAAGAAAAAAAAGAGAT
1 ATG--AAAAAAAGAAAAAAAAGAGAG
20080118 ATG--AAAAAGAAAAAAA
1 ATGAAAAAAAGAAAAAAA
20080134 GAAAAAAAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
22 13 0.34
25 3 0.08
26 15 0.39
27 7 0.18
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.07
Consensus pattern (24 bp):
ATGAAAAAAAGAAAAAAAAGAGAG
Found at i:20080140 original size:29 final size:29
Alignment explanation
Indices: 20080075--20080165 Score: 103
Period size: 29 Copynumber: 3.0 Consensus size: 29
20080065 TCATGAAAAT
* *
20080075 AAAAAAGAAAAAGAGAGATGAAAAAAAAAGAA
1 AAAAAAGAAAAAGA-AAAT-AGAAAAAAAG-A
* *
20080107 AAAAAAGAGATATGAAAA-AGAAAAAAAGA
1 AAAAAAGA-AAAAGAAAATAGAAAAAAAGA
20080136 AAAAAAGAAAAAGAAAATAGAAAAAAAGA
1 AAAAAAGAAAAAGAAAATAGAAAAAAAGA
20080165 A
1 A
20080166 GAAAGATCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
28 7 0.14
29 21 0.41
30 9 0.18
32 10 0.20
33 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.04
Consensus pattern (29 bp):
AAAAAAGAAAAAGAAAATAGAAAAAAAGA
Found at i:20080145 original size:22 final size:22
Alignment explanation
Indices: 20080097--20080165 Score: 56
Period size: 24 Copynumber: 3.1 Consensus size: 22
20080087 GAGAGATGAA
*
20080097 AAAAAAAGAAAAA-AAAGAGATATG
1 AAAAAAAGAAAAAGAAA-A-A-AAG
20080121 AAAAAGAA-AAAAAGAAAAAAAG
1 AAAAA-AAGAAAAAGAAAAAAAG
20080143 --AAAAAGAAAATAGAAAAAAAG
1 AAAAAAAGAAAA-AGAAAAAAAG
20080164 AA
1 AA
20080166 GAAAGATCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
19 2 0.05
20 7 0.18
21 10 0.26
22 2 0.05
23 1 0.03
24 11 0.29
25 5 0.13
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.04
Consensus pattern (22 bp):
AAAAAAAGAAAAAGAAAAAAAG
Found at i:20080171 original size:22 final size:21
Alignment explanation
Indices: 20080075--20080159 Score: 50
Period size: 23 Copynumber: 3.8 Consensus size: 21
20080065 TCATGAAAAT
* *
20080075 AAAAAAGAAAAAGAGAGATGAAA
1 AAAAAAGAAAAAGA-AAAT-AGA
*
20080098 AAAAAAGAAAAAAAAGAGATATGA
1 AAAAAAGAAAAAGAA-A-ATA-GA
20080122 AAAAGAA-AAAAAGAAAA-A-A
1 AAAA-AAGAAAAAGAAAATAGA
20080141 AGAAAAAGAAAATAGAAAA
1 A-AAAAAGAAAA-AGAAAA
20080160 AAAGAAGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
19 4 0.08
20 7 0.14
21 7 0.14
22 2 0.04
23 15 0.29
24 14 0.27
25 2 0.04
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (21 bp):
AAAAAAGAAAAAGAAAATAGA
Found at i:20081620 original size:41 final size:39
Alignment explanation
Indices: 20081522--20081638 Score: 112
Period size: 41 Copynumber: 3.0 Consensus size: 39
20081512 TACAATTTAG
* *
20081522 AATATTGGGGCATTTTGAAGGCCCAATTCAA-ACATATC
1 AATATTGGGGCATTTTGAAGGCCCAATTCAACAGAAATC
* * * * * *
20081560 CAT-GTGGGACATCTCGAAGGCCCATTTCAATCAGAAATAC
1 AATATTGGGGCATTTTGAAGGCCCAATTCAA-CAGAAAT-C
*
20081600 AATATTGGGGCATTTTGAAGGCCTAATTCAAACAGAAAT
1 AATATTGGGGCATTTTGAAGGCCCAATTC-AACAGAAAT
20081639 GATCTATGTG
Statistics
Matches: 59, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
37 22 0.37
38 2 0.03
39 4 0.07
40 3 0.05
41 26 0.44
42 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (39 bp):
AATATTGGGGCATTTTGAAGGCCCAATTCAACAGAAATC
Found at i:20083664 original size:117 final size:122
Alignment explanation
Indices: 20083458--20083780 Score: 469
Period size: 117 Copynumber: 2.7 Consensus size: 122
20083448 TCACTCGATG
* * * *
20083458 GATCAACATTGCCAGGTAGAGTTCATAATGAGAATAACTCATATGAAGAGGAAGAAGAAGTTCAT
1 GATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCAT
**
20083523 AATGAGAAGAACTTGTTCAACCTTTTTCTCGACTCTATCACAG-A-A-AGAGAT-A-
66 AATGAGAAGAACTTGTTCAACCTTTGGCTCGACTCTATCACAGAAGATAGAGATCAT
* *
20083575 GATCAGCATTGCCAGGAAGAGTTCATAATGAGAAGAATTCATCTGAAGAGGAAGAAGAAGTTCAT
1 GATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCAT
* *
20083640 AATGAGAAGAACTTGTTCAACCTTTGGCTTGACTCTATCACAGAAGGATATAGATCAT
66 AATGAGAAGAACTTGTTCAACCTTTGGCTCGACTCTATCACAGAA-GATAGAGATCAT
* **
20083698 CATCAACATTTTCA-GATAGAGTTCATAATGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCA
1 GATCAACATTGCCAGGA-AGAGTTCATAATGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCA
20083762 TAATGAGAAGAACTTGTTC
65 TAATGAGAAGAACTTGTTC
20083781 GATCTTAGCT
Statistics
Matches: 185, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
117 100 0.54
118 1 0.01
120 1 0.01
121 5 0.03
122 3 0.02
123 75 0.41
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (122 bp):
GATCAACATTGCCAGGAAGAGTTCATAATGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTGGCTCGACTCTATCACAGAAGATAGAGATCAT
Found at i:20083844 original size:139 final size:137
Alignment explanation
Indices: 20083699--20084061 Score: 428
Period size: 139 Copynumber: 2.6 Consensus size: 137
20083689 ATAGATCATC
* * *
20083699 ATCAACATTTTCAGATAGAGTTCATAATGAGAAGAAATCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTAATA
* * * * * * *
20083764 ATGAGAAGAACTTGTTCGATCTTAG-CTTGATTCATCGCCTATGTAGTTGAATTAAAGAAGAACC
66 ATGAGAAGAACTTGTTCAACCTT-GCCTTAATTCATCACATATGAAGTTGAATCAAAG-A-AACC
20083828 TCACTTGAGG
128 TCACTTGAGG
* *
20083838 ATCAACATTTCCAGA-GGAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTAAT
1 ATCAACATTTCCAGATAG-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTAAT
* *
20083902 AATGAGAAAAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGTTGAATCAAAGACACCTC
65 AATGAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGTTGAATCAAAGAAACCTC
*
20083967 TCTTGAGG
130 ACTTGAGG
* ** * *
20083975 ATCAACATTCCCAG-TGGAAGAGTTCATAATGAGAAGAACT-AGTCCAAAGAGAAAGAAAAAGTT
1 ATCAACATTTCCAGAT---AGAGTTCATAATGAGAAGAACTCA-TCTGAAGAGGAAGAAGAAGTT
* *
20084038 TATAATGAGAAGAATTTGTTCAAC
62 AATAATGAGAAGAACTTGTTCAAC
20084062 TCCAGCTTAA
Statistics
Matches: 192, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
137 25 0.13
138 4 0.02
139 162 0.84
140 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (137 bp):
ATCAACATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTAATA
ATGAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGTTGAATCAAAGAAACCTCA
CTTGAGG
Found at i:20084200 original size:3 final size:3
Alignment explanation
Indices: 20084186--20084249 Score: 51
Period size: 3 Copynumber: 22.0 Consensus size: 3
20084176 TGTCCCGTTT
* * * * * *
20084186 TTA TTT TTA TTA TTA TTA TAA TTA TTG TAA ATA TGA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
20084234 TTA -TA TAA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA
20084250 CAGGCCCAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 4
0.71 0.22 0.06
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:20087396 original size:41 final size:41
Alignment explanation
Indices: 20087348--20087572 Score: 238
Period size: 41 Copynumber: 5.5 Consensus size: 41
20087338 TTGTAAACAC
* * *
20087348 AAACGCCACTAAAGTACGAATCTATAGCTGCATTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * * *
20087389 AAACGCCACTAAAGTATGAGTCTTTAACGACGGTTGTATAG
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
*
20087430 AAACGCCACTAAAGTACGAGTCTATAGCGGCATTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* *
20087471 AAATGCCACTAAAGTAC-ACGTCTATAGCGGTGTTTGTATAA
1 AAACGCCACTAAAGTACGA-GTCTATAGCGGCGTTTGTATAA
* * * * * *
20087512 AAATGTCACTAAAGTAC-AATATTTAGCGGCGTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
20087552 AAATGCCAATAAAGTATGAGT
1 AAACGCCACTAAAGTACGAGT
20087573 ATTTAGTGGC
Statistics
Matches: 153, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
40 32 0.21
41 121 0.79
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:20087485 original size:82 final size:82
Alignment explanation
Indices: 20087348--20087577 Score: 275
Period size: 82 Copynumber: 2.8 Consensus size: 82
20087338 TTGTAAACAC
* *
20087348 AAACGCCACTAAAGTACGAATCTATAGCTGCATTTGTATAAAAACGCCACTAAAGTATGAGTCTT
1 AAACGCCACTAAAGTACGAATCTATAGCGGCATTTGTATAAAAATGCCACTAAAGTATGAGTCTT
*
20087413 TAACGACGGTTGTATAG
66 TAACGACGGTTGTATAA
* *
20087430 AAACGCCACTAAAGTACGAGTCTATAGCGGCATTTGTATAAAAATGCCACTAAAGTA-CACGTCT
1 AAACGCCACTAAAGTACGAATCTATAGCGGCATTTGTATAAAAATGCCACTAAAGTATGA-GTCT
* * ** *
20087494 ATAGCGGTGTTTGTATAA
65 TTAACGACGGTTGTATAA
* * * * * * * *
20087512 AAATGTCACTAAAGTAC-AATATTTAGCGGCGTTTATATAAAAATGCCAATAAAGTATGAGTATT
1 AAACGCCACTAAAGTACGAATCTATAGCGGCATTTGTATAAAAATGCCACTAAAGTATGAGTCTT
20087576 TA
66 TA
20087578 GTGGCATTTT
Statistics
Matches: 125, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
81 39 0.31
82 86 0.69
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (82 bp):
AAACGCCACTAAAGTACGAATCTATAGCGGCATTTGTATAAAAATGCCACTAAAGTATGAGTCTT
TAACGACGGTTGTATAA
Found at i:20088728 original size:16 final size:16
Alignment explanation
Indices: 20088691--20088731 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
20088681 AAAAATGAAG
*
20088691 AATAAA-AATAAGTAAA
1 AATAAATAA-AAGGAAA
20088707 AA-AAATAAAAGGAAA
1 AATAAATAAAAGGAAA
20088722 AATAAATAAA
1 AATAAATAAA
20088732 TAAGTAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (16 bp):
AATAAATAAAAGGAAA
Found at i:20088751 original size:2 final size:2
Alignment explanation
Indices: 20088744--20088772 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20088734 AGTAAATGAA
20088744 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20088773 AATGAGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20088839 original size:18 final size:18
Alignment explanation
Indices: 20088790--20088843 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 18
20088780 AAACTAGAAA
*
20088790 AATAATAATCATAACAATAAT
1 AATAGTAAT-ATAA-AAT-AT
20088811 AATAGTAATATGAAAATAT
1 AATAGTAATAT-AAAATAT
20088830 AATA-TAATATAAAA
1 AATAGTAATATAAAA
20088844 AAAACCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 4 0.13
18 6 0.19
19 6 0.19
20 5 0.16
21 10 0.32
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
AATAGTAATATAAAATAT
Found at i:20088844 original size:18 final size:19
Alignment explanation
Indices: 20088794--20088844 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
20088784 TAGAAAAATA
*
20088794 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
*
20088814 AGTAATATGAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
20088833 ATAATATAAAAA
1 ATAATATAAAAA
20088845 AAACCAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 6 0.22
20 7 0.26
21 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:20089074 original size:19 final size:19
Alignment explanation
Indices: 20089052--20089112 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 19
20089042 AAAAAAGTAT
20089052 ATATATATAAAAATAATAA
1 ATATATATAAAAATAATAA
*
20089071 ATATAGTATTAAAAAATAACCAA
1 ATATA-TA-T-AAAAATAA-TAA
20089094 ATGA-ATATAAAAA-AATAA
1 AT-ATATATAAAAATAATAA
20089112 A
1 A
20089113 AAAATATATG
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
18 3 0.09
19 7 0.20
20 7 0.20
21 2 0.06
22 10 0.29
23 5 0.14
24 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (19 bp):
ATATATATAAAAATAATAA
Found at i:20089088 original size:22 final size:22
Alignment explanation
Indices: 20089060--20089145 Score: 61
Period size: 22 Copynumber: 3.8 Consensus size: 22
20089050 ATATATATAT
20089060 AAAAATAATAAATATAGTATTA
1 AAAAATAATAAATATAGTATTA
* *
20089082 AAAAATAACCAAATGA-A-TATAA
1 AAAAATAA-TAAAT-ATAGTATTA
*
20089104 AAAAATAAAAAAATATATGTA-TA
1 AAAAAT-AATAAATATA-GTATTA
* *
20089127 GATAATAATAATATATAGT
1 AAAAATAATAA-ATATAGT
20089146 GTAAGAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
21 1 0.02
22 29 0.58
23 17 0.34
24 3 0.06
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (22 bp):
AAAAATAATAAATATAGTATTA
Found at i:20089710 original size:37 final size:37
Alignment explanation
Indices: 20089617--20089718 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
20089607 ATGCTTGTGG
* * ** * *
20089617 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
20089654 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
20089691 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
20089719 TAGGACGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:20090644 original size:106 final size:106
Alignment explanation
Indices: 20090459--20090989 Score: 687
Period size: 106 Copynumber: 5.1 Consensus size: 106
20090449 TAGCATTTTT
* * * * **
20090459 TCGAGTCTAATATCCTACGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGAC
1 TCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGAC
20090524 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
66 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
* **
20090565 TCGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCCAAAATTGGGAAATTATTTGTTGAC
1 TCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGAC
*
20090630 AATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
66 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
* * * *
20090671 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTAAC
1 TCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGAC
*
20090736 AACCAGCCGTCCCTTCGTTTGTGAAGTTGAACTTGTGCTGTC
66 AACCAGCCGTCCCTTCG-TTGTGAAGTTGAACTTGTGTTGTC
* ** * *
20090778 TCGAGTCTAATATCCTTCACTGTGAAGTTAAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGAC
1 TCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGAC
* * * **
20090837 AATCAGCCGCCCCTTCGTCGTGAAGTTGAGTTTGTGTTGTC
66 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
* * * * * * * *
20090878 TTGGGTCCAAGATCATTCGTTGTGAAGTTGAACTTGGCTCTGAAATTGAGAAGTTGTTTGTTGAC
1 TCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGAC
* *
20090943 AACCAGCGGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTC
66 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
*
20090984 TTGAGT
1 TCGAGT
20090990 GGCACGATAT
Statistics
Matches: 368, Mismatches: 50, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
100 52 0.14
101 25 0.07
102 2 0.01
103 3 0.01
104 3 0.01
105 2 0.01
106 220 0.60
107 61 0.17
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
TCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGAC
AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
Found at i:20090906 original size:207 final size:211
Alignment explanation
Indices: 20090480--20090989 Score: 724
Period size: 207 Copynumber: 2.4 Consensus size: 211
20090470 ATCCTACGTC
* ** * *
20090480 GTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACAACCAGCCGTCCCTTCGTTGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGT
** *
20090545 GAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCCAAAA
66 GAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCACTGTGAAGTTAAAATTGACTCCAAAA
* *
20090610 TTGGGAAATTATTTGTTGACAATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGA
131 TT-GGAAATTATTTGTTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGA
* *
20090675 GTCCAATATCCTTCGCT
195 GTCCAAGATCATTCGCT
*
20090692 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTAACAACCAGCCGTCCCTTCGTTTG
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCG-TTG
* * **
20090757 TGAAGTTGAACTTGTGCTGTCTCGAGTCTAATATCCTTCACTGTGAAGTTAAAATTGACT-CTGA
65 TGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCACTGTGAAGTTAAAATTGACTCCAAA
** * *
20090821 A-T-GAAA-T-TTTGTTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAGTTTGTGTTGTCTTGG
130 ATTGGAAATTATTTGTTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGA
*
20090882 GTCCAAGATCATTCGTT
195 GTCCAAGATCATTCGCT
* * * *
20090899 GTGAAGTTGAACTTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCATTGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGT
*
20090964 GAAGTTGAACTTGTGTTGTCTTGAGT
66 GAAGTTGAACTTGTGTTGTCTCGAGT
20090990 GGCACGATAT
Statistics
Matches: 268, Mismatches: 29, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
206 28 0.10
207 118 0.44
208 1 0.00
209 4 0.01
211 1 0.00
212 58 0.22
213 58 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (211 bp):
GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGT
GAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCACTGTGAAGTTAAAATTGACTCCAAAA
TTGGAAATTATTTGTTGACAATCAGCCGCCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAG
TCCAAGATCATTCGCT
Found at i:20091819 original size:22 final size:22
Alignment explanation
Indices: 20091794--20091892 Score: 162
Period size: 22 Copynumber: 4.5 Consensus size: 22
20091784 TTATGTTTGG
*
20091794 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
20091816 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
20091838 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* *
20091860 TCATAGGTTTGGCAGTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
20091882 TCAACGGTTTG
1 TCAAAGGTTTG
20091893 ATGGGGTAGT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 72 1.00
ACGTcount: A:0.21, C:0.13, G:0.28, T:0.37
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:20092587 original size:172 final size:173
Alignment explanation
Indices: 20092292--20092634 Score: 566
Period size: 172 Copynumber: 2.0 Consensus size: 173
20092282 TAGGCCCAAT
* * *
20092292 CAAGTATTTCAGGGTGTTGAACCAAGGATCAATTCATTCTAATGCCTTCAATCATGTCCTGCTTA
1 CAAGTATTTCAGGGTGTTGAACCAAAGATCAATTCATTATAATGCCTTCAA-CA-GTCCTGCTCA
20092357 AAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCGGGAATGATTG
64 AAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCGGGAATGATTG
20092422 TGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTTCAAA
129 TGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTTCAAA
* * *
20092467 CAAGTGTTTCAGGGTGTTGAACCAAAGATCAATTCATTATGATGTCTTC-A-A-TCCTGCTCAAA
1 CAAGTATTTCAGGGTGTTGAACCAAAGATCAATTCATTATAATGCCTTCAACAGTCCTGCTCAAA
*
20092529 ATGTTTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATGATTG
66 ATG--TCTCTCTCTTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCGGGAATGATTG
20092594 TGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 TGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
20092635 TTTTAGGGAA
Statistics
Matches: 159, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
170 13 0.08
172 101 0.64
174 1 0.01
175 44 0.28
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (173 bp):
CAAGTATTTCAGGGTGTTGAACCAAAGATCAATTCATTATAATGCCTTCAACAGTCCTGCTCAAA
ATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCGGGAATGATTGTG
CTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTTCAAA
Found at i:20092732 original size:19 final size:19
Alignment explanation
Indices: 20092681--20092732 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
20092671 TTCTTTTTGA
* *
20092681 TTTTTGTTCTTGTTTCTCT
1 TTTTTCTTCTTTTTTCTCT
*
20092700 TTTTTCTTTGTTTTTTGCT-T
1 TTTTTC-TTCTTTTTT-CTCT
20092720 TTTTTCTTCTTTT
1 TTTTTCTTCTTTT
20092733 CTTTTTTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 11 0.41
20 14 0.52
21 2 0.07
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (19 bp):
TTTTTCTTCTTTTTTCTCT
Found at i:20096208 original size:19 final size:19
Alignment explanation
Indices: 20096175--20096211 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
20096165 TGCAGATGAT
20096175 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
20096194 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
20096212 TTAGTAGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:20097370 original size:2 final size:2
Alignment explanation
Indices: 20097363--20097397 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
20097353 AATAAATGAA
20097363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20097398 AATGAGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20097685 original size:19 final size:21
Alignment explanation
Indices: 20097663--20097710 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
20097653 ATATTTTTTA
*
20097663 AAAAAATATATATATA-TA-T
1 AAAAAATATAAATATAGTATT
20097682 -AAAAATAATAAATATAGTATT
1 AAAAAAT-ATAAATATAGTATT
20097703 AAAAAATA
1 AAAAAATA
20097711 ACCAAATGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 6 0.25
19 8 0.33
20 2 0.08
21 2 0.08
22 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
AAAAAATATAAATATAGTATT
Found at i:20097686 original size:21 final size:21
Alignment explanation
Indices: 20097662--20097708 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
20097652 AATATTTTTT
*
20097662 AAAAAAATATATATA-TATATA
1 AAAAAAATAAATATAGTAT-TA
*
20097683 AAAATAATAAATATAGTATTA
1 AAAAAAATAAATATAGTATTA
20097704 AAAAA
1 AAAAA
20097709 TAACCAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAAAAATAAATATAGTATTA
Found at i:20097711 original size:19 final size:19
Alignment explanation
Indices: 20097661--20097711 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
20097651 AAATATTTTT
20097661 TAAAAAAATATATATATATA
1 TAAAAAAATA-ATATATATA
20097681 TAAAAATAATAA-ATATAGTA
1 TAAAAA-AATAATATATA-TA
*
20097701 TTAAAAAATAA
1 TAAAAAAATAA
20097712 CCAAATGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 10 0.36
20 14 0.50
21 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
TAAAAAAATAATATATATA
Found at i:20097855 original size:15 final size:16
Alignment explanation
Indices: 20097835--20097871 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
20097825 GACAATAATG
20097835 TAAATAATAAATA-AA
1 TAAATAATAAATACAA
*
20097850 TAAAT-ATATATACAA
1 TAAATAATAAATACAA
20097865 TAAATAA
1 TAAATAA
20097872 AAGGATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.32
15 12 0.63
16 1 0.05
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAATAATAAATACAA
Found at i:20098277 original size:37 final size:37
Alignment explanation
Indices: 20098236--20098332 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
20098226 ATGCTTGTGG
* ** *
20098236 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAACAAAACTCT
* ** *
20098273 ATCCTATTTTTAGGAGTTTGAATCCTAACAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAACAAAACTCT
20098310 ATCCTATTTTTAGGAGTTTAAAT
1 ATCCTATTTTTAGGAGTTTAAAT
20098333 CTTAGTAGGA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAACAAAACTCT
Found at i:20106274 original size:24 final size:24
Alignment explanation
Indices: 20106238--20106307 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
20106228 CATATTAATA
20106238 ATTTGAATGAATGTTTGTGATTGT
1 ATTTGAATGAATGTTTGTGATTGT
* * * * *
20106262 ATTTAAATTAATGTTTATAATTTT
1 ATTTGAATGAATGTTTGTGATTGT
20106286 ATTTGAATGAATGTTTGTGATT
1 ATTTGAATGAATGTTTGTGATT
20106308 AATTTTTATT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (24 bp):
ATTTGAATGAATGTTTGTGATTGT
Found at i:20109095 original size:2 final size:2
Alignment explanation
Indices: 20109088--20109115 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20109078 CCTTTATGAT
20109088 TA 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 TA
20109116 ATTTAATTAA
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):
TA
Found at i:20109242 original size:13 final size:12
Alignment explanation
Indices: 20109224--20109257 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20109214 TATATTGAAG
20109224 TTTTATTTTCTTA
1 TTTTATTTTC-TA
*
20109237 TTTTATCTTCTA
1 TTTTATTTTCTA
20109249 TTTTATTTT
1 TTTTATTTT
20109258 TTGTGAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTTTCTA
Found at i:20109322 original size:5 final size:5
Alignment explanation
Indices: 20109309--20109365 Score: 71
Period size: 5 Copynumber: 11.4 Consensus size: 5
20109299 TTCTTCCCTT
* * *
20109309 TTTTA TTTTT TTTTA TTTTG TTTTA TTTTA TTTTA TTTTCA TTTT- TTTAA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA
20109359 TTTTA TT
1 TTTTA TT
20109366 ATTTTTCCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
4 3 0.07
5 36 0.82
6 5 0.11
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.81
Consensus pattern (5 bp):
TTTTA
Done.