Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008229.1 Hibiscus syriacus cultivar Beakdansim tig00110865_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: 3634043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 17
Found at i:12377 original size:15 final size:15
Alignment explanation
Indices: 12357--12387 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12347 CCACTAGCCT
12357 CCCAATTACCATTGA
1 CCCAATTACCATTGA
*
12372 CCCAATTACTATTGA
1 CCCAATTACCATTGA
12387 C
1 C
12388 ATTAGCATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.29
Consensus pattern (15 bp):
CCCAATTACCATTGA
Found at i:14912 original size:3 final size:3
Alignment explanation
Indices: 14900--14950 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
14890 CTACAATAAC
14900 ATT A-T ATT ATT ATT ATTT ATT ATT ATT ATT ATT ATT -TT ATT -TT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
14943 ATT -TT ATT
1 ATT ATT ATT
14951 TACACATATT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 8 0.19
3 32 0.74
4 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
ATT
Found at i:14915 original size:6 final size:6
Alignment explanation
Indices: 14900--14950 Score: 65
Period size: 5 Copynumber: 9.0 Consensus size: 6
14890 CTACAATAAC
14900 ATTA-T ATTATT ATTATTT ATTATT ATTATT ATTATT -TTATT -TTATT
1 ATTATT ATTATT ATTA-TT ATTATT ATTATT ATTATT ATTATT ATTATT
14946 -TTATT
1 ATTATT
14951 TACACATATT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.43
6 19 0.43
7 6 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
ATTATT
Found at i:21880 original size:37 final size:36
Alignment explanation
Indices: 21803--21940 Score: 152
Period size: 36 Copynumber: 3.8 Consensus size: 36
21793 TATCTTCTTA
* * *
21803 AAAAACAAAGTGTCGTCTCGCTAGAGACAGTTT-TCTT
1 AAAAACAAA-TTTCGTCTCGCTTGAGACAATTTCTC-T
*
21840 AAAAACAAATTTTGTCTCGCTTGAGACAACTTTCTCT
1 AAAAACAAATTTCGTCTCGCTTGAGACAA-TTTCTCT
* * * *
21877 AAAAACAAATTTTGTATCGCTTAAAACAATTTCTCT
1 AAAAACAAATTTCGTCTCGCTTGAGACAATTTCTCT
**
21913 CGAAACAAATTTCGTCTCGCTTGAGACA
1 AAAAACAAATTTCGTCTCGCTTGAGACA
21941 TTTTTTCTGA
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
36 45 0.52
37 39 0.45
38 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (36 bp):
AAAAACAAATTTCGTCTCGCTTGAGACAATTTCTCT
Found at i:21920 original size:15 final size:17
Alignment explanation
Indices: 21900--21931 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
21890 GTATCGCTTA
21900 AAAC-AATTTC-TCTCG
1 AAACAAATTTCGTCTCG
21915 AAACAAATTTCGTCTCG
1 AAACAAATTTCGTCTCG
21932 CTTGAGACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 6 0.40
17 5 0.33
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.31
Consensus pattern (17 bp):
AAACAAATTTCGTCTCG
Found at i:21960 original size:37 final size:36
Alignment explanation
Indices: 21803--21961 Score: 128
Period size: 36 Copynumber: 4.3 Consensus size: 36
21793 TATCTTCTTA
* * *
21803 AAAAACAAAGTGTCGTCTCGCTAGAGACAGTTT-TCTT
1 AAAAACAAA-TTTCGTCTCGCTTGAGACA-TTTCTCTG
*
21840 AAAAACAAATTTTGTCTCGCTTGAGACAACTTTCTCT-
1 AAAAACAAATTTCGTCTCGCTTGAGAC-A-TTTCTCTG
* * * *
21877 AAAAACAAATTTTGTATCGCTTAAAACAATTTCTCTCG
1 AAAAACAAATTTCGTCTCGCTTGAGAC-ATTTCTCT-G
*
21915 --AAACAAATTTCGTCTCGCTTGAGACATTTTTTCTG
1 AAAAACAAATTTCGTCTCGCTTGAGACA-TTTCTCTG
* *
21950 AGATACAAATTT
1 AAAAACAAATTT
21962 AAATTTGTTT
Statistics
Matches: 102, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
35 2 0.02
36 49 0.48
37 48 0.47
38 3 0.03
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.35
Consensus pattern (36 bp):
AAAAACAAATTTCGTCTCGCTTGAGACATTTCTCTG
Found at i:22340 original size:32 final size:33
Alignment explanation
Indices: 22287--22352 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
22277 AAACAAAATC
22287 TTTGAGTATGTTTCTTCTGAAACAAAAC-CATA
1 TTTGAGTATGTTTCTTCTGAAACAAAACACATA
* * *
22319 TTTGCGTATGTTT-TATTTGAAATAAAACACATA
1 TTTGAGTATGTTTCT-TCTGAAACAAAACACATA
22352 T
1 T
22353 CTTTGAGATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 1 0.03
32 23 0.79
33 5 0.17
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (33 bp):
TTTGAGTATGTTTCTTCTGAAACAAAACACATA
Found at i:23137 original size:3 final size:3
Alignment explanation
Indices: 23125--23157 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
23115 CTACAAAAAC
23125 ATT A-T ATT ATT ATT ATTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
23158 TGCATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:23147 original size:13 final size:13
Alignment explanation
Indices: 23129--23154 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23119 AAAAACATTA
23129 TATTATTATTATT
1 TATTATTATTATT
23142 TATTATTATTATT
1 TATTATTATTATT
23155 ATTTGCATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:25020 original size:5 final size:5
Alignment explanation
Indices: 25003--25047 Score: 65
Period size: 5 Copynumber: 9.0 Consensus size: 5
24993 TTTTTACCTC
*
25003 TTTT- TTTTA TTTTG TTTTA TTTTA TTTTA TTTTA TTTTA TCTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA
25048 CAAAAAATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 4 0.11
5 29 0.78
6 4 0.11
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:29671 original size:4 final size:4
Alignment explanation
Indices: 29659--29711 Score: 83
Period size: 4 Copynumber: 13.8 Consensus size: 4
29649 TACATCAACT
*
29659 CATA TATA CATA CATA C--A CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
29705 CATA CAT
1 CATA CAT
29712 GACGCATGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
4 43 0.96
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:30118 original size:37 final size:37
Alignment explanation
Indices: 30041--30200 Score: 162
Period size: 36 Copynumber: 4.3 Consensus size: 37
30031 TATCTTCTTA
* * *
30041 AAAAACAAAGTGTCGTCTCGCTAGAGACAGTTTTCT-T
1 AAAAACAAA-TTTCGTCTCGCTTGAGACAATTTTCTCT
* * *
30078 AAAAACAAATTTTGTCTCGCTGGAGACAACTTTCTCT
1 AAAAACAAATTTCGTCTCGCTTGAGACAATTTTCTCT
* * * *
30115 AAAAACAAATTTTGTATTGCTTGAAACAA-TTTCTCT
1 AAAAACAAATTTCGTCTCGCTTGAGACAATTTTCTCT
* * *
30151 TAAAACAAATTTCATCTCGCTTGAGACATTTTTCTCT
1 AAAAACAAATTTCGTCTCGCTTGAGACAATTTTCTCT
*
30188 AAGATACAAATTT
1 AA-AAACAAATTT
30201 AAATTTGTTT
Statistics
Matches: 102, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
36 50 0.49
37 43 0.42
38 9 0.09
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (37 bp):
AAAAACAAATTTCGTCTCGCTTGAGACAATTTTCTCT
Found at i:30526 original size:67 final size:66
Alignment explanation
Indices: 30324--30540 Score: 221
Period size: 67 Copynumber: 3.3 Consensus size: 66
30314 CAAAATTGAT
* * * * *
30324 AATCTTTGAGTCTTTTTCTCTTGAAATAAGTTTTGTCTCTCTTGAGACAA-TTCTTCTAGCGAAA
1 AATCTTTGAGTATGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTT-TAGAGAAA
30388 TC-
65 -CA
* * * * * * *
30390 -ATCTTTGAGT-CGTTTCCCTTGAAACAAATTTTGTCTATTTTGAGACAGTTGCTTTTGA-AATA
1 AATCTTTGAGTATGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTTTAGAGAA-A
30452 CA
65 CA
*
30454 TAATCTTTGAGTATGTTTCTC-TGAAAACAAATTGTTGTCTCTCTTGAGACAATTTCTTTCGAGA
1 -AATCTTTGAGTATGTTTCTCTTG-AAACAAATT-TTGTCTCTCTTGAGACAATTTCTTTAGAGA
30518 AACA
63 AACA
30522 AATCTTTGAGTATGTTTCT
1 AATCTTTGAGTATGTTTCT
30541 TCTAAAACAA
Statistics
Matches: 124, Mismatches: 18, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
63 3 0.02
64 33 0.27
65 14 0.11
66 12 0.10
67 34 0.27
68 26 0.21
69 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (66 bp):
AATCTTTGAGTATGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTTTAGAGAAAC
A
Found at i:31146 original size:135 final size:131
Alignment explanation
Indices: 30726--31169 Score: 393
Period size: 132 Copynumber: 3.4 Consensus size: 131
30716 GTAGGAACCG
** * * * ** * *
30726 TGTCATCCCTTGACCAAACCTCCTCATCATGTAGGAGTTGTATCA-CCCTAGATAACCACCCGTC
1 TGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAACCGTC
* * * * * *
30790 CTCATCTCGTATGAACCATGCTATCGCCCTTCCTAAAGATGGCCAGAACTCTTTC-TCATGTATG
66 CTCATCACGTAAGAACCATGTTATCACTC-TCCTAAAGAT-GCCAGAACTC-TTCATCGTGTATG
*
30854 AG-T
128 AGAA
* * * **
30857 TGTTTCA-CCCCCGACCAGACCTCCTCATCACGTAGGAGCCATGTCACCCC-AGATAATCAGTCG
1 TG--TCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAACCG
* ** * * *
30920 TCCTCATCACGTAAGAACCGTGTTATCA-TC-CCTAAAGATGGTATATCATCCTCATCGTGTA-G
64 TCCTCATCACGTAAGAACCATGTTATCACTCTCCTAAAGATGCCAGAAC-TCTTCATCGTGTATG
30982 A-AA
128 AGAA
* *
30985 TCGTGTCATCCCTCGACCAGATCTCCTCATCATGTAGGAGCCGTGTCACCCCTAGATAACCAACC
1 ---TGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAACC
* * * * *
31050 GTCATCATCGCGTAGGAACCAAGTTATCACTCTCCTTAAAGATAGCCAAGAACTCTTCATCGCGT
63 GTCCTCATCACGTAAGAACCATGTTATCACTCTCC-TAAAGAT-GCC-AGAACTCTTCATCGTGT
31115 ATGAGCAA
125 ATGAG-AA
*
31123 TGTCATCCCCCAACCAGATCTCCTCATCACGTAGGAGCCGTGTCACC
1 TGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACC
31170 TTTAAACGTC
Statistics
Matches: 249, Mismatches: 45, Indels: 34
0.76 0.14 0.10
Matches are distributed among these distances:
128 8 0.03
129 20 0.08
130 39 0.16
131 38 0.15
132 66 0.27
133 8 0.03
134 7 0.03
135 56 0.22
136 5 0.02
138 2 0.01
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.25
Consensus pattern (131 bp):
TGTCATCCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAACCGTC
CTCATCACGTAAGAACCATGTTATCACTCTCCTAAAGATGCCAGAACTCTTCATCGTGTATGAGA
A
Found at i:31380 original size:3 final size:3
Alignment explanation
Indices: 31372--31415 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
31362 AACATTATAT
* *
31372 TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA GTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31416 TTTTACACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:41727 original size:160 final size:158
Alignment explanation
Indices: 41509--41937 Score: 493
Period size: 160 Copynumber: 2.7 Consensus size: 158
41499 GTCTGCTGAG
* * *
41509 AGAGAATAAA-TTCATAATGGGAAGAACTTTTCAGTCTTTGCTCGATTCCATCACAGAAGGAGAT
1 AGAGAA-AAAGTTCATAATGAGAAGAACTTTTCAGCCTTTGCTCAATTCCATCACAGAAGGAG-T
41573 T-GATCAACATTTTCAAAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAGCCTTTGCTCGATTC
64 TAGATCAACATTTTCAAAAAAAGAA-TTCATAATGAGAAGAACTTGTTCAGCCTTTGCTCGATTC
* * * * *
41637 AATCACAGAATGATATAAATTAGCAGTTCCA
128 AATCACAAAAAGAGATAAATCAACAGTTCCA
* * * * *
41668 ATAGAAGAAGTTCATAATGATAAAAACTTGTTCAGCCTTTGCTCAATTCCATCACAGAAGAAGTT
1 AGAGAAAAAGTTCATAATGAGAAGAACTT-TTCAGCCTTTGCTCAATTCCATCACAGAAGGAGTT
* * * * * *
41733 AAATCAACATTTTTAAGAAAAGAAATTCATAATGAGAAGAACTTGTTTAGTCTTTGCTCGATTCC
65 AGATCAACATTTTCAAAAAAAG-AATTCATAATGAGAAGAACTTGTTCAGCCTTTGCTCGATTCA
* ** * *
41798 ATCATAAAAAGAGATTGATCAATATTTCCA
129 ATCACAAAAAGAGATAAATCAACAGTTCCA
* * * * * *
41828 AGATAAAAAGTTCATAATGAGAAGAACTTTTTCAACCATTCCTCAATTCCATCACATAATGAGTT
1 AGAGAAAAAGTTCATAATGAGAAGAAC-TTTTCAGCCTTTGCTCAATTCCATCACAGAAGGAGTT
* *
41893 AGATCAACATTTTCAAAAAAAGGAATTCATAATGAAAATAACTTG
65 AGATCAACATTTTCAAAAAAA-GAATTCATAATGAGAAGAACTTG
41938 ATCAACATCT
Statistics
Matches: 224, Mismatches: 40, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
158 2 0.01
159 23 0.10
160 194 0.87
161 5 0.02
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (158 bp):
AGAGAAAAAGTTCATAATGAGAAGAACTTTTCAGCCTTTGCTCAATTCCATCACAGAAGGAGTTA
GATCAACATTTTCAAAAAAAGAATTCATAATGAGAAGAACTTGTTCAGCCTTTGCTCGATTCAAT
CACAAAAAGAGATAAATCAACAGTTCCA
Found at i:41943 original size:80 final size:79
Alignment explanation
Indices: 41517--41937 Score: 404
Period size: 80 Copynumber: 5.3 Consensus size: 79
41507 AGAGAGAATA
* * * *
41517 AATTCATAATGGGAAGAACTT-TTCAGTCTTTGCTCGATTCCATCACAGAAGGAGATT-GATCAA
1 AATTCATAATGAGAAGAACTTGTTCAGCCTTTGCTCAATTCCATCACAGAATGAG-TTAGATCAA
41580 CATTTTCAAAAAAAG
65 CATTTTCAAAAAAAG
* * * *
41595 AAGTTCATAATGAGAAGAACTTGTTCAGCCTTTGCTCGATTCAATCACAGAATGA-TATAAATTA
1 AA-TTCATAATGAGAAGAACTTGTTCAGCCTTTGCTCAATTCCATCACAGAATGAGT-TAGATCA
* * * * *
41659 GCAGTTCCAATAGAAG
64 ACATTTTCAAAAAAAG
* * *
41675 AAGTTCATAATGATAAAAACTTGTTCAGCCTTTGCTCAATTCCATCACAGAA-GAAGTTAAATCA
1 AA-TTCATAATGAGAAGAACTTGTTCAGCCTTTGCTCAATTCCATCACAGAATG-AGTTAGATCA
* *
41739 ACATTTTTAAGAAAAG
64 ACATTTTCAAAAAAAG
* * * * * *
41755 AAATTCATAATGAGAAGAACTTGTTTAGTCTTTGCTCGATTCCATCATAAAAAGAGATT-GATCA
1 -AATTCATAATGAGAAGAACTTGTTCAGCCTTTGCTCAATTCCATCACAGAATGAG-TTAGATCA
* *
41819 ATATTTCCAAGATAAAA-
64 ACATTTTCAA-A-AAAAG
* * * * * *
41836 AGTTCATAATGAGAAGAACTTTTTCAACCATTCCTCAATTCCATCACATAATGAGTTAGATCAAC
1 AATTCATAATGAGAAGAACTTGTTCAGCCTTTGCTCAATTCCATCACAGAATGAGTTAGATCAAC
41901 ATTTTCAAAAAAAGG
66 ATTTTCAAAAAAA-G
* *
41916 AATTCATAATGAAAATAACTTG
1 AATTCATAATGAGAAGAACTTG
41938 ATCAACATCT
Statistics
Matches: 278, Mismatches: 51, Indels: 26
0.78 0.14 0.07
Matches are distributed among these distances:
78 7 0.03
79 23 0.08
80 238 0.86
81 6 0.02
82 4 0.01
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (79 bp):
AATTCATAATGAGAAGAACTTGTTCAGCCTTTGCTCAATTCCATCACAGAATGAGTTAGATCAAC
ATTTTCAAAAAAAG
Found at i:43358 original size:3 final size:3
Alignment explanation
Indices: 43350--43382 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
43340 TATGACCCGC
43350 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43383 CAGACTCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:43447 original size:22 final size:24
Alignment explanation
Indices: 43404--43452 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
43394 ATTGTTTTGC
*
43404 CTACTGACGTTTTCTACCTTTTAA
1 CTACTGACGTTTTCTAACTTTTAA
* *
43428 CTACT-AC-TTTTCTAATTTTTTA
1 CTACTGACGTTTTCTAACTTTTAA
43450 CTA
1 CTA
43453 TTAACCACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 15 0.68
23 2 0.09
24 5 0.23
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.51
Consensus pattern (24 bp):
CTACTGACGTTTTCTAACTTTTAA
Found at i:43635 original size:34 final size:34
Alignment explanation
Indices: 43589--43665 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 34
43579 TGACTTTTAT
43589 TTTATTTTTATTTCTAATG-CTACTAACCACTAACA
1 TTTA-TTTTATTTCTAATGTC-ACTAACCACTAACA
* ** *
43624 TTTATTTTATTTTTAATGTCACTAACTGCTAACT
1 TTTATTTTATTTCTAATGTCACTAACCACTAACA
43658 TTTATTTT
1 TTTATTTT
43666 TCACATTCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 32 0.86
35 5 0.14
ACGTcount: A:0.27, C:0.16, G:0.04, T:0.53
Consensus pattern (34 bp):
TTTATTTTATTTCTAATGTCACTAACCACTAACA
Found at i:46564 original size:21 final size:21
Alignment explanation
Indices: 46538--46591 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
46528 TCCTTAAAGA
46538 GTGGTCATTCGGGACATATAT
1 GTGGTCATTCGGGACATATAT
* *
46559 GTGGTCATTCGGTACATCTAT
1 GTGGTCATTCGGGACATATAT
* *
46580 GTTGTCCTTCGG
1 GTGGTCATTCGG
46592 AACAAATTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.37
Consensus pattern (21 bp):
GTGGTCATTCGGGACATATAT
Found at i:53701 original size:21 final size:21
Alignment explanation
Indices: 53611--53737 Score: 112
Period size: 21 Copynumber: 6.0 Consensus size: 21
53601 CCTTTGGAAT
*
53611 ATATATGTGGTTC-TTCGAGAC
1 ATATATGTGG-TCATTCGGGAC
* * * * *
53632 ACATATTTGGTCATTTGGAAT
1 ATATATGTGGTCATTCGGGAC
* * **
53653 ATATATGTGATCCTTTAGGAC
1 ATATATGTGGTCATTCGGGAC
* * *
53674 ATATATGTAGTCCTTCGGGAT
1 ATATATGTGGTCATTCGGGAC
*
53695 ATTTATGTGGTCATTCGGGAC
1 ATATATGTGGTCATTCGGGAC
53716 ATATATGTGGTCATTCGGGAC
1 ATATATGTGGTCATTCGGGAC
53737 A
1 A
53738 AATTCTATGT
Statistics
Matches: 82, Mismatches: 23, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
20 2 0.02
21 80 0.98
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (21 bp):
ATATATGTGGTCATTCGGGAC
Found at i:53702 original size:42 final size:42
Alignment explanation
Indices: 53582--53735 Score: 114
Period size: 42 Copynumber: 3.7 Consensus size: 42
53572 TATGTGGTTT
* * * * * *
53582 TTCAGGATATATATGTAATCCTTTGGAATATATATGTGGTTC-
1 TTCAGGACATATATGTAGTCATTCGGGATATATATGT-GATCA
* * * * * *
53624 TTC-GAGACACATATTTGGTCATTTGGAATATATATGTGATCC
1 TTCAG-GACATATATGTAGTCATTCGGGATATATATGTGATCA
* * * *
53666 TTTAGGACATATATGTAGTCCTTCGGGATATTTATGTGGTCA
1 TTCAGGACATATATGTAGTCATTCGGGATATATATGTGATCA
* *
53708 TTCGGGACATATATGTGGTCATTCGGGA
1 TTCAGGACATATATGTAGTCATTCGGGA
53736 CAAATTCTAT
Statistics
Matches: 88, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
41 4 0.05
42 83 0.94
43 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (42 bp):
TTCAGGACATATATGTAGTCATTCGGGATATATATGTGATCA
Found at i:53706 original size:63 final size:63
Alignment explanation
Indices: 53588--53724 Score: 150
Period size: 63 Copynumber: 2.2 Consensus size: 63
53578 GTTTTTCAGG
* * * * * *
53588 ATATATATGTAATCCTTTGGAATATATATGTGGTTCTTCGAGACACATATTTGGTCATTTGGA
1 ATATATATGTGATCCTTTGGAACATATATGTAGTCCTTCGAGACACATATGTGGTCATTCGGA
* * ** *
53651 ATATATATGTGATCCTTTAGG-ACATATATGTAGTCCTTCGGGATATTTATGTGGTCATTCGGG
1 ATATATATGTGATCCTTT-GGAACATATATGTAGTCCTTCGAGACACATATGTGGTCATTCGGA
*
53714 ACATATATGTG
1 ATATATATGTG
53725 GTCATTCGGG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
63 59 0.97
64 2 0.03
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (63 bp):
ATATATATGTGATCCTTTGGAACATATATGTAGTCCTTCGAGACACATATGTGGTCATTCGGA
Found at i:57155 original size:13 final size:13
Alignment explanation
Indices: 57137--57161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57127 TTGAATATAC
57137 TTAGAAAATCTTT
1 TTAGAAAATCTTT
57150 TTAGAAAATCTT
1 TTAGAAAATCTT
57162 AAAATTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTAGAAAATCTTT
Found at i:57980 original size:20 final size:20
Alignment explanation
Indices: 57943--57982 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
57933 CTCAAAATCA
* *
57943 TTTTTGAAAATTTCATTTTG
1 TTTTTGAAAATCTAATTTTG
57963 TTTTTGAAAATCTAATTTTG
1 TTTTTGAAAATCTAATTTTG
57983 CTTACAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.57
Consensus pattern (20 bp):
TTTTTGAAAATCTAATTTTG
Found at i:58625 original size:64 final size:64
Alignment explanation
Indices: 58549--58693 Score: 168
Period size: 64 Copynumber: 2.3 Consensus size: 64
58539 GCTCCATCTA
* ** * ** *
58549 ATGCATCAATGCAC-CCTTGAATAAATTGAATTTTAAATGCATTTTGTGTACTGATGCACA-AGG
1 ATGCATCGATGCACTCC-TGAATAAATTGAACATCAAATGCATTTTGTGTACCAATGCACAGA-C
58612 C
64 C
** *
58613 ATGCATCGATGCACTCCTGAATATTTTGAACATCGAATGCATTTTGTGTACCAATGCACAGACC
1 ATGCATCGATGCACTCCTGAATAAATTGAACATCAAATGCATTTTGTGTACCAATGCACAGACC
58677 ATGCATCGATGCACTCC
1 ATGCATCGATGCACTCC
58694 AGGCTCATTT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
64 66 0.96
65 3 0.04
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (64 bp):
ATGCATCGATGCACTCCTGAATAAATTGAACATCAAATGCATTTTGTGTACCAATGCACAGACC
Found at i:58705 original size:64 final size:65
Alignment explanation
Indices: 58584--58722 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 65
58574 TTGAATTTTA
** * *
58584 AATGCATTTTGTGTACTGATGCACAAGGCATGCATCGATGCACTCCTGAATATTTTG-AACATCG
1 AATGCATTTTGTGTACCAATGCACAAGCCATGCATCGATGCACTCCAGAATATTTTGAAACATCG
** *
58648 AATGCATTTTGTGTACCAATGCAC-AGACCATGCATCGATGCACTCCAGGCTCA-TTTGAAATAT
1 AATGCATTTTGTGTACCAATGCACAAG-CCATGCATCGATGCACTCCAGAAT-ATTTTGAAACAT
58711 CG
64 CG
*
58713 AATGTATTTT
1 AATGCATTTT
58723 ATGCATCGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
63 2 0.03
64 46 0.72
65 16 0.25
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (65 bp):
AATGCATTTTGTGTACCAATGCACAAGCCATGCATCGATGCACTCCAGAATATTTTGAAACATCG
Found at i:60703 original size:21 final size:21
Alignment explanation
Indices: 60678--60717 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
60668 AAGACTTTAT
60678 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
60699 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
60718 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:64569 original size:23 final size:22
Alignment explanation
Indices: 64539--64612 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
64529 ATACTAGTTA
64539 GTGCATCGATACATCCCTTGAAT
1 GTGCATCGATACA-CCCTTGAAT
* * *
64562 GTGCATCGATTCA-CCATGAAG
1 GTGCATCGATACACCCTTGAAT
*
64583 GTGCA-CTGATGCACTCCTTGAAT
1 GTGCATC-GATACAC-CCTTGAAT
64606 GTGCATC
1 GTGCATC
64613 AATGCACTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
20 1 0.02
21 16 0.39
23 23 0.56
24 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (22 bp):
GTGCATCGATACACCCTTGAAT
Found at i:67406 original size:64 final size:63
Alignment explanation
Indices: 67269--67411 Score: 184
Period size: 64 Copynumber: 2.3 Consensus size: 63
67259 GCACTATCTA
** * *
67269 ATGCATCGATGCAC-CCTTGAATAAATTGAATTTTGAATGCATTGTGTACCGATGCACAAGGC
1 ATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATTGTGTACCGATGCACAAGCC
**
67331 ATGCATCGATGCACTCC-TGAATATTTTGAACATCGAATGCATTTTGTGTACCGATGCAC-AGAC
1 ATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCA--TTGTGTACCGATGCACAAG-C
67394 C
63 C
67395 ATGCATCGATGCACTCC
1 ATGCATCGATGCACTCC
67412 AGGCTCATTT
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
62 33 0.46
63 4 0.06
64 34 0.48
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATTGTGTACCGATGCACAAGCC
Found at i:67454 original size:65 final size:64
Alignment explanation
Indices: 67316--67455 Score: 156
Period size: 65 Copynumber: 2.2 Consensus size: 64
67306 TGCATTGTGT
* * ** * *
67316 ACCGATGCACA-AGGCATGCATCGATGCACTCCTGAATATTTTGAACATCGAATGCATTTTGTGT
1 ACCGATGCACAGA-CCATGCATCGATGCACTCCAGAATATTTAAAACATCGAATGCATTTTATGA
** * *
67380 ACCGATGCACAGACCATGCATCGATGCACTCCAGGCTCATTTAAAAGATCGAATGTATTTTATGA
1 ACCGATGCACAGACCATGCATCGATGCACTCCAGAAT-ATTTAAAACATCGAATGCATTTTATGA
*
67445 ATCGATGCACA
1 ACCGATGCACA
67456 CCTAGTATAT
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
64 31 0.49
65 32 0.51
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (64 bp):
ACCGATGCACAGACCATGCATCGATGCACTCCAGAATATTTAAAACATCGAATGCATTTTATGA
Found at i:69734 original size:18 final size:19
Alignment explanation
Indices: 69711--69749 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
69701 GTTGGAATAT
69711 GGGGG-TTCGAAACCTATA
1 GGGGGTTTCGAAACCTATA
* *
69729 GGGGGTTTTGAAACCTTTA
1 GGGGGTTTCGAAACCTATA
69748 GG
1 GG
69750 CCAATTTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.23, C:0.13, G:0.36, T:0.28
Consensus pattern (19 bp):
GGGGGTTTCGAAACCTATA
Found at i:71528 original size:17 final size:17
Alignment explanation
Indices: 71503--71538 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
71493 TTTTTTGAAA
71503 ATTTAAAATGATTTTAT
1 ATTTAAAATGATTTTAT
* *
71520 ATTTTAAATTATTTTAT
1 ATTTAAAATGATTTTAT
71537 AT
1 AT
71539 ATTTTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTAAAATGATTTTAT
Found at i:75252 original size:24 final size:25
Alignment explanation
Indices: 75219--75275 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
75209 GTTCACGAGC
* * *
75219 AAGCTCGTTTATGATCTCCTTTA-T
1 AAGCTTGTTTATGAGCTCATTTATT
75243 AAGCTTGTTTATGAGCTCATTTATT
1 AAGCTTGTTTATGAGCTCATTTATT
75268 AA-CTTGTT
1 AAGCTTGTT
75276 CATTTATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.90
25 3 0.10
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (25 bp):
AAGCTTGTTTATGAGCTCATTTATT
Found at i:75511 original size:22 final size:23
Alignment explanation
Indices: 75481--75544 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 23
75471 TCGAATATAT
75481 AAACGAACGATAAACAAACACTA
1 AAACGAACGATAAACAAACACTA
* *
75504 AAAC-AACGCTAAACGAACACT-
1 AAACGAACGATAAACAAACACTA
* * *
75525 AAATGAACGCTAAACGAACA
1 AAACGAACGATAAACAAACA
75545 TGTACATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.08
22 30 0.81
23 4 0.11
ACGTcount: A:0.56, C:0.23, G:0.11, T:0.09
Consensus pattern (23 bp):
AAACGAACGATAAACAAACACTA
Found at i:77561 original size:26 final size:26
Alignment explanation
Indices: 77521--77574 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
77511 CTTAGCATGT
* * * *
77521 AATGTTAATTGAAAGCTTGTTCTGGA
1 AATGGTAATTCAAAGCTTGATCTAGA
77547 AATGGTAATTCAAAGCTTGATCTAGA
1 AATGGTAATTCAAAGCTTGATCTAGA
77573 AA
1 AA
77575 CCAATTGGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.33
Consensus pattern (26 bp):
AATGGTAATTCAAAGCTTGATCTAGA
Found at i:104480 original size:30 final size:28
Alignment explanation
Indices: 104438--104509 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 28
104428 AAATTATAAG
104438 TAATAT-TTATAAAATT-AATGTATAAAA
1 TAATATATTATAAAATTAAATGTA-AAAA
104465 CTAATATATTAATAAAATTAAAATGTAAAAA
1 -TAATATATT-ATAAAATT-AAATGTAAAAA
*
104496 TGATATATTATAAA
1 TAATATATTATAAA
104510 TAATCTTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 6 0.15
29 7 0.18
30 16 0.41
31 4 0.10
32 6 0.15
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (28 bp):
TAATATATTATAAAATTAAATGTAAAAA
Found at i:104577 original size:14 final size:14
Alignment explanation
Indices: 104553--104589 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
104543 TATCTATAAA
104553 ATAAATA-TAT-TT
1 ATAAATATTATATT
104565 ATAAAT-TTATATT
1 ATAAATATTATATT
104578 ATAAATATTATA
1 ATAAATATTATA
104590 CAACTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.41
13 8 0.36
14 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATAAATATTATATT
Found at i:107218 original size:37 final size:36
Alignment explanation
Indices: 107143--107218 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
107133 TTTTTATATT
*
107143 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
107179 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
107216 TTT
1 TTT
107219 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:107400 original size:20 final size:20
Alignment explanation
Indices: 107364--107401 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
107354 ATCCTATTCC
**
107364 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
107384 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
107402 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:109255 original size:23 final size:24
Alignment explanation
Indices: 109214--109270 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
109204 TAAGCTTAAT
*
109214 TAAAATAATTAAAACAACAAAAAA
1 TAAAATAAATAAAACAACAAAAAA
*
109238 TAAAATAAAT-AAACAACATAAAA
1 TAAAATAAATAAAACAACAAAAAA
109261 TAAAAATAAA
1 T-AAAATAAA
109271 AATAAACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 13 0.43
24 17 0.57
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (24 bp):
TAAAATAAATAAAACAACAAAAAA
Found at i:109278 original size:23 final size:23
Alignment explanation
Indices: 109214--109282 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
109204 TAAGCTTAAT
* *
109214 TAAAATAATTAAAACAACAAAAAA
1 TAAAATAAAT-AAACAACATAAAA
109238 TAAAATAAATAAACAACATAAAA
1 TAAAATAAATAAACAACATAAAA
109261 TAAAAATAAA-AATA-AACATAAA
1 T-AAAATAAATAA-ACAACATAAA
109283 TACAAGGACC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
23 23 0.56
24 18 0.44
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.17
Consensus pattern (23 bp):
TAAAATAAATAAACAACATAAAA
Found at i:111073 original size:60 final size:62
Alignment explanation
Indices: 110941--111122 Score: 221
Period size: 60 Copynumber: 3.0 Consensus size: 62
110931 TCGATTGAGC
* * * * *
110941 ATTGTTGATTCGAAGTGTTGTGTGAATTGAGTAA-AAGAAATGTTATCCCCTATGGTAGGGC-
1 ATTGCTGATTCGAAGTGTTG-GTGAATTGAGCAATAAGAAATGTTAACCCCTCTGGTGGGGCG
* * *
111002 ATTGCTAATTCGAAGTGTTGGT-AATTGAGCAATAGGAAATGTTAACCTCTCTGGTGGGGCG
1 ATTGCTGATTCGAAGTGTTGGTGAATTGAGCAATAAGAAATGTTAACCCCTCTGGTGGGGCG
* * *
111063 GTT-CTGATTCGAAGTGTT-GTGAATCGAGCAATAAGAAAAGTTAACCCCTCTGGTGGGGCG
1 ATTGCTGATTCGAAGTGTTGGTGAATTGAGCAATAAGAAATGTTAACCCCTCTGGTGGGGCG
111123 TTGTTCGTTT
Statistics
Matches: 104, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
59 11 0.11
60 73 0.70
61 20 0.19
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (62 bp):
ATTGCTGATTCGAAGTGTTGGTGAATTGAGCAATAAGAAATGTTAACCCCTCTGGTGGGGCG
Found at i:111251 original size:39 final size:39
Alignment explanation
Indices: 111144--111274 Score: 174
Period size: 39 Copynumber: 3.4 Consensus size: 39
111134 AAGAAAAATA
* *
111144 ATCTCAAGTGAGAT-AAATCTTCTATTTTGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTATTTCGAGTGAAACT
* * * *
111182 ATCTCAAGCAAGATAAAAATCTTTTGTTTCGAATGAAACT
1 ATCTCAAGCGAGAT-AAAATCTTCTATTTCGAGTGAAACT
* *
111222 ATATCAAGCGAGATAAAATCTTCTATTTCGAGTGGAACT
1 ATCTCAAGCGAGATAAAATCTTCTATTTCGAGTGAAACT
111261 ATCTCAAGCGAGAT
1 ATCTCAAGCGAGAT
111275 GTTTATCCCT
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
38 12 0.15
39 34 0.44
40 32 0.41
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (39 bp):
ATCTCAAGCGAGATAAAATCTTCTATTTCGAGTGAAACT
Found at i:111488 original size:38 final size:39
Alignment explanation
Indices: 111431--111526 Score: 131
Period size: 39 Copynumber: 2.5 Consensus size: 39
111421 GTTTTAAGGA
* ** *
111431 AAACAATCTCAAGTAAGAT-AAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGTG
*
111469 AAATTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGTG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGTG
*
111508 AAACTATCTCAAACGAGAT
1 AAACTATCTCAAGCGAGAT
111527 GTTGATCCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
38 15 0.30
39 35 0.70
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGTG
Found at i:111596 original size:59 final size:60
Alignment explanation
Indices: 111525--111656 Score: 133
Period size: 59 Copynumber: 2.2 Consensus size: 60
111515 CTCAAACGAG
* * *
111525 ATGTTGAT-CCCTCAAATGAGGCGTCACTGATTTGAAATATTGTGAATCGAGCAA-AGGAA
1 ATGTT-ATCCCCTCAAATGAGGCATCACTAATTCGAAATATTGTGAATCGAGCAATAGGAA
*** * ** * *
111584 ATGTTATCCCCTCTGGTGGGGCATTGCTAATTCGAAGTGTTGTGAATCGAGCAATAGGAA
1 ATGTTATCCCCTCAAATGAGGCATCACTAATTCGAAATATTGTGAATCGAGCAATAGGAA
*
111644 ATGTTAACCCCTC
1 ATGTTATCCCCTC
111657 TGGTGGGGCG
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
58 2 0.03
59 40 0.68
60 17 0.29
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (60 bp):
ATGTTATCCCCTCAAATGAGGCATCACTAATTCGAAATATTGTGAATCGAGCAATAGGAA
Found at i:111659 original size:252 final size:251
Alignment explanation
Indices: 111177--111776 Score: 855
Period size: 252 Copynumber: 2.4 Consensus size: 251
111167 ATTTTGAGTG
* * * * *
111177 AAACTATCTCAAGCAAGATAAAAATCTTTTGTTTCGAATGAAACTATATCAAGCGAGATAAAATC
1 AAACAATCTCAAGTAAGAT--AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATC
* * * *
111242 TTCTATTTCGAGTGGAACTATCTCAAGCGAGATGTTTATCCCTCAAGTGAGGCATCGATGATTCG
64 TTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGTTGATCCCTCAAATGAGGCATCGATGATTCG
* * * *
111307 AAATATTGTGAATCGAGAAAAGGATATATTATCCCCTCTGGTGGGGCGTTGTTGATCTGAAGTGT
129 AAATATTGTGAATCGAGAAAAGGAAATATTATCCCCTCTGGTGGGGCATTGCTAATCTGAAGTGT
* *
111372 TGTGAATCGAGCAATAGAAAATTTTAACTCCTCTGGTGGGGCGTTGTTCGTTTTAAGGA
194 TGTGAATCGAGCAATAGAAAATGTTAACCCCTCTGGTGGGGCGTTGTTCGTTTTAA-GA
*
111431 AAACAATCTCAAGTAAGATAAATCTTCTGTTTCGAGTGAAATTATCTCAAGCGAGATAAAATCTT
1 AAACAATCTCAAGTAAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
* * * *
111496 CTGTTTCAAGTGAAACTATCTCAAACGAGATGTTGATCCCTCAAATGAGGCGTC-ACTGATTTGA
66 CTGTTTCGAGTGAAACTATCTCAAGCGAGATGTTGATCCCTCAAATGAGGCATCGA-TGATTCGA
* *
111560 AATATTGTGAATCGAGCAAAGGAAATGTTATCCCCTCTGGTGGGGCATTGCTAAT-TCGAAGTGT
130 AATATTGTGAATCGAGAAAAGGAAATATTATCCCCTCTGGTGGGGCATTGCTAATCT-GAAGTGT
* *
111624 TGTGAATCGAGCAATAGGAAATGTTAACCCCTCTGGTGGGGCGTTGTTTGTTTTAAGA
194 TGTGAATCGAGCAATAGAAAATGTTAACCCCTCTGGTGGGGCGTTGTTCGTTTTAAGA
* * * *
111682 AAACAATCTCTAGTGAGATAAATCTTCTGTTTCAAGTGAAACTATCTCAAGCTAGAT-AAATCTT
1 AAACAATCTCAAGTAAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
* * *
111746 TTGTTTTGAGTGAAACTCTCTCAAGCGAGAT
66 CTGTTTCGAGTGAAACTATCTCAAGCGAGAT
111777 AAAATATTAT
Statistics
Matches: 310, Mismatches: 34, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
250 33 0.11
251 56 0.18
252 204 0.66
254 17 0.05
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (251 bp):
AAACAATCTCAAGTAAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
CTGTTTCGAGTGAAACTATCTCAAGCGAGATGTTGATCCCTCAAATGAGGCATCGATGATTCGAA
ATATTGTGAATCGAGAAAAGGAAATATTATCCCCTCTGGTGGGGCATTGCTAATCTGAAGTGTTG
TGAATCGAGCAATAGAAAATGTTAACCCCTCTGGTGGGGCGTTGTTCGTTTTAAGA
Found at i:111729 original size:38 final size:38
Alignment explanation
Indices: 111682--111853 Score: 211
Period size: 38 Copynumber: 4.5 Consensus size: 38
111672 TGTTTTAAGA
* * *
111682 AAACAATCTCTAGTGAGATAAATCTTCTGTTTCAAGTG
1 AAACTATCTCAAGTGAGATAAATCTTCTGTTTCGAGTG
* *
111720 AAACTATCTCAAGCT-AGATAAATCTTTTGTTTTGAGTG
1 AAACTATCTCAAG-TGAGATAAATCTTCTGTTTCGAGTG
* * * *
111758 AAACTCTCTCAAGCGAGATAAAATATTATGTTTCGAGTG
1 AAACTATCTCAAGTGAGAT-AAATCTTCTGTTTCGAGTG
* * *
111797 AAACTATCTCAAGCGAGATAAATCTTCTATTTCCAGTG
1 AAACTATCTCAAGTGAGATAAATCTTCTGTTTCGAGTG
111835 AAACTATCTCAAGTGAGAT
1 AAACTATCTCAAGTGAGAT
111854 GTTGATCCCT
Statistics
Matches: 115, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
38 80 0.70
39 35 0.30
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (38 bp):
AAACTATCTCAAGTGAGATAAATCTTCTGTTTCGAGTG
Found at i:111797 original size:77 final size:76
Alignment explanation
Indices: 111682--111853 Score: 218
Period size: 77 Copynumber: 2.2 Consensus size: 76
111672 TGTTTTAAGA
* * * * * * *
111682 AAACAATCTCTAGTGAGATAAATCTTCTGTTTCAAGTGAAACTATCTCAAGCTAGATAAATCTTT
1 AAACTATCTCAAGCGAGATAAATATTATGTTTCAAGTGAAACTATCTCAAGCGAGATAAATCTTC
* **
111747 TGTTTTGAGTG
66 TATTTCCAGTG
* *
111758 AAACTCTCTCAAGCGAGATAAAATATTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAATCTT
1 AAACTATCTCAAGCGAGAT-AAATATTATGTTTCAAGTGAAACTATCTCAAGCGAGATAAATCTT
111823 CTATTTCCAGTG
65 CTATTTCCAGTG
*
111835 AAACTATCTCAAGTGAGAT
1 AAACTATCTCAAGCGAGAT
111854 GTTGATCCCT
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
76 15 0.19
77 66 0.81
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (76 bp):
AAACTATCTCAAGCGAGATAAATATTATGTTTCAAGTGAAACTATCTCAAGCGAGATAAATCTTC
TATTTCCAGTG
Found at i:112050 original size:42 final size:41
Alignment explanation
Indices: 111938--112050 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 41
111928 TCCAAAGGTC
* * *
111938 TTATGGATGGCCTGAAGGACTTATCATCTTGCTCGAAAGAC
1 TTATAGATGGCCTGAAGGACTTATCATCATGCTCGAAAGAA
* * * *
111979 TTATAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGAA
1 TTATAGATGGCCTGAAGGACTT-ATCATCATGCTCGAAAGAA
* *
112021 TTATTGATGGCATGAAGGACTTACTCATCA
1 TTATAGATGGCCTGAAGGACTTA-TCATCA
112051 AGAAACCCTT
Statistics
Matches: 57, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
41 19 0.33
42 38 0.67
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (41 bp):
TTATAGATGGCCTGAAGGACTTATCATCATGCTCGAAAGAA
Found at i:115726 original size:24 final size:26
Alignment explanation
Indices: 115681--115731 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
115671 ACAAGGCCAG
*
115681 ACAAAAGGAAATCAATGTTAGTAGAA
1 ACAAAAAGAAATCAATGTTAGTAGAA
*
115707 ACAAAAAG-AATCAA-GTTAGTTGAA
1 ACAAAAAGAAATCAATGTTAGTAGAA
115731 A
1 A
115732 TGATTAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
25 6 0.26
26 7 0.30
ACGTcount: A:0.55, C:0.08, G:0.18, T:0.20
Consensus pattern (26 bp):
ACAAAAAGAAATCAATGTTAGTAGAA
Found at i:117659 original size:23 final size:23
Alignment explanation
Indices: 117615--117672 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
117605 CTTAATTAAA
117615 AAAATAAAAT--AAATAAATAAT
1 AAAATAAAATAAAAATAAATAAT
*
117636 AACATAAAATAAAAATGAAA-AAT
1 AAAATAAAATAAAAAT-AAATAAT
117659 AAAATAAACATAAA
1 AAAATAAA-ATAAA
117673 TAGAAGGACC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 9 0.29
23 14 0.45
24 8 0.26
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (23 bp):
AAAATAAAATAAAAATAAATAAT
Found at i:121996 original size:23 final size:23
Alignment explanation
Indices: 121947--121996 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
121937 TATGGCTATT
* **
121947 AATTAAGAAGAAAATTGGCCTTT
1 AATTAAGAAGAAAATTGGACTGA
121970 AATTAAGGAAGAAAA-TGGACTGA
1 AATTAA-GAAGAAAATTGGACTGA
121993 AATT
1 AATT
121997 GAGGCCGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (23 bp):
AATTAAGAAGAAAATTGGACTGA
Found at i:122006 original size:23 final size:23
Alignment explanation
Indices: 121980--122028 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
121970 AATTAAGGAA
121980 GAAAATGG-ACTGAAATTGAGGCC
1 GAAAATGGCA-TGAAATTGAGGCC
* * *
122003 GAAAGTGGCATGGAATTTAGGCC
1 GAAAATGGCATGAAATTGAGGCC
122026 GAA
1 GAA
122029 TATTGGCCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.37, C:0.12, G:0.33, T:0.18
Consensus pattern (23 bp):
GAAAATGGCATGAAATTGAGGCC
Found at i:122061 original size:7 final size:7
Alignment explanation
Indices: 122049--122096 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
122039 AAGCCGAAGT
122049 TATAATA
1 TATAATA
122056 TATAATA
1 TATAATA
122063 TATAATA
1 TATAATA
*
122070 TTTAAGTTA
1 TATAA--TA
*
122079 TTTAATA
1 TATAATA
122086 TTATAATA
1 -TATAATA
122094 TAT
1 TAT
122097 GAAATGAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
7 23 0.64
8 6 0.17
9 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (7 bp):
TATAATA
Found at i:122273 original size:14 final size:14
Alignment explanation
Indices: 122239--122274 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
122229 TAAGATATGA
122239 TTTTTT-AATAATG
1 TTTTTTAAATAATG
122252 TTTGTTTAAATAATG
1 TTT-TTTAAATAATG
122267 TTTTTTAA
1 TTTTTTAA
122275 TTGACAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 8 0.38
15 10 0.48
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (14 bp):
TTTTTTAAATAATG
Found at i:126130 original size:23 final size:23
Alignment explanation
Indices: 126074--126136 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
126064 AATGATTCAG
*
126074 TACTGACTGATTCAGCAAAACAC
1 TACTGAATGATTCAGCAAAACAC
* * *
126097 TACTGACTGATTCAGCAAAATAG
1 TACTGAATGATTCAGCAAAACAC
**
126120 TGTTGAATGATTCAGCA
1 TACTGAATGATTCAGCA
126137 CAGAAGTACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (23 bp):
TACTGAATGATTCAGCAAAACAC
Found at i:129727 original size:29 final size:29
Alignment explanation
Indices: 129687--129747 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
129677 AATTCATTAT
*
129687 TCTTTTATTCAACAGTGTTTAACCATTCA
1 TCTTTTACTCAACAGTGTTTAACCATTCA
*
129716 TCTTTTACTCAACAGTGTTTAACCGTTCA
1 TCTTTTACTCAACAGTGTTTAACCATTCA
129745 TCT
1 TCT
129748 AATTGGCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.08, T:0.44
Consensus pattern (29 bp):
TCTTTTACTCAACAGTGTTTAACCATTCA
Found at i:129801 original size:110 final size:110
Alignment explanation
Indices: 129631--129828 Score: 256
Period size: 110 Copynumber: 1.8 Consensus size: 110
129621 TATTTAGACT
* * * * ** *
129631 TTCATCTAACTTGCGTATTTGACACTTTTCTGTCAAATGTACATCTAATTCATTATTCTTTTATT
1 TTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGCACATCTAAGCCATTATTCTTTTACT
**
129696 CAACAGTGTTTAACCATTCATCTTTTACTCAACAGTGTTTAACCG
66 CAACAGTACTTAACCATTCATCTTTTACTCAACAGTGTTTAACCG
*
129741 TTCATCTAA-TTGGCATAATTGACACATTTCTGTCAAATGCACAGT-TAGGCCATTATTCTTTTA
1 TTCATCTAACTT-GCATAATTGACACATTTCTGTCAAATGCACA-TCTAAGCCATTATTCTTTTA
* *
129804 CTCAACGGTACTTAACCGTTCATCT
64 CTCAACAGTACTTAACCATTCATCT
129829 AACTGACATA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
109 2 0.03
110 71 0.96
111 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (110 bp):
TTCATCTAACTTGCATAATTGACACATTTCTGTCAAATGCACATCTAAGCCATTATTCTTTTACT
CAACAGTACTTAACCATTCATCTTTTACTCAACAGTGTTTAACCG
Found at i:129995 original size:79 final size:81
Alignment explanation
Indices: 129716--130017 Score: 473
Period size: 81 Copynumber: 3.8 Consensus size: 81
129706 TAACCATTCA
* ** *
129716 TCTTTTACTCAACAGTGTTTAACCGTTCATCTAATTGGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
129781 ACAGTTAGGCCATTAT
66 ACAGTTAGGCCATTAT
* * *
129797 TCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGACATAATTGATACATTTATGTCAAATGC
1 TCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
**
129862 ACAACTAGGCCATTAT
66 ACAGTTAGGCCATTAT
*
129878 TCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
129943 ACAGTTAGGCCATT-T
66 ACAGTTAGGCCATTAT
* * *
129958 T-TTTTACTCAATGGTACTTAACTGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAA
1 TCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGTCAA
130018 TTAACAGTTT
Statistics
Matches: 204, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
79 57 0.28
80 2 0.01
81 145 0.71
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (81 bp):
TCTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
ACAGTTAGGCCATTAT
Found at i:130129 original size:68 final size:68
Alignment explanation
Indices: 129982--130240 Score: 385
Period size: 68 Copynumber: 3.8 Consensus size: 68
129972 TACTTAACTG
* * ** * *
129982 TTCATCTAACTGGCATAATTGACACCTTTCTGTC-AATTAACAGTTTGGCCTCAAAGGCATTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
130046 GCT
66 GCT
* *
130049 TTCATCTAACTGGCATAAATGATACATTTCTGTCAAATGCACGGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
130114 CCT
66 GCT
*
130117 TTCATCTAACTGGCATAAATGACACATTTCTTTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
130182 GCT
66 GCT
* * * *
130185 TTCATCTAATTGGCATAAATGATACATTTATGCCAAATGCACAGTTAGGCCTCAAA
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAA
130241 TCTTTTATCT
Statistics
Matches: 173, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
67 31 0.18
68 142 0.82
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
GCT
Found at i:135645 original size:18 final size:17
Alignment explanation
Indices: 135615--135648 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
135605 TTTTTATCCA
135615 TTTATTTTTATTATTAG
1 TTTATTTTTATTATTAG
135632 TTTATTTATTATTATTA
1 TTTATTT-TTATTATTA
135649 AATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTATTTTTATTATTAG
Found at i:136988 original size:17 final size:15
Alignment explanation
Indices: 136962--137000 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 15
136952 CTTTATTACT
136962 TTTTACATTTTATTATA
1 TTTTA-ATTTTATT-TA
136979 GTTTTAATTTTATTTA
1 -TTTTAATTTTATTTA
136995 TTTTAA
1 TTTTAA
137001 ACATTGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 2 0.10
17 8 0.38
18 5 0.24
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTAATTTTATTTA
Found at i:137312 original size:28 final size:28
Alignment explanation
Indices: 137265--137321 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
137255 AATATTTTAC
137265 TTTATATATTGTAATTATTTTTATAAATGT
1 TTTATATATTGTAATTATTTTT-T-AATGT
*
137295 TTTA-ATATT-TATTTATTTTTTAATGT
1 TTTATATATTGTAATTATTTTTTAATGT
137321 T
1 T
137322 AAGAAAAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 6 0.23
27 1 0.04
28 10 0.38
29 5 0.19
30 4 0.15
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (28 bp):
TTTATATATTGTAATTATTTTTTAATGT
Found at i:137937 original size:2 final size:2
Alignment explanation
Indices: 137930--137970 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
137920 TATTTTCATA
137930 AT AT AT 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 AT AT AT A
137971 GTATTTTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:140393 original size:2 final size:2
Alignment explanation
Indices: 140386--140431 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
140376 TTTATTTTAT
140386 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
140428 TA TA
1 TA TA
140432 CATAACCATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:141751 original size:10 final size:10
Alignment explanation
Indices: 141715--141743 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
141705 TCCTTTACCA
141715 TTTATTTATT
1 TTTATTTATT
141725 TTTATTTATT
1 TTTATTTATT
141735 TTTATTTAT
1 TTTATTTAT
141744 CTCTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTATT
Found at i:151680 original size:105 final size:105
Alignment explanation
Indices: 151495--152361 Score: 1581
Period size: 105 Copynumber: 8.3 Consensus size: 105
151485 AGGTTTTACC
151495 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
151560 ACGAAGGGACAGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
151600 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
151665 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* ** *
151705 CAGAGCCAATTTCAACTTCACAATGATTGATATTGGAATCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
151770 ACGAAGGGACCGGTGGTTGTCAACAAACATTGCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
151810 CAGAGCCAATTTCAACTTTACAACGAAGCATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
151875 ACGAAGGGACCGCTAGTTGTCAACAAACATTGCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
151915 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
151980 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
**
152020 CAGAGCCAATTTCAACTTCACAACGATTGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
152085 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
152125 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
152190 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
152230 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
152295 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
152335 CAGAGCCAATTTCAACTTCACGACGAA
1 CAGAGCCAATTTCAACTTCACAACGAA
152362 TGATCCAGGC
Statistics
Matches: 735, Mismatches: 27, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 735 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:155980 original size:20 final size:20
Alignment explanation
Indices: 155919--155988 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
155909 AGAGTTTGAT
155919 GTTGAAAAGGAAAAATGTGA
1 GTTGAAAAGGAAAAATGTGA
*
155939 GTTAAAAAGGAAAAATGTGA
1 GTTGAAAAGGAAAAATGTGA
* * *
155959 GTTGCAAAGGAAAACTGGGA
1 GTTGAAAAGGAAAAATGTGA
155979 GTTGGAAAAG
1 GTT-GAAAAG
155989 AAGAATTTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 38 0.88
21 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.31, T:0.19
Consensus pattern (20 bp):
GTTGAAAAGGAAAAATGTGA
Found at i:156674 original size:15 final size:15
Alignment explanation
Indices: 156654--156685 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
156644 GATCAATACC
*
156654 TTTTGCATACATTCA
1 TTTTGCACACATTCA
156669 TTTTGCACACATTCA
1 TTTTGCACACATTCA
156684 TT
1 TT
156686 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCACACATTCA
Found at i:164002 original size:13 final size:13
Alignment explanation
Indices: 163961--163990 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
163951 ATATTATGCT
*
163961 TGAAGGAAAAAAA
1 TGAAGAAAAAAAA
163974 TGAAGAAAAAAAA
1 TGAAGAAAAAAAA
163987 TGAA
1 TGAA
163991 AATGAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (13 bp):
TGAAGAAAAAAAA
Found at i:164377 original size:21 final size:20
Alignment explanation
Indices: 164353--164393 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
164343 TATCTTTTTG
*
164353 AAATTCAATTTGTTTTGTTCA
1 AAATTCAATTTATTTT-TTCA
*
164374 AAATTTAATTTATTTTTTCA
1 AAATTCAATTTATTTTTTCA
164394 CATAAACATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (20 bp):
AAATTCAATTTATTTTTTCA
Found at i:165734 original size:113 final size:113
Alignment explanation
Indices: 165536--165982 Score: 641
Period size: 113 Copynumber: 4.0 Consensus size: 113
165526 TAGAAAAAAT
* * * *
165536 TTGAATTCATCACTTGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCAACTGA
1 TTGAATTCATCACTCGATGGATCATCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
165601 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
165649 TTGAATTCATCACTTGATGGATTATCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCACTCGATGGATCATCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
* *
165714 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * ** * * *
165762 TTGAATTCAACAC-CCATTGGATCAAAATTTCCAGGTAGAATTCATAATGAAAAGGACTCATCTG
1 TTGAATTCATCACTCGA-TGGATCATCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTG
* *
165826 AACAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC-AACCTTTTGC
* * * *
165876 TTGAATTCATCACTCGATGGATCAAT-TTTTCCA-GAAGTGTTCATAATGAGAAGAACTCGTCTG
1 TTGAATTCATCACTCGATGGATC-ATCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTG
*
165939 AAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTT
165983 AATTTAATTT
Statistics
Matches: 300, Mismatches: 30, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
111 6 0.02
112 30 0.10
113 228 0.76
114 33 0.11
115 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
TTGAATTCATCACTCGATGGATCATCATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:165976 original size:20 final size:20
Alignment explanation
Indices: 165913--165977 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 20
165903 TTTCCAGAAG
165913 TGTTCATAATGAGAAGAACT
1 TGTTCATAATGAGAAGAACT
* * * *
165933 CGTCTGAAGAAGGAGAAGAA--
1 TGT-T-CATAATGAGAAGAACT
165953 -GTTCATAATGAGAAGAACT
1 TGTTCATAATGAGAAGAACT
165972 TGTTCA
1 TGTTCA
165978 ACCTTAATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
17 11 0.33
18 1 0.03
19 2 0.06
20 7 0.21
21 1 0.03
22 11 0.33
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.25
Consensus pattern (20 bp):
TGTTCATAATGAGAAGAACT
Found at i:166348 original size:3 final size:3
Alignment explanation
Indices: 166334--166414 Score: 69
Period size: 3 Copynumber: 27.3 Consensus size: 3
166324 TTGTTTTCAT
* * * * * *
166334 TTA TTT TTA TTA TTA GT- TTA TTTA TTA TAA ATA TTA TTA TAA ATA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
166379 TT- TTA TT- TTA TTTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA T
166415 AAATTTATAT
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
2 5 0.08
3 50 0.82
4 6 0.10
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:166389 original size:35 final size:36
Alignment explanation
Indices: 166341--166408 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
166331 CATTTATTTT
166341 TATTATTAGTTTATTTATTATAAATATTATTATAAA
1 TATTATTAGTTTATTTATTATAAATATTATTATAAA
* * *
166377 TATT-TTATTTTATTTATTATTATTATTATTAT
1 TATTATTAGTTTATTTATTATAAATATTATTAT
166409 TATTATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 25 0.86
36 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (36 bp):
TATTATTAGTTTATTTATTATAAATATTATTATAAA
Found at i:167733 original size:17 final size:15
Alignment explanation
Indices: 167707--167745 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 15
167697 CTTTATTACT
167707 TTTTACATTTTATTATA
1 TTTTA-ATTTTATT-TA
167724 GTTTTAATTTTATTTA
1 -TTTTAATTTTATTTA
167740 TTTTAA
1 TTTTAA
167746 ACATTGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 2 0.10
17 8 0.38
18 5 0.24
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTAATTTTATTTA
Found at i:168006 original size:24 final size:24
Alignment explanation
Indices: 167979--168059 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
167969 GCACTTAACA
167979 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
168003 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
168025 -TGCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
168047 GTGCATCGATGCA
1 GTGCATCGATGCA
168060 CAGGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:170315 original size:17 final size:17
Alignment explanation
Indices: 170293--170336 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
170283 GAGAAATATT
170293 AAGTGTTAAAAAGGGAG
1 AAGTGTTAAAAAGGGAG
170310 AAGTGTTAAAAAGGGAG
1 AAGTGTTAAAAAGGGAG
170327 AAGTGTTAAA
1 AAGTGTTAAA
170337 GTAAGGGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (17 bp):
AAGTGTTAAAAAGGGAG
Found at i:170787 original size:45 final size:46
Alignment explanation
Indices: 170738--170826 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 46
170728 AAACATCGAG
* * *
170738 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAA
1 TGCATTTGATGCATCGATGCACAAGACCATACATCGATGCACTCAA
170783 TGCATTTGATGCATCGATGCACAAGACCATACATCGATGCACTC
1 TGCATTTGATGCATCGATGCACAAGACCATACATCGATGCACTC
170827 TAAGTGCACC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.52
46 19 0.47
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATACATCGATGCACTCAA
Found at i:171684 original size:58 final size:58
Alignment explanation
Indices: 171622--171820 Score: 285
Period size: 58 Copynumber: 3.5 Consensus size: 58
171612 CTTACAATTT
* * * *
171622 GTATGAATTTCTTATCTTTATGCACACAAAGTGTCTAATACGGAAATTCACACACTAA
1 GTATGAATTTCTTATCTTTTTGCACACAAAGTGCCCAATACGGAAATTCACACACTTA
* * **
171680 GTATGAATTTCTTCTCTTTTTGCGCACAAAGTGCCCAATACATAAATTCACACACTTA
1 GTATGAATTTCTTATCTTTTTGCACACAAAGTGCCCAATACGGAAATTCACACACTTA
* *
171738 GTATGAATTTCTTCTCTTTTTGCACACAAAGTGCCCAATACGGAAATTCATACACTTA
1 GTATGAATTTCTTATCTTTTTGCACACAAAGTGCCCAATACGGAAATTCACACACTTA
*
171796 GTATGAATTCCTTA-C-TTTTGCACAC
1 GTATGAATTTCTTATCTTTTTGCACAC
171821 TTTGTGCCAT
Statistics
Matches: 127, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
56 10 0.08
57 1 0.01
58 116 0.91
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (58 bp):
GTATGAATTTCTTATCTTTTTGCACACAAAGTGCCCAATACGGAAATTCACACACTTA
Found at i:172162 original size:20 final size:20
Alignment explanation
Indices: 172116--172162 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
172106 TCAATAGTAT
*
172116 CGATACAACTACCCTGGTAC
1 CGATACTACTACCCTGGTAC
172136 CGATACTACTACCCTGGTAC
1 CGATACTACTACCCTGGTAC
*
172156 TGATACT
1 CGATACT
172163 TCTATACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.26
Consensus pattern (20 bp):
CGATACTACTACCCTGGTAC
Found at i:172299 original size:95 final size:94
Alignment explanation
Indices: 172145--172354 Score: 258
Period size: 95 Copynumber: 2.2 Consensus size: 94
172135 CCGATACTAC
* * * *
172145 TACCCTGGTACTGATACTTCTATACTATGGTACAGATACCCCCTTACAGTATCGATACCAATTTT
1 TACCATGGTATTGATACTACCATACTATGGTACAGATACCCCCTTACAGTATCGATACCAATTTT
* * * *
172210 AGGTTCGAAGTTTCCTAGTATCGATATCCT
66 AGCTTC-AAGATACCTAGTATCGATACCCT
** * *
172240 TACCATGGTATTGATACTACCATACTATGGTACCTATACCCCCTTCCGGTATCGATACCAATTTT
1 TACCATGGTATTGATACTACCATACTATGGTACAGATACCCCCTTACAGTATCGATACCAATTTT
** * *
172305 AGCTTCTTGATACTTGGTATCGATACCCT
66 AGCTTCAAGATACCTAGTATCGATACCCT
*
172334 TACCATGGTATCGATACTACC
1 TACCATGGTATTGATACTACC
172355 TCGTCGGTAT
Statistics
Matches: 98, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
94 36 0.37
95 62 0.63
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (94 bp):
TACCATGGTATTGATACTACCATACTATGGTACAGATACCCCCTTACAGTATCGATACCAATTTT
AGCTTCAAGATACCTAGTATCGATACCCT
Found at i:176545 original size:29 final size:29
Alignment explanation
Indices: 176507--176563 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
176497 TTCATTATTC
* *
176507 TTTTATTCAACAGTGTTTAACCATTCATG
1 TTTTACTCAACAATGTTTAACCATTCATG
* *
176536 TTTTACTCAATAATGTTTAACCGTTCAT
1 TTTTACTCAACAATGTTTAACCATTCAT
176564 CTAACTACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.46
Consensus pattern (29 bp):
TTTTACTCAACAATGTTTAACCATTCATG
Found at i:176928 original size:81 final size:81
Alignment explanation
Indices: 176552--176931 Score: 474
Period size: 81 Copynumber: 4.7 Consensus size: 81
176542 TCAATAATGT
* * * * *
176552 TTAACCGTTCATCTAACT-ACATAATTGGCACATTTTTATCAAATGCACAGTTAGGCCATTATTC
1 TTAACCATTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCATTATTC
*
176616 TTTTACTCAACAGTAC
66 TTTTACTCAACGGTAC
** *
176632 TTAACCATTCATCTAACTGACATAATTGACACCTTTCTGAAAAATGCACAGCTAGGCCATTATTC
1 TTAACCATTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCATTATTC
*
176697 TTTTACTCAACGATAC
66 TTTTACTCAACGGTAC
** * * * *
176713 TTAAATATTCATCTAACTGGCATAACTAACACCTTTCTGTCAAATGCACAGCTAGGCCATTATTC
1 TTAACCATTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCATTATTC
176778 TTTTACTCAACGGTAC
66 TTTTACTCAACGGTAC
* * * * * * *
176794 TTAACCATTCACCTAAATAACATAACTAACACCTTTTTGTCAAATGCACAGTTAAGCCATTATTC
1 TTAACCATTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCATTATTC
*
176859 TTTTACTCAATGGTAC
66 TTTTACTCAACGGTAC
** * * * * *
176875 TTAACTGTTCATCTAACTGGCATAATTGACACCTTTATGTCAATTGTATAGTTAGGC
1 TTAACCATTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
176932 TTCAAAGGCA
Statistics
Matches: 258, Mismatches: 41, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
80 17 0.07
81 241 0.93
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35
Consensus pattern (81 bp):
TTAACCATTCATCTAACTGACATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCATTATTC
TTTTACTCAACGGTAC
Found at i:180738 original size:27 final size:28
Alignment explanation
Indices: 180675--180743 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 28
180665 AACCCGACCC
* *
180675 AACCTGACCCGAATATCACACTTAAAAAA
1 AACCCGACCCGAATATAACACTT-AAAAA
180704 AACCCGACCCGAATATAACACTT-AAAA
1 AACCCGACCCGAATATAACACTTAAAAA
180731 AACCCGACCCGAA
1 AACCCGACCCGAA
180744 CAAAATAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 17 0.45
29 21 0.55
ACGTcount: A:0.46, C:0.32, G:0.09, T:0.13
Consensus pattern (28 bp):
AACCCGACCCGAATATAACACTTAAAAA
Found at i:181119 original size:186 final size:186
Alignment explanation
Indices: 180795--181138 Score: 537
Period size: 186 Copynumber: 1.8 Consensus size: 186
180785 AAAATCCGAC
* * *
180795 CCGACCCGACCCAAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTACCTTAATCTGACTC
1 CCGACCCGACCCAAAATAATAAAAAAATATTTTTATTTAATAAAAACAATACCTTAATCCGACCC
* * * *
180860 GACCCGAATTATATATATTTTTGGGTCAGTCTGGTTTTTTTCACCTTAAACCTGAACCTGACCCG
66 GACCCGAATTATATATATTTTCGGGTCAGTCCGGTTTTTTTCACCCTAAACCTGAACCCGACCCG
*
180925 ATCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAACAAAATAAAGTTTCAT
131 ACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAACAAAATAAAGTTTCAT
* *
180981 CCGACCCGACCCGAAATAATAAAAAAATTTTTTTATTTAATAAAAACAATGA-CTTAATCCGACC
1 CCGACCCGACCCAAAATAATAAAAAAATATTTTTATTTAATAAAAACAAT-ACCTTAATCCGACC
* * * **
181045 CGACTCGAATTATATATATTTTCGTGTCGGTCCGGTTTTTTTCACCCTAAACCTGAACCCGACTT
65 CGACCCGAATTATATATATTTTCGGGTCAGTCCGGTTTTTTTCACCCTAAACCTGAACCCGACCC
181110 GACCCGACCCGAATATCACACTTAAAAAA
130 GACCCGACCCGAATATCACACTTAAAAAA
181139 TCCGGCCCGA
Statistics
Matches: 142, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
186 141 0.99
187 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (186 bp):
CCGACCCGACCCAAAATAATAAAAAAATATTTTTATTTAATAAAAACAATACCTTAATCCGACCC
GACCCGAATTATATATATTTTCGGGTCAGTCCGGTTTTTTTCACCCTAAACCTGAACCCGACCCG
ACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAACAAAATAAAGTTTCAT
Found at i:181403 original size:210 final size:213
Alignment explanation
Indices: 181154--181578 Score: 703
Period size: 210 Copynumber: 2.0 Consensus size: 213
181144 CCCGACTCGA
* * *
181154 CCCGAATATCACACTTAGAAAACCTGATCCGAACCGAACAAAATAAAGTTTCATCTGACCCGATC
1 CCCGAATATCACACTTAGAAAA-C-AACCCGAACCGAACAAAATAAAGTTTCATCTGACCCGACC
*
181219 TGAATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAA
64 CGAATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAA
* * *
181284 TAAAACCAGTGACTTAATCCAACCCGACCCGAATTATATATATTTTCGGGTCGGTCCG-GTTTTT
129 TAAAAACAATGACTTAATCCAACCCGACCCGAATTATATATATTTTCGGGTCGATCCGAGTTTTT
*
181348 TCACCCTAAACCCGAACCCG
194 TCACCCTAAACCAGAACCCG
*
181368 CCCGAATATCACACTTA-AAAA-AACCCGACCCGAACAAAATAAAGTTTCATCTGACCCGACCCG
1 CCCGAATATCACACTTAGAAAACAACCCGAACCGAACAAAATAAAGTTTCATCTGACCCGACCCG
181431 AATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATA
66 AATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATA
* * *
181496 AAAACAATGACTTAATCCGACCCGACCTGAATTATATATATTTTCGGGTCGATCCGATTTTTTTC
131 AAAACAATGACTTAATCCAACCCGACCCGAATTATATATATTTTCGGGTCGATCCGAGTTTTTTC
181561 ACCCTAAACCAGAACCCG
196 ACCCTAAACCAGAACCCG
181579 ACCCAAAATA
Statistics
Matches: 198, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
210 153 0.77
211 24 0.12
213 4 0.02
214 17 0.09
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.25
Consensus pattern (213 bp):
CCCGAATATCACACTTAGAAAACAACCCGAACCGAACAAAATAAAGTTTCATCTGACCCGACCCG
AATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATA
AAAACAATGACTTAATCCAACCCGACCCGAATTATATATATTTTCGGGTCGATCCGAGTTTTTTC
ACCCTAAACCAGAACCCG
Found at i:182321 original size:9 final size:9
Alignment explanation
Indices: 182307--182340 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
182297 TAAAAGGGAA
182307 AAATAAAAT
1 AAATAAAAT
182316 AAATAAAAT
1 AAATAAAAT
182325 AAAT-AAAT
1 AAATAAAAT
182333 AAGATAAA
1 AA-ATAAA
182341 GGAAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:182328 original size:13 final size:13
Alignment explanation
Indices: 182306--182340 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
182296 GTAAAAGGGA
182306 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
182320 AAAATAAATAAAT
1 AAAATAAATAAAT
*
182333 AAGATAAA
1 AAAATAAA
182341 GGAAAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:183252 original size:37 final size:37
Alignment explanation
Indices: 183202--183290 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
183192 GTGCTTGTGG
* * * *
183202 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACT-CT
1 ATCCTATTTTTAGGAATTTAAATCCTAGCA-AAATGCT
* * *
183239 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAATTTAAATCCTAGCAAAATGCT
183276 ATCCTATTTTTAGGA
1 ATCCTATTTTTAGGA
183291 GTTTGAATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
36 3 0.07
37 41 0.93
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAATTTAAATCCTAGCAAAATGCT
Found at i:184149 original size:105 final size:105
Alignment explanation
Indices: 183850--184821 Score: 1408
Period size: 105 Copynumber: 9.3 Consensus size: 105
183840 CATTGTTCCA
* * ** * *
183850 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * *
183914 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * *
183956 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
184016 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
184056 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
184121 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
184161 AGTCCAATATCCTTAGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
***
184226 AGCGGTCCCTTCGTCGTGAAGTTGAACTTATATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
184266 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
184326 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
184366 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
184431 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
184471 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
184536 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
184576 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAGTTGTTGTTGACAAC
184641 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
184682 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAC
* * * * *
184747 CAGCCGTCCCTTCGTTGTGATGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
184788 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
184822 CGCGGATGGC
Statistics
Matches: 793, Mismatches: 57, Indels: 29
0.90 0.06 0.03
Matches are distributed among these distances:
100 170 0.21
101 6 0.01
102 8 0.01
103 1 0.00
104 10 0.01
105 388 0.49
106 185 0.23
107 3 0.00
109 22 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:184320 original size:205 final size:206
Alignment explanation
Indices: 183850--184821 Score: 1353
Period size: 205 Copynumber: 4.6 Consensus size: 206
183840 CATTGTTCCA
* * * *
183850 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAA-C-TGAAA-T-TTTGTTGACAAC
* * *
183915 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
61 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
**
183980 TTGAAATTGAATCTGA-A-T-GAAA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
126 TTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
*
184040 AACTTGCGTTGTCTGG
191 AACTTGCATTGTCTGG
* * * * *
184056 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAACT--GAAATT-TTGTTGACAACC
* *
184121 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTAGTTGTGAAGT
62 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGT
184186 TGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
127 TGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
**
184251 ACTTATATTGTCTGG
192 ACTTGCATTGTCTGG
* *
184266 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA-TGAAATTTTGTTGACAAGCAGCG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAACTGAAATTTTGTTGACAACCAGCG
*
184330 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
66 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAA
184395 ATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
131 ATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
184460 GCATTGTCTGG
196 GCATTGTCTGG
* *
184471 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ACT--GAAATT-TTGTTGACAACC
* *
184536 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
62 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGT
* * * *
184601 TGAAATTGGCTCTGAAATTGGGAAAATTGTTTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
127 TGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
*
184666 AACTTGCGTTGTCTGG
191 AACTTGCATTGTCTGG
*
184682 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AACTGA-AA--T-TTTGTTGACAAC
* * * * * *
184747 CAGCCGTCCCTTCGTTGTGATGTTGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCGTG
61 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGT-CCA--ATATCCTTCGTTGTG
*
184812 GAGTTGAAAT
123 AAGTTGAAAT
184822 CGCGGATGGC
Statistics
Matches: 697, Mismatches: 47, Indels: 35
0.89 0.06 0.04
Matches are distributed among these distances:
204 1 0.00
205 275 0.39
206 48 0.07
207 2 0.00
208 5 0.01
209 11 0.02
210 179 0.26
211 99 0.14
212 52 0.07
213 4 0.01
215 21 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (206 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAACTGAAATTTTGTTGACAACCAGCG
GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAA
ATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCATTGTCTGG
Found at i:184476 original size:310 final size:310
Alignment explanation
Indices: 183850--184821 Score: 1473
Period size: 310 Copynumber: 3.1 Consensus size: 310
183840 CATTGTTCCA
* * ** *
183850 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAA-TTGTTTATTGACA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-A-TTGGAAAGTTG-TTGTTGACA
* * * *
183913 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGA
63 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGA
**
183978 AGTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
128 AGTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* * *
184043 TTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTT
193 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTT
*
184108 GTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAG
258 GTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTAG
* *
184161 AGTCCAATATCCTTAGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
* *
184226 AGCGGTCCCTTCGTCGTGAAGTTGAACTTATATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
184291 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
131 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
184356 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTT
196 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTT
* *
184421 GTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
261 GTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTAG
*
184471 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
*
184536 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
* *
184601 TGAAATTGGCTCTGAAATTGGGAAAATTGTTTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
131 TGAAATTGGCTCTG-AA-T--G-AAATT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
*
184666 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGA
190 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGA-A
* * * * ** *
184730 AGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGATGTTGAACTTGTGTTGTCTCG
254 AGTTG-TTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTAG
* * *
184788 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
184822 CGCGGATGGC
Statistics
Matches: 608, Mismatches: 40, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
310 384 0.63
311 42 0.07
312 2 0.00
314 1 0.00
315 7 0.01
316 99 0.16
317 48 0.08
318 3 0.00
320 22 0.04
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (310 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTT
GTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTAG
Found at i:185273 original size:29 final size:28
Alignment explanation
Indices: 185208--185274 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
185198 GCCTGTCTGG
*
185208 AATCTTGATTCTTGAATCTTCAAATTTTGA
1 AATC-TGA-TCTTGAATCTTCAAATGTTGA
***
185238 TCCCTGATCTTGAATTCTTCAAATGTTGA
1 AATCTGATCTTGAA-TCTTCAAATGTTGA
185267 AATCTGAT
1 AATCTGAT
185275 GTGCACATTC
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
28 7 0.24
29 21 0.72
30 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.43
Consensus pattern (28 bp):
AATCTGATCTTGAATCTTCAAATGTTGA
Found at i:185556 original size:67 final size:68
Alignment explanation
Indices: 185412--185582 Score: 213
Period size: 68 Copynumber: 2.5 Consensus size: 68
185402 GGAAACGATC
* * * *
185412 TCAAAGATATCTGTTGTTTCATGAGAAACGGTCTCAAGGGAAACAAATTTATGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAA
185477 TAAAT
64 TAAAT
** * * *
185482 TTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATT-TGTTTTAGGGGAAATA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATA
185546 AAT
66 AAT
*
185549 TCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAG
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAG
185583 ATAGCCGAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 22 0.25
66 3 0.03
67 23 0.26
68 31 0.35
69 3 0.03
70 6 0.07
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.33
Consensus pattern (68 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATA
AAT
Found at i:185609 original size:36 final size:35
Alignment explanation
Indices: 185558--185838 Score: 236
Period size: 36 Copynumber: 8.0 Consensus size: 35
185548 TTCAAAGATT
* * *
185558 TTGTTTCAAGGGAAACTGTCTCAAGATAGCCGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
185594 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * ** *
185629 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAAACGGTAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * **
185667 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
185696 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
185731 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
*
185768 TTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
185803 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
185839 CTCTTTTAGT
Statistics
Matches: 198, Mismatches: 31, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.01
29 16 0.08
30 1 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 10 0.05
36 131 0.66
37 32 0.16
38 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:185670 original size:138 final size:137
Alignment explanation
Indices: 185506--185812 Score: 382
Period size: 138 Copynumber: 2.2 Consensus size: 137
185496 TTTCAAGAGT
* * ** * *
185506 AACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAAACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * *
185571 AACTGTCTCAAGATAGCCGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
66 AACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGT
185635 TCCAAAAGA
129 TCCAAAAGA
*** * *
185644 AACTGTCTCAAGGGAAACGGTATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAAACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * *
185709 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
66 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
* *
185774 TAAGAGA
131 CAAAAGA
* *
185781 AACTGTCTCAAGAGAGACAAAATTTGTTTCAA
1 AACTGTCTCAAGGGAAACAAAATTTGTTTCAA
185813 GGGAAACTGT
Statistics
Matches: 142, Mismatches: 26, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
137 41 0.29
138 101 0.71
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (137 bp):
AACTGTCTCAAGGGAAACAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
CAAAAGA
Found at i:185782 original size:102 final size:102
Alignment explanation
Indices: 185594--185782 Score: 263
Period size: 102 Copynumber: 1.9 Consensus size: 102
185584 TAGCCGAAAA
*
185594 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
**
185659 AACGGTATTTGTTTCAAAGAAAACATATTCAAATATT
66 AACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
* * * ** *
185696 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA-TTTCAAGGGAAACTGTCTCAAGATA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
* *
185760 GACGAAATTTGTTTTAAGAGAAA
66 AACGAAATTTGTTTCAA-AGAAA
185783 CTGTCTCAAG
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
101 33 0.44
102 42 0.56
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (102 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
AACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
Found at i:185879 original size:71 final size:72
Alignment explanation
Indices: 185707--185880 Score: 230
Period size: 72 Copynumber: 2.4 Consensus size: 72
185697 TGTTTCAAGG
* * ** *
185707 GAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAACTCT
185772 TTTAAGA
66 TTTAAGA
185779 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAACTCT
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAACTCT
*
185843 TTT-AGT
66 TTTAAGA
*
185849 GAAAAC-GATCTCAAGCGAGAC-AAATCTTGTTT
1 G-AAACTG-TCTCAAGAGAGACAAAAT-TTGTTT
185881 TAAGAAAAAC
Statistics
Matches: 92, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
70 8 0.09
71 30 0.33
72 54 0.59
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (72 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAAACTCT
TTTAAGA
Found at i:185888 original size:35 final size:35
Alignment explanation
Indices: 185708--185888 Score: 188
Period size: 36 Copynumber: 5.1 Consensus size: 35
185698 GTTTCAAGGG
* * *
185708 AAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGG
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTTAA-GA
* *
185744 AAACTGTCTCAAGATAGACGAAATTTGTTTTAAGA
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGA
* *
185779 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
1 -AAACTGTCTCAAGAGAGACAAAATTTGTTTTAA-GA
* * *
185816 AAACTGTCTCAAGAGAGACAAAA-CTCTTTTAGTGA
1 AAACTGTCTCAAGAGAGACAAAATTTGTTTTA-AGA
*
185851 AAAC-GATCTCAAGCGAGAC-AAATCTTGTTTTAAGA
1 AAACTG-TCTCAAGAGAGACAAAAT-TTGTTTTAAGA
185886 AAA
1 AAA
185889 ACAATCATGA
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
34 4 0.03
35 28 0.23
36 88 0.73
37 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (35 bp):
AAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGA
Found at i:186344 original size:18 final size:18
Alignment explanation
Indices: 186317--186352 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
186307 TGTTGAATCC
* *
186317 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
186335 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
186353 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:186777 original size:22 final size:22
Alignment explanation
Indices: 186752--186802 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
186742 TTATGTTTGG
186752 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
186774 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
186796 TCAAAGG
1 TCAAAGG
186803 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:187426 original size:20 final size:21
Alignment explanation
Indices: 187403--187462 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
187393 TTTTGTCCCT
*
187403 TTTTTTATTTTTGTTCTTT-C
1 TTTTTTATTCTTGTTCTTTCC
* *
187423 TTTTTTGTTCTTGTTTTTTCC
1 TTTTTTATTCTTGTTCTTTCC
*
187444 TTTTTTTCTTCTT-TTCTTT
1 -TTTTTTATTCTTGTTCTTT
187463 TTTCTTTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 16 0.48
21 6 0.18
22 11 0.33
ACGTcount: A:0.02, C:0.13, G:0.05, T:0.80
Consensus pattern (21 bp):
TTTTTTATTCTTGTTCTTTCC
Found at i:187449 original size:10 final size:9
Alignment explanation
Indices: 187419--187465 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
187409 ATTTTTGTTC
187419 TTTCTTTTT
1 TTTCTTTTT
187428 TGTTCTTGTTT
1 T-TTCTT-TTT
*
187439 TTTCCTTTT
1 TTTCTTTTT
*
187448 TTTC-TTCT
1 TTTCTTTTT
187456 TTTCTTTTT
1 TTTCTTTTT
187465 T
1 T
187466 CTTTTTGCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
8 7 0.22
9 12 0.38
10 9 0.28
11 4 0.12
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:190503 original size:9 final size:9
Alignment explanation
Indices: 190489--190522 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
190479 GTAAAAGGGA
190489 AAATAAAAT
1 AAATAAAAT
190498 AAATAAAAT
1 AAATAAAAT
190507 AAAT-AAAT
1 AAATAAAAT
190515 AAGATAAA
1 AA-ATAAA
190523 GGAAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:190512 original size:13 final size:13
Alignment explanation
Indices: 190488--190522 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
190478 GGTAAAAGGG
190488 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
190502 AAAATAAATAAAT
1 AAAATAAATAAAT
*
190515 AAGATAAA
1 AAAATAAA
190523 GGAAAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:190825 original size:2 final size:2
Alignment explanation
Indices: 190784--190808 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
190774 AACGAAAATA
190784 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 A
190809 AAGTTATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:191445 original size:37 final size:37
Alignment explanation
Indices: 191395--191483 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
191385 GTGCTTGTGG
* * * *
191395 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACT-CT
1 ATCCTATTTTTAGGAATTTAAATCCTAGCA-AAATGCT
* * *
191432 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAATTTAAATCCTAGCAAAATGCT
191469 ATCCTATTTTTAGGA
1 ATCCTATTTTTAGGA
191484 GTTTGAATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
36 3 0.07
37 41 0.93
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAATTTAAATCCTAGCAAAATGCT
Found at i:192155 original size:24 final size:21
Alignment explanation
Indices: 192098--192148 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
192088 AATATTGATG
192098 TATCATCATAAAATAATACCA
1 TATCATCATAAAATAATACCA
192119 TATCATCATAAAATAATACCA
1 TATCATCATAAAATAATACCA
192140 TATCATCAT
1 TATCATCAT
192149 TAGAAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (21 bp):
TATCATCATAAAATAATACCA
Found at i:201024 original size:27 final size:27
Alignment explanation
Indices: 200986--201044 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
200976 TTTTAGTATT
*
200986 GTGTTCATGTTTGTTTTTCTTTTTTAA
1 GTGTTCATGTTTGTTTTTCTTTTTAAA
201013 GTGTTCATGTTTGTTTTTCTTTTTAAA
1 GTGTTCATGTTTGTTTTTCTTTTTAAA
201040 GTGTT
1 GTGTT
201045 TGTAATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.12, C:0.07, G:0.17, T:0.64
Consensus pattern (27 bp):
GTGTTCATGTTTGTTTTTCTTTTTAAA
Found at i:201401 original size:34 final size:34
Alignment explanation
Indices: 201363--201444 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
201353 TAAATGAGCT
*
201363 TATAAATGAGTCGATAAATGAGCTTGTTCGTGAA
1 TATAAATGAGTCGATAAACGAGCTTGTTCGTGAA
*
201397 TATAAATGAGTCGATAAACGAGCTTGTTTGTGAA
1 TATAAATGAGTCGATAAACGAGCTTGTTCGTGAA
*
201431 TATAAATGAATCGA
1 TATAAATGAGTCGA
201445 ACACACATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.32
Consensus pattern (34 bp):
TATAAATGAGTCGATAAACGAGCTTGTTCGTGAA
Found at i:214897 original size:5 final size:5
Alignment explanation
Indices: 214887--214943 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
214877 TGACCGGTCT
* *
214887 GACCC GACCC GA-CC GA-TC GA-CC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACCC
214936 GACCC GAC
1 GACCC GAC
214944 AGTTGACCGT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
4 10 0.22
5 31 0.69
7 4 0.09
ACGTcount: A:0.21, C:0.51, G:0.23, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:214948 original size:22 final size:22
Alignment explanation
Indices: 214887--214951 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
214877 TGACCGGTCT
*
214887 GACCCGACCCGACCGATCGA-CC
1 GACCCGACCCGACCG-TTGACCC
214909 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
214931 GACCCGACCCGACAGTTGACC
1 GACCCGACCCGACCGTTGACC
214952 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 3 0.08
22 37 0.93
ACGTcount: A:0.22, C:0.48, G:0.23, T:0.08
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:227467 original size:27 final size:27
Alignment explanation
Indices: 227413--227468 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
227403 CCGCCATCAC
* *
227413 CACTTTGAACTTGAAACTCCATAGCAT
1 CACTTTGAACTTGAAACTCCACAACAT
* *
227440 CACTTTGAGCTTGAAAGTCCACAACAT
1 CACTTTGAACTTGAAACTCCACAACAT
227467 CA
1 CA
227469 ATATCTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCACAACAT
Found at i:227738 original size:30 final size:30
Alignment explanation
Indices: 227676--227738 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
227666 GAACTGGCGA
* *
227676 TTCACACCGGTTTTGTTAGTTCCCAGTCGG
1 TTCACACCGGTTTTGCTAGTTCCCAGACGG
227706 TTCACACCGGTTTTGCCT-GTTCCCA-ACAGG
1 TTCACACCGGTTTTG-CTAGTTCCCAGAC-GG
227736 TTC
1 TTC
227739 TATAGGTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.03
30 27 0.93
31 1 0.03
ACGTcount: A:0.14, C:0.30, G:0.21, T:0.35
Consensus pattern (30 bp):
TTCACACCGGTTTTGCTAGTTCCCAGACGG
Found at i:227826 original size:25 final size:25
Alignment explanation
Indices: 227797--227850 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
227787 GGACAGGCAT
227797 CCGGTTCCTGGTTCAACAGGTCTAA
1 CCGGTTCCTGGTTCAACAGGTCTAA
227822 CCGGTTCCTGGTTCAACAGGTCTAA
1 CCGGTTCCTGGTTCAACAGGTCTAA
227847 CCGG
1 CCGG
227851 CCAGTCCGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.19, C:0.30, G:0.26, T:0.26
Consensus pattern (25 bp):
CCGGTTCCTGGTTCAACAGGTCTAA
Found at i:228789 original size:57 final size:57
Alignment explanation
Indices: 228709--229036 Score: 541
Period size: 57 Copynumber: 5.8 Consensus size: 57
228699 ATGGCACTGA
*
228709 GTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTT
* * *
228766 GTGTACAAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTT
* *
228823 GTGTGCAAAAAGTTCAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTT
228880 GTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTT
* * * * *
228937 GTGTACAAAAAGTTAAGAAATTCATAATAAGTTTACG-ATTTCCGTATGAGTAATTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTT
*
228993 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCC
1 GTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCC
229037 ATAAGGACAC
Statistics
Matches: 255, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
56 50 0.20
57 205 0.80
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (57 bp):
GTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTT
Found at i:247164 original size:23 final size:24
Alignment explanation
Indices: 247134--247180 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
247124 TATTATATCA
*
247134 TATTATTATTATTG-TATTTTTTT
1 TATTATTATTAATGCTATTTTTTT
247157 TATTATTATTAATGCTATTTTTTT
1 TATTATTATTAATGCTATTTTTTT
247181 ACAATTACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (24 bp):
TATTATTATTAATGCTATTTTTTT
Done.