Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008357.1 Hibiscus syriacus cultivar Beakdansim tig00111096_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: 1459476
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 7
Found at i:1215815 original size:22 final size:23
Alignment explanation
Indices: 1215766--1215817 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1215756 TGGCCCTGCA
*
1215766 AAATAATAATAAAAAATATTAAT
1 AAATAATAATAAAAAATATAAAT
* *
1215789 -TATAATAATAATAAATA-AAAT
1 AAATAATAATAAAAAATATAAAT
1215810 AAATAATA
1 AAATAATA
1215818 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AAATAATAATAAAAAATATAAAT
Found at i:1216233 original size:37 final size:37
Alignment explanation
Indices: 1216183--1216259 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
1216173 AAGGGTTTTT
*
1216183 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTG
* *
1216220 TTTCAAGGGAAACTATCTCTAGAGAGACAAAACTTTG
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTG
1216257 TTT
1 TTT
1216260 TGAGTACATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (37 bp):
TTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTG
Found at i:1216277 original size:47 final size:47
Alignment explanation
Indices: 1216223--1216315 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
1216213 AACTTTGTTT
1216223 CAAGGGAAACTATCTCTAGAGAGACAAAACTTTGTTTTGAGTACATA
1 CAAGGGAAACTATCTCTAGAGAGACAAAACTTTGTTTTGAGTACATA
*
1216270 CAAGGGAAATTATCTCTAGAGAGACAAAACTTTGTTTTGAGTACAT
1 CAAGGGAAACTATCTCTAGAGAGACAAAACTTTGTTTTGAGTACAT
1216316 TAGTCTTAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (47 bp):
CAAGGGAAACTATCTCTAGAGAGACAAAACTTTGTTTTGAGTACATA
Found at i:1216607 original size:124 final size:124
Alignment explanation
Indices: 1216387--1216623 Score: 359
Period size: 124 Copynumber: 1.9 Consensus size: 124
1216377 CTTGTTCCTG
* * *
1216387 AAGATGAATATTGCTGGTGGGTACGATTCCATTCGTCGTGAAGTTAAAACCGTGGATGGCCCCTT
1 AAGATGAATATTGCTGGTGGGCACGATTCCATTCATCGTGAAGTTAAAACCGTGGATGGCCCCTC
*
1216452 CGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTA
66 CGTCGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTA
* * * *
1216511 AAGATGAATGA-TGCTTGTGTGCACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGCCCCT
1 AAGATGAAT-ATTGCTGGTGGGCACGATTCCATTCATCGTGAAGTTAAAACCGTGGATGGCCCCT
* * *
1216575 CCGTCGTGGAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGGAGTTGA
65 CCGTCGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCATGAAGTTGA
1216624 GCCTTGAATT
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
124 100 0.99
125 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (124 bp):
AAGATGAATATTGCTGGTGGGCACGATTCCATTCATCGTGAAGTTAAAACCGTGGATGGCCCCTC
CGTCGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTA
Found at i:1216615 original size:34 final size:34
Alignment explanation
Indices: 1216576--1216657 Score: 146
Period size: 34 Copynumber: 2.4 Consensus size: 34
1216566 ATGGCCCCTC
*
1216576 CGTCGTGGAGTTGAGCCTTGAATTGGATATCCTT
1 CGTCGTGGAGTTGAGCCTTGAATTGGATATCATT
1216610 CGTCGTGGAGTTGAGCCTTGAATTGGATATCATT
1 CGTCGTGGAGTTGAGCCTTGAATTGGATATCATT
*
1216644 CGTCGTGAAGTTGA
1 CGTCGTGGAGTTGA
1216658 AATCCAATGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (34 bp):
CGTCGTGGAGTTGAGCCTTGAATTGGATATCATT
Found at i:1219036 original size:13 final size:13
Alignment explanation
Indices: 1219018--1219043 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1219008 CTTAATTACA
1219018 AAAAAATAAAAAT
1 AAAAAATAAAAAT
1219031 AAAAAATAAAAAT
1 AAAAAATAAAAAT
1219044 TCAATTCAAA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:1220753 original size:26 final size:26
Alignment explanation
Indices: 1220722--1220771 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1220712 AAAAATATTA
1220722 TATTATTATTATTATTATATATTACC
1 TATTATTATTATTATTATATATTACC
* *
1220748 TATTATTATTATTGTTATTTATTA
1 TATTATTATTATTATTATATATTA
1220772 TTATTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (26 bp):
TATTATTATTATTATTATATATTACC
Found at i:1220769 original size:10 final size:10
Alignment explanation
Indices: 1220722--1220776 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
1220712 AAAAATATTA
1220722 TATTA-TTAT
1 TATTATTTAT
1220731 TATTA-TTAT
1 TATTATTTAT
**
1220740 ATATTACCTAT
1 -TATTATTTAT
1220751 TATTA-TTAT
1 TATTATTTAT
*
1220760 TGTTATTTAT
1 TATTATTTAT
1220770 TATTATT
1 TATTATT
1220777 AATAATAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
9 16 0.41
10 20 0.51
11 3 0.08
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.64
Consensus pattern (10 bp):
TATTATTTAT
Found at i:1220797 original size:3 final size:3
Alignment explanation
Indices: 1220717--1220777 Score: 70
Period size: 3 Copynumber: 19.7 Consensus size: 3
1220707 CTTAAAAAAA
* *
1220717 TAT TA- TAT TAT TAT TAT TAT TAT ATAT TACC TAT TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT TAT TAT TAT
1220763 TATT TAT TAT TAT TA
1 TA-T TAT TAT TAT TA
1220778 ATAATAATAG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 2 0.04
3 40 0.80
4 8 0.16
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1222667 original size:13 final size:13
Alignment explanation
Indices: 1222636--1222700 Score: 62
Period size: 13 Copynumber: 4.9 Consensus size: 13
1222626 AAGGTAATTA
1222636 ATTTTCTTT-TTTT
1 ATTTT-TTTATTTT
*
1222649 AATTTTTTATTTT
1 ATTTTTTTATTTT
*
1222662 ATTTTTTTATTTG
1 ATTTTTTTATTTT
*
1222675 ATTTATTTAATATTT
1 ATTT-TTTTAT-TTT
1222690 A-TTTTTTATTT
1 ATTTTTTTATTT
1222701 CTTATCTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
12 5 0.12
13 28 0.65
14 7 0.16
15 3 0.07
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (13 bp):
ATTTTTTTATTTT
Found at i:1222668 original size:7 final size:7
Alignment explanation
Indices: 1222643--1222727 Score: 50
Period size: 7 Copynumber: 12.1 Consensus size: 7
1222633 TTAATTTTCT
1222643 TTTTTTAA
1 TTTTTT-A
1222651 TTTTTTA
1 TTTTTTA
1222658 --TTTTA
1 TTTTTTA
1222663 TTTTTT-
1 TTTTTTA
* *
1222669 TATTTGA
1 TTTTTTA
1222676 TTTATTTA
1 TTT-TTTA
* *
1222684 ATATTTA
1 TTTTTTA
1222691 TTTTTTA
1 TTTTTTA
*
1222698 TTTCTTA
1 TTTTTTA
* **
1222705 TCTAATA
1 TTTTTTA
1222712 TTTTTTA
1 TTTTTTA
1222719 CTTTTTTA
1 -TTTTTTA
1222727 T
1 T
1222728 GGATAGTTTA
Statistics
Matches: 57, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
5 5 0.09
6 4 0.07
7 31 0.54
8 17 0.30
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (7 bp):
TTTTTTA
Found at i:1222700 original size:22 final size:22
Alignment explanation
Indices: 1222654--1222700 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
1222644 TTTTTAATTT
*
1222654 TTTATTTTATTTTTTTATTTGA
1 TTTATTTTATTTATTTATTTGA
1222676 TTTATTTAATATTTATTT-TTT-A
1 TTTATTT--TATTTATTTATTTGA
1222698 TTT
1 TTT
1222701 CTTATCTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 11 0.50
23 3 0.14
24 8 0.36
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTATTTTATTTATTTATTTGA
Found at i:1222705 original size:25 final size:27
Alignment explanation
Indices: 1222659--1222714 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
1222649 AATTTTTTAT
* *
1222659 TTTATTTTTTTATTTGATTTATTTAATA
1 TTTATTTTTTTATTT-ACTTATCTAATA
1222687 TTTA-TTTTTTATTT-CTTATCTAATA
1 TTTATTTTTTTATTTACTTATCTAATA
1222712 TTT
1 TTT
1222715 TTTACTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 12 0.46
27 10 0.38
28 4 0.15
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTATTTTTTTATTTACTTATCTAATA
Found at i:1227111 original size:240 final size:240
Alignment explanation
Indices: 1226645--1227268 Score: 868
Period size: 240 Copynumber: 2.6 Consensus size: 240
1226635 TCGAGATTGT
* * * *
1226645 ATTTCAACTTCACAATAAAGGATATCT-AACTC-AAAGCAACATACAATACTTGGATTTCAACTT
1 ATTTCAACTTCACGACAAAGGATAT-TGGACTCGAAA-C-A-ATACAA-GCTTGGATTTCAACTT
* * * * * *
1226708 CACGGCGAAGGATA-T----TCAAGGTTCAACTTCACAACGAATGGGTTATCTACGATTTTAGCT
61 CACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAATGGGTCATCCACGATTTCAACT
* * * *
1226768 TCACGACGAATGATATCGTGTCAACTCTAGATTGGATTTCAACTTCACGACGAATGATATCCAAT
126 TCACGACGAAGGATATTGTGCCAACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAAT
* * * *
1226833 TCAAAGCTCAACTTCACGGCGAAGGGGCTTCCCAGTTTCATTCATATCCA
191 TCAAAGCTCAACTTCAAGGCGAAAGGGCTTCCCAGTTTCATTCAGAGCCA
1226883 ATTTCAACTTCACGACAAAGGATATTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGA
1 ATTTCAACTTCACGACAAAGGATATTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGA
* *
1226948 CGAAGGATATTCAAGTCAAGGCTCAACTTCAGAACGAATGGGTCATCCACGATTTCAACTTCATG
66 CGAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAATGGGTCATCCACGATTTCAACTTCACG
1227013 ACGAAGGATATTGTGCCAACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAA
131 ACGAAGGATATTGTGCCAACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAA
* *
1227078 GCTCAACTTCAAGGCTAAAGGGCTTCCCAGTTTCATTCAGAGCTA
196 GCTCAACTTCAAGGCGAAAGGGCTTCCCAGTTTCATTCAGAGCCA
* * * *
1227123 ATTTCAACTTTACGGCGAAGGATATTGGACTCGAAACAATACAAGCTTGAATTTCAACTTCACGA
1 ATTTCAACTTCACGACAAAGGATATTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGA
* * * *
1227188 CGAAGGATATTCAAGTTAAGGCTCAACTTCACAAAGAATGAGCCATCCACGATTTCAACTTCACG
66 CGAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAATGGGTCATCCACGATTTCAACTTCACG
1227253 ACGAAGGGA-ATTGTGC
131 ACGAA-GGATATTGTGC
1227269 TCACCAGTAA
Statistics
Matches: 346, Mismatches: 32, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
235 28 0.08
236 7 0.02
237 2 0.01
238 28 0.08
239 3 0.01
240 275 0.79
241 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (240 bp):
ATTTCAACTTCACGACAAAGGATATTGGACTCGAAACAATACAAGCTTGGATTTCAACTTCACGA
CGAAGGATATTCAAGTCAAGGCTCAACTTCACAACGAATGGGTCATCCACGATTTCAACTTCACG
ACGAAGGATATTGTGCCAACTCTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAA
GCTCAACTTCAAGGCGAAAGGGCTTCCCAGTTTCATTCAGAGCCA
Found at i:1227334 original size:124 final size:124
Alignment explanation
Indices: 1227173--1227520 Score: 527
Period size: 124 Copynumber: 2.8 Consensus size: 124
1227163 ACAAGCTTGA
* * * * *
1227173 ATTTCAACTTCACGACGAAGGATATTCAAGTTAAGGCTCAACTTCACAAAGAATGAGCCATCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAATGGGCCATCCAC
* * * *
1227238 GATTTCAACTTCACGACGAAGGGAATTGTGCTCACCAGTAACATTCATCTTTAGATTGG
66 GATTTCAACTTCACGACGAAGGGAATCGTGCCCACCAGCAACATTCATCTTCAGATTGG
* * *
1227297 ATTTCAACTTCATGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGTAGGGGCCATCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAATGGGCCATCCAC
* *
1227362 GGTTTCAACTTCACGACGAAGGGAATCGTTCCCACCAGCAACATTCATCTTCAGATTGG
66 GATTTCAACTTCACGACGAAGGGAATCGTGCCCACCAGCAACATTCATCTTCAGATTGG
* * *
1227421 ATTTCAACTTCACGACGAAGGATTTCCAATTCAAGGCTCAACTTCACAACGAATGGGCCCTCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAATGGGCCATCCAC
1227486 GATTTCAACTTCACGACGAA-GGATATCGTGCCCAC
66 GATTTCAACTTCACGACGAAGGGA-ATCGTGCCCAC
1227521 AAGAAGCAAT
Statistics
Matches: 201, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
123 3 0.01
124 198 0.99
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (124 bp):
ATTTCAACTTCACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAATGGGCCATCCAC
GATTTCAACTTCACGACGAAGGGAATCGTGCCCACCAGCAACATTCATCTTCAGATTGG
Found at i:1227851 original size:167 final size:168
Alignment explanation
Indices: 1227571--1228003 Score: 679
Period size: 167 Copynumber: 2.6 Consensus size: 168
1227561 GATATCGTGT
*
1227571 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCAAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* * * * *
1227636 CGCTAATCTCCAAAGCACATTATTTGTAGCATAACTCAAGGCTAAAAGGGTTATCTGCCAACAAA
66 CGCTCAGCTCCAAGGCACATTATTTGAAGCATAACTCAAGGATAAAAGGGTTATCTGCCAACAAA
* * *
1227701 ATACCTTCGAGTTTGACTACGCTCAGCTTCAAGGCACA
131 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
*
1227739 TCATTTGCAACATAGCTCAAGGAAAGAA-GGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* *
1227803 CGCTCAGCTCCAAGGCACATCATTTGAAGTATAACTCAAGGATAAAAGGGTTATCTGCCAACAAA
66 CGCTCAGCTCCAAGGCACATTATTTGAAGCATAACTCAAGGATAAAAGGGTTATCTGCCAACAAA
* *
1227868 AGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACG
131 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
* * *
1227906 TCATTTGCTACATAGCTCAAGGCAATAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* * *
1227971 CCCTCAGCTCTAAGGCACATTATTTGCAGCATA
66 CGCTCAGCTCCAAGGCACATTATTTGAAGCATA
1228004 TCTTAGGTCG
Statistics
Matches: 241, Mismatches: 23, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
167 151 0.63
168 90 0.37
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (168 bp):
TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACATTATTTGAAGCATAACTCAAGGATAAAAGGGTTATCTGCCAACAAA
AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
Found at i:1228020 original size:84 final size:84
Alignment explanation
Indices: 1227571--1228137 Score: 565
Period size: 84 Copynumber: 6.7 Consensus size: 84
1227561 GATATCGTGT
* * * * *
1227571 TCATTTGCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCAAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* * *
1227636 CGCTAATCTCCAAAGCACA
66 CGCTCAGCTCCAAGGCACA
* * * *
1227655 TTATTTGTAGCATAACTCAAGGCTAA-AAGGGTTATCTGCCAACAAAATACCTTCGAGTTTGACT
1 TCATTTGCAGCATAACTCAAGGC-AAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
*
1227719 ACGCTCAGCTTCAAGGCACA
65 ACGCTCAGCTCCAAGGCACA
* * * * *
1227739 TCATTTGCAACATAGCTCAAGGAAAGAA-GGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
1227803 CGCTCAGCTCCAAGGCACA
66 CGCTCAGCTCCAAGGCACA
* * * *
1227822 TCATTTGAAGTATAACTCAAGG-ATAAAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACT
1 TCATTTGCAGCATAACTCAAGGCA-AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
*
1227886 ACGCTCAGCTCCAAGGCACG
65 ACGCTCAGCTCCAAGGCACA
* * *
1227906 TCATTTGCTA-CATAGCTCAAGGCAATAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACT
1 TCATTTGC-AGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
* *
1227970 ACCCTCAGCTCTAAGGCACA
65 ACGCTCAGCTCCAAGGCACA
* * * * * * * * * * *
1227990 TTATTTGCAGCATATCT-TAGGTCGAGAAGGGATATCTACCAACCAAAGACCATCAAGTTCAATT
1 TCATTTGCAGCATAACTCAAGG-CAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
** *
1228054 ACATTCAGCT-CAAGGACATA
65 ACGCTCAGCTCCAAGG-CACA
* * * * * *
1228074 TCAAATTTACAACATAACCCAAGGCGAGAAAGGTTATCTGTCAAACAAAA-A-CTGTCGAGTTCG
1 TC--ATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTG-CCAACAAAAGACCT-TCGAGTTCG
1228137 A
62 A
1228138 TTCCATTCAG
Statistics
Matches: 397, Mismatches: 72, Indels: 26
0.80 0.15 0.05
Matches are distributed among these distances:
82 1 0.00
83 81 0.20
84 267 0.67
85 5 0.01
86 33 0.08
87 10 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (84 bp):
TCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACA
Found at i:1228474 original size:3 final size:3
Alignment explanation
Indices: 1228468--1228517 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
1228458 AACAATTACC
* *
1228468 TAT TAT TAT TAT TATT TGT TAT TAT TAT TAT AAT TAT T-T TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1228513 T-T TAT
1 TAT TAT
1228518 AGGGCCCATG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1228493 original size:22 final size:20
Alignment explanation
Indices: 1228468--1228518 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1228458 AACAATTACC
* *
1228468 TATTATTATTATTATT-TGT
1 TATTATTATTATAATTATTT
1228487 TATTATTATTATAATTATTT
1 TATTATTATTATAATTATTT
1228507 TATTATT-TTATA
1 TATTATTATTATA
1228519 GGGCCCATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 20 0.69
20 9 0.31
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTATTATTATAATTATTT
Found at i:1230506 original size:19 final size:19
Alignment explanation
Indices: 1230478--1230521 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1230468 AATAGTAATT
* *
1230478 AATTTGAATTGAATTTTTA
1 AATTTCAATTGAAATTTTA
*
1230497 AATTTCAATTTAAATTTTA
1 AATTTCAATTGAAATTTTA
*
1230516 ATTTTC
1 AATTTC
1230522 GCAAATAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (19 bp):
AATTTCAATTGAAATTTTA
Found at i:1231870 original size:16 final size:16
Alignment explanation
Indices: 1231800--1231878 Score: 50
Period size: 20 Copynumber: 4.4 Consensus size: 16
1231790 ATATAATAAT
1231800 AATAATAATTAAATATATA
1 AATAA-AATTAAA-A-ATA
*
1231819 AATGTAAAATTAAATATA
1 AA--TAAAATTAAAAATA
*
1231837 AATAAACAATGACTAAAATA
1 AAT-AA-AATTA--AAAATA
*
1231857 AATAAAATTAAAAATT
1 AATAAAATTAAAAATA
1231873 AATAAA
1 AATAAA
1231879 TAAAAGTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
16 12 0.24
17 2 0.04
18 13 0.27
19 4 0.08
20 15 0.31
21 3 0.06
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
AATAAAATTAAAAATA
Found at i:1233989 original size:72 final size:74
Alignment explanation
Indices: 1233872--1234045 Score: 280
Period size: 72 Copynumber: 2.4 Consensus size: 74
1233862 GAGGTCTTAT
* * *
1233872 CATCTTACACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATC-AAAAGCTCCC-AAGGCT
1 CATCTTGCACTGTAGGTCTTACAGATGTCCCAGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1233935 TTTTGAAAA
66 TTTTGAAAA
*
1233944 CATCTTGCACTGTAGGTCTTACAGATGTCCCAGAGGCTTTAAATATCAAAAAGCTCCCGAAGGTT
1 CATCTTGCACTGTAGGTCTTACAGATGTCCCAGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1234009 TTTTGAAAA
66 TTTTGAAAA
* *
1234018 CATCATGCACTGTAGGTTTTACAGATGT
1 CATCTTGCACTGTAGGTCTTACAGATGT
1234046 GGGAAATAGT
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
72 44 0.47
73 10 0.11
74 40 0.43
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (74 bp):
CATCTTGCACTGTAGGTCTTACAGATGTCCCAGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
TTTTGAAAA
Found at i:1234042 original size:74 final size:72
Alignment explanation
Indices: 1233879--1234045 Score: 271
Period size: 74 Copynumber: 2.3 Consensus size: 72
1233869 TATCATCTTA
* *
1233879 CACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAGCTCCCAAGGCTTTTTGAAAA
1 CACTGTAGGTCTTACAGATGTCCCAGAGGCTTTAAATATCAAAAGCTCCCAAGGCTTTTTGAAAA
*
1233944 CATCTTG
66 CATCATG
*
1233951 CACTGTAGGTCTTACAGATGTCCCAGAGGCTTTAAATATCAAAAAGCTCCCGAAGGTTTTTTGAA
1 CACTGTAGGTCTTACAGATGTCCCAGAGGCTTTAAATATC-AAAAGCTCCC-AAGGCTTTTTGAA
1234016 AACATCATG
64 AACATCATG
*
1234025 CACTGTAGGTTTTACAGATGT
1 CACTGTAGGTCTTACAGATGT
1234046 GGGAAATAGT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
72 38 0.43
73 10 0.11
74 40 0.45
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (72 bp):
CACTGTAGGTCTTACAGATGTCCCAGAGGCTTTAAATATCAAAAGCTCCCAAGGCTTTTTGAAAA
CATCATG
Found at i:1235809 original size:9 final size:9
Alignment explanation
Indices: 1235795--1235833 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
1235785 TTTTCTATAT
1235795 ATTTTTTTC
1 ATTTTTTTC
1235804 A-TTTTTTC
1 ATTTTTTTC
1235812 A---TTTTC
1 ATTTTTTTC
1235818 ATTTTTTTC
1 ATTTTTTTC
1235827 ATTTTTT
1 ATTTTTT
1235834 AAGCATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 6 0.22
8 8 0.30
9 13 0.48
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (9 bp):
ATTTTTTTC
Found at i:1235810 original size:8 final size:8
Alignment explanation
Indices: 1235797--1235833 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1235787 TTCTATATAT
1235797 TTTTTTCA
1 TTTTTTCA
1235805 TTTTTTCA
1 TTTTTTCA
1235813 --TTTTCA
1 TTTTTTCA
1235819 TTTTTTTCA
1 -TTTTTTCA
1235828 TTTTTT
1 TTTTTT
1235834 AAGCATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
6 6 0.23
8 14 0.54
9 6 0.23
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:1235816 original size:14 final size:15
Alignment explanation
Indices: 1235799--1235831 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1235789 CTATATATTT
1235799 TTTTCA-TTTTTTCA
1 TTTTCATTTTTTTCA
1235813 TTTTCATTTTTTTCA
1 TTTTCATTTTTTTCA
1235828 TTTT
1 TTTT
1235832 TTAAGCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCATTTTTTTCA
Found at i:1242971 original size:26 final size:26
Alignment explanation
Indices: 1242920--1242984 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
1242910 TTAATACTTG
1242920 AAAATAA-A-ATAAAAATATTAATAA
1 AAAATAATATATAAAAATATTAATAA
*
1242944 AAAATAATATATATAAATATT-ATGAA
1 AAAATAATATATAAAAATATTAAT-AA
1242970 AATAATAAGTATATA
1 AA-AATAA-TATATA
1242985 GGAAAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
24 7 0.20
25 3 0.09
26 14 0.40
27 5 0.14
28 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (26 bp):
AAAATAATATATAAAAATATTAATAA
Found at i:1242982 original size:24 final size:24
Alignment explanation
Indices: 1242918--1242982 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
1242908 ATTTAATACT
*
1242918 TGAAAATAA-AATAAAAATATTAA
1 TGAAAATAATAATATAAATATTAA
*
1242941 TAAAAAATAATATATATAAATATT-A
1 T-GAAAATAATA-ATATAAATATTAA
1242966 TGAAAATAATAAGTATA
1 TGAAAATAATAA-TATA
1242983 TAGGAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
23 2 0.06
24 20 0.57
25 3 0.09
26 10 0.29
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (24 bp):
TGAAAATAATAATATAAATATTAA
Found at i:1242997 original size:28 final size:26
Alignment explanation
Indices: 1242920--1242998 Score: 67
Period size: 26 Copynumber: 3.0 Consensus size: 26
1242910 TTAATACTTG
*
1242920 AAAATAA-A-ATAAAAATATTAAT-AA
1 AAAATAATATATAGAAATATT-ATGAA
*
1242944 AAAATAATATATATAAATATTATGAA
1 AAAATAATATATAGAAATATTATGAA
*
1242970 AATAATAAGTATATAGGAAA-ATTTTGAA
1 AA-AATAA-TATATA-GAAATATTATGAA
1242998 A
1 A
1242999 GGAAAGAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
24 7 0.15
25 3 0.07
26 14 0.30
27 5 0.11
28 14 0.30
29 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.30
Consensus pattern (26 bp):
AAAATAATATATAGAAATATTATGAA
Found at i:1245178 original size:3 final size:3
Alignment explanation
Indices: 1245172--1245243 Score: 110
Period size: 3 Copynumber: 24.0 Consensus size: 3
1245162 TATTTTTTAT
1245172 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -ATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* *
1245220 TAA TAA TAT TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
1245244 AAGCAGATGG
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
2 1 0.02
3 63 0.97
4 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1258335 original size:27 final size:25
Alignment explanation
Indices: 1258299--1258365 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 25
1258289 ATATGTTTTC
* *
1258299 TTTTCGTTTTCTTTACTATTATTATTT
1 TTTTCTTTTTCTTTA-TATTATTA-TA
* *
1258326 TTTTCTTTTTGATTTATATTTTTATA
1 TTTTCTTTTT-CTTTATATTATTATA
1258352 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
1258366 CTTTTTTCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 3 0.09
26 11 0.32
27 16 0.47
28 4 0.12
ACGTcount: A:0.13, C:0.09, G:0.03, T:0.75
Consensus pattern (25 bp):
TTTTCTTTTTCTTTATATTATTATA
Found at i:1259080 original size:19 final size:19
Alignment explanation
Indices: 1259056--1259097 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
1259046 TAAGTTACAA
1259056 TTGATGAAGTT-ATGAGATT
1 TTGATGAAGTTGA-GAGATT
1259075 TTGATGAAGTTGAGAGATT
1 TTGATGAAGTTGAGAGATT
1259094 TTGA
1 TTGA
1259098 ATTTATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (19 bp):
TTGATGAAGTTGAGAGATT
Found at i:1259236 original size:13 final size:13
Alignment explanation
Indices: 1259192--1259236 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
1259182 TACTTTTTAT
1259192 ATTAATTATAATC
1 ATTAATTATAATC
*
1259205 CTTATATTATAAATC
1 ATTA-ATTAT-AATC
1259220 -TTAATTATAATC
1 ATTAATTATAATC
1259232 ATTAA
1 ATTAA
1259237 ATTAATTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 8 0.29
15 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTAATTATAATC
Found at i:1260810 original size:13 final size:13
Alignment explanation
Indices: 1260784--1260852 Score: 50
Period size: 13 Copynumber: 5.0 Consensus size: 13
1260774 ATATTCATAC
**
1260784 ATATTATATTTAT
1 ATATTATAAGTAT
1260797 ATATTATAAGTAT
1 ATATTATAAGTAT
**
1260810 A-ATATATACTTAT
1 ATAT-TATAAGTAT
1260823 ATTATATATAAGTAT
1 A-TAT-TATAAGTAT
1260838 ATACTTATAATGTAT
1 ATA-TTATAA-GTAT
1260853 GCATAAGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
12 2 0.04
13 20 0.44
14 7 0.16
15 16 0.36
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (13 bp):
ATATTATAAGTAT
Found at i:1260831 original size:15 final size:14
Alignment explanation
Indices: 1260771--1260832 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 14
1260761 ATATACATGA
*
1260771 ATTATATTCATACAT
1 ATTATATT-ATATAT
1260786 ATTATATT-TATAT
1 ATTATATTATATAT
1260799 ATTATAAGTATAATATAT
1 ATTAT-A-T-T-ATATAT
1260817 ACTTATATTATATAT
1 A-TTATATTATATAT
1260832 A
1 A
1260833 AGTATATACT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
15 16 0.40
16 2 0.05
17 1 0.03
18 7 0.17
19 4 0.10
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (14 bp):
ATTATATTATATAT
Found at i:1260858 original size:25 final size:23
Alignment explanation
Indices: 1260808--1260863 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
1260798 TATTATAAGT
*
1260808 ATAA-TATATACTTATATTATAT
1 ATAAGTATATACTTATATTATAC
*
1260830 ATAAGTATATACTTATAATGTATGC
1 ATAAGTATATACTTAT-AT-TATAC
1260855 ATAAGTATA
1 ATAAGTATA
1260864 ATGTACATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 4 0.14
23 11 0.38
24 2 0.07
25 12 0.41
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (23 bp):
ATAAGTATATACTTATATTATAC
Found at i:1266967 original size:8 final size:8
Alignment explanation
Indices: 1266954--1266979 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1266944 ATGATGTAAT
1266954 TTTTTTTA
1 TTTTTTTA
1266962 TTTTTTTA
1 TTTTTTTA
1266970 TTTTTTTA
1 TTTTTTTA
1266978 TT
1 TT
1266980 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1280268 original size:24 final size:24
Alignment explanation
Indices: 1280240--1280328 Score: 142
Period size: 24 Copynumber: 3.7 Consensus size: 24
1280230 TTTCTATTAT
* *
1280240 AATACCTGACTTGGATTCTGATCG
1 AATACTTGACCTGGATTCTGATCG
*
1280264 GATACTTGACCTGGATTCTGATCG
1 AATACTTGACCTGGATTCTGATCG
*
1280288 AATACTTGACCTGGATTCTGATAG
1 AATACTTGACCTGGATTCTGATCG
1280312 AATACTTGACCTGGATT
1 AATACTTGACCTGGATT
1280329 ATGTTTTGAT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (24 bp):
AATACTTGACCTGGATTCTGATCG
Found at i:1281239 original size:28 final size:27
Alignment explanation
Indices: 1281184--1281239 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1281174 ACTTAATATC
* * *
1281184 ATTTATAAAATTATTTTTTTACTGAAA
1 ATTTATAAAATTATTCTTTTAATAAAA
*
1281211 ATTTATTAAATTATCTCTTTTAATAAAA
1 ATTTATAAAATTAT-TCTTTTAATAAAA
1281239 A
1 A
1281240 AAATTCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (27 bp):
ATTTATAAAATTATTCTTTTAATAAAA
Found at i:1285997 original size:58 final size:58
Alignment explanation
Indices: 1285802--1285989 Score: 349
Period size: 58 Copynumber: 3.2 Consensus size: 58
1285792 ACCATATCTC
*
1285802 AACTTTTTGCACACGAAGTGCCCAATACGAAAATTCATACACTTAGTATGAATTTCTT
1 AACTTTTTGCACACGAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTT
*
1285860 AACTTTTTGCACACGAAGTGCCCAATACAGAAATTCATACACTTAGTATGAATTTCTT
1 AACTTTTTGCACACGAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTT
*
1285918 AATTTTTTGCACACGAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTT
1 AACTTTTTGCACACGAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTT
1285976 AACTTTTTGCACAC
1 AACTTTTTGCACAC
1285990 TTAGTGCCAT
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 125 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.34
Consensus pattern (58 bp):
AACTTTTTGCACACGAAGTGCCCAATACGGAAATTCATACACTTAGTATGAATTTCTT
Found at i:1286390 original size:19 final size:19
Alignment explanation
Indices: 1286355--1286391 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1286345 GATATTACAA
*
1286355 TACTATGGTACCTATACCC
1 TACTATGGTACCGATACCC
*
1286374 TACTATGGTATCGATACC
1 TACTATGGTACCGATACC
1286392 ATTTTTTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (19 bp):
TACTATGGTACCGATACCC
Found at i:1286441 original size:20 final size:20
Alignment explanation
Indices: 1286416--1286464 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1286406 TTTTGAAATA
1286416 GTATCGATACCTTCCCTTT-G
1 GTATCGATA-CTTCCCTTTCG
1286436 GTATCGATACTTCCCTTTCG
1 GTATCGATACTTCCCTTTCG
*
1286456 ATATCGATA
1 GTATCGATA
1286465 TTGATTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.39
Consensus pattern (20 bp):
GTATCGATACTTCCCTTTCG
Found at i:1287460 original size:49 final size:48
Alignment explanation
Indices: 1287397--1287495 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 48
1287387 GGTACAAAAT
1287397 TGATTAGTTATAAATGAATATTTATAATTAAGATGGATTCAAATTGTGA
1 TGATTAGTTATAAATGAATATTTATAATTAAGAT-GATTCAAATTGTGA
1287446 TGATTAGTTATAAATGAATATTTATAATTAAGATGATTCAAATTGTGA
1 TGATTAGTTATAAATGAATATTTATAATTAAGATGATTCAAATTGTGA
1287494 TG
1 TG
1287496 TTGACAAGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 16 0.32
49 34 0.68
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.41
Consensus pattern (48 bp):
TGATTAGTTATAAATGAATATTTATAATTAAGATGATTCAAATTGTGA
Found at i:1289586 original size:108 final size:108
Alignment explanation
Indices: 1289189--1289586 Score: 327
Period size: 108 Copynumber: 3.7 Consensus size: 108
1289179 CCTATTTTCT
* * * * * * * * * *
1289189 CCTTTTCCTGGAGCAAATGGTGGAATAGCAACTCCCTTTGATAATATCAT-AAAATTCAAACCAT
1 CCTTTTGCAGGAGCAGATGGTGGAATAGGAATTTCCTTCGGTAATAT-TTCAAAGTTCAAACCAT
*** * * * * *
1289253 TGGTAGGTTGACTTGTTTGAGATGTCATCGGAGGCTTATTTATA
65 TACCAGATTGACTTGGTTGAGATGACATTGGAGGCTTATGTATA
* * * * ** *
1289297 CCTTTTTCAAGAGCAGATGAG-GGAATAGAAACTTCCTTCGGTAATATCCCAAAGTTCAAACTAT
1 CCTTTTGCAGGAGCAGATG-GTGGAATAGGAATTTCCTTCGGTAATATTTCAAAGTTCAAACCAT
* * * * ** *
1289361 TACTAGATTCACTT-GTCTGGGAAGGGATTGGAGACTTATGTATA
65 TACCAGATTGACTTGGT-TGAGATGACATTGGAGGCTTATGTATA
* * * * *
1289405 CGTTTTGCAGGAGCAGATGGTGGAATAGGAATCTCCATGGGTAATATTTCAAAGTTCAAGCCATT
1 CCTTTTGCAGGAGCAGATGGTGGAATAGGAATTTCCTTCGGTAATATTTCAAAGTTCAAACCATT
* *
1289470 GCTC-GATTGACTTGGTTGAGATGACATTGGAGGTTTATGTATA
66 AC-CAGATTGACTTGGTTGAGATGACATTGGAGGCTTATGTATA
* * * * * *
1289513 CCTTTTGCGGGAGCAGACGGTGGAATAGGAATTTTCTTCGGCAATATTTCAAAGGTCAAACCATC
1 CCTTTTGCAGGAGCAGATGGTGGAATAGGAATTTCCTTCGGTAATATTTCAAAGTTCAAACCATT
1289578 ACCAGATTG
66 ACCAGATTG
1289587 GGAGAGCCTT
Statistics
Matches: 226, Mismatches: 57, Indels: 14
0.76 0.19 0.05
Matches are distributed among these distances:
107 3 0.01
108 220 0.97
109 3 0.01
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.31
Consensus pattern (108 bp):
CCTTTTGCAGGAGCAGATGGTGGAATAGGAATTTCCTTCGGTAATATTTCAAAGTTCAAACCATT
ACCAGATTGACTTGGTTGAGATGACATTGGAGGCTTATGTATA
Found at i:1291037 original size:11 final size:11
Alignment explanation
Indices: 1290996--1291039 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1290986 TTCGTCCCTT
*
1290996 TATAATATATA
1 TATATTATATA
* *
1291007 GTATATTAAACA
1 -TATATTATATA
1291019 TATATTATATA
1 TATATTATATA
1291030 TATATTATAT
1 TATATTATAT
1291040 TACTAATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 19 0.70
12 8 0.30
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (11 bp):
TATATTATATA
Found at i:1291980 original size:21 final size:21
Alignment explanation
Indices: 1291941--1291981 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1291931 TTTCGTCGAA
*
1291941 TTTTTATTATTATTGTTTTCC
1 TTTTTATTAATATTGTTTTCC
1291962 TTTTTATTTAATATT-TTTTC
1 TTTTTA-TTAATATTGTTTTC
1291982 ATTATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTTATTAATATTGTTTTCC
Found at i:1293000 original size:16 final size:16
Alignment explanation
Indices: 1292981--1293012 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1292971 CACTAACTAT
*
1292981 TTTCATTTTTATTTTC
1 TTTCATTTTAATTTTC
1292997 TTTCATTTTAATTTTC
1 TTTCATTTTAATTTTC
1293013 ATCATTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTCATTTTAATTTTC
Found at i:1294652 original size:98 final size:95
Alignment explanation
Indices: 1294399--1294654 Score: 363
Period size: 95 Copynumber: 2.7 Consensus size: 95
1294389 ATAATATCAT
* * * *
1294399 ATATATAATAAAGCTTAAGCTGTCCCTCTAAAGCAATTGGTTAAACGTCCTGACTTTATGGATAA
1 ATATATAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAA
*
1294464 GATTCAACTAGTCTGATAAAGGTGATTATA
66 GATTCAACTAGCCTGATAAAGGTGATTATA
*
1294494 ATATATAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAA
1 ATATATAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAA
* *
1294559 TATTCAGCTAGCCTGATAAAGGTGATTATA
66 GATTCAACTAGCCTGATAAAGGTGATTATA
* *
1294589 ATATCT-ATACAATGACATTGAGCTGCCCCTCTAGAGCAATTGGTTAAACGCCCCGGA-TTTATG
1 ATATATAATA-AA-G-C-TTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCC-GACTTTATG
1294652 GAT
61 GAT
1294655 TCAGCTAGCC
Statistics
Matches: 145, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
94 3 0.02
95 94 0.65
96 1 0.01
97 1 0.01
98 44 0.30
99 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (95 bp):
ATATATAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGATAA
GATTCAACTAGCCTGATAAAGGTGATTATA
Found at i:1296015 original size:83 final size:82
Alignment explanation
Indices: 1295790--1296749 Score: 1005
Period size: 83 Copynumber: 11.5 Consensus size: 82
1295780 GAAACTATTG
* *
1295790 GCAGCATAACTCAAGGCTAGAAAGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCAT-ACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* *
1295855 GTTCAAAGGCACAACATTT
65 GCTC-AAGGCACATCATTT
* * * * * * * *
1295874 GCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCTAACCAAAGACCTTCGAGTTTGACTACGCTCA
1 GCAGCATA-CTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
1295939 ACTACAAGGCACATCATTT
65 GCT-CAAGGCACATCATTT
* * * *
1295958 GCAACATCACTCAAGGCTA-AAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACACTCA
1 GCAGCAT-ACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1296022 GCTCCAAGGCACATCATTT
65 GCT-CAAGGCACATCATTT
* * ** * *
1296041 ACAACATAACTCAAGGCTAGAAGGATTATTTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCAT-ACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1296105 GCTCAAAGGCACATCATTT
65 GCTC-AAGGCACATCATTT
* * * * * * * * *
1296124 GCAACATAGCTTAAGTCGAGAGGGGCTATCTACCAACCAAAAGACCTTTGAGTTTGACTACACTC
1 GCAGCATA-CTCAAGGCTAGAAGGGCTATCTGCCAA-CAAAAGACCTTCGAGTTCGATTACACTC
1296189 AGCTCCAA-GCACATCATTT
64 AGCT-CAAGGCACATCATTT
** ** * * * * * * *
1296208 ATAATATAACTCAATGCAAGAAGGGCTATTTGCCAAAAAAAGACCTTTGAGTTCGACTACGCTCA
1 GCAGCAT-ACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1296273 GCTCAAGGCACATCATTT
65 GCTCAAGGCACATCATTT
** * *
1296291 GCAGCATAACTCAAGGCTAGAAGGATTATCTACCAACAAAAGGCCTTCGAGTTCGATTACACTCA
1 GCAGCAT-ACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
1296356 GCTCAAAGGCACAACATTT
65 GCTC-AAGGCACATCATTT
* * * * * * *
1296375 GTAGCATAGCTCAAGGCGAGAAGGGCTATATGCCAATAAAAGACCTTCGAGTTTGACTACGCTCA
1 GCAGCATA-CTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1296440 GCTCCAAGGCACATCATTT
65 GCT-CAAGGCACATCATTT
* * *
1296459 GCAGCATAACTCAA-GCTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAATTCGATTACACTCA
1 GCAGCAT-ACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1296523 GCTCAAAGGCACATCATTT
65 GCTC-AAGGCACATCATTT
* * * *
1296542 GCAACATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATA-CTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* **
1296607 GCTTAAAGGTGCATCATTT
65 GC-TCAAGGCACATCATTT
* * * *
1296626 GTAGCATTACTCAAGGTTAGAA-GGTTATCTG-CAACAAAAGACCTGCGAGTTCGATTACACTCA
1 GCAGCA-TACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
1296689 GCTCAAAGGCACGTCATTTT
65 GCTC-AAGGCACATCA-TTT
* * *
1296709 ACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAA
1 GCAGCATA-CTCAAGGCTAGAAGGGCTATCTGCCAACAAAA
1296750 TTGTCGAGTT
Statistics
Matches: 728, Mismatches: 123, Indels: 49
0.81 0.14 0.05
Matches are distributed among these distances:
81 1 0.00
82 50 0.07
83 329 0.45
84 302 0.41
85 45 0.06
86 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (82 bp):
GCAGCATACTCAAGGCTAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAG
CTCAAGGCACATCATTT
Found at i:1296276 original size:251 final size:252
Alignment explanation
Indices: 1295794--1296749 Score: 1225
Period size: 251 Copynumber: 3.8 Consensus size: 252
1295784 CTATTGGCAG
*
1295794 CATAACTCAAGGCTAGAAAGG-TTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGTT
1 CATAACTCAAGGCTAG-AAGGATTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCT
*
1295858 CAAAGGCACAACATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCTAACC-AAAGACCTTC
65 CAAAGGCACAACATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAAGACCTTC
* * *
1295922 GAGTTTGACTACGCTCAACTACAAGGCACATCATTTGCAACATCACTCAAGGCTA-AAGGGTTAT
130 GAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAA-GCTAGAAGGGTTAT
*
1295986 CTGCCAACAAAAGACCTTTGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAA
194 CTGCCAACAAAAGACCTTTGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAA
* *
1296045 CATAACTCAAGGCTAGAAGGATTATTTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAACTCAAGGCTAGAAGGATTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* * * * *
1296109 AAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAGGGGCTATCTACCAACCAAAAGACCTTTG
66 AAAGGCACAACATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAAGACCTTCG
* ** * * * *
1296174 AGTTTGACTACACTCAGCTCCAA-GCACATCATTTATAATATAACTCAATGCAAGAAGGGCTATT
131 AGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAA-GCTAGAAGGGTTATC
* * *
1296238 TGCCAAAAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTGCAG
195 TGCCAACAAAAGACCTTTGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAA
* *
1296295 CATAACTCAAGGCTAGAAGGATTATCTACCAACAAAAGGCCTTCGAGTTCGATTACACTCAGCTC
1 CATAACTCAAGGCTAGAAGGATTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
* * * * *
1296360 AAAGGCACAACATTTGTAGCATAGCTCAAGGCGAGAAGGGCTATATGCCAA-TAAAAGACCTTCG
66 AAAGGCACAACATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAAGACCTTCG
*
1296424 AGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGCTAGAAGGGTTATCT
131 AGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGCTAGAAGGGTTATCT
* * *
1296489 GCCAACAAAAGACCTTTGAATTCGATTACACTCAGCTCAAAGGCACATCATTTGCAA
196 GCCAACAAAAGACCTTTGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAA
* * * * ** *
1296546 CATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTT
1 CATAACTCAAGGCTAGAAGGATTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
** * * * * * *
1296611 AAAGGTGCATCATTTGTAGCATTA-CTCAAGGT-TAGAA-GGTTATCTG-CAA-CAAAAGACCTG
66 AAAGGCACAACATTTGCAGCA-TAGCTTAA-GTCGAGAAGGGCTATCTGCCAACCAAAAGACCTT
* * * * * * * * * *
1296671 CGAGTTCGATTACACTCAGCTCAAAGGCACGTCATTTTACAGCATAGCTCAAGGCAAGAAGGGCT
129 CGAGTTTGACTACGCTCAGCTCCAAGGCACATCA-TTTGCAACATAACTCAA-GCTAGAAGGGTT
*
1296736 ATCTGTCAACAAAA
192 ATCTGCCAACAAAA
1296750 TTGTCGAGTT
Statistics
Matches: 615, Mismatches: 80, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
249 41 0.07
250 254 0.41
251 317 0.52
252 3 0.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (252 bp):
CATAACTCAAGGCTAGAAGGATTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
AAAGGCACAACATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAAGACCTTCG
AGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGCTAGAAGGGTTATCT
GCCAACAAAAGACCTTTGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAA
Found at i:1296323 original size:167 final size:167
Alignment explanation
Indices: 1295790--1296749 Score: 1149
Period size: 167 Copynumber: 5.7 Consensus size: 167
1295780 GAAACTATTG
*
1295790 GCAGCATAACTCAAGGCTAGAAAGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * * * **
1295855 GTTCAAAGGCACAACATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCTAACCAAAGACCT
66 GCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCGAGAAGGGCTATCTGCCAAAAAAAGACCT
* *
1295920 TCGAGTTTGACTACGCTCAACTACAAGGCACATCATTT
131 TCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTT
* * * *
1295958 GCAACATCACTCAAGGCTA-AAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * ** * * *
1296022 GCTCCAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGATTATTTGTC-AACAAAGACCT
66 GCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCGAGAAGGGCTATCTGCCAAAAAAAGACCT
* *
1296086 TCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT
131 TCGAGTTCGACTACGCTCAGCTC-AAGGCACATCATTT
* * * * * * * * * * *
1296124 GCAACATAGCTTAAGTCGAGAGGGGCTATCTACCAACCAAAAGACCTTTGAGTTTGACTACACTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAAGACCTTCGAGTTCGATTACACTC
* ** * * * * *
1296189 AGCTCCAA-GCACATCATTTATAATATAACTCAATGCAAGAAGGGCTATTTGCCAAAAAAAGACC
65 AGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCGAGAAGGGCTATCTGCCAAAAAAAGACC
*
1296253 TTTGAGTTCGACTACGCTCAGCTCAAGGCACATCATTT
130 TTCGAGTTCGACTACGCTCAGCTCAAGGCACATCATTT
* * *
1296291 GCAGCATAACTCAAGGCTAGAAGGATTATCTACCAACAAAAGGCCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * *
1296356 GCTCAAAGGCACAACATTTGTAGCATAGCTCAAGGCGAGAAGGGCTATATGCCAATAAAAGACCT
66 GCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCGAGAAGGGCTATCTGCCAAAAAAAGACCT
*
1296421 TCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTT
131 TCGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTT
* *
1296459 GCAGCATAACTCAA-GCTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAATTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * *
1296523 GCTCAAAGGCACATCATTTGCAACATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAAGACCT
66 GCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCGAGAAGGGCTATCTGCCAAAAAAAGACCT
* * * **
1296588 TCGAGTTCGATTACACTCAGCTTAAAGGTGCATCATTT
131 TCGAGTTCGACTACGCTCAGC-TCAAGGCACATCATTT
* * * *
1296626 GTAGCATTACTCAAGGTTAGAA-GGTTATCTG-CAACAAAAGACCTGCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * * * *
1296689 GCTCAAAGGCACGTCATTTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAA
66 GCTCAAAGGCACATCA-TTTGCAACATAGCTCAAGGCGAGAAGGGCTATCTGCCAAAAAAA
1296750 TTGTCGAGTT
Statistics
Matches: 684, Mismatches: 99, Indels: 19
0.85 0.12 0.02
Matches are distributed among these distances:
165 1 0.00
166 131 0.19
167 434 0.63
168 118 0.17
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (167 bp):
GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
GCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCGAGAAGGGCTATCTGCCAAAAAAAGACCT
TCGAGTTCGACTACGCTCAGCTCAAGGCACATCATTT
Found at i:1298269 original size:13 final size:12
Alignment explanation
Indices: 1298240--1298283 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1298230 ATTTTATTAA
1298240 TATTTTTTTCAT
1 TATTTTTTTCAT
*
1298252 TATTTTTTTCTT
1 TATTTTTTTCAT
*
1298264 TGATTTATTT-AT
1 T-ATTTTTTTCAT
1298276 TATTTTTT
1 TATTTTTT
1298284 ATCAAACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 6 0.22
12 14 0.52
13 7 0.26
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (12 bp):
TATTTTTTTCAT
Found at i:1301638 original size:29 final size:31
Alignment explanation
Indices: 1301570--1301635 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 31
1301560 TGTTCAAAGT
* * *
1301570 TTGGCCATCAACCAAGATGAAATTTCTAATAAG
1 TTGGCCACCAACCAAGATGAAATTTC--ACAAC
1301603 TTGGCCACCAACCAAGATGAAATTTC-CAAC
1 TTGGCCACCAACCAAGATGAAATTTCACAAC
1301633 TTG
1 TTG
1301636 CCAACTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 5 0.17
33 25 0.83
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (31 bp):
TTGGCCACCAACCAAGATGAAATTTCACAAC
Found at i:1306418 original size:29 final size:31
Alignment explanation
Indices: 1306353--1306415 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
1306343 TCAAAGTTTA
* *
1306353 GCCATCAACCAAGATGAAATTTCCAATAAGTTG
1 GCCACCAACCAAGATGAAATTTCC-A-AACTTG
1306386 GCCACCAACCAAGATGAAATTTCC-AACTTG
1 GCCACCAACCAAGATGAAATTTCCAAACTTG
1306416 CCAACTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 5 0.18
33 23 0.82
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.22
Consensus pattern (31 bp):
GCCACCAACCAAGATGAAATTTCCAAACTTG
Found at i:1307034 original size:108 final size:108
Alignment explanation
Indices: 1306906--1307113 Score: 299
Period size: 108 Copynumber: 1.9 Consensus size: 108
1306896 TACGAGGACC
* * **
1306906 AGATGGTGGCATAGTAACTCCCTTCGCTAATATCTCAAAATCCAAACCATTGTTAGATTGACTTG
1 AGATGGTGGAATAGGAACTCCCTTCGCTAATATCTCAAAATCCAAACCATTACTAGATTGACTTG
1306971 CTTGGGATAACGTTGGAAGCCTATTTCCACCTTTTCCAGGAGT
66 CTTGGGATAACGTTGGAAGCCTATTTCCACCTTTTCCAGGAGT
* * * * * * *
1307014 AGATGGTGGAATAGGAACTCCCTTTGGTAATATCTCAAAGTTCAAGCTATTACTAGTTTGACTTG
1 AGATGGTGGAATAGGAACTCCCTTCGCTAATATCTCAAAATCCAAACCATTACTAGATTGACTTG
* *
1307079 CTTGGGATGACGTTGGAGGCCTATTTCCACCTTTT
66 CTTGGGATAACGTTGGAAGCCTATTTCCACCTTTT
1307114 TCGAGAGCAG
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
108 87 1.00
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (108 bp):
AGATGGTGGAATAGGAACTCCCTTCGCTAATATCTCAAAATCCAAACCATTACTAGATTGACTTG
CTTGGGATAACGTTGGAAGCCTATTTCCACCTTTTCCAGGAGT
Found at i:1308015 original size:50 final size:50
Alignment explanation
Indices: 1307930--1308048 Score: 188
Period size: 50 Copynumber: 2.4 Consensus size: 50
1307920 TAACTTATAG
*
1307930 GAGATGTACATACTTACA-CAGTGTAAGTATGTGTTT-ATTTTTAGGTTGA
1 GAGATGTATATACTTACACCAGTGTAAGTATGTGTTTCA-TTTTAGGTTGA
*
1307979 GAGATGTATATACTTACACCAGTGTAAGTATGTGTTTCATTTTAGGTTGG
1 GAGATGTATATACTTACACCAGTGTAAGTATGTGTTTCATTTTAGGTTGA
*
1308029 GAGATGTATATAGTTACACC
1 GAGATGTATATACTTACACC
1308049 TCGTTATAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
49 17 0.26
50 47 0.72
51 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (50 bp):
GAGATGTATATACTTACACCAGTGTAAGTATGTGTTTCATTTTAGGTTGA
Found at i:1308731 original size:41 final size:40
Alignment explanation
Indices: 1308686--1308946 Score: 131
Period size: 41 Copynumber: 6.4 Consensus size: 40
1308676 ATTAACGGCG
* *
1308686 TTTTTTCAAAAACGCTGCTACAAACTCGTACTTTAGTGGCA
1 TTTTTTAAAAAACGCTGCTACAAAC-CATACTTTAGTGGCA
* * * * * *
1308727 TTTTTTTACAATCGCCGCTACAGACCATACTATAGTGGC-
1 TTTTTTAAAAAACGCTGCTACAAACCATACTTTAGTGGCA
* * *
1308766 GTTTTTAGACAAACGTCT-TTA-AATACTCATACTTTAGTGGC-
1 TTTTTTA-AAAAACG-CTGCTACAA-AC-CATACTTTAGTGGCA
*
1308807 GTTTTTAAACAAACG-TCGCTACAGAACCATACTTTAGTGGCA
1 TTTTTTAAA-AAACGCT-GCTACA-AACCATACTTTAGTGGCA
* * * * *
1308849 -TTTTTAGATAAATGCCGTTA-AATACTCATACTTTAGTGGCG
1 TTTTTTA-AAAAACGCTGCTACAA-AC-CATACTTTAGTGGCA
* * * * * **
1308890 TTTTTTAAAAAATGCCGCAACATACTCATATTTTAGTGGTG
1 TTTTTTAAAAAACGCTGCTACAAAC-CATACTTTAGTGGCA
*
1308931 TTTATTAAATAAACGC
1 TTTTTTAAA-AAACGC
1308947 CTCTATTTGT
Statistics
Matches: 174, Mismatches: 29, Indels: 33
0.74 0.12 0.14
Matches are distributed among these distances:
39 8 0.05
40 26 0.15
41 123 0.71
42 16 0.09
43 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (40 bp):
TTTTTTAAAAAACGCTGCTACAAACCATACTTTAGTGGCA
Found at i:1308767 original size:81 final size:82
Alignment explanation
Indices: 1308682--1308907 Score: 219
Period size: 82 Copynumber: 2.8 Consensus size: 82
1308672 TAACATTAAC
* * ** *
1308682 GGCGTTTTTTCAAAAACG-CTGCTACAA-ACTCGTACTTTAGTGGCATTTTTTTACAATCGCCGC
1 GGCGTTTTTACAAAAACGTCT-CTA-AATACTCATACTTTAGTGGCATTTTTAAACAAACGCCGC
1308745 TACAG-ACCATACTATAGT
64 TACAGAACCATACTATAGT
* * * * *
1308763 GGCGTTTTTAGACAAACGTCTTTAAATACTCATACTTTAGTGGCGTTTTTAAACAAACGTCGCTA
1 GGCGTTTTTACAAAAACGTCTCTAAATACTCATACTTTAGTGGCATTTTTAAACAAACGCCGCTA
*
1308828 CAGAACCATACTTTAGT
66 CAGAACCATACTATAGT
* * * * * * *
1308845 GGCATTTTTAGATAAATGCCGT-TAAATACTCATACTTTAGTGGCGTTTTTTAAA-AAATGCCGC
1 GGCGTTTTTACAAAAACGTC-TCTAAATACTCATACTTTAGTGGC-ATTTTTAAACAAACGCCGC
1308908 AACATACTCA
Statistics
Matches: 122, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
80 2 0.02
81 52 0.43
82 59 0.48
83 9 0.07
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (82 bp):
GGCGTTTTTACAAAAACGTCTCTAAATACTCATACTTTAGTGGCATTTTTAAACAAACGCCGCTA
CAGAACCATACTATAGT
Found at i:1308870 original size:82 final size:81
Alignment explanation
Indices: 1308709--1308907 Score: 256
Period size: 82 Copynumber: 2.4 Consensus size: 81
1308699 GCTGCTACAA
* * ** * *
1308709 ACTCGTACTTTAGTGGCATTTTTTTACAATCGCCGCTACAGACCATACTATAGTGGCGTTTTTAG
1 ACTCATACTTTAGTGGCGTTTTTAAACAAACGCCGCTACAGACCATACTATAGTGGCATTTTTAG
* *
1308774 ACAAACGTCTTTAAAT
66 ACAAACGCCGTTAAAT
* *
1308790 ACTCATACTTTAGTGGCGTTTTTAAACAAACGTCGCTACAGAACCATACTTTAGTGGCATTTTTA
1 ACTCATACTTTAGTGGCGTTTTTAAACAAACGCCGCTACAG-ACCATACTATAGTGGCATTTTTA
* *
1308855 GATAAATGCCGTTAAAT
65 GACAAACGCCGTTAAAT
*
1308872 ACTCATACTTTAGTGGCGTTTTTTAAA-AAATGCCGC
1 ACTCATACTTTAGTGGCG-TTTTTAAACAAACGCCGC
1308908 AACATACTCA
Statistics
Matches: 102, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
81 35 0.34
82 59 0.58
83 8 0.08
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (81 bp):
ACTCATACTTTAGTGGCGTTTTTAAACAAACGCCGCTACAGACCATACTATAGTGGCATTTTTAG
ACAAACGCCGTTAAAT
Found at i:1311172 original size:41 final size:41
Alignment explanation
Indices: 1311127--1311445 Score: 336
Period size: 41 Copynumber: 7.8 Consensus size: 41
1311117 CTTAAAATGT
* * * *
1311127 CGCTAAAGATTCGTACTTTAGTGGCGTTTTTATAAAAATGC
1 CGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
* * * * *
1311168 CGCTATAGAATCATACTTTAGCGGTGTTTTTATACAAATGC
1 CGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
* * ** *
1311209 CACTATAGACTCGTACTCTAGCCGTGTTTTTATACAAACGC
1 CGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
* * * * * * *
1311250 CACTATATACTCGCACTTTAGTGACATTTTTATACAAAGGA
1 CGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
* *
1311291 CGCTATAGACTTGTACTTTAGCGGCGTTTTTATACAAACGC
1 CGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
* * * * *
1311332 CGTTATATACTCATACTTTAGTGGCATTTTCATACAAACG-
1 CGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
*
1311372 CGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAGACGC
1 CGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
* *
1311413 CGCTA-AGGACTTGTACTTTATTGGCGTTTTTAT
1 CGCTATA-GACTCGTACTTTAGTGGCGTTTTTAT
1311446 TCAATCTGAT
Statistics
Matches: 230, Mismatches: 46, Indels: 4
0.82 0.16 0.01
Matches are distributed among these distances:
40 35 0.15
41 195 0.85
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (41 bp):
CGCTATAGACTCGTACTTTAGTGGCGTTTTTATACAAACGC
Found at i:1313306 original size:21 final size:21
Alignment explanation
Indices: 1313280--1313338 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
1313270 TGATTTATTA
*
1313280 TTATGGATTTCAAGTTTCTTG
1 TTATGGATTTCAAGTTTCTCG
*
1313301 TTATGGATTTCAAGTTTGTCG
1 TTATGGATTTCAAGTTTCTCG
*
1313322 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
1313339 ATTGGATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.20, C:0.08, G:0.22, T:0.49
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTCG
Found at i:1313941 original size:21 final size:21
Alignment explanation
Indices: 1313903--1313953 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1313893 ATATAGTATT
1313903 AAATAA-AAATAATAATAGAA
1 AAATAAGAAATAATAATAGAA
1313923 AAATAAGAAAT-ATATATAGAA
1 AAATAAGAAATAATA-ATAGAA
*
1313944 ACATATAGAA
1 AAATA-AGAA
1313954 CAAAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 9 0.33
21 14 0.52
22 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.22
Consensus pattern (21 bp):
AAATAAGAAATAATAATAGAA
Found at i:1314130 original size:2 final size:2
Alignment explanation
Indices: 1314125--1314161 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1314115 AAATACTTAA
1314125 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 A
1314162 ATAATAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1315669 original size:105 final size:107
Alignment explanation
Indices: 1315472--1315703 Score: 324
Period size: 105 Copynumber: 2.2 Consensus size: 107
1315462 ATCTTCTGTC
* * * **
1315472 GTGAAGTTGAAGTTGGTTCTGGAACTGGGAAATTGTTTTGTTGACAGTCAGCCGTCCCTTCGTTG
1 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTG
* *
1315537 TGAAGTTGAACTTGTGCTGTCTCGAGTCCAATGCCCTTCAAT
66 TAAAGTTGAACTTGTGCTGTCTCGAGTCCAATACCCTTCAAT
*
1315579 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TTTGTTGACAACCAGCCG-CCCTTCGTTG
1 GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTG
* * * * **
1315642 TAAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCTTTCGCT
66 TAAAGTTGAACTTGTGCTGTCTCGAGTCCAATACCCTTCAAT
1315684 GTGAAGTTGAAATTGGCTCT
1 GTGAAGTTGAAATTGGCTCT
1315704 AGCTAAAACC
Statistics
Matches: 111, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
105 64 0.58
106 16 0.14
107 31 0.28
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (107 bp):
GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTTGTTGACAACCAGCCGTCCCTTCGTTG
TAAAGTTGAACTTGTGCTGTCTCGAGTCCAATACCCTTCAAT
Found at i:1316149 original size:31 final size:31
Alignment explanation
Indices: 1316114--1316241 Score: 82
Period size: 31 Copynumber: 3.9 Consensus size: 31
1316104 AGGAAATAAA
1316114 CTCAAA-GATTTTGTGTTTCAAGAGAAACTGT
1 CTCAAACGATTTTGTGTTTCAAGAGAAACT-T
** * *
1316145 CTCAAGGGAGACGAAATT-TGTTTCAAGGGAAACAAT
1 CTC-A---A-ACGATTTTGTGTTTCAAGAGAAAC-TT
*
1316181 CTCAAA-GGTTTTGTGTTTCAAGAGAAACATT
1 CTCAAACGATTTTGTGTTTCAAGAGAAAC-TT
* * *
1316212 TTCAAAGGTTTTTTGTGTTTCAAGAGAAAC
1 CTCAAACG-ATTTTGTGTTTCAAGAGAAAC
1316242 AATTTCAAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
30 3 0.04
31 25 0.33
32 3 0.04
33 20 0.26
35 2 0.03
36 19 0.25
37 4 0.05
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (31 bp):
CTCAAACGATTTTGTGTTTCAAGAGAAACTT
Found at i:1316198 original size:67 final size:68
Alignment explanation
Indices: 1316028--1316208 Score: 213
Period size: 67 Copynumber: 2.6 Consensus size: 68
1316018 ACAGAATTCA
* * * *
1316028 TTTCAAGGGAAACGATCTTAAAGATATATGTTGTTT-AATGAGAAACGGCCTCAAGTGAGACAAA
1 TTTCAAGGGAAACAATCTCAAAGAT-TTTG-TGTTTCAA-GAGAAACGGCCTCAAGGGAGACAAA
1316092 ATTTTG
63 ATTTTG
* * * * * * *
1316098 TTTTAAAGGAAATAAACTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAA-T
1 TTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAGGGAGACAAAATT
1316162 TTG
66 TTG
*
1316165 TTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAAC
1 TTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAAC
1316209 ATTTTCAAAG
Statistics
Matches: 94, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
67 43 0.46
68 27 0.29
69 5 0.05
70 19 0.20
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.30
Consensus pattern (68 bp):
TTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAGGGAGACAAAATT
TTG
Found at i:1316268 original size:36 final size:33
Alignment explanation
Indices: 1316163--1316277 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
1316153 AGACGAAATT
* *
1316163 TGTTTCAAGGGAAACAATCTCAAAGG--TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
*
1316194 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
1316227 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG--T-TTTTTG
1316263 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
1316278 TGTATCAAGG
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 23 0.31
33 30 0.40
35 1 0.01
36 21 0.28
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.37
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
Found at i:1316375 original size:38 final size:36
Alignment explanation
Indices: 1316318--1316432 Score: 158
Period size: 37 Copynumber: 3.1 Consensus size: 36
1316308 CAAGGATTGA
* * *
1316318 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAA-TT
* *
1316355 TGTTTTAAGAAAAACATGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGAAAAAC-TGTCTCAAGAGAGACAAAATT
*
1316392 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATT
1316428 TGTTT
1 TGTTT
1316433 AATGTAAAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
36 25 0.36
37 27 0.39
38 17 0.25
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.30
Consensus pattern (36 bp):
TGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATT
Found at i:1316501 original size:30 final size:30
Alignment explanation
Indices: 1316446--1316502 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1316436 GTAAAACATA
*
1316446 TTCAAAGATTTTGTTTCAAGGGAAACTATT
1 TTCAAAGATTTTGTTTCAAGAGAAACTATT
*
1316476 TTCAAAG-TTTATGTTTCAATAGAAACT
1 TTCAAAGATTT-TGTTTCAAGAGAAACT
1316503 GTCTCAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (30 bp):
TTCAAAGATTTTGTTTCAAGAGAAACTATT
Found at i:1316646 original size:37 final size:37
Alignment explanation
Indices: 1316588--1316840 Score: 158
Period size: 37 Copynumber: 7.4 Consensus size: 37
1316578 TCAATGTTTA
* *
1316588 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* *
1316625 TGTTTCAAGGGAAACTATCTCAAGAGAGAC--AA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* * *
1316659 TATTTCAAGGGAAA-TGCTTTCAA---TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAATTT
*
1316687 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* * *
1316725 TGTTCCAAGGGAAA-TGTTTTCAA---TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAATTT
*
1316753 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* *
1316791 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
**
1316827 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
1316841 TGTTTTTAAT
Statistics
Matches: 166, Mismatches: 25, Indels: 51
0.69 0.10 0.21
Matches are distributed among these distances:
28 5 0.03
29 34 0.20
30 4 0.02
31 1 0.01
32 2 0.01
33 1 0.01
34 21 0.13
35 2 0.01
36 16 0.10
37 74 0.45
38 6 0.04
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:1316694 original size:100 final size:99
Alignment explanation
Indices: 1316392--1316738 Score: 465
Period size: 100 Copynumber: 3.5 Consensus size: 99
1316382 AGACAAAATT
* **
1316392 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT-AATGTAAAACATAT-TC-A-A-A
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAA-GGGAAAC-TATCTCAAGAGA
* * * *
1316452 G--ATTTTGTTTCAAGGGAAACTATTTTCAAAGTTTA
64 GACAATTTATTTCAAGGGAAA-TGTTTTCAATGTTTA
* *
1316487 TGTTTCAATAGAAACTGTCTCAAAGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
*
1316552 CAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
66 C--AATTTATTTCAAGGGAAATGTTTTCAATGTTTA
*
1316588 TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
1316653 ACAATTTATTTCAAGGGAAATGCTTTCAATGTTTA
65 ACAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
*
1316688 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAA
1316739 TGTTTTCAAT
Statistics
Matches: 225, Mismatches: 17, Indels: 15
0.88 0.07 0.06
Matches are distributed among these distances:
94 3 0.01
95 45 0.20
96 3 0.01
97 1 0.00
98 2 0.01
100 80 0.36
101 44 0.20
102 47 0.21
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (99 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
CAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:1316756 original size:166 final size:166
Alignment explanation
Indices: 1316523--1316908 Score: 605
Period size: 166 Copynumber: 2.3 Consensus size: 166
1316513 AGACAAAATT
* * *
1316523 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT-TTCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-TTGTTCAAGGGAAATGTTTTCAATGTTT
*
1316587 ATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
65 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
*
1316652 GAC-AATTTATTTCAAGGGAAATGCTTTCAATGTTTA
130 GACAAATTCATTTCAAGGGAAATGCTTTCAATGTTTA
*
1316688 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTT-CAAGGGAAATGTTTTCAATGTTT
1316753 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
65 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
* *
1316818 GACAAAATTCATTTCAAGGGAAATGTTTTTAATGTTTA
130 GAC-AAATTCATTTCAAGGGAAATGCTTTCAATGTTTA
* * *
1316856 TGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTTCTGTTTCGAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTT-TG-TTCAAGGGAAA
1316909 CTATCTCAAG
Statistics
Matches: 203, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
164 1 0.00
165 35 0.17
166 90 0.44
168 62 0.31
169 3 0.01
170 10 0.05
171 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (166 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAATTCATTTCAAGGGAAATGCTTTCAATGTTTA
Found at i:1316759 original size:66 final size:65
Alignment explanation
Indices: 1316625--1316804 Score: 276
Period size: 66 Copynumber: 2.8 Consensus size: 65
1316615 GACAAAATTT
* * *
1316625 TGTTTCAAGGGAAACTATCTCAAGAGAGAC--AATTTAT-TTCAAGGGAAATGCTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT-TGTTCAAGGGAAATGCTTTCAATGTTT
1316687 A
65 A
*
1316688 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTT-CAAGGGAAATGCTTTCAATGTTT
1316753 A
65 A
1316754 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG-TTCAAGGGAAA
1316805 CTATCTCAAG
Statistics
Matches: 108, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
63 27 0.25
64 1 0.01
65 7 0.06
66 71 0.66
67 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCAAGGGAAATGCTTTCAATGTTTA
Found at i:1316866 original size:102 final size:105
Alignment explanation
Indices: 1316688--1316929 Score: 357
Period size: 102 Copynumber: 2.3 Consensus size: 105
1316678 TCAATGTTTA
* * * *
1316688 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTATGTTCCAAGGGAAATGTTTTCAATGTTT
*
1316753 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT-
66 ATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTC
*
1316791 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT-TT-CAAGGGAAATGTTTTTAATGTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT-ATGTTCCAAGGGAAATGTTTTCAATGTT
*
1316854 TATGTTTAAAGAGAAACTGTCTCAAGTGAGACAAAACTTTC
65 TATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTC
* * *
1316895 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
1316930 CTTGTTTTAA
Statistics
Matches: 126, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
102 55 0.44
103 38 0.30
104 33 0.26
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (105 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTATGTTCCAAGGGAAATGTTTTCAATGTTT
ATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAACTTTC
Found at i:1318433 original size:183 final size:183
Alignment explanation
Indices: 1318125--1318474 Score: 637
Period size: 183 Copynumber: 1.9 Consensus size: 183
1318115 GGTTTAACTA
1318125 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
* **
1318190 AGTGTCCGAGCAATGTCATGGTTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
*
1318255 CTATAACCAATTGTCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
* *
1318308 AAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAATCAGTGGAGCAAACACCGAATTGCCA
1 AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
*
1318373 AGTGTCTGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
66 AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
1318438 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
1318475 CGGATTTAAT
Statistics
Matches: 160, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 160 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (183 bp):
AAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTGCCA
AGTGTCCGAGCAATGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTTCCT
CTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATCACTG
Found at i:1322447 original size:19 final size:20
Alignment explanation
Indices: 1322423--1322463 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1322413 ACATAGTATT
1322423 AAATAA-AAATA-ATAATAGA
1 AAATAAGAAATATAT-ATAGA
1322442 AAATAAGAAATATATATAGA
1 AAATAAGAAATATATATAGA
1322462 AA
1 AA
1322464 CATATAGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 12 0.60
21 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (20 bp):
AAATAAGAAATATATATAGA
Found at i:1322612 original size:2 final size:2
Alignment explanation
Indices: 1322548--1322594 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1322538 AAATAATGAC
1322548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1322590 AT AT A
1 AT AT A
1322595 AGAAAAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1322673 original size:2 final size:2
Alignment explanation
Indices: 1322666--1322698 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1322656 GTATACTTAA
1322666 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 A
1322699 CTAATATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1324079 original size:26 final size:26
Alignment explanation
Indices: 1324002--1324079 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 26
1323992 ATCTTTTATA
1324002 TTACTATCAATCTTTTATATT-AAA-
1 TTACTATCAATCTTTTATATTAAAAT
* ** * *
1324026 GTACCCTC-ACCTATTTAT-TTAATTAT
1 TTACTATCAATCT-TTTATATTAA-AAT
1324052 TTACTATCAATCTTTTATATTAAAAT
1 TTACTATCAATCTTTTATATTAAAAT
1324078 TT
1 TT
1324080 TAATTTATCA
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
23 5 0.13
24 11 0.29
25 1 0.03
26 14 0.37
27 7 0.18
ACGTcount: A:0.33, C:0.15, G:0.01, T:0.50
Consensus pattern (26 bp):
TTACTATCAATCTTTTATATTAAAAT
Found at i:1328063 original size:21 final size:21
Alignment explanation
Indices: 1328039--1328083 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1328029 TAAACTTTGA
*
1328039 TTTGTTGTTATGGATTTCAAG
1 TTTGTTGTTATGGATGTCAAG
1328060 TTTGTTGTTATGGATGTCAAG
1 TTTGTTGTTATGGATGTCAAG
1328081 TTT
1 TTT
1328084 ATTGGATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.04, G:0.24, T:0.53
Consensus pattern (21 bp):
TTTGTTGTTATGGATGTCAAG
Found at i:1328316 original size:44 final size:44
Alignment explanation
Indices: 1328268--1328366 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
1328258 TTTTACAGTC
* * * *
1328268 ACAAATACCACTATATGTCATAACATTTAGTGGCGTTTTTGGGA
1 ACAAACACCACTATATGTCAGAACATTTAGCGGCGTTTTTGGAA
* * * *
1328312 ACAAACACCTCTATATGTCGGAATATTTAGCGGCGTTTTTTGAA
1 ACAAACACCACTATATGTCAGAACATTTAGCGGCGTTTTTGGAA
*
1328356 ACAAACGCCAC
1 ACAAACACCAC
1328367 AAAAGATAAG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.30
Consensus pattern (44 bp):
ACAAACACCACTATATGTCAGAACATTTAGCGGCGTTTTTGGAA
Found at i:1329599 original size:21 final size:21
Alignment explanation
Indices: 1329573--1329624 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1329563 TGAGTCAAGT
1329573 GTCAGATTCGATATTATTGAG
1 GTCAGATTCGATATTATTGAG
1329594 GTCAGATTCGATATTATTGAG
1 GTCAGATTCGATATTATTGAG
1329615 GTCAGATTCG
1 GTCAGATTCG
1329625 TGGTTTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.37
Consensus pattern (21 bp):
GTCAGATTCGATATTATTGAG
Found at i:1331463 original size:37 final size:35
Alignment explanation
Indices: 1331382--1331667 Score: 274
Period size: 37 Copynumber: 7.9 Consensus size: 35
1331372 AAACTATATA
* * *
1331382 TATATATATATGTTTT-TAAAATTGTTTTTGAAAT
1 TATATATATATGTTTTCAAAAATTGTTTTTAAAAC
1331416 TATATAATATATGTTTTCAAAAATTGTTTTTCAAAAC
1 TATAT-ATATATGTTTTCAAAAATTGTTTTT-AAAAC
* *
1331453 TATAATATATATATTTTCAAAAATTGTTTTTAAAAT
1 TAT-ATATATATGTTTTCAAAAATTGTTTTTAAAAC
*
1331489 TATATAATATATGTTTTCAAAAATTGTTTTTTTAAAC
1 TATAT-ATATATGTTTTCAAAAATTG-TTTTTAAAAC
* * * *
1331526 TATATATTATACGTTTTAAAAAATAGATTTTCAAAAC
1 TATATA-TATATGTTTTCAAAAATTG-TTTTTAAAAC
* *
1331563 TATATAGTATATATATGTTCAAAAATTGTTTTT-AAAT
1 TATATA-TATATGT-T-TTCAAAAATTGTTTTTAAAAC
* * *
1331600 TATATATAT-TGCTTTCAAAAATTGTGTTCTCAAAC
1 TATATATATATGTTTTCAAAAATTGT-TTTTAAAAC
* *
1331635 T-TGATATTATACGTTTTCAAAAATTATTTTTAA
1 TAT-ATA-TATATGTTTTCAAAAATTGTTTTTAA
1331668 CCGATTTTAA
Statistics
Matches: 208, Mismatches: 30, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
33 12 0.06
34 10 0.05
35 21 0.10
36 49 0.24
37 100 0.48
38 7 0.03
39 9 0.04
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (35 bp):
TATATATATATGTTTTCAAAAATTGTTTTTAAAAC
Found at i:1331489 original size:73 final size:72
Alignment explanation
Indices: 1331380--1331665 Score: 278
Period size: 73 Copynumber: 3.9 Consensus size: 72
1331370 CAAAACTATA
** **
1331380 TATATATATATATGTTTTTAAAATTGTTTTTGAAATTATATAATATATGTTTTCAAAAATTGTTT
1 TATATATATATAT-TTTCAAAAATTGTTTTCAAAATTATATAATATATGTTTTCAAAAATTGTTT
1331445 TTCAAAAC
65 TTCAAAAC
*
1331453 TATAATATATATATTTTCAAAAATTGTTTTTAAAATTATATAATATATGTTTTCAAAAATTGTTT
1 TAT-ATATATATATTTTCAAAAATTGTTTTCAAAATTATATAATATATGTTTTCAAAAATTGTTT
**
1331518 TTTTAAAC
65 TTCAAAAC
* * * * *
1331526 TATATAT-TATACGTTTTAAAAAATAGATTTTCAAAACTATATAGTATATATATGTTCAAAAATT
1 TATATATATATA--TTTTCAAAAATTG-TTTTCAAAATTATATA--ATATATGTTTTCAAAAATT
*
1331590 GTTTTT--AAAT
61 GTTTTTCAAAAC
** * * *
1331600 TATATATAT-TGCTTTCAAAAATTGTGTTCTCAAACTTGATAT--TATACGTTTTCAAAAATTAT
1 TATATATATATATTTTCAAAAATTGT-TT-TCAAAATT-ATATAATATATGTTTTCAAAAATTGT
1331662 TTTT
63 TTTT
1331666 AACCGATTTT
Statistics
Matches: 181, Mismatches: 22, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
70 20 0.11
71 5 0.03
72 16 0.09
73 77 0.43
74 39 0.22
75 1 0.01
76 23 0.13
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.49
Consensus pattern (72 bp):
TATATATATATATTTTCAAAAATTGTTTTCAAAATTATATAATATATGTTTTCAAAAATTGTTTT
TCAAAAC
Found at i:1332245 original size:2 final size:2
Alignment explanation
Indices: 1332238--1332275 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1332228 GATCTTGTTC
1332238 AT AT AT AT A- 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 A
1332276 AGCATTTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1333189 original size:179 final size:179
Alignment explanation
Indices: 1332856--1333221 Score: 673
Period size: 180 Copynumber: 2.0 Consensus size: 179
1332846 TAAGACAAGG
1332856 TAAAAACAAGGGAAATAAAAGATAATTAAACGACAAAGCATGTAATGAAGAACTAAACTTATCCT
1 TAAAAACAAGGGAAATAAAAGATAATTAAACGACAAAGCATGTAAT--AGAACTAAACTTATCCT
1332921 ATTTAAAGTGGGCGGCCAAGGTCCGAAGAATAAATTCATTGAAAGATAGAAATTTAAGGATCACA
64 ATTTAAAGTGGGCGGCCAAGGTCCGAAGAATAAATTCATTGAAAGATAGAAATTTAAGGATCACA
1332986 ACGGTGAAGACGGTATTGAAATCAGATGGTT-GATTGAAGGGAAAATAATT
129 ACGGTGAAGACGGTATTGAAATCAGATGGTTGGATTGAAGGGAAAATAATT
1333036 TAAAAACAAGGGAAATAAAAGATAATTAAACGACAAAGCATGTAAT-GAACTAAACTTATCCTAT
1 TAAAAACAAGGGAAATAAAAGATAATTAAACGACAAAGCATGTAATAGAACTAAACTTATCCTAT
1333100 TTAAAGTGGGCGGCCAAGGTCCGAAGAATAATATTCATTGAAAAGATAGAAATTTAAGGATCACA
66 TTAAAGTGGGCGGCCAAGGTCCGAAGAATAA-ATTCATTG-AAAGATAGAAATTTAAGGATCACA
1333165 ACGGTGAAGACGGTATTGAAATCAGATGGTTGGATTGAAGGGAAAATAATT
129 ACGGTGAAGACGGTATTGAAATCAGATGGTTGGATTGAAGGGAAAATAATT
*
1333216 TGAAAA
1 TAAAAA
1333222 TTTAGCCCCG
Statistics
Matches: 182, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
177 49 0.27
178 8 0.04
179 55 0.30
180 70 0.38
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.23
Consensus pattern (179 bp):
TAAAAACAAGGGAAATAAAAGATAATTAAACGACAAAGCATGTAATAGAACTAAACTTATCCTAT
TTAAAGTGGGCGGCCAAGGTCCGAAGAATAAATTCATTGAAAGATAGAAATTTAAGGATCACAAC
GGTGAAGACGGTATTGAAATCAGATGGTTGGATTGAAGGGAAAATAATT
Found at i:1343934 original size:31 final size:31
Alignment explanation
Indices: 1343875--1343934 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1343865 ATCAATGTCC
**
1343875 AAGTGACAACAACTTAATAAAATGATAACGT
1 AAGTGACAACAACTTAATAAAACAATAACGT
* *
1343906 AAGTGACCAGAACTTAATAAAACAATAAC
1 AAGTGACAACAACTTAATAAAACAATAAC
1343935 ATAAAATGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.20
Consensus pattern (31 bp):
AAGTGACAACAACTTAATAAAACAATAACGT
Found at i:1346674 original size:45 final size:45
Alignment explanation
Indices: 1346625--1346769 Score: 175
Period size: 45 Copynumber: 3.2 Consensus size: 45
1346615 TAATCCAAGG
* * *
1346625 CTTTTGATTATTGGGTTGTCAAAAGTAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTGGGTTGACAAAAATAAAATCAAAGGATTAATTC
* * *
1346670 CTTTTGATTATTGTGTTGCCAAAAATAAAATCAAAGGATTAATTA
1 CTTTTGATTATTGGGTTGACAAAAATAAAATCAAAGGATTAATTC
* * *
1346715 CTTTCGATTATTGGATT-ACAAAAATTAAAAATAAAAGGATTAATTC
1 CTTTTGATTATTGGGTTGACAAAAA-T-AAAATCAAAGGATTAATTC
*
1346761 CTTTAGATT
1 CTTTTGATT
1346770 TCTGTTTGTT
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
44 6 0.07
45 55 0.64
46 25 0.29
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (45 bp):
CTTTTGATTATTGGGTTGACAAAAATAAAATCAAAGGATTAATTC
Found at i:1346972 original size:58 final size:57
Alignment explanation
Indices: 1346893--1347238 Score: 376
Period size: 58 Copynumber: 6.0 Consensus size: 57
1346883 TCTTGTGCTA
* * *
1346893 ATTCTAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTTCTTGAAAATCTTAAATG
1 ATTCTAACTTTGTAA-AAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATG
* * *
1346951 ATTCTAACTTTGTAAGAAAAATAAATTGTTAAAATTTATTTCCTTGAAAATCTTGAATG
1 ATTCTAACTTTGTAA-AAAAATAAATTGTT-AAATTTATTTTCTTGAGAATCTTAAATG
* ** ** * * *
1347010 ATTTTAACTTTACG-AGGAAAATAAATTGTCGAATTTATTTTCTTGAGAATCATAGACG
1 ATTCTAACTTT--GTAAAAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATG
* *
1347068 ATTCTATCATT-TAAAAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATG
1 ATTCTAACTTTGTAAAAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATG
* * *
1347124 ATTAT-ATTTTGTAAAATTTAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATG
1 ATTCTAACTTTGTAAAA--AAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATG
* * * *
1347182 ATTCT-ATTTTGTTAAAGTAAATAAATTGTTAAATTTATTTTATTGTGAATCTTAAAT
1 ATTCTAACTTTG-TAAA-AAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAAT
1347239 AAAGAAATAA
Statistics
Matches: 244, Mismatches: 35, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
55 2 0.01
56 46 0.19
58 143 0.59
59 51 0.21
60 1 0.00
61 1 0.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (57 bp):
ATTCTAACTTTGTAAAAAAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATG
Found at i:1347147 original size:114 final size:114
Alignment explanation
Indices: 1346909--1347238 Score: 392
Period size: 114 Copynumber: 2.9 Consensus size: 114
1346899 ACTTTGTAAG
* *
1346909 GAAAATAAATTGTTGAATTTATTTTCTTGAAAATCTTAAATGATTCTAACTTTGTAAGAAAAATA
1 GAAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAATGATTCTATCTTT-TAA-AAAAATA
* * * * * *
1346974 AATTGTTAAAATTTATTTCCTTGAAAATCTTGAATGATTTTAACTTTACGAG
64 AATTGTT-AAATTTATTTTCTTGAGAATCTTAAATGATTATAACTTTACAAA
* * * * *
1347026 GAAAATAAATTGTCGAATTTATTTTCTTGAGAATCATAGACGATTCTATCATTTAAAAAAATAAA
1 GAAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAATGATTCTATCTTTTAAAAAAATAAA
**
1347091 TTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTATATTTTGTA-AAA
66 TTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTATAACTT-TACAAA
*** * * *
1347140 TTTAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTCTATTTTGTTAAAGTAAATA
1 GAAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAATGATTCTATCTT-TTAAA-AAAATA
* *
1347205 AATTGTTAAATTTATTTTATTGTGAATCTTAAAT
64 AATTGTTAAATTTATTTTCTTGAGAATCTTAAAT
1347239 AAAGAAATAA
Statistics
Matches: 182, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
114 75 0.41
115 21 0.12
116 40 0.22
117 46 0.25
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (114 bp):
GAAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAATGATTCTATCTTTTAAAAAAATAAA
TTGTTAAATTTATTTTCTTGAGAATCTTAAATGATTATAACTTTACAAA
Found at i:1347238 original size:31 final size:31
Alignment explanation
Indices: 1347145--1347238 Score: 72
Period size: 31 Copynumber: 3.2 Consensus size: 31
1347135 TAAAATTTAA
* *
1347145 TAAATTGTTAAATTTATTTTCTTGAGAATCT
1 TAAATTGTTAAATTTATTTTATTGTGAATCT
** * ** *
1347176 TAAA-TGATTCTATTT-TGTTAAAGT-AA--A
1 TAAATTG-TTAAATTTATTTTATTGTGAATCT
1347203 TAAATTGTTAAATTTATTTTATTGTGAATCT
1 TAAATTGTTAAATTTATTTTATTGTGAATCT
1347234 TAAAT
1 TAAAT
1347239 AAAGAAATAA
Statistics
Matches: 43, Mismatches: 14, Indels: 12
0.62 0.20 0.17
Matches are distributed among these distances:
27 10 0.23
28 8 0.19
29 4 0.09
30 6 0.14
31 15 0.35
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.50
Consensus pattern (31 bp):
TAAATTGTTAAATTTATTTTATTGTGAATCT
Found at i:1347298 original size:92 final size:87
Alignment explanation
Indices: 1347173--1347352 Score: 216
Period size: 92 Copynumber: 2.0 Consensus size: 87
1347163 TTCTTGAGAA
* * * * *
1347173 TCTTAAATGATTCTATTTTGTTAAAGTAAATAAATTGTTAAATTTATTTTATTGTGAATCTTAAA
1 TCTTAAATGATTCTATCTTGTAAAAGAAAATAAATCGTTAAATTTATTTT-CT-T--ATCTTAAA
1347238 TAAAGAAATAAATTGTTGGATTTATTT
62 -AAAGAAATAAATTGTTGGATTTATTT
* * * * * *
1347265 TCTTATATGATTTTATCTTGTAAAAGAAAATAAATCGTTAGATTTATTTTCTTATTTTTAAAAGG
1 TCTTAAATGATTCTATCTTGTAAAAGAAAATAAATCGTTAAATTTATTTTCTTATCTTAAAAAAG
1347330 AAATAAATTGTTGGATTTATTT
66 AAATAAATTGTTGGATTTATTT
1347352 T
1 T
1347353 GTTGTTTTAT
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
87 26 0.34
88 6 0.08
90 1 0.01
91 1 0.01
92 43 0.56
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (87 bp):
TCTTAAATGATTCTATCTTGTAAAAGAAAATAAATCGTTAAATTTATTTTCTTATCTTAAAAAAG
AAATAAATTGTTGGATTTATTT
Found at i:1347427 original size:39 final size:39
Alignment explanation
Indices: 1347286--1347474 Score: 181
Period size: 39 Copynumber: 4.9 Consensus size: 39
1347276 TTTATCTTGT
* *
1347286 AAAAGAAAATAAATCGTTAGATTTATTTTCTTATTTTT-
1 AAAAGGAAATAAATCGTTGGATTTATTTTCTTATTTTTG
* * *
1347324 AAAAGGAAATAAATTGTTGGATTTATTTTGTTGTTTTATG
1 AAAAGGAAATAAATCGTTGGATTTATTTTCTTATTTT-TG
* * * * *
1347364 -AAAGTAAATAAATCATT-AAGTTTATTTTCCTGTTTTATG
1 AAAAGGAAATAAATCGTTGGA-TTTATTTTCTTATTTT-TG
* * *
1347403 AAAA-GAGATAAATCGATGGATTTATTTT-TATATTTTGG
1 AAAAGGAAATAAATCGTTGGATTTATTTTCT-TATTTTTG
*
1347441 AAAAGGAAATAAATCGTTGAATTTATTTTCTTAT
1 AAAAGGAAATAAATCGTTGGATTTATTTTCTTAT
1347475 GAATCTTATA
Statistics
Matches: 121, Mismatches: 22, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
38 38 0.31
39 78 0.64
40 5 0.04
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (39 bp):
AAAAGGAAATAAATCGTTGGATTTATTTTCTTATTTTTG
Found at i:1347430 original size:78 final size:77
Alignment explanation
Indices: 1347287--1347430 Score: 184
Period size: 77 Copynumber: 1.9 Consensus size: 77
1347277 TTATCTTGTA
* * * *
1347287 AAAGAAAATAAATCGTTAGATTTATTTTCTTATTTTTAAAAGGAAATAAATTGTTGGATTTATTT
1 AAAGAAAATAAATCATTAGATTTATTTTCCTATTTTTAAAAGGAAATAAATCGATGGATTTATTT
1347352 TGTTGTTTTATG
66 TGTTGTTTTATG
* * *
1347364 AAAGTAAATAAATCATTA-AGTTTATTTTCCTGTTTTATGAAAA-GAGATAAATCGATGGATTTA
1 AAAGAAAATAAATCATTAGA-TTTATTTTCCTATTTT-T-AAAAGGAAATAAATCGATGGATTTA
1347427 TTTT
63 TTTT
1347431 TATATTTTGG
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
76 1 0.02
77 30 0.53
78 22 0.39
79 4 0.07
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (77 bp):
AAAGAAAATAAATCATTAGATTTATTTTCCTATTTTTAAAAGGAAATAAATCGATGGATTTATTT
TGTTGTTTTATG
Found at i:1347523 original size:97 final size:98
Alignment explanation
Indices: 1347403--1347669 Score: 331
Period size: 97 Copynumber: 2.7 Consensus size: 98
1347393 CTGTTTTATG
* * * * *
1347403 AAAAGAGATAAATCGAT-GGATTTATTTTTATATTTTGGAAAAGGAAATAAATCGTTGAATTTAT
1 AAAAGAAATAAATC-ATAGAATTTATTTTCATATTTTGTAAAAGAAAATAAATCGTTGAATTTAT
* * * *
1347467 TTTCTTATGAATCTTATATGATTTTGTTTTGT-A
65 TTTCCTATGAATCTTATATGATTATGATATGTAA
* * * * * * *
1347500 AAATGAAATAAATCGTCGAATTTATTTTCCTGTTTTGTAAAAGAAAATAAATCGTTAAATTTACT
1 AAAAGAAATAAATCATAGAATTTATTTTCATATTTTGTAAAAGAAAATAAATCGTTGAATTTATT
1347565 TTCCTATGAATCTTATATGATTATGATATGTAA
66 TTCCTATGAATCTTATATGATTATGATATGTAA
* * * *
1347598 AAAAGAAATATATCATAGAATTTATTTTCATATTTTGTAAAAGAAAACAAATCATTGGATTTATT
1 AAAAGAAATAAATCATAGAATTTATTTTCATATTTTGTAAAAGAAAATAAATCGTTGAATTTATT
1347663 TTCCTAT
66 TTCCTAT
1347670 TTTGTAAAAG
Statistics
Matches: 142, Mismatches: 26, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
96 1 0.01
97 79 0.56
98 62 0.44
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (98 bp):
AAAAGAAATAAATCATAGAATTTATTTTCATATTTTGTAAAAGAAAATAAATCGTTGAATTTATT
TTCCTATGAATCTTATATGATTATGATATGTAA
Found at i:1347538 original size:39 final size:39
Alignment explanation
Indices: 1347491--1347569 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 39
1347481 TATATGATTT
* *
1347491 TGTTTTGTAAAATG-AAATAAATCGTCGAATTTATTTTCC
1 TGTTTTGTAAAA-GAAAATAAATCGTCAAATTTACTTTCC
*
1347530 TGTTTTGTAAAAGAAAATAAATCGTTAAATTTACTTTCC
1 TGTTTTGTAAAAGAAAATAAATCGTCAAATTTACTTTCC
1347569 T
1 T
1347570 ATGAATCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 35 0.97
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.43
Consensus pattern (39 bp):
TGTTTTGTAAAAGAAAATAAATCGTCAAATTTACTTTCC
Found at i:1347660 original size:39 final size:39
Alignment explanation
Indices: 1347598--1347728 Score: 165
Period size: 39 Copynumber: 3.4 Consensus size: 39
1347588 TGATATGTAA
* * * *
1347598 AAAAG-AAATATATCATAGAATTTATTTTCATATTTTGT
1 AAAAGAAAATAAATCATTGGATTTATTTTCCTATTTTGT
*
1347636 AAAAGAAAACAAATCATTGGATTTATTTTCCTATTTTGT
1 AAAAGAAAATAAATCATTGGATTTATTTTCCTATTTTGT
* * * * *
1347675 AAAAGGAAATAAACCGTTGTATTTATTTTCCTGTTTTGT
1 AAAAGAAAATAAATCATTGGATTTATTTTCCTATTTTGT
1347714 AAAAGAAAATAAATC
1 AAAAGAAAATAAATC
1347729 GGTGGATTGA
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
38 5 0.06
39 74 0.94
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (39 bp):
AAAAGAAAATAAATCATTGGATTTATTTTCCTATTTTGT
Found at i:1351931 original size:22 final size:21
Alignment explanation
Indices: 1351901--1351947 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1351891 TTTTACTTCA
* *
1351901 AAACTCCAAATCTCAAACTCCT
1 AAACCCCAAATC-CAAAATCCT
*
1351923 AAACCCCAAATCCAAAATTCT
1 AAACCCCAAATCCAAAATCCT
1351944 AAAC
1 AAAC
1351948 TCTAATTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (21 bp):
AAACCCCAAATCCAAAATCCT
Found at i:1352947 original size:26 final size:27
Alignment explanation
Indices: 1352918--1352978 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
1352908 GTTAAATTTG
* *
1352918 AAAATTTTATTTAAAATTAAAATATT-
1 AAAATTTTATTTAAAATAAAAAAATTC
* **
1352944 AAAATTATATTTTTAATAAAAAAATTC
1 AAAATTTTATTTAAAATAAAAAAATTC
1352971 AAAATTTT
1 AAAATTTT
1352979 TGAAAATCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
AAAATTTTATTTAAAATAAAAAAATTC
Found at i:1357599 original size:18 final size:18
Alignment explanation
Indices: 1357565--1357607 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1357555 GTATTGGTCA
*
1357565 TGAGGAATATCAGAATGC
1 TGAGGAATATCAAAATGC
1357583 TGAGGCAAT-TCAAAATGC
1 TGAGG-AATATCAAAATGC
1357601 T-AGGAAT
1 TGAGGAAT
1357608 CCAGCAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.13
17 3 0.13
18 14 0.61
19 3 0.13
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.23
Consensus pattern (18 bp):
TGAGGAATATCAAAATGC
Found at i:1365190 original size:13 final size:14
Alignment explanation
Indices: 1365174--1365206 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1365164 AAAACCCCAT
1365174 ATGAAATG-AAAAA
1 ATGAAATGAAAAAA
1365187 ATG-AATGAAAAAA
1 ATGAAATGAAAAAA
1365200 ATGAAAT
1 ATGAAAT
1365207 TGTGAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.22
13 11 0.61
14 3 0.17
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (14 bp):
ATGAAATGAAAAAA
Found at i:1369738 original size:72 final size:72
Alignment explanation
Indices: 1369621--1369767 Score: 276
Period size: 72 Copynumber: 2.0 Consensus size: 72
1369611 GTGTAGTTGC
* *
1369621 TTGTCCATCGTCTTCTCATGGACAGCGTGTACATCCAAATCTATATGTTTGGATTGAGTGCAATA
1 TTGTCCATCATCTTCTCATGGACAGCGTGTACATCCAAATCTATATGTTTGGATTGACTGCAATA
1369686 GACAGGG
66 GACAGGG
1369693 TTGTCCATCATCTTCTCATGGACAGCGTGTACATCCAAATCTATATGTTTGGATTGACTGCAATA
1 TTGTCCATCATCTTCTCATGGACAGCGTGTACATCCAAATCTATATGTTTGGATTGACTGCAATA
1369758 GACAGGG
66 GACAGGG
1369765 TTG
1 TTG
1369768 GCACTTGTTG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (72 bp):
TTGTCCATCATCTTCTCATGGACAGCGTGTACATCCAAATCTATATGTTTGGATTGACTGCAATA
GACAGGG
Found at i:1372312 original size:13 final size:13
Alignment explanation
Indices: 1372294--1372323 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1372284 TTTTGATGAT
1372294 CATGCTCTGATAC
1 CATGCTCTGATAC
1372307 CATGCTCTGATAC
1 CATGCTCTGATAC
1372320 CATG
1 CATG
1372324 TATGAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (13 bp):
CATGCTCTGATAC
Found at i:1377026 original size:14 final size:14
Alignment explanation
Indices: 1377007--1377033 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1376997 GAATTAAATG
1377007 AAATAAAAAAATAA
1 AAATAAAAAAATAA
1377021 AAATAAAAAAATA
1 AAATAAAAAAATA
1377034 TAATGGCAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
AAATAAAAAAATAA
Found at i:1380376 original size:20 final size:20
Alignment explanation
Indices: 1380351--1380399 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1380341 TTCCACAGCT
1380351 TGGCTATCAGTTTTAGGGCA
1 TGGCTATCAGTTTTAGGGCA
1380371 TGGCTATCAGTTTTAGGGCA
1 TGGCTATCAGTTTTAGGGCA
*
1380391 TGGCGATCA
1 TGGCTATCA
1380400 ATTATCTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.33
Consensus pattern (20 bp):
TGGCTATCAGTTTTAGGGCA
Found at i:1400402 original size:27 final size:27
Alignment explanation
Indices: 1400346--1400396 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1400336 GCGGAGCTAG
* *
1400346 AAAATTTATTTTAGGATGTCAAATTAA
1 AAAAATTACTTTAGGATGTCAAATTAA
1400373 AAAAATTACTTTAGG-TGTCAAATT
1 AAAAATTACTTTAGGATGTCAAATT
1400397 TCAAAAGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (27 bp):
AAAAATTACTTTAGGATGTCAAATTAA
Found at i:1404640 original size:2 final size:2
Alignment explanation
Indices: 1404633--1404669 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1404623 GATAAATCTA
1404633 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1404670 ACTAATATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1408237 original size:17 final size:17
Alignment explanation
Indices: 1408217--1408255 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1408207 ATTTCAAAGT
1408217 TATAATTATATAAAAAA
1 TATAATTATATAAAAAA
* *
1408234 TATATTTATATATAAAA
1 TATAATTATATAAAAAA
1408251 TATAA
1 TATAA
1408256 ATAAAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAATTATATAAAAAA
Found at i:1408568 original size:3 final size:3
Alignment explanation
Indices: 1408554--1408618 Score: 61
Period size: 3 Copynumber: 23.3 Consensus size: 3
1408544 TATTTTTATA
* *
1408554 AAT AAT AA- AAT AAT AAT AAT GA- AAT AAT AATT AA- AAC AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
1408596 AA- AAT AAT AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1408619 TTGCAAATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
2 11 0.21
3 39 0.74
4 3 0.06
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:1408570 original size:11 final size:11
Alignment explanation
Indices: 1408553--1408618 Score: 66
Period size: 11 Copynumber: 6.0 Consensus size: 11
1408543 TTATTTTTAT
1408553 AAATAATAA-A
1 AAATAATAATA
*
1408563 ATAATAATAATG
1 A-AATAATAATA
1408575 AAATAATAATTA
1 AAATAATAA-TA
*
1408587 AAACAATAA-A
1 AAATAATAATA
1408597 AAATAATAATA
1 AAATAATAATA
1408608 ATAA-AATAATA
1 A-AATAATAATA
1408619 TTGCAAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
10 10 0.21
11 25 0.53
12 12 0.26
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (11 bp):
AAATAATAATA
Found at i:1408663 original size:29 final size:28
Alignment explanation
Indices: 1408631--1408701 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
1408621 GCAAATAATG
1408631 ATTAAAATAAAAGGAAATAAAAAT-ATAGT
1 ATTAAAATAAAA--AAATAAAAATCATAGT
* *
1408660 ATTAAAATGTAAAATATTAAAAATCATAGT
1 ATTAAAA--TAAAAAAATAAAAATCATAGT
1408690 A-TAAAATAAAAA
1 ATTAAAATAAAAA
1408702 CAAACTAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 5 0.14
29 20 0.56
30 6 0.17
31 5 0.14
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.27
Consensus pattern (28 bp):
ATTAAAATAAAAAAATAAAAATCATAGT
Found at i:1409795 original size:39 final size:39
Alignment explanation
Indices: 1409734--1409810 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
1409724 ACCTGGCAGT
* *
1409734 GCTGGAAGCTGTTGCAACTGATGCGTGGAGGGGCTGCTC
1 GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTC
* *
1409773 GCTGGAAGCTGCTGGAAATGATGTGTGGAGGGGCTGCT
1 GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCT
1409811 GGATGGAGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.43, T:0.23
Consensus pattern (39 bp):
GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTC
Found at i:1410429 original size:22 final size:22
Alignment explanation
Indices: 1410404--1410458 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1410394 AATAAAGCTT
*
1410404 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAAAGAATCTA
* *
1410426 TCATCTTTAAAAAAAGAGTCTA
1 TCATCTTTGAAAAAAGAATCTA
1410448 TCATCTTTGAA
1 TCATCTTTGAA
1410459 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAAAGAATCTA
Found at i:1410900 original size:54 final size:54
Alignment explanation
Indices: 1410818--1410983 Score: 253
Period size: 54 Copynumber: 3.1 Consensus size: 54
1410808 AGAATAGCAG
** * *
1410818 GTTCGTAAAACATTTGACGGCGCATTCATCCTTTCCAGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCAGTGGTTTCTGCTCAGAT
* *
1410872 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTAGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCAGTGGTTTCTGCTCAGAT
*
1410926 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTA-TGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCC-AGTGGTTTCTGCTCAGAT
1410980 GTTC
1 GTTC
1410984 TCAATCATTG
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 102 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCAGTGGTTTCTGCTCAGAT
Found at i:1413252 original size:114 final size:113
Alignment explanation
Indices: 1413047--1413386 Score: 590
Period size: 114 Copynumber: 3.0 Consensus size: 113
1413037 GATCATGCAG
* * * * *
1413047 TTCATCTTTTAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAA-TCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
* *
1413112 ACACTTCCAGAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAA
65 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
1413161 TTCATCTTTCAGATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCA-ATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1413226 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
65 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
1413275 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTC-AATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1413340 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
65 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
1413387 CATGGCACTT
Statistics
Matches: 217, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
114 215 0.99
115 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (113 bp):
TTCATCTTTCAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:1421393 original size:18 final size:18
Alignment explanation
Indices: 1421356--1421390 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1421346 AGGATTTTAA
*
1421356 ATATATATATTATTTATT
1 ATATATATATTATATATT
1421374 ATATATATA-TATATATT
1 ATATATATATTATATATT
1421391 TATTTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATATATATTATATATT
Found at i:1421484 original size:12 final size:11
Alignment explanation
Indices: 1421412--1421486 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 11
1421402 ATTATAAAAT
* *
1421412 AATAATAATGA
1 AATAATATTAA
1421423 AATAATGATTAA
1 AATAAT-ATTAA
* **
1421435 AACAATAAAAA
1 AATAATATTAA
*
1421446 TAATAATAATAA
1 -AATAATATTAA
*
1421458 AATAATATTGCA
1 AATAATATT-AA
1421470 AATAATGATTAA
1 AATAAT-ATTAA
1421482 AATAA
1 AATAA
1421487 AAGGAAATAA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
11 17 0.34
12 30 0.60
13 3 0.06
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (11 bp):
AATAATATTAA
Found at i:1422646 original size:39 final size:39
Alignment explanation
Indices: 1422585--1422661 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
1422575 ACCTGGCAGT
* *
1422585 GCTGGAAGCTGTTGCAACTGATGCGTGGAGGGGCTGCTC
1 GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTC
* *
1422624 GCTGGAAGCTGCTGGAAATGATGTGTGGAGGGGCTGCT
1 GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCT
1422662 GGATGGAGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.43, T:0.23
Consensus pattern (39 bp):
GCTGGAAGCTGCTGCAAATGATGCGTGGAGGGGCTGCTC
Found at i:1428586 original size:20 final size:20
Alignment explanation
Indices: 1428558--1428596 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1428548 CCAAATTCGC
1428558 AACGCGAATATGTAAATCGA
1 AACGCGAATATGTAAATCGA
* *
1428578 AACGTGAATTTGTAAATCG
1 AACGCGAATATGTAAATCG
1428597 TAACACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (20 bp):
AACGCGAATATGTAAATCGA
Found at i:1428623 original size:20 final size:20
Alignment explanation
Indices: 1428598--1428880 Score: 176
Period size: 20 Copynumber: 14.1 Consensus size: 20
1428588 TGTAAATCGT
1428598 AACACATAAGTCAAATTCGC
1 AACACATAAGTCAAATTCGC
*
1428618 AACACAGAAGTCAAATTCGC
1 AACACATAAGTCAAATTCGC
* *
1428638 AACGCGAT-AGTCAAATTCGT
1 AACAC-ATAAGTCAAATTCGC
* *
1428658 AACGCA-ATAGTCATATTCGC
1 AACACATA-AGTCAAATTCGC
1428678 AACAC-TGAAGTCAAATTCGC
1 AACACAT-AAGTCAAATTCGC
* ** *
1428698 AACGCGAATCTGT-AAAAT-GC
1 AACAC--ATAAGTCAAATTCGC
* * **
1428718 AGCGCGAATTTGT-AAA-TCGC
1 AACAC--ATAAGTCAAATTCGC
*
1428738 AACACAGAAGTCAAATTCGC
1 AACACATAAGTCAAATTCGC
*
1428758 AACACAAAAGTCAAATTCGC
1 AACACATAAGTCAAATTCGC
*
1428778 AACGCGAT-AGTCAAATTCGC
1 AACAC-ATAAGTCAAATTCGC
*
1428798 AA-AGCGAT-AGTCAAATTCGT
1 AACA-C-ATAAGTCAAATTCGC
* *
1428818 AACA-TTGAATTTCAAATTCGC
1 AACACAT-AA-GTCAAATTCGC
*
1428839 AACACAAAAGTCAAATTCGC
1 AACACATAAGTCAAATTCGC
*
1428859 AACGCGAT-AGTCAAATTCGC
1 AACAC-ATAAGTCAAATTCGC
1428879 AA
1 AA
1428881 AGCACGTTTA
Statistics
Matches: 212, Mismatches: 32, Indels: 38
0.75 0.11 0.13
Matches are distributed among these distances:
18 4 0.02
19 5 0.02
20 176 0.83
21 24 0.11
22 2 0.01
23 1 0.00
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.21
Consensus pattern (20 bp):
AACACATAAGTCAAATTCGC
Done.