Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008953.1 Hibiscus syriacus cultivar Beakdansim tig00112281_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: 2822058
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 15
Found at i:2695914 original size:26 final size:26
Alignment explanation
Indices: 2695884--2695986 Score: 111
Period size: 26 Copynumber: 3.8 Consensus size: 26
2695874 TTCATCCATT
*
2695884 TTTTATTTATATTTTTATTATTATTTA
1 TTTTA-TTATATTATTATTATTATTTA
* * *
2695911 -TTTATTATAAATGTTATTA-TAATTA
1 TTTTATTAT-ATTATTATTATTATTTA
2695936 TTTTATTATATTATTATTATTAATATTA
1 TTTTATTATATTATTATTATT-AT-TTA
2695964 TTCTTATTATATTATTATTATTA
1 TT-TTATTATATTATTATTATTA
2695987 AAATAAATAA
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
25 17 0.27
26 21 0.33
27 1 0.02
28 6 0.09
29 19 0.30
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (26 bp):
TTTTATTATATTATTATTATTATTTA
Found at i:2695931 original size:37 final size:36
Alignment explanation
Indices: 2695890--2695985 Score: 95
Period size: 37 Copynumber: 2.5 Consensus size: 36
2695880 CATTTTTTAT
*
2695890 TTATATTTTTATTATTATTTATTTATTATAAATGTTA
1 TTATATTTTTATTATTATTTA-TTATTATAAATATTA
* *
2695927 TTATAATTATT-TTATTATATTATTATTATTAATATTA
1 TTAT-ATTTTTATTATTAT-TTATTATTATAAATATTA
*
2695964 TTCTTATTATATTATTATTATT
1 TT-ATATT-T-TTATTATTATT
2695986 AAAATAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
37 29 0.60
38 9 0.19
39 3 0.06
40 7 0.15
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (36 bp):
TTATATTTTTATTATTATTTATTATTATAAATATTA
Found at i:2696376 original size:17 final size:18
Alignment explanation
Indices: 2696343--2696376 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2696333 GCAGAAAACA
*
2696343 AAGAGATGAACAATGACC
1 AAGAGATGAAAAATGACC
2696361 AAGAGA-GAAAAATGAC
1 AAGAGATGAAAAATGAC
2696377 AACCACCACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.12, G:0.24, T:0.09
Consensus pattern (18 bp):
AAGAGATGAAAAATGACC
Found at i:2696741 original size:29 final size:29
Alignment explanation
Indices: 2696699--2696758 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
2696689 AGAGAGGGTG
2696699 GAGCATTTTTATTCTCTCTCACTTAGAGA
1 GAGCATTTTTATTCTCTCTCACTTAGAGA
2696728 GAGCATTTTTATTCTCTCTCACTTAGAGA
1 GAGCATTTTTATTCTCTCTCACTTAGAGA
2696757 GA
1 GA
2696759 ATGAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (29 bp):
GAGCATTTTTATTCTCTCTCACTTAGAGA
Found at i:2697001 original size:2 final size:2
Alignment explanation
Indices: 2696994--2697037 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2696984 TTGACATAAT
2696994 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2697036 TA
1 TA
2697038 GGTAAATAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2697827 original size:23 final size:23
Alignment explanation
Indices: 2697801--2697844 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2697791 TCTATTATGG
2697801 TATTTAAAAATAAATAAATATCT
1 TATTTAAAAATAAATAAATATCT
* * *
2697824 TATTTATAAATATATATATAT
1 TATTTAAAAATAAATAAATAT
2697845 ATATATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTTAAAAATAAATAAATATCT
Found at i:2697840 original size:2 final size:2
Alignment explanation
Indices: 2697828--2697865 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2697818 ATATCTTATT
*
2697828 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2697866 ATAAAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2697894 original size:17 final size:18
Alignment explanation
Indices: 2697874--2697912 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2697864 TAATAAAAAT
*
2697874 TATTATA-TTCTTATTAA
1 TATTATATTTATTATTAA
2697891 TATT-TATTTATTATTAA
1 TATTATATTTATTATTAA
2697908 TATTA
1 TATTA
2697913 AAGAAAAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTATATTTATTATTAA
Found at i:2704816 original size:10 final size:10
Alignment explanation
Indices: 2704798--2704828 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2704788 TTTATTTTGA
2704798 TTATGTTATT
1 TTATGTTATT
*
2704808 TTATTTTATT
1 TTATGTTATT
2704818 TTATGTTATT
1 TTATGTTATT
2704828 T
1 T
2704829 GTTGATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (10 bp):
TTATGTTATT
Found at i:2704823 original size:20 final size:19
Alignment explanation
Indices: 2704786--2704828 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
2704776 TTATTTTATA
2704786 ATTTTATTTTGATTATGTT
1 ATTTTATTTTGATTATGTT
2704805 ATTTTATTTT-ATTTTATGTT
1 ATTTTATTTTGA--TTATGTT
2704825 ATTT
1 ATTT
2704829 GTTGATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.05
19 10 0.45
20 11 0.50
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (19 bp):
ATTTTATTTTGATTATGTT
Found at i:2709296 original size:21 final size:21
Alignment explanation
Indices: 2709259--2709378 Score: 150
Period size: 21 Copynumber: 5.7 Consensus size: 21
2709249 GGGTCTACGC
*
2709259 GGTCCTTCGGGATAATACAGT
1 GGTCCTTCGGGACAATACAGT
* *
2709280 GGTCTTTCAGGACAATACAGT
1 GGTCCTTCGGGACAATACAGT
* *
2709301 GATCCTTCGGGATAATACAGT
1 GGTCCTTCGGGACAATACAGT
**
2709322 GGTCCTTCGGGACAATACAAC
1 GGTCCTTCGGGACAATACAGT
* * *
2709343 AGTCCTTCGGGATAATATAGT
1 GGTCCTTCGGGACAATACAGT
2709364 GGTCCTTCGGGACAA
1 GGTCCTTCGGGACAA
2709379 ATTTCATATG
Statistics
Matches: 81, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 81 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (21 bp):
GGTCCTTCGGGACAATACAGT
Found at i:2709320 original size:42 final size:42
Alignment explanation
Indices: 2709260--2709378 Score: 177
Period size: 42 Copynumber: 2.8 Consensus size: 42
2709250 GGTCTACGCG
* * **
2709260 GTCCTTCGGGATAATACAGTGGTCTTTCAGGACAATAC-AGT
1 GTCCTTCGGGATAATACAGTGGTCCTTCGGGACAATACAACA
2709301 GATCCTTCGGGATAATACAGTGGTCCTTCGGGACAATACAACA
1 G-TCCTTCGGGATAATACAGTGGTCCTTCGGGACAATACAACA
*
2709344 GTCCTTCGGGATAATATAGTGGTCCTTCGGGACAA
1 GTCCTTCGGGATAATACAGTGGTCCTTCGGGACAA
2709379 ATTTCATATG
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 1 0.01
42 68 0.96
43 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (42 bp):
GTCCTTCGGGATAATACAGTGGTCCTTCGGGACAATACAACA
Found at i:2713664 original size:21 final size:22
Alignment explanation
Indices: 2713640--2713683 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2713630 TAAAGCAGTA
2713640 CTGTAGC-AGGGAATCAGTTCC
1 CTGTAGCAAGGGAATCAGTTCC
*
2713661 CTGTAGCAAGGGAATCGGTTCC
1 CTGTAGCAAGGGAATCAGTTCC
2713683 C
1 C
2713684 CTCTGACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.23
Consensus pattern (22 bp):
CTGTAGCAAGGGAATCAGTTCC
Found at i:2720123 original size:15 final size:15
Alignment explanation
Indices: 2720103--2720184 Score: 103
Period size: 15 Copynumber: 5.5 Consensus size: 15
2720093 TTCCAGAAAA
*
2720103 TGAATTATTGGAATT
1 TGAATTACTGGAATT
2720118 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
2720133 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
*
2720148 TGAATTACTAGAATT
1 TGAATTACTGGAATT
**
2720163 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
2720177 TGAATTAC
1 TGAATTAC
2720185 ATTTCTGTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
14 11 0.19
15 46 0.81
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:2720162 original size:45 final size:44
Alignment explanation
Indices: 2720098--2720184 Score: 129
Period size: 45 Copynumber: 2.0 Consensus size: 44
2720088 TGGTTTTCCA
* * **
2720098 GAAAATGAATTATTGGAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTAGAATTTGAATT-CTGGAAAATGAATTACTG
2720143 GAAAATGAATTACTAGAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTAGAATTTGAATTCTGGAAAATGAATTAC
2720185 ATTTCTGTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
44 14 0.37
45 24 0.63
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.34
Consensus pattern (44 bp):
GAAAATGAATTACTAGAATTTGAATTCTGGAAAATGAATTACTG
Found at i:2720182 original size:29 final size:30
Alignment explanation
Indices: 2720103--2720184 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
2720093 TTCCAGAAAA
* ** *
2720103 TGAATTATTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTAGAATT
2720133 TGAATTACTGGAAAATGAATTACTAGAATT
1 TGAATTACTGGAAAATGAATTACTAGAATT
2720163 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
2720185 ATTTCTGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 16 0.33
30 32 0.67
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTAGAATT
Found at i:2720190 original size:20 final size:20
Alignment explanation
Indices: 2720167--2720236 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
2720157 AGAATTTGAA
2720167 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
2720187 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
2720207 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
2720227 TTCTGGAAAA
1 TTCTGGAAAA
2720237 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:2720428 original size:28 final size:28
Alignment explanation
Indices: 2720395--2720552 Score: 126
Period size: 28 Copynumber: 5.5 Consensus size: 28
2720385 CTTTACTAAA
*
2720395 ATATTATTAAATATATAAATAATATTAT
1 ATATTATTAAATATAAAAATAATATTAT
*
2720423 -TCATTATTAAATATAAAAAAAATTATTAT
1 AT-ATTATTAAATATAAAAATAA-TATTAT
2720452 ATATTATTAAA-ATAAAATATAATATCT-T
1 ATATTATTAAATATAAAA-ATAATAT-TAT
** * *
2720480 ATATTATT-AATATAATTGATTATTTTAT
1 ATATTATTAAATATAA-AAATAATATTAT
* * * *
2720508 ATAATATTAAAAATAAATATATTATTAT
1 ATATTATTAAATATAAAAATAATATTAT
*
2720536 AAATATTAATAAATATA
1 --ATATTATTAAATATA
2720553 TTTAAATATT
Statistics
Matches: 102, Mismatches: 17, Indels: 20
0.73 0.12 0.14
Matches are distributed among these distances:
27 4 0.04
28 60 0.59
29 25 0.25
30 13 0.13
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (28 bp):
ATATTATTAAATATAAAAATAATATTAT
Found at i:2720447 original size:26 final size:27
Alignment explanation
Indices: 2720396--2720457 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
2720386 TTTACTAAAA
*
2720396 TATTATTAAATATATAAATAATATTAT
1 TATTATTAAATATATAAATAAAATTAT
2720423 TCATTATTAAATATA-AAA-AAAATTAT
1 T-ATTATTAAATATATAAATAAAATTAT
2720449 TATATATTA
1 TAT-TATTA
2720458 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 2 0.06
26 13 0.41
27 4 0.12
28 13 0.41
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
TATTATTAAATATATAAATAAAATTAT
Found at i:2720476 original size:23 final size:23
Alignment explanation
Indices: 2720436--2720481 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2720426 TTATTAAATA
*
2720436 TAAAAAAAATTATTATATATTAT
1 TAAAAAAAATTATAATATATTAT
*
2720459 TAAAATAAAA-TATAATATCTTAT
1 TAAAA-AAAATTATAATATATTAT
2720482 ATTATTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAAAAAAATTATAATATATTAT
Found at i:2720533 original size:18 final size:18
Alignment explanation
Indices: 2720506--2720540 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2720496 TGATTATTTT
2720506 ATATAATATTAAAAATAA
1 ATATAATATTAAAAATAA
* *
2720524 ATATATTATTATAAATA
1 ATATAATATTAAAAATA
2720541 TTAATAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAATATTAAAAATAA
Found at i:2720546 original size:20 final size:20
Alignment explanation
Indices: 2720506--2720571 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
2720496 TGATTATTTT
* *
2720506 ATATAATATTA-AAA-ATAA
1 ATATATTATTATAAATATTA
2720524 ATATATTATTATAAATATTA
1 ATATATTATTATAAATATTA
*
2720544 ATAAATATATT-TAAATATTTA
1 ATATAT-TATTATAAATA-TTA
2720565 ATA-ATTA
1 ATATATTA
2720572 ATATTTGATG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 10 0.24
19 5 0.12
20 16 0.39
21 10 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATATTATTATAAATATTA
Found at i:2720565 original size:21 final size:21
Alignment explanation
Indices: 2720519--2720577 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
2720509 TAATATTAAA
2720519 AATAAATATATTATTATAAATATT
1 AATAAATA-A-TATT-TAAATATT
2720543 AATAAAT-ATATTTAAATATTT
1 AATAAATAATATTTAAATA-TT
*
2720564 AATAATTAATATTT
1 AATAAATAATATTT
2720578 GATGAAAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 6 0.19
21 12 0.38
22 7 0.22
24 7 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATAAATAATATTTAAATATT
Found at i:2720808 original size:42 final size:42
Alignment explanation
Indices: 2720749--2720868 Score: 231
Period size: 42 Copynumber: 2.9 Consensus size: 42
2720739 ATGATTTACA
*
2720749 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
2720791 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
2720833 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
2720869 TTCGGGGAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:2724265 original size:24 final size:24
Alignment explanation
Indices: 2724238--2724283 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2724228 ATGTTACTAT
2724238 AATTATATAATT-AAATTAATTAAA
1 AATTATAT-ATTAAAATTAATTAAA
* *
2724262 AATTTTATTTTAAAATTAATTA
1 AATTATATATTAAAATTAATTA
2724284 TATTAGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 2 0.11
24 17 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATTATATATTAAAATTAATTAAA
Found at i:2726091 original size:27 final size:27
Alignment explanation
Indices: 2726053--2726113 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
2726043 CTAATTAATA
2726053 TAAGGTAAATTAAGGCCTTTTCTAACT
1 TAAGGTAAATTAAGGCCTTTTCTAACT
2726080 TAAGGTAAATTAAGGCCTTTTCTAACT
1 TAAGGTAAATTAAGGCCTTTTCTAACT
2726107 TAAGGTA
1 TAAGGTA
2726114 TCAAATTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (27 bp):
TAAGGTAAATTAAGGCCTTTTCTAACT
Found at i:2726730 original size:16 final size:17
Alignment explanation
Indices: 2726709--2726740 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2726699 ACTTAATTAA
2726709 AATAAAAAAAA-AGTAC
1 AATAAAAAAAATAGTAC
2726725 AATAAAAAAAATAGTA
1 AATAAAAAAAATAGTA
2726741 AAAACAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (17 bp):
AATAAAAAAAATAGTAC
Found at i:2726735 original size:25 final size:24
Alignment explanation
Indices: 2726707--2726759 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 24
2726697 AAACTTAATT
2726707 AAAATA-AAAAAAAAGTACAATAAAA
1 AAAATAGAAAAAAAA-TAC-ATAAAA
*
2726732 AAAATAGTAAAAACAATACATAAAA
1 AAAATAG-AAAAAAAATACATAAAA
2726757 AAA
1 AAA
2726760 CTTGAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 15 0.60
26 3 0.12
27 7 0.28
ACGTcount: A:0.77, C:0.06, G:0.04, T:0.13
Consensus pattern (24 bp):
AAAATAGAAAAAAAATACATAAAA
Found at i:2726742 original size:12 final size:13
Alignment explanation
Indices: 2726713--2726759 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
2726703 AATTAAAATA
2726713 AAAAAAAAGTACAAT
1 AAAAAAAA-TAC-AT
*
2726728 AAAAAAAATA-GT
1 AAAAAAAATACAT
*
2726740 AAAAACAATACAT
1 AAAAAAAATACAT
2726753 AAAAAAA
1 AAAAAAA
2726760 CTTGAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 10 0.37
13 7 0.26
14 2 0.07
15 8 0.30
ACGTcount: A:0.77, C:0.06, G:0.04, T:0.13
Consensus pattern (13 bp):
AAAAAAAATACAT
Found at i:2727369 original size:115 final size:107
Alignment explanation
Indices: 2727167--2727459 Score: 342
Period size: 115 Copynumber: 2.7 Consensus size: 107
2727157 TTGTGCAATA
* * * **
2727167 AAATAAAAGTTAGTAGTTAGCAGAGTTCGAACCATAATAATGTGGGTCTTACCCCGGATTAGGTC
1 AAATAAAA--TAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCTTACCCCGGATCGGGTC
*
2727232 ATCACAAGGTCGAATCGAATAATGCAAACAAATATATAAAAAAAT
64 ACCACAAGGTCGAATCGAATAATGCAAAC-AATATATAAAAAAAT
2727277 AAAACAAATAAAAAATAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCTTACCCCGGATC
1 -----AAAT--AAAATAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCTTACCCCGGATC
**
2727342 GGGTCACCACAAGGTCGAATCGAATAATTTAAACAATATATAAAAAAAT
59 GGGTCACCACAAGGTCGAATCGAATAATGCAAACAATATATAAAAAAAT
* * * * **
2727391 AAGT----TGGTGGTTGGCATAGTCTAAACCATAATAATGTGGATCTTACCCCGGATCGGGTCAC
1 AAATAAAATAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCTTACCCCGGATCGGGTCAC
2727452 CACAAGGT
66 CACAAGGT
2727460 TGAGTAATAG
Statistics
Matches: 162, Mismatches: 14, Indels: 16
0.84 0.07 0.08
Matches are distributed among these distances:
103 60 0.37
109 3 0.02
114 15 0.09
115 80 0.49
117 4 0.02
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (107 bp):
AAATAAAATAGTGGTTAGCAGAGTCCGAACCATAATAATGTGGATCTTACCCCGGATCGGGTCAC
CACAAGGTCGAATCGAATAATGCAAACAATATATAAAAAAAT
Found at i:2728120 original size:13 final size:13
Alignment explanation
Indices: 2728090--2728128 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2728080 CAAGCATACT
**
2728090 AACACCCTAAATT
1 AACACCCTAAACC
*
2728103 GACACCCTAAACC
1 AACACCCTAAACC
2728116 AACACCCTAAACC
1 AACACCCTAAACC
2728129 GACGTACAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.44, C:0.41, G:0.03, T:0.13
Consensus pattern (13 bp):
AACACCCTAAACC
Found at i:2729985 original size:24 final size:24
Alignment explanation
Indices: 2729958--2730004 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2729948 GCATGACATT
2729958 GTACATAGATATTTTATACATCAA
1 GTACATAGATATTTTATACATCAA
*
2729982 GTACATAGATGTTTTATACATCA
1 GTACATAGATATTTTATACATCA
2730005 TCAGGAAGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (24 bp):
GTACATAGATATTTTATACATCAA
Found at i:2731820 original size:132 final size:130
Alignment explanation
Indices: 2731539--2731873 Score: 411
Period size: 132 Copynumber: 2.5 Consensus size: 130
2731529 TGGCAATATT
* * * * *
2731539 GATCCACCTCATGCTGTGATTGAATCGAACATAATGCCAGTGCTGATCTACCTCCTTCTGTGATA
1 GATCCACCTCATTCTGTGATGGAATCGAAGAT-ATGTCGGTGCTGATCTACCTCCTTCTGTGATA
* * ** * *
2731604 GAAAT-GAGCAAAATGTGATGTTTTTCCAACTCCTTATGCGATGGATTTGAGTGAAATGAAAATG
65 G-AATCGAGCAAAAAGTGATATTGATCCAACTCCTTATGCGATGGATTTGAGCGAAATAAAAATG
2731668 TC
129 TC
* *
2731670 GATCCACATCATTCTGTGATGGAATCGAATGATATGTCGGTGCTGATCTACCTCATTCTGTGATA
1 GATCCACCTCATTCTGTGATGGAATCGAA-GATATGTCGGTGCTGATCTACCTCCTTCTGTGATA
* * * **
2731735 GAATCGAGCAAAAAGTTGATATTGATGCAATTTCTTATGTTATGGATTTGAGCGAAATAAAAATG
65 GAATCGAGCAAAAAG-TGATATTGATCCAACTCCTTATGCGATGGATTTGAGCGAAATAAAAATG
2731800 TC
129 TC
* * * * *
2731802 GATCCACCTCCTTCTGTGATGGAATTGAACGAGATGTTGGTACTGATCTACCTCCTTCTGTGATA
1 GATCCACCTCATTCTGTGATGGAATCGAA-GATATGTCGGTGCTGATCTACCTCCTTCTGTGATA
2731867 GAATCGA
65 GAATCGA
2731874 CTAAAAAATA
Statistics
Matches: 175, Mismatches: 26, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
130 3 0.02
131 65 0.37
132 107 0.61
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (130 bp):
GATCCACCTCATTCTGTGATGGAATCGAAGATATGTCGGTGCTGATCTACCTCCTTCTGTGATAG
AATCGAGCAAAAAGTGATATTGATCCAACTCCTTATGCGATGGATTTGAGCGAAATAAAAATGTC
Found at i:2731965 original size:108 final size:108
Alignment explanation
Indices: 2731776--2731981 Score: 331
Period size: 108 Copynumber: 1.9 Consensus size: 108
2731766 TTCTTATGTT
* * * **
2731776 ATGGATTTGAGCGAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATTGAACGAGATGTTG
1 ATGGATTTGAGCGAAATAAAAACGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCA
2731841 GTACTGATCTACCTCCTTCTGTGATAGAATCGACTAAAAAATA
66 GTACTGATCTACCTCCTTCTGTGATAGAATCGACTAAAAAATA
* *
2731884 ATGGATTTGAGTGAAATGAAAACGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCA
1 ATGGATTTGAGCGAAATAAAAACGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCA
**
2731949 GTGTTGATCTACCTCCTTCTGTGATAGAATCGA
66 GTACTGATCTACCTCCTTCTGTGATAGAATCGA
2731982 GAAAAAAAGT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
108 89 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (108 bp):
ATGGATTTGAGCGAAATAAAAACGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATATCA
GTACTGATCTACCTCCTTCTGTGATAGAATCGACTAAAAAATA
Found at i:2732921 original size:54 final size:52
Alignment explanation
Indices: 2732863--2732967 Score: 149
Period size: 52 Copynumber: 2.0 Consensus size: 52
2732853 TATAGTTTTC
* *
2732863 AAGAAACCCCT-AAAATTAGGCTTAGCTTCTTTTAAAAATTCATTTAAAAACATA
1 AAGAAACCCCTAAAAATTAGGCTTAG--T-TTCTAAAAACTCATTTAAAAACATA
*
2732917 AAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAACTCATTTGAAAACAT
1 AAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAACTCATTTAAAAACAT
2732968 CATGCCCGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
52 21 0.45
53 1 0.02
54 11 0.23
55 14 0.30
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.30
Consensus pattern (52 bp):
AAGAAACCCCTAAAAATTAGGCTTAGTTTCTAAAAACTCATTTAAAAACATA
Found at i:2733094 original size:42 final size:41
Alignment explanation
Indices: 2732965--2733094 Score: 127
Period size: 42 Copynumber: 3.1 Consensus size: 41
2732955 CATTTGAAAA
* * *
2732965 CATCATGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTAT
1 CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTTAT
* * * * *
2733006 CATCTTGCTCGAAAGACTTATAGATGACCCGAAGAATTTAAA
1 CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTT-AT
* * *
2733048 CATCATGCTCGAAAGATTTGCTA-ATGGCCCAAAGGACTTACT
1 CATCATGCTCGAAAGACTT-ATAGATGGCCCGAAGGACTTA-T
2733090 CATCA
1 CATCA
2733095 AGAAACCCTT
Statistics
Matches: 70, Mismatches: 16, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
41 33 0.47
42 35 0.50
43 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.25
Consensus pattern (41 bp):
CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTTAT
Found at i:2733634 original size:263 final size:262
Alignment explanation
Indices: 2732958--2733688 Score: 1038
Period size: 262 Copynumber: 2.8 Consensus size: 262
2732948 AAAAACTCAT
* *
2732958 TTGAAAACATCATGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGAC
1 TTGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGAC
* * * * *
2733023 TTATAGATGACCCGAAGAATTTAAACATCATGCTCGAAAGATTTGCTAATGGCCCAAAGGACTTA
66 TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAATTACTGATGGCCCAAAGGACTTA
2733088 CTCATCAAGAAACCCTTGAAAATCAAGCTT-TTTTCTTAGTTGTCATCAAGGAACCCCTACATAT
131 CTCATCAAGAAACCCTTGAAAATCAAGCTTATTTT-TTAGTTGTCATCAAGGAACCCCTACATAT
* * *
2733152 CACGTTGGTCCCTCGAGTGAGGTGACGTTGATTCAACTCCATATATGATGAATCGAGTATCGAAA
195 CACGTTGGTCCCTCGAGTGAGGTGACGTTGATTCAAATCCATATATGATGAATCAAGTAGCGAAA
2733217 ATG
260 ATG
* * * * * * *
2733220 TTGAAAACATCCTGCCCAAAGGAT-TTATGGATGACCCGAAGGTCTTATTATTTTGCTCAAAAGT
1 TTGAAAACATCATGCCCGAAGG-TCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGA
* * * *
2733284 CTTATAAATGGCCCGAAAGACTTAAGCATCATGCTCGAAAGACA-TACTGATGGCCCAAAGGACT
65 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA-ATTACTGATGGCCCAAAGGACT
* *
2733348 TACTCATCAAGAAACCCTTGAAAATCAAGCTTATTTTTTAGTTGTCATTAAGGAAACCCTACATA
129 TACTCATCAAGAAACCCTTGAAAATCAAGCTTATTTTTTAGTTGTCATCAAGGAACCCCTACATA
* * * * *
2733413 TCACGTTGGTCCCTTGAGTGAGGTGACGCTTGATTCAAATCTATATGTGATGAATCAAGTGGCTA
194 TCACGTTGGTCCCTCGAGTGAGGTGACG-TTGATTCAAATCCATATATGATGAATCAAGTAGCGA
2733478 AAATG
258 AAATG
* * *
2733483 TTGAAAATATCATGCCCGAAGGTCTTATGGATGGCCTGAAGGACTTATCATCTTGCTCTAAAGAC
1 TTGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGAC
* * * * *
2733548 TTACAGATGATCTGAAGGATTTACGCATCATGCTCGAACGAATTACTGATGGCCCGAAA-GACTT
66 TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAATTACTGATGGCCC-AAAGGACTT
* *
2733612 ACTCATCAAGAAACCCTTGAAAATCAAGCTCAGTTTATTAGTTGTCATCAAGGAACCCCTACATA
130 ACTCATCAAGAAACCCTTGAAAATCAAGCTTA-TTTTTTAGTTGTCATCAAGGAACCCCTACATA
2733677 TCACGTTGGTCC
194 TCACGTTGGTCC
2733689 ATCAAGCTTA
Statistics
Matches: 410, Mismatches: 51, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
262 194 0.47
263 172 0.42
264 44 0.11
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (262 bp):
TTGAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGAC
TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAATTACTGATGGCCCAAAGGACTTA
CTCATCAAGAAACCCTTGAAAATCAAGCTTATTTTTTAGTTGTCATCAAGGAACCCCTACATATC
ACGTTGGTCCCTCGAGTGAGGTGACGTTGATTCAAATCCATATATGATGAATCAAGTAGCGAAAA
TG
Found at i:2735075 original size:28 final size:28
Alignment explanation
Indices: 2735043--2735106 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
2735033 GATAAAAGGC
2735043 TCAGGCTGACTTGGGAAAGTAATGTGTT
1 TCAGGCTGACTTGGGAAAGTAATGTGTT
* * * * *
2735071 TCAGGTTAATTTGGGGAGGTAATGTGTT
1 TCAGGCTGACTTGGGAAAGTAATGTGTT
2735099 TCAGGCTG
1 TCAGGCTG
2735107 GATTCTTGCG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.22, C:0.09, G:0.34, T:0.34
Consensus pattern (28 bp):
TCAGGCTGACTTGGGAAAGTAATGTGTT
Found at i:2735127 original size:15 final size:16
Alignment explanation
Indices: 2735107--2735141 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2735097 TTTCAGGCTG
*
2735107 GATTCTTGCGTTC-TT
1 GATTCTAGCGTTCATT
2735122 GATTCTAGCGTTCATT
1 GATTCTAGCGTTCATT
2735138 GATT
1 GATT
2735142 AAATGAAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.14, C:0.17, G:0.20, T:0.49
Consensus pattern (16 bp):
GATTCTAGCGTTCATT
Found at i:2739492 original size:2 final size:2
Alignment explanation
Indices: 2739485--2739551 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
2739475 TTTTTAAAAC
2739485 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
2739527 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2739552 CCCCCATCCC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2739738 original size:24 final size:24
Alignment explanation
Indices: 2739711--2739762 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2739701 AACGGATATA
*
2739711 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
2739735 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
2739759 TCAA
1 TCAA
2739763 GTAATAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:2739825 original size:24 final size:24
Alignment explanation
Indices: 2739734--2739825 Score: 125
Period size: 24 Copynumber: 3.8 Consensus size: 24
2739724 CATAAATCAG
* *
2739734 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAA
2739758 GTCAAGTAAT-AGATCAGAATCCAA
1 GTCAAGT-ATCAGATCAGAATCCAA
*
2739782 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
2739806 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
2739826 TCAAATCGAA
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
23 5 0.08
24 55 0.89
25 2 0.03
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:2739841 original size:48 final size:48
Alignment explanation
Indices: 2739735--2739843 Score: 116
Period size: 48 Copynumber: 2.3 Consensus size: 48
2739725 ATAAATCAGG
* * *
2739735 TCAAGTATCATATCAGAAATCAGGTCAAGTAATAGATCAGAATCCAAG
1 TCAAGAATCAGATCAGAAATCAGGTCAAGTAATAGATCAGAATCCAAA
* * *
2739783 TCAAGTATCAGATCAG-AATCCATGTCAAGT-ATCAGATCAGAATTCAAA
1 TCAAGAATCAGATCAGAAAT-CAGGTCAAGTAAT-AGATCAGAATCCAAA
2739831 TCGAA-AATCAGAT
1 TC-AAGAATCAGAT
2739844 AAAATATTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
47 5 0.09
48 46 0.87
49 2 0.04
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (48 bp):
TCAAGAATCAGATCAGAAATCAGGTCAAGTAATAGATCAGAATCCAAA
Found at i:2742321 original size:7 final size:7
Alignment explanation
Indices: 2742309--2742348 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
2742299 TGGTCAACGC
2742309 CGGTCAA
1 CGGTCAA
2742316 CGGTCAA
1 CGGTCAA
2742323 CGGGTCAA
1 C-GGTCAA
*
2742331 CAGTCAA
1 CGGTCAA
2742338 CGGGTCAA
1 C-GGTCAA
2742346 CGG
1 CGG
2742349 GTCGGGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 16 0.55
8 13 0.45
ACGTcount: A:0.28, C:0.28, G:0.33, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:2742330 original size:8 final size:8
Alignment explanation
Indices: 2742300--2742364 Score: 68
Period size: 8 Copynumber: 8.5 Consensus size: 8
2742290 TCAAAGTTTT
2742300 GGTCAACG
1 GGTCAACG
2742308 CCGGTCAAC-
1 --GGTCAACG
2742317 GGTCAACG
1 GGTCAACG
2742325 GGTCAAC-
1 GGTCAACG
*
2742332 AGTCAACG
1 GGTCAACG
2742340 GGTCAACG
1 GGTCAACG
2742348 GGT---CG
1 GGTCAACG
2742353 GGTCAACG
1 GGTCAACG
2742361 GGTC
1 GGTC
2742365 GGGTCAACAG
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
5 5 0.10
7 13 0.27
8 23 0.48
10 7 0.15
ACGTcount: A:0.23, C:0.28, G:0.35, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:2742330 original size:15 final size:15
Alignment explanation
Indices: 2742300--2742348 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
2742290 TCAAAGTTTT
2742300 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
2742317 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
*
2742332 AGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
2742347 GG
1 GG
2742349 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 22 0.73
17 8 0.27
ACGTcount: A:0.27, C:0.29, G:0.33, T:0.12
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:2742369 original size:18 final size:18
Alignment explanation
Indices: 2742359--2742418 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
2742349 GTCGGGTCAA
2742359 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
2742377 -----CGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
* *
2742390 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACAGGT
2742408 CGGGTCGGGTC
1 CGGGTCGGGTC
2742419 GGGTTGTGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
13 13 0.38
18 21 0.62
ACGTcount: A:0.15, C:0.22, G:0.47, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:2742412 original size:13 final size:13
Alignment explanation
Indices: 2742338--2742395 Score: 98
Period size: 13 Copynumber: 4.5 Consensus size: 13
2742328 CAACAGTCAA
2742338 CGGGTCAACGGGT
1 CGGGTCAACGGGT
2742351 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
2742364 CGGGTCAACAGGT
1 CGGGTCAACGGGT
*
2742377 CGGGTCAACAGGT
1 CGGGTCAACGGGT
2742390 CGGGTC
1 CGGGTC
2742396 GGGTAAACGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.17, C:0.24, G:0.43, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:2744014 original size:17 final size:16
Alignment explanation
Indices: 2743976--2744014 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2743966 TAATTAAAAT
*
2743976 AAAATAAAAAAGTACA
1 AAAATAAAAAAGTAAA
*
2743992 ATAATAAAAACAGTAAA
1 AAAATAAAAA-AGTAAA
2744009 AAAATA
1 AAAATA
2744015 GTAAAAACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.15
Consensus pattern (16 bp):
AAAATAAAAAAGTAAA
Found at i:2744394 original size:14 final size:13
Alignment explanation
Indices: 2744375--2744410 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
2744365 AAAGTGCTAG
2744375 AAAATAAAAAAAA
1 AAAATAAAAAAAA
2744388 TAAAATAAAAAAAA
1 -AAAATAAAAAAAA
2744402 AGAAATAAA
1 A-AAATAAA
2744411 TTGCTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 1 0.05
14 20 0.95
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (13 bp):
AAAATAAAAAAAA
Found at i:2746915 original size:23 final size:24
Alignment explanation
Indices: 2746877--2746925 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
2746867 GAATTCGATT
* *
2746877 AAATTACAGAGTTTTTTTTTATTA
1 AAATTACAAAGTTTTTTTTTAATA
2746901 AAATTACAAAG-TTTTTTTTAATA
1 AAATTACAAAGTTTTTTTTTAATA
2746924 AA
1 AA
2746926 CCATACCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (24 bp):
AAATTACAAAGTTTTTTTTTAATA
Found at i:2747289 original size:3 final size:3
Alignment explanation
Indices: 2747281--2747375 Score: 163
Period size: 3 Copynumber: 31.7 Consensus size: 3
2747271 TTTTTATCCA
* *
2747281 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2747329 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2747376 AATATATATT
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2747879 original size:28 final size:27
Alignment explanation
Indices: 2747817--2747891 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
2747807 ACCCCAACCT
* * *
2747817 GAAAAAAAGAAAGAGAACGGGACAGAGA
1 GAAAAAAAAAAAGAGAA-GAGACAGACA
* *
2747845 GACAAAAAAAAAGAAGAAGAGAGAGACA
1 GAAAAAAAAAAAG-AGAAGAGACAGACA
*
2747873 GAAAAAAAAACAGAGAAGA
1 GAAAAAAAAAAAGAGAAGA
2747892 TACAAACTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 6 0.15
28 29 0.74
29 4 0.10
ACGTcount: A:0.67, C:0.07, G:0.27, T:0.00
Consensus pattern (27 bp):
GAAAAAAAAAAAGAGAAGAGACAGACA
Found at i:2760190 original size:11 final size:11
Alignment explanation
Indices: 2760166--2760201 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2760156 ATTATGCTTG
*
2760166 AAGAGAAAAGAA
1 AAGA-AAAAAAA
2760178 AAGAAAAAAAA
1 AAGAAAAAAAA
2760189 AAGAAAAAAAA
1 AAGAAAAAAAA
2760200 AA
1 AA
2760202 AAAGGGGGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:2760192 original size:16 final size:15
Alignment explanation
Indices: 2760171--2760204 Score: 59
Period size: 15 Copynumber: 2.2 Consensus size: 15
2760161 GCTTGAAGAG
2760171 AAAAGAAAAGAAAAAA
1 AAAAGAAAA-AAAAAA
2760187 AAAAGAAAAAAAAAA
1 AAAAGAAAAAAAAAA
2760202 AAA
1 AAA
2760205 GGGGGGGGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAAAA
Found at i:2760573 original size:19 final size:21
Alignment explanation
Indices: 2760540--2760582 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2760530 TTCAAGTTCA
*
2760540 ATTTATTGGAGATTC-AATTT
1 ATTTATTGGAAATTCAAATTT
2760560 ATTT-TTGGAAATTCAAATTT
1 ATTTATTGGAAATTCAAATTT
2760580 ATT
1 ATT
2760583 CTTTTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.51
Consensus pattern (21 bp):
ATTTATTGGAAATTCAAATTT
Found at i:2761442 original size:84 final size:84
Alignment explanation
Indices: 2761343--2761991 Score: 1246
Period size: 84 Copynumber: 7.7 Consensus size: 84
2761333 CATTAACTGA
2761343 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
2761408 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
2761427 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
2761492 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
2761511 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
2761576 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
2761595 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
2761660 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
2761679 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
2761744 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
2761763 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
2761828 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
*
2761847 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTAGCAG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
2761912 AACCAATCATTGAATTTGG
66 AACCAATCATTGAATTTGG
* * * *
2761931 AAGATGAATTTGC-CAATAGCATCTTTTGAAAGTGTTCTTTGAGTTATCTAATCTGGTTTGG
1 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGG
2761992 TAAAAATTAC
Statistics
Matches: 559, Mismatches: 6, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
83 43 0.08
84 516 0.92
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.37
Consensus pattern (84 bp):
AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
AACCAATCATTGAATTTGG
Found at i:2762924 original size:113 final size:113
Alignment explanation
Indices: 2762721--2764098 Score: 1766
Period size: 113 Copynumber: 12.0 Consensus size: 113
2762711 CAAAGATTCA
* * * *
2762721 AATCTATCATTTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
2762786 AGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
2762834 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* **
2762899 AGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCCA
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * *
2762947 AATCTATCATTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
2763012 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
2763060 AATCCATCATTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
2763125 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * * *
2763173 AATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTG
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTG
* * * * * *
2763237 AAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCAT-
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * *
2763288 AATTCTATCGCAGAAGGAGATAGATTAGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
1 AA-TCCAT--C------A-TTTGA-T-GGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
* **
2763353 CTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCCA
54 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * *
2763413 AATCTATCATTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
2763478 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
2763526 AATCCATCATTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
2763591 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * * *
2763639 AATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCATCTG
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTG
* * * * * *
2763703 AAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCAT-
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * * *
2763754 AATTCTATCGCAGAAGGAGATAGATTAGCATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAA
1 AA-TCCAT--C------A-TTTGA-T-GGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
2763819 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
54 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
2763879 AATCCATCATTTGATGGATTAGC-TTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
2763943 AGGAAGAAGAAGTTCAT-ATGAGAAGAATTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * * *
2763990 AATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTG
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTG
* *
2764054 AAGAAGAAAGAAGAAGTTCATAAT-AGAAGAACTTGTTCAA-CTTTT
62 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
2764099 GCATAATTCT
Statistics
Matches: 1121, Mismatches: 102, Indels: 83
0.86 0.08 0.06
Matches are distributed among these distances:
111 49 0.04
112 84 0.07
113 618 0.55
114 7 0.01
115 52 0.05
116 116 0.10
118 2 0.00
122 2 0.00
124 113 0.10
125 12 0.01
126 2 0.00
127 62 0.06
128 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:2763149 original size:24 final size:23
Alignment explanation
Indices: 2763106--2763150 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
2763096 GTTCATAATG
*
2763106 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
2763129 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
2763151 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:2763615 original size:24 final size:23
Alignment explanation
Indices: 2763572--2763616 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
2763562 GTTCATAATG
*
2763572 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
2763595 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
2763617 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:2763722 original size:466 final size:466
Alignment explanation
Indices: 2762851--2764100 Score: 2267
Period size: 466 Copynumber: 2.7 Consensus size: 466
2762841 CATTTGATGG
2762851 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCAT
1 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCAT
2762916 AATGAGAAGAATTTGTTCAACCTTTTACCCAAATCTATCATTTGATGGATTATCTTTTCCAGAGA
66 AATGAGAAGAATTTGTTCAACCTTTTACCCAAATCTATCATTTGATGGATTATCTTTTCCAGAGA
2762981 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
131 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
2763046 CAACCTTTTACCTGAATCCATCATTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAG
196 CAACCTTTTACCTGAATCCATCATTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAG
2763111 AATTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAAT
261 AATTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAAT
*
2763176 TCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
326 TCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGA
2763241 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCATAATTCTATCGCAGAAGGA
391 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCATAATTCTATCGCAGAAGGA
2763306 GATAGATTAGC
456 GATAGATTAGC
2763317 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCAT
1 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCAT
2763382 AATGAGAAGAATTTGTTCAACCTTTTACCCAAATCTATCATTTGATGGATTATCTTTTCCAGAGA
66 AATGAGAAGAATTTGTTCAACCTTTTACCCAAATCTATCATTTGATGGATTATCTTTTCCAGAGA
2763447 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
131 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
2763512 CAACCTTTTACCTGAATCCATCATTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAG
196 CAACCTTTTACCTGAATCCATCATTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAG
2763577 AATTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAAT
261 AATTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAAT
2763642 TCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGA
326 TCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGA
2763707 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCATAATTCTATCGCAGAAGGA
391 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCATAATTCTATCGCAGAAGGA
2763772 GATAGATTAGC
456 GATAGATTAGC
* *
2763783 ATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCAT
** * *
2763848 AATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATTAGC-TTTCCAGAGA
66 AATGAGAAGAATTTGTTCAACCTTTTACCCAAATCTATCATTTGATGGATTATCTTTTCCAGAGA
*
2763912 AAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCAT-ATGAGAAGAATTTGTT
131 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * * * * * *
2763976 CAACCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAA
196 CAACCTTTTACCTGAATCCATCATTTGATGGATTAGCTTTTCCAGAG-AAAGTTCATAATGAGAA
* *
2764040 GAACTCGTCATCTGAAGAAGAAAGAAGAAGTTCATAAT-AGAAGAACTTGTTCAA-CTTTTGC
260 GAA-T--TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
2764101 ATAATTCTAT
Statistics
Matches: 762, Mismatches: 18, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
463 1 0.00
464 73 0.10
465 65 0.09
466 593 0.78
467 30 0.04
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (466 bp):
ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCAT
AATGAGAAGAATTTGTTCAACCTTTTACCCAAATCTATCATTTGATGGATTATCTTTTCCAGAGA
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
CAACCTTTTACCTGAATCCATCATTTGATGGATTAGCTTTTCCAGAGAAAGTTCATAATGAGAAG
AATTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAAT
TCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGA
AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTTGCATAATTCTATCGCAGAAGGA
GATAGATTAGC
Found at i:2763906 original size:112 final size:112
Alignment explanation
Indices: 2763789--2764098 Score: 457
Period size: 112 Copynumber: 2.8 Consensus size: 112
2763779 TAGCATCAGC
2763789 CTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 CTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* *
2763854 AAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATTAG
66 AAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAA
*
2763901 CTTTCCAGAGAAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCAT-ATGAG
1 CTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * *
2763965 AAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAA
66 AAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAA
* * *
2764012 CATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAAGAAGAAGTTCATA
1 C-TTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATA
*
2764076 AT-AGAAGAACTTGTTCAA-CTTTT
61 ATGAGAAGAATTTGTTCAACCTTTT
2764099 GCATAATTCT
Statistics
Matches: 181, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
111 49 0.27
112 83 0.46
114 5 0.03
115 42 0.23
116 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (112 bp):
CTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCAA
Found at i:2763952 original size:23 final size:23
Alignment explanation
Indices: 2763924--2763967 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2763914 GTTCATAATG
*
2763924 AGAAGAA-TTCATCTGAAGAAGGA
1 AGAAGAAGTTCATATG-AGAAGGA
2763947 AGAAGAAGTTCATATGAGAAG
1 AGAAGAAGTTCATATGAGAAG
2763968 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.48, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAAGTTCATATGAGAAGGA
Found at i:2764423 original size:3 final size:3
Alignment explanation
Indices: 2764415--2764508 Score: 145
Period size: 3 Copynumber: 31.3 Consensus size: 3
2764405 TTTTTTATCC
*
2764415 ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
2764463 ATC ATT ATT ACT ATT ATT ATTT ATT A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
2764508 A
1 A
2764509 AATATATATT
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
2 2 0.02
3 78 0.94
4 3 0.04
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2764432 original size:9 final size:9
Alignment explanation
Indices: 2764415--2764520 Score: 92
Period size: 9 Copynumber: 11.6 Consensus size: 9
2764405 TTTTTTATCC
*
2764415 ATTATTATT
1 ATTAATATT
2764424 ATTAATATT
1 ATTAATATT
*
2764433 ATTATTATT
1 ATTAATATT
*
2764442 ATTATTATT
1 ATTAATATT
*
2764451 ATTATTATT
1 ATTAATATT
2764460 ATT-ATCATT
1 ATTAAT-ATT
*
2764469 ATTACTATT
1 ATTAATATT
2764478 ATT-AT-TT
1 ATTAATATT
2764485 ATTATATTATT
1 ATTA-A-TATT
*
2764496 ATTATTATT
1 ATTAATATT
2764505 ATTAAATATAT
1 ATT-AATAT-T
2764516 ATTAA
1 ATTAA
2764521 ATATATATAA
Statistics
Matches: 82, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
7 5 0.06
8 2 0.02
9 57 0.70
10 8 0.10
11 10 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTAATATT
Found at i:2764518 original size:11 final size:11
Alignment explanation
Indices: 2764504--2764528 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2764494 TTATTATTAT
2764504 TATTAAATATA
1 TATTAAATATA
2764515 TATTAAATATA
1 TATTAAATATA
2764526 TAT
1 TAT
2764529 AATAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TATTAAATATA
Found at i:2776277 original size:18 final size:19
Alignment explanation
Indices: 2776236--2776277 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
2776226 CTATATTAGG
*
2776236 GTATAGATACTCTACCATGG
1 GTATAGATACTCTA-CATGA
*
2776256 GTATTGATACTCT-CATGA
1 GTATAGATACTCTACATGA
2776274 GTAT
1 GTAT
2776278 CAATACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
20 12 0.60
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (19 bp):
GTATAGATACTCTACATGA
Found at i:2778969 original size:22 final size:22
Alignment explanation
Indices: 2778941--2778984 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2778931 TGACAACATT
*
2778941 TGCTTTCTCTGGTTGATAGTCA
1 TGCTTTCTCTGGTTCATAGTCA
2778963 TGCTTTCTCTGGTTCATAGTCA
1 TGCTTTCTCTGGTTCATAGTCA
2778985 ATTACACAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (22 bp):
TGCTTTCTCTGGTTCATAGTCA
Found at i:2782959 original size:43 final size:43
Alignment explanation
Indices: 2782884--2782978 Score: 147
Period size: 43 Copynumber: 2.2 Consensus size: 43
2782874 CTTCCAACCG
* *
2782884 AACACACCATAATGTGTAAGATTCCCAGAACCATACACCCACT
1 AACACACCATAATGTGTAAGATTCCCAAAACCATACACCCACC
*
2782927 AACACACCATAATGTGT-AGGTTCCCCAAAACCATACACCCACC
1 AACACACCATAATGTGTAAGATT-CCCAAAACCATACACCCACC
2782970 AACACACCA
1 AACACACCA
2782979 AGTAAGGCCC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
42 4 0.08
43 44 0.92
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (43 bp):
AACACACCATAATGTGTAAGATTCCCAAAACCATACACCCACC
Found at i:2783107 original size:24 final size:24
Alignment explanation
Indices: 2783090--2783212 Score: 185
Period size: 24 Copynumber: 5.1 Consensus size: 24
2783080 ATCAAAACAT
* *
2783090 AATCCATGTCAAGTATCATATCAA
1 AATCCATGTCAAGTATCAGATCAG
* *
2783114 AATCCAAGTCAAGTATCATATCAG
1 AATCCATGTCAAGTATCAGATCAG
*
2783138 AATCCAAGTCAAGTATCAGATCAG
1 AATCCATGTCAAGTATCAGATCAG
2783162 AATCCATGTC-AGATATCAGATCAG
1 AATCCATGTCAAG-TATCAGATCAG
2783186 AATCCATGTCAAGTATCAGATCAG
1 AATCCATGTCAAGTATCAGATCAG
2783210 AAT
1 AAT
2783213 TCAAATCGAA
Statistics
Matches: 93, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
23 2 0.02
24 89 0.96
25 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (24 bp):
AATCCATGTCAAGTATCAGATCAG
Found at i:2783228 original size:48 final size:47
Alignment explanation
Indices: 2783090--2783230 Score: 183
Period size: 48 Copynumber: 2.9 Consensus size: 47
2783080 ATCAAAACAT
* * *
2783090 AATCCATGTCAAGTATCATATCAAAATCCAAGTCAAGTATCATATCAG
1 AATCCATGTCAAGTATCAGATCAGAATCCAAGTCAA-TATCAGATCAG
* *
2783138 AATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGATATCAGATCAG
1 AATCCATGTCAAGTATCAGATCAGAATCCAAGTCA-ATATCAGATCAG
* * *
2783186 AATCCATGTCAAGTATCAGATCAGAATTCAAATCGAAAATCAGAT
1 AATCCATGTCAAGTATCAGATCAGAATCCAAGTC-AATATCAGAT
2783231 AAAATATTCA
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
48 79 0.98
49 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (47 bp):
AATCCATGTCAAGTATCAGATCAGAATCCAAGTCAATATCAGATCAG
Found at i:2783228 original size:72 final size:72
Alignment explanation
Indices: 2783090--2783230 Score: 187
Period size: 72 Copynumber: 2.0 Consensus size: 72
2783080 ATCAAAACAT
* * * *
2783090 AATCCATGTCAAGTATCATATCAAAATCCAAGTCAAGTATCATATCAGAATCCAAGTCAAGTATC
1 AATCCATGTCAAGTATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAAGAATC
2783155 AGATCAG
66 AGATCAG
* * *
2783162 AATCCATGTC-AGATATCAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATCGAA-AA
1 AATCCATGTCAAG-TATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATC-AAGAA
2783225 TCAGAT
64 TCAGAT
2783231 AAAATATTCA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
71 2 0.03
72 56 0.93
73 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (72 bp):
AATCCATGTCAAGTATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAAGAATC
AGATCAG
Found at i:2785805 original size:18 final size:18
Alignment explanation
Indices: 2785768--2785806 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2785758 CAACGGTCAA
*
2785768 CGGGTCGGGTCAACATGT
1 CGGGTCGGGTCAACAGGT
*
2785786 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
2785804 CGG
1 CGG
2785807 ATAAACGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:2788130 original size:24 final size:24
Alignment explanation
Indices: 2788117--2788235 Score: 177
Period size: 24 Copynumber: 5.0 Consensus size: 24
2788107 AAACATAATT
*
2788117 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
*
2788141 CAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
2788165 CAAGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
2788189 CATGTC-AGATATCAGATCAGAATC
1 CATGTCAAG-TATCATATCAGAATC
*
2788213 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
2788236 TCAAATCGAA
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
23 2 0.02
24 84 0.95
25 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.26
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:2788251 original size:48 final size:48
Alignment explanation
Indices: 2788120--2788253 Score: 128
Period size: 48 Copynumber: 2.8 Consensus size: 48
2788110 CATAATTCAT
* * ** * *
2788120 GTCAAGTATCATATCAAAATCCAGGTCA-AGTATCATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAAATCAGA-AATCAGATCAGAATCCAA
* ** * *
2788168 GTCAAGTATCATATCAGAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAAATCAGAAATCAGATCAGAATCCAA
*
2788216 GTCAAGTATCAGATCAGAATTCAAATC-GAAAATCAGAT
1 GTCAAGTATCAGATCAGAATCCAAATCAG-AAATCAGAT
2788254 AAAATATTCA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 1 0.01
48 73 0.97
49 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAAATCAGAAATCAGATCAGAATCCAA
Found at i:2790794 original size:18 final size:18
Alignment explanation
Indices: 2790773--2790811 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2790763 CGCCGGTCAA
*
2790773 CGGGTCGGGTCAACAGGT
1 CGGGTAGGGTCAACAGGT
*
2790791 CGGGTAGGGTCAACGGGT
1 CGGGTAGGGTCAACAGGT
2790809 CGG
1 CGG
2790812 ATAAACGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.49, T:0.15
Consensus pattern (18 bp):
CGGGTAGGGTCAACAGGT
Found at i:2790818 original size:13 final size:13
Alignment explanation
Indices: 2790802--2790826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2790792 GGGTAGGGTC
2790802 AACGGGTCGGATA
1 AACGGGTCGGATA
2790815 AACGGGTCGGAT
1 AACGGGTCGGAT
2790827 TATGACCGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.40, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGATA
Found at i:2791865 original size:16 final size:16
Alignment explanation
Indices: 2791836--2791869 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2791826 GAAGGAGATA
2791836 AGGGACAAAGGAGGCT
1 AGGGACAAAGGAGGCT
2791852 AGGGACAAAGGAGGCT
1 AGGGACAAAGGAGGCT
2791868 AG
1 AG
2791870 AAATGGGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.44, T:0.06
Consensus pattern (16 bp):
AGGGACAAAGGAGGCT
Found at i:2795683 original size:11 final size:11
Alignment explanation
Indices: 2795667--2795693 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2795657 ATTATAGGTG
2795667 TATGGATAATA
1 TATGGATAATA
2795678 TATGGATAATA
1 TATGGATAATA
2795689 TATGG
1 TATGG
2795694 TCAGTAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (11 bp):
TATGGATAATA
Found at i:2796292 original size:37 final size:38
Alignment explanation
Indices: 2796236--2796403 Score: 184
Period size: 37 Copynumber: 4.5 Consensus size: 38
2796226 TTATCTAAGG
2796236 ATTTATATTCAATTAAAATAAAAATATATTA-TTATAA
1 ATTTATATTCAATTAAAATAAAAATATATTATTTATAA
* * * *
2796273 ATTTATATTTAATTGAAATAGAAATGTATTATTTATAA
1 ATTTATATTCAATTAAAATAAAAATATATTATTTATAA
** *
2796311 ATTTATATTTGA-TAAAAT-AAAATATATTATTTATGA
1 ATTTATATTCAATTAAAATAAAAATATATTATTTATAA
** *
2796347 ATTTATATTCAATTAAAATACGAGTATATTA-TTA-AGA
1 ATTTATATTCAATTAAAATAAAAATATATTATTTATA-A
* *
2796384 ATTTATATTCATTTGAAATA
1 ATTTATATTCAATTAAAATA
2796404 TAATATTGTA
Statistics
Matches: 110, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
36 25 0.23
37 60 0.55
38 25 0.23
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTATATTCAATTAAAATAAAAATATATTATTTATAA
Found at i:2797432 original size:19 final size:20
Alignment explanation
Indices: 2797399--2797436 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2797389 ACCATAATTT
2797399 ATTTTTAGTATATTTTAATA
1 ATTTTTAGTATATTTTAATA
*
2797419 ATTTTTATTA-ATTTTAAT
1 ATTTTTAGTATATTTTAAT
2797437 TTTTTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
ATTTTTAGTATATTTTAATA
Found at i:2799497 original size:37 final size:37
Alignment explanation
Indices: 2799432--2799595 Score: 156
Period size: 37 Copynumber: 4.4 Consensus size: 37
2799422 TTAATTAAGG
* * * *
2799432 ATTTATATTTAATTAAAATGTGAA-ATATTA-CTACAA
1 ATTTATATTCAATT-AAATATAAATATATTATTTACAA
* * *
2799468 ATTTATACTCGATTGAAATA-AGAATATATTATTTATAA
1 ATTTATATTCAATT-AAATATA-AATATATTATTTACAA
* **
2799506 ATTTATATTTAATTAAATATAAATATATTATTTATGA
1 ATTTATATTCAATTAAATATAAATATATTATTTACAA
*
2799543 ATTTATATTCAATTAAAATATAAATATACTA-TTACAA
1 ATTTATATTCAATT-AAATATAAATATATTATTTACAA
*
2799580 ATTTATATTCGATTAA
1 ATTTATATTCAATTAA
2799596 TTATTTATTT
Statistics
Matches: 106, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
36 19 0.18
37 56 0.53
38 31 0.29
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (37 bp):
ATTTATATTCAATTAAATATAAATATATTATTTACAA
Found at i:2799534 original size:74 final size:74
Alignment explanation
Indices: 2799432--2799588 Score: 176
Period size: 74 Copynumber: 2.1 Consensus size: 74
2799422 TTAATTAAGG
* * * *
2799432 ATTTATATTTAATTAAAATGTGAAATATTA-CTACAAATTTATACTCGATTGAAATA-AGAATAT
1 ATTTATATTTAATTAAAATATAAAATATTATCTACAAATTTATACTCAATTAAAATATA-AATAT
* *
2799495 ATTATTTATAA
65 ACTA-TTACAA
* ** *
2799506 ATTTATATTTAATT-AAATATAAATATATTATTTATGAATTTATATTCAATTAAAATATAAATAT
1 ATTTATATTTAATTAAAATATAAA-ATATTATCTACAAATTTATACTCAATTAAAATATAAATAT
2799570 ACTATTACAA
65 ACTATTACAA
2799580 ATTTATATT
1 ATTTATATT
2799589 CGATTAATTA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
73 7 0.10
74 34 0.49
75 28 0.40
76 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (74 bp):
ATTTATATTTAATTAAAATATAAAATATTATCTACAAATTTATACTCAATTAAAATATAAATATA
CTATTACAA
Found at i:2802080 original size:24 final size:25
Alignment explanation
Indices: 2802042--2802103 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
2802032 AAGCATTAAA
*
2802042 AATAATAATAATAAAAAAAGA-GAAT
1 AATAA-AATAATAAAAAAAGACAAAT
**
2802067 AATAAAATAATAAATCAAGACAAAT
1 AATAAAATAATAAAAAAAGACAAAT
2802092 AA-AAAATAATAA
1 AATAAAATAATAA
2802104 TAATAGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 23 0.70
25 10 0.30
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (25 bp):
AATAAAATAATAAAAAAAGACAAAT
Found at i:2802981 original size:37 final size:36
Alignment explanation
Indices: 2802872--2803140 Score: 268
Period size: 37 Copynumber: 7.5 Consensus size: 36
2802862 GTCTTGGTTT
*
2802872 ACTATATATTATATATTTTTCAAAAATG-ATTTAAA
1 ACTATATATTATATATTTTTCAAAAATGTTTTTAAA
* *
2802907 AATAT-TA-TATA-AGTTTTCAAAAAGTGTTTTTAAA
1 ACTATATATTATATATTTTTCAAAAA-TGTTTTTAAA
2802941 ACTATATATTATATAATTTTTCAAAAATGTTTTTAAA
1 ACTATATATTATAT-ATTTTTCAAAAATGTTTTTAAA
* *
2802978 ACTATATATTATATAAGTTTTTTGAAAAATGTTTTAAAA
1 ACTATATATTATAT-A--TTTTTCAAAAATGTTTTTAAA
* * *
2803017 ACTATATATTATATATATATTC-AAAATGATTTCAAA
1 ACTATATATTATATAT-TTTTCAAAAATGTTTTTAAA
* * * *
2803053 ACCATATATTATATATATTTTCAAAAGTATTTTAAAA
1 ACTATATATTATATAT-TTTTCAAAAATGTTTTTAAA
* * *
2803090 ACTATACATTATATATGTTTTCAAAAA---ATTCAAA
1 ACTATATATTATATAT-TTTTCAAAAATGTTTTTAAA
2803124 ACTATATA-TATATATTT
1 ACTATATATTATATATTT
2803141 CGAAATGTTT
Statistics
Matches: 200, Mismatches: 24, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
32 13 0.06
33 13 0.06
34 24 0.12
35 6 0.03
36 37 0.19
37 62 0.31
38 12 0.06
39 33 0.17
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
ACTATATATTATATATTTTTCAAAAATGTTTTTAAA
Found at i:2803091 original size:112 final size:109
Alignment explanation
Indices: 2802872--2803110 Score: 276
Period size: 112 Copynumber: 2.2 Consensus size: 109
2802862 GTCTTGGTTT
*
2802872 ACTATATATTATAT-A--TTTTTCAAAAATGATTTAAAAATATTATATAAGTTTTCAAAAAGTGT
1 ACTATATATTATATAAGTTTTTTCAAAAATGATTTAAAAATATTATATAAGTTTTCAAAAAGTGA
* * * *
2802934 TTTTAAAACTATATATTATATAATTTTTCAAAAATGTTTTTAAA
66 TTTCAAAACCATATATTATATAATTTTTCAAAAATATTTTAAAA
* *
2802978 ACTATATATTATATAAGTTTTTTGAAAAATGTTTTAAAAACTATATATTATATA-TATATTC-AA
1 ACTATATATTATATAAGTTTTTTCAAAAATGATTTAAAAA-TAT-TA-TATA-AGT-T-TTCAAA
*
2803041 AA-TGATTTCAAAACCATATATTATAT-ATATTTTCAAAAGTATTTTAAAA
60 AAGTGATTTCAAAACCATATATTATATAAT-TTTTCAAAAATATTTTAAAA
* *
2803090 ACTATACATTATATATGTTTT
1 ACTATATATTATATAAGTTTT
2803111 CAAAAAATTC
Statistics
Matches: 113, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
106 14 0.12
107 1 0.01
109 20 0.18
110 3 0.03
111 4 0.04
112 62 0.55
113 6 0.05
114 3 0.03
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (109 bp):
ACTATATATTATATAAGTTTTTTCAAAAATGATTTAAAAATATTATATAAGTTTTCAAAAAGTGA
TTTCAAAACCATATATTATATAATTTTTCAAAAATATTTTAAAA
Found at i:2803135 original size:75 final size:74
Alignment explanation
Indices: 2802908--2803136 Score: 213
Period size: 73 Copynumber: 3.1 Consensus size: 74
2802898 TGATTTAAAA
*
2802908 ATATTATATA-AGTTTTCAAAAAGTGTTTTTAAAACTATATATTATATAATTTTTCAAAAATGTT
1 ATATTATATATA-TTTTC-AAAAGTGTTTTAAAAACTATATATTATAT-ATTTTTCAAAAA---T
*
2802972 TTTAAAACTATATAT
60 TTCAAAACTATATAT
* * * *
2802987 -TA-TATA-AGTTTTTTGAAAAATGTTTTAAAAACTATATATTATATATATATTCAAAATGATTT
1 ATATTATATA-TATTTTCAAAAGTGTTTTAAAAACTATATATTATATAT-TTTTCAAAA--ATTT
*
2803049 CAAAAC----CAT
62 CAAAACTATATAT
* * *
2803058 ATATTATATATATTTTCAAAAGTATTTTAAAAACTATACATTATATATGTTTTCAAAAAATTCAA
1 ATATTATATATATTTTCAAAAGTGTTTTAAAAACTATATATTATATAT-TTTTCAAAAATTTCAA
2803123 AACTATATAT
65 AACTATATAT
2803133 ATAT
1 ATAT
2803137 ATTTCGAAAT
Statistics
Matches: 122, Mismatches: 16, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
71 11 0.09
72 2 0.02
73 45 0.37
74 1 0.01
75 16 0.13
76 36 0.30
77 8 0.07
78 3 0.02
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (74 bp):
ATATTATATATATTTTCAAAAGTGTTTTAAAAACTATATATTATATATTTTTCAAAAATTTCAAA
ACTATATAT
Found at i:2803228 original size:30 final size:31
Alignment explanation
Indices: 2803167--2803233 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
2803157 CTAGATGGTA
* * * *
2803167 TATATATTTTAGAAAACCGTTTTCTAAAAAT
1 TATATTTTTTAAAAAAACATTTTCTAAAAAT
2803198 TATATTTTTTAAAAAAACATTTTC-AAAAAT
1 TATATTTTTTAAAAAAACATTTTCTAAAAAT
2803228 TATATT
1 TATATT
2803234 ATATTACTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (31 bp):
TATATTTTTTAAAAAAACATTTTCTAAAAAT
Found at i:2803251 original size:2 final size:2
Alignment explanation
Indices: 2803244--2803274 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2803234 ATATTACTAA
2803244 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 A
2803275 AAGCAAATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2803996 original size:80 final size:79
Alignment explanation
Indices: 2803837--2804484 Score: 702
Period size: 79 Copynumber: 8.0 Consensus size: 79
2803827 AAATTTAATA
* * * * * *
2803837 TGCCTTTGAGCTGAATGTAATCGAACTTGAAGGTCTTTTGTTAGCAGACATCCCTTCTCGTCTTG
1 TGCC-TTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTG---GCAGATAACCCTTCTAGCCTTG
2803902 AGCTATGCTGCAAATGATG
61 AGCTATGCTGCAAATGATG
* * * * * * ** *
2803921 CGCCTTTGAGCTGTGTGTAATCAAACTCGAAGGACTTTGGCAGATAGCCCTTATTTCCTTGAACT
1 TGCC-TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGCT
*
2803986 AAGCTGCAAATGATG
65 ATGCTGCAAATGATG
* * * * *
2804001 TGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTGACAGATAACCCTTCTTGCCTTAAGCT
1 TGCC-TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGCT
* **
2804066 ATGTTATAAATGATG
65 ATGCTGCAAATGATG
* * * * *
2804081 TGCCTTGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGTATATAACCCTTCTAGCATTGAGGTA
1 TGCCTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGCTA
*
2804146 TACTGCAAATGATG
66 TGCTGCAAATGATG
* * *
2804160 TGCCTTAAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTTA
1 TGCCTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGCTA
* *
2804225 TGTTGCAAATGATA
66 TGCTGCAAATGATG
* **
2804239 TGCCTTGAGCTGAGTGTAATCGAACTCGAAGGTTTTTTTTTACAGATAACCCTTCTAGCCTTGAG
1 TGCCTTGAGCTGAGTGTAATCGAACTCGAAGG---TCTTTGGCAGATAACCCTTCTAGCCTTGAG
* * *
2804304 TTATGTTGTAAATGATG
63 CTATGCTGCAAATGATG
* * * *
2804321 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTATAACCTTAAGTT
1 TGCC-TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGCT
*
2804386 ATGCTGCAGATGATG
65 ATGCTGCAAATGATG
* * * *
2804401 TGCCTTGAGCTGAGTGTAATCGAACTTGAAGGTATTTGTTGATAGATAACCCTTTTAGCCTTGAG
1 TGCCTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTAGCCTTGAG
* *
2804466 TTATGCTGTAAATGATG
63 CTATGCTGCAAATGATG
2804483 TG
1 TG
2804485 TAACATCCTC
Statistics
Matches: 481, Mismatches: 76, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
79 192 0.40
80 145 0.30
81 1 0.00
82 82 0.17
83 32 0.07
84 29 0.06
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (79 bp):
TGCCTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGCTA
TGCTGCAAATGATG
Found at i:2804388 original size:162 final size:161
Alignment explanation
Indices: 2803837--2804484 Score: 703
Period size: 162 Copynumber: 4.0 Consensus size: 161
2803827 AAATTTAATA
* * * * * * *
2803837 TGCCTTTGAGCTGAATGTAATCGAACTTGAAGGTCTTTTGTTAGCAGACATCCCTTCTCGTCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTG---GCAGATAACCCTTCTAGCCTTA
* * * * * ** ***
2803902 AGCTATGCTGCAAATGATGCGCCTTTGAGCTGTGTGTAATCAAACTCGAAGG--ACTTTGGCAGA
62 AGTTATGTTGCAAATGATGTGCC-TTGAGCTGAGTGTAATCGAACTCGAAGGTTTTTTTTTAAGA
* * ** ** * *
2803965 TAGCCCTTATTTCCTTGAACTAAGCTGCAAATGATG
126 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
* * * * *
2804001 TGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTGACAGATAACCCTTCTTGCCTTAAGCT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTAAGTT
** * * ** *
2804066 ATGTTATAAATGATGTGCCTTGAGCTAAGTGTAATCGAACTCGAAGG-TCTTTGGT-ATATAACC
66 ATGTTGCAAATGATGTGCCTTGAGCTGAGTGTAATCGAACTCGAAGGTTTTTTTTTAAGATAACC
* * * *
2804129 CTTCTAGCATTGAGGTATACTGCAAATGATG
131 CTTCTAGCCTTGAGTTATGCTGTAAATGATG
* * *
2804160 TGCC-TTAAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGCAGATAACCCTTCTAGCCTTGAGTT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTAAGTT
*
2804224 ATGTTGCAAATGATATGCCTTGAGCTGAGTGTAATCGAACTCGAAGGTTTTTTTTTACAGATAAC
66 ATGTTGCAAATGATGTGCCTTGAGCTGAGTGTAATCGAACTCGAAGGTTTTTTTTTA-AGATAAC
*
2804289 CCTTCTAGCCTTGAGTTATGTTGTAAATGATG
130 CCTTCTAGCCTTGAGTTATGCTGTAAATGATG
* *
2804321 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTATAACCTTAAGTT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTAAGTT
* * * * * *
2804386 ATGCTGCAGATGATGTGCCTTGAGCTGAGTGTAATCGAACTTGAAGGTATTTGTTGATAGATAAC
66 ATGTTGCAAATGATGTGCCTTGAGCTGAGTGTAATCGAACTCGAAGGTTTTTTTTTA-AGATAAC
*
2804451 CCTTTTAGCCTTGAGTTATGCTGTAAATGATG
130 CCTTCTAGCCTTGAGTTATGCTGTAAATGATG
2804483 TG
1 TG
2804485 TAACATCCTC
Statistics
Matches: 414, Mismatches: 65, Indels: 12
0.84 0.13 0.02
Matches are distributed among these distances:
158 95 0.23
159 63 0.15
160 38 0.09
161 37 0.09
162 144 0.35
163 4 0.01
164 33 0.08
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (161 bp):
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTAGCCTTAAGTT
ATGTTGCAAATGATGTGCCTTGAGCTGAGTGTAATCGAACTCGAAGGTTTTTTTTTAAGATAACC
CTTCTAGCCTTGAGTTATGCTGTAAATGATG
Found at i:2805238 original size:21 final size:21
Alignment explanation
Indices: 2805196--2805238 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2805186 TTTTCGGGCT
* * *
2805196 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
2805217 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
2805238 A
1 A
2805239 CGAATATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:2805298 original size:66 final size:66
Alignment explanation
Indices: 2805196--2805366 Score: 245
Period size: 66 Copynumber: 2.6 Consensus size: 66
2805186 TTTTCGGGCT
* * *
2805196 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCCTCAACGAATATGATTTCCAGAATGC
1 AGGGGAATCGATACCCA--CAGGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGC
2805260 TAG
64 TAG
*
2805263 AGGGGAATCGATACCCCCAGGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTA
1 AGGGGAATCGATACCCACAGGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTA
2805328 G
66 G
* ** *
2805329 TGGGGAATCGATACCCAGGGGGGGGAACCGATTCCCCC
1 AGGGGAATCGATACCCACAGGGGGGAACCGATACCCCC
2805367 ATGAAAAAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
65 2 0.02
66 77 0.82
67 15 0.16
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (66 bp):
AGGGGAATCGATACCCACAGGGGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTA
G
Found at i:2806044 original size:23 final size:23
Alignment explanation
Indices: 2805978--2806036 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
2805968 ATCATTATAT
*
2805978 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
2806000 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
2806023 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
2806037 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:2812104 original size:21 final size:21
Alignment explanation
Indices: 2812062--2812104 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2812052 TTTTCGGGCT
* * *
2812062 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
2812083 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
2812104 A
1 A
2812105 CGAATATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:2812158 original size:65 final size:65
Alignment explanation
Indices: 2812084--2812231 Score: 244
Period size: 65 Copynumber: 2.3 Consensus size: 65
2812074 ACCCATTCAA
*
2812084 GGGGAACCGATACCCCCTCAACGAATATGATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA-
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATA-CCCCAG
2812148 G
65 G
*
2812149 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGTGGGGAATCGATACCCCAGG
1 GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCA-G
2812214 G
65 G
*
2812215 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
2812232 ATGAAAAAAA
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
64 5 0.06
65 56 0.72
66 17 0.22
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.16
Consensus pattern (65 bp):
GGGGAACCGATACCCCCTCAACGAATATGAATTCCAGAATGCTAGAGGGGAATCGATACCCCAGG
Found at i:2812870 original size:22 final size:23
Alignment explanation
Indices: 2812838--2812896 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 23
2812828 ATCATTATAT
* *
2812838 GGCACTACGGTGTAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
2812860 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
2812883 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
2812897 TTTATACGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 19 0.56
23 15 0.44
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:2812904 original size:23 final size:23
Alignment explanation
Indices: 2812838--2812904 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
2812828 ATCATTATAT
* * *
2812838 GGCACTACGGTGTAATTCTAC-G
1 GGCACTTCGGTGCAATTATACGG
*
2812860 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTATACGG
*
2812883 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCAATTATACG
2812905 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 19 0.47
23 21 0.52
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGG
Found at i:2813632 original size:83 final size:82
Alignment explanation
Indices: 2813459--2813773 Score: 379
Period size: 83 Copynumber: 3.9 Consensus size: 82
2813449 TGGGGGTGAC
* * *
2813459 ATGATGTGTCTTTGAGCTAAGTGTAATCGAACTCGAAGGTCTTTG--GA-AGATAGCCCTTCT-G
1 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAG
* * * *
2813520 CCTTAAGCTATGTGCAA
66 CCTTGAGTTATATGAAA
* * * *
2813537 ATGATGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGTATTTGTTGACAAATAACCATTCTAG
1 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAG
* *
2813602 CCTTGGGTTATACTGTAA
66 CCTTGAGTTATA-TGAAA
* *
2813620 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTGTGTTGGCAGATAACCCTT-TA
1 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTT-TGTTGACAGATAACCCTTCTA
2813684 GCCTTGAGTTATGATGAAA
65 GCCTTGAGTTAT-ATGAAA
* * * * *
2813703 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAATGTCTTTTGGTGGCAGATAACCCTTATT
1 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTA
2813768 GCCTTG
65 GCCTTG
2813774 GGCTATGTTG
Statistics
Matches: 204, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
78 41 0.20
80 2 0.01
81 10 0.05
82 9 0.04
83 117 0.57
84 25 0.12
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (82 bp):
ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAG
CCTTGAGTTATATGAAA
Found at i:2817792 original size:59 final size:59
Alignment explanation
Indices: 2817672--2817799 Score: 140
Period size: 59 Copynumber: 2.2 Consensus size: 59
2817662 AGATATATAT
* *
2817672 ATAATAAATAAGCATTAAAATAATAATAATAATAATAAACAAAACAATAGAATAATAAA
1 ATAATAAATAAGCATTAAAATAAAAATAATAATAATAAACAAAACAAGAGAATAATAAA
*
2817731 ATAATAAATCAAG-ATTAATAA-AAAAATAATAATAGA-AAA-AAAATCAGAGAGAA-AATTAA
1 ATAATAAAT-AAGCATTAA-AATAAAAATAATAATA-ATAAACAAAA-CA-AGAGAATAATAAA
2817790 ATAAGTAAAT
1 ATAA-TAAAT
2817800 TGAAAAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
58 4 0.07
59 40 0.67
60 16 0.27
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.23
Consensus pattern (59 bp):
ATAATAAATAAGCATTAAAATAAAAATAATAATAATAAACAAAACAAGAGAATAATAAA
Found at i:2818876 original size:3 final size:3
Alignment explanation
Indices: 2818868--2818902 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2818858 AAGAAATTAG
* *
2818868 TAA TAA TAA AAA AAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2818903 TAACATAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:2818969 original size:33 final size:33
Alignment explanation
Indices: 2818924--2819253 Score: 187
Period size: 33 Copynumber: 9.5 Consensus size: 33
2818914 ATAATATATA
*
2818924 TATATATATATATATTTCAAAAATATTTTTAAAC
1 TATATAT-TATATATTTCAAAAATATTTTAAAAC
* * * *
2818958 TATATATTATAT-TTTTAATATTTTTTTCAAAAC
1 TATATATTATATATTTCAAAAATATTTT-AAAAC
*
2818991 TATATATTATATAATTTTCAAAAATGA-TTTAAAAA
1 TATATATTATAT-A-TTTCAAAAAT-ATTTTAAAAC
*
2819026 TATATA-TA-AGT-TTTCAAAAAATGTTTTTAAAAC
1 TATATATTATA-TATTTC-AAAAAT-ATTTTAAAAC
*
2819059 TATATA-TATAATTTTTCAAAAATATTTTTAAAAC
1 TATATATTAT-ATATTTCAAAAATA-TTTTAAAAC
*
2819093 TATATATTATAGAAGTTTTTTTTCAAAAATATTTTAAAAAC
1 TATATATTAT---A----TATTTCAAAAATATTTT-AAAAC
*
2819134 TATATTATATATATATTTTC-AAAATGATTTCAAAAC
1 TATA-TAT-TATATA-TTTCAAAAAT-ATTTTAAAAC
* * * *
2819170 TTTATGTATATATATTTTTAAAAGTATTTTCAAAAAC
1 TATATAT-TATATA-TTTCAAAAATATTTT--AAAAC
*
2819207 TATATATTATATGTTTTC-AAAAT-TTTTCAAAA-
1 TATATATTATAT-ATTTCAAAAATATTTT-AAAAC
*
2819239 T-TATAATATATATTT
1 TATATATTATATATTT
2819254 TCGAAATGTT
Statistics
Matches: 240, Mismatches: 28, Indels: 60
0.73 0.09 0.18
Matches are distributed among these distances:
30 3 0.01
31 13 0.05
32 19 0.08
33 41 0.17
34 36 0.15
35 39 0.16
36 36 0.15
37 20 0.08
40 5 0.02
41 22 0.09
42 3 0.01
43 3 0.01
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (33 bp):
TATATATTATATATTTCAAAAATATTTTAAAAC
Found at i:2819011 original size:68 final size:69
Alignment explanation
Indices: 2818920--2819104 Score: 204
Period size: 68 Copynumber: 2.7 Consensus size: 69
2818910 AACTATAATA
* * *
2818920 TATATATATATATATATATTTCAAAAATATTTTTAAACTATATATTATA-TTTT-TAATATTTTT
1 TATATAT-TATATA-AT-TTTCAAAAATATTTTTAAACTATATATTATAGTTTTAAAAAATGTTT
2818983 TTCAAAAC
63 TT-AAAAC
* *
2818991 TATATATTATATAATTTTCAAAAATGA-TTTAAAAATATATA-TA-AGTTTTCAAAAAATGTTTT
1 TATATATTATATAATTTTCAAAAAT-ATTTTTAAACTATATATTATAGTTTT-AAAAAATGTTTT
2819053 TAAAAC
64 TAAAAC
*
2819059 TATATA-TATA-ATTTTTCAAAAATATTTTTAAAACTATATATTATAG
1 TATATATTATATAATTTTCAAAAATATTTTT-AAACTATATATTATAG
2819105 AAGTTTTTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
65 1 0.01
66 16 0.16
67 19 0.19
68 35 0.36
69 14 0.14
70 6 0.06
71 7 0.07
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (69 bp):
TATATATTATATAATTTTCAAAAATATTTTTAAACTATATATTATAGTTTTAAAAAATGTTTTTA
AAAC
Found at i:2819030 original size:35 final size:35
Alignment explanation
Indices: 2818920--2819283 Score: 221
Period size: 35 Copynumber: 10.3 Consensus size: 35
2818910 AACTATAATA
*
2818920 TATATATATATATATATATTTCAAAAATATTTTTAAAC
1 TATATAT-TATATA-AT-TTTCAAAAATATTTTAAAAC
* * *
2818958 TATATATTATAT--TTTT-AATATTTTTTTCAAAAC
1 TATATATTATATAATTTTCAAAAATATTTT-AAAAC
2818991 TATATATTATATAATTTTCAAAAATGA-TTTAAAA-
1 TATATATTATATAATTTTCAAAAAT-ATTTTAAAAC
* *
2819025 -ATATA-TATA-AGTTTTCAAAAAATGTTTTTAAAAC
1 TATATATTATATAATTTTC-AAAAAT-ATTTTAAAAC
*
2819059 TATATA-TATA-ATTTTTCAAAAATATTTTTAAAAC
1 TATATATTATATAATTTTCAAAAATA-TTTTAAAAC
*
2819093 TATATATTATAGAAGTTTTTTTTCAAAAATATTTTAAAAAC
1 TATATATTATATAA-----TTTTCAAAAATATTTT-AAAAC
*
2819134 TATAT-TATATATATATTTTC-AAAATGATTTCAAAAC
1 TATATAT-TATATA-ATTTTCAAAAAT-ATTTTAAAAC
* *
2819170 T-T-TATGTATATATATTTTTAAAAGTATTTTCAAAAAC
1 TATATAT-TATATA-ATTTTCAAAAATATTTT--AAAAC
*
2819207 TATATATTATAT-GTTTTC-AAAAT-TTTTCAAAA-
1 TATATATTATATAATTTTCAAAAATATTTT-AAAAC
* * * *
2819239 T-TATAATATAT-ATTTTC-GAAATGTTTTCGAAAC
1 TATATATTATATAATTTTCAAAAATATTTT-AAAAC
*
2819272 TATATAATATAT
1 TATATATTATAT
2819284 TTTAGAAAAC
Statistics
Matches: 270, Mismatches: 26, Indels: 64
0.75 0.07 0.18
Matches are distributed among these distances:
31 24 0.09
32 28 0.10
33 36 0.13
34 37 0.14
35 49 0.18
36 27 0.10
37 20 0.07
38 13 0.05
39 3 0.01
40 5 0.02
41 27 0.10
42 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (35 bp):
TATATATTATATAATTTTCAAAAATATTTTAAAAC
Found at i:2819298 original size:34 final size:33
Alignment explanation
Indices: 2819118--2819305 Score: 114
Period size: 32 Copynumber: 5.5 Consensus size: 33
2819108 TTTTTTTTCA
* * **
2819118 AAAATATTTTAAAAACTATATTATATATATATTTTC
1 AAAATGTTTTCAAAACTATA-TA-ATATAT-TTTAG
* *
2819154 AAAATGATTTCAAAACTTTATGTATATATATTTTTA-
1 AAAATGTTTTCAAAAC--TATATA-ATATA-TTTTAG
* * * **
2819190 AAAGTATTTTCAAAAACTATATATTATATGTTTTC
1 AAAATGTTTTC-AAAACTATATAATATAT-TTTAG
* *
2819225 AAAAT-TTTTCAAAATTATA-ATATATATTTTCG
1 AAAATGTTTTCAAAACTATATA-ATATATTTTAG
*
2819257 -AAATGTTTTCGAAACTATATAATATATTTTAG
1 AAAATGTTTTCAAAACTATATAATATATTTTAG
2819289 AAAACTGTTTTCTAAAA
1 AAAA-TGTTTTC-AAAA
2819306 ATTATATTTT
Statistics
Matches: 120, Mismatches: 20, Indels: 25
0.73 0.12 0.15
Matches are distributed among these distances:
31 4 0.03
32 26 0.22
33 18 0.15
34 19 0.16
35 12 0.10
36 21 0.17
37 16 0.13
38 4 0.03
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (33 bp):
AAAATGTTTTCAAAACTATATAATATATTTTAG
Found at i:2819320 original size:16 final size:16
Alignment explanation
Indices: 2819296--2819337 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 16
2819286 TAGAAAACTG
*
2819296 TTTTCTAAAAATTATA
1 TTTTTTAAAAATTATA
2819312 TTTTTTAAAAA--ATA
1 TTTTTTAAAAATTATA
2819326 -TTTTTAAAAATT
1 TTTTTTAAAAATT
2819338 TTTTATACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 10 0.43
14 3 0.13
16 10 0.43
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTTTAAAAATTATA
Found at i:2819333 original size:29 final size:31
Alignment explanation
Indices: 2819278--2819337 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
2819268 AAACTATATA
* *
2819278 ATATATTTTAGAAAACTGTTTTCTAAAAATT
1 ATATATTTTAGAAAAATATTTTCTAAAAATT
*
2819309 ATATTTTTTA-AAAAATATTTT-TAAAAATT
1 ATATATTTTAGAAAAATATTTTCTAAAAATT
2819338 TTTTATACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.31
30 9 0.35
31 9 0.35
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (31 bp):
ATATATTTTAGAAAAATATTTTCTAAAAATT
Done.