Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007992.1 Hibiscus syriacus cultivar Beakdansim tig00110442_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: 1314873
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:832381 original size:36 final size:36
Alignment explanation
Indices: 832326--832410 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 36
832316 TTAATGTTTT
* * * * * *
832326 ATCTGATTTCTGATTTGGATTCTGTTCTGATTTCTG
1 ATCTGAATTCTTATATGGATTCTGTTATGATATATG
*
832362 ATCTGAATTCTTATATGGATTGTGTTATGATATATG
1 ATCTGAATTCTTATATGGATTCTGTTATGATATATG
*
832398 TTCTGAATT-TTAT
1 ATCTGAATTCTTAT
832411 TTTGATTTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
35 4 0.10
36 37 0.90
ACGTcount: A:0.21, C:0.09, G:0.18, T:0.52
Consensus pattern (36 bp):
ATCTGAATTCTTATATGGATTCTGTTATGATATATG
Found at i:836868 original size:24 final size:24
Alignment explanation
Indices: 836808--836916 Score: 105
Period size: 24 Copynumber: 4.5 Consensus size: 24
836798 TAATGTTTTA
*
836808 TCTGATTTCCGAT-TTAAATTCTGT
1 TCTGATTTCTGATCTT-AATTCTGT
*
836832 TATGATTTCTGATCTTAATTCTGT
1 TCTGATTTCTGATCTTAATTCTGT
* *
836856 TCTGATTTTTGATC-TAGATTTTGT
1 TCTGATTTCTGATCTTA-ATTCTGT
* * * *
836880 TCTGATATATGTTCTGAATTCTGT
1 TCTGATTTCTGATCTTAATTCTGT
*
836904 TTTGATTTCTGAT
1 TCTGATTTCTGAT
836917 ATCTCCGTTT
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.93
25 3 0.04
ACGTcount: A:0.19, C:0.12, G:0.15, T:0.54
Consensus pattern (24 bp):
TCTGATTTCTGATCTTAATTCTGT
Found at i:836904 original size:12 final size:12
Alignment explanation
Indices: 836824--836914 Score: 51
Period size: 12 Copynumber: 7.6 Consensus size: 12
836814 TTCCGATTTA
*
836824 AATTCTGTTATG
1 AATTCTGTTCTG
* * *
836836 ATTTCTGATCTT
1 AATTCTGTTCTG
836848 AATTCTGTTCTG
1 AATTCTGTTCTG
* * *
836860 ATTTTTGATCT-
1 AATTCTGTTCTG
*
836871 AGATTTTGTTCTG
1 A-ATTCTGTTCTG
*
836884 -ATATATGTTCTG
1 AAT-TCTGTTCTG
*
836896 AATTCTGTTTTG
1 AATTCTGTTCTG
*
836908 ATTTCTG
1 AATTCTG
836915 ATATCTCCGT
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
11 3 0.05
12 54 0.92
13 2 0.03
ACGTcount: A:0.19, C:0.11, G:0.15, T:0.55
Consensus pattern (12 bp):
AATTCTGTTCTG
Found at i:839629 original size:21 final size:21
Alignment explanation
Indices: 839603--839650 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
839593 TTGATATAGT
839603 CTTGAGTAAAGTGCTCTAGAA
1 CTTGAGTAAAGTGCTCTAGAA
*
839624 CTTGAGTAAAGTTCTCTAGAA
1 CTTGAGTAAAGTGCTCTAGAA
839645 CTTGAG
1 CTTGAG
839651 ACAAGAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (21 bp):
CTTGAGTAAAGTGCTCTAGAA
Found at i:849214 original size:23 final size:23
Alignment explanation
Indices: 849188--849233 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
849178 AATTTTGGCT
849188 TTTTTGCTTCTTCTTTTTTTGAA
1 TTTTTGCTTCTTCTTTTTTTGAA
** * *
849211 TTTTTTTTTGTTTTTTTTTTGAA
1 TTTTTGCTTCTTCTTTTTTTGAA
849234 AAAAATAGCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.09, C:0.07, G:0.09, T:0.76
Consensus pattern (23 bp):
TTTTTGCTTCTTCTTTTTTTGAA
Found at i:849217 original size:11 final size:12
Alignment explanation
Indices: 849201--849233 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
849191 TTGCTTCTTC
849201 TTTTTTTGAATT
1 TTTTTTTGAATT
*
849213 TTTTTTTG-TTT
1 TTTTTTTGAATT
849224 TTTTTTTGAA
1 TTTTTTTGAA
849234 AAAAATAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:855532 original size:40 final size:41
Alignment explanation
Indices: 855449--855932 Score: 340
Period size: 41 Copynumber: 11.8 Consensus size: 41
855439 TAGCGGCATT
* *
855449 TTTAGTGGCGTTTTT-TGAACAAATGCCG-TAAATACTCATAC
1 TTTAGTGGCGTTTTTAT--ATAAACGCCGCTAAATACTCATAC
* * *
855490 TTTAGTGGCATTTTTATATAAACGCTGCTAAATACT-AAAC
1 TTTAGTGGCGTTTTTATATAAACGCCGCTAAATACTCATAC
* * *
855530 TTTAGTGGCGTTTTTGTACAAACGCCGCTAAA-ACTCGTAC
1 TTTAGTGGCGTTTTTATATAAACGCCGCTAAATACTCATAC
* * * * * *
855570 GTTAGTGGCATTTTTTATATAAATGCTGCTAAATA-TTATAT
1 TTTAGTGGC-GTTTTTATATAAACGCCGCTAAATACTCATAC
* * **
855611 TTTAGTGGCGTTTTAATCACAAACGCCGCTAAATACTGGTAC
1 TTTAGTGGCGTTTTTAT-ATAAACGCCGCTAAATACTCATAC
* * *
855653 TTTAGTGGCGTTTCTATATAAACGCCGCTAAATAAT-GTA-
1 TTTAGTGGCGTTTTTATATAAACGCCGCTAAATACTCATAC
* ** * * * * **
855692 TTGTAGTGGCATTAGTATAAAAATGCCGCCAAAGACTTGTAC
1 TT-TAGTGGCGTTTTTATATAAACGCCGCTAAATACTCATAC
* * * * **
855734 TTTAGTGGCGTTTTAAGCACAAACGCC-CTAAAAACTGTTAC
1 TTTAGTGGCGTTTTTA-TATAAACGCCGCTAAATACTCATAC
* * * **
855775 TTTAATGGCGTTTTTATATAAACACCACTAAATA-TTGTAC
1 TTTAGTGGCGTTTTTATATAAACGCCGCTAAATACTCATAC
* * * *
855815 TTTAGTGGCGTTTTTGCT-TAAAACGCCACCAAATACTGATAC
1 TTTAGTGGCGTTTTT-ATAT-AAACGCCGCTAAATACTCATAC
* * * * **
855857 TTTAGTGGCGTTTTAACCACAAACGCTGCTAAATACTTGTAC
1 TTTAGTGGCGTTTTTA-TATAAACGCCGCTAAATACTCATAC
* *
855899 TTTAGTGGCGTATTTATATAAACGCCACTAAATA
1 TTTAGTGGCGTTTTTATATAAACGCCGCTAAATA
855933 AATAAAGCCA
Statistics
Matches: 345, Mismatches: 81, Indels: 34
0.75 0.18 0.07
Matches are distributed among these distances:
39 5 0.01
40 109 0.32
41 153 0.44
42 78 0.23
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATATAAACGCCGCTAAATACTCATAC
Found at i:855590 original size:81 final size:81
Alignment explanation
Indices: 855449--855932 Score: 341
Period size: 81 Copynumber: 5.9 Consensus size: 81
855439 TAGCGGCATT
* * *
855449 TTTAGTGGCGTTTTTTGAACAAATGCCG-TAAATACTCATACTTTAGTGGCATTTTTATATAAAC
1 TTTAGTGGCG-TTTTTGTACAAACGCCGCTAAATACTCGTACTTTAGTGGCATTTTTATATAAAC
855513 GCTGCTAAATACTAAAC
65 GCTGCTAAATACTAAAC
* *
855530 TTTAGTGGCGTTTTTGTACAAACGCCGCTAAA-ACTCGTACGTTAGTGGCATTTTTTATATAAAT
1 TTTAGTGGCGTTTTTGTACAAACGCCGCTAAATACTCGTACTTTAGTGGCA-TTTTTATATAAAC
* * *
855594 GCTGCTAAATATTATAT
65 GCTGCTAAATACTAAAC
** * * *
855611 TTTAGTGGCGTTTTAATCACAAACGCCGCTAAATACTGGTACTTTAGTGGCGTTTCTATATAAAC
1 TTTAGTGGCGTTTTTGT-ACAAACGCCGCTAAATACTCGTACTTTAGTGGCATTTTTATATAAAC
* * **
855676 GCCGCTAAATAATGTA-
65 GCTGCTAAATACTAAAC
* ** * * * * * * * * * *
855692 TTGTAGTGGCATTAGTATAAAAATGCCGCCAAAGACTTGTACTTTAGTGGCGTTTTAAGCACAAA
1 TT-TAGTGGCGTTTTTGTACAAACGCCGCTAAATACTCGTACTTTAGTGGCATTTTTA-TATAAA
* * **
855757 CGC-CCTAAAAACTGTTAC
64 CGCTGCTAAATACT-AAAC
* * * * * * * *
855775 TTTAATGGCGTTTTTATATAAACACCACTAAATA-TTGTACTTTAGTGGCGTTTTTGCT-TAAAA
1 TTTAGTGGCGTTTTTGTACAAACGCCGCTAAATACTCGTACTTTAGTGGCATTTTT-ATAT-AAA
** * *
855838 CGCCACCAAATACTGATAC
64 CGCTGCTAAATACT-AAAC
*** * * * *
855857 TTTAGTGGCGTTTTAACCACAAACGCTGCTAAATACTTGTACTTTAGTGGCGTATTTATATAAAC
1 TTTAGTGGCGTTTT-TGTACAAACGCCGCTAAATACTCGTACTTTAGTGGCATTTTTATATAAAC
**
855922 GCCACTAAATA
65 GCTGCTAAATA
855933 AATAAAGCCA
Statistics
Matches: 325, Mismatches: 64, Indels: 26
0.78 0.15 0.06
Matches are distributed among these distances:
80 31 0.10
81 123 0.38
82 105 0.32
83 45 0.14
84 21 0.06
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (81 bp):
TTTAGTGGCGTTTTTGTACAAACGCCGCTAAATACTCGTACTTTAGTGGCATTTTTATATAAACG
CTGCTAAATACTAAAC
Found at i:855699 original size:123 final size:123
Alignment explanation
Indices: 855451--855933 Score: 475
Period size: 123 Copynumber: 3.9 Consensus size: 123
855441 GCGGCATTTT
* * * * * *
855451 TAGTGGCGTTTTTTGA-ACAAATGCCG-TAAATACTCATACTTTAGTGGCATTTTTAT-ATAAAC
1 TAGTGGCATTTTTT-ATA-AAATGCCGCCAAATACTTATACTTTAGTGGCGTTTTAATCACAAAC
* ** * * * * *
855513 GCTGCTAAATACT-AAACTTTAGTGGCGTTTTTGTACAAACGCCGCTAAA-ACTCGTA-CG
64 GCCGCTAAATACTGGTACTTTAGTGGCGTTTTTATATAAACGCCACTAAATAAT-GTATTG
* * *
855571 TTAGTGGCATTTTTTATATAAATGCTGCTAAATA-TTATATTTTAGTGGCGTTTTAATCACAAAC
1 -TAGTGGCATTTTTTATA-AAATGCCGCCAAATACTTATACTTTAGTGGCGTTTTAATCACAAAC
* *
855635 GCCGCTAAATACTGGTACTTTAGTGGCGTTTCTATATAAACGCCGCTAAATAATGTATTG
64 GCCGCTAAATACTGGTACTTTAGTGGCGTTTTTATATAAACGCCACTAAATAATGTATTG
** * * *
855695 TAGTGGCA-TTAGTATAAAAATGCCGCCAAAGACTTGTACTTTAGTGGCGTTTTAAGCACAAACG
1 TAGTGGCATTTTTTAT-AAAATGCCGCCAAATACTTATACTTTAGTGGCGTTTTAATCACAAACG
* * * * *
855759 CC-CTAAAAACTGTTACTTTAATGGCGTTTTTATATAAACACCACTAAATATTGTACTT-
65 CCGCTAAATACTGGTACTTTAGTGGCGTTTTTATATAAACGCCACTAAATAATGTA-TTG
* * * * *
855817 TAGTGGCGTTTTTGCT-TAAAACGCCACCAAATACTGATACTTTAGTGGCGTTTTAACCACAAAC
1 TAGTGGCATTTTT--TATAAAATGCCGCCAAATACTTATACTTTAGTGGCGTTTTAATCACAAAC
* * *
855881 GCTGCTAAATACTTGTACTTTAGTGGCGTATTTATATAAACGCCACTAAATAA
64 GCCGCTAAATACTGGTACTTTAGTGGCGTTTTTATATAAACGCCACTAAATAA
855934 ATAAAGCCAA
Statistics
Matches: 301, Mismatches: 48, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
120 1 0.00
121 40 0.13
122 93 0.31
123 120 0.40
124 46 0.15
125 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (123 bp):
TAGTGGCATTTTTTATAAAATGCCGCCAAATACTTATACTTTAGTGGCGTTTTAATCACAAACGC
CGCTAAATACTGGTACTTTAGTGGCGTTTTTATATAAACGCCACTAAATAATGTATTG
Found at i:858582 original size:12 final size:12
Alignment explanation
Indices: 858565--858589 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
858555 AAATAATTAG
858565 TTAGTTAGTTAA
1 TTAGTTAGTTAA
858577 TTAGTTAGTTAA
1 TTAGTTAGTTAA
858589 T
1 T
858590 CCACCTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTAGTTAGTTAA
Found at i:860103 original size:42 final size:42
Alignment explanation
Indices: 860056--860316 Score: 288
Period size: 43 Copynumber: 6.1 Consensus size: 42
860046 AAGGTAATTA
* *
860056 GCGGCGTTTGTTCCAAAAACGCCGCTATAAATCTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACATTTT
* * * * *
860098 ACGGCGTTTGCTCCAAAAAATGCCACTATAGATCTCACATTTT
1 GCGGCGTTTGTTCC-AAAAACGCCGCTATAGATCTGACATTTT
* * * *
860141 GCGGCGTTTGTTCAAAAAATGCCTCTATAGGTCTGACATTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACATTTT
* * *
860183 GCGGCGTTTATTCCACAAACACCGCTATAGATCTCGACATTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACATTTT
* * * *
860226 GCGGCGTTTGTTCCAAAAAAACGCCGTTATAGATATCAACCTTTT
1 GCGGCGTTTGTTCC--AAAAACGCCGCTATAGATCT-GACATTTT
* *
860271 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATAGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACATTTT
860314 GCG
1 GCG
860317 AAAAACGCCG
Statistics
Matches: 185, Mismatches: 30, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
42 64 0.35
43 84 0.45
45 37 0.20
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACATTTT
Found at i:860223 original size:85 final size:84
Alignment explanation
Indices: 860056--860316 Score: 283
Period size: 85 Copynumber: 3.0 Consensus size: 84
860046 AAGGTAATTA
* * * * * *
860056 GCGGCGTTTGTTCCAAAAACGCCGCTATAAATCTGACCTTTTACGGCGTTTGCTCCAAAAAATGC
1 GCGGCGTTTGTTCAAAAAACGCCTCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAACA--C
*
860121 CACTATAGATCTC-ACATTTT
64 CGCTATAGATCTCGACATTTT
* * * *
860141 GCGGCGTTTGTTCAAAAAATGCCTCTATAGGTCTGACATTTTGCGGCGTTTATTCCACAAACACC
1 GCGGCGTTTGTTCAAAAAACGCCTCTATAGATCTGACCTTTTGCGGCGTTTGTTCCA-AAACACC
860206 GCTATAGATCTCGACATTTT
65 GCTATAGATCTCGACATTTT
* *
860226 GCGGCGTTTGTTCCAAAAAAACGCCGT-TATAGATATCAACCTTTTGCGGCGTTTGTTCCAAAAA
1 GCGGCGTTTGTT-C-AAAAAACGCC-TCTATAGATCT-GACCTTTTGCGGCGTTTGTTCC-AAAA
* * * *
860290 CGCCGCTATAGATATAGACCTTTT
61 CACCGCTATAGATCTCGACATTTT
860314 GCG
1 GCG
860317 AAAAACGCCG
Statistics
Matches: 148, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
84 13 0.09
85 67 0.45
86 5 0.03
87 16 0.11
88 46 0.31
89 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (84 bp):
GCGGCGTTTGTTCAAAAAACGCCTCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAACACCG
CTATAGATCTCGACATTTT
Found at i:860326 original size:32 final size:32
Alignment explanation
Indices: 860285--860348 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
860275 CGTTTGTTCC
*
860285 AAAAACGCCGCTATAGATATAGACCTTTTGCG
1 AAAAACGCCGCTATAGATATAGACCTATTGCG
* *
860317 AAAAACGCCGCTATAGATCTTGACCTATTGCG
1 AAAAACGCCGCTATAGATATAGACCTATTGCG
860349 GCGTTTTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (32 bp):
AAAAACGCCGCTATAGATATAGACCTATTGCG
Found at i:861161 original size:27 final size:26
Alignment explanation
Indices: 861130--861195 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
861120 CATTTTTGCT
*
861130 ATATATATTATTATTATTTTAATATAG
1 ATATATATTATTATTAGTTT-ATATAG
* *
861157 ATATATA-TACTATTAGTTTATATAT
1 ATATATATTATTATTAGTTTATATAG
861182 ATATATATATATTA
1 ATATATAT-TATTA
861196 CTAATATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 12 0.36
26 10 0.30
27 11 0.33
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (26 bp):
ATATATATTATTATTAGTTTATATAG
Found at i:861205 original size:29 final size:28
Alignment explanation
Indices: 861129--861205 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 28
861119 CCATTTTTGC
*
861129 TATATATATTATTATTATTT-TAATATA
1 TATATATATTACTATTATTTATAATATA
*
861156 GATATATA-TACTATTAGTTTATATATATA
1 TATATATATTACTATTA-TTTATA-ATATA
*
861185 TATATATATTACTAATATTTA
1 TATATATATTACTATTATTTA
861206 AAAAAATACA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
26 7 0.17
27 10 0.24
28 2 0.05
29 16 0.38
30 7 0.17
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (28 bp):
TATATATATTACTATTATTTATAATATA
Found at i:864441 original size:15 final size:15
Alignment explanation
Indices: 864421--864451 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
864411 AGTTCACACC
864421 TAAATTAATTTGATG
1 TAAATTAATTTGATG
864436 TAAATTAATTTGATG
1 TAAATTAATTTGATG
864451 T
1 T
864452 CATTGCTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (15 bp):
TAAATTAATTTGATG
Found at i:864478 original size:29 final size:29
Alignment explanation
Indices: 864444--864502 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
864434 TGTAAATTAA
864444 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
*
864473 TTTGATGTCATTTCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
864502 T
1 T
864503 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:874138 original size:20 final size:20
Alignment explanation
Indices: 874102--874140 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
874092 ATTTGTTTTA
874102 TTTTCTATTTATGTATATTAT
1 TTTTCTATTTA-GTATATTAT
874123 TTTTCTACTTTA-TATATT
1 TTTTCTA-TTTAGTATATT
874141 TTATATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTCTATTTAGTATATTAT
Found at i:874144 original size:22 final size:22
Alignment explanation
Indices: 874097--874171 Score: 73
Period size: 27 Copynumber: 3.3 Consensus size: 22
874087 CTTGTATTTG
*
874097 TTTTA-TTTTCTA-TTTATGTA
1 TTTTATTTTTCTACTTTATATA
*
874117 TATTATTTTTCTACTTTATATA
1 TTTTATTTTTCTACTTTATATA
874139 TTTTATATTATTTTTCTACTTTATATA
1 ---T-T-TTATTTTTCTACTTTATATA
874166 TTTTAT
1 TTTTAT
874172 GATGTATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
20 4 0.09
21 7 0.16
22 11 0.24
23 1 0.02
24 1 0.02
25 1 0.02
27 20 0.44
ACGTcount: A:0.24, C:0.07, G:0.01, T:0.68
Consensus pattern (22 bp):
TTTTATTTTTCTACTTTATATA
Found at i:874146 original size:27 final size:27
Alignment explanation
Indices: 874115--874171 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
874105 TCTATTTATG
874115 TATATTATTTTTCTACTTTATATATTT
1 TATATTATTTTTCTACTTTATATATTT
874142 TATATTATTTTTCTACTTTATATATTT
1 TATATTATTTTTCTACTTTATATATTT
874169 TAT
1 TAT
874172 GATGTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (27 bp):
TATATTATTTTTCTACTTTATATATTT
Found at i:883058 original size:20 final size:21
Alignment explanation
Indices: 883030--883084 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
883020 TTGAACCGAC
*
883030 CTGATTCAACTC-GAATAGAA
1 CTGAGTCAACTCTGAATAGAA
* *
883050 CTGAGTCAAC-CTGAATTGAC
1 CTGAGTCAACTCTGAATAGAA
883070 CTGAGTCAACT-TGAA
1 CTGAGTCAACTCTGAA
883085 CTGGTCTGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (21 bp):
CTGAGTCAACTCTGAATAGAA
Found at i:883285 original size:12 final size:13
Alignment explanation
Indices: 883268--883301 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
883258 TGCATATACA
883268 ATTTAAGT-ATTT
1 ATTTAAGTGATTT
883280 ATTTAAGTGATTT
1 ATTTAAGTGATTT
*
883293 AATTAAGTG
1 ATTTAAGTG
883302 CATCTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (13 bp):
ATTTAAGTGATTT
Found at i:888364 original size:15 final size:16
Alignment explanation
Indices: 888340--888401 Score: 74
Period size: 15 Copynumber: 3.9 Consensus size: 16
888330 TTTGGCTCTT
888340 TTTTTGTTTTTTTGCC
1 TTTTTGTTTTTTTGCC
888356 TTTTT-TTTTTTTGCC
1 TTTTTGTTTTTTTGCC
**
888371 TTTTT-TTGCTTTTTGTT
1 TTTTTGTT--TTTTTGCC
888388 TTTTTGTTTTTTTG
1 TTTTTGTTTTTTTG
888402 AAAAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
15 17 0.41
16 11 0.27
17 11 0.27
18 2 0.05
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.81
Consensus pattern (16 bp):
TTTTTGTTTTTTTGCC
Found at i:888374 original size:33 final size:34
Alignment explanation
Indices: 888327--888401 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
888317 AAATTTTGGC
* *
888327 TTTTTTGGCTCTTTTTTTGTTTTTTTGCCTTTTT-
1 TTTTTTTGCTCTTTTTTTG-CTTTTTGCCTTTTTG
**
888361 TTTTTTTGC-CTTTTTTTGCTTTTTGTTTTTTTG
1 TTTTTTTGCTCTTTTTTTGCTTTTTGCCTTTTTG
888394 TTTTTTTG
1 TTTTTTTG
888402 AAAAAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 11 0.31
33 17 0.47
34 8 0.22
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.79
Consensus pattern (34 bp):
TTTTTTTGCTCTTTTTTTGCTTTTTGCCTTTTTG
Found at i:888392 original size:9 final size:8
Alignment explanation
Indices: 888338--888401 Score: 69
Period size: 8 Copynumber: 8.0 Consensus size: 8
888328 TTTTTGGCTC
888338 TTTTTTTG
1 TTTTTTTG
888346 TTTTTTTG
1 TTTTTTTG
**
888354 CCTTTTT-
1 TTTTTTTG
888361 TTTTTTTG
1 TTTTTTTG
888369 CCTTTTTTTG
1 --TTTTTTTG
*
888379 -CTTTTTG
1 TTTTTTTG
888386 TTTTTTTG
1 TTTTTTTG
888394 TTTTTTTG
1 TTTTTTTG
888402 AAAAAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
7 11 0.24
8 27 0.59
10 8 0.17
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.81
Consensus pattern (8 bp):
TTTTTTTG
Found at i:912484 original size:27 final size:27
Alignment explanation
Indices: 912454--912535 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 27
912444 TTGTAGATAT
* *
912454 ATGTTTAGGGATTTTTTTTGTTTAAAA
1 ATGTTTAGGGATTTCTTCTGTTTAAAA
* *
912481 ATGTTTAGGGGTTTCTTCT-ATTAAAA
1 ATGTTTAGGGATTTCTTCTGTTTAAAA
* *
912507 ATAATTTAGGGATTTCTTCTGTTAAAAA
1 AT-GTTTAGGGATTTCTTCTGTTTAAAA
912535 A
1 A
912536 ATTTAGGAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
26 8 0.18
27 31 0.69
28 6 0.13
ACGTcount: A:0.30, C:0.05, G:0.17, T:0.48
Consensus pattern (27 bp):
ATGTTTAGGGATTTCTTCTGTTTAAAA
Found at i:912533 original size:26 final size:25
Alignment explanation
Indices: 912457--912547 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 25
912447 TAGATATATG
* * *
912457 TTTAGGGATTTTTTTTGTTTAAAAATG
1 TTTAGGGATTTCTTCTG-TTAAAAA-A
* *
912484 TTTAGGGGTTTCTTCTATTAAAAATAA
1 TTTAGGGATTTCTTCTGTT-AAAA-AA
912511 TTTAGGGATTTCTTCTGTTAAAAAAA
1 TTTAGGGATTTCTTCTGTT-AAAAAA
*
912537 TTTAGGAATTT
1 TTTAGGGATTT
912548 AATATATATG
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
26 14 0.26
27 39 0.72
28 1 0.02
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.48
Consensus pattern (25 bp):
TTTAGGGATTTCTTCTGTTAAAAAA
Found at i:912862 original size:15 final size:15
Alignment explanation
Indices: 912812--912862 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
912802 TGTATATATG
912812 TGTTTATTGAT-TTCA
1 TGTTTATTGATATT-A
*
912827 TGTTTACTGATTATATA
1 TGTTTATTGA-TAT-TA
912844 TGTTTATTGATATTA
1 TGTTTATTGATATTA
912859 TGTT
1 TGTT
912863 GATATATGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 15 0.48
16 4 0.13
17 11 0.35
18 1 0.03
ACGTcount: A:0.24, C:0.04, G:0.14, T:0.59
Consensus pattern (15 bp):
TGTTTATTGATATTA
Found at i:912909 original size:27 final size:27
Alignment explanation
Indices: 912864--912935 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
912854 TATTATGTTG
* * *
912864 ATATATG-TTATGATTATAAGCCATGT
1 ATATATGTTTCTGATTATAAGCCACGA
**
912890 ATATATGTTTCTGATTATAAGTTACGA
1 ATATATGTTTCTGATTATAAGCCACGA
*
912917 ATATATGTTTCGGATTATA
1 ATATATGTTTCTGATTATA
912936 TATGTGAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 7 0.18
27 32 0.82
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (27 bp):
ATATATGTTTCTGATTATAAGCCACGA
Found at i:912966 original size:17 final size:17
Alignment explanation
Indices: 912944--912987 Score: 65
Period size: 15 Copynumber: 2.7 Consensus size: 17
912934 TATATGTGAA
912944 TATATGTGTTTACTAAT
1 TATATGTGTTTACTAAT
*
912961 TATA--TGTTTACTTAT
1 TATATGTGTTTACTAAT
912976 TATATGTGTTTA
1 TATATGTGTTTA
912988 GTATATATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 14 0.58
17 10 0.42
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (17 bp):
TATATGTGTTTACTAAT
Found at i:912994 original size:15 final size:15
Alignment explanation
Indices: 912943--912995 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
912933 ATATATGTGA
912943 ATATATGTGTTTACT
1 ATATATGTGTTTACT
*
912958 A-ATTATATGTTTACTT
1 ATA-TATGTGTTTAC-T
*
912974 ATTATATGTGTTTAGT
1 A-TATATGTGTTTACT
912990 ATATAT
1 ATATAT
912996 CTTTTATGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 1 0.03
15 16 0.52
16 4 0.13
17 9 0.29
18 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (15 bp):
ATATATGTGTTTACT
Found at i:913105 original size:26 final size:26
Alignment explanation
Indices: 913075--913129 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
913065 TTGTTCATAT
*
913075 TATGTTAAATGATTATATCATAATAA
1 TATGTTAAATAATTATATCATAATAA
* * *
913101 TATGTTTACTAATTATATCTTAATAA
1 TATGTTAAATAATTATATCATAATAA
913127 TAT
1 TAT
913130 ATGTTGGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (26 bp):
TATGTTAAATAATTATATCATAATAA
Found at i:913866 original size:21 final size:20
Alignment explanation
Indices: 913842--913907 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
913832 ATGAATATGT
913842 TGAACATGAAATTAATGATGC
1 TGAACAT-AAATTAATGATGC
* *
913863 TGAACCTAAAGTTAATGATGT
1 TGAACATAAA-TTAATGATGC
* *
913884 TAAACATAAAATTAATGATCC
1 TGAACAT-AAATTAATGATGC
913905 TGA
1 TGA
913908 CCCATATGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
20 3 0.08
21 30 0.83
22 3 0.08
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (20 bp):
TGAACATAAATTAATGATGC
Found at i:918386 original size:13 final size:13
Alignment explanation
Indices: 918368--918395 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
918358 ACCTAAACCT
918368 AAATTTAACCATC
1 AAATTTAACCATC
918381 AAATTTAACCATC
1 AAATTTAACCATC
918394 AA
1 AA
918396 TTTTTTGGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATTTAACCATC
Found at i:919462 original size:15 final size:15
Alignment explanation
Indices: 919442--919487 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
919432 TACAGTCACC
919442 GAGTCAACTCAGTCT
1 GAGTCAACTCAGTCT
*
919457 GAGTCATCTCAGTCT
1 GAGTCAACTCAGTCT
*
919472 GAGTCGACTC-GTCT
1 GAGTCAACTCAGTCT
919486 GA
1 GA
919488 CTTTGACCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 6 0.21
15 22 0.79
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (15 bp):
GAGTCAACTCAGTCT
Found at i:926233 original size:12 final size:12
Alignment explanation
Indices: 926213--926282 Score: 72
Period size: 12 Copynumber: 5.8 Consensus size: 12
926203 GATACATGAC
*
926213 CTGAATTCTGTT
1 CTGATTTCTGTT
926225 CTGATTTCTGATT
1 CTGATTTCTG-TT
926238 -TGGA-TTCTGTT
1 CT-GATTTCTGTT
*
926249 CTGATATCTGTT
1 CTGATTTCTGTT
*
926261 TTGATTTCTGTT
1 CTGATTTCTGTT
*
926273 TTGATTTCTG
1 CTGATTTCTG
926283 ATATCTCCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
11 4 0.08
12 42 0.84
13 4 0.08
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.56
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:926235 original size:7 final size:7
Alignment explanation
Indices: 926223--926284 Score: 50
Period size: 7 Copynumber: 10.0 Consensus size: 7
926213 CTGAATTCTG
926223 TTCTGAT
1 TTCTGAT
926230 TTCTGAT
1 TTCTGAT
*
926237 TT-GGA-
1 TTCTGAT
926242 TTCTG--
1 TTCTGAT
926247 TTCTGAT
1 TTCTGAT
*
926254 ATCTG-T
1 TTCTGAT
926260 TT-TGAT
1 TTCTGAT
926266 TTCTG-T
1 TTCTGAT
926272 TT-TGAT
1 TTCTGAT
926278 TTCTGAT
1 TTCTGAT
926285 ATCTCCATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
5 11 0.25
6 14 0.32
7 19 0.43
ACGTcount: A:0.13, C:0.11, G:0.18, T:0.58
Consensus pattern (7 bp):
TTCTGAT
Found at i:926244 original size:24 final size:24
Alignment explanation
Indices: 926217--926284 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
926207 CATGACCTGA
926217 ATTCTGTTCTGATTTCTGATTTGG
1 ATTCTGTTCTGATTTCTGATTTGG
* *
926241 ATTCTGTTCTGATATCTG-TTTTG
1 ATTCTGTTCTGATTTCTGATTTGG
*
926264 ATTTCTGTTTTGATTTCTGAT
1 A-TTCTGTTCTGATTTCTGAT
926285 ATCTCCATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 5 0.13
24 32 0.84
25 1 0.03
ACGTcount: A:0.13, C:0.12, G:0.18, T:0.57
Consensus pattern (24 bp):
ATTCTGTTCTGATTTCTGATTTGG
Found at i:926560 original size:27 final size:27
Alignment explanation
Indices: 926530--926626 Score: 86
Period size: 27 Copynumber: 3.3 Consensus size: 27
926520 TTCTGATATC
*
926530 CTGATCTCATTCATCCGAAATATTTCA
1 CTGAACTCATTCATCCGAAATATTTCA
* *
926557 CTGAACTGAAAGATCATTGTCCGTATATATATTTCA
1 CTGAACT--CA-TTCA---TCCG-A-A-ATATTTCA
926593 CTGAACTCATTCATCCGAAATATTTCA
1 CTGAACTCATTCATCCGAAATATTTCA
926620 CTGAACT
1 CTGAACT
926627 GAAAGATCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
27 21 0.38
28 1 0.02
29 2 0.04
30 7 0.12
33 7 0.12
34 2 0.04
35 1 0.02
36 15 0.27
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (27 bp):
CTGAACTCATTCATCCGAAATATTTCA
Found at i:927429 original size:2 final size:2
Alignment explanation
Indices: 927424--927484 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
927414 ACACACACAC
927424 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
*
927466 AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT A
927485 CCCCCATCCC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:927678 original size:24 final size:24
Alignment explanation
Indices: 927651--927745 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 24
927641 GATATCAAAA
*
927651 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
927675 ATCATAACAGAATCCA-AGTTAGGA-
1 ATCAAAACAGAATTCAGA-TCA-GAT
* *
927699 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* *
927723 GTCAAAACAGAATTCAAATCAGA
1 ATCAAAACAGAATTCAGATCAGA
927746 AATTAGATAA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
23 3 0.05
24 49 0.89
25 3 0.05
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:930303 original size:19 final size:19
Alignment explanation
Indices: 930281--930382 Score: 124
Period size: 19 Copynumber: 5.6 Consensus size: 19
930271 CTAGGCGGCT
*
930281 CGGCTCTGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
*
930300 CGGCTCGGCTTAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
*
930319 CGTCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
* *
930338 TGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
930357 CGGCTCGG-T----TCAAA
1 CGGCTCGGCTCAGCTCAAA
930371 CGGCTCGGCTCA
1 CGGCTCGGCTCA
930383 AACGGCTCCT
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
14 12 0.17
15 1 0.01
18 1 0.01
19 57 0.80
ACGTcount: A:0.19, C:0.34, G:0.26, T:0.21
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:930360 original size:14 final size:14
Alignment explanation
Indices: 930343--930390 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
930333 TCAAATGGCT
* *
930343 CGGCTCAGCTCAAG
1 CGGCTCGGCTCAAA
*
930357 CGGCTCGGTTCAAA
1 CGGCTCGGCTCAAA
930371 CGGCTCGGCTCAAA
1 CGGCTCGGCTCAAA
930385 CGGCTC
1 CGGCTC
930391 CTCAGGCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.19, C:0.35, G:0.29, T:0.17
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:932719 original size:7 final size:7
Alignment explanation
Indices: 932699--932740 Score: 66
Period size: 7 Copynumber: 5.7 Consensus size: 7
932689 CCGTTTACCC
932699 GACCGTT
1 GACCGTT
932706 GACCCGTT
1 GA-CCGTT
932714 GACCGTT
1 GACCGTT
932721 GACCGTT
1 GACCGTT
932728 GACCCGTT
1 GA-CCGTT
932736 GACCG
1 GACCG
932741 GCATTGACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 19 0.58
8 14 0.42
ACGTcount: A:0.14, C:0.33, G:0.29, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:932727 original size:22 final size:22
Alignment explanation
Indices: 932699--932740 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
932689 CCGTTTACCC
932699 GACCGTTGACCCGTTGACCGTT
1 GACCGTTGACCCGTTGACCGTT
932721 GACCGTTGACCCGTTGACCG
1 GACCGTTGACCCGTTGACCG
932741 GCATTGACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.33, G:0.29, T:0.24
Consensus pattern (22 bp):
GACCGTTGACCCGTTGACCGTT
Found at i:932740 original size:15 final size:15
Alignment explanation
Indices: 932699--932739 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
932689 CCGTTTACCC
932699 GACCGTTGACCCGTT
1 GACCGTTGACCCGTT
932714 GACCGTTGA-CCGTT
1 GACCGTTGACCCGTT
932728 GACCCGTTGACC
1 GA-CCGTTGACC
932740 GGCATTGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.29
15 16 0.67
16 1 0.04
ACGTcount: A:0.15, C:0.34, G:0.27, T:0.24
Consensus pattern (15 bp):
GACCGTTGACCCGTT
Found at i:935232 original size:24 final size:25
Alignment explanation
Indices: 935205--935259 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
935195 ATATTTTATC
*
935205 TGATTTC-CGACTTGAATTATGTTA
1 TGATTTCACGACCTGAATTATGTTA
* * *
935229 TGA-TACATGACCTGAATTCTGTTA
1 TGATTTCACGACCTGAATTATGTTA
935253 TGATTTC
1 TGATTTC
935260 TGATCTGATT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 2 0.08
24 20 0.83
25 2 0.08
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (25 bp):
TGATTTCACGACCTGAATTATGTTA
Found at i:935268 original size:12 final size:12
Alignment explanation
Indices: 935240--935308 Score: 77
Period size: 12 Copynumber: 5.8 Consensus size: 12
935230 GATACATGAC
*
935240 CTGAATTCTGTT
1 CTGATTTCTGTT
* *
935252 ATGATTTCTGAT
1 CTGATTTCTGTT
935264 CTGA-TTCTGTT
1 CTGATTTCTGTT
*
935275 CTGATATCTGTT
1 CTGATTTCTGTT
*
935287 CTGAATTCTGTT
1 CTGATTTCTGTT
*
935299 TTGATTTCTG
1 CTGATTTCTG
935309 ATATCTCCGT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
11 10 0.22
12 36 0.78
ACGTcount: A:0.16, C:0.14, G:0.17, T:0.52
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:935274 original size:23 final size:24
Alignment explanation
Indices: 935217--935310 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
935207 ATTTCCGACT
* * *
935217 TGAATTATGTTATGA-TACATGACC
1 TGAATTCTGTTATGATTTC-TGATC
935241 TGAATTCTGTTATGATTTCTGATC
1 TGAATTCTGTTATGATTTCTGATC
* * *
935265 TG-ATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTATGATTTCTGATC
*
935288 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTATGATTTCTGAT
935311 ATCTCCGTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
23 20 0.34
24 37 0.63
25 2 0.03
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATC
Found at i:937383 original size:18 final size:18
Alignment explanation
Indices: 937340--937396 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
937330 ACCGGTTACA
* *
937340 ACCCGACCCGACCCATTT
1 ACCCGACCCGACCCGTTG
* *
937358 ACCTGACCCAACCCGTTG
1 ACCCGACCCGACCCGTTG
*
937376 ACCCGACCCGAGCCGTTG
1 ACCCGACCCGACCCGTTG
937394 ACC
1 ACC
937397 GACGTTGACT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.21, C:0.47, G:0.18, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:944649 original size:97 final size:97
Alignment explanation
Indices: 944501--944681 Score: 263
Period size: 97 Copynumber: 1.9 Consensus size: 97
944491 TAGTAGATAA
* * * * * *
944501 ATATATATTTTAATAGAGTTTGATAATTACAATACTTATCTATCTTCTAAATATATAAACATATT
1 ATATATATATTAATAAAGTTTAATAATTAAAATAATTATCTATCTTCTAAATATACAAACATATT
944566 TCAACTAAGATTAGGTTCTATCACATATATAT
66 TCAACTAAGATTAGGTTCTATCACATATATAT
* * *
944598 ATATATATATTAATAAAGTTTAATAATTAAAATAATTATCTCTCTTTTAAATATACAAACCTATT
1 ATATATATATTAATAAAGTTTAATAATTAAAATAATTATCTATCTTCTAAATATACAAACATATT
* *
944663 TCAATTATGATTAGGTTCT
66 TCAACTAAGATTAGGTTCT
944682 GTAACTAGGG
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
97 73 1.00
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (97 bp):
ATATATATATTAATAAAGTTTAATAATTAAAATAATTATCTATCTTCTAAATATACAAACATATT
TCAACTAAGATTAGGTTCTATCACATATATAT
Found at i:957178 original size:16 final size:18
Alignment explanation
Indices: 957159--957200 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
957149 AATTTTTGTG
957159 ATTTTTTGGC-TTT-TTT
1 ATTTTTTGGCATTTGTTT
*
957175 ATTTTTCGGCATTTGTTT
1 ATTTTTTGGCATTTGTTT
*
957193 TTTTTTTG
1 ATTTTTTG
957201 TGTTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 9 0.43
17 3 0.14
18 9 0.43
ACGTcount: A:0.07, C:0.07, G:0.14, T:0.71
Consensus pattern (18 bp):
ATTTTTTGGCATTTGTTT
Found at i:963765 original size:2 final size:2
Alignment explanation
Indices: 963758--963810 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
963748 TGATACATTA
963758 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
963800 AT AT AT AT AT A
1 AT AT AT AT AT A
963811 CCAAATTATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:970644 original size:19 final size:19
Alignment explanation
Indices: 970622--970667 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
970612 TTGGACCCTT
*
970622 AGTGCATCGTTGCACTAAG
1 AGTGCATCGGTGCACTAAG
* *
970641 AGTGAATCGGTGCATTAAG
1 AGTGCATCGGTGCACTAAG
970660 AGTGCATC
1 AGTGCATC
970668 AATACATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.26
Consensus pattern (19 bp):
AGTGCATCGGTGCACTAAG
Found at i:970859 original size:65 final size:65
Alignment explanation
Indices: 970661--970861 Score: 174
Period size: 65 Copynumber: 3.1 Consensus size: 65
970651 TGCATTAAGA
* * * * * * * * ** *
970661 GTGCATCAATACATCAAGTGCATTCAATGTTTCAA-AATAGCCAGAGTACATTGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAAAATCCATAGTGCATCAATGCATGGTTG
** * **
970725 GTGCATCGATGCATCAAATGCATTCGATGTTTTTATAAAATCCTTAGTGCATCTTTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAAAATCCATAGTGCATCAATGCATGGT-T
970790 -
65 G
* ** * *
970790 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCAATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAAAATCCATAGTGCATCAATGCATGG-TT
970854 G
65 G
970855 GTGCATC
1 GTGCATC
970862 ACTCTGAAAA
Statistics
Matches: 108, Mismatches: 25, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
64 53 0.49
65 54 0.50
66 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAAAATCCATAGTGCATCAATGCATGGTTG
Found at i:986758 original size:56 final size:56
Alignment explanation
Indices: 986667--987551 Score: 865
Period size: 56 Copynumber: 15.8 Consensus size: 56
986657 CCTATACAGT
* * * * *
986667 TATTCTTCAACTCATGAATGAATTACGAT--AATTTGCACACGTA-TGGTATGTACGGC
1 TATTCATCAACTCATG-ATGAATTCCG-TGGATTTTGCACACATAGT-GCATGTACGGC
** * **
986723 TATTCATCAACTCATGATGAATTTTGTGGATTTTGCACACATATTGCATGTACGAA
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCATGTACGGC
* * * * * *
986779 TATTCATCAAGTCATGATGAATTCTGTGGA-TTTGAAACACACAGTGCCTGTACGAC
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTG-CACACATAGTGCATGTACGGC
* *
986835 TATTCATCAACTCATGGTGAATTCCGTGGATTTTGCACTCGA-AGTGTCA-GTACGGC
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACAC-ATAGTG-CATGTACGGC
* * * * * * *
986891 TATTCATCAAATCATGATGAATTTCATGGATTTTGTACACATAGAGCCTGTATGGC
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCATGTACGGC
* ** * * *
986947 TATTCATCAACTCATGATGAATTTCGTGGATTTTGTTCAAACAGTGCCTGTACGGC
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCATGTACGGC
* * * * *
987003 CATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAATGCTTTTACGAC
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCATGTACGGC
* * * * *
987059 TATTTATCAACTCATGATGAATTTCGTGAATTTTGCACACGTAGGGCATGTACGGC
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCATGTACGGC
* *
987115 TATTCATCAACTCATGATGAATTACGTGGATTTTGCACACATA-TGGCATGTACGGA
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGT-GCATGTACGGC
* * * *
987171 TATTCATCAAGTCATGATGAATTACGTGGATTTTGAACACATAGTGCCTGTACGGC
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCATGTACGGC
* * * * *
987227 TATTCATTAACTCATGATGAATTCTGTGGATTTTACACACGA-AGTGCCTGTACGTC
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACAC-ATAGTGCATGTACGGC
* ** * * *
987283 TATTCATCAACTCATGATGAATTTCGTGGATTTTATACACTTAGTTCATGTAAGGC
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCATGTACGGC
* ** * * * * ** *
987339 TATTTATTGA--CACGATGAATTCCATGGATTTTGTACATATAGTGCCCGTATGGC
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCATGTACGGC
* * * * *
987393 TATTCATGAACTCATGATGAATTCTGTGGATTTTGCACACATATTTTC-TGTACGAC
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATA-GTGCATGTACGGC
* * * * *
987449 TATTCATCAACTCATGATAAATTACGTAGATTTTGTACACATAGTGTATGTACGGC
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCATGTACGGC
* * ** *
987505 TATTAATCAACTCATGATTAATTATGTGGATTTTGCATACATAGTGC
1 TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGC
987552 CTATTATACA
Statistics
Matches: 685, Mismatches: 127, Indels: 34
0.81 0.15 0.04
Matches are distributed among these distances:
54 42 0.06
55 15 0.02
56 617 0.90
57 11 0.02
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (56 bp):
TATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATAGTGCATGTACGGC
Found at i:991324 original size:56 final size:56
Alignment explanation
Indices: 991271--991864 Score: 653
Period size: 56 Copynumber: 10.7 Consensus size: 56
991261 CTATACGGTA
* * * * *
991271 ATTCTTCAACTCATGAATGAATTTCAT-GAATTTGCGCACATAGTGCATGTACGGTT
1 ATTCATCAACTCATG-ATGAATTTCGTGGATTTTGCACACATAGTGCATGTACGGCT
* * * *
991327 ATTCATCAACTCATGAATGAATTCCAT-GAATTTGCACACATAGTG-ACTGTATGGCT
1 ATTCATCAACTCATG-ATGAATTTCGTGGATTTTGCACACATAGTGCA-TGTACGGCT
*
991383 ATTCATCAACTCATGATGAATTAT-GTGGATTTTGCACACATAGT-TATTGTACGGCT
1 ATTCATCAACTCATGATGAATT-TCGTGGATTTTGCACACATAGTGCA-TGTACGGCT
* * * *
991439 ATTCATCAACTCATGATGAATTCCATGGATTTTGCACACGTAGTGCCTGTACGGCT
1 ATTCATCAACTCATGATGAATTTCGTGGATTTTGCACACATAGTGCATGTACGGCT
* * *
991495 ATTCATCAACTCATGATGAATTCCGTGGATTTTGCACACATATTGCCTGTACGGCT
1 ATTCATCAACTCATGATGAATTTCGTGGATTTTGCACACATAGTGCATGTACGGCT
* * * * *
991551 ATTCATCAAGTC---AT-AA--T-ATGGATTTTGAACACATAGTGCCTGTACGACT
1 ATTCATCAACTCATGATGAATTTCGTGGATTTTGCACACATAGTGCATGTACGGCT
* * *
991600 ATTCATCAACTCATGACGAA-TTCTGTGGATTTTGCACACGTAGTGCCTGTACGGCT
1 ATTCATCAACTCATGATGAATTTC-GTGGATTTTGCACACATAGTGCATGTACGGCT
*
991656 ATTCATCAACTCATGATGAATTTCGTGGATTTTGCACACATAGTGCATGTACGACT
1 ATTCATCAACTCATGATGAATTTCGTGGATTTTGCACACATAGTGCATGTACGGCT
* * * * *
991712 ATTCATCAACTTATTATGAATTAT-TTGGATTTTGTAAACATAGTGCATGTACGTG-T
1 ATTCATCAACTCATGATGAATT-TCGTGGATTTTGCACACATAGTGCATGTACG-GCT
* * * * *
991768 GTTCATCAACTCATGATGAA-TTCTGTGGATTTTACACACATATTGCTTGTACGACT
1 ATTCATCAACTCATGATGAATTTC-GTGGATTTTGCACACATAGTGCATGTACGGCT
* *
991824 ATTCATCAAGTCATGATGAATTCCGTGGATTTTGCACACAT
1 ATTCATCAACTCATGATGAATTTCGTGGATTTTGCACACAT
991865 GGTGTCTGTA
Statistics
Matches: 464, Mismatches: 54, Indels: 40
0.83 0.10 0.07
Matches are distributed among these distances:
49 39 0.08
52 3 0.01
53 4 0.01
54 2 0.00
55 10 0.02
56 400 0.86
57 6 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (56 bp):
ATTCATCAACTCATGATGAATTTCGTGGATTTTGCACACATAGTGCATGTACGGCT
Found at i:991798 original size:273 final size:273
Alignment explanation
Indices: 991307--991837 Score: 764
Period size: 273 Copynumber: 1.9 Consensus size: 273
991297 TGAATTTGCG
** *
991307 CACATAGTGCATGTACGGTTATTCATCAACTCATGAATGAATTCCATGAATTTGCACACATAGTG
1 CACATAGTGCATGTACGACTATTCATCAACTCATGAACGAATTCCATGAATTTGCACACATAGTG
* * *
991372 ACTGTATGGCTATTCATCAACTCATGATGAATTATGTGGATTTTGCACACATAGTTATTGTACGG
66 ACTGTACGGCTATTCATCAACTCATGATGAATTATGTGGATTTTGCACACATAGTCATTGTACGA
* * * *
991437 CTATTCATCAACTCATGATGAATTCCATGGATTTTGCACACGTAGTGCCTGTACGGCTATTCATC
131 CTATTCATCAACTCATGATGAATTACATGGATTTTGCAAACATAGTGCATGTACGGCTATTCATC
* *
991502 AACTCATGATGAATTCCGTGGATTTTGCACACATATTGCCTGTACGGCTATTCATCAAGTCATAA
196 AACTCATGATGAATTCCGTGGATTTTACACACATATTGCCTGTACGACTATTCATCAAGTCATAA
991567 TATGGATTTTGAA
261 TATGGATTTTGAA
* ** * *
991580 CACATAGTGCCTGTACGACTATTCATCAACTCATG-ACGAATTCTGTGGATTTTGCACACGTAGT
1 CACATAGTGCATGTACGACTATTCATCAACTCATGAACGAATTCCAT-GAATTTGCACACATAGT
*
991644 GCCTGTACGGCTATTCATCAACTCATGATGAATT-TCGTGGATTTTGCACACATAGTGCA-TGTA
65 GACTGTACGGCTATTCATCAACTCATGATGAATTAT-GTGGATTTTGCACACATAGT-CATTGTA
* * ** * *
991707 CGACTATTCATCAACTTATTATGAATTATTTGGATTTTGTAAACATAGTGCATGTACGTG-TGTT
128 CGACTATTCATCAACTCATGATGAATTACATGGATTTTGCAAACATAGTGCATGTACG-GCTATT
* *
991771 CATCAACTCATGATGAATTCTGTGGATTTTACACACATATTGCTTGTACGACTATTCATCAAGTC
192 CATCAACTCATGATGAATTCCGTGGATTTTACACACATATTGCCTGTACGACTATTCATCAAGTC
991836 AT
257 AT
991838 GATGAATTCC
Statistics
Matches: 228, Mismatches: 26, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
272 9 0.04
273 217 0.95
274 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (273 bp):
CACATAGTGCATGTACGACTATTCATCAACTCATGAACGAATTCCATGAATTTGCACACATAGTG
ACTGTACGGCTATTCATCAACTCATGATGAATTATGTGGATTTTGCACACATAGTCATTGTACGA
CTATTCATCAACTCATGATGAATTACATGGATTTTGCAAACATAGTGCATGTACGGCTATTCATC
AACTCATGATGAATTCCGTGGATTTTACACACATATTGCCTGTACGACTATTCATCAAGTCATAA
TATGGATTTTGAA
Found at i:992220 original size:20 final size:22
Alignment explanation
Indices: 992192--992248 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 22
992182 ATTTCTGGCT
*
992192 CCATAGTATCGATACC-CT-TA
1 CCATGGTATCGATACCACTATA
992212 CCATGGTATCGATACCACTATA
1 CCATGGTATCGATACCACTATA
* *
992234 CTATGGTACCGATAC
1 CCATGGTATCGATAC
992249 TCTGCTATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 15 0.47
21 2 0.06
22 15 0.47
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (22 bp):
CCATGGTATCGATACCACTATA
Found at i:992246 original size:22 final size:20
Alignment explanation
Indices: 992201--992248 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
992191 TCCATAGTAT
*
992201 CGATACCCTTACCATGGTAT
1 CGATACCCTTACCATGGTAC
*
992221 CGATACCACTATACTATGGTAC
1 CGATACC-CT-TACCATGGTAC
992243 CGATAC
1 CGATAC
992249 TCTGCTATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.29
21 2 0.08
22 15 0.62
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (20 bp):
CGATACCCTTACCATGGTAC
Found at i:996088 original size:22 final size:22
Alignment explanation
Indices: 996063--996104 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
996053 ATATAATTGG
996063 TCTATGAGATATAGTTAATTCA
1 TCTATGAGATATAGTTAATTCA
* *
996085 TCTATGAGATGTATTTAATT
1 TCTATGAGATATAGTTAATT
996105 ATCATTTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (22 bp):
TCTATGAGATATAGTTAATTCA
Found at i:1003513 original size:16 final size:15
Alignment explanation
Indices: 1003490--1003519 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1003480 TTTGGTCAGA
1003490 GTTAACCATTGACTG
1 GTTAACCATTGACTG
1003505 GTTAGACCATTGACT
1 GTTA-ACCATTGACT
1003520 TTGACTGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (15 bp):
GTTAACCATTGACTG
Found at i:1008387 original size:22 final size:22
Alignment explanation
Indices: 1008353--1008403 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1008343 CTGAGTGGCA
*
1008353 TATGATATTTGTCCCTA-AGGACC
1 TATGA-ATATGTCCC-AGAGGACC
*
1008376 TGTGAATATGTCCCAGAGGACC
1 TATGAATATGTCCCAGAGGACC
1008398 TATGAA
1 TATGAA
1008404 ACCCTCAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.79
23 4 0.17
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (22 bp):
TATGAATATGTCCCAGAGGACC
Found at i:1015314 original size:22 final size:21
Alignment explanation
Indices: 1015285--1015325 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1015275 TGGCATATGA
*
1015285 GATTTGTCCCTAAGGACATGT
1 GATTTGTCCCGAAGGACATGT
*
1015306 GATTATGTCCCGAATGACAT
1 GATT-TGTCCCGAAGGACAT
1015326 ATGAAACGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (21 bp):
GATTTGTCCCGAAGGACATGT
Found at i:1016001 original size:64 final size:63
Alignment explanation
Indices: 1015925--1016085 Score: 196
Period size: 64 Copynumber: 2.5 Consensus size: 63
1015915 TCCTTAACAT
** * ** *
1015925 GTGTATCGATACACTAACTATGTATCGATACACAAATTATATTCGATGTTTTTCTTTACAAGAA
1 GTGTATCGATACACTTCCTATGTATCGATACACAAATTACATTAAATGTTTTTATTT-CAAGAA
* * * *
1015989 GTGTATCAATACACTTCCTATGTATCGATACAAAAATTACATTAAATGTTTTTATTTTAAGGA
1 GTGTATCGATACACTTCCTATGTATCGATACACAAATTACATTAAATGTTTTTATTTCAAGAA
* * *
1016052 GTGCATCGTTACACTTCCTGTGTATCGATACACA
1 GTGTATCGATACACTTCCTATGTATCGATACACA
1016086 CTAAATAATT
Statistics
Matches: 82, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
63 33 0.40
64 49 0.60
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (63 bp):
GTGTATCGATACACTTCCTATGTATCGATACACAAATTACATTAAATGTTTTTATTTCAAGAA
Found at i:1017080 original size:13 final size:13
Alignment explanation
Indices: 1017045--1017083 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1017035 TGATCGGTTA
1017045 GACCATTGACTTT
1 GACCATTGACTTT
1017058 GACCA--G--TTT
1 GACCATTGACTTT
1017067 GACCATTGACTTT
1 GACCATTGACTTT
1017080 GACC
1 GACC
1017084 GAAAAAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
9 8 0.36
11 2 0.09
13 12 0.55
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (13 bp):
GACCATTGACTTT
Found at i:1021622 original size:21 final size:22
Alignment explanation
Indices: 1021596--1021640 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1021586 CCATTGATTT
1021596 TGGTCAGA-GTTGACCATTGAC
1 TGGTCAGACGTTGACCATTGAC
*
1021617 TGGTCAGATCGTTGACCGTTGAC
1 TGGTCAGA-CGTTGACCATTGAC
1021640 T
1 T
1021641 TTGACAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
23 13 0.62
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (22 bp):
TGGTCAGACGTTGACCATTGAC
Found at i:1027741 original size:40 final size:40
Alignment explanation
Indices: 1027682--1027843 Score: 279
Period size: 40 Copynumber: 4.0 Consensus size: 40
1027672 TGCAGGTTTA
*
1027682 TAATACACTTCTGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
1027722 TAACACACTTCGGTGTATATGGTGGGCGCGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
1027762 TAATACACTTTGGTGTATATGGTGGACACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1027802 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1027842 TA
1 TA
1027844 GCACTATGGT
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 113 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1028015 original size:21 final size:21
Alignment explanation
Indices: 1027949--1028016 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
1027939 TAAGCATGCA
1027949 AATAAGCTTACGAGCTTATGG
1 AATAAGCTTACGAGCTTATGG
** *
1027970 AATAA--TGGCAAG-TATATTGG
1 AATAAGCTTACGAGCT-TA-TGG
1027990 TAATAAGCTTACGAGCTTATGG
1 -AATAAGCTTACGAGCTTATGG
1028012 AATAA
1 AATAA
1028017 AGGCAAGTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
18 1 0.03
19 6 0.17
20 3 0.09
21 15 0.43
22 3 0.09
23 6 0.17
24 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.29
Consensus pattern (21 bp):
AATAAGCTTACGAGCTTATGG
Found at i:1028085 original size:45 final size:45
Alignment explanation
Indices: 1027948--1028155 Score: 334
Period size: 45 Copynumber: 4.7 Consensus size: 45
1027938 GTAAGCATGC
*
1027948 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGT-
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
1027991 -AATAAGCTTACGAGCTTATGGAATAAA-GGCAAGTATATTGGTG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1028034 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
1028079 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
1028124 AAATAAGCTTACAAGCTTATGGGATAAATGGT
1 AAATAAGCTTACGAGCTTATGGAATAAATGGT
1028156 GAGAAATTTT
Statistics
Matches: 156, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
42 39 0.25
43 2 0.01
44 27 0.17
45 88 0.56
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:1031001 original size:22 final size:22
Alignment explanation
Indices: 1030962--1031020 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
1030952 TAAGAGCTAA
* *
1030962 AAAATAGAAAAAGAAAAAAAGAG
1 AAAAT-GAAAATGAAAAAAAAAG
1030985 TAAAATGAAAATGAAAAAAAAAG
1 -AAAATGAAAATGAAAAAAAAAG
*
1031008 AAAATAAAAATGA
1 AAAATGAAAATGA
1031021 TGATGAGAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 12 0.38
23 15 0.47
24 5 0.16
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (22 bp):
AAAATGAAAATGAAAAAAAAAG
Found at i:1034824 original size:40 final size:40
Alignment explanation
Indices: 1034765--1034846 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
1034755 TGCAGGTTTA
*
1034765 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGCGGGCACGACCTTATGTG
*
1034805 TAATACACTTCGGTTTATATGGCGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGCGGGCACGACCTTATGTG
1034845 TA
1 TA
1034847 GCACTACGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGCGGGCACGACCTTATGTG
Found at i:1035083 original size:45 final size:45
Alignment explanation
Indices: 1034954--1035159 Score: 310
Period size: 45 Copynumber: 4.6 Consensus size: 45
1034944 AGCATGAAAT
* * *
1034954 TAAGCTTATGAGCTTATAGAAT-AATGGCAAGTA-ATTGGTAAAA
1 TAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAA
* *
1034997 TAAGCTTACGAGTTTATGGAAT-AATGGCAAGTATATTGGTAAAA
1 TAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAA
1035041 TAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAA
1 TAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAA
* * *
1035086 TAAGATTACGAGCTTATGGAATAAGTGGTAAGTATTTTGGTAAAA
1 TAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAA
*
1035131 TAAGCTTACAAGCTTATGGAATAAATGGT
1 TAAGCTTACGAGCTTATGGAATAAATGGT
1035160 GAGAAATTTT
Statistics
Matches: 150, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
43 30 0.20
44 31 0.21
45 89 0.59
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (45 bp):
TAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAA
Found at i:1043734 original size:55 final size:54
Alignment explanation
Indices: 1043634--1043738 Score: 126
Period size: 55 Copynumber: 1.9 Consensus size: 54
1043624 TTTTCTAATT
1043634 TATGTTTCTGATTATATATCTGTGAATAAATGTGTTTATTGATATTATGTTGATA
1 TATGTTTCTGATTATATATCTGTGAATAAATGTGTTTATTGATATT-TGTTGATA
* * *
1043689 TATGTTTTCTGATTTTATGT-TGTGAATATATGT-TTCTGATT-ATATTTGTT
1 TATG-TTTCTGATTATATATCTGTGAATAAATGTGTT-T-ATTGATATTTGTT
1043739 TTCTGATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
54 6 0.14
55 22 0.50
56 16 0.36
ACGTcount: A:0.25, C:0.04, G:0.16, T:0.55
Consensus pattern (54 bp):
TATGTTTCTGATTATATATCTGTGAATAAATGTGTTTATTGATATTTGTTGATA
Found at i:1043738 original size:16 final size:17
Alignment explanation
Indices: 1043686--1043746 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 17
1043676 TATTATGTTG
1043686 ATATATGTTTTCTGATT
1 ATATATGTTTTCTGATT
*
1043703 -T-TATG--TTGTGA--
1 ATATATGTTTTCTGATT
1043714 ATATATG-TTTCTGATT
1 ATATATGTTTTCTGATT
*
1043730 ATATTTGTTTTCTGATT
1 ATATATGTTTTCTGATT
1043747 TTATGTTGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
12 1 0.03
13 9 0.26
14 5 0.14
15 4 0.11
16 7 0.20
17 9 0.26
ACGTcount: A:0.21, C:0.05, G:0.15, T:0.59
Consensus pattern (17 bp):
ATATATGTTTTCTGATT
Found at i:1043748 original size:44 final size:44
Alignment explanation
Indices: 1043686--1043777 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
1043676 TATTATGTTG
*
1043686 ATATATGTTTTCTGATTTTATGTTGTGAATATATGTTTCTGATT
1 ATATATGTTTTCTGATTTTATGTTGTGAATATATGTTTCTGAAT
* *
1043730 ATATTTGTTTTCTGATTTTATGTTGTGAATATATGTTTTTGAAT
1 ATATATGTTTTCTGATTTTATGTTGTGAATATATGTTTCTGAAT
1043774 ATAT
1 ATAT
1043778 CTGTGAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (44 bp):
ATATATGTTTTCTGATTTTATGTTGTGAATATATGTTTCTGAAT
Found at i:1043766 original size:28 final size:28
Alignment explanation
Indices: 1043730--1043809 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 28
1043720 GTTTCTGATT
*
1043730 ATATTTGTTTTCTGATTTTATGTTGTGA
1 ATATATGTTTTCTGATTTTATGTTGTGA
* * *
1043758 ATATATGTTTT-TGAATATAT-CTGTGA
1 ATATATGTTTTCTGATTTTATGTTGTGA
*
1043784 ATATATGTGTTTACTAATTTTATGTT
1 ATATATGT-TTT-CTGATTTTATGTT
1043810 TACTAGTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
26 13 0.32
27 10 0.25
28 10 0.25
29 6 0.15
30 1 0.03
ACGTcount: A:0.25, C:0.04, G:0.15, T:0.56
Consensus pattern (28 bp):
ATATATGTTTTCTGATTTTATGTTGTGA
Found at i:1043774 original size:14 final size:14
Alignment explanation
Indices: 1043686--1043777 Score: 62
Period size: 14 Copynumber: 6.4 Consensus size: 14
1043676 TATTATGTTG
1043686 ATATATGTTTTCTGA
1 ATATATGTTTT-TGA
* * *
1043701 TTTTATG-TTGTGA
1 ATATATGTTTTTGA
*
1043714 ATATATGTTTCTGA
1 ATATATGTTTTTGA
*
1043728 TTATATTTGTTTTCTGA
1 --ATATATGTTTT-TGA
* * *
1043745 TTTTATG-TTGTGA
1 ATATATGTTTTTGA
1043758 ATATATGTTTTTGA
1 ATATATGTTTTTGA
1043772 ATATAT
1 ATATAT
1043778 CTGTGAATAT
Statistics
Matches: 57, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
13 16 0.28
14 20 0.35
15 9 0.16
16 9 0.16
17 3 0.05
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (14 bp):
ATATATGTTTTTGA
Found at i:1043826 original size:17 final size:17
Alignment explanation
Indices: 1043785--1043828 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
1043775 TATCTGTGAA
1043785 TATATGTGTTTACTAAT
1 TATATGTGTTTACTAAT
* *
1043802 T-T-TATGTTTACTAGT
1 TATATGTGTTTACTAAT
1043817 TATATGTGTTTA
1 TATATGTGTTTA
1043829 GTATATATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
15 12 0.55
16 2 0.09
17 8 0.36
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.57
Consensus pattern (17 bp):
TATATGTGTTTACTAAT
Found at i:1044784 original size:21 final size:20
Alignment explanation
Indices: 1044744--1044801 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
1044734 TGTGATGAGC
1044744 ATGCT-AAACCTAAAATTAATA
1 ATGCTGAAA-CTAAAA-TAATA
*
1044765 ATGCTGAAACTGAAAATAATG
1 ATGCTGAAACT-AAAATAATA
* *
1044786 ATGTTGAACCTAAAAT
1 ATGCTGAAACTAAAAT
1044802 TAATTATGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 5 0.16
21 20 0.62
22 7 0.22
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (20 bp):
ATGCTGAAACTAAAATAATA
Found at i:1044805 original size:21 final size:21
Alignment explanation
Indices: 1044750--1044816 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
1044740 GAGCATGCTA
*
1044750 AACCTAAAATTAATAATGCTG
1 AACCTAAAATTAATAATGTTG
* *
1044771 AAACTGAAAA-TAATGATGTTG
1 AACCT-AAAATTAATAATGTTG
* *
1044792 AACCTAAAATTAATTATGTCG
1 AACCTAAAATTAATAATGTTG
1044813 AACC
1 AACC
1044817 ATCTGAGGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 4 0.11
21 30 0.79
22 4 0.11
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.28
Consensus pattern (21 bp):
AACCTAAAATTAATAATGTTG
Found at i:1054744 original size:93 final size:93
Alignment explanation
Indices: 1054575--1054746 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
1054565 CATATACATT
* * * * *
1054575 TGTATATTTTAATAGAGCTTGATCATTATAATAATTATCTCTCTTTTAAATATATAAACTTATTT
1 TGTATATTTTAATAGAGCTTGATAATTACAATAATTATCTCTCTTTTAAATATACAAACCTATTC
1054640 CAACTAAGATTAGGTTCTATCACATAAA
66 CAACTAAGATTAGGTTCTATCACATAAA
* *
1054668 TGTATATTTTAATAGAGTTTTATAATTACAATAATTATCTCTCTTTTAAATATACAAACCTATTC
1 TGTATATTTTAATAGAGCTTGATAATTACAATAATTATCTCTCTTTTAAATATACAAACCTATTC
* *
1054733 CAATTATGATTAGG
66 CAACTAAGATTAGG
1054747 CTTTGTAACC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (93 bp):
TGTATATTTTAATAGAGCTTGATAATTACAATAATTATCTCTCTTTTAAATATACAAACCTATTC
CAACTAAGATTAGGTTCTATCACATAAA
Found at i:1058034 original size:17 final size:17
Alignment explanation
Indices: 1058012--1058055 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
1058002 AACTGGTCCA
1058012 GTTCAATCAACAGTTCG
1 GTTCAATCAACAGTTCG
*
1058029 GTTCAATCAACGGTTCG
1 GTTCAATCAACAGTTCG
*
1058046 GTTCAGTCAA
1 GTTCAATCAA
1058056 TGGGTCAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (17 bp):
GTTCAATCAACAGTTCG
Found at i:1059736 original size:21 final size:20
Alignment explanation
Indices: 1059696--1059753 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
1059686 TGTGATGAGC
1059696 ATGCT-AAACCTAAAATTAATA
1 ATGCTGAAA-CTAAAA-TAATA
*
1059717 ATGCTGAAACTGAAAATAATG
1 ATGCTGAAACT-AAAATAATA
* *
1059738 ATGTTGAACCTAAAAT
1 ATGCTGAAACTAAAAT
1059754 TAATGATGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 5 0.16
21 20 0.62
22 7 0.22
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (20 bp):
ATGCTGAAACTAAAATAATA
Found at i:1059757 original size:21 final size:21
Alignment explanation
Indices: 1059702--1059768 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
1059692 GAGCATGCTA
* *
1059702 AACCTAAAATTAATAATGCTG
1 AACCTAAAATTAATGATGTTG
*
1059723 AAACTGAAAA-TAATGATGTTG
1 AACCT-AAAATTAATGATGTTG
*
1059744 AACCTAAAATTAATGATGTCG
1 AACCTAAAATTAATGATGTTG
1059765 AACC
1 AACC
1059769 ATCTGAGGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
20 4 0.10
21 31 0.79
22 4 0.10
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.27
Consensus pattern (21 bp):
AACCTAAAATTAATGATGTTG
Found at i:1065217 original size:28 final size:28
Alignment explanation
Indices: 1065176--1065229 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1065166 GATCGAACCG
* *
1065176 TTTACTTTGACCATAGTTGTCTTTGACT
1 TTTACCTTGACCATAGTTGACTTTGACT
*
1065204 TTTACCTTGGCCATAGTTGACTTTGA
1 TTTACCTTGACCATAGTTGACTTTGA
1065230 ATTTGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.46
Consensus pattern (28 bp):
TTTACCTTGACCATAGTTGACTTTGACT
Found at i:1070166 original size:59 final size:59
Alignment explanation
Indices: 1070074--1070202 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
1070064 CGTAGTGCTA
* * **
1070074 TCCCGAATATGACACATAAGGTCATGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
* * ** *
1070133 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
1070192 TCCCGAATATG
1 TCCCGAATATG
1070203 CAGCCTGATG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:1071240 original size:42 final size:41
Alignment explanation
Indices: 1071149--1071395 Score: 334
Period size: 42 Copynumber: 5.8 Consensus size: 41
1071139 CTATACACCA
* * *
1071149 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGGAAACT
*
1071193 GTAAGGTTTATCCTTGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
*
1071235 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
*
1071277 GTAAGGCTTACCTTCGCACACAGTAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
*
1071319 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
*
1071361 GTAAGGCTTACCTTCACACACAGCAAAGGGACCTG
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTG
1071396 ATAATACTTC
Statistics
Matches: 186, Mismatches: 12, Indels: 12
0.89 0.06 0.06
Matches are distributed among these distances:
41 8 0.04
42 145 0.78
43 19 0.10
44 14 0.08
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGGAAACT
Found at i:1071296 original size:84 final size:84
Alignment explanation
Indices: 1071149--1071395 Score: 381
Period size: 84 Copynumber: 2.9 Consensus size: 84
1071139 CTATACACCA
* * * * *
1071149 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACTGTAAGGTTTATCCTT-GCAC
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCT-GGTAAACTGTAAGGCTTA-CCTTCGCAC
1071212 ACAGCAAAGGGACCTGGGAAACT
62 ACAGCAAAGGGACCTGGGAAACT
1071235 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
*
1071300 TAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
*
1071319 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCACACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1071384 CAAAGGGACCTG
66 CAAAGGGACCTG
1071396 ATAATACTTC
Statistics
Matches: 151, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
83 4 0.03
84 117 0.77
85 14 0.09
86 16 0.11
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
CAAAGGGACCTGGGAAACT
Found at i:1072379 original size:29 final size:29
Alignment explanation
Indices: 1072347--1072419 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
1072337 CTTTTAAAAA
* * * *
1072347 TAATTACCAAAATAGCA-CACATTTCGAAT
1 TAATTCCCAAAATAGCACCAAAATT-AAAT
*
1072376 TAATTCCCAGAATAGCACCAAAATTAAAT
1 TAATTCCCAAAATAGCACCAAAATTAAAT
1072405 TAATTCCCAAAATAG
1 TAATTCCCAAAATAG
1072420 TACCGGTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 32 0.86
30 5 0.14
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.26
Consensus pattern (29 bp):
TAATTCCCAAAATAGCACCAAAATTAAAT
Found at i:1075554 original size:17 final size:17
Alignment explanation
Indices: 1075503--1075546 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
1075493 AACTGGTCCA
*
1075503 GTTCAGTCAACAGTTCG
1 GTTCAGTCAACGGTTCG
*
1075520 GTTCAATCAACGGTTCG
1 GTTCAGTCAACGGTTCG
1075537 GTTCAGTCAA
1 GTTCAGTCAA
1075547 TGGGTCGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (17 bp):
GTTCAGTCAACGGTTCG
Found at i:1086959 original size:26 final size:26
Alignment explanation
Indices: 1086923--1086980 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1086913 ACTTTTCCTC
* * * *
1086923 ATTTCGATAAAAGATTTCGAACGAAA
1 ATTTCCATAAAAGAATCCGAACAAAA
1086949 ATTTCCATAAAAGAATCCGAACAAAA
1 ATTTCCATAAAAGAATCCGAACAAAA
1086975 ATTTCC
1 ATTTCC
1086981 TTGAGGAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (26 bp):
ATTTCCATAAAAGAATCCGAACAAAA
Found at i:1089752 original size:90 final size:89
Alignment explanation
Indices: 1089600--1089772 Score: 276
Period size: 90 Copynumber: 1.9 Consensus size: 89
1089590 ACACTCCCTT
* *
1089600 TTATAGCCAAGTTACCCTATTCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
1089665 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
*
1089689 TTATATCCAAGTTACCCTAATCATACTGT-GGATTTTATTATTTCAAATTAATTAAATCTATATT
1 TTATAGCCAAGTTACCCTAATCATA-T-TAGGATTTTATTATTTCAAATTAATTAAATCTATATT
1089753 TAATTAATTGAAATTAAATA
64 TAATTAATTGAAATTAAATA
1089773 TTCAGGATTA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
89 23 0.30
90 53 0.69
91 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.45
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:1089911 original size:18 final size:18
Alignment explanation
Indices: 1089888--1089924 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1089878 TAGGTTCTTG
1089888 TAACGTTAGCAGTAATTA
1 TAACGTTAGCAGTAATTA
1089906 TAACGTTAGCAGTAATTA
1 TAACGTTAGCAGTAATTA
1089924 T
1 T
1089925 TAGAACAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (18 bp):
TAACGTTAGCAGTAATTA
Found at i:1096649 original size:90 final size:89
Alignment explanation
Indices: 1096497--1096669 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
1096487 ACACACCCTT
1096497 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
1096562 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* *
1096586 TTATATCCAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
1096651 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
1096670 TTTGGGATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 29 0.37
90 50 0.63
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.44
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:1096722 original size:13 final size:13
Alignment explanation
Indices: 1096704--1096728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1096694 TAATTAACTA
1096704 TAGATATATATTC
1 TAGATATATATTC
1096717 TAGATATATATT
1 TAGATATATATT
1096729 TTAGTAACGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TAGATATATATTC
Found at i:1096915 original size:18 final size:18
Alignment explanation
Indices: 1096892--1096933 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1096882 TTTATATCTA
*
1096892 GAATAGGCTCAAGTCTTG
1 GAATAGGCACAAGTCTTG
*
1096910 GAATAGTCACAAGTCTTG
1 GAATAGGCACAAGTCTTG
1096928 GAATAG
1 GAATAG
1096934 TCAGACTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.26
Consensus pattern (18 bp):
GAATAGGCACAAGTCTTG
Found at i:1096934 original size:18 final size:18
Alignment explanation
Indices: 1096901--1096936 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1096891 AGAATAGGCT
1096901 CAAGTCTTGGAATAGTCA
1 CAAGTCTTGGAATAGTCA
1096919 CAAGTCTTGGAATAGTCA
1 CAAGTCTTGGAATAGTCA
1096937 GACTTGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (18 bp):
CAAGTCTTGGAATAGTCA
Found at i:1099619 original size:15 final size:16
Alignment explanation
Indices: 1099601--1099630 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1099591 TGACCCGTTT
1099601 GATCCGA-TTTGACCC
1 GATCCGAGTTTGACCC
1099616 GATCCGAGTTTGACC
1 GATCCGAGTTTGACC
1099631 TGACCCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (16 bp):
GATCCGAGTTTGACCC
Found at i:1102993 original size:21 final size:21
Alignment explanation
Indices: 1102969--1103018 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1102959 AATACACCTT
1102969 GGATCATTTTTTATTATTGGG
1 GGATCATTTTTTATTATTGGG
1102990 GGATCATTTTTTATTATTGGG
1 GGATCATTTTTTATTATTGGG
1103011 GGATCATT
1 GGATCATT
1103019 GGTGAAGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.06, G:0.24, T:0.50
Consensus pattern (21 bp):
GGATCATTTTTTATTATTGGG
Found at i:1103935 original size:9 final size:9
Alignment explanation
Indices: 1103913--1103942 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1103903 ATTAAGTTCA
1103913 AACATCCA-
1 AACATCCAT
1103921 AACATCCAT
1 AACATCCAT
1103930 AACATCCAT
1 AACATCCAT
1103939 AACA
1 AACA
1103943 AACAAATCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (9 bp):
AACATCCAT
Found at i:1105882 original size:21 final size:21
Alignment explanation
Indices: 1105850--1105900 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
1105840 GATACAAGCT
*
1105850 GAGAAC-ACTTGAAGAAGTAC
1 GAGAACAACTTGAAGAAGTAA
1105870 GAGAACAACTTGAAGAAGTAA
1 GAGAACAACTTGAAGAAGTAA
*
1105891 GAGCACAACT
1 GAGAACAACT
1105901 ATCCAAGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.47, C:0.16, G:0.24, T:0.14
Consensus pattern (21 bp):
GAGAACAACTTGAAGAAGTAA
Found at i:1106084 original size:34 final size:33
Alignment explanation
Indices: 1106045--1106115 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 33
1106035 TTTTGTAAAG
*
1106045 GGGAAAGGTTCTA-TCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGT-TTAGCCCGTG-AAAAACTA
*
1106079 GGGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGTTTAGCCCGTGAAAAACTA
1106112 GGGA
1 GGGA
1106116 GTTGTAAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 11 0.32
34 22 0.65
35 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.25
Consensus pattern (33 bp):
GGGAAAGGTTCTAGTTTAGCCCGTGAAAAACTA
Found at i:1108794 original size:18 final size:17
Alignment explanation
Indices: 1108771--1108828 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 17
1108761 CAACAAATGG
1108771 TAACAATTAGTATCTTTT
1 TAACAATT-GTATCTTTT
1108789 TAACAATTGATATTCTTTTGT
1 TAACAATTG-TA-TC-TTT-T
1108810 TAACAATTGGTATCTTTT
1 TAACAATT-GTATCTTTT
1108828 T
1 T
1108829 CATTAAACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.03
18 12 0.34
19 5 0.14
20 5 0.14
21 11 0.31
22 1 0.03
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (17 bp):
TAACAATTGTATCTTTT
Found at i:1108828 original size:21 final size:20
Alignment explanation
Indices: 1108771--1108828 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 20
1108761 CAACAAATGG
*
1108771 TAACAATTAGTATC--TTTT
1 TAACAATTGGTATCTTTTTT
* *
1108789 TAACAATTGATATTCTTTTGT
1 TAACAATTGGTA-TCTTTTTT
1108810 TAACAATTGGTATCTTTTT
1 TAACAATTGGTATCTTTTT
1108829 CATTAAACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 10 0.31
19 2 0.06
20 6 0.19
21 14 0.44
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (20 bp):
TAACAATTGGTATCTTTTTT
Found at i:1109090 original size:20 final size:20
Alignment explanation
Indices: 1109065--1109110 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1109055 TTAATGTATA
1109065 AACAGTAAC-GATACTGTTTG
1 AACAGT-ACTGATACTGTTTG
*
1109085 AACAGTACTGATAGTGTTTG
1 AACAGTACTGATACTGTTTG
1109105 AACAGT
1 AACAGT
1109111 GATGAATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (20 bp):
AACAGTACTGATACTGTTTG
Found at i:1109169 original size:20 final size:21
Alignment explanation
Indices: 1109144--1109184 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1109134 AATTTCAGAA
*
1109144 TGCTACA-GGGTATCGATACC
1 TGCTACAGGGGTACCGATACC
1109164 TGCTACAGGGGTACCGATACC
1 TGCTACAGGGGTACCGATACC
1109185 GTTACTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (21 bp):
TGCTACAGGGGTACCGATACC
Found at i:1109547 original size:34 final size:33
Alignment explanation
Indices: 1109508--1109578 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
1109498 TTTTGTAAAG
*
1109508 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCGTG-AAAAACTA
* *
1109542 GGGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGTGAAAAACTA
1109575 GGGA
1 GGGA
1109579 GTTGTAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 11 0.32
34 23 0.68
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAGCCCGTGAAAAACTA
Found at i:1122177 original size:16 final size:16
Alignment explanation
Indices: 1122156--1122188 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1122146 TAAAGTTAAT
*
1122156 ATAATTTCAGAAAAAG
1 ATAATTCCAGAAAAAG
1122172 ATAATTCCAGAAAAAG
1 ATAATTCCAGAAAAAG
1122188 A
1 A
1122189 ATCTCCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (16 bp):
ATAATTCCAGAAAAAG
Found at i:1126562 original size:21 final size:21
Alignment explanation
Indices: 1126538--1126588 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1126528 AGTTGAAGCG
1126538 AGAGAAGCAGAGAGAGCAACA
1 AGAGAAGCAGAGAGAGCAACA
* * *
1126559 AGAGAAACAGAGAGAGCAGCG
1 AGAGAAGCAGAGAGAGCAACA
1126580 AGAGAAGCA
1 AGAGAAGCA
1126589 ACATTTCAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.51, C:0.14, G:0.35, T:0.00
Consensus pattern (21 bp):
AGAGAAGCAGAGAGAGCAACA
Found at i:1129263 original size:43 final size:44
Alignment explanation
Indices: 1129169--1129266 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
1129159 AAAACATTTA
* *
1129169 GCGACGTTTTTGCCTAAAACGCCACTAAATAACCCAAACCTATT
1 GCGACGTTTGTGACTAAAACGCCACTAAATAACCCAAACCTATT
* * ** *
1129213 GTGACGTTTGTGACTAAAATGCCGTTATATAA-CCAAACCTATT
1 GCGACGTTTGTGACTAAAACGCCACTAAATAACCCAAACCTATT
1129256 GCGACGTTTGT
1 GCGACGTTTGT
1129267 AGAGAAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
43 21 0.46
44 25 0.54
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (44 bp):
GCGACGTTTGTGACTAAAACGCCACTAAATAACCCAAACCTATT
Found at i:1142827 original size:20 final size:21
Alignment explanation
Indices: 1142799--1142850 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
1142789 GATTTAAGTA
* * *
1142799 GTATCGATACTGATGTGG-AG
1 GTATTGATACTGAAGAGGAAG
*
1142819 GTATTGATAC-CAAGAGGAAG
1 GTATTGATACTGAAGAGGAAG
1142839 GTATTGATACTG
1 GTATTGATACTG
1142851 TAATGGAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (21 bp):
GTATTGATACTGAAGAGGAAG
Found at i:1153054 original size:27 final size:27
Alignment explanation
Indices: 1153016--1153085 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
1153006 AACCCTATAT
*
1153016 ATATGTTTAGGGATTT-TTTTGTTTAAA
1 ATATGTTTAGGGATTTCTTCTG-TTAAA
*
1153043 ATATGTTTAGGGGTTTCTTCTGTTAAA
1 ATATGTTTAGGGATTTCTTCTGTTAAA
*
1153070 AT-TAATTTAGGGATTT
1 ATAT-GTTTAGGGATTT
1153086 AGTATATATG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 32 0.86
28 4 0.11
ACGTcount: A:0.26, C:0.03, G:0.20, T:0.51
Consensus pattern (27 bp):
ATATGTTTAGGGATTTCTTCTGTTAAA
Found at i:1153486 original size:13 final size:14
Alignment explanation
Indices: 1153472--1153648 Score: 75
Period size: 13 Copynumber: 12.6 Consensus size: 14
1153462 TATTATGTTG
1153472 ATATATGTTTCTGA
1 ATATATGTTTCTGA
* *
1153486 TTATATG-TTGTGA
1 ATATATGTTTCTGA
*
1153499 ATATATGTTTCTAGTT
1 ATATATGTTTCT-G-A
1153515 ATATATGTTTCATG-
1 ATATATGTTTC-TGA
*
1153529 ATAGTATG-TTGTGA
1 ATA-TATGTTTCTGA
*
1153543 ATATATGTTTCAG-
1 ATATATGTTTCTGA
* * *
1153556 AT-TATATCTGTGA
1 ATATATGTTTCTGA
1153569 ATATATGTGTTTACTGA
1 ATATA--TGTTT-CTGA
* * *
1153586 TTATATGTGTAT--
1 ATATATGTTTCTGA
*
1153598 ATATCT-TTTCTGA
1 ATATATGTTTCTGA
* * *
1153611 TTATATG-CTGTGA
1 ATATATGTTTCTGA
1153624 ATATATGTTTCTGA
1 ATATATGTTTCTGA
1153638 TTATATATGTT
1 --ATATATGTT
1153649 AATTGATATT
Statistics
Matches: 116, Mismatches: 29, Indels: 34
0.65 0.16 0.19
Matches are distributed among these distances:
11 3 0.03
12 10 0.09
13 35 0.30
14 27 0.23
15 9 0.08
16 24 0.21
17 8 0.07
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.51
Consensus pattern (14 bp):
ATATATGTTTCTGA
Found at i:1153491 original size:27 final size:28
Alignment explanation
Indices: 1153461--1153523 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
1153451 GCGTTTATGG
1153461 ATATTATGTTG-ATATATGTTTCT-GATT
1 ATATTATGTTGAATATATGTTTCTAG-TT
1153488 ATATGT-TG-TGAATATATGTTTCTAGTT
1 ATAT-TATGTTGAATATATGTTTCTAGTT
1153515 ATA-TATGTT
1 ATATTATGTT
1153524 TCATGATAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
25 1 0.03
26 4 0.13
27 24 0.77
28 2 0.06
ACGTcount: A:0.27, C:0.03, G:0.16, T:0.54
Consensus pattern (28 bp):
ATATTATGTTGAATATATGTTTCTAGTT
Found at i:1153543 original size:44 final size:43
Alignment explanation
Indices: 1153472--1153648 Score: 147
Period size: 44 Copynumber: 4.2 Consensus size: 43
1153462 TATTATGTTG
1153472 ATATATGTTTCTGATTATATGTTGTGAATATATGTTTCTAG-TT
1 ATATATGTTTCTGATTATATGTTGTGAATATATGTTTC-AGATT
1153515 ATATATGTTTCATGA-TAGTATGTTGTGAATATATGTTTCAGATT
1 ATATATGTTTC-TGATTA-TATGTTGTGAATATATGTTTCAGATT
* *** * * * *
1153559 ATATCTGTGAAT-A-TATGTGTTTACTGATTATATGTGT---A-T
1 ATATATGTTTCTGATTATATG-TT-GTGAATATATGTTTCAGATT
* * *
1153598 ATATCT-TTTCTGATTATATGCTGTGAATATATGTTTCTGATT
1 ATATATGTTTCTGATTATATGTTGTGAATATATGTTTCAGATT
1153640 ATATATGTT
1 ATATATGTT
1153649 AATTGATATT
Statistics
Matches: 105, Mismatches: 17, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
38 13 0.12
39 9 0.09
40 6 0.06
41 4 0.04
42 11 0.10
43 29 0.28
44 33 0.31
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.51
Consensus pattern (43 bp):
ATATATGTTTCTGATTATATGTTGTGAATATATGTTTCAGATT
Found at i:1153550 original size:28 final size:28
Alignment explanation
Indices: 1153515--1153643 Score: 139
Period size: 27 Copynumber: 4.8 Consensus size: 28
1153505 GTTTCTAGTT
*
1153515 ATATATGTTTCATGA-TAGTATGTTGTGA
1 ATATATGTTTCATGATTA-TATGCTGTGA
1153543 ATATATGTTTCA-GATTATAT-CTGTGA
1 ATATATGTTTCATGATTATATGCTGTGA
*
1153569 ATATATGTGTTTACTGATTATATG-TGT--
1 ATATATGT-TTCA-TGATTATATGCTGTGA
*
1153596 ATATATCTTTTC-TGATTATATGCTGTGA
1 ATATAT-GTTTCATGATTATATGCTGTGA
1153624 ATATATGTTTC-TGATTATAT
1 ATATATGTTTCATGATTATAT
1153644 ATGTTAATTG
Statistics
Matches: 87, Mismatches: 5, Indels: 19
0.78 0.05 0.17
Matches are distributed among these distances:
25 10 0.11
26 16 0.18
27 29 0.33
28 21 0.24
29 11 0.13
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (28 bp):
ATATATGTTTCATGATTATATGCTGTGA
Found at i:1153591 original size:71 final size:69
Alignment explanation
Indices: 1153435--1153593 Score: 182
Period size: 71 Copynumber: 2.3 Consensus size: 69
1153425 ATTGAATTTA
* * *
1153435 TGTTTACTGATTATATGCGTTTATGGATATTATGTTGATATATGTTTCTGATTATATGTTGTGAA
1 TGTTTACTGATTATAT--GTTTATGGATAGTATGTTGATATATGTTTCAGATTATATGCTGTGAA
1153500 TATATG
64 TATATG
* *
1153506 T-TTCTAGTTA-TATATGTTTCAT-GATAGTATGTTGTGAATATATGTTTCAGATTATAT-CTGT
1 TGTT-TACTGATTATATGTTT-ATGGATAGTATG-T-TG-ATATATGTTTCAGATTATATGCTGT
1153567 GAATATATG
61 GAATATATG
1153576 TGTTTACTGATTATATGT
1 TGTTTACTGATTATATGT
1153594 GTATATATCT
Statistics
Matches: 74, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
68 12 0.16
69 3 0.04
70 26 0.35
71 33 0.45
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.50
Consensus pattern (69 bp):
TGTTTACTGATTATATGTTTATGGATAGTATGTTGATATATGTTTCAGATTATATGCTGTGAATA
TATG
Found at i:1153641 original size:27 final size:27
Alignment explanation
Indices: 1153515--1153643 Score: 142
Period size: 28 Copynumber: 4.7 Consensus size: 27
1153505 GTTTCTAGTT
*
1153515 ATATATGTTTCATGA-TAGTATGTTGTGA
1 ATATATGTTTC-TGATTA-TATGCTGTGA
*
1153543 ATATATGTTTCAGATTATAT-CTGTGA
1 ATATATGTTTCTGATTATATGCTGTGA
1153569 ATATATGTGTTTACTGATTATATG-TGT--
1 ATATA--TGTTT-CTGATTATATGCTGTGA
*
1153596 ATATATCTTTTCTGATTATATGCTGTGA
1 ATATAT-GTTTCTGATTATATGCTGTGA
1153624 ATATATGTTTCTGATTATAT
1 ATATATGTTTCTGATTATAT
1153644 ATGTTAATTG
Statistics
Matches: 87, Mismatches: 5, Indels: 19
0.78 0.05 0.17
Matches are distributed among these distances:
25 12 0.14
26 16 0.18
27 23 0.26
28 24 0.28
29 12 0.14
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (27 bp):
ATATATGTTTCTGATTATATGCTGTGA
Found at i:1156636 original size:27 final size:27
Alignment explanation
Indices: 1156604--1156658 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
1156594 CAAACTTTTT
* *
1156604 CGTGTTTATATTTGTTTGACTTTTCAA
1 CGTGTTTATATATATTTGACTTTTCAA
1156631 CGTGTTTATATATATTTGACTTTTCAA
1 CGTGTTTATATATATTTGACTTTTCAA
1156658 C
1 C
1156659 CTCGGATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.53
Consensus pattern (27 bp):
CGTGTTTATATATATTTGACTTTTCAA
Done.