Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_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: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 49
Found at i:2958262 original size:32 final size:33
Alignment explanation
Indices: 2958189--2958262 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 33
2958179 ACCAACCCGA
* * *
2958189 TCGAGTTGGTTTTTTTCAAATTTTGAGTTTGGG
1 TCGAGTCGGATTTTTTCAAATTTTGAGTTCGGG
*
2958222 TCGGGTCGGATTTTTT-AAA-TTTGATGTTCGGG
1 TCGAGTCGGATTTTTTCAAATTTTGA-GTTCGGG
*
2958254 TTGAGTCGG
1 TCGAGTCGG
2958263 GTTTAGGGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
31 5 0.15
32 16 0.47
33 13 0.38
ACGTcount: A:0.15, C:0.08, G:0.31, T:0.46
Consensus pattern (33 bp):
TCGAGTCGGATTTTTTCAAATTTTGAGTTCGGG
Found at i:2965358 original size:21 final size:21
Alignment explanation
Indices: 2965329--2965399 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 21
2965319 CCCCCCATAA
2965329 ATTAATTTATGAAATGGCATT
1 ATTAATTTATGAAATGGCATT
* *** *
2965350 ATT-ATTT-TAAAACCCCCATAA
1 ATTAATTTATGAAA-TGGCAT-T
2965371 ATTAATTTATGAAATGGCATT
1 ATTAATTTATGAAATGGCATT
2965392 ATT-ATTTA
1 ATTAATTTA
2965400 AAAAAACCTA
Statistics
Matches: 36, Mismatches: 10, Indels: 9
0.65 0.18 0.16
Matches are distributed among these distances:
19 4 0.11
20 12 0.33
21 9 0.25
22 7 0.19
23 4 0.11
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.42
Consensus pattern (21 bp):
ATTAATTTATGAAATGGCATT
Found at i:2965379 original size:42 final size:43
Alignment explanation
Indices: 2965298--2965403 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 43
2965288 TTCGTAAAAT
2965298 AATGGCATTATTATTTTAAAACCCCCCATAAATTAATTTATGA
1 AATGGCATTATTATTTTAAAACCCCCCATAAATTAATTTATGA
2965341 AATGGCATTATTATTTTAAAA-CCCCCATAAATTAATTTATGA
1 AATGGCATTATTATTTTAAAACCCCCCATAAATTAATTTATGA
*
2965383 AATGGCATTATTATTTAAAAA
1 AATGGCATTATTATTTTAAAA
2965404 AACCTAAGCT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
42 41 0.66
43 21 0.34
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.38
Consensus pattern (43 bp):
AATGGCATTATTATTTTAAAACCCCCCATAAATTAATTTATGA
Found at i:2971017 original size:12 final size:12
Alignment explanation
Indices: 2971000--2971048 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
2970990 ATAAATCAAT
2971000 TAAACGAGCTTA
1 TAAACGAGCTTA
2971012 TAAACGAG-TTGA
1 TAAACGAGCTT-A
* *
2971024 TAAGCAAGCTTA
1 TAAACGAGCTTA
2971036 TAAACGAGCTTA
1 TAAACGAGCTTA
2971048 T
1 T
2971049 TCATGAACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 2 0.06
12 27 0.87
13 2 0.06
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (12 bp):
TAAACGAGCTTA
Found at i:2974344 original size:41 final size:41
Alignment explanation
Indices: 2974287--2974557 Score: 307
Period size: 41 Copynumber: 6.7 Consensus size: 41
2974277 TTTTTAGACA
* * * *
2974287 CGTTTTTAGACAAACGCCGCTATATACTCGTAATATAGTGG
1 CGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGG
* * *
2974328 CGTTTTTATACAAACGCCGCTAAAGACGCGTACTTTAGTGA
1 CGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGG
* *
2974369 CGTTTTTAATACAGAA-GCCGCTATAGACTCATATTTTAGTGG
1 CGTTTTT-ATACA-AACGCCGCTATAGACTCGTACTTTAGTGG
* * *
2974411 TGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGT--
1 CGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGG
* * *
2974450 -ATTTTTATATAAACGCCGCTAAAGACTCGTACTTTAGTGG
1 CGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGG
* ** *
2974490 CGTTTTTATATAAACATCGCTATAGACTCGTACTTTAGTGA
1 CGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGG
**
2974531 CACTTTTATACAAACGCCGCTATAGAC
1 CGTTTTTATACAAACGCCGCTATAGAC
2974558 CTATGCTTTA
Statistics
Matches: 196, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
38 35 0.18
40 2 0.01
41 125 0.64
42 32 0.16
43 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (41 bp):
CGTTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGG
Found at i:2974417 original size:83 final size:82
Alignment explanation
Indices: 2974286--2974557 Score: 345
Period size: 83 Copynumber: 3.3 Consensus size: 82
2974276 ATTTTTAGAC
* * *
2974286 ACGTTTTTAGACAAACGCCGCTATATACTCGTAATATAGTGGCGTTTTTATACAAACGCCGCTAA
1 ACGTTTTTATACAAACGCCGCTATAGACTCGTAATTTAGTGGCGTTTTTATACAAACGCCGCTAA
*
2974351 AGACGCGTACTTTAGTG
66 AGACTCGTACTTTAGTG
* * *
2974368 ACGTTTTTAATACAGAA-GCCGCTATAGACTCATATTTTAGTGGTGTTTTTATACAAACGCCGCT
1 ACGTTTTT-ATACA-AACGCCGCTATAGACTCGTAATTTAGTGGCGTTTTTATACAAACGCCGCT
*
2974432 AAAGACTCATACTTTAGT-
64 AAAGACTCGTACTTTAGTG
* * * * ** *
2974450 A--TTTTTATATAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATATAAACATCGCTAT
1 ACGTTTTTATACAAACGCCGCTATAGACTCGTAATTTAGTGGCGTTTTTATACAAACGCCGCTAA
2974513 AGACTCGTACTTTAGTG
66 AGACTCGTACTTTAGTG
**
2974530 ACACTTTTATACAAACGCCGCTATAGAC
1 ACGTTTTTATACAAACGCCGCTATAGAC
2974558 CTATGCTTTA
Statistics
Matches: 163, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
78 2 0.01
79 60 0.37
80 6 0.04
82 31 0.19
83 62 0.38
84 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (82 bp):
ACGTTTTTATACAAACGCCGCTATAGACTCGTAATTTAGTGGCGTTTTTATACAAACGCCGCTAA
AGACTCGTACTTTAGTG
Found at i:2974568 original size:120 final size:121
Alignment explanation
Indices: 2974330--2974557 Score: 318
Period size: 121 Copynumber: 1.9 Consensus size: 121
2974320 TATAGTGGCG
2974330 TTTTTATACAAACGCCGCTAAAGACGCGTACTTTAGTGACGTTTTTAATACAGAAGCCGCTATAG
1 TTTTTATACAAACGCCGCTAAAGACGCGTACTTTAGTGACGTTTTTAATACAGAAGCCGCTATAG
* ****
2974395 ACTCATATTTTAGTGGTGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTA
66 ACTCATACTTTAGTGACACTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTA
* * * *
2974451 TTTTTATATAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATATA-A-ACA-TCGCTAT
1 TTTTTATACAAACGCCGCTAAAGACGCGTACTTTAGTGACGTTTTTA-ATACAGA-AGCCGCTAT
* *
2974513 AGACTCGTACTTTAGTGACACTTTTATACAAACGCCGCTATAGAC
64 AGACTCATACTTTAGTGACACTTTTATACAAACGCCGCTAAAGAC
2974558 CTATGCTTTA
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
120 45 0.48
121 46 0.49
122 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (121 bp):
TTTTTATACAAACGCCGCTAAAGACGCGTACTTTAGTGACGTTTTTAATACAGAAGCCGCTATAG
ACTCATACTTTAGTGACACTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTA
Found at i:2978095 original size:86 final size:85
Alignment explanation
Indices: 2977951--2978173 Score: 268
Period size: 86 Copynumber: 2.6 Consensus size: 85
2977941 GTAATTAGCA
* * * * * *
2977951 GCGTTTGTATCCAAAACGCCGCTATAAATCTGACATTTTGTGGCGTTTGTATAAAAAAACGCTGC
1 GCGTTTGTATCAAAAACACCGCTATAGATCTGACCTTTTGCGGCGTTTGTATAAAAAAACGCCGC
*
2978016 TATAAATCTG-ACTTTTTGCG
66 TATAAATATGAAC-TTTTGCG
* * * **
2978036 GCGTTTTTATCCAAAAATATCGCTATAGATCTGACCTTTTGCGGCGTTTGTATCCAAAAACGCCG
1 GCGTTTGTAT-CAAAAACACCGCTATAGATCTGACCTTTTGCGGCGTTTGTATAAAAAAACGCCG
*
2978101 CTATAGATATGAACTTTTGCG
65 CTATAAATATGAACTTTTGCG
* * * *
2978122 GCGTTTGTATCAAAAACACCACTATAGATATGATCTTTTGCGACGTTTGTAT
1 GCGTTTGTATCAAAAACACCGCTATAGATCTGACCTTTTGCGGCGTTTGTAT
2978174 TTCACAAACA
Statistics
Matches: 116, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
85 45 0.39
86 69 0.59
87 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (85 bp):
GCGTTTGTATCAAAAACACCGCTATAGATCTGACCTTTTGCGGCGTTTGTATAAAAAAACGCCGC
TATAAATATGAACTTTTGCG
Found at i:2978149 original size:42 final size:42
Alignment explanation
Indices: 2977951--2978173 Score: 227
Period size: 43 Copynumber: 5.2 Consensus size: 42
2977941 GTAATTAGCA
* * * *
2977951 GCGTTTGTATCCAAAACGCCGCTATAAATCTG-ACATTTTGTG
1 GCGTTTGTATCAAAAACACCGCTATAGATCTGAAC-TTTTGCG
* *
2977993 GCGTTTGTAT-AAAAAAACGCTGCTATAAATCTG-ACTTTTTGCG
1 GCGTTTGTATCAAAAACAC-C-GCTATAGATCTGAAC-TTTTGCG
* * * *
2978036 GCGTTTTTATCCAAAAATATCGCTATAGATCTGACCTTTTGCG
1 GCGTTTGTAT-CAAAAACACCGCTATAGATCTGAACTTTTGCG
* *
2978079 GCGTTTGTATCCAAAAACGCCGCTATAGATATGAACTTTTGCG
1 GCGTTTGTAT-CAAAAACACCGCTATAGATCTGAACTTTTGCG
* * *
2978122 GCGTTTGTATCAAAAACACCACTATAGATATGATCTTTTGCG
1 GCGTTTGTATCAAAAACACCGCTATAGATCTGAACTTTTGCG
*
2978164 ACGTTTGTAT
1 GCGTTTGTAT
2978174 TTCACAAACA
Statistics
Matches: 156, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
41 5 0.03
42 49 0.31
43 94 0.60
44 2 0.01
45 6 0.04
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (42 bp):
GCGTTTGTATCAAAAACACCGCTATAGATCTGAACTTTTGCG
Found at i:2979414 original size:19 final size:18
Alignment explanation
Indices: 2979388--2979426 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2979378 GGGATTTCGA
* *
2979388 TGAAATTTTAATTTAATT
1 TGAAAATTTAAATTAATT
2979406 TGAAAATTTAAATTAATT
1 TGAAAATTTAAATTAATT
2979424 TGA
1 TGA
2979427 TTTGGAGTCT
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:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (18 bp):
TGAAAATTTAAATTAATT
Found at i:2985558 original size:24 final size:25
Alignment explanation
Indices: 2985531--2985589 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
2985521 GTATTTAGTA
*
2985531 TTTAAATTATC-AATTTTTATTCGT
1 TTTAAATTATCAAACTTTTATTCGT
*
2985555 TTT-AA-TATCTAAACTTTTATTCTT
1 TTTAAATTATC-AAACTTTTATTCGT
2985579 TTTAAAATTAT
1 TTT-AAATTAT
2985590 ATCGAACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 4 0.14
23 2 0.07
24 17 0.61
26 2 0.07
27 3 0.11
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (25 bp):
TTTAAATTATCAAACTTTTATTCGT
Found at i:2988020 original size:28 final size:29
Alignment explanation
Indices: 2987982--2988037 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
2987972 GACATGGTAT
2987982 TTTTATATATTATTAAATATAAAATAATA
1 TTTTATATATTATTAAATATAAAATAATA
*
2988011 TTTTAT-TATTATTAAATTTAAAATAAT
1 TTTTATATATTATTAAATATAAAATAAT
2988038 CAACATCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTTATATATTATTAAATATAAAATAATA
Found at i:2993138 original size:57 final size:57
Alignment explanation
Indices: 2993050--2993162 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
2993040 TCATTCGTAT
2993050 AGATCAGGTAAAAGGAAAGGATATGATCTAAAGATTATATAAAGTATGAGACATTTG
1 AGATCAGGTAAAAGGAAAGGATATGATCTAAAGATTATATAAAGTATGAGACATTTG
* *
2993107 AGATCAGGTAAAAGGAGAGGATATGATCTAAAGATTATATAAAGTATGGGACATTT
1 AGATCAGGTAAAAGGAAAGGATATGATCTAAAGATTATATAAAGTATGAGACATTT
2993163 ATCATAAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.44, C:0.05, G:0.24, T:0.27
Consensus pattern (57 bp):
AGATCAGGTAAAAGGAAAGGATATGATCTAAAGATTATATAAAGTATGAGACATTTG
Found at i:2994522 original size:25 final size:24
Alignment explanation
Indices: 2994468--2994522 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
2994458 AATAAAGTGT
* *
2994468 CGTTCTCTTCAACCTTTCTGCTGC
1 CGTTCTCTTCAACCTTTCTACCGC
** *
2994492 TATTCTCTTCAAACTTTTCTACCGC
1 CGTTCTCTTC-AACCTTTCTACCGC
2994517 CGTTCT
1 CGTTCT
2994523 ACTCCACTAT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.13, C:0.35, G:0.09, T:0.44
Consensus pattern (24 bp):
CGTTCTCTTCAACCTTTCTACCGC
Found at i:2998664 original size:14 final size:14
Alignment explanation
Indices: 2998635--2998672 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2998625 ATTTTATATT
2998635 AAATTAA-AAATCA
1 AAATTAATAAATCA
*
2998648 AAATTAATAAATTA
1 AAATTAATAAATCA
2998662 AAATTCAATAA
1 AAATT-AATAA
2998673 CTAAATTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.32
14 10 0.45
15 5 0.23
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATTAATAAATCA
Found at i:2999896 original size:39 final size:38
Alignment explanation
Indices: 2999816--2999901 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 38
2999806 CTTTTTTTAT
* *
2999816 ATTTTTAATTTTGTAAAAAAATTATATAAATATTATGA
1 ATTTATAATTTTGTAAAAAAATTATATAAATATTATCA
* *
2999854 ATTTATAATTTTTTAAAGAAAA-TATATAAATATTTTACA
1 ATTTATAATTTTGTAAA-AAAATTATATAAATATTAT-CA
*
2999893 ATTTGTAAT
1 ATTTATAAT
2999902 ATTATACAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 28 0.68
39 13 0.32
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.48
Consensus pattern (38 bp):
ATTTATAATTTTGTAAAAAAATTATATAAATATTATCA
Found at i:3000060 original size:19 final size:20
Alignment explanation
Indices: 3000036--3000073 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3000026 CCAGTAATCC
3000036 TATTCCC-CTGGTAATCTTT
1 TATTCCCACTGGTAATCTTT
3000055 TATTCCCACTGGTAATCTT
1 TATTCCCACTGGTAATCTT
3000074 ACATTCCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.18, C:0.26, G:0.11, T:0.45
Consensus pattern (20 bp):
TATTCCCACTGGTAATCTTT
Found at i:3000079 original size:20 final size:19
Alignment explanation
Indices: 3000037--3000080 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
3000027 CAGTAATCCT
**
3000037 ATTCCCCTGGTAATCTTTT
1 ATTCCCCTGGTAATCTTAC
3000056 ATTCCCACTGGTAATCTTAC
1 ATTCCC-CTGGTAATCTTAC
3000076 ATTCC
1 ATTCC
3000081 GTGAACTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.20, C:0.30, G:0.09, T:0.41
Consensus pattern (19 bp):
ATTCCCCTGGTAATCTTAC
Found at i:3004882 original size:6 final size:6
Alignment explanation
Indices: 3004871--3004898 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3004861 TTGCATGTCC
3004871 TTTCAG TTTCAG TTTCAG TTTCAG TTTC
1 TTTCAG TTTCAG TTTCAG TTTCAG TTTC
3004899 CATTTTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.14, T:0.54
Consensus pattern (6 bp):
TTTCAG
Found at i:3010458 original size:55 final size:55
Alignment explanation
Indices: 3010399--3010898 Score: 343
Period size: 55 Copynumber: 9.1 Consensus size: 55
3010389 GTCAGGATAA
* *
3010399 ATAAGACTTGAAAAATCTTCA-AATAACGAG-CTTGCTCCCTATTCCTTCAG-GAAGT
1 ATAAGACTTGAACAATCTTCATAA-AACGAGTC-TGCTCCCTATTCATTCAGAG-AGT
* * * *
3010454 ATAAGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTATTCATTCAGAGAGT
1 ATAAGACTTGAACAATCTTCATAAAACGAGTCTGCTCCCTATTCATTCAGAGAGT
* * * * * *
3010509 ATAAGACTTGAACAATCTTAAAAAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGT
1 ATAAGACTTGAACAATCTT-CATAAAACGAGTCTGCTCCCTATTCATTCAGAGAGT
* * *
3010565 AT-AGAACTAAGAA-AATCTTCA-ATAAAC-AGGTCCGCTCCCTATTCTTTCAGAGAGT
1 ATAAG-ACT-TGAACAATCTTCATA-AAACGA-GTCTGCTCCCTATTCATTCAGAGAGT
* * * * *
3010620 ATAGGAC-T---CAATCTTTA-ACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGT
1 ATAAGACTTGAACAATCTTCATA-AAACGAGTCTGCTCCCTATTCATTCAGAGAGT
* * * * * * *
3010671 AT-AGAACTCGAGCAATCTTCATAAAACGGGTATGTTCTCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCATAAAACGAGTCTGCTCCCTATTCATTCAGAGAGT
* * * * *
3010726 AT-AGAACTCGAACAATCTTCA-ACAAACGTGTCCGCTCTCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCATA-AAACGAGTCTGCTCCCTATTCATTCAGAGAGT
* * * * *
3010781 AT-AGAACTCGAACAATCTTCATGAAACGAGTCCGCTCTCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCATAAAACGAGTCTGCTCCCTATTCATTCAGAGAGT
* * ** * *
3010836 AT-AGAACTCGAACAATCTTCA-ACGAACTTGTCCGCTCCCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCATA-AAACGAGTCTGCTCCCTATTCATTCAGAGAGT
*
3010891 ATAGGACT
1 ATAAGACT
3010899 CAATCTTCAA
Statistics
Matches: 379, Mismatches: 45, Indels: 42
0.81 0.10 0.09
Matches are distributed among these distances:
50 1 0.00
51 41 0.11
54 2 0.01
55 284 0.75
56 48 0.13
57 3 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (55 bp):
ATAAGACTTGAACAATCTTCATAAAACGAGTCTGCTCCCTATTCATTCAGAGAGT
Found at i:3010784 original size:110 final size:110
Alignment explanation
Indices: 3010432--3010899 Score: 594
Period size: 110 Copynumber: 4.3 Consensus size: 110
3010422 TAACGAGCTT
* * *
3010432 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTA
* * * * *
3010495 TTCATTCAGAGAGTATA-AGACTTGAACAATCTTAAAAAAAACGGGTCC
64 TTCCTTCAGAGAGTATAGA-ACTCGAACAATCTT-CAACAAACGTGTCC
* * * *
3010543 GCTCTCTATTCCTTCAGAGAGTATAGAACTAAGAA-AATCTTCA-ATAAACAGGTCCGCTCCCTA
1 GCTCCCTATTCCTTCAGAGAGTATAGAACT-CGAACAATCTTCATA-AAACGGGTCCGCTCTCTA
* * *
3010606 TTCTTTCAGAGAGTATAGGACT----CAATCTTTAACAAACGTGTCC
64 TTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* ** *
3010649 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTATGTTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
3010714 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * *
3010759 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAACGAGTCCGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
* *
3010824 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCC
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
*
3010869 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC
3010900 AATCTTCAAC
Statistics
Matches: 312, Mismatches: 34, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
105 2 0.01
106 81 0.26
107 8 0.03
110 151 0.48
111 65 0.21
112 5 0.02
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (110 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
Found at i:3010915 original size:55 final size:53
Alignment explanation
Indices: 3010465--3010915 Score: 397
Period size: 55 Copynumber: 8.3 Consensus size: 53
3010455 TAAGACTCGA
* * *
3010465 ACAATCTTCATA-AAATG-TGTCTGCTCTCTATTCATTCAGAGAGTATA-AGACTT
1 ACAATCTTCA-ACAAACGATGTCCGCTCTCTATTCCTTCAGAGAGTATAGA-AC-T
* * *
3010518 GAACAATCTTAAAAAAAACG-GGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 --ACAATCTT-CAACAAACGATGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
* * * * * *
3010573 AAGAAAATCTTCAATAAAC-AGGTCCGCTCCCTATTCTTTCAGAGAGTATAGGACT
1 ---ACAATCTTCAACAAACGATGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
* *
3010628 -CAATCTTTAACAAACG-TGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACT
1 ACAATCTTCAACAAACGATGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
* ** *
3010679 CGAGCAATCTTCATA-AAACG-GGTATGTTCTCTATTCCTTCAGAGAGTATAGAACT
1 --A-CAATCTTCA-ACAAACGATGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
3010734 CGAACAATCTTCAACAAACG-TGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 ---ACAATCTTCAACAAACGATGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
**
3010789 CGAACAATCTTCATGAAACGA-GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
1 ---ACAATCTTCAACAAACGATGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
* * * *
3010844 CGAACAATCTTCAACGAAC-TTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
1 ---ACAATCTTCAACAAACGATGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
3010899 -CAATCTTCAACAAACGA
1 ACAATCTTCAACAAACGA
3010916 GTTTGCTTCA
Statistics
Matches: 339, Mismatches: 41, Indels: 35
0.82 0.10 0.08
Matches are distributed among these distances:
51 58 0.17
54 1 0.00
55 236 0.70
56 43 0.13
57 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.28
Consensus pattern (53 bp):
ACAATCTTCAACAAACGATGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACT
Found at i:3012322 original size:40 final size:39
Alignment explanation
Indices: 3012278--3012429 Score: 123
Period size: 40 Copynumber: 3.8 Consensus size: 39
3012268 TTTATTCTTC
3012278 TTTTT-TTATTTTTCTCTTTCATTTTTTCTTCCATTTTCCA
1 TTTTTATTATTTTTCT-TTTCATTTTTTCTT-CATTTTCCA
* * * *
3012318 TTTTTTCTCTTTTTTTCTTTTCGTTTTTTCCATCATTTTTCC-
1 -TTTTTAT-TATTTTTCTTTTCATTTTTT-CTTCA-TTTTCCA
* * * *
3012360 TTTTTCTCATTTTTCTTTTCTTTTTTTTTTC-TTCTTCTCA
1 TTTTTATTATTTTTCTTTTCATTTTTTCTTCATT-TTC-CA
3012400 TTTTTATTATTATTT-TTTTCATTTTTTCTT
1 TTTTTATTATT-TTTCTTTTCATTTTTTCTT
3012430 TTTCTCTTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
37 2 0.02
38 3 0.03
39 3 0.03
40 39 0.43
41 15 0.16
42 13 0.14
43 16 0.18
ACGTcount: A:0.08, C:0.18, G:0.01, T:0.74
Consensus pattern (39 bp):
TTTTTATTATTTTTCTTTTCATTTTTTCTTCATTTTCCA
Found at i:3012331 original size:41 final size:41
Alignment explanation
Indices: 3012277--3012386 Score: 104
Period size: 42 Copynumber: 2.7 Consensus size: 41
3012267 TTTTATTCTT
* *
3012277 CTTTTTT-TATTTTTCTCTTTCATTTTTT-CTTCCA-TTTTC
1 CTTTTTTCTCTTTTTCTCTTTCATTTTTTCCAT-CATTTTTC
* *
3012316 CATTTTTTCTCTTTTTTTCTTTTCGTTTTTTCCATCATTTTTC
1 C-TTTTTTCTCTTTTTCTC-TTTCATTTTTTCCATCATTTTTC
*
3012359 C-TTTTTCTCATTTTTCT-TTTCTTTTTTT
1 CTTTTTTCTC-TTTTTCTCTTTCATTTTTT
3012387 TTTCTTCTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
39 1 0.02
40 16 0.27
41 16 0.27
42 18 0.31
43 8 0.14
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (41 bp):
CTTTTTTCTCTTTTTCTCTTTCATTTTTTCCATCATTTTTC
Found at i:3012388 original size:31 final size:30
Alignment explanation
Indices: 3012353--3012443 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 30
3012343 TTTTCCATCA
* *
3012353 TTTTTCCTTTTTCTCATTTTTCTTTTCTTTT
1 TTTTTCCTTTTTCTCATTTTTCTTAT-TATT
* * *
3012384 TTTTTTCTTCTTCTCATTTTTATTATTATT
1 TTTTTCCTTTTTCTCATTTTTCTTATTATT
* *
3012414 TTTTTCATTTTT-TC-TTTTTCTCTTTTATT
1 TTTTTCCTTTTTCTCATTTTTCT-TATTATT
3012443 T
1 T
3012444 CTTCTTCAAG
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
28 6 0.12
29 9 0.18
30 12 0.24
31 22 0.45
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTTTCCTTTTTCTCATTTTTCTTATTATT
Found at i:3012403 original size:19 final size:16
Alignment explanation
Indices: 3012369--3012446 Score: 50
Period size: 17 Copynumber: 4.5 Consensus size: 16
3012359 CTTTTTCTCA
3012369 TTTTTCTTTTCTTTTT
1 TTTTTCTTTTCTTTTT
3012385 TTTTTCTTCTTCTCATTTT
1 TTTTTCTT-TTCT--TTTT
* *
3012404 TATTATTATTTT-TTTCAT
1 T-TT-TTCTTTTCTTT-TT
*
3012422 TTTTTCTTTTTCTCTTT
1 TTTTTC-TTTTCTTTTT
*
3012439 TATTTCTT
1 TTTTTCTT
3012447 CTTCAAGTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
16 12 0.25
17 18 0.38
18 4 0.08
19 6 0.12
20 4 0.08
21 4 0.08
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTTTTCTTTTT
Found at i:3027462 original size:20 final size:20
Alignment explanation
Indices: 3027437--3027527 Score: 65
Period size: 20 Copynumber: 5.0 Consensus size: 20
3027427 TAAATTAAAT
3027437 ATTAGATAGGAA-CAGTTTTA
1 ATTAGATA-GAATCAGTTTTA
*
3027457 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
3027477 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
3027489 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
3027509 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
3027528 TTATTCTATT
Statistics
Matches: 54, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 5 0.09
20 35 0.65
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.44
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:3027555 original size:53 final size:52
Alignment explanation
Indices: 3027436--3027588 Score: 263
Period size: 53 Copynumber: 2.9 Consensus size: 52
3027426 CTAAATTAAA
* *
3027436 TATTAGATAGGAACAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
3027488 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
*
3027541 TATTAGATATGATCATTTTTAATTAGATAGAATCA-TTTTTATTCTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATT
3027589 GCTAATTTTA
Statistics
Matches: 97, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 13 0.13
52 34 0.35
53 50 0.52
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:3027567 original size:20 final size:20
Alignment explanation
Indices: 3027542--3027581 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3027532 TCTATTAGTT
3027542 ATTAGATATG-ATCATTTTTA
1 ATTAGATA-GAATCATTTTTA
3027562 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
3027582 TTCTATTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:3037391 original size:19 final size:19
Alignment explanation
Indices: 3037367--3037405 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3037357 GGGGGATGGT
3037367 AAGTCTATTTCGTTTTGGA
1 AAGTCTATTTCGTTTTGGA
3037386 AAGTCTATTTCGTTTTGGA
1 AAGTCTATTTCGTTTTGGA
3037405 A
1 A
3037406 TGATGTTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46
Consensus pattern (19 bp):
AAGTCTATTTCGTTTTGGA
Found at i:3042484 original size:19 final size:19
Alignment explanation
Indices: 3042457--3042495 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3042447 TGGGAAAATG
*
3042457 TTATTTCTTTTGAATGAAA
1 TTATGTCTTTTGAATGAAA
3042476 TTATGTCTTTTGAATGAAA
1 TTATGTCTTTTGAATGAAA
3042495 T
1 T
3042496 GTTGTTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.51
Consensus pattern (19 bp):
TTATGTCTTTTGAATGAAA
Found at i:3046818 original size:36 final size:35
Alignment explanation
Indices: 3046735--3046849 Score: 160
Period size: 34 Copynumber: 3.2 Consensus size: 35
3046725 GCACCGTAGG
* * * *
3046735 TATGTGGCTTCAAGCCTTCATAATTCAGTTCGAGA
1 TATGTGGCCTCGAGCTTTCATAATTCAGCTCGAGA
3046770 T-TGTGGCCTCGAGCTTTCATAATTCAGCTCGAGA
1 TATGTGGCCTCGAGCTTTCATAATTCAGCTCGAGA
3046804 TCATGTGGCCTCGAGCTTTCATAATTCAGCTCGAAGA
1 T-ATGTGGCCTCGAGCTTTCATAATTCAGCTCG-AGA
3046841 CTATGTGGC
1 -TATGTGGC
3046850 TAACTCGCTA
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
34 30 0.42
35 1 0.01
36 30 0.42
37 10 0.14
38 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (35 bp):
TATGTGGCCTCGAGCTTTCATAATTCAGCTCGAGA
Found at i:3052107 original size:220 final size:221
Alignment explanation
Indices: 3051725--3052164 Score: 873
Period size: 220 Copynumber: 2.0 Consensus size: 221
3051715 GTCGGACGAT
3051725 ATAAGCTCAGCTCACAGGTTTTTCAGCTGGAAGTTGGATTATTATCAAATGCTCGATAAAAGTCA
1 ATAAGCTCAGCTCACAGGTTTTTCAGCTGGAAGTTGGATTATTATCAAATGCTCGATAAAAGTCA
3051790 ACTTGTTAATCTTCTCGATTTCCTTTCCTAATCGCAGGCTCGATCCAAAACCGAAACCGCAAGAG
66 ACTTGTTAATCTTCTCGATTTCCTTTCCTAATCGCAGGCTCGATCCAAAACCGAAACCGCAAGAG
3051855 TGAAGGCGGCGCAAGAGGCACACAAAGAACTTAAAAACGCTAGGCAAGAAGCGTTGCAGAGAAAG
131 TGAAGGCGGCGCAAGAGGCACACAAAGAACTTAAAAACGCTAGGCAAGAAGCGTTGCAGAGAAAG
3051920 AAGGCAGAG-AGAAGAAGATGTTGGG
196 AAGGCAGAGAAGAAGAAGATGTTGGG
3051945 ATAAGCTCAGCTCACAGGTTTTTCAGCTGGAAGTTGGATTATTATCAAATGCTCGATAAAAGTCA
1 ATAAGCTCAGCTCACAGGTTTTTCAGCTGGAAGTTGGATTATTATCAAATGCTCGATAAAAGTCA
3052010 ACTTGTTAATCTTCTCGATTTCCTTTCCTAATCGCAGGCTCGATCCAAAACCGAAACCGCAAGAG
66 ACTTGTTAATCTTCTCGATTTCCTTTCCTAATCGCAGGCTCGATCCAAAACCGAAACCGCAAGAG
3052075 TGAAGGCGGCGCAAGAGGCACACAAAGAACTTAAAAACGCTAGGCAAGAAGCGTTGCAGAGAAAG
131 TGAAGGCGGCGCAAGAGGCACACAAAGAACTTAAAAACGCTAGGCAAGAAGCGTTGCAGAGAAAG
3052140 AAGGCAGAGAAGAAGAAGATGTTGG
196 AAGGCAGAGAAGAAGAAGATGTTGG
3052165 AGGAGGCAGA
Statistics
Matches: 219, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
220 204 0.93
221 15 0.07
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (221 bp):
ATAAGCTCAGCTCACAGGTTTTTCAGCTGGAAGTTGGATTATTATCAAATGCTCGATAAAAGTCA
ACTTGTTAATCTTCTCGATTTCCTTTCCTAATCGCAGGCTCGATCCAAAACCGAAACCGCAAGAG
TGAAGGCGGCGCAAGAGGCACACAAAGAACTTAAAAACGCTAGGCAAGAAGCGTTGCAGAGAAAG
AAGGCAGAGAAGAAGAAGATGTTGGG
Found at i:3052926 original size:22 final size:21
Alignment explanation
Indices: 3052900--3052941 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
3052890 AATTTATGGA
*
3052900 AACATTGTAAAGAATAATAAAC
1 AACATTATAAAGAAT-ATAAAC
3052922 AACATTATAAAGAATATAAA
1 AACATTATAAAGAATATAAA
3052942 TATAAACGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (21 bp):
AACATTATAAAGAATATAAAC
Found at i:3057617 original size:2 final size:2
Alignment explanation
Indices: 3057604--3057634 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3057594 ATAAAATACC
*
3057604 AT AT AC 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
3057635 AACCTACCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3060371 original size:42 final size:42
Alignment explanation
Indices: 3060312--3060431 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
3060302 TTTCCCTGAA
*
3060312 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
* *
3060354 TTCCCATGTTTGTTTCACATAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
3060396 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
3060432 TGTAATTCAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:3060654 original size:30 final size:29
Alignment explanation
Indices: 3060612--3060686 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 29
3060602 CAAAATATTA
*
3060612 ATTATTAAAATAT-TTAAAATATTTATTAAT
1 ATTA-TAAAATATAATAAAATATTT-TTAAT
**
3060642 ATTATAATAATATAATATTATATTTTTAAT
1 ATTATAA-AATATAATAAAATATTTTTAAT
3060672 ATTATATAAA-ATAAT
1 ATTATA-AAATATAAT
3060687 CAATTATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 8 0.21
30 22 0.56
31 9 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTATAAAATATAATAAAATATTTTTAAT
Found at i:3060655 original size:8 final size:8
Alignment explanation
Indices: 3060605--3060677 Score: 53
Period size: 8 Copynumber: 9.1 Consensus size: 8
3060595 TTTTCATCAA
3060605 AATATTA-
1 AATATTAT
* *
3060612 ATTATTAA
1 AATATTAT
*
3060620 AATATTTAA
1 AATA-TTAT
3060629 AATATTTATT
1 AATA-TTA-T
3060639 AATATTAT
1 AATATTAT
*
3060647 AATAATAT
1 AATATTAT
3060655 AATATTAT
1 AATATTAT
*
3060663 -AT-TTTT
1 AATATTAT
3060669 AATATTAT
1 AATATTAT
3060677 A
1 A
3060678 TAAAATAATC
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
6 3 0.06
7 10 0.19
8 22 0.41
9 15 0.28
10 4 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (8 bp):
AATATTAT
Found at i:3060673 original size:49 final size:47
Alignment explanation
Indices: 3060620--3060732 Score: 115
Period size: 51 Copynumber: 2.3 Consensus size: 47
3060610 TAATTATTAA
**
3060620 AATATTTAAAATATTTATTAATATTATAATAATATA-ATATTATATTTTT
1 AATATTTAAAATATCAATT-ATATTATAAT-ATA-AGATATTATATTTTT
3060669 AATATTATATAAAATAATCAATTATATTATAATATAAGATATTATATTTTT
1 AATA-T-T-TAAAAT-ATCAATTATATTATAATATAAGATATTATATTTTT
3060720 -AT-TTTAATAATAT
1 AATATTTAA-AATAT
3060733 ATAATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 15
0.77 0.03 0.21
Matches are distributed among these distances:
46 5 0.09
47 4 0.07
48 1 0.02
49 4 0.07
50 4 0.07
51 17 0.30
52 16 0.29
53 5 0.09
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (47 bp):
AATATTTAAAATATCAATTATATTATAATATAAGATATTATATTTTT
Found at i:3060693 original size:31 final size:31
Alignment explanation
Indices: 3060630--3060703 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
3060620 AATATTTAAA
*
3060630 ATATTTATTAATATTATAATAATATAATATT
1 ATATTTATTAATATTATAATAAAATAATATT
3060661 ATATTT-TTAATATTAT-ATAAAATAATCAATT
1 ATATTTATTAATATTATAATAAAATAAT--ATT
3060692 ATA-TTA-TAATAT
1 ATATTTATTAATAT
3060704 AAGATATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 9 0.23
30 18 0.46
31 12 0.31
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (31 bp):
ATATTTATTAATATTATAATAAAATAATATT
Found at i:3060734 original size:24 final size:23
Alignment explanation
Indices: 3060702--3060748 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
3060692 ATATTATAAT
* *
3060702 ATAAGATATTATATTTTTATTTTA
1 ATAAGATATAATAATTTT-TTTTA
*
3060726 ATAATATATAATAATTTTTTTTA
1 ATAAGATATAATAATTTTTTTTA
3060749 TATTTAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATAAGATATAATAATTTTTTTTA
Found at i:3060744 original size:26 final size:28
Alignment explanation
Indices: 3060713--3060790 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 28
3060703 TAAGATATTA
3060713 TATTTTTATTTTAATAATATATAATAAT
1 TATTTTTATTTTAATAATATATAATAAT
*
3060741 TTTTTTTATATTTAATAATGA-ATAATAA-
1 TATTTTTAT-TTTAATAAT-ATATAATAAT
*
3060769 TATTTATATATTTCAATAATAT
1 TATTT-T-TATTTTAATAATAT
3060791 TTTAGTAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
28 13 0.31
29 25 0.60
30 4 0.10
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
TATTTTTATTTTAATAATATATAATAAT
Found at i:3060792 original size:11 final size:10
Alignment explanation
Indices: 3060722--3060792 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
3060712 ATATTTTTAT
3060722 TTTAATAATA
1 TTTAATAATA
*
3060732 TATAATAAT-
1 TTTAATAATA
** *
3060741 TTTTTTTATA
1 TTTAATAATA
3060751 TTTAATAATGA
1 TTTAATAAT-A
*
3060762 -ATAATAATA
1 TTTAATAATA
3060771 TTT-AT-ATA
1 TTTAATAATA
3060779 TTTCAATAATA
1 TTT-AATAATA
3060790 TTT
1 TTT
3060793 TAGTAAAGAT
Statistics
Matches: 45, Mismatches: 10, Indels: 11
0.68 0.15 0.17
Matches are distributed among these distances:
8 6 0.13
9 8 0.18
10 24 0.53
11 7 0.16
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (10 bp):
TTTAATAATA
Found at i:3060981 original size:20 final size:20
Alignment explanation
Indices: 3060956--3061019 Score: 119
Period size: 20 Copynumber: 3.2 Consensus size: 20
3060946 TTTCCAGATG
3060956 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
3060976 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
3060996 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
3061016 TTTT
1 TTTT
3061020 TTAGAATTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.44
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:3061034 original size:40 final size:40
Alignment explanation
Indices: 3060956--3061034 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
3060946 TTTCCAGATG
* **
3060956 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
** *
3060996 TTTTACAGAAATGTAATTCATTTTTTAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
3061035 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:3061060 original size:30 final size:30
Alignment explanation
Indices: 3061008--3061089 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
3060998 TTACAGAAAT
*
3061008 GTAATTCATTTTTTAG-AATTCAAATTCCA
1 GTAATTCATTTTCTAGTAATTCAAATTCCA
*
3061037 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCTAGTAATTCAAATTCCA
**
3061067 GTAATTCAAATTCTAGTAATTCA
1 GTAATTCATTTTCTAGTAATTCA
3061090 TTTTCTGGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 14 0.30
30 33 0.70
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTCTAGTAATTCAAATTCCA
Found at i:3061095 original size:15 final size:15
Alignment explanation
Indices: 3061024--3061089 Score: 105
Period size: 15 Copynumber: 4.4 Consensus size: 15
3061014 CATTTTTTAG
3061024 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
**
3061039 AATTCATTTTCCAGT
1 AATTCAAATTCCAGT
3061054 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
*
3061069 AATTCAAATTCTAGT
1 AATTCAAATTCCAGT
3061084 AATTCA
1 AATTCA
3061090 TTTTCTGGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:3067793 original size:20 final size:20
Alignment explanation
Indices: 3067768--3067834 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
3067758 AATTCACAAT
3067768 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
** * *
3067788 GCGAATTGGGAAATTCGCAAT
1 GCGAATAAGTAAA-TCGCAAC
3067809 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
3067829 GCGAAT
1 GCGAAT
3067835 TGGGAAAATC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
GCGAATAAGTAAATCGCAAC
Found at i:3067803 original size:41 final size:41
Alignment explanation
Indices: 3067758--3067853 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
3067748 CGATTTTCCC
*
3067758 AATTCACAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
3067799 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
3067840 AAATCGCAATGCGA
1 AATTCGCAATGCGA
3067854 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:3067807 original size:21 final size:20
Alignment explanation
Indices: 3067778--3067853 Score: 89
Period size: 21 Copynumber: 3.7 Consensus size: 20
3067768 GCGAATAAGT
3067778 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATTGGG
* ** *
3067798 AAATTCGCAATGCGAATAAGT
1 AAA-TCGCAACGCGAATTGGG
3067819 AAATCGCAACGCGAATTGGG
1 AAATCGCAACGCGAATTGGG
*
3067839 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
3067854 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (20 bp):
AAATCGCAACGCGAATTGGG
Found at i:3067866 original size:41 final size:41
Alignment explanation
Indices: 3067780--3067914 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
3067770 GAATAAGTAA
* * *
3067780 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
3067821 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
3067862 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
3067903 TTCGCAACGCGA
1 ATCGCAACGCGA
3067915 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:3067867 original size:20 final size:20
Alignment explanation
Indices: 3067842--3067936 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
3067832 AATTGGGAAA
*
3067842 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
3067862 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
3067883 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
3067903 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
3067923 TTCGCAACGCGATA
1 ATCGCAACGCGATA
3067937 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:3068152 original size:22 final size:22
Alignment explanation
Indices: 3068124--3068167 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3068114 CACTCTCTCA
3068124 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
3068146 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
3068168 TATCTAAATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:3068456 original size:20 final size:20
Alignment explanation
Indices: 3068431--3068468 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3068421 CGATTCTCTC
3068431 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
3068451 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
3068469 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:3069809 original size:18 final size:18
Alignment explanation
Indices: 3069788--3069832 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3069778 TCCACTTCGG
*
3069788 GAGCCATCACCTCGTCC-A
1 GAGCCATCACCTC-ACCTA
*
3069806 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCTA
3069824 GAGCCATCA
1 GAGCCATCA
3069833 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.27, C:0.40, G:0.16, T:0.18
Consensus pattern (18 bp):
GAGCCATCACCTCACCTA
Found at i:3070358 original size:19 final size:20
Alignment explanation
Indices: 3070304--3070370 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
3070294 TAGTTTACTT
* *
3070304 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
3070324 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
3070344 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
3070363 TCGCAACG
1 TCGCAACG
3070371 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:3070378 original size:14 final size:14
Alignment explanation
Indices: 3070359--3070416 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3070349 ATGCGAAATG
3070359 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3070373 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
3070389 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3070405 AAAATCGCAACG
1 AAAATCGCAACG
3070417 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3070401 original size:32 final size:33
Alignment explanation
Indices: 3070343--3070433 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
3070333 GGAAATGGCT
*
3070343 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
3070376 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
3070408 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
3070434 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:3070427 original size:19 final size:19
Alignment explanation
Indices: 3070304--3070438 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
3070294 TAGTTTACTT
* **
3070304 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
3070324 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
3070344 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3070363 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
3070377 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
3070395 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
3070409 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3070428 TCGCAATGCGA
1 TCGCAACGCGA
3070439 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3070469 original size:14 final size:14
Alignment explanation
Indices: 3070450--3070507 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3070440 TTGTGTTTCG
3070450 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3070464 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
3070480 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
3070496 CGTTGCGATTTT
1 CGTTGCGATTTT
3070508 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3070484 original size:32 final size:33
Alignment explanation
Indices: 3070445--3070523 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
3070435 GCGATTTGTG
3070445 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
3070477 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
3070510 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
3070524 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:3070522 original size:19 final size:19
Alignment explanation
Indices: 3070466--3070565 Score: 77
Period size: 19 Copynumber: 5.5 Consensus size: 19
3070456 GATTTTGTCG
*
3070466 TTGCGA-TTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
*
3070484 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
3070498 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
***
3070517 TTGCGATAGCCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
** *
3070537 TTGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
3070556 TTGCGATTTT
1 TTGCGATTTT
3070566 AAGTATCGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
14 6 0.09
15 3 0.04
16 4 0.06
17 4 0.06
18 9 0.13
19 23 0.34
20 18 0.27
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3070538 original size:20 final size:19
Alignment explanation
Indices: 3070508--3070562 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
3070498 TTGCGATTTT
3070508 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
*
3070527 CATTTCCGCATTGCGATAGT
1 CATTT-CGCATTGCGATAGC
*
3070547 CATTTCGCGTTGCGAT
1 CATTTCGCATTGCGAT
3070563 TTTAAGTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:3072452 original size:14 final size:14
Alignment explanation
Indices: 3072433--3072468 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3072423 ATTGTTTAAT
3072433 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3072447 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3072461 TGATTTGT
1 TGATTTGT
3072469 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3072594 original size:14 final size:15
Alignment explanation
Indices: 3072575--3072651 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
3072565 CGAAATGGCT
3072575 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
3072589 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
3072607 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
3072626 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
3072640 ATCGCAATGCGA
1 ATCGCAA-GCGA
3072652 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:3072607 original size:19 final size:19
Alignment explanation
Indices: 3072585--3072651 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
3072575 ATCGCAACGA
3072585 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3072604 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3072622 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
3072636 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
3072652 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:3072727 original size:20 final size:20
Alignment explanation
Indices: 3072677--3072727 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
3072667 GCGATATTCT
* *
3072677 CGTTGCGATAACCATTTTCG
1 CGTTGCGATAGCCATTTTCA
3072697 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGCCATTTTCA
3072717 CGTTGCGATAG
1 CGTTGCGATAG
3072728 TCAAATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:3073112 original size:14 final size:14
Alignment explanation
Indices: 3073093--3073128 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3073083 ATTGTTTAAT
3073093 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3073107 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3073121 TGATTTGT
1 TGATTTGT
3073129 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3073278 original size:19 final size:19
Alignment explanation
Indices: 3073250--3073303 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
3073240 AACGAGAAAA
*
3073250 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3073269 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3073288 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
3073304 TCGTTGCGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3074442 original size:24 final size:24
Alignment explanation
Indices: 3074386--3074444 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
3074376 AGTCAGTATT
* *
3074386 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
3074410 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
3074434 CGAATTTTGAT
1 CGAAATTTGAT
3074445 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:3074636 original size:12 final size:12
Alignment explanation
Indices: 3074619--3074643 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3074609 ATATAATCCT
3074619 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3074631 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3074643 G
1 G
3074644 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3076960 original size:19 final size:19
Alignment explanation
Indices: 3076938--3077035 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
3076928 GGAAATTACT
3076938 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3076957 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3076971 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
3076990 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
3077004 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3077023 ATCGCAACGCGAA
1 ATCGCAATGCGAA
3077036 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3076980 original size:33 final size:33
Alignment explanation
Indices: 3076938--3077031 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
3076928 GGAAATTACT
3076938 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3076971 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3077004 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3077032 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3077213 original size:14 final size:14
Alignment explanation
Indices: 3077194--3077230 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3077184 CATCAATTAA
3077194 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3077208 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3077222 ACAAATCAA
1 ACAAATCAA
3077231 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3078653 original size:21 final size:21
Alignment explanation
Indices: 3078587--3078653 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3078577 GTGAATCGGG
*
3078587 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
3078607 CTTCTTCAACGATGACAGTGGC
1 C-TCTTGAACGGTGGGAGGGGA
3078629 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
3078650 CTCT
1 CTCT
3078654 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.88
22 3 0.09
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:3078672 original size:42 final size:41
Alignment explanation
Indices: 3078587--3078709 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
3078577 GTGAATCGGG
* * * * *
3078587 CTCTTGAATGGTGGGA-GGGACTTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGAC-TC-TCGAGGATGATAGGGGC
3078629 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
3078671 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
3078710 CGAGTCGAGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.84
43 7 0.10
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:3080774 original size:19 final size:19
Alignment explanation
Indices: 3080710--3080880 Score: 199
Period size: 19 Copynumber: 9.1 Consensus size: 19
3080700 TCTTTTGGTT
*
3080710 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
3080729 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
3080749 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
** *
3080769 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
3080787 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3080802 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
3080822 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3080841 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3080860 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3080879 GA
1 GA
3080881 TTTTGGTTTC
Statistics
Matches: 135, Mismatches: 9, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
14 10 0.07
15 2 0.01
18 2 0.01
19 70 0.52
20 49 0.36
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3080834 original size:39 final size:38
Alignment explanation
Indices: 3080710--3080880 Score: 199
Period size: 39 Copynumber: 4.6 Consensus size: 38
3080700 TCTTTTGGTT
* *
3080710 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** ** *
3080749 GGAAATGACTATCGCAACGCGAAATGACTATCGCGAC-C
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
3080787 ---A-GACAATCGCAACGCGAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAA-CGC
3080822 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
3080860 GAAATGAAAATCGCAATGCGA
1 GAAATGAAAATCGCAACGCGA
3080881 TTTTGGTTTC
Statistics
Matches: 113, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
33 26 0.23
34 2 0.02
35 1 0.01
38 25 0.22
39 41 0.36
40 18 0.16
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:3080909 original size:19 final size:19
Alignment explanation
Indices: 3080876--3080946 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
3080866 AAAATCGCAA
**
3080876 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
3080895 TGCGATTTTTATTTCGCGT
1 TGCGATTTTCATTTCGCGT
**
3080914 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
*
3080934 TGCGATTCTCATT
1 TGCGATTTTCATT
3080947 CTCGAAACTA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 28 0.64
20 16 0.36
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:3081547 original size:20 final size:20
Alignment explanation
Indices: 3081462--3081575 Score: 111
Period size: 20 Copynumber: 5.7 Consensus size: 20
3081452 CGCTAAGTAA
* *
3081462 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
** * *
3081482 ATCGTGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
3081502 ATCTCGTTGCGATTCTTTATT
1 ATCGCATTGCGA-TAGTCAGT
3081523 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
3081543 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
3081563 ATCGCATTGCGAT
1 ATCGCATTGCGAT
3081576 TTTCCCAATT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 65 0.83
21 13 0.17
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:3081564 original size:61 final size:61
Alignment explanation
Indices: 3081462--3081576 Score: 158
Period size: 61 Copynumber: 1.9 Consensus size: 61
3081452 CGCTAAGTAA
* ** * *
3081462 ATCGCGTTGCGAAAGTCAGTATCGTGTTGCGAAAGTAAGTATCTCGTTGCGATTCTTTATT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATTCTTTATT
* * *
3081523 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATT
3081577 TTCCCAATTC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATTCTTTATT
Found at i:3081594 original size:61 final size:61
Alignment explanation
Indices: 3081462--3081596 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 61
3081452 CGCTAAGTAA
* ** * * * *
3081462 ATCGCGTTGCGAAAGTCAGTATCGTGTTGCGAAAGTAAGTATCTCGTTGCGATTCTTTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATTCTTCAAT
* * *
3081523 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATT-TTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATTCTT--CAAT
3081585 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
3081597 TTACTTATTC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
60 2 0.03
61 57 0.93
62 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCGATTCTTCAAT
Found at i:3099330 original size:24 final size:24
Alignment explanation
Indices: 3099303--3099371 Score: 122
Period size: 24 Copynumber: 2.9 Consensus size: 24
3099293 TCATTTTATG
3099303 CTCTACCCTTAACTTGAAACTATA
1 CTCTACCCTTAACTTGAAACTATA
3099327 CTCTA-CCTCTAACTTGAAACTATA
1 CTCTACCCT-TAACTTGAAACTATA
3099351 CTCTACCCTTAACTTGAAACT
1 CTCTACCCTTAACTTGAAACT
3099372 CTAAGTTAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.07
24 37 0.86
25 3 0.07
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.33
Consensus pattern (24 bp):
CTCTACCCTTAACTTGAAACTATA
Found at i:3100272 original size:13 final size:15
Alignment explanation
Indices: 3100232--3100272 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
3100222 ATTTTTGTCA
*
3100232 AAATTTTAAAATTCT
1 AAATTATAAAATTCT
*
3100247 AAATTATATAATT-T
1 AAATTATAAAATTCT
3100261 AAA-TATAAAATT
1 AAATTATAAAATT
3100273 ATAGATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 8 0.35
14 4 0.17
15 11 0.48
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATTATAAAATTCT
Found at i:3100685 original size:19 final size:20
Alignment explanation
Indices: 3100657--3100695 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3100647 TAATAAAGTA
*
3100657 TTATCTAAAATATT-ATTTT
1 TTATCAAAAATATTAATTTT
3100676 TTATCAAAAATATTAATTTT
1 TTATCAAAAATATTAATTTT
3100696 GTTAACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATCAAAAATATTAATTTT
Found at i:3107053 original size:17 final size:18
Alignment explanation
Indices: 3107033--3107073 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3107023 AAATTATATT
3107033 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
3107050 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
3107068 ATTAAA
1 AGTAAA
3107074 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:3114998 original size:10 final size:10
Alignment explanation
Indices: 3114978--3115031 Score: 65
Period size: 10 Copynumber: 5.4 Consensus size: 10
3114968 TTAATTTTAC
*
3114978 AAATATAAAA
1 AAATACAAAA
3114988 AAAT-CAGAAA
1 AAATACA-AAA
3114998 AAATACAAAA
1 AAATACAAAA
*
3115008 AAATTCAAAA
1 AAATACAAAA
*
3115018 AATTACAAAA
1 AAATACAAAA
3115028 AAAT
1 AAAT
3115032 TAGTATGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 1 0.03
10 34 0.92
11 2 0.05
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.17
Consensus pattern (10 bp):
AAATACAAAA
Found at i:3115031 original size:11 final size:11
Alignment explanation
Indices: 3114995--3115033 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
3114985 AAAAAATCAG
3114995 AAAAAA-TACA
1 AAAAAATTACA
3115005 AAAAAATT-C-
1 AAAAAATTACA
3115014 AAAAAATTACA
1 AAAAAATTACA
3115025 AAAAAATTA
1 AAAAAATTA
3115034 GTATGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.31
10 8 0.31
11 10 0.38
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAAATTACA
Found at i:3115032 original size:20 final size:21
Alignment explanation
Indices: 3114978--3115032 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
3114968 TTAATTTTAC
*
3114978 AAATATAAAAAAA-TCAGAAA
1 AAATACAAAAAAATTCAGAAA
3114998 AAATACAAAAAAATTCA-AAA
1 AAATACAAAAAAATTCAGAAA
*
3115018 AATTACAAAAAAATT
1 AAATACAAAAAAATT
3115033 AGTATGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 29 0.91
21 3 0.09
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (21 bp):
AAATACAAAAAAATTCAGAAA
Found at i:3121192 original size:2 final size:2
Alignment explanation
Indices: 3121185--3121216 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3121175 AAGCAAACTC
3121185 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
3121217 GTGCGCGCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3128529 original size:14 final size:14
Alignment explanation
Indices: 3128510--3128538 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3128500 CGAGTCTGGA
3128510 GAACATAAATGAAC
1 GAACATAAATGAAC
3128524 GAACATAAATGAAC
1 GAACATAAATGAAC
3128538 G
1 G
3128539 GATTAGCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (14 bp):
GAACATAAATGAAC
Found at i:3128832 original size:18 final size:19
Alignment explanation
Indices: 3128797--3128833 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3128787 CACGGAATGT
3128797 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
3128817 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
3128834 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:3129400 original size:24 final size:24
Alignment explanation
Indices: 3129368--3129424 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
3129358 GCCAACCAAA
3129368 CATGGGAATGTGGGATTCCCATCC
1 CATGGGAATGTGGGATTCCCATCC
3129392 CATGGGAATGTGGGATTCCCATCC
1 CATGGGAATGTGGGATTCCCATCC
3129416 CATGGGAAT
1 CATGGGAAT
3129425 CCCACATTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.25
Consensus pattern (24 bp):
CATGGGAATGTGGGATTCCCATCC
Found at i:3129433 original size:24 final size:24
Alignment explanation
Indices: 3129382--3129433 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3129372 GGAATGTGGG
*****
3129382 ATTCCCATCCCATGGGAATGTGGG
1 ATTCCCATCCCATGGGAATCCCAC
3129406 ATTCCCATCCCATGGGAATCCCAC
1 ATTCCCATCCCATGGGAATCCCAC
3129430 ATTC
1 ATTC
3129434 TTTGAACCAA
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:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (24 bp):
ATTCCCATCCCATGGGAATCCCAC
Found at i:3133842 original size:44 final size:44
Alignment explanation
Indices: 3133792--3133882 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
3133782 TCTGCTATAG
3133792 TCGTGTTGTGATTTACTTATTACTATCGGTTTCTACAAGATCGA
1 TCGTGTTGTGATTTACTTATTACTATCGGTTTCTACAAGATCGA
3133836 TCGTGTTGTGATTTACTTATTACTATCGGTTTCTACAAGATCGA
1 TCGTGTTGTGATTTACTTATTACTATCGGTTTCTACAAGATCGA
3133880 TCG
1 TCG
3133883 CAGCATTTCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (44 bp):
TCGTGTTGTGATTTACTTATTACTATCGGTTTCTACAAGATCGA
Found at i:3141061 original size:3 final size:3
Alignment explanation
Indices: 3141053--3141083 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3141043 TTAACCCTCC
3141053 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
3141084 CTCCTTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:3147536 original size:34 final size:31
Alignment explanation
Indices: 3147498--3147561 Score: 76
Period size: 34 Copynumber: 2.0 Consensus size: 31
3147488 ATAAGAATAA
3147498 ATAAAGTAAT-AAAATAAATGTAAAAGGAAAAAGG
1 ATAAAG-AATAAAAATAAA-G-AAAA-GAAAAAGG
*
3147532 ATAAAGGATAAAAATAAAGAAAAGAAAAAG
1 ATAAAGAATAAAAATAAAGAAAAGAAAAAG
3147562 AAAAACAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 7 0.25
32 4 0.14
33 3 0.11
34 14 0.50
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (31 bp):
ATAAAGAATAAAAATAAAGAAAAGAAAAAGG
Found at i:3147605 original size:18 final size:17
Alignment explanation
Indices: 3147573--3147609 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
3147563 AAAACAATAA
*
3147573 ATAAATAAAAGTAAAAT
1 ATAAAAAAAAGTAAAAT
3147590 ATAAAAAAATAGTAAAAT
1 ATAAAAAAA-AGTAAAAT
3147608 AT
1 AT
3147610 GTAAGGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (17 bp):
ATAAAAAAAAGTAAAAT
Found at i:3147713 original size:24 final size:24
Alignment explanation
Indices: 3147686--3147733 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3147676 ACTAATAATG
3147686 AAAAT-AATATATACAAATATATAA
1 AAAATAAATATATA-AAATATATAA
*
3147710 AAAATAAATATATAATATATATAA
1 AAAATAAATATATAAAATATATAA
3147734 TAATAACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
AAAATAAATATATAAAATATATAA
Found at i:3147739 original size:15 final size:15
Alignment explanation
Indices: 3147689--3147739 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3147679 AATAATGAAA
3147689 ATAATATATACAAATAT
1 ATAATATAT--AAATAT
* *
3147706 ATAAAAAATAAATAT
1 ATAATATATAAATAT
3147721 ATAATATATATAATA-
1 ATAATATATA-AATAT
3147736 ATAA
1 ATAA
3147740 CAAAGGTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 18 0.62
16 4 0.14
17 7 0.24
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAATATATAAATAT
Found at i:3149619 original size:101 final size:102
Alignment explanation
Indices: 3149376--3149779 Score: 614
Period size: 102 Copynumber: 4.0 Consensus size: 102
3149366 TATTTTGTGC
* * * *
3149376 TTCAAGGGAAACGTTTTCAAAGTTTATATTCCAAGAGAAATTGTCTCAA-AGGAGACAAAATTTT
1 TTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGA-GAGACAAAATTTT
* *
3149440 GTTTCAAGGGAAACTATCTAAAGAGAGACAAAATTCAT
65 GTTTCAAAGGAAACTATCTCAAGAGAGACAAAATTCAT
* *
3149478 TTCAAGGGAGATGTTTTCAAAGTTTATGTTTCAAGAGAAACTCTCTCAAGAGAGACAAAATTTTG
1 TTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTG
*
3149543 TTTAAAAGGAAACTATCTCAAGAGAG-CAAAATTCAT
66 TTTCAAAGGAAACTATCTCAAGAGAGACAAAATTCAT
* * *
3149579 TTCAAGGGAAATGTTTTCAATGTCTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
1 TTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTG
* *
3149644 TTTCAAGGGAAACTATCCCAAGAGAGACAAAATTCAT
66 TTTCAAAGGAAACTATCTCAAGAGAGACAAAATTCAT
* * *
3149681 TTCAAGGGAAATGTTTTCAATGTTAATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
1 TTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTG
* *
3149746 TTTCAAAGGAAACTATCTCAAGCGAGATAAAATT
66 TTTCAAAGGAAACTATCTCAAGAGAGACAAAATT
3149780 TTCTTTAAAA
Statistics
Matches: 277, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
101 93 0.34
102 183 0.66
103 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (102 bp):
TTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTG
TTTCAAAGGAAACTATCTCAAGAGAGACAAAATTCAT
Found at i:3149656 original size:37 final size:37
Alignment explanation
Indices: 3149605--3149781 Score: 140
Period size: 37 Copynumber: 5.0 Consensus size: 37
3149595 TCAATGTCTA
*
3149605 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* * *
3149642 TGTTTCAAGGGAAACTATCCCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
** * * **
3149678 CATTTCAAGGGAAA-TGTTTTCAA---TG--TTAA---
1 TGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAATTT
*
3149707 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* * * *
3149744 TGTTTCAAAGGAAACTATCTCAAGCGAGATAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
3149781 T
1 T
3149782 CTTTAAAAAC
Statistics
Matches: 106, Mismatches: 24, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
29 16 0.15
30 2 0.02
31 2 0.02
32 1 0.01
33 1 0.01
34 2 0.02
35 1 0.01
36 18 0.17
37 63 0.59
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:3149730 original size:203 final size:203
Alignment explanation
Indices: 3149376--3149767 Score: 649
Period size: 203 Copynumber: 1.9 Consensus size: 203
3149366 TATTTTGTGC
* *
3149376 TTCAAGGGAAACGTTTTCAAAGTTTATATTCCAAGAGAAATTGTCTCAAAGGAGACAAAATTTTG
1 TTCAAGGGAAACGTTTTCAAAGTCTATATTCCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTG
* * *
3149441 TTTCAAGGGAAACTATCTAAAGAGAGACAAAATTCATTTCAAGGGAGATGTTTTCAAAGTTTATG
66 TTTCAAGGGAAACTATCCAAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAAAGTTAATG
3149506 TTTCAAGAGAAACTCTCTCAAGAGAGACAAAATTTTGTTTAAAAGGAAACTATCTCAAGAGAGCA
131 TTTCAAGAGAAACTCTCTCAAGAGAGACAAAATTTTGTTTAAAAGGAAACTATCTCAAGAGAGCA
3149571 AAATTCAT
196 AAATTCAT
* * * * *
3149579 TTCAAGGGAAATGTTTTCAATGTCTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
1 TTCAAGGGAAACGTTTTCAAAGTCTATATTCCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTG
* *
3149644 TTTCAAGGGAAACTATCCCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTAATG
66 TTTCAAGGGAAACTATCCAAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAAAGTTAATG
* * *
3149709 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAAGGAAACTATCTCAAG
131 TTTCAAGAGAAACTCTCTCAAGAGAGACAAAATTTTGTTTAAAAGGAAACTATCTCAAG
3149768 CGAGATAAAA
Statistics
Matches: 174, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
203 174 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (203 bp):
TTCAAGGGAAACGTTTTCAAAGTCTATATTCCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTG
TTTCAAGGGAAACTATCCAAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAAAGTTAATG
TTTCAAGAGAAACTCTCTCAAGAGAGACAAAATTTTGTTTAAAAGGAAACTATCTCAAGAGAGCA
AAATTCAT
Found at i:3151403 original size:95 final size:94
Alignment explanation
Indices: 3151234--3151417 Score: 253
Period size: 95 Copynumber: 1.9 Consensus size: 94
3151224 ATGTAAATAC
* * **
3151234 CTTTATCAGGGTAGTTGAATCTTATCCATAAAGCCGGGGAGTTTAACAAATTGCCTTAGAGGGAC
1 CTTTATCAGGCTAGTTGAATATTATCCATAAAGCAAGGGAGTTTAACAAATTGCCTTAGAGGGAC
* *
3151299 ATCTTAAGCTTTATTATATAGTATAATCAT
66 AACTCAAGCTTTATTATATA-TATAATCAT
* *
3151329 CTTTATCAGGCTAGTTGAATATTATCCATAAAGCAAGGGCGTTTAACCAATTG-CTCTAGAGGGA
1 CTTTATCAGGCTAGTTGAATATTATCCATAAAGCAAGGGAGTTTAACAAATTGCCT-TAGAGGGA
* *
3151393 TAACTCAAGCTTTATTGTATATATA
65 CAACTCAAGCTTTATTATATATATA
3151418 TAATATTATA
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
94 6 0.08
95 72 0.92
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (94 bp):
CTTTATCAGGCTAGTTGAATATTATCCATAAAGCAAGGGAGTTTAACAAATTGCCTTAGAGGGAC
AACTCAAGCTTTATTATATATATAATCAT
Found at i:3155842 original size:17 final size:17
Alignment explanation
Indices: 3155820--3155884 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
3155810 ACAGATTACA
3155820 TCCTTCGGGATGATAGG
1 TCCTTCGGGATGATAGG
* **
3155837 TCCTTCGGGACACAGATAACA
1 TCCTTCGGG--A-TGAT-AGG
*
3155858 TCCTTTGGGATGATAGG
1 TCCTTCGGGATGATAGG
3155875 TCCTTCGGGA
1 TCCTTCGGGA
3155885 CATAGTTTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
17 19 0.53
18 3 0.08
19 2 0.06
20 3 0.08
21 9 0.25
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (17 bp):
TCCTTCGGGATGATAGG
Found at i:3155850 original size:38 final size:38
Alignment explanation
Indices: 3155808--3155886 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
3155798 TATGATAGGT
*
3155808 ACACAGATTACATCCTTCGGGATGATAGGTCCTTCGGG
1 ACACAGATAACATCCTTCGGGATGATAGGTCCTTCGGG
*
3155846 ACACAGATAACATCCTTTGGGATGATAGGTCCTTCGGG
1 ACACAGATAACATCCTTCGGGATGATAGGTCCTTCGGG
3155884 ACA
1 ACA
3155887 TAGTTTATAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (38 bp):
ACACAGATAACATCCTTCGGGATGATAGGTCCTTCGGG
Found at i:3157452 original size:15 final size:14
Alignment explanation
Indices: 3157434--3157496 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 14
3157424 GGAAAAAAGG
3157434 ATAAAAATAAAGAAA
1 ATAAAAATAAA-AAA
*
3157449 ATAAAAAGAAAAACA
1 ATAAAAATAAAAA-A
3157464 ATAAAAA-AAATAAA
1 ATAAAAATAAA-AAA
3157478 AGTAAAATATAAAAAA
1 A-TAAAA-ATAAAAAA
3157494 ATA
1 ATA
3157497 GTAAAATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
14 7 0.17
15 27 0.64
16 5 0.12
17 3 0.07
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (14 bp):
ATAAAAATAAAAAA
Found at i:3157456 original size:24 final size:24
Alignment explanation
Indices: 3157439--3157494 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
3157429 AAAGGATAAA
*
3157439 AATAAAGAAAATAAAAAGAAAAAC
1 AATAAAAAAAATAAAAAGAAAAAC
*
3157463 AATAAAAAAAAT-AAAAGTAAAA-
1 AATAAAAAAAATAAAAAGAAAAAC
*
3157485 TATAAAAAAA
1 AATAAAAAAA
3157495 TAGTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 9 0.31
23 9 0.31
24 11 0.38
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.12
Consensus pattern (24 bp):
AATAAAAAAAATAAAAAGAAAAAC
Found at i:3157471 original size:22 final size:22
Alignment explanation
Indices: 3157436--3157494 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
3157426 AAAAAAGGAT
*
3157436 AAAAATAAAGAAAATAAAAAGAA
1 AAAAATAAAAAAAAT-AAAAGAA
*
3157459 AAACAATAAAAAAAATAAAAGTA
1 AAA-AATAAAAAAAATAAAAGAA
*
3157482 AAATATAAAAAAA
1 AAAAATAAAAAAA
3157495 TAGTAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.28
23 12 0.38
24 11 0.34
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (22 bp):
AAAAATAAAAAAAATAAAAGAA
Found at i:3157501 original size:24 final size:22
Alignment explanation
Indices: 3157435--3157502 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
3157425 GAAAAAAGGA
3157435 TAAAAATAAAGAAAATA-AAAAG
1 TAAAAATAAA-AAAATATAAAAG
*
3157457 AAAAACAATAAAAAAA-ATAAAAG
1 -TAAA-AATAAAAAAATATAAAAG
3157480 TAAAATATAAAAAAATAGTAAAA
1 TAAAA-ATAAAAAAATA-TAAAA
3157503 TATATAAGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
21 1 0.03
22 13 0.34
23 13 0.34
24 11 0.29
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (22 bp):
TAAAAATAAAAAAATATAAAAG
Found at i:3157515 original size:21 final size:19
Alignment explanation
Indices: 3157470--3157531 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 19
3157460 AACAATAAAA
3157470 AAAATAAAAGTAAAATATA-
1 AAAA-AAAAGTAAAATATAT
*
3157489 AAAAAATAGTAAAATATAT
1 AAAAAAAAGTAAAATATAT
*
3157508 AAGGAAAAAAGTAAAAGATAT
1 AA--AAAAAAGTAAAATATAT
3157529 AAA
1 AAA
3157532 TAATACAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 13 0.35
19 7 0.19
21 17 0.46
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (19 bp):
AAAAAAAAGTAAAATATAT
Found at i:3157631 original size:17 final size:17
Alignment explanation
Indices: 3157585--3157631 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
3157575 AATAATGAAA
* *
3157585 ATAATATATACAAATAT
1 ATAATATATATAAATAG
* *
3157602 ATAAAATAAATAAATAG
1 ATAATATATATAAATAG
3157619 ATAATATATATAA
1 ATAATATATATAA
3157632 TAATAACAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
ATAATATATATAAATAG
Found at i:3167806 original size:15 final size:15
Alignment explanation
Indices: 3167786--3167817 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3167776 CTCGTATCCC
*
3167786 TTTTTTCTTTTTCTT
1 TTTTTTCTTCTTCTT
3167801 TTTTTTCTTCTTCTT
1 TTTTTTCTTCTTCTT
3167816 TT
1 TT
3167818 GGAGTCTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTCTTCTTCTT
Found at i:3170902 original size:27 final size:28
Alignment explanation
Indices: 3170847--3170903 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
3170837 AGAAATGTTG
*
3170847 TTTTTAATAAATATAATAATATTTTAAA
1 TTTTTAATAAATATAATAATATTTAAAA
3170875 TTTTTAA-AAAT-TAAATAA-ATTTCAAAA
1 TTTTTAATAAATAT-AATAATATTT-AAAA
3170902 TT
1 TT
3170904 ATAAGAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 5 0.19
27 14 0.54
28 7 0.27
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTTTAATAAATATAATAATATTTAAAA
Found at i:3171079 original size:20 final size:20
Alignment explanation
Indices: 3171041--3171079 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3171031 TGAAAAGCAG
* *
3171041 TATAATTTAGGCAAGTATTT
1 TATAATTAAGCCAAGTATTT
*
3171061 TATAATTAAGCCAATTATT
1 TATAATTAAGCCAAGTATT
3171080 GTTTGTAAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (20 bp):
TATAATTAAGCCAAGTATTT
Found at i:3174297 original size:4 final size:4
Alignment explanation
Indices: 3174288--3174324 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
3174278 TTAAGTTTAG
3174288 ATTA ATTA ATTA ATTA ATTA ATTA ATTA A-TA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
3174325 AAAAATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
ATTA
Found at i:3175210 original size:22 final size:20
Alignment explanation
Indices: 3175175--3175215 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
3175165 TTTAATCAGA
3175175 TATAATTTTTATATTTTATT
1 TATAATTTTTATATTTTATT
3175195 TATAATATTTTAATATTTTAT
1 TATAAT-TTTT-ATATTTTAT
3175216 GTGGAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 4 0.21
22 9 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATAATTTTTATATTTTATT
Found at i:3182086 original size:48 final size:50
Alignment explanation
Indices: 3182033--3182127 Score: 140
Period size: 48 Copynumber: 1.9 Consensus size: 50
3182023 GGTCGTTTTC
*
3182033 TCTCTAACAGTTGATGATGTG-AAATTTT-TTATTTAATATAAAATAATA
1 TCTCTAACAGCTGATGATGTGCAAATTTTATTATTTAATATAAAATAATA
* * *
3182081 TCTCTAACAGCTGATGATGTGCCATTTTTATTATTTAATGTAAAATA
1 TCTCTAACAGCTGATGATGTGCAAATTTTATTATTTAATATAAAATA
3182128 TTTAATTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 20 0.49
49 5 0.12
50 16 0.39
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (50 bp):
TCTCTAACAGCTGATGATGTGCAAATTTTATTATTTAATATAAAATAATA
Found at i:3183146 original size:59 final size:59
Alignment explanation
Indices: 3183080--3183201 Score: 151
Period size: 59 Copynumber: 2.1 Consensus size: 59
3183070 ATGGAGTCTG
*
3183080 AATAAAATTAAAATATTTAAAAATTT-GAGAATT-AGTTTAAA-ATGAGATCATAGTTTAAA
1 AATAAAATTAAAATATTCAAAAATTTAGAG-ATTGA-TTTAAACATGA-ATCATAGTTTAAA
* * *
3183139 AATAAAATTAAAATGTTCAAAAGTTTAGAGATTGATTTAAACTATGAATCGTAGTTTAAA
1 AATAAAATTAAAATATTCAAAAATTTAGAGATTGATTTAAAC-ATGAATCATAGTTTAAA
3183199 AAT
1 AAT
3183202 GTGTGATGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
59 32 0.58
60 19 0.35
61 4 0.07
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.35
Consensus pattern (59 bp):
AATAAAATTAAAATATTCAAAAATTTAGAGATTGATTTAAACATGAATCATAGTTTAAA
Found at i:3186464 original size:30 final size:31
Alignment explanation
Indices: 3186430--3186495 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
3186420 GGACAAAAGA
*
3186430 AAGTTTA-GTACCAAATT-CAACCTTCAGGTC
1 AAGTTTAGGTACCAAATTGC-ACCTTCAAGTC
*
3186460 AAGTTTAGGTACTAAATTGCACCTTCAAGTC
1 AAGTTTAGGTACCAAATTGCACCTTCAAGTC
3186491 AAGTT
1 AAGTT
3186496 CAACTACCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 7 0.22
31 24 0.75
32 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (31 bp):
AAGTTTAGGTACCAAATTGCACCTTCAAGTC
Done.