Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007957.1 Hibiscus syriacus cultivar Beakdansim tig00110384_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: 8646418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 43
Found at i:3083311 original size:42 final size:41
Alignment explanation
Indices: 3083230--3083330 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 41
3083220 AGGTTTTATG
* * * *
3083230 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTACA
* * *
3083271 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGACTTACA
*
3083313 GATGGCCCGAAGAACTTA
1 GATGGCCCGAAGGACTTA
3083331 TAAATTGTGA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
41 16 0.33
42 33 0.67
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTACA
Found at i:3083519 original size:215 final size:214
Alignment explanation
Indices: 3083047--3083597 Score: 922
Period size: 215 Copynumber: 2.6 Consensus size: 214
3083037 CTCTCTTATT
* * *
3083047 AAGGCTTAAAAATTACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGGCCCGAAGG
1 AAGGCTTAAAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* *
3083112 ACTTATAAATTGTGAAATTTTGAATATCACATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAAC
66 ACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAAC
* * *
3083177 ATCATTTTTCATTTTCAAATTCATGTGAAAATATCCTACCCGAAGGTTTTATGGATGGCCCGAAG
131 ATCATTTTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATAGATCGCCCGAAG
3083242 GACTTATCATCTTGCTCTA
196 GACTTATCATCTTGCTCTA
* *
3083261 AAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGA
1 AAGGCTTAAAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* *
3083326 ACTTATAAATTGTGAAATTTTGAAAATCGCATTCTTAGTTTTCAAAAATTTCATCTTCTTAAAAC
66 ACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAAC
* * *
3083391 GTCATTTTTTCATTTTCAAATTCTTGTGAAAACATCCTACCTGAAGGTTTTATAGATCGCCCGAA
131 ATCA-TTTTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATAGATCGCCCGAA
3083456 GGACTTATCATCTTGCTCTA
195 GGACTTATCATCTTGCTCTA
*
3083476 AAGGCTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTAAAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* * *
3083541 ACATATAAATCGTGAAATTTTGAAAATCACATTCTTCGTTTTAAAAAATTTCATCTT
66 ACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTTCATCTT
3083598 TGTTGATTTA
Statistics
Matches: 314, Mismatches: 22, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
214 124 0.39
215 190 0.61
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (214 bp):
AAGGCTTAAAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
ACTTATAAATTGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTTCATCTTCTTAAAAC
ATCATTTTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTTATAGATCGCCCGAAG
GACTTATCATCTTGCTCTA
Found at i:3083537 original size:42 final size:41
Alignment explanation
Indices: 3083440--3083542 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 41
3083430 CCTGAAGGTT
* * * * *
3083440 TTATAGATCGCCCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGAC
* *
3083481 TTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAC
1 TTATAGATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGAC
3083523 TTACT-GATGGCCCGAAGGAC
1 TTA-TAGATGGCCCGAAGGAC
3083543 ATATAAATCG
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 19 0.37
42 31 0.61
43 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (41 bp):
TTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGAC
Found at i:3084648 original size:29 final size:29
Alignment explanation
Indices: 3084606--3084663 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3084596 TGAAATTACT
3084606 CCCCCTTACTTTAACACTTCTCCCATTTA
1 CCCCCTTACTTTAACACTTCTCCCATTTA
3084635 CCCCCTTACTTTAACACTTCTCCCATTTA
1 CCCCCTTACTTTAACACTTCTCCCATTTA
3084664 TCATTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.41, G:0.00, T:0.38
Consensus pattern (29 bp):
CCCCCTTACTTTAACACTTCTCCCATTTA
Found at i:3087012 original size:20 final size:21
Alignment explanation
Indices: 3086966--3087026 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
3086956 TCCCCTATGG
3086966 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
3086989 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
3087009 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
3087027 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:3092838 original size:37 final size:37
Alignment explanation
Indices: 3092741--3092859 Score: 145
Period size: 37 Copynumber: 3.2 Consensus size: 37
3092731 TTTATGGACG
* *
3092741 GATTTGCTTTACTACTCTTCGGTGAAGGCTTAAGA-T
1 GATTTGCTTCACTACTTTTCGGTGAAGGCTTAAGATT
* *
3092777 GGTTTACTTCACTACTCTTT-GGTGAAGGCTTAAGATT
1 GATTTGCTTCACTACT-TTTCGGTGAAGGCTTAAGATT
*
3092814 GATTTGCTTCACT-CATTTTCGGTGAAGGCTTAAAATT
1 GATTTGCTTCACTAC-TTTTCGGTGAAGGCTTAAGATT
3092851 GACTTTGCT
1 GA-TTTGCT
3092860 CCAATCTCAT
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
36 32 0.45
37 33 0.46
38 6 0.08
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (37 bp):
GATTTGCTTCACTACTTTTCGGTGAAGGCTTAAGATT
Found at i:3094848 original size:33 final size:32
Alignment explanation
Indices: 3094810--3094874 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 32
3094800 ACAGACATAA
*
3094810 AACAAAA-AATGGGT-TAGTACACATAATATAAAC
1 AACAAAATAATGAGTATAGTA-ACA-AATA-AAAC
3094843 AACAAAATAATGAGTATAGTAACAAATAAAAC
1 AACAAAATAATGAGTATAGTAACAAATAAAAC
3094875 CTACCCTCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 4 0.14
33 11 0.38
34 9 0.31
35 5 0.17
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (32 bp):
AACAAAATAATGAGTATAGTAACAAATAAAAC
Found at i:3095021 original size:46 final size:46
Alignment explanation
Indices: 3094965--3095054 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
3094955 AAAAAAATAT
3094965 TAACCGCATGATATCTAATTCGCATGCTTGTTCGAGAAAACAAACC
1 TAACCGCATGATATCTAATTCGCATGCTTGTTCGAGAAAACAAACC
* *
3095011 TAACCGCATGATTTCTAGTTCGCATGCTTGTTCGAGAAAACAAA
1 TAACCGCATGATATCTAATTCGCATGCTTGTTCGAGAAAACAAA
3095055 AATAAATGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (46 bp):
TAACCGCATGATATCTAATTCGCATGCTTGTTCGAGAAAACAAACC
Found at i:3105333 original size:17 final size:17
Alignment explanation
Indices: 3105303--3105340 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3105293 TTATAAATAA
3105303 AAAATATATAAAAATCT
1 AAAATATATAAAAATCT
*
3105320 AAAATATA-AGAAAATTT
1 AAAATATATA-AAAATCT
3105337 AAAA
1 AAAA
3105341 ATTTCATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAATATATAAAAATCT
Found at i:3105661 original size:17 final size:17
Alignment explanation
Indices: 3105639--3105676 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
3105629 AGATGTTAGG
3105639 TTGTAACCTTCTTCATC
1 TTGTAACCTTCTTCATC
3105656 TTGTAACCTTCTTCATC
1 TTGTAACCTTCTTCATC
3105673 TTGT
1 TTGT
3105677 CAAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.16, C:0.26, G:0.08, T:0.50
Consensus pattern (17 bp):
TTGTAACCTTCTTCATC
Found at i:3106045 original size:6 final size:6
Alignment explanation
Indices: 3106036--3106063 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3106026 GGCGGCGGCG
3106036 GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACC
3106064 CGAGACGAGA
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:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:3106712 original size:22 final size:22
Alignment explanation
Indices: 3106685--3106778 Score: 122
Period size: 22 Copynumber: 4.4 Consensus size: 22
3106675 AATTTGGAAA
3106685 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
3106707 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
3106729 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
3106748 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
3106770 ATCGCAACG
1 ATCGCAACG
3106779 CGAACTGGAA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 13 0.22
20 2 0.03
21 2 0.03
22 42 0.71
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:3106761 original size:41 final size:41
Alignment explanation
Indices: 3106707--3106880 Score: 169
Period size: 41 Copynumber: 4.2 Consensus size: 41
3106697 ACTGTAGACT
* *
3106707 ATCGCAACAACAACTGTAGACTATCGCAA-CGAATTTGGAAA
1 ATCGCAACGACAACTGTAGACTATCGCAACCGAA-CTGGAAA
3106748 ATCGCAACGACAACTGTAGACTATCGCAACGCGAACTGGAAA
1 ATCGCAACGACAACTGTAGACTATCGCAAC-CGAACTGGAAA
* * * *
3106790 ATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAACTGAAAA
1 ATCGCAACGACAACTGT-AGACTATCGCAAC-CGAACTGGAAA
** * *
3106831 ATCGCAACG-TGATTTTCA-ACTATCGCAACGCGAACTGGAAA
1 ATCGCAACGACAACTGT-AGACTATCGCAAC-CGAACTGGAAA
3106872 ATCGCAACG
1 ATCGCAACG
3106881 CGATTTTCAA
Statistics
Matches: 122, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
41 102 0.84
42 16 0.13
43 4 0.03
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.18
Consensus pattern (41 bp):
ATCGCAACGACAACTGTAGACTATCGCAACCGAACTGGAAA
Found at i:3106795 original size:20 final size:20
Alignment explanation
Indices: 3106742--3106883 Score: 106
Period size: 20 Copynumber: 6.9 Consensus size: 20
3106732 GCAACGAATT
3106742 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAC
**
3106762 TGTAGACTATCGCAACGCGAAC
1 TG--GAAAATCGCAACGCGAAC
**
3106784 TGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGAAC
** *
3106804 TTCAACTATCGCAACGCGAAC
1 TGGAA-AATCGCAACGCGAAC
* * **
3106825 TGAAAAATCGCAACGTGATT
1 TGGAAAATCGCAACGCGAAC
** *
3106845 TTCAACTATCGCAACGCGAAC
1 TGGAA-AATCGCAACGCGAAC
3106866 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
3106884 TTTTCAACTA
Statistics
Matches: 91, Mismatches: 26, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
20 45 0.49
21 30 0.33
22 16 0.18
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAC
Found at i:3106815 original size:82 final size:81
Alignment explanation
Indices: 3106726--3106907 Score: 251
Period size: 82 Copynumber: 2.2 Consensus size: 81
3106716 ACAACTGTAG
*
3106726 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAACTGGAAA
1 ACTATCGCAACGAATTTGAAAAATCGCAACG-CAACTGTCA-ACTATCGCAACGCGAACTGGAAA
3106790 ATCGCAACGCGATTTTCA
64 ATCGCAACGCGATTTTCA
* ** * *
3106808 ACTATCGCAACGCGAA-CTGAAAAATCGCAACGTGATTTTCAACTATCGCAACGCGAACTGGAAA
1 ACTATCGCAA--CGAATTTGAAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAACTGGAAA
3106872 ATCGCAACGCGATTTTCA
64 ATCGCAACGCGATTTTCA
3106890 ACTATCGCAACGATATTT
1 ACTATCGCAACGA-ATTT
3106908 TCAATTATCG
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
80 3 0.03
81 1 0.01
82 65 0.74
83 15 0.17
84 4 0.05
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (81 bp):
ACTATCGCAACGAATTTGAAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAACTGGAAAAT
CGCAACGCGATTTTCA
Found at i:3106816 original size:21 final size:21
Alignment explanation
Indices: 3106790--3106925 Score: 123
Period size: 21 Copynumber: 6.6 Consensus size: 21
3106780 GAACTGGAAA
3106790 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** * **
3106811 ATCGCAACGCGA-ACTGAAAA
1 ATCGCAACGCGATTTTCAACT
*
3106831 ATCGCAACGTGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
3106852 ATCGCAACGCGAACTGGAA-A
1 ATCGCAACGCGATTTTCAACT
3106872 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** *
3106893 ATCGCAACGATATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
*
3106914 ATCGTAACGCGA
1 ATCGCAACGCGA
3106926 ATTTACGATA
Statistics
Matches: 85, Mismatches: 28, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
20 29 0.34
21 56 0.66
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:3106819 original size:63 final size:62
Alignment explanation
Indices: 3106670--3106798 Score: 181
Period size: 63 Copynumber: 2.1 Consensus size: 62
3106660 TTAACTATCA
* **
3106670 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACAACAACTGTAGACTATCG
1 CAACGAATTTGCAAAATCGCAACGACAACTGTAGACTATCGCAACAACAACTG-AGAAAATCG
* *
3106733 CAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAAC-GCGAACTG-GAAAATCG
1 CAACGAATTTGCAAAATCGCAACGACAACTGTAGACTATCGCAACAAC-AACTGAGAAAATCG
3106794 CAACG
1 CAACG
3106799 CGATTTTCAA
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
61 11 0.18
62 1 0.02
63 50 0.81
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (62 bp):
CAACGAATTTGCAAAATCGCAACGACAACTGTAGACTATCGCAACAACAACTGAGAAAATCG
Found at i:3106886 original size:41 final size:41
Alignment explanation
Indices: 3106767--3106901 Score: 252
Period size: 41 Copynumber: 3.3 Consensus size: 41
3106757 ACAACTGTAG
3106767 ACTATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCA
* *
3106808 ACTATCGCAACGCGAACTGAAAAATCGCAACGTGATTTTCA
1 ACTATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCA
3106849 ACTATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCA
3106890 ACTATCGCAACG
1 ACTATCGCAACG
3106902 ATATTTTCAA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 90 1.00
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCA
Found at i:3115776 original size:67 final size:67
Alignment explanation
Indices: 3115692--3115820 Score: 231
Period size: 67 Copynumber: 1.9 Consensus size: 67
3115682 CTTAATTCCC
* *
3115692 TTTTGTGTTTCATTTGTCGATGCAATCAGATTTATTCGTATCTATTTTAGTCTCTTTGTTGATTC
1 TTTTGTGGTTCATTTGTCGATGCAATCAGATTTATTCGTATCTATTTTAGTCTCTTGGTTGATTC
3115757 TT
66 TT
*
3115759 TTTTGTGGTTCGTTTGTCGATGCAATCAGATTTATTCGTATCTATTTTAGTCTCTTGGTTGA
1 TTTTGTGGTTCATTTGTCGATGCAATCAGATTTATTCGTATCTATTTTAGTCTCTTGGTTGA
3115821 GTTTTTTACC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.16, C:0.13, G:0.18, T:0.53
Consensus pattern (67 bp):
TTTTGTGGTTCATTTGTCGATGCAATCAGATTTATTCGTATCTATTTTAGTCTCTTGGTTGATTC
TT
Found at i:3118048 original size:26 final size:26
Alignment explanation
Indices: 3117998--3118048 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3117988 CAATTTAATA
* *
3117998 TAAAAATTATATACATATTTTATAAC
1 TAAAAATTACATACATATTTCATAAC
3118024 TAAAAATTACATAC-TATGTTCATAA
1 TAAAAATTACATACATAT-TTCATAA
3118049 TAATATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (26 bp):
TAAAAATTACATACATATTTCATAAC
Found at i:3120762 original size:107 final size:104
Alignment explanation
Indices: 3120709--3121437 Score: 1183
Period size: 107 Copynumber: 6.9 Consensus size: 104
3120699 TGTCTACTCC
* * *
3120709 CTATTTCTTCAGGGAGTAGAACTTC-AACAATAATCTTCTTACGGGTCCACTCTCTTTTTCTTCA
1 CTATTTCTTCAGGGAGTAGAAC-TCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCA
* *
3120773 GGGAGTAGAACTCAAACAATAATCTTCCTATGGGTCCGCTCT
65 GGGAGTAGAACTCGAAC-A-AATCTTCCTACGGGTCCGCTCT
*
3120815 CTTTTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCA
1 CTATTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCA
3120880 GGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCT
65 GGGAGTAGAACTCGAAC-A-AATCTTCCTACGGGTCCGCTCT
3120922 CTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCA
1 CTATTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCA
3120987 GGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCT
65 GGGAGTAGAACTCGAAC-A-AATCTTCCTACGGGTCCGCTCT
*
3121029 CTTTTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCA
1 CTATTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCA
*
3121094 GGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCT
65 GGGAGTAGAACTCGAAC-A-AATCTTCCTACGGGTCCGCTCT
3121136 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAG
1 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAG
3121201 GGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCT
66 GGAGT-AGAACTCGAAC-A-AATCTTCCTACGGGTCCGCTCT
*
3121243 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAG
1 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAG
3121308 GGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCT
66 GGAGT-AGAACTCGAAC-A-AATCTTCCTACGGGTCCGCTCT
* *
3121350 CTATTTCTTCAGGGAGTATAACTCGAACAATAATCTTCCTATGGGTCCGCTCTCTATTTCTTCAG
1 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAG
3121415 GGAGTAGAACTCGAAC-AATCTTC
66 GGAGTAGAACTCGAACAAATCTTC
3121438 TGTTGCTTCA
Statistics
Matches: 605, Mismatches: 15, Indels: 9
0.96 0.02 0.01
Matches are distributed among these distances:
103 7 0.01
106 82 0.14
107 516 0.85
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (104 bp):
CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAG
GGAGTAGAACTCGAACAAATCTTCCTACGGGTCCGCTCT
Found at i:3120843 original size:160 final size:158
Alignment explanation
Indices: 3120709--3121433 Score: 1222
Period size: 160 Copynumber: 4.5 Consensus size: 158
3120699 TGTCTACTCC
* * *
3120709 CTATTTCTTCAGGGAGTAGAACTTC-AACAATAATCTTCTTACGGGTCCACTCTCTTTTTCTTCA
1 CTATTTCTTCAGGGAGTAGAAC-TCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCA
* * *
3120773 GGGAGTAGAACTCAAACAATAATCTTCCTATGGGTCCGCTCTCTTTTTCTTCAGGGAGTAAGAAC
65 GGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAAGAAC
3120838 TCGAACAATAATCTTCCTACGGGTCCGCTCT
130 TCGAAC-A-AATCTTCCTACGGGTCCGCTCT
3120869 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAG
1 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAG
3120934 GGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGT-AGAAC
66 GGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAAGAAC
3120998 TCGAACAATAATCTTCCTACGGGTCCGCTCT
130 TCGAAC-A-AATCTTCCTACGGGTCCGCTCT
*
3121029 CTTTTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCA
1 CTATTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCA
*
3121094 GGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTATTTCTTCAGGGAGT-AGAAC
65 GGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAAGAAC
3121158 TCGAACAATAATCTTCCTACGGGTCCGCTCT
130 TCGAAC-A-AATCTTCCTACGGGTCCGCTCT
3121189 CTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCA
1 CTATTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCA
*
3121254 GGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGGAGTAAGAAC
65 GGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAAGAAC
3121319 TCGAACAATAATCTTCCTACGGGTCCGCTCT
130 TCGAAC-A-AATCTTCCTACGGGTCCGCTCT
* *
3121350 CTATTTCTTCAGGGAGTATAACTCGAACAATAATCTTCCTATGGGTCCGCTCTCTATTTCTTCAG
1 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAG
3121415 GGAGTAGAACTCGAACAAT
66 GGAGTAGAACTCGAACAAT
3121434 CTTCTGTTGC
Statistics
Matches: 548, Mismatches: 13, Indels: 8
0.96 0.02 0.01
Matches are distributed among these distances:
159 2 0.00
160 390 0.71
161 156 0.28
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (158 bp):
CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAG
GGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAAGAACT
CGAACAAATCTTCCTACGGGTCCGCTCT
Found at i:3121125 original size:267 final size:267
Alignment explanation
Indices: 3120709--3121433 Score: 1346
Period size: 267 Copynumber: 2.7 Consensus size: 267
3120699 TGTCTACTCC
* *
3120709 CTATTTCTTCAGGGAGTAGAACTTC-AACAATAATCTTCTTACGGGTCCACTCTCTTTTTCTTCA
1 CTATTTCTTCAGGGAGTAGAAC-TCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCA
* * *
3120773 GGGAGT-AGAACTCAAACAATAATCTTCCTATGGGTCCGCTCTCTTTTTCTTCAGGGAGTAAGAA
65 GGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGT-AGAA
3120837 CTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAATAA
129 CTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAATAA
3120902 TCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGG
194 TCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGG
3120967 GTCCGCTCT
259 GTCCGCTCT
3120976 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAG
1 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAG
3121041 GGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAGAACT
66 GGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAGAACT
*
3121106 CGAACAATAATCTTCCTACGGGTCTGCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATC
131 CGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATC
3121171 TTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGT
196 TTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGT
3121236 CCGCTCT
261 CCGCTCT
3121243 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAG
1 CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAG
*
3121308 GGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTATAACT
66 GGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAGAACT
*
3121373 CGAACAATAATCTTCCTATGGGTCCGCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAAT
131 CGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAAT
3121434 CTTCTGTTGC
Statistics
Matches: 447, Mismatches: 9, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
266 2 0.00
267 395 0.88
268 50 0.11
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (267 bp):
CTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAG
GGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAGAACT
CGAACAATAATCTTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATC
TTCCTACGGGTCCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGT
CCGCTCT
Found at i:3122795 original size:11 final size:11
Alignment explanation
Indices: 3122781--3122865 Score: 75
Period size: 11 Copynumber: 7.3 Consensus size: 11
3122771 TTTTGTTTTG
3122781 TTTTTTTC-TT
1 TTTTTTTCATT
3122791 ATTTTTTTCATT
1 -TTTTTTTCATT
3122803 TTTTTTTCATT
1 TTTTTTTCATT
*
3122814 TTTTCATTT-TTT
1 TTTT--TTTCATT
*
3122826 CATTTTTTTAATTT
1 --TTTTTTTCA-TT
3122840 TTATTTTTCATT
1 TT-TTTTTCATT
3122852 TTTTTTTCATT
1 TTTTTTTCATT
3122863 TTT
1 TTT
3122866 CATCTTCATG
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
11 35 0.56
12 13 0.21
13 9 0.14
14 6 0.10
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTTCATT
Found at i:3122804 original size:7 final size:7
Alignment explanation
Indices: 3122794--3122868 Score: 56
Period size: 8 Copynumber: 11.1 Consensus size: 7
3122784 TTTTCTTATT
3122794 TTTTTCA
1 TTTTTCA
3122801 -TTTT--
1 TTTTTCA
3122805 TTTTTCA
1 TTTTTCA
3122812 TTTTTTCA
1 -TTTTTCA
3122820 TTTTTTCA
1 -TTTTTCA
*
3122828 TTTTTTTAA
1 --TTTTTCA
3122837 TTTTT-A
1 TTTTTCA
3122843 TTTTTCA
1 TTTTTCA
3122850 -TTTT--
1 TTTTTCA
3122854 TTTTTCA
1 TTTTTCA
3122861 TTTTTCA
1 TTTTTCA
3122868 T
1 T
3122869 CTTCATGCAA
Statistics
Matches: 58, Mismatches: 1, Indels: 18
0.75 0.01 0.23
Matches are distributed among these distances:
5 8 0.14
6 14 0.24
7 14 0.24
8 15 0.26
9 7 0.12
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCA
Found at i:3122804 original size:19 final size:19
Alignment explanation
Indices: 3122782--3122841 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
3122772 TTTGTTTTGT
3122782 TTTTTTCTTATTTTTTTCA
1 TTTTTTCTTATTTTTTTCA
*
3122801 TTTTTTTTTCA-TTTTTTCA
1 TTTTTTCTT-ATTTTTTTCA
*
3122820 TTTTTTC--ATTTTTTTAA
1 TTTTTTCTTATTTTTTTCA
3122837 TTTTT
1 TTTTT
3122842 ATTTTTCATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 1 0.03
17 12 0.33
19 22 0.61
20 1 0.03
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTCTTATTTTTTTCA
Found at i:3122824 original size:38 final size:38
Alignment explanation
Indices: 3122782--3122855 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 38
3122772 TTTGTTTTGT
*
3122782 TTTTTTCTTATTTTTTTCA-TTTT-TTTTTCATTTTTTCA
1 TTTTTTC--ATTTTTTTAATTTTTATTTTTCATTTTTTCA
3122820 TTTTTTCATTTTTTTAATTTTTATTTTTCATTTTTT
1 TTTTTTCATTTTTTTAATTTTTATTTTTCATTTTTT
3122856 TTTCATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 9 0.27
37 4 0.12
38 20 0.61
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (38 bp):
TTTTTTCATTTTTTTAATTTTTATTTTTCATTTTTTCA
Found at i:3122865 original size:8 final size:8
Alignment explanation
Indices: 3122804--3122855 Score: 72
Period size: 8 Copynumber: 6.8 Consensus size: 8
3122794 TTTTTCATTT
3122804 TTTTTTCA
1 TTTTTTCA
3122812 TTTTTTCA
1 TTTTTTCA
3122820 TTTTTTCA
1 TTTTTTCA
*
3122828 TTTTTTTA
1 TTTTTTCA
*
3122836 ATTTTT-A
1 TTTTTTCA
3122843 -TTTTTCA
1 TTTTTTCA
3122850 TTTTTT
1 TTTTTT
3122856 TTTCATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 5 0.12
7 2 0.05
8 33 0.82
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCA
Found at i:3131308 original size:26 final size:26
Alignment explanation
Indices: 3131258--3131308 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3131248 CACTTTAATA
* *
3131258 TAAAAATTATATACATATTTTATAAC
1 TAAAAATTACATACATATTTCATAAC
3131284 TAAAAATTACATAC-TATGTTCATAA
1 TAAAAATTACATACATAT-TTCATAA
3131309 TAATATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (26 bp):
TAAAAATTACATACATATTTCATAAC
Found at i:3133769 original size:3 final size:3
Alignment explanation
Indices: 3133756--3133793 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
3133746 TATATTAGAT
3133756 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3133794 CGGATAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3135091 original size:18 final size:18
Alignment explanation
Indices: 3135068--3135108 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3135058 TACACAAAGT
3135068 CCTCCACCGCCTTCC-CCA
1 CCTCCACCGCC-TCCACCA
*
3135086 CCTCCACCGTCTCCACCA
1 CCTCCACCGCCTCCACCA
3135104 CCTCC
1 CCTCC
3135109 GGCATGTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.12, C:0.66, G:0.05, T:0.17
Consensus pattern (18 bp):
CCTCCACCGCCTCCACCA
Found at i:3135196 original size:18 final size:18
Alignment explanation
Indices: 3135175--3135219 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
3135165 TGCAGTATCC
3135175 GCCACCGTCACCGAAAAA
1 GCCACCGTCACCGAAAAA
3135193 GCCACCGTCACCGAAAAA
1 GCCACCGTCACCGAAAAA
*
3135211 GCCGCCGTC
1 GCCACCGTC
3135220 CAGTTGCTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.31, C:0.42, G:0.20, T:0.07
Consensus pattern (18 bp):
GCCACCGTCACCGAAAAA
Found at i:3135488 original size:18 final size:19
Alignment explanation
Indices: 3135452--3135489 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3135442 ATAATTTATT
3135452 ATTTTCTTTTAGGACAAGA
1 ATTTTCTTTTAGGACAAGA
* *
3135471 ATTTTTTTTTCGGA-AAGA
1 ATTTTCTTTTAGGACAAGA
3135489 A
1 A
3135490 AGTTATTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (19 bp):
ATTTTCTTTTAGGACAAGA
Found at i:3136395 original size:22 final size:23
Alignment explanation
Indices: 3136370--3136413 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3136360 TTTTTATGGC
* *
3136370 TAAAATTATG-TATTTTTAATAA
1 TAAAATTAAGTTATTTTCAATAA
3136392 TAAAATTAAGTTATTTTCAATA
1 TAAAATTAAGTTATTTTCAATA
3136414 TTATAGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (23 bp):
TAAAATTAAGTTATTTTCAATAA
Found at i:3137404 original size:19 final size:20
Alignment explanation
Indices: 3137380--3137418 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3137370 TTTTTTGTAC
*
3137380 TTAAATTTTAA-TAAAAATA
1 TTAAATATTAAGTAAAAATA
3137399 TTAAATATTAAGTAAAAATA
1 TTAAATATTAAGTAAAAATA
3137419 CCATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TTAAATATTAAGTAAAAATA
Found at i:3137596 original size:16 final size:17
Alignment explanation
Indices: 3137562--3137596 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3137552 TAAAATCAAC
3137562 TTAATTTATGAATAGAT
1 TTAATTTATGAATAGAT
*
3137579 TTAATTTAT-AATATAT
1 TTAATTTATGAATAGAT
3137595 TT
1 TT
3137597 GTTTCAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TTAATTTATGAATAGAT
Found at i:3146264 original size:18 final size:18
Alignment explanation
Indices: 3146241--3146311 Score: 70
Period size: 18 Copynumber: 3.6 Consensus size: 18
3146231 TGCAAAATAG
3146241 GTATCGATACCCAAAGGA
1 GTATCGATACCCAAAGGA
*
3146259 GTATCGATACTACCTTACATAGTA
1 GTATCGATAC--CC--A-A-AGGA
*
3146283 GTATCAATACCCAAAGGA
1 GTATCGATACCCAAAGGA
3146301 GTATCGATACC
1 GTATCGATACC
3146312 ATGATCTTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 23 0.53
19 1 0.02
20 3 0.07
22 3 0.07
23 1 0.02
24 12 0.28
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.24
Consensus pattern (18 bp):
GTATCGATACCCAAAGGA
Found at i:3147426 original size:15 final size:17
Alignment explanation
Indices: 3147389--3147426 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
3147379 ATTAATGAAA
3147389 TTATGTTATTTGTACTT
1 TTATGTTATTTGTACTT
*
3147406 TAATGTTA-TTG-ACTT
1 TTATGTTATTTGTACTT
3147421 TTATGT
1 TTATGT
3147427 AAACAATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 9 0.47
16 3 0.16
17 7 0.37
ACGTcount: A:0.21, C:0.05, G:0.13, T:0.61
Consensus pattern (17 bp):
TTATGTTATTTGTACTT
Found at i:3148521 original size:172 final size:172
Alignment explanation
Indices: 3148235--3148580 Score: 676
Period size: 172 Copynumber: 2.0 Consensus size: 172
3148225 TACATATAAT
3148235 AATTAAGAAGTAAAGAATAAGAAAAATGTAATTTATTGCAAAAAGCATGGATAGAAAAGCGATTT
1 AATTAAGAAGTAAAGAATAAGAAAAATGTAATTTATTGCAAAAAGCATGGATAGAAAAGCGATTT
3148300 ATTATTTTTTTCAGGAAATGAAAATCCTCAATTCCGTTGAAGGTTGCTT-AATAAGTTTGCTTTT
66 ATTATTTTTTTCAGGAAATGAAAATCCTCAATTCCGTTGAAGGTTGCTTAAATAAGTTTGCTTTT
3148364 TTCCCTCATCGGAAAAAAAGTTAAATCTGGAAGGACACATACA
131 TTCCCTCATCGG-AAAAAAGTTAAATCTGGAAGGACACATACA
3148407 AATTAAGAAGTAAAGAATAAGAAAAATGTAATTTATTGCAAAAAGCATGGATAGAAAAGCGATTT
1 AATTAAGAAGTAAAGAATAAGAAAAATGTAATTTATTGCAAAAAGCATGGATAGAAAAGCGATTT
3148472 ATTATTTTTTTCAGGAAATGAAAATCCTCAATTCCGTTGAAGGTTGCTTAAATAAGTTTGCTTTT
66 ATTATTTTTTTCAGGAAATGAAAATCCTCAATTCCGTTGAAGGTTGCTTAAATAAGTTTGCTTTT
3148537 TTCCCTCATCGGAAAAAAGTTAAATCTGGAAGGACACATACA
131 TTCCCTCATCGGAAAAAAGTTAAATCTGGAAGGACACATACA
3148579 AA
1 AA
3148581 AATGTTATTT
Statistics
Matches: 173, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
172 146 0.84
173 27 0.16
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.31
Consensus pattern (172 bp):
AATTAAGAAGTAAAGAATAAGAAAAATGTAATTTATTGCAAAAAGCATGGATAGAAAAGCGATTT
ATTATTTTTTTCAGGAAATGAAAATCCTCAATTCCGTTGAAGGTTGCTTAAATAAGTTTGCTTTT
TTCCCTCATCGGAAAAAAGTTAAATCTGGAAGGACACATACA
Found at i:3148806 original size:20 final size:20
Alignment explanation
Indices: 3148781--3148833 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3148771 GATTTTCCAG
*
3148781 AATCACAACGCGAATATGA-A
1 AATCACAACGCGAACAT-ATA
3148801 AATCACAACGCGAACATATA
1 AATCACAACGCGAACATATA
*
3148821 AATCGCAACGCGA
1 AATCACAACGCGA
3148834 TTCTGACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.47, C:0.25, G:0.15, T:0.13
Consensus pattern (20 bp):
AATCACAACGCGAACATATA
Found at i:3148889 original size:20 final size:20
Alignment explanation
Indices: 3148842--3149035 Score: 194
Period size: 20 Copynumber: 9.6 Consensus size: 20
3148832 GATTCTGACT
*
3148842 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
* *
3148863 ATTGCAACTCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
3148883 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
3148904 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
3148924 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
3148944 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
3148964 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
3148984 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
3149004 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
3149025 ATCGCAACGCG
1 ATCGCAACGCG
3149036 ATTTTTAAAG
Statistics
Matches: 140, Mismatches: 27, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
20 96 0.69
21 44 0.31
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:3148957 original size:40 final size:41
Alignment explanation
Indices: 3148842--3149035 Score: 302
Period size: 40 Copynumber: 4.8 Consensus size: 41
3148832 GATTCTGACT
* * * *
3148842 ATCGCAACGAGTATCCGTAAAATTGCAACTCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
3148883 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
3148924 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
3148964 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
3149004 ATCGCAACGACAATACGTAAAATCGCAACGCG
1 ATCGCAACGAGAATACGTAAAATCGCAACGCG
3149036 ATTTTTAAAG
Statistics
Matches: 141, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 76 0.54
41 65 0.46
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:3149057 original size:80 final size:81
Alignment explanation
Indices: 3148842--3149048 Score: 265
Period size: 81 Copynumber: 2.6 Consensus size: 81
3148832 GATTCTGACT
** * * * * * *
3148842 ATCGCAACGAGTATCCGTAAAATTGCAACTCGTATCCGTAAATCGCAACGACAATACGTAAAATC
1 ATCGCAACGACAATACGT-AAATCGCAACGCGTATCTGTAAAGCGCAACGAGAATACGTAAAATC
3148907 GCAACGCGTATCCGTAA
65 GCAACGCGTATCCGTAA
* *
3148924 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGT-AAATCG
1 ATCGCAACGACAATACGTAAATCGCAACGCGTATCTGTAAAGCGCAACGAGAATACGTAAAATCG
*
3148988 CAATGCGTATCCGTAA
66 CAACGCGTATCCGTAA
* *
3149004 ATCGCAACGACAATACGTAAAATCGCAACGCG-ATTTTTAAAGCGC
1 ATCGCAACGACAATACGT-AAATCGCAACGCGTATCTGTAAAGCGC
3149049 CATTAGAATC
Statistics
Matches: 113, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
80 48 0.42
81 49 0.43
82 16 0.14
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (81 bp):
ATCGCAACGACAATACGTAAATCGCAACGCGTATCTGTAAAGCGCAACGAGAATACGTAAAATCG
CAACGCGTATCCGTAA
Found at i:3149619 original size:20 final size:20
Alignment explanation
Indices: 3149594--3149665 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
3149584 TTCTAAACTT
* *
3149594 AAAATCGTAACATGAAAATG
1 AAAATCGCAACACGAAAATG
3149614 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
3149634 ACTATCGCAACGA-GAGAAATC
1 AAAATCGCAAC-ACGA-AAATG
3149655 AAAATCGCAAC
1 AAAATCGCAAC
3149666 GAGAGAATCG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.51, C:0.19, G:0.15, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:3149676 original size:14 final size:14
Alignment explanation
Indices: 3149655--3149718 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 14
3149645 GAGAGAAATC
3149655 AAAATCGCAACGAG
1 AAAATCGCAACGAG
*
3149669 AGAATCGCAACGTGAAATG
1 AAAATCGCAAC--G--A-G
3149688 AAAATCGCAACGAG
1 AAAATCGCAACGAG
* *
3149702 ATAATCGCAACGCG
1 AAAATCGCAACGAG
3149716 AAA
1 AAA
3149719 CCAAAATCGC
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.62
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.28
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAG
Found at i:3149692 original size:33 final size:33
Alignment explanation
Indices: 3149649--3149729 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 33
3149639 CGCAACGAGA
*
3149649 GAAATCAAAATCGCAACGAGAGAATCGCAACGT
1 GAAATCAAAATCGCAACGAGAGAATCGCAACGC
* *
3149682 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATCAAAATCGCAACGAGAGAATCGCAACGC
*
3149715 GAAACCAAAATCGCA
1 GAAATCAAAATCGCA
3149730 TTGCGATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
GAAATCAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3149747 original size:19 final size:19
Alignment explanation
Indices: 3149725--3149870 Score: 123
Period size: 19 Copynumber: 8.1 Consensus size: 19
3149715 GAAACCAAAA
*
3149725 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3149744 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
3149758 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
3149777 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3149791 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3149810 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
3149829 TCTGCGTTGCGATAGTCATT
1 TC-GCGTTGCGATTTTCATT
*
3149849 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3149869 TC
1 TC
3149871 AACCAAAAGA
Statistics
Matches: 103, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
14 20 0.19
16 5 0.05
17 5 0.05
19 40 0.39
20 31 0.30
21 2 0.02
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3149766 original size:14 final size:14
Alignment explanation
Indices: 3149747--3149803 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3149737 TTTCATTTCG
3149747 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
3149761 CGTTGCGATTTTAATTTCG
1 CGTTGCGA---T--TCTCT
3149780 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3149794 CGTTGCGATT
1 CGTTGCGATT
3149804 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 21 0.62
16 1 0.03
17 1 0.03
19 11 0.32
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3149772 original size:33 final size:33
Alignment explanation
Indices: 3149730--3149821 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
3149720 CAAAATCGCA
3149730 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
3149763 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3149796 TTGCGATTTTCATTTCGCGTTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
3149822 AGTCATTTCT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3149868 original size:20 final size:19
Alignment explanation
Indices: 3149791--3149861 Score: 97
Period size: 20 Copynumber: 3.6 Consensus size: 19
3149781 GTTGCGATTC
**
3149791 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATAGTCATT
*
3149810 TCGCGTTGCGATAGTCATT
1 TCTCGTTGCGATAGTCATT
3149829 TCTGCGTTGCGATAGTCATT
1 TCT-CGTTGCGATAGTCATT
3149849 CTCTCGTTGCGAT
1 -TCTCGTTGCGAT
3149862 TTTCATTTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 18 0.39
20 25 0.54
21 3 0.07
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.42
Consensus pattern (19 bp):
TCTCGTTGCGATAGTCATT
Found at i:3152325 original size:20 final size:20
Alignment explanation
Indices: 3152302--3152340 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3152292 GAATCTCATT
3152302 GCGATTTAC-TAAATCGCAAC
1 GCGA-TTACGTAAATCGCAAC
3152322 GCGATTACGTAAATCGCAA
1 GCGATTACGTAAATCGCAA
3152341 TACGAATACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
GCGATTACGTAAATCGCAAC
Found at i:3152350 original size:20 final size:20
Alignment explanation
Indices: 3152311--3152351 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3152301 TGCGATTTAC
* *
3152311 TAAATCGCAACGCGATTACG
1 TAAATCGCAACACGAATACG
*
3152331 TAAATCGCAATACGAATACG
1 TAAATCGCAACACGAATACG
3152351 T
1 T
3152352 GCGAATACGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (20 bp):
TAAATCGCAACACGAATACG
Found at i:3152392 original size:20 final size:20
Alignment explanation
Indices: 3152369--3152477 Score: 121
Period size: 20 Copynumber: 5.3 Consensus size: 20
3152359 CGTATTCGCA
3152369 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
**
3152389 TTGCGATTTATAGATACGCG
1 TTGCGATTTACGGATACGCG
* * *
3152409 TTGCAATTTTACGTAT-TGTCG
1 TTGCGA-TTTACGGATACG-CG
*
3152430 TTGCGATTTACGAATACGCG
1 TTGCGATTTACGGATACGCG
*
3152450 TTGCGATTTTACGGATACTCG
1 TTGCGA-TTTACGGATACGCG
3152471 TTGCGAT
1 TTGCGAT
3152478 AGTCAGAATC
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
20 41 0.56
21 32 0.44
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGGATACGCG
Found at i:3152420 original size:41 final size:41
Alignment explanation
Indices: 3152375--3152500 Score: 132
Period size: 41 Copynumber: 3.0 Consensus size: 41
3152365 CGCATTGCGA
3152375 TTTACGGATACGCGTTGCGATTTATAG-ATACGCGTTGCAAT
1 TTTACGGATACGCGTTGCGATTTA-AGAATACGCGTTGCAAT
* * * *
3152416 TTTACGTAT-TGTCGTTGCGATTTACGAATACGCGTTGCGAT
1 TTTACGGATACG-CGTTGCGATTTAAGAATACGCGTTGCAAT
* * *
3152457 TTTACGGATACTCGTTGCGATAGTCAGAAT-CGCGTTGCGAAT
1 TTTACGGATACGCGTTGCGAT-TTAAGAATACGCGTTGC-AAT
3152499 TT
1 TT
3152501 ATATGTTGCG
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
40 2 0.03
41 58 0.84
42 9 0.13
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (41 bp):
TTTACGGATACGCGTTGCGATTTAAGAATACGCGTTGCAAT
Found at i:3152493 original size:61 final size:60
Alignment explanation
Indices: 3152364--3152501 Score: 145
Period size: 61 Copynumber: 2.2 Consensus size: 60
3152354 GAATACGTAT
* * * * *
3152364 TCGCATTGCGATTTACGGATACGCGTTGCGATTTATAGATACGCGTTGCAATTTTACGTA
1 TCGCGTTGCGATTTACGAATACGCGTTGCGATTTATAGATACGCGTTGCAATGTCACGAA
* * *
3152424 TTGTCGTTGCGATTTACGAATACGCGTTGCGATTT-TACGGATACTCGTTGCGATAGTCA-GAA
1 TCG-CGTTGCGATTTACGAATACGCGTTGCGATTTATA--GATACGCGTTGCAAT-GTCACGAA
3152486 TCGCGTTGCGAATTTA
1 TCGCGTTGCG-ATTTA
3152502 TATGTTGCGT
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
60 4 0.06
61 36 0.56
62 22 0.34
63 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGAATACGCGTTGCGATTTATAGATACGCGTTGCAATGTCACGAA
Found at i:3152537 original size:20 final size:20
Alignment explanation
Indices: 3152362--3152538 Score: 94
Period size: 20 Copynumber: 8.8 Consensus size: 20
3152352 GCGAATACGT
* * *
3152362 ATTCGCATTGCGATTTACGG
1 ATTCGCGTTGCGATTTTCAG
*
3152382 ATACGCGTTGCGATTTAT-AG
1 ATTCGCGTTGCGATTT-TCAG
* *
3152402 ATACGCGTTGCAATTTT-ACG
1 ATTCGCGTTGCGATTTTCA-G
*
3152422 TATT-GTCGTTGCGATTTAC-G
1 -ATTCG-CGTTGCGATTTTCAG
* *
3152442 AATACGCGTTGCGATTTTACGG
1 -ATTCGCGTTGCGATTTT-CAG
* * **
3152464 ATACTCGTTGCGATAGTCAG
1 ATTCGCGTTGCGATTTTCAG
* * *
3152484 AATCGCGTTGCGAATTT-AT
1 ATTCGCGTTGCGATTTTCAG
* *
3152503 ATGTTGCGTTGCGATTTTCAT
1 AT-TCGCGTTGCGATTTTCAG
3152524 ATTCGCGTTGCGATT
1 ATTCGCGTTGCGATT
3152539 CTGGAAAATC
Statistics
Matches: 121, Mismatches: 26, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
19 4 0.03
20 84 0.69
21 32 0.26
22 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTTCAG
Found at i:3152734 original size:12 final size:12
Alignment explanation
Indices: 3152717--3152741 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3152707 TAGGAGAAAG
3152717 AAATAATATTTT
1 AAATAATATTTT
3152729 AAATAATATTTT
1 AAATAATATTTT
3152741 A
1 A
3152742 TTAAAAATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:3154239 original size:18 final size:18
Alignment explanation
Indices: 3154218--3154269 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
3154208 AATAATAAAT
3154218 TAATTTAAATAAAATTGA
1 TAATTTAAATAAAATTGA
* * *
3154236 TAATTT-ATTAAAAATGT
1 TAATTTAAATAAAATTGA
3154253 TATATTTATAATAAAAT
1 TA-ATTTA-AATAAAAT
3154270 AATAGAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
17 10 0.38
18 10 0.38
20 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
TAATTTAAATAAAATTGA
Found at i:3156240 original size:28 final size:28
Alignment explanation
Indices: 3156209--3156262 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
3156199 GCTCACAATG
* * *
3156209 ATATTTTGGCAATTTTATACATATAAGT
1 ATATTTTGACAATTTAATACACATAAGT
*
3156237 ATATTTTGATAATTTAATACACATAA
1 ATATTTTGACAATTTAATACACATAA
3156263 AAGGATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (28 bp):
ATATTTTGACAATTTAATACACATAAGT
Found at i:3158431 original size:187 final size:189
Alignment explanation
Indices: 3158114--3158483 Score: 726
Period size: 187 Copynumber: 2.0 Consensus size: 189
3158104 GCTCGTATGT
3158114 GGGAGTCACTTTCAGATCCATCCGACGTGCTAATCAGCATAGTCACAACCCCTCCAATCAATTGT
1 GGGAGTCACTTTCAGATCCATCCGACGTGCTAATCAGCATAGTCACAACCCCTCCAATCAATTGT
3158179 CCAGCGGCCGCGTCATTCACCGGGAACGAACGGGTGAAGTTTCACCAGGGAAAACACAAGCTCTC
66 CCAGCGGCCGCGTCATTCACCGGGAACGAACGGGTGAAGTTTCACCAGGGAAAACACAAGCTCTC
3158244 TACTCAGTTTATCGCATTTTTTGATAGCCATGATTATCCCCTTGCCTCACCTCCACCGC
131 TACTCAGTTTATCGCATTTTTTGATAGCCATGATTATCCCCTTGCCTCACCTCCACCGC
3158303 GGGAGTCACTTTCAGATCCAT-CGACGTGCTAATCAGCATAGTCAC-ACCCCTCCAATCAATTGT
1 GGGAGTCACTTTCAGATCCATCCGACGTGCTAATCAGCATAGTCACAACCCCTCCAATCAATTGT
3158366 CCAGCGGCCGCGTCATTCACCGGGAACGAACGGGTGAAGTTTCACCAGGGAAAACACAAGCTCTC
66 CCAGCGGCCGCGTCATTCACCGGGAACGAACGGGTGAAGTTTCACCAGGGAAAACACAAGCTCTC
3158431 TACTCAGTTTATCGCATTTTTTGATAGCCATGATTATCCCCTTGCCTCACCTC
131 TACTCAGTTTATCGCATTTTTTGATAGCCATGATTATCCCCTTGCCTCACCTC
3158484 ACCTCCACCG
Statistics
Matches: 181, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
187 136 0.75
188 24 0.13
189 21 0.12
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (189 bp):
GGGAGTCACTTTCAGATCCATCCGACGTGCTAATCAGCATAGTCACAACCCCTCCAATCAATTGT
CCAGCGGCCGCGTCATTCACCGGGAACGAACGGGTGAAGTTTCACCAGGGAAAACACAAGCTCTC
TACTCAGTTTATCGCATTTTTTGATAGCCATGATTATCCCCTTGCCTCACCTCCACCGC
Found at i:3158854 original size:22 final size:22
Alignment explanation
Indices: 3158829--3158883 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
3158819 ACTGACCAAC
* *
3158829 GACTTTGACCAGA-GTTGACTTT
1 GACTTTGACCA-ACATTGAATTT
3158851 GAC-TTGACCAACATTGAATTT
1 GACTTTGACCAACATTGAATTT
*
3158872 AACTTTGACCAA
1 GACTTTGACCAA
3158884 AAAGTCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 16 0.57
22 11 0.39
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (22 bp):
GACTTTGACCAACATTGAATTT
Found at i:3160051 original size:21 final size:21
Alignment explanation
Indices: 3160025--3160068 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3160015 AGTTAGTACG
*
3160025 ATTTGACT-CAAATTCATGATA
1 ATTTGA-TACAAATTCATAATA
*
3160046 ATTTGATAGAAATTCATAATA
1 ATTTGATACAAATTCATAATA
3160067 AT
1 AT
3160069 GAAAACTACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (21 bp):
ATTTGATACAAATTCATAATA
Found at i:3165406 original size:17 final size:17
Alignment explanation
Indices: 3165384--3165426 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
3165374 TCCGGTATTT
3165384 GTGTTAAAAGCTATAAA
1 GTGTTAAAAGCTATAAA
3165401 GTGTTAAAAGCTATAAA
1 GTGTTAAAAGCTATAAA
3165418 GTGTTAAAA
1 GTGTTAAAA
3165427 TCTGGTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.30
Consensus pattern (17 bp):
GTGTTAAAAGCTATAAA
Found at i:3167988 original size:70 final size:70
Alignment explanation
Indices: 3167884--3168082 Score: 265
Period size: 70 Copynumber: 2.8 Consensus size: 70
3167874 GCATATCTGG
* * *
3167884 TTTAGCACTACAGTGTATATAAAGGACACTTAGTGCAAGTGGTGGGCACAACCATATGTGTCATA
1 TTTAGCACTATAGTGTATATAAAGGACACTTAGTGCAAGTGGTGGGCACGACCTTATGTGTCATA
3167949 TTCGA
66 TTCGA
* * *
3167954 TTTAGCACTATAGTGTATATAAAGGACACTTAGTGCAGGTGGTGGGCATGACCTTACGTGTCATA
1 TTTAGCACTATAGTGTATATAAAGGACACTTAGTGCAAGTGGTGGGCACGACCTTATGTGTCATA
*
3168019 TTCGG
66 TTCGA
** * * *
3168024 TTTAATAATATAGTGTATAATCAAGGACACTTAGTGTATA-TGGTGGGCACGACCTTATG
1 TTTAGCACTATAGTGTAT-ATAAAGGACACTTAGTGCA-AGTGGTGGGCACGACCTTATG
3168083 CGTATTGACA
Statistics
Matches: 112, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
70 78 0.70
71 34 0.30
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (70 bp):
TTTAGCACTATAGTGTATATAAAGGACACTTAGTGCAAGTGGTGGGCACGACCTTATGTGTCATA
TTCGA
Found at i:3169305 original size:188 final size:191
Alignment explanation
Indices: 3168988--3169367 Score: 739
Period size: 188 Copynumber: 2.0 Consensus size: 191
3168978 GAGACATATA
3168988 TAACTTGTTTAATAACCATCAAAATACCCAACAAATTAGAACTTCAAATATAATAATTAATGGGT
1 TAACTTGTTTAATAACCATCAAAATACCCAACAAATTAGAACTTCAAATATAATAATTAATGGGT
3169053 AATACAAAAAACATACACTAAAGCAATTAATGCATAGGAGATAATTCCATAATTCCTCATATCTA
66 AATACAAAAAACATACACTAAAGCAATTAATGCATAGGAGATAATTCCATAATTCCTCATATCTA
3169118 TAGCTAATGATCACA-AAGC-ATAGAAAATTAAT-AAACGAACATAAGCTGTCATAGCGTT
131 TAGCTAATGATCACATAAGCAATAGAAAATTAATAAAACGAACATAAGCTGTCATAGCGTT
3169176 TAACTTGTTTAATAACCATCAAAATACCCAACAAATTAGAACTTCAAATATAATAATTAATGGGT
1 TAACTTGTTTAATAACCATCAAAATACCCAACAAATTAGAACTTCAAATATAATAATTAATGGGT
3169241 AATACAAAAAACATACACTAAAGCAATTAATGCATAGGAGATAATTCCATAATTCCTCATATCTA
66 AATACAAAAAACATACACTAAAGCAATTAATGCATAGGAGATAATTCCATAATTCCTCATATCTA
3169306 TAGCTAATGATCACATAAGCAATAGAAAATTAATAAAACGAACATAAGCTGTCATAGCGTT
131 TAGCTAATGATCACATAAGCAATAGAAAATTAATAAAACGAACATAAGCTGTCATAGCGTT
3169367 T
1 T
3169368 TCCCGGAGGA
Statistics
Matches: 189, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
188 145 0.77
189 4 0.02
190 13 0.07
191 27 0.14
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.27
Consensus pattern (191 bp):
TAACTTGTTTAATAACCATCAAAATACCCAACAAATTAGAACTTCAAATATAATAATTAATGGGT
AATACAAAAAACATACACTAAAGCAATTAATGCATAGGAGATAATTCCATAATTCCTCATATCTA
TAGCTAATGATCACATAAGCAATAGAAAATTAATAAAACGAACATAAGCTGTCATAGCGTT
Found at i:3170249 original size:30 final size:30
Alignment explanation
Indices: 3170215--3170350 Score: 152
Period size: 30 Copynumber: 4.5 Consensus size: 30
3170205 GAACAACAAC
* *
3170215 AACTTAAAGGACCAAAATAGCAAAAATTGA
1 AACTTAAAGGACTAAAATAGCAAAAATAGA
3170245 AACTTAAAGGACTAAAATAGCAAAAATCA-A
1 AACTTAAAGGACTAAAATAGCAAAAAT-AGA
* *
3170275 AACTTAAAGGA-TGAAAATGGCACAAATAGA
1 AACTTAAAGGACT-AAAATAGCAAAAATAGA
* *
3170305 AATTTAAAGGGA-TAAAATAGTAAAAATAGA
1 AACTTAAA-GGACTAAAATAGCAAAAATAGA
* *
3170335 AACTTAAGGGTCTAAA
1 AACTTAAAGGACTAAA
3170351 CATTAATTAA
Statistics
Matches: 90, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
29 4 0.04
30 82 0.91
31 4 0.04
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (30 bp):
AACTTAAAGGACTAAAATAGCAAAAATAGA
Found at i:3171701 original size:3 final size:3
Alignment explanation
Indices: 3171693--3171770 Score: 147
Period size: 3 Copynumber: 25.7 Consensus size: 3
3171683 TGTAGTTGTA
3171693 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3171741 AAT AAT AAT AAAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
3171771 ACATTTTATC
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 71 0.96
4 3 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3172203 original size:83 final size:83
Alignment explanation
Indices: 3172055--3172252 Score: 238
Period size: 83 Copynumber: 2.4 Consensus size: 83
3172045 ATCTTTAGGA
*
3172055 AGGGTGATAACACAGTTCCTACGTGATGAGGACAACTGGTTATCTAGGGGTGAAACGACACCTAC
1 AGGG-GATGACACAGTTCCTACGTGATGAGGACAACTGGTTATCTAGGGGTGAAACGACACCTAC
*
3172120 GCGATGAGGAGGTCT-GAT
65 GCGATGAGGAGGTATGGAT
* * * ** *
3172138 CGGTGGATGACACAGTTCCTACGTGATGAGG-CTGACTGGTTATCTAGGGTTGACGCGACTCCTA
1 AGG-GGATGACACAGTTCCTACGTGATGAGGAC-AACTGGTTATCTAGGGGTGAAACGACACCTA
* *
3172202 CGTGATGAGGAGGTATGGTT
64 CGCGATGAGGAGGTATGGAT
* **
3172222 AGGGGATGACACAATTCCTACGCAATGAGGA
1 AGGGGATGACACAGTTCCTACGTGATGAGGA
3172253 TGACAGACTA
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
82 1 0.01
83 91 0.94
84 5 0.05
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.23
Consensus pattern (83 bp):
AGGGGATGACACAGTTCCTACGTGATGAGGACAACTGGTTATCTAGGGGTGAAACGACACCTACG
CGATGAGGAGGTATGGAT
Found at i:3172637 original size:67 final size:65
Alignment explanation
Indices: 3172478--3172646 Score: 178
Period size: 67 Copynumber: 2.5 Consensus size: 65
3172468 GATTTTTTTC
* *
3172478 TCAAAAGAAATTGTCTCAAGAGAGACAAAACTTTGATTTGTTTCCAAAGAAACAACCTCAAAATT
1 TCAAAAGAAACTGTCTCAAAAGAGACAAAA---T--TTTGTTTCCAAAGAAACAACCTCAAAATT
3172543 TTCCT
61 TTCCT
* * *
3172548 TCAAAAGAAACTTTCTCAAAAGAGATAAAATTTTGTTTCCAAAGACACAGA-CTCAAATATTTTT
1 TCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTCCAAAGAAACA-ACCTCAAA-A-TTTT
**
3172612 GTT
63 CCT
* *
3172615 TCAAGATAAACTGTCTCAAAAGAGACAAAATT
1 TCAAAAGAAACTGTCTCAAAAGAGACAAAATT
3172647 CATTTTAAGA
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
65 23 0.27
66 2 0.02
67 34 0.40
70 26 0.31
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (65 bp):
TCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTCCAAAGAAACAACCTCAAAATTTTCCT
Found at i:3173617 original size:93 final size:93
Alignment explanation
Indices: 3173495--3173680 Score: 372
Period size: 93 Copynumber: 2.0 Consensus size: 93
3173485 CTTCGGAGAG
3173495 ATATTTATTGAATCCCAAGATACTTCTAGAGAACTTATCTTGTTTGAAAATGTTTTCTTCCTTTG
1 ATATTTATTGAATCCCAAGATACTTCTAGAGAACTTATCTTGTTTGAAAATGTTTTCTTCCTTTG
3173560 GATTTTCAAAATTTTGAAAATATAAAAA
66 GATTTTCAAAATTTTGAAAATATAAAAA
3173588 ATATTTATTGAATCCCAAGATACTTCTAGAGAACTTATCTTGTTTGAAAATGTTTTCTTCCTTTG
1 ATATTTATTGAATCCCAAGATACTTCTAGAGAACTTATCTTGTTTGAAAATGTTTTCTTCCTTTG
3173653 GATTTTCAAAATTTTGAAAATATAAAAA
66 GATTTTCAAAATTTTGAAAATATAAAAA
3173681 GATTTTTGAA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (93 bp):
ATATTTATTGAATCCCAAGATACTTCTAGAGAACTTATCTTGTTTGAAAATGTTTTCTTCCTTTG
GATTTTCAAAATTTTGAAAATATAAAAA
Found at i:3178845 original size:30 final size:30
Alignment explanation
Indices: 3178811--3178880 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
3178801 AAATTATAAC
* *
3178811 GACCAAAATAAGAACAA-GAACAACTTAAAG
1 GACCAAAATAACAAAAACGAA-AACTTAAAG
* *
3178841 GACCAAAATCACAAAAACTAAAACTTAAAG
1 GACCAAAATAACAAAAACGAAAACTTAAAG
*
3178871 GACTAAAATA
1 GACCAAAATA
3178881 GTAAAAATAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 31 0.94
31 2 0.06
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.13
Consensus pattern (30 bp):
GACCAAAATAACAAAAACGAAAACTTAAAG
Found at i:3178887 original size:30 final size:30
Alignment explanation
Indices: 3178832--3178957 Score: 100
Period size: 30 Copynumber: 4.2 Consensus size: 30
3178822 GAACAAGAAC
* *
3178832 AACTTAAAGGACCAAAATCA-CAAAAACTA-A
1 AACTTAAAGGACTAAAAT-AGTAAAAAC-AGA
*
3178862 AACTTAAAGGACTAAAATAGTAAAAATAGA
1 AACTTAAAGGACTAAAATAGTAAAAACAGA
* *
3178892 AACTT-AAGG-GTATAAATAG-AAAATACATA
1 AACTTAAAGGACTA-AAATAGTAAAA-ACAGA
* * * *
3178921 CATTTAAAGGGCTAAAACAGTAAAAACAGA
1 AACTTAAAGGACTAAAATAGTAAAAACAGA
3178951 AACTTAA
1 AACTTAA
3178958 GGGTTTAAAC
Statistics
Matches: 76, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
28 6 0.08
29 18 0.24
30 46 0.61
31 6 0.08
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.19
Consensus pattern (30 bp):
AACTTAAAGGACTAAAATAGTAAAAACAGA
Found at i:3178908 original size:29 final size:29
Alignment explanation
Indices: 3178876--3178966 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
3178866 TAAAGGACTA
3178876 AAATAGTAAAAATAGAAACTTAAGGGTAT
1 AAATAGTAAAAATAGAAACTTAAGGGTAT
* *
3178905 AAATAG--AAAATACATACATTTAAAGGGCTA-
1 AAATAGTAAAAATAGA-A-ACTT-AAGGG-TAT
* * *
3178935 AAACAGTAAAAACAGAAACTTAAGGGTTT
1 AAATAGTAAAAATAGAAACTTAAGGGTAT
3178964 AAA
1 AAA
3178967 CATTAATTAC
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
27 7 0.15
28 2 0.04
29 17 0.35
30 13 0.27
31 3 0.06
32 6 0.12
ACGTcount: A:0.55, C:0.08, G:0.15, T:0.22
Consensus pattern (29 bp):
AAATAGTAAAAATAGAAACTTAAGGGTAT
Found at i:3179627 original size:24 final size:24
Alignment explanation
Indices: 3179600--3179648 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3179590 GTAACCCACT
* *
3179600 AGATCTAACTGAATACCCTTTGAA
1 AGATCTAACTAAATACCCTTCGAA
3179624 AGATCTAACTAAATACCCTTCGAA
1 AGATCTAACTAAATACCCTTCGAA
3179648 A
1 A
3179649 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (24 bp):
AGATCTAACTAAATACCCTTCGAA
Found at i:3181498 original size:131 final size:131
Alignment explanation
Indices: 3181334--3181596 Score: 526
Period size: 131 Copynumber: 2.0 Consensus size: 131
3181324 ATTTCATAAC
3181334 ATATGTAAAACTGTCTAAAGACTGCCTAATTTAAAAACTCAAACAATTAACTTTAAAACATAATA
1 ATATGTAAAACTGTCTAAAGACTGCCTAATTTAAAAACTCAAACAATTAACTTTAAAACATAATA
3181399 ATATTAAATACTATTCATTTATACTATCAAGCATAAACAATACTAACCAAATTTAAGGCATTTAT
66 ATATTAAATACTATTCATTTATACTATCAAGCATAAACAATACTAACCAAATTTAAGGCATTTAT
3181464 A
131 A
3181465 ATATGTAAAACTGTCTAAAGACTGCCTAATTTAAAAACTCAAACAATTAACTTTAAAACATAATA
1 ATATGTAAAACTGTCTAAAGACTGCCTAATTTAAAAACTCAAACAATTAACTTTAAAACATAATA
3181530 ATATTAAATACTATTCATTTATACTATCAAGCATAAACAATACTAACCAAATTTAAGGCATTTAT
66 ATATTAAATACTATTCATTTATACTATCAAGCATAAACAATACTAACCAAATTTAAGGCATTTAT
3181595 A
131 A
3181596 A
1 A
3181597 ATTACTATTA
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 132 1.00
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (131 bp):
ATATGTAAAACTGTCTAAAGACTGCCTAATTTAAAAACTCAAACAATTAACTTTAAAACATAATA
ATATTAAATACTATTCATTTATACTATCAAGCATAAACAATACTAACCAAATTTAAGGCATTTAT
A
Found at i:3182012 original size:20 final size:20
Alignment explanation
Indices: 3181975--3182015 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3181965 CTCATTATTT
**
3181975 TATAAAATCATGACAATCAA
1 TATAAAATCACAACAATCAA
*
3181995 TATAAAATCACAATAATCAA
1 TATAAAATCACAACAATCAA
3182015 T
1 T
3182016 CATTATTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.27
Consensus pattern (20 bp):
TATAAAATCACAACAATCAA
Found at i:3184330 original size:29 final size:28
Alignment explanation
Indices: 3184243--3184330 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 28
3184233 CAAAATATAT
* *
3184243 AACTTTTAAAATTATATTTTTGGTCCCTA
1 AACTTTTAAAATTATA-TTTTGGACACTA
* * *
3184272 AAC-TTTACAAAGTTTATACTTTAGAAACTA
1 AACTTTTA-AAA--TTATATTTTGGACACTA
*
3184302 AACTTTTAAAACTTATATTTTGGGCACTA
1 AACTTTTAAAA-TTATATTTTGGACACTA
3184331 GCCAAATTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
28 4 0.09
29 19 0.42
30 13 0.29
31 9 0.20
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (28 bp):
AACTTTTAAAATTATATTTTGGACACTA
Found at i:3198682 original size:418 final size:419
Alignment explanation
Indices: 3197905--3198742 Score: 1624
Period size: 418 Copynumber: 2.0 Consensus size: 419
3197895 AAGAATTTCA
*
3197905 AGCTTAGTTTGAGATAGCCAAGGTAAAAACCTTAATCTTCATTCCTCAAGTTTTAATTCAAGCAC
1 AGCTTAGTTTGAGATAGCCAAGGTAAAAACCTTAATCTGCATTCCTCAAGTTTTAATTCAAGCAC
3197970 CAAATCTCAAGTTTTGGTCATACTTTCCAAAAATGGGTTTTATGGAGGTTTTTAAGAATCAAGTG
66 CAAATCTCAAGTTTTGGTCATACTTTCCAAAAATGGGTTTTATGGAGGTTTTTAAGAATCAAGTG
*
3198035 ATTCTAGCTCGTTTTTAGTGGATTCAAGTTATAGGAAGTGTTTTTAACTCCATATTGAACTCCTA
131 ATTCTAGCTCGTTTTTAGTGGATTCAAGTTATAGGAAGTGTTTTTAACTCCAAATTGAACTCCTA
3198100 AATAAGTTAGTAATCCATTTCTCTTGCATTTGATTATTGAAAGAAGTGGGGGAGAGCTCCAATGC
196 AATAAGTTAGTAATCCATTTCTCTTGCATTTGATTATTGAAAGAAGTGGGGGAGAGCTCCAATGC
3198165 TAGAGGTAAAGAGAAGGCGACTCCTAGTTGAGTTTGGAGAGACTTTAGAAGCCAAGGGAACAAGG
261 TAGAGGTAAAGAGAAGGCGACTCCTAGTTGAGTTTGGAGAGACTTTAGAAGCCAAGGGAACAAGG
3198230 TAACACACTCACTACTTCTTACAAATTGTGGGTCATTA-AAATGTATCCTAGCTAAAGAGTTTAG
326 TAACACACTCACTACTTCTTACAAATTGTGGGTCATTAGAAATGTATCCTAGCTAAAGAGTTTAG
3198294 TTATGAAGCTTAGTGATGTATTTCTTGGT
391 TTATGAAGCTTAGTGATGTATTTCTTGGT
3198323 AGCTTAGTTTGAGATAGCCAAGGTAAAAACCTTAATCTGCATTCCTCAAGTTTTAATTCAAGCAC
1 AGCTTAGTTTGAGATAGCCAAGGTAAAAACCTTAATCTGCATTCCTCAAGTTTTAATTCAAGCAC
3198388 CAAATCTCAAGTTTTGGTCATACTTTCCAAAAATGGGTTTTATGGAGGTTTTTAAGAATCAAGTG
66 CAAATCTCAAGTTTTGGTCATACTTTCCAAAAATGGGTTTTATGGAGGTTTTTAAGAATCAAGTG
3198453 ATTCTAGCTCGTTTTTAGTGGATTCAAGTTATAGGAAGTGTTTTTAACTCCAAATTGAACTCCTA
131 ATTCTAGCTCGTTTTTAGTGGATTCAAGTTATAGGAAGTGTTTTTAACTCCAAATTGAACTCCTA
*
3198518 AATAAGTTAGTAATCTATTTCTCTTGCATTTGATTATTGAAAGAAGTGGGGGAGAGCTCCAATGC
196 AATAAGTTAGTAATCCATTTCTCTTGCATTTGATTATTGAAAGAAGTGGGGGAGAGCTCCAATGC
*
3198583 TAGAGGTAAAGAGAAGGTGACTCCTAGTTGAGTTTGGAGAGACTTTAGAAGCCAAGGGAACAAGG
261 TAGAGGTAAAGAGAAGGCGACTCCTAGTTGAGTTTGGAGAGACTTTAGAAGCCAAGGGAACAAGG
*
3198648 TAACACACTCACTACTTCTTACAAATTGTGGGTCATTAGAAATGTATCCTAGCTAAAGCGTTTAG
326 TAACACACTCACTACTTCTTACAAATTGTGGGTCATTAGAAATGTATCCTAGCTAAAGAGTTTAG
3198713 TTATGAAGCTTAGTGATGTATTTCTTGGT
391 TTATGAAGCTTAGTGATGTATTTCTTGGT
3198742 A
1 A
3198743 TATTTCATAA
Statistics
Matches: 414, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
418 359 0.87
419 55 0.13
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (419 bp):
AGCTTAGTTTGAGATAGCCAAGGTAAAAACCTTAATCTGCATTCCTCAAGTTTTAATTCAAGCAC
CAAATCTCAAGTTTTGGTCATACTTTCCAAAAATGGGTTTTATGGAGGTTTTTAAGAATCAAGTG
ATTCTAGCTCGTTTTTAGTGGATTCAAGTTATAGGAAGTGTTTTTAACTCCAAATTGAACTCCTA
AATAAGTTAGTAATCCATTTCTCTTGCATTTGATTATTGAAAGAAGTGGGGGAGAGCTCCAATGC
TAGAGGTAAAGAGAAGGCGACTCCTAGTTGAGTTTGGAGAGACTTTAGAAGCCAAGGGAACAAGG
TAACACACTCACTACTTCTTACAAATTGTGGGTCATTAGAAATGTATCCTAGCTAAAGAGTTTAG
TTATGAAGCTTAGTGATGTATTTCTTGGT
Found at i:3199210 original size:20 final size:20
Alignment explanation
Indices: 3199187--3199236 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3199177 CCCTTAAGAG
*
3199187 AGTATCGATACCAA-AGCGGT
1 AGTATCGATACCAAGAG-GCT
*
3199207 AGTATCTATACCAAGAGGCT
1 AGTATCGATACCAAGAGGCT
3199227 AGTATCGATA
1 AGTATCGATA
3199237 TCATAATATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (20 bp):
AGTATCGATACCAAGAGGCT
Found at i:3199839 original size:21 final size:21
Alignment explanation
Indices: 3199806--3199861 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
3199796 ATTATCTAAT
*
3199806 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
*
3199827 AAACATGAAATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
3199848 GAACTTGAACTCCA
1 AAACTTGAAATCCA
3199862 ATAATAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.48, C:0.27, G:0.07, T:0.18
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:3208413 original size:41 final size:41
Alignment explanation
Indices: 3208368--3208658 Score: 189
Period size: 41 Copynumber: 7.1 Consensus size: 41
3208358 TCGAGATCAT
**
3208368 CTAAAGTATGAGTCTTTAGCGATATTTGTATAAAAACGCCA
1 CTAAAGTATGAGTCTTTAGCGGCATTTGTATAAAAACGCCA
* * *
3208409 CTAAAGTATGAGTCTATAGCGGCGTTTGTATAAAAACGTCA
1 CTAAAGTATGAGTCTTTAGCGGCATTTGTATAAAAACGCCA
* * * *
3208450 CTAAAGTATGATTCGTTAGCGGCATTTGTATATAAACACCA
1 CTAAAGTATGAGTCTTTAGCGGCATTTGTATAAAAACGCCA
* * * * * **
3208491 TTAAAGT-TCAATTTTATAGTGGCATTTGTATAAAAAAACCA
1 CTAAAGTATGAGTCTT-TAGCGGCATTTGTATAAAAACGCCA
* **** * *
3208532 CTACAGTATGAGT-TGTTATTTACGTTTGTATACAAACGCCA
1 CTAAAGTATGAGTCT-TTAGCGGCATTTGTATAAAAACGCCA
* * * * * * * * *
3208573 CGAAAGTCTGAGTTTTTAGCAGCGTCTGTATACAAACTCCC
1 CTAAAGTATGAGTCTTTAGCGGCATTTGTATAAAAACGCCA
* *
3208614 CTAAAGTA--AGTCTTTTA-TGGCGTTTGT-TCATAAAACGCCA
1 CTAAAGTATGAGTC-TTTAGCGGCATTTGTAT-A-AAAACGCCA
3208654 CTAAA
1 CTAAA
3208659 AATGCTTCTA
Statistics
Matches: 193, Mismatches: 50, Indels: 15
0.75 0.19 0.06
Matches are distributed among these distances:
38 1 0.01
39 11 0.06
40 19 0.10
41 157 0.81
42 5 0.03
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (41 bp):
CTAAAGTATGAGTCTTTAGCGGCATTTGTATAAAAACGCCA
Found at i:3209187 original size:24 final size:23
Alignment explanation
Indices: 3209113--3209193 Score: 80
Period size: 24 Copynumber: 3.6 Consensus size: 23
3209103 TATAACCCCG
3209113 TGCATCGATGCACATTCAAGGCG-
1 TGCATCGATGCACATTCAAGG-GA
* *
3209136 TGCATCGGTGCATCA-TC-A-TGA
1 TGCATCGATGCA-CATTCAAGGGA
*
3209157 TGAATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
3209181 TGCATCGATGCAC
1 TGCATCGATGCAC
3209194 TTTTAAGTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
20 3 0.07
21 12 0.26
22 1 0.02
23 14 0.30
24 16 0.35
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:3212817 original size:71 final size:70
Alignment explanation
Indices: 3212739--3212885 Score: 285
Period size: 71 Copynumber: 2.1 Consensus size: 70
3212729 TACTTCTAAT
3212739 GATTTTACCATTTGAAGTTCTTTGAGGACTTCTATGATTGTAGTTTCTAAAACTTTTCTTAACAC
1 GATTTTACCATTTGAAGTTCTTTGAGGACTTCTATGATTGTAGTTTCTAAAACTTTTCTTAACAC
3212804 AGTTGG
66 AGTT-G
3212810 GATTTTACCATTTGAAGTTCTTTGAGGACTTCTATGATTGTAGTTTCTAAAACTTTTCTTAACAC
1 GATTTTACCATTTGAAGTTCTTTGAGGACTTCTATGATTGTAGTTTCTAAAACTTTTCTTAACAC
3212875 AGTTG
66 AGTTG
3212880 GATTTT
1 GATTTT
3212886 GAATTCTCAC
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 7 0.09
71 69 0.91
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (70 bp):
GATTTTACCATTTGAAGTTCTTTGAGGACTTCTATGATTGTAGTTTCTAAAACTTTTCTTAACAC
AGTTG
Found at i:3215108 original size:18 final size:17
Alignment explanation
Indices: 3215054--3215102 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3215044 TTGGACCCTT
* *
3215054 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
3215072 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
3215090 AGTGCATTCGATG
1 AGTGCA-TCGATG
3215103 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:3216679 original size:78 final size:78
Alignment explanation
Indices: 3216550--3216707 Score: 262
Period size: 78 Copynumber: 2.0 Consensus size: 78
3216540 GTAGCGTAAT
**
3216550 ATGCTTAGTCTTGTAAGAGCTTTTGAGAGATTGTCATTTTCTAAGTATAGATACCTAGTATCGAG
1 ATGCTTAGTCTTGTAAGAGAATTTGAGAGATTGTCATTTTCTAAGTATAGATACCTAGTATCGAG
*
3216615 AGAGTTTTGTTAG
66 AGAGTTATGTTAG
* * *
3216628 ATGCTTAGTCTTGTAAGAGAATTTGAGATATTTTCATTTTCTAAGTATAGATACCTAGTATTGAG
1 ATGCTTAGTCTTGTAAGAGAATTTGAGAGATTGTCATTTTCTAAGTATAGATACCTAGTATCGAG
3216693 AGAGTTATGTTAG
66 AGAGTTATGTTAG
3216706 AT
1 AT
3216708 TTACATGACC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.41
Consensus pattern (78 bp):
ATGCTTAGTCTTGTAAGAGAATTTGAGAGATTGTCATTTTCTAAGTATAGATACCTAGTATCGAG
AGAGTTATGTTAG
Found at i:3226175 original size:44 final size:44
Alignment explanation
Indices: 3226092--3226203 Score: 172
Period size: 44 Copynumber: 2.6 Consensus size: 44
3226082 AAATGAATGA
* * * *
3226092 ATAAATGAAAATGCATAA-GGTGCATTATTGGCAGAAAGGTGTC
1 ATAAATGAAAAAGCATAACGATGTATTATTGGCAGAAAGGTGCC
*
3226135 ATAAATGAAAACGCATAACGATGTATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAAAGCATAACGATGTATTATTGGCAGAAAGGTGCC
3226179 ATAAATGAAAAAGCATAACGATGTA
1 ATAAATGAAAAAGCATAACGATGTA
3226204 GTGCCACCAA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
43 17 0.27
44 46 0.73
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (44 bp):
ATAAATGAAAAAGCATAACGATGTATTATTGGCAGAAAGGTGCC
Found at i:3226264 original size:48 final size:48
Alignment explanation
Indices: 3226212--3226353 Score: 196
Period size: 48 Copynumber: 3.0 Consensus size: 48
3226202 TAGTGCCACC
* * * *
3226212 AATGAAAAATAAATGCATAATGGTGCATTTTGGCAGAAAGATGTCACT-
1 AATGAAAATTAAATGCATAACGGTGCGTTTTGGCAGAAAGATGCCA-TA
* *
3226260 AATGAAAATTAAATGCATAACGGTGCGTTTTGGCATAAAGGTGCCATA
1 AATGAAAATTAAATGCATAACGGTGCGTTTTGGCAGAAAGATGCCATA
* *
3226308 AATGAAACTTAAATGCATAACGGTGCGTTTTGGCAGAAAGGTGCCA
1 AATGAAAATTAAATGCATAACGGTGCGTTTTGGCAGAAAGATGCCA
3226354 CTCCTGGTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
47 1 0.01
48 84 0.99
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (48 bp):
AATGAAAATTAAATGCATAACGGTGCGTTTTGGCAGAAAGATGCCATA
Found at i:3228085 original size:35 final size:35
Alignment explanation
Indices: 3228019--3228086 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
3228009 AACATAATCC
* *
3228019 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTACATTCTAAACCCTAAATTACAAAATAAT
* *
3228054 TCAATTACATTTTAAACCCTAAATTATAAAATA
1 TCAATTACATTCTAAACCCTAAATTACAAAATA
3228087 TTTTAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCTAAATTACAAAATAAT
Found at i:3228131 original size:36 final size:35
Alignment explanation
Indices: 3228087--3228159 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 35
3228077 TTATAAAATA
3228087 TTTTAATTTAGGGTTTAAAATATAATTAAAGTATT
1 TTTTAATTTAGGGTTTAAAATATAATTAAAGTATT
* * * *
3228122 TTTTGAATTTAGGGTTTAGAATCTAATTGAAGTGTT
1 TTTT-AATTTAGGGTTTAAAATATAATTAAAGTATT
3228158 TT
1 TT
3228160 AGAATTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
35 4 0.12
36 29 0.88
ACGTcount: A:0.33, C:0.01, G:0.16, T:0.49
Consensus pattern (35 bp):
TTTTAATTTAGGGTTTAAAATATAATTAAAGTATT
Found at i:3241824 original size:158 final size:159
Alignment explanation
Indices: 3241536--3241853 Score: 629
Period size: 158 Copynumber: 2.0 Consensus size: 159
3241526 TATCCATTCG
3241536 GCTTGCTTAGAAAATTAGCAATAACATTGTTAATGACCTTAATATATAAAGCTTCAAAATTAAAA
1 GCTTGCTTAGAAAATTAGCAATAACATTGTTAATGACCTTAATATATAAAGCTTCAAAATTAAAA
3241601 GTACTTAACTCATTATACCATCTAATTCTTCTAGGTATTGTCTTCAATTTTTTTGATAAAAATAA
66 GTACTTAACTCATTATACCATCTAATTCTTCTAGGTATTGTCTTCAATTTTTTTGATAAAAATAA
3241666 AGGTCTCTTTAAA-CCCCATCATACAAAA
131 AGGTCTCTTTAAACCCCCATCATACAAAA
3241694 GCTTGCTTAGAAAATTAGCAATAACATTGTTAATGACCTTAATATATAAAGCTTCAAAATTAAAA
1 GCTTGCTTAGAAAATTAGCAATAACATTGTTAATGACCTTAATATATAAAGCTTCAAAATTAAAA
3241759 GTACTTAACTCATTATACCATCTAATTCTTCTAGGTATTGTCTTCAATTTTTTTGATAAAAATAA
66 GTACTTAACTCATTATACCATCTAATTCTTCTAGGTATTGTCTTCAATTTTTTTGATAAAAATAA
3241824 AGGTCTCTTTAAACCCCCATCATACAAAA
131 AGGTCTCTTTAAACCCCCATCATACAAAA
3241853 G
1 G
3241854 TCATATTAAA
Statistics
Matches: 159, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
158 143 0.90
159 16 0.10
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (159 bp):
GCTTGCTTAGAAAATTAGCAATAACATTGTTAATGACCTTAATATATAAAGCTTCAAAATTAAAA
GTACTTAACTCATTATACCATCTAATTCTTCTAGGTATTGTCTTCAATTTTTTTGATAAAAATAA
AGGTCTCTTTAAACCCCCATCATACAAAA
Found at i:3244412 original size:3 final size:3
Alignment explanation
Indices: 3244404--3244482 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
3244394 TTTTCGTCCC
3244404 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3244451 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3244483 AATAATAATT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 73 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3249009 original size:47 final size:47
Alignment explanation
Indices: 3248938--3249033 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
3248928 AAAAAGACAA
*
3248938 TGTCATGAAGGAAGCTGCTGCCCAAGAAAATAATGTGGCTCATAAAC
1 TGTCATGAAGGAAGCTGCTACCCAAGAAAATAATGTGGCTCATAAAC
3248985 TGTCATGAAGGAAGCTGCTACCCAAGAAAATAATGTGGCTCATAAAC
1 TGTCATGAAGGAAGCTGCTACCCAAGAAAATAATGTGGCTCATAAAC
3249032 TG
1 TG
3249034 GTTGATTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (47 bp):
TGTCATGAAGGAAGCTGCTACCCAAGAAAATAATGTGGCTCATAAAC
Found at i:3253585 original size:15 final size:15
Alignment explanation
Indices: 3253567--3253596 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3253557 CTCAGAGATC
3253567 AAATTCATTCGAGAA
1 AAATTCATTCGAGAA
3253582 AAATTCATTCGAGAA
1 AAATTCATTCGAGAA
3253597 CAACGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (15 bp):
AAATTCATTCGAGAA
Found at i:3253656 original size:9 final size:9
Alignment explanation
Indices: 3253620--3253659 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
3253610 TCCAAATACA
3253620 AGAAAAAAT
1 AGAAAAAAT
*
3253629 AGAAGAAAAA
1 AGAA-AAAAT
3253639 AGAAAAAAT
1 AGAAAAAAT
3253648 AGAAAAAAT
1 AGAAAAAAT
3253657 AGA
1 AGA
3253660 GGAAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (9 bp):
AGAAAAAAT
Found at i:3253665 original size:19 final size:19
Alignment explanation
Indices: 3253619--3253655 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3253609 TTCCAAATAC
3253619 AAGAAAAAATAGAAGAAAA
1 AAGAAAAAATAGAAGAAAA
3253638 AAGAAAAAATAGAA-AAAA
1 AAGAAAAAATAGAAGAAAA
3253656 TAGAGGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (19 bp):
AAGAAAAAATAGAAGAAAA
Found at i:3256105 original size:42 final size:41
Alignment explanation
Indices: 3256050--3256139 Score: 117
Period size: 42 Copynumber: 2.2 Consensus size: 41
3256040 AAGTCCTTTA
** * *
3256050 GGCCATCAATAAGTCTTTCGAGCACGATGATTAAATCCTTTG
1 GGCCATCTGTAAGTCTTTCGAGCAAGATGA-TAAATCCTTCG
* *
3256092 GGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCG
1 GGCCATCTGTAAGTCTTTCGAGCAAGATGATAAATCCTTCG
3256133 GGCCATC
1 GGCCATC
3256140 CATAAGACCT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 15 0.37
42 26 0.63
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (41 bp):
GGCCATCTGTAAGTCTTTCGAGCAAGATGATAAATCCTTCG
Found at i:3256358 original size:258 final size:258
Alignment explanation
Indices: 3255884--3256811 Score: 1438
Period size: 258 Copynumber: 3.6 Consensus size: 258
3255874 GAGCAAGATG
*
3255884 ATAAGCCCTTCA-GT-AGAATGTTTTCACATGAATTGTGAAAATGAGAAAGCGATTTCCAAAGTT
1 ATAAGACCTTCAGGTAAG-ATGTTTTCACATGAATTGTGAAAATGAGAAAGCGATTTCCAAAGTT
*
3255947 TCTCATTTAAATCTTTTCTGAAAATAAAATTTTTGAAAAGTAAGAAAGCT-ATTACCAAAGTTTC
65 TCTCATTTAAATCTTTTCTGAAAATGAAATTTTTGAAAAGTAAGAAAG-TGATTACCAAAGTTTC
* * *
3256011 TTACCCACTAAACTATTTCCCAAATTGGTAAGTCCTTTAGGCCATCAATAAGTCTTTCGAGCACG
129 TTACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTTAGGCCATCAGTAAGTCTTTCGAGCATG
* *
3256076 ATGATTAAATCCTTTGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
194 ATGATTAAATCCATCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
* * *
3256141 ATAAGACCTTCAGGTAAGATGTTTTTACATGAATTGTGAAAATGAGAAATCGATTTCCAAAGTGT
1 ATAAGACCTTCAGGTAAGATGTTTTCACATGAATTGTGAAAATGAGAAAGCGATTTCCAAAGTTT
3256206 CTCATTTAAATCTTTTCTGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTACCAAAGTTTCTT
66 CTCATTTAAATCTTTTCTGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTACCAAAGTTTCTT
*
3256271 ACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGAT
131 ACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTTAGGCCATCAGTAAGTCTTTCGAGCATGAT
* * * *
3256336 GATTAAATCCATCGGGTCATCTGTAAGCCTTTCGAGCAAGATAAAAAGTCCTTCGGGCAATCC
196 GATTAAATCCATCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
* *
3256399 ATAAGACCTTCGGGTAAGATGTTTTCACATGAATTGTGAAAATAAGAAAGCGATTTCCAAAGTTT
1 ATAAGACCTTCAGGTAAGATGTTTTCACATGAATTGTGAAAATGAGAAAGCGATTTCCAAAGTTT
3256464 CTCATTTAAATCTTTTCTGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTACCAAAGTTTCTT
66 CTCATTTAAATCTTTTCTGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTACCAAAGTTTCTT
* *
3256529 ACCAAGTAAACTATTTCCCAAATTGGTAAGTCCTTCA-GCCATCAGTAAGTCTTTCGAGCATGAT
131 ACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTTAGGCCATCAGTAAGTCTTTCGAGCATGAT
* * * *
3256593 GATTAAAT-CATTCGGGTCATCTATAAGGT-GTTCGAACAAGATGATTAGTCCTTCGGGCCATCC
196 GATTAAATCCA-TCGGGTCATCTGTAA-GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
* * * *
3256656 ATAAAACCTTCGGGTAGGAT-TTTTCACATGAATTGTGAAAATGAGAAAACGATTTCCAAAGTTT
1 ATAAGACCTTCAGGTAAGATGTTTTCACATGAATTGTGAAAATGAGAAAGCGATTTCCAAAGTTT
* * * * * * *
3256720 CTCATTTAAATATTTTTCAGAAAAAGAAATTTTAGAAAAGTAAAAAAAGTGATTTCAAAAGTTTC
66 CTCATTTAAAT-CTTTTCTGAAAATGAAATTTTTGAAAAGT-AAGAAAGTGATTACCAAAGTTTC
*
3256785 TTACCCAGTAAACTATTTCCAAAATTG
129 TTACCCAGTAAACTATTTCCCAAATTG
3256812 ATCTGACTAC
Statistics
Matches: 620, Mismatches: 44, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
256 55 0.09
257 132 0.21
258 431 0.70
259 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (258 bp):
ATAAGACCTTCAGGTAAGATGTTTTCACATGAATTGTGAAAATGAGAAAGCGATTTCCAAAGTTT
CTCATTTAAATCTTTTCTGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTACCAAAGTTTCTT
ACCCAGTAAACTATTTCCCAAATTGGTAAGTCCTTTAGGCCATCAGTAAGTCTTTCGAGCATGAT
GATTAAATCCATCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
Found at i:3261795 original size:22 final size:21
Alignment explanation
Indices: 3261756--3261803 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
3261746 TAAGAATTAC
*
3261756 TTTTTCTTTTCATTTTTTAGGG
1 TTTTTCTTTTCATTTTTT-GAG
*
3261778 TTTTTTTTTTC-TTATTTTGAG
1 TTTTTCTTTTCATT-TTTTGAG
3261799 TTTTT
1 TTTTT
3261804 ACTATAGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.08, C:0.06, G:0.10, T:0.75
Consensus pattern (21 bp):
TTTTTCTTTTCATTTTTTGAG
Found at i:3261832 original size:2 final size:2
Alignment explanation
Indices: 3261825--3261850 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3261815 TGAGGAGATC
3261825 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
3261851 CATTGGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3263755 original size:2 final size:2
Alignment explanation
Indices: 3263744--3263794 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
3263734 TTCTCTAATC
3263744 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3263783 AT AT AT AT AT AT
1 AT AT AT AT AT AT
3263795 TTCTTCATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3264833 original size:2 final size:2
Alignment explanation
Indices: 3264826--3264856 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3264816 TTAATCAATG
3264826 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3264857 TCAATGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3270272 original size:66 final size:68
Alignment explanation
Indices: 3270166--3270300 Score: 256
Period size: 66 Copynumber: 2.0 Consensus size: 68
3270156 GCAAAAACAT
3270166 AGTAGACGATACACTACCACGAAGGTATACTCTTACCTATCAAACTCATACTACT-TT-TGAGAA
1 AGTAGACGATACACTACCACGAAGGTATACTCTTACCTATCAAACTCATACTACTATTCTGAGAA
3270229 TTG
66 TTG
3270232 AGTAGACGATACACTACCACGAAGGTATACTCTTACCTATCAAACTCATACTACTATTCTGAGAA
1 AGTAGACGATACACTACCACGAAGGTATACTCTTACCTATCAAACTCATACTACTATTCTGAGAA
3270297 TTG
66 TTG
3270300 A
1 A
3270301 ACATATCAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
66 55 0.82
67 2 0.03
68 10 0.15
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (68 bp):
AGTAGACGATACACTACCACGAAGGTATACTCTTACCTATCAAACTCATACTACTATTCTGAGAA
TTG
Found at i:3271933 original size:11 final size:11
Alignment explanation
Indices: 3271906--3271950 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
3271896 TTGCAATTCC
3271906 TTTATCTT-TT
1 TTTATCTTGTT
3271916 TTTATCTTGTT
1 TTTATCTTGTT
* *
3271927 TTAATCTTATTT
1 TTTATCTT-GTT
3271939 TTTATCTTGTT
1 TTTATCTTGTT
3271950 T
1 T
3271951 CCAGCACCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 8 0.28
11 12 0.41
12 9 0.31
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.73
Consensus pattern (11 bp):
TTTATCTTGTT
Found at i:3273967 original size:40 final size:41
Alignment explanation
Indices: 3273866--3273979 Score: 164
Period size: 39 Copynumber: 2.9 Consensus size: 41
3273856 TTCCCCGAAA
* *
3273866 TCCCGTGTTTGTTTCA-TGTAATTCATTTTTCGGAAAATGTT
1 TCCCGTGTTTGTTTCACT-TAATTCGTTTTCCGGAAAATGTT
*
3273907 T-CC-TGTTTGTTTCACGTAATTCGTTTTCCGGAAAAT-TT
1 TCCCGTGTTTGTTTCACTTAATTCGTTTTCCGGAAAATGTT
3273945 TCCCGTGTTTGTTTCACTTAATTCGTTTTCCGGAA
1 TCCCGTGTTTGTTTCACTTAATTCGTTTTCCGGAA
3273980 CGTATTCATT
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
38 3 0.05
39 31 0.47
40 31 0.47
41 1 0.02
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.47
Consensus pattern (41 bp):
TCCCGTGTTTGTTTCACTTAATTCGTTTTCCGGAAAATGTT
Found at i:3274265 original size:22 final size:20
Alignment explanation
Indices: 3274240--3274283 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
3274230 ATTATATAAA
*
3274240 TAATAATATTATAGTTTTTATT
1 TAATAATA-TATAATTTTT-TT
3274262 TAATAATATATAATTTTTTT
1 TAATAATATATAATTTTTTT
3274282 TA
1 TA
3274284 TATTTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 9 0.43
22 8 0.38
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TAATAATATATAATTTTTTT
Found at i:3274626 original size:20 final size:20
Alignment explanation
Indices: 3274597--3274646 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
3274587 TCATAAAACG
3274597 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
* *
3274617 TTTTCTAGAAATTTAATTCA
1 TTTTCCAGAAATGTAATTCA
3274637 TTTTCCAGAA
1 TTTTCCAGAA
3274647 TTCAAATTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:3274672 original size:29 final size:30
Alignment explanation
Indices: 3274630--3274701 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
3274620 TCTAGAAATT
3274630 TAATTCATTTTCCAG-AATTCAAATTCCAA
1 TAATTCATTTTCCAGTAATTCAAATTCCAA
*
3274659 TAATTCATTTTCCAGTAATTCAAATTCCAG
1 TAATTCATTTTCCAGTAATTCAAATTCCAA
3274689 TAATTCATTTTCC
1 TAATTCATTTTCC
3274702 GGAAACTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 15 0.37
30 26 0.63
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (30 bp):
TAATTCATTTTCCAGTAATTCAAATTCCAA
Found at i:3274701 original size:15 final size:15
Alignment explanation
Indices: 3274630--3274701 Score: 92
Period size: 15 Copynumber: 4.9 Consensus size: 15
3274620 TCTAGAAATT
3274630 TAATTCATTTTCCAG
1 TAATTCATTTTCCAG
** *
3274645 -AATTCAAATTCCAA
1 TAATTCATTTTCCAG
3274659 TAATTCATTTTCCAG
1 TAATTCATTTTCCAG
**
3274674 TAATTCAAATTCCAG
1 TAATTCATTTTCCAG
3274689 TAATTCATTTTCC
1 TAATTCATTTTCC
3274702 GGAAACTAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
14 11 0.24
15 35 0.76
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (15 bp):
TAATTCATTTTCCAG
Found at i:3275386 original size:171 final size:168
Alignment explanation
Indices: 3275101--3275439 Score: 633
Period size: 171 Copynumber: 2.0 Consensus size: 168
3275091 TCGGGTTAAT
*
3275101 CTTTAGATTTTCAATTTAATTTGAGTTGGGTTAAGTATGGGTCCAATCAAGTATATATAAAATTA
1 CTTTAGATTTTCAATTTAATTTGAGTTGAGTTAAGTATGGGTCCAATCAAGTATATATAAAATTA
3275166 TTAATATATTCTTATAAGAAAATATATATTTTTCTTTTTCAATCTTATCATTTAAGTTCAAGTAC
66 TTAATATATTCTTATAAGAAAATATATATTTTTCTTTTTCAATCTTATCATTTAAGTTCAAGTAC
3275231 AACTTTAAAAAATTCTATGTTTCATATTACACTATCATTTA
131 AACTTTAAAAAA-T-TA-GTTTCATATTACACTATCATTTA
3275272 CTTTAGATTTTCAATTTAATTTGAGTTGAGTTAAGTATGGGTCCAATCAAGTATATATAAAATTA
1 CTTTAGATTTTCAATTTAATTTGAGTTGAGTTAAGTATGGGTCCAATCAAGTATATATAAAATTA
*
3275337 TTAATATATTCTTATAAGAAAATATATATTTTTCTTTTTCAATCTTATCATTTAAGTTCAAGTGC
66 TTAATATATTCTTATAAGAAAATATATATTTTTCTTTTTCAATCTTATCATTTAAGTTCAAGTAC
3275402 AACTTTAAAAAATTAGTTTCATATTACACTATCATTTA
131 AACTTTAAAAAATTAGTTTCATATTACACTATCATTTA
3275440 TTAATGACAA
Statistics
Matches: 166, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
168 23 0.14
169 2 0.01
170 1 0.01
171 140 0.84
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (168 bp):
CTTTAGATTTTCAATTTAATTTGAGTTGAGTTAAGTATGGGTCCAATCAAGTATATATAAAATTA
TTAATATATTCTTATAAGAAAATATATATTTTTCTTTTTCAATCTTATCATTTAAGTTCAAGTAC
AACTTTAAAAAATTAGTTTCATATTACACTATCATTTA
Found at i:3276506 original size:126 final size:126
Alignment explanation
Indices: 3276276--3276538 Score: 501
Period size: 126 Copynumber: 2.1 Consensus size: 126
3276266 ATTTCAAAGT
*
3276276 TATTGAATCATACATAGAGAGATCTTTTAAACGTGAAAATGTTATATTGACCATTCGGCTATTAC
1 TATTTAATCATACATAGAGAGATCTTTTAAACGTGAAAATGTTATATTGACCATTCGGCTATTAC
3276341 TAAAGGTGATGATTAACTAGTAGTGTAATATAAAAAGAGAATAAAACATGCAGCATTTTAC
66 TAAAGGTGATGATTAACTAGTAGTGTAATATAAAAAGAGAATAAAACATGCAGCATTTTAC
3276402 TATTTAATCATACATAGAGAGATCTTTTAAACGTGAAAATGTTATATTGACCATTCGGCTATTAC
1 TATTTAATCATACATAGAGAGATCTTTTAAACGTGAAAATGTTATATTGACCATTCGGCTATTAC
*
3276467 TAAAGGTGATGATTAACTAGTAGTGTAATATAAAAAGAGAATAAAACATGCATCATTTTAC
66 TAAAGGTGATGATTAACTAGTAGTGTAATATAAAAAGAGAATAAAACATGCAGCATTTTAC
3276528 TATTT-ATCATA
1 TATTTAATCATA
3276539 TTATTAAAAA
Statistics
Matches: 135, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
125 6 0.04
126 129 0.96
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (126 bp):
TATTTAATCATACATAGAGAGATCTTTTAAACGTGAAAATGTTATATTGACCATTCGGCTATTAC
TAAAGGTGATGATTAACTAGTAGTGTAATATAAAAAGAGAATAAAACATGCAGCATTTTAC
Found at i:3281240 original size:68 final size:65
Alignment explanation
Indices: 3281136--3281448 Score: 227
Period size: 65 Copynumber: 4.6 Consensus size: 65
3281126 TTGATAAAAA
* * * * * *
3281136 CTTTGAGATTGTTTTCCTCGAAACAAAGTTTTGTCTC-CTTTGAGATAGTTTCTCTTGAAATAAA
1 CTTTGAGATTGTTTCCCTTGAAATAAA-TTTTGTCTCTC-TTAAGACAATTTCTCTTG--A-AAA
3281200 ACCAT
61 ACCAT
* * * * *
3281205 CTTTGAGATTGTTTCCCTTAAAATGAATTTTGTCTCTCTTAAGACAATTTTTCTTGAAACATCAT
1 CTTTGAGATTGTTTCCCTTGAAATAAATTTTGTCTCTCTTAAGACAATTTCTCTTGAAAAACCAT
* * *
3281270 CTTTAAGTTTGTTTCCCTTGAAATAAATTTTGTCTATCTTAAGACAATTTCTCTTGAAACAAAAT
1 CTTTGAGATTGTTTCCCTTGAAATAAATTTTGTCTCTCTTAAGACAATTTCTCTTG-----AAA-
**
3281335 TAAAAAT
60 -AACCAT
* * * * * * *
3281342 CTTTAAG-TCTGTTTCCCTTGAAACAATGTTTTATCTCTCTTGAGACAATTTCCCTTGAAACACC
1 CTTTGAGAT-TGTTTCCCTTGAAATAA-ATTTTGTCTCTCTTAAGACAATTTCTCTTGAAAAACC
3281406 AAT
64 -AT
* * *
3281409 CTTTGAG-TCTGTTGCTCTTGAAACAAATTTTGTCTCTCTT
1 CTTTGAGAT-TGTTTCCCTTGAAATAAATTTTGTCTCTCTT
3281449 GAAATGGTTT
Statistics
Matches: 199, Mismatches: 34, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
65 56 0.28
66 14 0.07
67 25 0.13
68 26 0.13
69 23 0.12
70 3 0.02
71 1 0.01
72 26 0.13
73 25 0.13
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (65 bp):
CTTTGAGATTGTTTCCCTTGAAATAAATTTTGTCTCTCTTAAGACAATTTCTCTTGAAAAACCAT
Found at i:3281810 original size:135 final size:131
Alignment explanation
Indices: 3281473--3281819 Score: 421
Period size: 131 Copynumber: 2.6 Consensus size: 131
3281463 TGAAACTATT
* * * *
3281473 ATTCCTAAAGATGACCCGTCGTCCTCATCACGTAAGAATCGTGTCATCCCCCCGACCAGACCTCC
1 ATTCCTAAAGATGACCAGTCGTCCTCATCACGTAGGAACCGTGTCAT-CCCCTGACCAGACCTCC
* * * * *
3281538 TCATCACGTAGGATCCATGTCAACCTCAGATAACCAGTCGTCTTCATCACGCAGGAACTGTGTTA
65 TCATCACGTAGGAGCCATATCAACCTCAGATAACCAGCCGTCCTCATCACGCAGGAACCGTGTTA
3281603 TC
130 TC
* * * *
3281605 ATTCCTAAA-ACTGGCCAGCCATCCTCATCACGTAGGATCCGTGTCATCCCCTGACCAGACCTCC
1 ATTCCTAAAGA-TGACCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCC
* *
3281669 TCATCACGTA-GAGGCCATATC-ACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGT
65 TCATCACGTAGGA-GCCATATCAACCTC-AGATAACCAGCCGTCCTCATCACGCAGGAACCGTGT
3281732 TATCACC
128 TAT---C
* * * * *
3281739 ATTCCCTAAAGATGTCCAGTTGTCCTCATTACGTAGGAACCGTGTCATCCACTGACCAGATCTCC
1 ATT-CCTAAAGATGACCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCC
3281804 TCATCACGTAGGAGCC
65 TCATCACGTAGGAGCC
3281820 GTGTCACCCT
Statistics
Matches: 183, Mismatches: 23, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
130 6 0.03
131 68 0.37
132 38 0.21
134 4 0.02
135 64 0.35
136 3 0.02
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.24
Consensus pattern (131 bp):
ATTCCTAAAGATGACCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCT
CATCACGTAGGAGCCATATCAACCTCAGATAACCAGCCGTCCTCATCACGCAGGAACCGTGTTAT
C
Found at i:3281840 original size:135 final size:131
Alignment explanation
Indices: 3281473--3281833 Score: 438
Period size: 135 Copynumber: 2.7 Consensus size: 131
3281463 TGAAACTATT
* * * *
3281473 ATTCCTAAAGATGACCCGTCGTCCTCATCACGTAAGAATCGTGTCATCCCCCCGACCAGACCTCC
1 ATTCCTAAAGATGACCAGTCGTCCTCATCACGTAGGAACCGTGTCAT-CCCCTGACCAGACCTCC
* * * * * *
3281538 TCATCACGTAGGATCCATGTCAACCTCAGATAACCAGTCGTCTTCATCACGCAGGAACTGTGTTA
65 TCATCACGTAGGAGCCATGTCACCCTTAGATAACCAGCCGTCCTCATCACGCAGGAACCGTGTTA
3281603 TC
130 TC
* * * *
3281605 ATTCCTAAA-ACTGGCCAGCCATCCTCATCACGTAGGATCCGTGTCATCCCCTGACCAGACCTCC
1 ATTCCTAAAGA-TGACCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCC
* * *
3281669 TCATCACGTA-GAGGCCATATCACCCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTT
65 TCATCACGTAGGA-GCCATGTCACCCTTAGATAACCAGCCGTCCTCATCACGCAGGAACCGTGTT
3281733 ATCACC
129 AT---C
* * * * *
3281739 ATTCCCTAAAGATGTCCAGTTGTCCTCATTACGTAGGAACCGTGTCATCCACTGACCAGATCTCC
1 ATT-CCTAAAGATGACCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCC
*
3281804 TCATCACGTAGGAGCCGTGTCACCCTTAGA
65 TCATCACGTAGGAGCCATGTCACCCTTAGA
3281834 CGACCAGAAC
Statistics
Matches: 193, Mismatches: 28, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
130 2 0.01
131 71 0.37
132 38 0.20
134 4 0.02
135 75 0.39
136 3 0.02
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.24
Consensus pattern (131 bp):
ATTCCTAAAGATGACCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCT
CATCACGTAGGAGCCATGTCACCCTTAGATAACCAGCCGTCCTCATCACGCAGGAACCGTGTTAT
C
Found at i:3288000 original size:38 final size:37
Alignment explanation
Indices: 3287960--3288128 Score: 170
Period size: 38 Copynumber: 4.6 Consensus size: 37
3287950 ATTTAAAAAT
3287960 TATATATACGTTTTCAAAAAATGTTTTCAAAACTATA
1 TATATATACGTTTTCAAAAAATGTTTTCAAAACTATA
* * *
3287997 TTATATATATGTTTTTC-AAAAATGTTTTTAAAACCATA
1 -TATATATACG-TTTTCAAAAAATGTTTTCAAAACTATA
** * *
3288035 TAT-TATACGTTTTCAAAACTTTTTTTAAAAACTATA
1 TATATATACGTTTTCAAAAAATGTTTTCAAAACTATA
* *
3288071 TAT-TATACGTTTTCAAAAATAAGTTTCCAAAAACTATA
1 TATATATACGTTTTCAAAAA-ATGTTTTC-AAAACTATA
3288109 TATTATATA--TTTT-AAAAAAT
1 TA-TATATACGTTTTCAAAAAAT
3288129 TATATTTGAA
Statistics
Matches: 109, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
35 5 0.05
36 40 0.37
37 11 0.10
38 43 0.39
39 6 0.06
40 4 0.04
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (37 bp):
TATATATACGTTTTCAAAAAATGTTTTCAAAACTATA
Found at i:3288066 original size:36 final size:35
Alignment explanation
Indices: 3287951--3288090 Score: 158
Period size: 36 Copynumber: 3.9 Consensus size: 35
3287941 TCCAAGAATA
* *
3287951 TTTAAAAAT-TATA-TATACGTTTTCAAAAAATGTT
1 TTTAAAACTATATATTATACGTTTTC-AAAAATTTT
* * *
3287985 TTCAAAACTATATTATATATATGTTTTTCAAAAATGTT
1 TTTAAAACTATA-TAT-TATACG-TTTTCAAAAATTTT
* *
3288023 TTTAAAACCATATATTATACGTTTTCAAAACTTTT
1 TTTAAAACTATATATTATACGTTTTCAAAAATTTT
3288058 TTTAAAAACTATATATTATACGTTTTCAAAAAT
1 TTT-AAAACTATATATTATACGTTTTCAAAAAT
3288091 AAGTTTCCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
34 7 0.08
35 17 0.19
36 34 0.38
37 3 0.03
38 24 0.27
39 5 0.06
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.45
Consensus pattern (35 bp):
TTTAAAACTATATATTATACGTTTTCAAAAATTTT
Found at i:3288104 original size:74 final size:74
Alignment explanation
Indices: 3287960--3288128 Score: 186
Period size: 74 Copynumber: 2.3 Consensus size: 74
3287950 ATTTAAAAAT
* *
3287960 TATA-TATACGTTTTCAAAAAATGTTTTCAAAACTATATTATATATATGTTTTTCAAAAATGTTT
1 TATATTATACGTTTTCAAAAAATGTTTTAAAAACTATATTATATATACGTTTTTCAAAAATGTTT
**
3288024 TTAAAACCA
66 CAAAAACCA
** *
3288033 TATATTATACGTTTTCAAAACTTTTTTTAAAAACTATA-TAT-TATACG-TTTTCAAAAATAAGT
1 TATATTATACGTTTTCAAAAAATGTTTTAAAAACTATATTATATATACGTTTTTCAAAAAT--GT
*
3288095 TTCCAAAAACTA
64 TT-CAAAAACCA
**
3288107 TATATTATATATTTT-AAAAAAT
1 TATATTATACGTTTTCAAAAAAT
3288129 TATATTTGAA
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
71 11 0.14
72 5 0.06
73 16 0.20
74 48 0.60
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (74 bp):
TATATTATACGTTTTCAAAAAATGTTTTAAAAACTATATTATATATACGTTTTTCAAAAATGTTT
CAAAAACCA
Found at i:3289202 original size:30 final size:30
Alignment explanation
Indices: 3289168--3289263 Score: 122
Period size: 30 Copynumber: 3.2 Consensus size: 30
3289158 TTTGATTGAA
* *
3289168 TTTAGGGTCAAACTGATATTTTATCTAAAG
1 TTTAGGGTCAAAATAATATTTTATCTAAAG
*
3289198 TTTAGGGTTAAAATAATATTTTATCTAAAG
1 TTTAGGGTCAAAATAATATTTTATCTAAAG
* * * *
3289228 TTTA-AGTCAAATTAATATTCTATCAAAAG
1 TTTAGGGTCAAAATAATATTTTATCTAAAG
3289257 TTTAGGG
1 TTTAGGG
3289264 GTAAAATTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 24 0.43
30 32 0.57
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.41
Consensus pattern (30 bp):
TTTAGGGTCAAAATAATATTTTATCTAAAG
Found at i:3293141 original size:19 final size:18
Alignment explanation
Indices: 3293080--3293140 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 18
3293070 AGATTTGACC
3293080 AAAAGTTTCAAAACTTTGGT
1 AAAAGTTTCAAAAC-TT-GT
*
3293100 AAGAGTTTCAAAACTTGT
1 AAAAGTTTCAAAACTTGT
3293118 GAAAAGTTTCAAAACTTGT
1 -AAAAGTTTCAAAACTTGT
3293137 AAAA
1 AAAA
3293141 ATAGTATACT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.16
19 19 0.50
20 13 0.34
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (18 bp):
AAAAGTTTCAAAACTTGT
Found at i:3293957 original size:43 final size:42
Alignment explanation
Indices: 3293892--3294005 Score: 183
Period size: 43 Copynumber: 2.7 Consensus size: 42
3293882 AAGGCACCCA
* *
3293892 ACAATTTCAAATATGTTGAAAAAAAGCAAGAAGAAAAAATAC
1 ACAACTTCAAACATGTTGAAAAAAAGCAAGAAGAAAAAATAC
*
3293934 ACAACTTCAACACATGTTGAAAAAAAACAAGAAGAAAAAATAC
1 ACAACTTCAA-ACATGTTGAAAAAAAGCAAGAAGAAAAAATAC
*
3293977 ACAATTTCAAACATGTTGAAAAAAAGCAA
1 ACAACTTCAAACATGTTGAAAAAAAGCAA
3294006 TAAAAAATGT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 27 0.41
43 39 0.59
ACGTcount: A:0.59, C:0.13, G:0.11, T:0.18
Consensus pattern (42 bp):
ACAACTTCAAACATGTTGAAAAAAAGCAAGAAGAAAAAATAC
Found at i:3298687 original size:96 final size:98
Alignment explanation
Indices: 3298570--3298763 Score: 374
Period size: 97 Copynumber: 2.0 Consensus size: 98
3298560 AAAGCTGAAA
3298570 ATAAAACATTGACCGAGCTGAT-GTTGACTGTAAGAACTTTACACGAGAACTTTATGACCGT-TC
1 ATAAAACATTGACCGAGCTGATAGTTGACTGTAAGAACTTTACACGAGAACTTTATGACCGTGTC
3298633 GAGTCTTTTGAGAAAGAAAATGGCCAATATTAC
66 GAGTCTTTTGAGAAAGAAAATGGCCAATATTAC
3298666 ATAAAACATTGACCGAGCTGATAGTTGACTGTAAGAACTTTACACGAGAACTTTATGACCGTGTC
1 ATAAAACATTGACCGAGCTGATAGTTGACTGTAAGAACTTTACACGAGAACTTTATGACCGTGTC
3298731 GAGTCTTTTGAGAAAGAAAATGGCCAATATTAC
66 GAGTCTTTTGAGAAAGAAAATGGCCAATATTAC
3298764 CTACAGCTTC
Statistics
Matches: 96, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
96 22 0.23
97 39 0.41
98 35 0.36
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (98 bp):
ATAAAACATTGACCGAGCTGATAGTTGACTGTAAGAACTTTACACGAGAACTTTATGACCGTGTC
GAGTCTTTTGAGAAAGAAAATGGCCAATATTAC
Done.