Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008165.1 Hibiscus syriacus cultivar Beakdansim tig00110745_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: 2894944
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 11
Found at i:6384 original size:21 final size:22
Alignment explanation
Indices: 6358--6400 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6348 TCTAATATCT
6358 AATATTTT-AAATTTCAAATAA
1 AATATTTTAAAATTTCAAATAA
*
6379 AATATTTTAAAATTTGAAATAA
1 AATATTTTAAAATTTCAAATAA
6401 TTTAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AATATTTTAAAATTTCAAATAA
Found at i:6409 original size:16 final size:17
Alignment explanation
Indices: 6378--6412 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6368 ATTTCAAATA
*
6378 AAATATTTTAAAATTTG
1 AAATAATTTAAAATTTG
*
6395 AAATAATTTAAATTTTG
1 AAATAATTTAAAATTTG
6412 A
1 A
6413 GTTAGAGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
AAATAATTTAAAATTTG
Found at i:6835 original size:40 final size:40
Alignment explanation
Indices: 6732--7227 Score: 334
Period size: 40 Copynumber: 12.1 Consensus size: 40
6722 TTGAATAAAT
* * * * *
6732 GCCGCAAAAGATC-TAACTTTAGAGGCGTTTGTATAAAAAG
1 GCCGCTAAAGATCGT-ACTTTAGTGGCGTTTTTATACAAAC
* * *
6772 GCCGCAAAATATCTTACTTTAGTGGC-TTTTGTATACAAAC
1 GCCGCTAAAGATCGTACTTTAGTGGCGTTTT-TATACAAAC
* * *
6812 GCCGCTAAAGATAGTACTATAGTGGCGTTTTTACACAAAC
1 GCCGCTAAAGATCGTACTTTAGTGGCGTTTTTATACAAAC
* * *
6852 TCCGCTATAGAATCATACTTTAG-GAGCGGTTTTTATACAAAC
1 GCCGCTAAAG-ATCGTACTTTAGTG-GC-GTTTTTATACAAAC
6894 GCCGCT-AAGACTCGTACTTTAGTGGCGTTTTTTATA-AAA-
1 GCCGCTAAAGA-TCGTACTTTAGTGGCG-TTTTTATACAAAC
* * * * *
6933 GCACTGTTATAA-CTCGTACTGTAGTGGCGTTTGTATAAAAAC
1 GC-C-GCTA-AAGATCGTACTTTAGTGGCGTTTTTATACAAAC
* * *
6975 GCCGCTATAA-CTCATACTTTAGTGGCGTTTTTATTCAAAC
1 GCCGCTA-AAGATCGTACTTTAGTGGCGTTTTTATACAAAC
* * *
7015 GCCGCTATAGACTCGTACTTTAGTGGCGATTTTTTTTATAAAC
1 GCCGCTAAAGA-TCGTACTTTAGTGGCG--TTTTTATACAAAC
* **
7058 GCCGCTATAGACTCGTACTTTAGTGGTATTTTT-TACAAAC
1 GCCGCTAAAGA-TCGTACTTTAGTGGCGTTTTTATACAAAC
* * *
7098 GCCGCTAAAGACTCGTTCTTTCGTGGCGTTTTTGTTTACAAAC
1 GCCGCTAAAGA-TCGTACTTTAGTGGCG-TTTT-TATACAAAC
* * * *
7141 G-CGCTATAA-ACTTGTACTTTAGTGGCATTTTTAAACAAAT
1 GCCGCTA-AAGA-TCGTACTTTAGTGGCGTTTTTATACAAAC
* * * *
7181 GCC-ATGAAAAACTTGTACTTTAATGGCGTTTGTGT-TACAAAC
1 GCCGCT-AAAGA-TCGTACTTTAGTGGCGTTT-T-TATACAAAC
7223 GCCGC
1 GCCGC
7228 AAATTTAAAG
Statistics
Matches: 370, Mismatches: 57, Indels: 55
0.77 0.12 0.11
Matches are distributed among these distances:
39 6 0.02
40 157 0.42
41 108 0.29
42 50 0.14
43 49 0.13
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (40 bp):
GCCGCTAAAGATCGTACTTTAGTGGCGTTTTTATACAAAC
Found at i:6926 original size:41 final size:42
Alignment explanation
Indices: 6786--7172 Score: 399
Period size: 40 Copynumber: 9.4 Consensus size: 42
6776 CAAAATATCT
* * *
6786 TACTTTAGTGGC-TTTTGTATACAAACGCCGCTAAAGA-TAG
1 TACTTTAGTGGCGTTTTTTATACAAACGCCGCTATAGACTCG
* * * * *
6826 TACTATAGTGGCG-TTTTTACACAAACTCCGCTATAGAATCA
1 TACTTTAGTGGCGTTTTTTATACAAACGCCGCTATAGACTCG
*
6867 TACTTTAG-GAGCGGTTTTTATACAAACGCCGCTA-AGACTCG
1 TACTTTAGTG-GCGTTTTTTATACAAACGCCGCTATAGACTCG
*
6908 TACTTTAGTGGCGTTTTTTATA-AAA-GCACTGTTATA-ACTCG
1 TACTTTAGTGGCGTTTTTTATACAAACGC-C-GCTATAGACTCG
* * * *
6949 TACTGTAGTGGCG-TTTGTATAAAAACGCCGCTATA-ACTCA
1 TACTTTAGTGGCGTTTTTTATACAAACGCCGCTATAGACTCG
*
6989 TACTTTAGTGGCG-TTTTTATTCAAACGCCGCTATAGACTCG
1 TACTTTAGTGGCGTTTTTTATACAAACGCCGCTATAGACTCG
* *
7030 TACTTTAGTGGCGATTTTTTTTATAAACGCCGCTATAGACTCG
1 TACTTTAGTGGCG-TTTTTTATACAAACGCCGCTATAGACTCG
*
7073 TACTTTAGT-G-GTATTTTT-TACAAACGCCGCTAAAGACTCG
1 TACTTTAGTGGCGT-TTTTTATACAAACGCCGCTATAGACTCG
* * * * *
7113 TTCTTTCGTGGCGTTTTTGTTTACAAACG-CGCTATAAACTTG
1 TACTTTAGTGGCGTTTTT-TATACAAACGCCGCTATAGACTCG
*
7155 TACTTTAGTGGCATTTTT
1 TACTTTAGTGGCGTTTTT
7173 AAACAAATGC
Statistics
Matches: 293, Mismatches: 36, Indels: 34
0.81 0.10 0.09
Matches are distributed among these distances:
39 2 0.01
40 111 0.38
41 87 0.30
42 51 0.17
43 42 0.14
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (42 bp):
TACTTTAGTGGCGTTTTTTATACAAACGCCGCTATAGACTCG
Found at i:6993 original size:81 final size:83
Alignment explanation
Indices: 6786--7172 Score: 314
Period size: 82 Copynumber: 4.7 Consensus size: 83
6776 CAAAATATCT
* * * * * **
6786 TACTTTAGTGGC-TTTTGTATACAAACGCCGCTAAAGA-TAGTACTATAGTGGCG-TTTTTACAC
1 TACTGTAGTGGCGTTTT-TATAAAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTTATTC
** * *
6848 AAACTCCGCTATAGAATCA
65 AAAAGCCGCTATAGACTCG
* *
6867 TACTTTAG-GAGCGGTTTTTATACAAACGCCGCTA-AGACTCGTACTTTAGTGGCGTTTTTTA-T
1 TACTGTAGTG-GC-GTTTTTATAAAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTTATT
*
6929 -AAAAGCACTGTTATA-ACTCG
64 CAAAAGC-C-GCTATAGACTCG
* *
6949 TACTGTAGTGGCGTTTGTATAAAAACGCCGCTATA-ACTCATACTTTAGTGGCG-TTTTTATTCA
1 TACTGTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTTATTCA
*
7012 AACGCCGCTATAGACTCG
66 AAAGCCGCTATAGACTCG
* * * **
7030 TACTTTAGTGGCGATTTTTTTTATAAACGCCGCTATAGACTCGTACTTTAGTGGTATTTTTTA--
1 TACTGTAGTGGCG--TTTTTATAAAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTTATT
* *
7093 CAAACGCCGCTAAAGACTCG
64 CAAAAGCCGCTATAGACTCG
* * * * * * * *
7113 TTCTTTCGTGGCGTTTTTGTTTACAAACG-CGCTATAAACTTGTACTTTAGTGGCATTTTT
1 TACTGTAGTGGCG-TTTT-TATAAAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTT
7173 AAACAAATGC
Statistics
Matches: 261, Mismatches: 28, Indels: 33
0.81 0.09 0.10
Matches are distributed among these distances:
80 12 0.05
81 72 0.28
82 82 0.31
83 74 0.28
84 15 0.06
85 6 0.02
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (83 bp):
TACTGTAGTGGCGTTTTTATAAAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTTATTCA
AAAGCCGCTATAGACTCG
Found at i:7036 original size:163 final size:165
Alignment explanation
Indices: 6786--7092 Score: 417
Period size: 163 Copynumber: 1.9 Consensus size: 165
6776 CAAAATATCT
* * *
6786 TACTTTAGTGGCTTTTGTATACAAACGCCGCTAAAGATAGTACTATAGTGGCGTTTTTACACAAA
1 TACTGTAGTGGCGTTTGTATAAAAACGCCGCTAAAGATAGTACTATAGTGGCGTTTTTACACAAA
*
6851 CTCCGCTATAGAATCATACTTTAG-GAGCG-GTTTTTATACAAACGCCGCTA-AGACTCGTACTT
66 CGCCGCTATAGAATCATACTTTAGTG-GCGAGTTTTTATACAAACGCCGCTATAGACTCGTACTT
*
6913 TAGTGGCGTTTTTTATAAAAGCACTGTTATAACTCG
130 TAGTGGCATTTTTTATAAAAGCACTGTTATAACTCG
* * **
6949 TACTGTAGTGGCGTTTGTATAAAAACGCCGCTATAA-CTCA-TACTTTAGTGGCGTTTTTATTCA
1 TACTGTAGTGGCGTTTGTATAAAAACGCCGCTA-AAGAT-AGTACTATAGTGGCGTTTTTACACA
* * * * *
7012 AACGCCGCTATAGACTCGTACTTTAGTGGCGATTTTTTTTATAAACGCCGCTATAGACTCGTACT
64 AACGCCGCTATAGAATCATACTTTAGTGGCGAGTTTTTATACAAACGCCGCTATAGACTCGTACT
*
7077 TTAGTGGTATTTTTTA
129 TTAGTGGCATTTTTTA
7093 CAAACGCCGC
Statistics
Matches: 124, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
163 77 0.62
164 22 0.18
165 25 0.20
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (165 bp):
TACTGTAGTGGCGTTTGTATAAAAACGCCGCTAAAGATAGTACTATAGTGGCGTTTTTACACAAA
CGCCGCTATAGAATCATACTTTAGTGGCGAGTTTTTATACAAACGCCGCTATAGACTCGTACTTT
AGTGGCATTTTTTATAAAAGCACTGTTATAACTCG
Found at i:7179 original size:83 final size:85
Alignment explanation
Indices: 6786--7227 Score: 327
Period size: 83 Copynumber: 5.4 Consensus size: 85
6776 CAAAATATCT
* * * * * *
6786 TACTTTAGTGGC---TTTTGTATACAAACGCCGCTA-AAGA-TAGTACTATAGTGGCGTTTTTAC
1 TACTTTAGTGGCGATTTTTGTTTAAAAACGCCGCTATAA-ACTCGTACTTTAGTGGCATTTTTAT
* * * *
6846 ACAAACTCCGCTATAGAATCA
65 ACAAACGCCGCTAAAGACTCG
* * * * *
6867 TACTTTAG-GAGCG-GTTTT-TATACAAACGCCGCTA-AGACTCGTACTTTAGTGGCGTTTTTTA
1 TACTTTAGTG-GCGATTTTTGTTTAAAAACGCCGCTATAAACTCGTACTTTAGTGGC-ATTTTTA
* *
6928 TA-AAA-GCACTGTTATA-ACTCG
64 TACAAACGC-C-GCTAAAGACTCG
* * * * *
6949 TACTGTAGTGGCG---TTTGTATAAAAACGCCGCTAT-AACTCATACTTTAGTGGCGTTTTTATT
1 TACTTTAGTGGCGATTTTTGTTTAAAAACGCCGCTATAAACTCGTACTTTAGTGGCATTTTTATA
*
7010 CAAACGCCGCTATAGACTCG
66 CAAACGCCGCTAAAGACTCG
* * *
7030 TACTTTAGTGGCGATTTTT-TTTATAAACGCCGCTATAGACTCGTACTTTAGTGGTATTTTT-TA
1 TACTTTAGTGGCGATTTTTGTTTAAAAACGCCGCTATAAACTCGTACTTTAGTGGCATTTTTATA
7093 CAAACGCCGCTAAAGACTCG
66 CAAACGCCGCTAAAGACTCG
* * * * *
7113 TTCTTTCGTGGCG-TTTTTGTTTACAAACG-CGCTATAAACTTGTACTTTAGTGGCATTTTTAAA
1 TACTTTAGTGGCGATTTTTGTTTAAAAACGCCGCTATAAACTCGTACTTTAGTGGCATTTTTATA
* * * *
7176 CAAATGCC-ATGAAAAACTTG
66 CAAACGCCGCT-AAAGACTCG
* * *
7196 TACTTTAATGGCG-TTTGTG-TTACAAACGCCGC
1 TACTTTAGTGGCGATTTTTGTTTAAAAACGCCGC
7228 AAATTTAAAG
Statistics
Matches: 300, Mismatches: 40, Indels: 40
0.79 0.11 0.11
Matches are distributed among these distances:
80 16 0.05
81 64 0.21
82 92 0.31
83 105 0.35
84 23 0.08
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (85 bp):
TACTTTAGTGGCGATTTTTGTTTAAAAACGCCGCTATAAACTCGTACTTTAGTGGCATTTTTATA
CAAACGCCGCTAAAGACTCG
Found at i:7219 original size:82 final size:81
Alignment explanation
Indices: 6786--7224 Score: 292
Period size: 82 Copynumber: 5.4 Consensus size: 81
6776 CAAAATATCT
* * *
6786 TACTTTAGTGGC--TTTTGTATACAAACGCCGCTA-AAGA-TAGTACTATAGTGGCGTTTTTACA
1 TACTTTAGTGGCGTTTTTGT-TACAAACG-CGCTATAA-ACTCGTACTTTAGTGGCATTTTTA-A
* * * *
6847 CAAACTCCGCTATAGAA-TCA
62 CAAACGCCGATA-AAAACTCG
* * * * *
6867 TACTTTAG-GAGCGGTTTTT-ATACAAACGCCGCTA-AGACTCGTACTTTAGTGGCGTTTTTTAT
1 TACTTTAGTG-GC-GTTTTTGTTACAAACG-CGCTATAAACTCGTACTTTAGTGGCATTTTTAAC
* * *
6929 AAAAGCACTG-TTATAACTCG
63 AAACGC-C-GATAAAAACTCG
* * * * *
6949 TACTGTAGTGGCG--TTTGTATAAAAACGCCGCTAT-AACTCATACTTTAGTGGCGTTTTTATTC
1 TACTTTAGTGGCGTTTTTGT-TACAAACG-CGCTATAAACTCGTACTTTAGTGGCATTTTTA-AC
* * *
7011 AAACGCCGCTATAGACTCG
63 AAACGCCGATAAAAACTCG
* * * * *
7030 TACTTTAGTGGCGATTTTTTTTATAAACGCCGCTATAGACTCGTACTTTAGTGGTATTTTTTACA
1 TACTTTAGTGGCG-TTTTTGTTACAAACG-CGCTATAAACTCGTACTTTAGTGGCATTTTTAACA
* *
7095 AACGCCGCTAAAGACTCG
64 AACGCCGATAAAAACTCG
* * *
7113 TTCTTTCGTGGCGTTTTTGTTTACAAACGCGCTATAAACTTGTACTTTAGTGGCATTTTTAAACA
1 TACTTTAGTGGCGTTTTTG-TTACAAACGCGCTATAAACTCGTACTTTAGTGGCATTTTT-AACA
* *
7178 AATGCC-ATGAAAAACTTG
64 AACGCCGAT-AAAAACTCG
* *
7196 TACTTTAATGGCGTTTGTGTTACAAACGC
1 TACTTTAGTGGCGTTTTTGTTACAAACGC
7225 CGCAAATTTA
Statistics
Matches: 287, Mismatches: 50, Indels: 41
0.76 0.13 0.11
Matches are distributed among these distances:
79 3 0.01
80 2 0.01
81 74 0.26
82 96 0.33
83 84 0.29
84 28 0.10
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (81 bp):
TACTTTAGTGGCGTTTTTGTTACAAACGCGCTATAAACTCGTACTTTAGTGGCATTTTTAACAAA
CGCCGATAAAAACTCG
Found at i:10576 original size:43 final size:43
Alignment explanation
Indices: 10528--10644 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 43
10518 ATGGTAATTA
*
10528 GCGGCGTTTGTATCCAAAAACGCCGCTAAATATCT-AACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTAAAGATCTCAACCTTTT
* *
10571 GCGGCGTTTGTT-CAAAACACGCCGCTATAGATCTCGACCTTTT
1 GCGGCGTTTGTTCCAAAA-ACGCCGCTAAAGATCTCAACCTTTT
* *
10614 ---GCGTTTGTTCCAAAAATGCCGCTATAGATCT
1 GCGGCGTTTGTTCCAAAAACGCCGCTAAAGATCT
10645 TGAACTATGG
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
40 24 0.36
41 10 0.15
42 15 0.22
43 18 0.27
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (43 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTAAAGATCTCAACCTTTT
Found at i:12073 original size:15 final size:15
Alignment explanation
Indices: 12053--12090 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
12043 TCTTTGCATT
*
12053 GAACTTGACAAATTC
1 GAACTTGAAAAATTC
12068 GAACTTGAAAAATTC
1 GAACTTGAAAAATTC
12083 GAACTTGA
1 GAACTTGA
12091 TTTGATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (15 bp):
GAACTTGAAAAATTC
Found at i:14488 original size:55 final size:55
Alignment explanation
Indices: 14404--14770 Score: 504
Period size: 55 Copynumber: 6.7 Consensus size: 55
14394 CAAATGATAA
* * * **
14404 GTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTAGAACAAACTTCGGCAAACGT
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGT
* * *
14459 GTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGG
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGT
*
14514 GTTTGCTCCCTATTCGTTCAGGGAGTAT-AGAACTCGAACAATCTTCAACAAACGT
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAAG-ACTCGAACAATCTTCAACAAACGT
** * *
14569 GTCTGCTCCCTATTATTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGG
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGT
* ***
14624 GTCCGCTCCCTATTCGTTCAGGGAGTAT-AGAACTCGAACAATCTTCAGTGAACGT
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAAG-ACTCGAACAATCTTCAACAAACGT
* *
14679 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCAAACAATCTTCAACTAACGT
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGT
* * *
14734 GTCTGCTCCCTATTCTTTCAGAGAGTATAGGACTCGA
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGA
14771 TCTTCATAAA
Statistics
Matches: 277, Mismatches: 31, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
54 4 0.01
55 269 0.97
56 4 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (55 bp):
GTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGT
Found at i:14840 original size:37 final size:37
Alignment explanation
Indices: 14781--14856 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
14771 TCTTCATAAA
14781 ATGAGTTTGCTTCACTACTCTTCCGTGAAGCCTTATAG
1 ATGAGTTTGCTTCACTACTCTTCCGTGAAGCCTTA-AG
* *
14819 ATGA-TTTTCTTCACTACTCTTCCGTGAAGGCTTAAG
1 ATGAGTTTGCTTCACTACTCTTCCGTGAAGCCTTAAG
14855 AT
1 AT
14857 TGAATTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 4 0.11
37 28 0.78
38 4 0.11
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.38
Consensus pattern (37 bp):
ATGAGTTTGCTTCACTACTCTTCCGTGAAGCCTTAAG
Found at i:16173 original size:9 final size:9
Alignment explanation
Indices: 16130--16336 Score: 109
Period size: 9 Copynumber: 21.9 Consensus size: 9
16120 TGAACCCCCC
16130 TTTTATTTCT
1 TTTTATTT-T
16140 TTTTATTTT
1 TTTTATTTT
*
16149 TCTT-TTTT
1 TTTTATTTT
** *
16157 CATCATTTT
1 TTTTATTTT
16166 TTTTATTTT
1 TTTTATTTT
*
16175 TTTCTCTTTCT
1 TTT-TATTT-T
16186 TCTTT-TTTCAT
1 T-TTTATTT--T
16197 TTTTCATTTT
1 TTTT-ATTTT
16207 ATTTTATTTT
1 -TTTTATTTT
*
16217 TTCTTCTTTT
1 TT-TTATTTT
16227 TTTTA-TTT
1 TTTTATTTT
*
16235 TTTTA-ATT
1 TTTTATTTT
16243 TTTTATTTT
1 TTTTATTTT
* *
16252 CTTCATTTT
1 TTTTATTTT
16261 CTTTTCATTTT
1 -TTTT-ATTTT
* *
16272 CTTCATTTT
1 TTTTATTTT
*
16281 TTTCATTTT
1 TTTTATTTT
*
16290 TTTCATTTTTT
1 TTT--TATTTT
16301 TTTTCATTTT
1 TTTT-ATTTT
16311 TTTTCA-TTT
1 TTTT-ATTTT
*
16320 TTTCATTTT
1 TTTTATTTT
*
16329 TTCTATTT
1 TTTTATTT
16337 CTTCTTTAAG
Statistics
Matches: 155, Mismatches: 26, Indels: 33
0.72 0.12 0.15
Matches are distributed among these distances:
8 21 0.14
9 62 0.40
10 46 0.30
11 21 0.14
12 5 0.03
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTATTTT
Found at i:16257 original size:54 final size:53
Alignment explanation
Indices: 16199--16330 Score: 161
Period size: 54 Copynumber: 2.6 Consensus size: 53
16189 TTTTTCATTT
*
16199 TTCATTTTATTTT-ATTTTTTCTTC-TTTTTTTTATTTTTTTAATTTTTTATTTTC
1 TTCATTTTATTTTCA--TTTTCTTCATTTTTTTCATTTTTTTAATTTTTT-TTTTC
* *
16253 TTCATTTTCTTTTCATTTTCTTCATTTTTTTCATTTTTTTCA--TTTTTTTT-
1 TTCATTTTATTTTCATTTTCTTCATTTTTTTCATTTTTTTAATTTTTTTTTTC
16303 TTCATTTT-TTTTCATTTT-TTCATTTTTT
1 TTCATTTTATTTTCATTTTCTTCATTTTTT
16331 CTATTTCTTC
Statistics
Matches: 73, Mismatches: 3, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
48 10 0.14
49 10 0.14
50 8 0.11
51 4 0.05
52 4 0.05
53 8 0.11
54 28 0.38
55 1 0.01
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (53 bp):
TTCATTTTATTTTCATTTTCTTCATTTTTTTCATTTTTTTAATTTTTTTTTTC
Found at i:19814 original size:2 final size:2
Alignment explanation
Indices: 19807--19836 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19797 GAAAGAGAAG
*
19807 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19837 GGGAGGATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28964 original size:22 final size:22
Alignment explanation
Indices: 28934--28984 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
28924 ACAAAGGCAG
28934 AAGCGATATTTTCAATCGAATC
1 AAGCGATATTTTCAATCGAATC
*
28956 AGGCGATATTTTCAATCGAATC
1 AAGCGATATTTTCAATCGAATC
28978 AAGCGAT
1 AAGCGAT
28985 TTTCAGACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (22 bp):
AAGCGATATTTTCAATCGAATC
Found at i:38750 original size:73 final size:75
Alignment explanation
Indices: 38625--38782 Score: 187
Period size: 74 Copynumber: 2.1 Consensus size: 75
38615 ATGATAAGGG
* * * *
38625 GTATCGATACCAAGAAACATCGAATCTAATTTTGATATCGATACCGGTA-GGGGAATCAATACCC
1 GTATCGATACCAAGAAACATCGAACCTAATTTTGATATCGATACCCGAAGGGGGAATCAATACCA
* *
38689 TAGTATGGTA
66 TAGTATAGAA
* * * **
38699 GTATCGATACCAA-CAACATCGAACCT-ATTTTCGGTATCGATACCCGAAGGGGGTATCGGTACC
1 GTATCGATACCAAGAAACATCGAACCTAATTTT-GATATCGATACCCGAAGGGGGAATCAATACC
38762 ATAGTATAGAA
65 ATAGTATAGAA
38773 GTATCGATAC
1 GTATCGATAC
38783 AAGGGTAGTA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
72 5 0.07
73 24 0.34
74 42 0.59
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (75 bp):
GTATCGATACCAAGAAACATCGAACCTAATTTTGATATCGATACCCGAAGGGGGAATCAATACCA
TAGTATAGAA
Found at i:39211 original size:58 final size:58
Alignment explanation
Indices: 39130--39291 Score: 220
Period size: 58 Copynumber: 2.8 Consensus size: 58
39120 TGGCACTTCG
* * * *
39130 TGTGCAAAATG-TTAAAAATTCATACTAAGTGTATGAATTTCCGTAT-AGACACTTTA
1 TGTGCTAAATGATAAAAAATTCATACTAAGTGTATGAATTTCCGCATCAGACACCTTA
* * *
39186 TGTGCTAACATGATAAAAAATTCATACTAAGTGTATGAATTTCTGCATCGGGCACCTTA
1 TGTGCTAA-ATGATAAAAAATTCATACTAAGTGTATGAATTTCCGCATCAGACACCTTA
* *
39245 TGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCAGCAT
1 TGTGCTAAATGATAAAAAATTCATACTAAGTGTATGAATTTCCGCAT
39292 GTGAAATATA
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
56 7 0.07
57 3 0.03
58 69 0.73
59 15 0.16
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (58 bp):
TGTGCTAAATGATAAAAAATTCATACTAAGTGTATGAATTTCCGCATCAGACACCTTA
Found at i:39312 original size:58 final size:56
Alignment explanation
Indices: 39136--39312 Score: 153
Period size: 58 Copynumber: 3.1 Consensus size: 56
39126 TTCGTGTGCA
* * * *
39136 AAATGTTAAAAATTCATACTAAGTGTATGAATTTCCGTAT-AGACACTTTATGTGCTA-
1 AAATGATAAAAATTCATACTAAGTGTATGAATTTCAGCATGAGA-AC-TTATG-GGTAT
* * * * * *
39193 ACATGATAAAAAATTCATACTAAGTGTATGAATTTCTGCATCGGGCACCTTATGTG-CT
1 AAATGAT-AAAAATTCATACTAAGTGTATGAATTTCAGCAT-GAG-AACTTATGGGTAT
* *
39251 AAATGATAAGAAATTCATACTAAGTGTATGAATTTCAGCATGTGAAATATATGGGTAT
1 AAATGATAA-AAATTCATACTAAGTGTATGAATTTCAGCATGAGAACT-TATGGGTAT
39309 AAAT
1 AAAT
39313 ATTAGAACTG
Statistics
Matches: 96, Mismatches: 16, Indels: 15
0.76 0.13 0.12
Matches are distributed among these distances:
56 2 0.02
57 14 0.15
58 72 0.75
59 5 0.05
60 2 0.02
61 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (56 bp):
AAATGATAAAAATTCATACTAAGTGTATGAATTTCAGCATGAGAACTTATGGGTAT
Found at i:43362 original size:72 final size:71
Alignment explanation
Indices: 43280--43452 Score: 186
Period size: 72 Copynumber: 2.4 Consensus size: 71
43270 CCAATGAGGT
*
43280 AGTATCGATACCAT-GATAAGAGTATCAATACCAAGAAACATCGAATCTAATTTTGGTATCGATA
1 AGTATCGATACCATAG-TAAGAGTATCAATACCAAGAAACATC-AACCTAATTTTGGTATCGATA
43344 CCGGTAGA
64 CCGGTAGA
* * ** * *
43352 AGTATCGATACCCTAGTAAGGGTATTTATACCAGGAAACATCAACCTATTTTTGGTATCGATACC
1 AGTATCGATACCATAGTAAGAGTATCAATACCAAGAAACATCAACCTAATTTTGGTATCGATACC
* * *
43417 CGAAGGG
66 GGTA-GA
* *
43424 GGTATCGGTACCATAGTATAGAAGTATCA
1 AGTATCGATACCATAGTA-AG-AGTATCA
43453 GTACTAGGGT
Statistics
Matches: 81, Mismatches: 16, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
71 23 0.28
72 51 0.63
73 3 0.04
74 4 0.05
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (71 bp):
AGTATCGATACCATAGTAAGAGTATCAATACCAAGAAACATCAACCTAATTTTGGTATCGATACC
GGTAGA
Found at i:43888 original size:59 final size:59
Alignment explanation
Indices: 43800--43962 Score: 267
Period size: 59 Copynumber: 2.8 Consensus size: 59
43790 CAAATGGAAT
* *
43800 TTCGTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCA-C
1 TTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACC
* *
43858 TTCGTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCTGTATCGGGCACC
1 TTCGTGTGCTAA-ATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACC
43918 TT-GTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTC
1 TTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTC
43963 AATATGGGTA
Statistics
Matches: 99, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
58 45 0.45
59 51 0.52
60 3 0.03
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (59 bp):
TTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACC
Found at i:44511 original size:68 final size:68
Alignment explanation
Indices: 44329--44511 Score: 298
Period size: 67 Copynumber: 2.7 Consensus size: 68
44319 GAATAAAGGA
*
44329 CTAACTGTGCATATGACATAAAGGTGTTATTTAT-TCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CTAACTGTGCATATGACATAAAGGTGTCATTTATGT-CAGTTAGATGAAAGGCTAAGTGCCTTTG
44393 AGGC
65 AGGC
* * *
44397 CTAAC-GTGCATATGAAAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATATGACATAAAGGTGTCATTTATGTCAGTTAGATGAAAGGCTAAGTGCCTTTGA
44461 GGC
66 GGC
*
44464 CTAACTGTGCATATGACATAAAGGTGTCAATTATGTCAGTTAGATGAA
1 CTAACTGTGCATATGACATAAAGGTGTCATTTATGTCAGTTAGATGAA
44512 CATTAAACAC
Statistics
Matches: 105, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
67 62 0.59
68 43 0.41
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (68 bp):
CTAACTGTGCATATGACATAAAGGTGTCATTTATGTCAGTTAGATGAAAGGCTAAGTGCCTTTGA
GGC
Found at i:44685 original size:79 final size:79
Alignment explanation
Indices: 44464--44695 Score: 331
Period size: 78 Copynumber: 2.9 Consensus size: 79
44454 CCTTTGAGGC
* * *
44464 CTAACTGTGCATATGACATAAAGGTGTCAATTATGTCAGTTAGATGAACATTAAACACTGTTGAG
1 CTAACTGTGCAT-TGGCAGAAAGATGTCAATTATGTCAGTTAGATGAACATTAAACACTGTTGAG
44529 TAAAAGAATAATGGT
65 TAAAAGAATAATGGT
* * ** * *
44544 CTAATTGTGCATTGGCAG-AAGATGTCAATTATGTCGGTTAGACAAACATTAAACACTATTGAGA
1 CTAACTGTGCATTGGCAGAAAGATGTCAATTATGTCAGTTAGATGAACATTAAACACTGTTGAGT
44608 AAAAGAATAATGGT
66 AAAAGAATAATGGT
* * *
44622 CTAACTGTGCATTGGCAGAAAGATATCAATTATGCCAGTTAGATGAACGTTAAACACTGTTGAGT
1 CTAACTGTGCATTGGCAGAAAGATGTCAATTATGTCAGTTAGATGAACATTAAACACTGTTGAGT
*
44687 AAGAGAATA
66 AAAAGAATA
44696 CATAAATTAT
Statistics
Matches: 132, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
78 71 0.54
79 50 0.38
80 11 0.08
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (79 bp):
CTAACTGTGCATTGGCAGAAAGATGTCAATTATGTCAGTTAGATGAACATTAAACACTGTTGAGT
AAAAGAATAATGGT
Found at i:45810 original size:9 final size:9
Alignment explanation
Indices: 45798--45855 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 9
45788 AAGAGTGATA
45798 AGGACGATG
1 AGGACGATG
* *
45807 AGGAGGAGG
1 AGGACGATG
*
45816 AGGAGGATG
1 AGGACGATG
**
45825 TCGACGATG
1 AGGACGATG
*
45834 AGGAGGATG
1 AGGACGATG
*
45843 AAGACGATG
1 AGGACGATG
45852 AGGA
1 AGGA
45856 GGAGCATGGC
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.34, C:0.07, G:0.48, T:0.10
Consensus pattern (9 bp):
AGGACGATG
Found at i:45824 original size:18 final size:18
Alignment explanation
Indices: 45815--45858 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
45805 TGAGGAGGAG
**
45815 GAGGAGGATGTCGACGAT
1 GAGGAGGATGAAGACGAT
45833 GAGGAGGATGAAGACGAT
1 GAGGAGGATGAAGACGAT
45851 GAGGAGGA
1 GAGGAGGA
45859 GCATGGCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.34, C:0.07, G:0.48, T:0.11
Consensus pattern (18 bp):
GAGGAGGATGAAGACGAT
Found at i:48681 original size:26 final size:28
Alignment explanation
Indices: 48611--48703 Score: 89
Period size: 26 Copynumber: 3.6 Consensus size: 28
48601 AGTCAAATTA
48611 AATAAAA-AT-TTTAAA-ATATTTGAAT
1 AATAAAATATATTTAAATATATTTGAAT
* *
48636 --TAAAATAT-TTAAAATATATTT-ATT
1 AATAAAATATATTTAAATATATTTGAAT
48660 AATAAAATATATTTAAAT-TATTTGAAT
1 AATAAAATATATTTAAATATATTTGAAT
48687 AA-AAGAAT-TATTTAAAT
1 AATAA-AATATATTTAAAT
48704 GTGATAATTG
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
23 5 0.09
24 9 0.16
25 6 0.11
26 24 0.42
27 13 0.23
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (28 bp):
AATAAAATATATTTAAATATATTTGAAT
Found at i:50106 original size:24 final size:25
Alignment explanation
Indices: 50079--50144 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
50069 TGCAATGGTG
*
50079 CTAATATAGGAGTACACGAA-TGCA
1 CTAATATAGGAGTACACAAATTGCA
*
50103 CTAAT-TCAGGAGTGC-CAAATTGCA
1 CTAATAT-AGGAGTACACAAATTGCA
* *
50127 CTAATACAAGAGTACACA
1 CTAATATAGGAGTACACA
50145 TTTGTACTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
23 4 0.12
24 27 0.82
25 2 0.06
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (25 bp):
CTAATATAGGAGTACACAAATTGCA
Found at i:50153 original size:24 final size:24
Alignment explanation
Indices: 50120--50192 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
50110 AGGAGTGCCA
*
50120 AATTGCACTAATACAAGAGTACAC
1 AATTGTACTAATACAAGAGTACAC
* * * * *
50144 ATTTGTACTAAAACGAGAGTGCAT
1 AATTGTACTAATACAAGAGTACAC
*
50168 AATTGTACTAATTACATGAGTACAC
1 AATTGTACTAA-TACAAGAGTACAC
50193 GAATGAACTA
Statistics
Matches: 36, Mismatches: 12, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
24 28 0.78
25 8 0.22
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.27
Consensus pattern (24 bp):
AATTGTACTAATACAAGAGTACAC
Found at i:56249 original size:10 final size:10
Alignment explanation
Indices: 56221--56263 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
56211 ATTGATTTTG
56221 GATT-GAATT
1 GATTGGAATT
56230 GATATGGAATT
1 GAT-TGGAATT
56241 GATTGGAATT
1 GATTGGAATT
**
56251 GCGTGGAATT
1 GATTGGAATT
56261 GAT
1 GAT
56264 GTTAGGAGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 3 0.11
10 17 0.61
11 8 0.29
ACGTcount: A:0.30, C:0.02, G:0.30, T:0.37
Consensus pattern (10 bp):
GATTGGAATT
Found at i:60246 original size:27 final size:28
Alignment explanation
Indices: 60208--60272 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
60198 TATAACTCAA
60208 AAACCCAAAATCA-AAACCCCATTCGTG
1 AAACCCAAAATCAGAAACCCCATTCGTG
*
60235 AAACCCAAAATCAGAACCCCCATTCGTG
1 AAACCCAAAATCAGAAACCCCATTCGTG
60263 AAACCCAAAA
1 AAACCCAAAA
60273 CAACCTCTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 13 0.36
28 23 0.64
ACGTcount: A:0.46, C:0.34, G:0.08, T:0.12
Consensus pattern (28 bp):
AAACCCAAAATCAGAAACCCCATTCGTG
Found at i:66054 original size:25 final size:25
Alignment explanation
Indices: 66009--66079 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
65999 AAAGCCCGAA
66009 GCTTTGTTTATTTTTTTCTTTCGATT
1 GCTTTGTTTA-TTTTTTCTTTCGATT
* *
66035 GCTTTGTTTATTTTTACTTTCGGTT
1 GCTTTGTTTATTTTTTCTTTCGATT
*
66060 GCCTTGTTTATTTTTTCTTT
1 GCTTTGTTTATTTTTTCTTT
66080 TGGTTTGTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 31 0.76
26 10 0.24
ACGTcount: A:0.07, C:0.13, G:0.13, T:0.68
Consensus pattern (25 bp):
GCTTTGTTTATTTTTTCTTTCGATT
Found at i:66585 original size:2 final size:2
Alignment explanation
Indices: 66580--66794 Score: 241
Period size: 2 Copynumber: 110.5 Consensus size: 2
66570 AAACAAATGA
* * * *
66580 AT AT AT AT AT AT AT AT AT AT A- AT AT AT GT GT -T AT AA AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
66620 AT -T AT AA AA AT A- AT AA AT AT A- AT AT AT AA AT AT AC ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
66660 -T A- AT AT AT AT AT ACT AT A- AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
66700 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
*
66743 AT AT A- AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66784 AT AT AT AT AT A
1 AT AT AT AT AT A
66795 CTACACATAA
Statistics
Matches: 184, Mismatches: 17, Indels: 24
0.82 0.08 0.11
Matches are distributed among these distances:
1 9 0.05
2 170 0.92
3 5 0.03
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (2 bp):
AT
Found at i:67659 original size:25 final size:25
Alignment explanation
Indices: 67630--67695 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
67620 AAGCCCCAAA
*
67630 CTTTGTTGATTTTTTCCTTCGGTTG
1 CTTTGTTTATTTTTTCCTTCGGTTG
* *
67655 CTTTGTTTATTTTTGCTTTCGGTTG
1 CTTTGTTTATTTTTTCCTTCGGTTG
*
67680 CTTTATTTATTTTTTC
1 CTTTGTTTATTTTTTC
67696 TTTCAGTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.06, C:0.14, G:0.15, T:0.65
Consensus pattern (25 bp):
CTTTGTTTATTTTTTCCTTCGGTTG
Found at i:67698 original size:25 final size:25
Alignment explanation
Indices: 67638--67699 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
67628 AACTTTGTTG
* *
67638 ATTTTTTCCTTCGGTTGCTTTGTTT
1 ATTTTTTCTTTCGGTTGCTTTATTT
*
67663 ATTTTTGCTTTCGGTTGCTTTATTT
1 ATTTTTTCTTTCGGTTGCTTTATTT
67688 ATTTTTTCTTTC
1 ATTTTTTCTTTC
67700 AGTTTATGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.06, C:0.15, G:0.13, T:0.66
Consensus pattern (25 bp):
ATTTTTTCTTTCGGTTGCTTTATTT
Found at i:68222 original size:2 final size:2
Alignment explanation
Indices: 68217--68252 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
68207 AAGCAAATGA
68217 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68253 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68257 original size:2 final size:2
Alignment explanation
Indices: 68252--68300 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
68242 TATATATATA
*
68252 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
68294 TG TG TG T
1 TG TG TG T
68301 TATAAATAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:68334 original size:2 final size:2
Alignment explanation
Indices: 68318--68554 Score: 145
Period size: 2 Copynumber: 125.5 Consensus size: 2
68308 AAGTTATAAC
* *
68318 AT AT A- AT AA AT AT AT AT AT TT AT AT AT ACT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
68359 AT AT AT AT AT AT A- AT AG A- AT AT AA AT AA AT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
68397 AT A- AT AT AT AT AT AT AT AA AT AT ACT AT A- AC AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
*
68437 A- AT AT AT -T AT AT A- AT AT AA AT AT ACT AT A- AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
*
68475 -T A- AT AA AT A- AT AT -T AT A- AT AT AT AT AT ACT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * * * *
68512 AT AA AT TT ACT AC AC AT AA AA ACT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A
68555 AAAAAGATCG
Statistics
Matches: 185, Mismatches: 24, Indels: 52
0.71 0.09 0.20
Matches are distributed among these distances:
1 20 0.11
2 154 0.83
3 11 0.06
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:68382 original size:77 final size:76
Alignment explanation
Indices: 68301--68514 Score: 228
Period size: 75 Copynumber: 2.8 Consensus size: 76
68291 GTGTGTGTGT
* *
68301 TATAAATAAGTTATAACATATAATAAATATATATATTTATATATACTATATAATATATATATATA
1 TATAAATAA-ATATAATATATAATAAATATATATATTTATATATACTATATAATATATATATATA
68366 TATATAATAGAA
65 TATATAATAGAA
* *
68378 TATAAATAAATATAATA-AT-ATAATATATATATATATAAATATACTATA-ACATATA-ATATA-
1 TATAAATAAATATAATATATAATAA-ATATATATATTTATATATACTATATA-ATATATATATAT
* *
68438 ATATATTATATAA
64 ATATATAATAGAA
* * * *
68451 TATAAATATACTATAATATATAATTAATAAATA-ATATTATAATATA-TATATACTATAT-TATA
1 TATAAATA-AATATAATATATAATAAATATATATAT-TTAT-ATATACTATATAATATATATATA
68513 TA
63 TA
68515 AATTTACTAC
Statistics
Matches: 115, Mismatches: 12, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
73 19 0.17
74 20 0.17
75 51 0.44
76 16 0.14
77 9 0.08
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (76 bp):
TATAAATAAATATAATATATAATAAATATATATATTTATATATACTATATAATATATATATATAT
ATATAATAGAA
Found at i:68453 original size:73 final size:74
Alignment explanation
Indices: 68312--68514 Score: 208
Period size: 73 Copynumber: 2.8 Consensus size: 74
68302 ATAAATAAGT
* *
68312 TATAACAT-ATAATA-AATATATATATTTATATATACTATATAATATATATATATATATATAATA
1 TATAATATAATAATATAATATATATATTTAAATATACTATATAATATATATATATATATATAATA
68375 GAATATAAA
66 GAATATAAA
*
68384 TA-AATATAATAATATAATATATATATATATAAATATACTATA-ACATATA-ATATA-ATATATT
1 TATAATATAATAATATAATATATATAT-T-TAAATATACTATATA-ATATATATATATATATATA
*
68445 ATATAATATAAA
63 ATAGAATATAAA
* * *
68457 TATACTATAAT-ATATAATTAATAAATAATATTATAATATA-TATATACTATAT-TATATA
1 TATAATATAATAATATAA-T-ATATAT-AT-TTA-AATATACTATATAATATATATATATA
68515 AATTTACTAC
Statistics
Matches: 111, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
71 4 0.04
72 8 0.07
73 36 0.32
74 15 0.14
75 36 0.32
76 12 0.11
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (74 bp):
TATAATATAATAATATAATATATATATTTAAATATACTATATAATATATATATATATATATAATA
GAATATAAA
Found at i:68554 original size:94 final size:93
Alignment explanation
Indices: 68341--68554 Score: 200
Period size: 97 Copynumber: 2.3 Consensus size: 93
68331 ATATATTTAT
*
68341 ATATACTATA-TA-ATATATATATATATAT----ATAATAGAATATAAATAAATATAATAATATA
1 ATATAATATACTATATATATATATATATATATATATAATAGAATATAAATAAATATAATAATATA
68400 ATATATATATATATAAATATACTATAAC
66 ATATATATATATATAAATATACTATAAC
* * * *
68428 ATATAATATAATATATTATATAATATAAATATACTATAATATATA-ATTAATAAAT-AATATTAT
1 ATATAATATACTATA-TATAT-ATATATATATA-TAT-ATA-ATAGAAT-ATAAATAAATATAAT
* *
68491 AATATATATATACTATATTATATAAATTTACTA-CAC
60 AATATA-ATATA-TATA-TATATAAATATACTATAAC
68527 ATA-AA-A-ACTATATATATATATATATATA
1 ATATAATATACTATATATATATATATATATA
68555 AAAAAGATCG
Statistics
Matches: 104, Mismatches: 8, Indels: 23
0.77 0.06 0.17
Matches are distributed among these distances:
87 9 0.09
88 2 0.02
89 1 0.01
90 5 0.05
91 9 0.09
94 10 0.10
95 5 0.05
96 5 0.05
97 19 0.18
98 16 0.15
99 9 0.09
100 14 0.13
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (93 bp):
ATATAATATACTATATATATATATATATATATATATAATAGAATATAAATAAATATAATAATATA
ATATATATATATATAAATATACTATAAC
Found at i:69933 original size:2 final size:2
Alignment explanation
Indices: 69923--70185 Score: 117
Period size: 2 Copynumber: 140.5 Consensus size: 2
69913 AAACAAAGGA
* * * *
69923 AT AT A- AT AT AT AT AT AT A- AT AT AT AT GT GT -T AT AG AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
69962 ACT AT A- AC AT AT A- AT A- AA AT AT AT AT AT AT AT ACT AT A- AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* *
70002 AT A- AT AT A- AA AT AA AT AT A- AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
70040 AT AA AT AT ACT AT A- AC AT AT A- AT A- AT AT A- AT AT AT -T AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
70078 AT A- AT AT AA AT AT ACT AT A- AT AT AT A- AT -T A- AT AA AT A-
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
70115 AT AT -T AT A- AT AT AT AT ACT AT AT -T AT AT AA AT TT ACT AC AC
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT
* * *
70156 AT AA AA ACT AT AA AT AT AT AT AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A
70186 AGAAAGATCA
Statistics
Matches: 202, Mismatches: 27, Indels: 64
0.69 0.09 0.22
Matches are distributed among these distances:
1 25 0.12
2 165 0.82
3 12 0.06
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (2 bp):
AT
Found at i:70027 original size:43 final size:44
Alignment explanation
Indices: 69922--70136 Score: 191
Period size: 43 Copynumber: 5.0 Consensus size: 44
69912 AAAACAAAGG
* **
69922 AATATAATATATATATATAATATATATGTGTTATAGATA-AACTATAA
1 AATATAATATA-ATATAT-ATATATATATAATATA-ATATAA-TATAA
* *
69969 CATATAATA-AA-ATATATATATATATACTATAATATAATATAA
1 AATATAATATAATATATATATATATATAATATAATATAATATAA
*
70011 AATA-AATATAATATATATATATATATAATATAAATATACTATAA
1 AATATAATATAATATATATATATATATAATAT-AATATAATATAA
* *
70055 CATAT-A-ATAATATA-ATATATTATATAATATAAATATACTATAA
1 AATATAATATAATATATATATA-TATATAATAT-AATATAATATAA
* * *
70098 TATATAAT-TAATAAATA-ATAT-TATAATAT-ATATACTATA
1 AATATAATATAATATATATATATATATAATATAATATAATATA
70137 TTATATAAAT
Statistics
Matches: 149, Mismatches: 10, Indels: 25
0.81 0.05 0.14
Matches are distributed among these distances:
40 10 0.07
41 4 0.03
42 26 0.17
43 69 0.46
44 29 0.19
45 2 0.01
46 1 0.01
47 8 0.05
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (44 bp):
AATATAATATAATATATATATATATATAATATAATATAATATAA
Found at i:70099 original size:76 final size:73
Alignment explanation
Indices: 69980--70186 Score: 194
Period size: 76 Copynumber: 2.8 Consensus size: 73
69970 ATATAATAAA
* *
69980 ATATATATATATATACTATAATATAATATAAAATAAATATAATATATATATATATATAATA-TA-
1 ATATA-ATATA-ATA-TATTATATAATATAAAAT-ACTATAATATATATATATATATAATATTAT
70043 AATATACTATAACAT
62 AATATA-TAT-AC-T
*
70058 ATAATAATATAATATATTATATAATATAAATATACTATAATATATA-ATTAATAAATAATATTAT
1 AT-ATAATATAATATATTATATAATATAAA-ATACTATAATATATATA-T-ATATATAATATTAT
70122 AATATATATACT
62 AATATATATACT
* * *
70134 ATATTATATAA-AT-TTACTA-CACATAAAA-ACTATAAATATATATATATATATAA
1 ATATAATATAATATATTA-TATAATATAAAATACTAT-AATATATATATATATATAA
70187 GAAAGATCAG
Statistics
Matches: 113, Mismatches: 7, Indels: 25
0.78 0.05 0.17
Matches are distributed among these distances:
71 12 0.11
72 10 0.09
73 10 0.09
74 4 0.04
75 9 0.08
76 31 0.27
77 16 0.14
78 12 0.11
79 9 0.08
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (73 bp):
ATATAATATAATATATTATATAATATAAAATACTATAATATATATATATATATAATATTATAATA
TATATACT
Found at i:70181 original size:54 final size:55
Alignment explanation
Indices: 70016--70185 Score: 150
Period size: 58 Copynumber: 3.0 Consensus size: 55
70006 TATAAAATAA
* *
70016 ATATAATATATATATATA-TATAATATAAATATACTATAACATATA-ATAATATAATATATT
1 ATATAATATA-A-ATATACTACAATAT-AA-A-ACTATAA-ATATATATAATAT-ATATACT
* * *
70076 ATATAATATAAATATACTATAATATATAATTAATAAATAATATTATAATATATATACT
1 ATATAATATAAATATACTACAATATAAAACT-ATAAAT-ATA-TATAATATATATACT
* *
70134 ATATTATATAAATTTACTACACATA-AAAACTATAAATATATAT-ATATATATA
1 ATATAATATAAATATACTACA-ATATAAAACTATAAATATATATAATATATATA
70186 AGAAAGATCA
Statistics
Matches: 96, Mismatches: 8, Indels: 18
0.79 0.07 0.15
Matches are distributed among these distances:
54 9 0.09
55 3 0.03
56 7 0.07
57 14 0.15
58 34 0.35
59 19 0.20
60 10 0.10
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (55 bp):
ATATAATATAAATATACTACAATATAAAACTATAAATATATATAATATATATACT
Found at i:74284 original size:13 final size:13
Alignment explanation
Indices: 74266--74320 Score: 83
Period size: 13 Copynumber: 4.2 Consensus size: 13
74256 TGCGTCATAA
74266 ATTTATGACGTGC
1 ATTTATGACGTGC
* *
74279 ATTTATGACATAC
1 ATTTATGACGTGC
74292 ATTTATGACGTGC
1 ATTTATGACGTGC
*
74305 ATTTATGACGTTC
1 ATTTATGACGTGC
74318 ATT
1 ATT
74321 GAGCATCATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (13 bp):
ATTTATGACGTGC
Found at i:74320 original size:26 final size:26
Alignment explanation
Indices: 74261--74313 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
74251 AACTGTGCGT
*
74261 CATAAATTTATGACGTGCATTTATGA
1 CATACATTTATGACGTGCATTTATGA
74287 CATACATTTATGACGTGCATTTATGA
1 CATACATTTATGACGTGCATTTATGA
74313 C
1 C
74314 GTTCATTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (26 bp):
CATACATTTATGACGTGCATTTATGA
Found at i:87965 original size:12 final size:12
Alignment explanation
Indices: 87904--87965 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
87894 AAAAAGGTTT
87904 AAAA-AATAAAA
1 AAAAGAATAAAA
87915 AGAAAG-ATAAAA
1 A-AAAGAATAAAA
* *
87927 GAAAGAATAATA
1 AAAAGAATAAAA
*
87939 CAAA-AATAAAA
1 AAAAGAATAAAA
87950 AAAAGAATAAAGA
1 AAAAGAATAAA-A
87963 AAA
1 AAA
87966 CTTAAATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
11 14 0.34
12 23 0.56
13 4 0.10
ACGTcount: A:0.79, C:0.02, G:0.10, T:0.10
Consensus pattern (12 bp):
AAAAGAATAAAA
Found at i:89267 original size:2 final size:2
Alignment explanation
Indices: 89257--89473 Score: 106
Period size: 2 Copynumber: 118.5 Consensus size: 2
89247 AAACAAATAA
* *
89257 AT AT A- AT AT AT AT TT A- AT A- AT AT A- AT AT A- AC 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
* * *
89293 AT A- AC AT AT A- AT AA AT AT A- AT AT GT AT AT AT AT AT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
89333 AT AT A- AT AT AA AT AT A- AT GT A- AC AT AT A- AT -T AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
89369 AT AT AT AT AT AT AT ACT AT GT A- AT AT A- AT AT AA AT AT ACT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT
*
89411 A- AT AT AT A- AT AA AT A- AGT A- AT AT -T AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
*
89448 AT ACT AT AT -T AT AT AA AT AT A- AT AT A
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT A
89474 CATAAAAACT
Statistics
Matches: 164, Mismatches: 21, Indels: 60
0.67 0.09 0.24
Matches are distributed among these distances:
1 25 0.15
2 130 0.79
3 9 0.05
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:89321 original size:6 final size:6
Alignment explanation
Indices: 89257--89473 Score: 106
Period size: 5 Copynumber: 39.5 Consensus size: 6
89247 AAACAAATAA
* * *
89257 ATATA- ATATAT ATTTA- ATA-AT ATA-AT ATA-AC ATAT-T ATA-AC
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * *
89298 ATATA- ATAAAT ATA-AT ATGTAT ATATAT ATATACT ATATA- ATATAA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATA-T ATATAT ATATAT
* *
89344 ATATA- ATGTA- ACATAT A-AT-T ATATA- ATATAT ATATAT ATACTAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATA-TAT
* * *
89388 GTA-AT ATA-AT ATAAAT ATACTAT A-ATAT ATA-AT AAATA- AGTA-AT
1 ATATAT ATATAT ATATAT ATA-TAT ATATAT ATATAT ATATAT A-TATAT
*
89432 AT-TAT A-ATAT ATATAT ATACTAT AT-TAT ATAAAT ATA-AT ATA
1 ATATAT ATATAT ATATAT ATA-TAT ATATAT ATATAT ATATAT ATA
89474 CATAAAAACT
Statistics
Matches: 170, Mismatches: 17, Indels: 50
0.72 0.07 0.21
Matches are distributed among these distances:
4 3 0.02
5 91 0.54
6 57 0.34
7 19 0.11
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (6 bp):
ATATAT
Found at i:89359 original size:58 final size:59
Alignment explanation
Indices: 89253--89477 Score: 252
Period size: 58 Copynumber: 3.9 Consensus size: 59
89243 TAAAAAACAA
* *
89253 ATAA-ATATA-ATATATATTTAATAATATAATATAACATAT--TATAACATATAATAAAT
1 ATAATATATATATATATATATACTAATATAATATAA-ATATAATATAACATATAATAAAT
* * *
89309 ATAATATGTATATATATATATACT-ATATAATATAAATATAATGTAACATATAAT-TAT
1 ATAATATATATATATATATATACTAATATAATATAAATATAATATAACATATAATAAAT
* * *
89366 ATAATATATATATATATACTAT-GTAATATAATATAAATATACTATAATATATAATAAAT
1 ATAATATATATATATATA-TATACTAATATAATATAAATATAATATAACATATAATAAAT
*
89425 AAGTAATATTATAATATATATATATACT-ATATTATATAAATATAATAT-ACATA
1 -A-TAATA-TAT-ATATATATATATACTAATATAATATAAATATAATATAACATA
89478 AAAACTATAT
Statistics
Matches: 142, Mismatches: 15, Indels: 19
0.81 0.09 0.11
Matches are distributed among these distances:
56 8 0.06
57 35 0.25
58 53 0.37
59 2 0.01
60 1 0.01
61 9 0.06
62 24 0.17
63 10 0.07
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (59 bp):
ATAATATATATATATATATATACTAATATAATATAAATATAATATAACATATAATAAAT
Found at i:89474 original size:23 final size:23
Alignment explanation
Indices: 89303--89474 Score: 98
Period size: 23 Copynumber: 7.7 Consensus size: 23
89293 ATAACATATA
89303 ATAAATATAATATGTA-TATATATAT
1 ATAAATATAATA--TACTATAT-TAT
* * *
89328 ATACTATATAATATA-AATATAAT
1 ATA-AATATAATATACTATATTAT
*
89351 GTAACATATAAT-TA-TATA--AT
1 ATAA-ATATAATATACTATATTAT
* * *
89371 ATATATAT-ATATACTATGTAAT
1 ATAAATATAATATACTATATTAT
*
89393 AT-AATATAAATATACTATAATAT
1 ATAAATAT-AATATACTATATTAT
*
89416 AT-AATA-AATA-AGTAATATTAT
1 ATAAATATAATATACT-ATATTAT
*
89437 A-ATATATATATATACTATATTAT
1 ATAAATATA-ATATACTATATTAT
89460 ATAAATATAATATAC
1 ATAAATATAATATAC
89475 ATAAAAACTA
Statistics
Matches: 115, Mismatches: 18, Indels: 30
0.71 0.11 0.18
Matches are distributed among these distances:
18 2 0.02
19 6 0.05
20 9 0.08
21 18 0.16
22 10 0.09
23 45 0.39
24 14 0.12
25 3 0.03
26 8 0.07
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAAATATAATATACTATATTAT
Found at i:89487 original size:44 final size:44
Alignment explanation
Indices: 89396--89489 Score: 102
Period size: 44 Copynumber: 2.1 Consensus size: 44
89386 ATGTAATATA
* * *
89396 ATATAAATATACTATAATATATAATAAATAAGTAATATTATAAT
1 ATATAAATATACTATAATATATAATAAATAAGTAACATAAAAAT
* * *
89440 ATATATATATACTATATTATATAA-ATATAA-TATACATAAAAACT
1 ATATAAATATACTATAATATATAATAAATAAGTA-ACATAAAAA-T
89484 ATATAA
1 ATATAA
89490 TAAAAAGATT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
42 2 0.05
43 11 0.27
44 28 0.68
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (44 bp):
ATATAAATATACTATAATATATAATAAATAAGTAACATAAAAAT
Found at i:89487 original size:120 final size:115
Alignment explanation
Indices: 89274--89491 Score: 305
Period size: 120 Copynumber: 1.9 Consensus size: 115
89264 ATATATTTAA
*
89274 TAATATAATATAACATATTATAACATATAATAAATATAATATGTATATATATATATACTATATAA
1 TAATATAATATAACATATTATAACATATAATAAATATAATATATATATATATATATACTATATAA
* * *
89339 TATAAATATAATGTAACATATAATTATATAATATATATATATATACTATG
66 TATAAATATAATATAACATAAAACTATATAATATATATATATATACTATG
*
89389 TAATATAATATAA-ATATACTATAATATATAATAAATAAGTAATATTATAATATATATATATACT
1 TAATATAATATAACATAT--TATAACATATAATAAAT-A-TAATA-TAT-ATATATATATATACT
*
89453 ATATTATATAAATATAATAT-ACATAAAAACTATATAATA
60 ATATAATATAAATATAATATAACAT-AAAACTATATAATA
89492 AAAAGATTGG
Statistics
Matches: 90, Mismatches: 6, Indels: 9
0.86 0.06 0.09
Matches are distributed among these distances:
114 4 0.04
115 13 0.14
116 16 0.18
117 1 0.01
118 5 0.06
119 6 0.07
120 45 0.50
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (115 bp):
TAATATAATATAACATATTATAACATATAATAAATATAATATATATATATATATATACTATATAA
TATAAATATAATATAACATAAAACTATATAATATATATATATATACTATG
Found at i:99789 original size:20 final size:19
Alignment explanation
Indices: 99755--99793 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
99745 CAAACATTAA
*
99755 ATTTACACCGGTAGAACAT
1 ATTTACACCGATAGAACAT
99774 ATTTATCACCGATAGAACAT
1 ATTTA-CACCGATAGAACAT
99794 GAAATAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (19 bp):
ATTTACACCGATAGAACAT
Found at i:110083 original size:39 final size:39
Alignment explanation
Indices: 110028--110110 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
110018 TATTTTATGT
* ** *
110028 TTATTTTGCTACTACTTTTATGTTCTTGTTGCTTCATGA
1 TTATTTTGCTAATACTTTTATGTGATCGTTGCTTCATGA
*
110067 TTATTTTTCTAATACTTTTATGTGATCGTTGCTTCATGA
1 TTATTTTGCTAATACTTTTATGTGATCGTTGCTTCATGA
110106 TTATT
1 TTATT
110111 AGTAGAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.18, C:0.13, G:0.12, T:0.57
Consensus pattern (39 bp):
TTATTTTGCTAATACTTTTATGTGATCGTTGCTTCATGA
Found at i:115857 original size:18 final size:18
Alignment explanation
Indices: 115831--115865 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
115821 TCGAAAGGAC
*
115831 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
115849 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
115866 CCTGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:123824 original size:3 final size:3
Alignment explanation
Indices: 123811--123896 Score: 142
Period size: 3 Copynumber: 29.3 Consensus size: 3
123801 TGTAAAACAA
123811 AAT AA- AAT AAT AAT AAT AAT AA- AACT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
123854 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
123897 GATTAAAATT
Statistics
Matches: 79, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
2 6 0.08
3 71 0.90
4 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:124331 original size:133 final size:134
Alignment explanation
Indices: 124076--124345 Score: 416
Period size: 134 Copynumber: 2.0 Consensus size: 134
124066 ACACAGCTCA
* * * *
124076 TACGCGTTGAAGAGTTCTGGTCGAGGGATGACACGACTCATACGTGATGAAGAGTTATGGTCATC
1 TACGCGATGAAGAGATCTAGTCGAGGGATGACACGACTCATACGTGATAAAGAGTTATGGTCATC
* *
124141 TTTAGGAAGGGTGATAACTCAGTTCCTACGTGATGAGGATGACTGGTTATCTAGGGGTGACATGA
66 TTTAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGGTGACATGA
124206 CTCC
131 CTCC
* * * * * *
124210 TACGCGATGAGGAGATCTAGTCGGGGGATGACACGGCTTATATGTGATAAAGAGTTCTGGTCATC
1 TACGCGATGAAGAGATCTAGTCGAGGGATGACACGACTCATACGTGATAAAGAGTTATGGTCATC
*
124275 TTTAGGAA-GGTGATAACTCAGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGGTGACATGG
66 TTTAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGGTGACATGA
124339 CTCC
131 CTCC
124343 TAC
1 TAC
124346 ATGTTGAAGA
Statistics
Matches: 123, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
133 60 0.49
134 63 0.51
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (134 bp):
TACGCGATGAAGAGATCTAGTCGAGGGATGACACGACTCATACGTGATAAAGAGTTATGGTCATC
TTTAGGAAGGGTGATAACTCAGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGGTGACATGA
CTCC
Found at i:124373 original size:133 final size:134
Alignment explanation
Indices: 124102--124390 Score: 391
Period size: 133 Copynumber: 2.2 Consensus size: 134
124092 CTGGTCGAGG
* *
124102 GATGACACGACTCATACGTGATGAAGAGTTATGGTCATCTTTAGGAAGGGTGATAACTCAGTTCC
1 GATGACACGGCTCATACGTGATAAAGAGTTATGGTCATCTTTAGGAAGGGTGATAACTCAGTTCC
* * * * * *
124167 TACGTGATGAGGATGACTGGTTATCTAGGGGTGACATGACTCCTACGCGATGAGGAGATCTAGTC
66 TACGCGATGAGGACGACTGGTTATCTAGGGGTGACATGACTCCTACACGATGAAGAGATATAGGC
* *
124232 GGGG
131 AGGA
* * *
124236 GATGACACGGCTTATATGTGATAAAGAGTTCTGGTCATCTTTAGGAA-GGTGATAACTCAGTTCC
1 GATGACACGGCTCATACGTGATAAAGAGTTATGGTCATCTTTAGGAAGGGTGATAACTCAGTTCC
* * * * *
124300 TACGCGATGAGGACGACTGGTTATCTAGGGGTGACATGGCTCCTACATGTTGAAGAGGTATGGGC
66 TACGCGATGAGGACGACTGGTTATCTAGGGGTGACATGACTCCTACACGATGAAGAGATATAGGC
124365 AGGA
131 AGGA
* *
124369 GATGACACGGTTCCTACGTGAT
1 GATGACACGGCTCATACGTGAT
124391 GAGGAAGGCT
Statistics
Matches: 133, Mismatches: 22, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
133 91 0.68
134 42 0.32
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.27
Consensus pattern (134 bp):
GATGACACGGCTCATACGTGATAAAGAGTTATGGTCATCTTTAGGAAGGGTGATAACTCAGTTCC
TACGCGATGAGGACGACTGGTTATCTAGGGGTGACATGACTCCTACACGATGAAGAGATATAGGC
AGGA
Found at i:124462 original size:28 final size:29
Alignment explanation
Indices: 124430--124500 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
124420 GGTTTTAAGG
* *
124430 GAAACCGACTCAAAGATTTGTTTCAA-AA
1 GAAACAGACTCAAAGATTTGTCTCAAGAA
124458 GAAACAGACTCAAAGATTTGTCTCAAGAA
1 GAAACAGACTCAAAGATTTGTCTCAAGAA
*
124487 -AAACAAACTCAAAG
1 GAAACAGACTCAAAG
124501 GTGATGTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
28 37 0.95
29 2 0.05
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (29 bp):
GAAACAGACTCAAAGATTTGTCTCAAGAA
Found at i:124683 original size:32 final size:31
Alignment explanation
Indices: 124636--124723 Score: 101
Period size: 32 Copynumber: 2.9 Consensus size: 31
124626 CAAAGATCGG
* *
124636 TGTTTCGAGAGAAACAAACTCAAAGATTTTTT
1 TGTTTCAAGAAAAACAAACTCAAAGA-TTTTT
*
124668 TGTTTCAAGAAAAACATACTCAAAGA-TTTT
1 TGTTTCAAGAAAAACAAACTCAAAGATTTTT
*
124698 TGTTTCAAGGGAAAA-AAA-TCAAAGAT
1 TGTTTCAA-GAAAAACAAACTCAAAGAT
124724 GATAAATTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
29 7 0.14
30 14 0.29
31 5 0.10
32 23 0.47
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (31 bp):
TGTTTCAAGAAAAACAAACTCAAAGATTTTT
Found at i:124966 original size:31 final size:31
Alignment explanation
Indices: 124928--125002 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 31
124918 TCAAAATTTG
*
124928 TTTCAAGAGAAAC-AACTCAAAGATGGTTT-TA
1 TTTCAAGAGAAACAAAATCAAAGAT--TTTGTA
124959 TTTCAAGAGAAACAAAATCAAAGATTTTGTA
1 TTTCAAGAGAAACAAAATCAAAGATTTTGTA
*
124990 TTTCTAGAGAAAC
1 TTTCAAGAGAAAC
125003 TGCCTCAAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 3 0.08
31 27 0.68
32 10 0.25
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (31 bp):
TTTCAAGAGAAACAAAATCAAAGATTTTGTA
Found at i:125505 original size:36 final size:36
Alignment explanation
Indices: 125408--125495 Score: 142
Period size: 36 Copynumber: 2.5 Consensus size: 36
125398 GTGAGAACAC
125408 ATTTGTTTTTAGAGAAATTGTCTCAAACGAGACAAA
1 ATTTGTTTTTAGAGAAATTGTCTCAAACGAGACAAA
* *
125444 AATTGTTTTTAGAGAAATTGTCTCAAGCGAGACAAA
1 ATTTGTTTTTAGAGAAATTGTCTCAAACGAGACAAA
*
125480 GTTTGTTTTT-GAGAAA
1 ATTTGTTTTTAGAGAAA
125496 ACGATCTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 6 0.12
36 42 0.88
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.35
Consensus pattern (36 bp):
ATTTGTTTTTAGAGAAATTGTCTCAAACGAGACAAA
Found at i:125697 original size:107 final size:107
Alignment explanation
Indices: 125517--125814 Score: 424
Period size: 107 Copynumber: 2.8 Consensus size: 107
125507 TGAGATCAAC
* * * *
125517 TTTGTTT-AACGTGAAACAAATTCGAAATTTGTATTCTCAAAGG--AAAATGTCGCAAACGATAC
1 TTTGTTTCAA-GTGAATCAAATTCGAAATTTGTA-TATCAAAGGAAAAAATGTCTCAAACGAGAC
125579 GAAATTTGTTTTGAAAGAAATAACAATATCAAGTGAGATTAATT
64 GAAATTTGTTTTGAAAGAAATAACAATATCAAGTGAGATTAATT
*
125623 TTTGTTTCAAGTGAATCAAATTCAAAATTTGTATATCAAAGGAAAAAATGTCTCAAACGAGACGA
1 TTTGTTTCAAGTGAATCAAATTCGAAATTTGTATATCAAAGGAAAAAATGTCTCAAACGAGACGA
* *
125688 AATTTGTTTTGAAATAAATAACAATCTCAAGTGAGATTAATT
66 AATTTGTTTTGAAAGAAATAACAATATCAAGTGAGATTAATT
* * * *
125730 TTTTTTTCAAGTGAATCAAATTCGAAATTTATATATCAAAGGAAAAAAATGTCTCAAGCAAGACG
1 TTTGTTTCAAGTGAATCAAATTCGAAATTTGTATATCAAAGG-AAAAAATGTCTCAAACGAGACG
*
125795 AATTTTGTTTT-AAGAGAAAT
65 AAATTTGTTTTGAA-AGAAAT
125815 TGTCTTAAAT
Statistics
Matches: 173, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
105 8 0.05
106 28 0.16
107 102 0.59
108 35 0.20
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (107 bp):
TTTGTTTCAAGTGAATCAAATTCGAAATTTGTATATCAAAGGAAAAAATGTCTCAAACGAGACGA
AATTTGTTTTGAAAGAAATAACAATATCAAGTGAGATTAATT
Found at i:125929 original size:36 final size:36
Alignment explanation
Indices: 125855--125937 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 36
125845 ATTCTAAAAA
*
125855 TTTATGAGAAATGTATCAAGCGAGAAAGAATTTGTT
1 TTTATGAGAAATGTATCAAGCGAGAAAGAATTTATT
* *
125891 TTTA-GAGAAATTGTCTCAAGCGAGACAA-AGTTTATT
1 TTTATGAGAAA-TGTATCAAGCGAGA-AAGAATTTATT
*
125927 TTTTTGAGAAA
1 TTTATGAGAAA
125938 ACGATCTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 6 0.15
36 26 0.65
37 8 0.20
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.35
Consensus pattern (36 bp):
TTTATGAGAAATGTATCAAGCGAGAAAGAATTTATT
Found at i:126075 original size:35 final size:34
Alignment explanation
Indices: 126007--126125 Score: 143
Period size: 34 Copynumber: 3.5 Consensus size: 34
125997 AAGGAAAAGC
*
126007 GTCTCAAGCGAGACGAATTT-TTTTTCAAGAAATT
1 GTCTCAAGCGAGACAAATTTGTTTTTCAA-AAATT
*
126041 GTCTCAAACGAGACAAAATTTGTTTTT-AGAAAATT
1 GTCTCAAGCGAGAC-AAATTTGTTTTTCA-AAAATT
* * *
126076 GTCTCAAGCAAGACAATTTTGTTTTTCAAAAGTT
1 GTCTCAAGCGAGACAAATTTGTTTTTCAAAAATT
*
126110 GTCTCTAGCGAGACAA
1 GTCTCAAGCGAGACAA
126126 CATCTTATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
34 43 0.59
35 24 0.33
36 6 0.08
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (34 bp):
GTCTCAAGCGAGACAAATTTGTTTTTCAAAAATT
Found at i:126456 original size:12 final size:13
Alignment explanation
Indices: 126424--126468 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
126414 TTTATGTATC
*
126424 ATGTATATATGTG
1 ATGTATGTATGTG
126437 TATGTATGTATGTG
1 -ATGTATGTATGTG
126451 -TGTATGTAT-TG
1 ATGTATGTATGTG
126462 ATGTATG
1 ATGTATG
126469 CTTTTCTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 2 0.07
12 15 0.52
14 12 0.41
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (13 bp):
ATGTATGTATGTG
Found at i:127705 original size:17 final size:17
Alignment explanation
Indices: 127676--127712 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
127666 TTGTCATCTT
127676 TTTGTTCTTTGCTCTTTC
1 TTTGTTCTTTGCT-TTTC
127694 TTTGTT-TTTGCTTTTC
1 TTTGTTCTTTGCTTTTC
127710 TTT
1 TTT
127713 TCTTTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 6 0.32
18 6 0.32
ACGTcount: A:0.00, C:0.16, G:0.11, T:0.73
Consensus pattern (17 bp):
TTTGTTCTTTGCTTTTC
Found at i:127710 original size:27 final size:27
Alignment explanation
Indices: 127680--127734 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
127670 CATCTTTTTG
*
127680 TTCTTTGCTCTTTCTTTGTTTTTGCTT
1 TTCTTTGCTCTTTCTTTGTTTTTCCTT
* * *
127707 TTCTTTTCTTTTTCTTTTTTTTTCCTT
1 TTCTTTGCTCTTTCTTTGTTTTTCCTT
127734 T
1 T
127735 GTTTTCCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.00, C:0.18, G:0.05, T:0.76
Consensus pattern (27 bp):
TTCTTTGCTCTTTCTTTGTTTTTCCTT
Found at i:127718 original size:16 final size:16
Alignment explanation
Indices: 127683--127740 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
127673 CTTTTTGTTC
127683 TTTGCTCTTTCTTTGT-T
1 TTTGCT-TTTCTTT-TCT
127700 TTTGCTTTTCTTTTCT
1 TTTGCTTTTCTTTTCT
* * *
127716 TTTTCTTTTTTTTTCC
1 TTTGCTTTTCTTTTCT
127732 TTTG-TTTTC
1 TTTGCTTTTC
127741 CTTTGCTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 5 0.14
16 24 0.69
17 6 0.17
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (16 bp):
TTTGCTTTTCTTTTCT
Found at i:127744 original size:27 final size:27
Alignment explanation
Indices: 127680--127753 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
127670 CATCTTTTTG
* * * *
127680 TTCTTTGCTCTTTCTTTGTTTTTGCTT
1 TTCTTTCCTTTTTCTTTTTTTTTCCTT
*
127707 TTCTTTTCTTTTTCTTTTTTTTTCCTT
1 TTCTTTCCTTTTTCTTTTTTTTTCCTT
127734 TGT-TTTCCTTTGCTTCTTTT
1 T-TCTTTCCTTT--TTCTTTT
127754 CTCTCTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
27 31 0.79
28 1 0.03
29 7 0.18
ACGTcount: A:0.00, C:0.19, G:0.07, T:0.74
Consensus pattern (27 bp):
TTCTTTCCTTTTTCTTTTTTTTTCCTT
Found at i:128229 original size:25 final size:26
Alignment explanation
Indices: 128180--128229 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
128170 AGATTACTTT
*
128180 GAGATGCCCCCACATTGTTTCTTCTC
1 GAGATGCCCCCACATTGTTTATTCTC
*
128206 GAGATG-CCCCACATTTTTTATTCT
1 GAGATGCCCCCACATTGTTTATTCT
128230 GGTAGGAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.18, C:0.30, G:0.14, T:0.38
Consensus pattern (26 bp):
GAGATGCCCCCACATTGTTTATTCTC
Found at i:128442 original size:28 final size:27
Alignment explanation
Indices: 128409--128462 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
128399 AGGTCAGAAA
*
128409 AATGTTTCAAAGTCTCAAGGATAAATGC
1 AATGTTTCAAAGTCTCAAAGA-AAATGC
*
128437 AATGTTTCAAGGTCTCAAAGAAAATG
1 AATGTTTCAAAGTCTCAAAGAAAATG
128463 AATATCACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (27 bp):
AATGTTTCAAAGTCTCAAAGAAAATGC
Found at i:132367 original size:15 final size:15
Alignment explanation
Indices: 132349--132379 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
132339 CCTCAGTTCC
132349 TCTCCCTTCTTCCTT
1 TCTCCCTTCTTCCTT
132364 TCTCCCTTCTTCCTT
1 TCTCCCTTCTTCCTT
132379 T
1 T
132380 TCGTTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTCCCTTCTTCCTT
Found at i:133056 original size:3 final size:3
Alignment explanation
Indices: 133043--133080 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
133033 TATAAAACAA
*
133043 AAT AA- AAT AAT AAT AAT AAT AAT ACT AAT ATAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AA
133081 AAATTAGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:133289 original size:3 final size:3
Alignment explanation
Indices: 133269--133311 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
133259 GACGGGCAAT
*
133269 TAA TAC TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
133312 ATTAAAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:136653 original size:11 final size:12
Alignment explanation
Indices: 136625--136658 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
136615 TATTTAAACG
136625 GGTATTGGGCCA
1 GGTATTGGGCCA
*
136637 GGTATTGGGTC-
1 GGTATTGGGCCA
136648 GGTATTGGGCC
1 GGTATTGGGCC
136659 GAGAATCAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.15, G:0.44, T:0.29
Consensus pattern (12 bp):
GGTATTGGGCCA
Found at i:136738 original size:24 final size:25
Alignment explanation
Indices: 136674--136738 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
136664 TCAGGCCGGG
136674 TATATATATATATATATTTAAATTAAA
1 TATATAT-TATAT-TATTTAAATTAAA
*
136701 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
136725 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
136739 ATATATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 19 0.56
25 2 0.06
26 1 0.03
27 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:148564 original size:68 final size:68
Alignment explanation
Indices: 148473--148809 Score: 480
Period size: 68 Copynumber: 5.0 Consensus size: 68
148463 ACTCAACGGT
* * * * *
148473 ACTTAACCGTTCATCTAATTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGTCAT-AA
1 ACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGG-CATCAA
148537 AGGC
65 AGGC
* *
148541 ACTTAGCCCTTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTCAAA
1 ACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCATCAAA
148606 GGC
66 GGC
* * * *
148609 ACTTAGCCTTTCATATAACTAGCATAAATGACACCTTTCTATCATATGCACAGTTAGGCCTCAAA
1 ACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCATCAAA
148674 GGC
66 GGC
* * *
148677 ACTTAGCCTTTAATCTAACTGGCATAAATGACACCTTTCTATCATATGCAAAGTTAGGCCA-CAA
1 ACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGG-CATCAA
148741 AGGC
65 AGGC
* * * *
148745 ACTTAACCTTTCATCTAACTGGTATAAATGACACCTTTCTGTCATATGCACAATTAGGCCTCAAA
1 ACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCATCAAA
148810 TCTTTTTACT
Statistics
Matches: 244, Mismatches: 22, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
67 3 0.01
68 240 0.98
69 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (68 bp):
ACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCATCAAA
GGC
Found at i:149104 original size:59 final size:59
Alignment explanation
Indices: 149025--149522 Score: 701
Period size: 59 Copynumber: 8.4 Consensus size: 59
149015 TTCCATATAA
* * * * *
149025 AAATTTATACACTTAATATGAATTTCTTACCATTTTAGCACAC-AAGGTGCCCAATACAG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAA-GTGCCCTATACGG
* * *
149084 AAATTCATATACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGCGCCCTATATGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* * * * *
149143 AAATTCATACACTCAATATGAATTTCTGAACATTTTAGCACATGAAGTGCCATATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* * *
149202 AAATTCATACACCTAGTATGAATTCCTTAACATTTTAGCACACGAAGTGCCCTATACAG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* * * * *
149261 AAATTCATACACATAGTATGAATTCCTTAATATTTTAGCACACGAAGTGCCTTATACTG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* *
149320 AAATTCATACACTTAGTATGAATTTCCTAACATTTTAGCACACAAAGTGCCCTATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* * * * * *
149379 AAGTTCAAACACTTAGTATGAATTACTCAACATTTTAGCACATGAAGAGCCCTATACGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
* *
149438 AAATTCATACACTTAGTATGAATTTCTTAATATTTTAGCACACGAAGTGCCCTATATGG
1 AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
149497 AAATTCATACACTTAGTATGAATTTC
1 AAATTCATACACTTAGTATGAATTTC
149523 ATAATTTTGC
Statistics
Matches: 387, Mismatches: 51, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
59 385 0.99
60 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (59 bp):
AAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGG
Found at i:149994 original size:95 final size:95
Alignment explanation
Indices: 149869--150051 Score: 251
Period size: 95 Copynumber: 1.9 Consensus size: 95
149859 TCTATACTAC
* * * *
149869 GGTATCGATACCCCCTTACGATATCGATACCAATTTTAGGTTCGAAGTT-TTCTAGTGTCGATAC
1 GGTACCGATACCCCCATACGATATCAATACCAATTTTAGGTTCGAAGTTGTT-TAGTATCGATAC
*
149933 CCTTACCATGGTATCAATTCTACCATACAAT
65 CCTTACCATGGTATCAATACTACCATACAAT
* * * *
149964 GGTACCGATACCCCCATCCGGTATCAATACCAATTTTAGGTTCGATGTTGTTTGGTATCGATACC
1 GGTACCGATACCCCCATACGATATCAATACCAATTTTAGGTTCGAAGTTGTTTAGTATCGATACC
* *
150029 CTTACTATGGTATCGATACTACC
66 CTTACCATGGTATCAATACTACC
150052 TTGTCGGTAT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
95 74 0.97
96 2 0.03
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (95 bp):
GGTACCGATACCCCCATACGATATCAATACCAATTTTAGGTTCGAAGTTGTTTAGTATCGATACC
CTTACCATGGTATCAATACTACCATACAAT
Found at i:153283 original size:28 final size:28
Alignment explanation
Indices: 153238--153298 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
153228 ATCACTTTAA
153238 AAAATTTAATTATCATTT-AAAAACCCAT
1 AAAATTTAATTATCATTTGAAAAA-CCAT
* *
153266 AAAATTTAGTT-TCAATTTGAAAAACTAT
1 AAAATTTAATTATC-ATTTGAAAAACCAT
153294 AAAAT
1 AAAAT
153299 ATGATATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 2 0.07
28 22 0.76
29 5 0.17
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAATTTAATTATCATTTGAAAAACCAT
Found at i:154131 original size:29 final size:29
Alignment explanation
Indices: 154084--154144 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
154074 AATTCATTAT
* * * * *
154084 TCTTTTATTCAAGAGTGTTTTACTGTTCA
1 TCTTTTACTCAACAATGTTTAACCGTTCA
154113 TCTTTTACTCAACAATGTTTAACCGTTCA
1 TCTTTTACTCAACAATGTTTAACCGTTCA
154142 TCT
1 TCT
154145 AACTGGCATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.48
Consensus pattern (29 bp):
TCTTTTACTCAACAATGTTTAACCGTTCA
Found at i:154310 original size:68 final size:68
Alignment explanation
Indices: 154201--154881 Score: 886
Period size: 68 Copynumber: 10.1 Consensus size: 68
154191 TATTCTTTTT
* * * * * * * *
154201 CTCAATGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGTACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCATATGCACAGTTA
154266 GGC
66 GGC
* * *
154269 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACATCTTTCTGTCATATGCATAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCATATGCACAGTTA
154334 GGC
66 GGC
* * *
154337 CTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAAATGACACCTTTCTATCATATACATAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCATATGCACAGTTA
154402 GGC
66 GGC
* * *
154405 CTCAAAGGCACTTAGCCTTTCATCTAACTGGAATAAATGACACATTTCTATCATATGCACCGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCATATGCACAGTTA
*
154470 AGC
66 GGC
* * * * *
154473 CTCAAAGACACTTAGCCTTTTATCTAACTGGCATAAATGACACCTATCTGTCATATGCACAATTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCATATGCACAGTTA
154538 GGC
66 GGC
* * * * *
154541 CTCAAAAGCACATAGCCTTTCATCTAACT-TCAT-AATGATACTTTTCTATCATATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCATATGCACAGTTA
154604 GGC
66 GGC
* * *** * *
154607 CTTAAAGGCACTTAGCCTTTCATCTAATTAATATAAATGACACATTTCTATCACATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCATATGCACAGTTA
*
154672 -AC
66 GGC
* * **
154674 CTC-AAGGCACTTAGCCTTTCATCTAACTGGCATAAATAACACCTTTCTGTCATAAACACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCATATGCACAGTTA
154738 GGC
66 GGC
* * * * *
154741 CTCAACGACATTTAGCCTTTCATCTAACT-ACATAAATGACATCTTTCTATCATATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCATATGCACAGTTA
154805 GGC
66 GGC
* * *
154808 CTCAAAGGCTCTTAGCCTTTAATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCATATGCACAGTTA
154873 GGC
66 GGC
*
154876 GTCAAA
1 CTCAAA
154882 TCTTTTAATT
Statistics
Matches: 529, Mismatches: 79, Indels: 10
0.86 0.13 0.02
Matches are distributed among these distances:
66 104 0.20
67 68 0.13
68 357 0.67
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTATCATATGCACAGTTA
GGC
Found at i:155169 original size:59 final size:59
Alignment explanation
Indices: 155106--155595 Score: 747
Period size: 59 Copynumber: 8.4 Consensus size: 59
155096 AAAAAATTAT
* * * **
155106 TACACTTAATATGAATTTCTTATCATTTTAGCACACAAAGTGCCCCGTATGGAAATTCA
1 TACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAATTCA
* * *
155165 TACACTTAGTATGAATTTATTAATATTTTAGCACACGAAGAGCCCTATATGGAAATTCA
1 TACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAATTCA
* *
155224 TACACTTAGTATGAATTTCTTAACATTTT---ACACGAAGTGCCCTTTACGGAAATTCA
1 TACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAATTCA
* *
155280 TACACTTAGTATGAATTCCTTAACATTTTAGCACACGAAGTGCCTTATATGGAAATTCA
1 TACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAATTCA
* * *
155339 TACACTTAGTATGAATTTCTTAACATTTTAGTACATGAAGTGCCTTATATGGAAATTCA
1 TACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAATTCA
* * *
155398 T--AGTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACGAAAATTCA
1 TACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAATTCA
* *
155455 TACACTTAGTATGAATTCCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAATTTA
1 TACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAATTCA
* *
155514 TACACTTAGTATGAATTTCGTAACATTTTAGTACACGAAGTGCCCTATATGGAAATTCA
1 TACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAATTCA
155573 TACACTTAGTATGAATTTCTTAA
1 TACACTTAGTATGAATTTCTTAA
155596 TTTTACACAC
Statistics
Matches: 390, Mismatches: 36, Indels: 10
0.89 0.08 0.02
Matches are distributed among these distances:
56 52 0.13
57 51 0.13
59 287 0.74
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (59 bp):
TACACTTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAATTCA
Found at i:155493 original size:175 final size:173
Alignment explanation
Indices: 155098--155603 Score: 768
Period size: 175 Copynumber: 2.9 Consensus size: 173
155088 TTCGCATAAA
* * * * **
155098 AAAATT-ATTACACTTAATATGAATTTCTTATCATTTTAGCACACAAAGTGCCCCGTATGGAAAT
1 AAAATTCA-TACACTTAGTATGAATTCCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAAT
* * * *
155162 TCATACACTTAGTATGAATTTATTAATATTTTAGCACACGAAGAGCCCTATATGGAAATTCATAC
65 TCATACACTTAGTATGAATTTCTTAACATTTTAGTACACGAAGTGCCCTATATGGAAATTCATA-
*
155227 ACTTAGTATGAATTTCTTAACATTTTACACGAAGTGCCCTTTACG
129 ACTTAGTATGAATTTCTTAACATTTTACACGAAGTGCCCTATACG
* *
155272 GAAATTCATACACTTAGTATGAATTCCTTAACATTTTAGCACACGAAGTGCCTTATATGGAAATT
1 AAAATTCATACACTTAGTATGAATTCCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAATT
* * *
155337 CATACACTTAGTATGAATTTCTTAACATTTTAGTACATGAAGTGCCTTATATGGAAATTCAT-AG
66 CATACACTTAGTATGAATTTCTTAACATTTTAGTACACGAAGTGCCCTATATGGAAATTCATAAC
155401 TTAGTATGAATTTCTTAACATTTTAGCACACGAAGTGCCCTATACG
131 TTAGTATGAATTTCTTAACATTTT---ACACGAAGTGCCCTATACG
155447 AAAATTCATACACTTAGTATGAATTCCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAATT
1 AAAATTCATACACTTAGTATGAATTCCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAATT
* *
155512 TATACACTTAGTATGAATTTCGTAACATTTTAGTACACGAAGTGCCCTATATGGAAATTCATACA
66 CATACACTTAGTATGAATTTCTTAACATTTTAGTACACGAAGTGCCCTATATGGAAATTCATA-A
155577 CTTAGTATGAATTTCTT-A-ATTTTACAC
130 CTTAGTATGAATTTCTTAACATTTTACAC
155604 ACTTAGTGCC
Statistics
Matches: 303, Mismatches: 23, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
172 29 0.10
174 111 0.37
175 145 0.48
176 1 0.00
177 17 0.06
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (173 bp):
AAAATTCATACACTTAGTATGAATTCCTTAACATTTTAGCACACGAAGTGCCCTATATGGAAATT
CATACACTTAGTATGAATTTCTTAACATTTTAGTACACGAAGTGCCCTATATGGAAATTCATAAC
TTAGTATGAATTTCTTAACATTTTACACGAAGTGCCCTATACG
Found at i:156124 original size:21 final size:21
Alignment explanation
Indices: 156098--156147 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
156088 CCTTACCATG
156098 GTATCGATACTGATTGAATCA
1 GTATCGATACTGATTGAATCA
* *
156119 GTATCGATACTGATTTAATTA
1 GTATCGATACTGATTGAATCA
156140 GTATCGAT
1 GTATCGAT
156148 GCTACTCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (21 bp):
GTATCGATACTGATTGAATCA
Found at i:171537 original size:19 final size:19
Alignment explanation
Indices: 171513--171559 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
171503 TGCATTGGGA
*
171513 TATGAATTTGAAA-ATAAGC
1 TATGAATATGAAATA-AAGC
*
171532 TATGAATATGAAATAAAGT
1 TATGAATATGAAATAAAGC
171551 TATGAATAT
1 TATGAATAT
171560 TAAACTAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 24 0.96
20 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.15, T:0.34
Consensus pattern (19 bp):
TATGAATATGAAATAAAGC
Found at i:171569 original size:19 final size:18
Alignment explanation
Indices: 171524--171569 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
171514 ATGAATTTGA
* *
171524 AAATAAGCTATGAATATG
1 AAATAAGTTATGAATATT
171542 AAATAAAGTTATGAATATT
1 AAAT-AAGTTATGAATATT
171561 AAACTAAGT
1 AAA-TAAGT
171570 GTCGAATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.17
19 19 0.79
20 1 0.04
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.30
Consensus pattern (18 bp):
AAATAAGTTATGAATATT
Found at i:174956 original size:37 final size:37
Alignment explanation
Indices: 174908--175214 Score: 254
Period size: 39 Copynumber: 7.9 Consensus size: 37
174898 TATATATAAG
* *
174908 ATATAGTATATAGTATTT-TATAAAATTTTGGAAACATAT
1 ATATAATATATAGT-TTTATA-AAAATTTT-AAAACATAT
*
174947 ATATAATATATAGTTTTTTTAAAAAATGTTTCGAAAACATAT
1 ATATAATATATAG-TTTTAT-AAAAAT-TTT--AAAACATAT
174989 ATATAATATATAGTTTT-TAAAAATATTTTAAAA-ATAT
1 ATATAATATATAGTTTTAT-AAAA-ATTTTAAAACATAT
175026 ATATAATATATAGTTTT-TGAAAATATTTTAAAAACATAT
1 ATATAATATATAGTTTTAT-AAAA-ATTTT-AAAACATAT
* *
175065 ATATAATATATAGTTTCTATAAAAAATTTGAAA-ATAT
1 ATATAATATATAGTTT-TATAAAAATTTTAAAACATAT
* * * *
175102 ATAAAACATATAGTTTT-TGAAAATGTTTTGAAAATATAT
1 ATATAATATATAGTTTTAT-AAAA-ATTTT-AAAACATAT
175141 ATATAATATATAGTTTT-TGAAAACATTTTAAAA-ATAT
1 ATATAATATATAGTTTTAT-AAAA-ATTTTAAAACATAT
* *
175178 ATATAATATACAGGTTTTGA-AAATATTTTTAAAACAT
1 ATATAATATATA-GTTTT-ATAAA-AATTTTAAAACAT
175215 TTTGAAAATA
Statistics
Matches: 233, Mismatches: 16, Indels: 38
0.81 0.06 0.13
Matches are distributed among these distances:
35 1 0.00
36 5 0.02
37 68 0.29
38 34 0.15
39 71 0.30
40 21 0.09
41 11 0.05
42 22 0.09
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.43
Consensus pattern (37 bp):
ATATAATATATAGTTTTATAAAAATTTTAAAACATAT
Found at i:174958 original size:39 final size:36
Alignment explanation
Indices: 174908--175214 Score: 287
Period size: 37 Copynumber: 7.9 Consensus size: 36
174898 TATATATAAG
* *
174908 ATATAGTATATAGTATTTTATAAAATTTTGGAAACATAT
1 ATATAATATATAGT-TTTTA-AAAATTTT-AAAACATAT
174947 ATATAATATATAGTTTTTTTAAAAAATGTTTCGAAAACATAT
1 ATATAATATATAG--TTTTT-AAAAAT-TTT--AAAACATAT
174989 ATATAATATATAGTTTTTAAAAATATTTTAAAA-ATAT
1 ATATAATATATAGTTTTT-AAAA-ATTTTAAAACATAT
175026 ATATAATATATAGTTTTTGAAAATATTTTAAAAACATAT
1 ATATAATATATAGTTTTT-AAAA-ATTTT-AAAACATAT
* *
175065 ATATAATATATAGTTTCTATAAAAAATTTGAAA-ATAT
1 ATATAATATATAGTTT-T-TAAAAATTTTAAAACATAT
* * * *
175102 ATAAAACATATAGTTTTTGAAAATGTTTTGAAAATATAT
1 ATATAATATATAGTTTTT-AAAA-ATTTT-AAAACATAT
175141 ATATAATATATAGTTTTTGAAAACATTTTAAAA-ATAT
1 ATATAATATATAGTTTTT-AAAA-ATTTTAAAACATAT
* *
175178 ATATAATATACAGGTTTTGAAAATATTTTTAAAACAT
1 ATATAATATATA-GTTTTTAAAA-A-TTTTAAAACAT
175215 TTTGAAAATA
Statistics
Matches: 234, Mismatches: 17, Indels: 34
0.82 0.06 0.12
Matches are distributed among these distances:
35 1 0.00
36 5 0.02
37 73 0.31
38 31 0.13
39 67 0.29
40 27 0.12
41 8 0.03
42 22 0.09
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.43
Consensus pattern (36 bp):
ATATAATATATAGTTTTTAAAAATTTTAAAACATAT
Found at i:175017 original size:11 final size:11
Alignment explanation
Indices: 175003--175059 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
174993 AATATATAGT
175003 TTTTAAAAATA
1 TTTTAAAAATA
175014 TTTTAAAAATA
1 TTTTAAAAATA
* *
175025 TATATAATATATA
1 T-TTTAA-AAATA
*
175038 GTTTTTGAAAATA
1 --TTTTAAAAATA
175051 TTTTAAAAA
1 TTTTAAAAA
175060 CATATATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
11 20 0.56
12 4 0.11
13 8 0.22
14 3 0.08
15 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:175080 original size:76 final size:76
Alignment explanation
Indices: 174908--175214 Score: 377
Period size: 76 Copynumber: 4.0 Consensus size: 76
174898 TATATATAAG
* * * * *
174908 ATATAGTATATAGTATTTTATAAAAT-TTTGGAAACATATATATAATATATAGTTTTTTTAAAAA
1 ATATAATATATAGT-TTTTA-AAAATATTT-TAAAAATATATATAATATATAG-TTTTTGAAAAT
174972 ATGTTTCGAAAACATAT
62 AT-TTT-GAAAACATAT
174989 ATATAATATATAGTTTTTAAAAATATTTTAAAAATATATATAATATATAGTTTTTGAAAATATTT
1 ATATAATATATAGTTTTTAAAAATATTTTAAAAATATATATAATATATAGTTTTTGAAAATATTT
*
175054 TAAAAACATAT
66 TGAAAACATAT
* * * *
175065 ATATAATATATAGTTTCTATAAAAA-A-TTTGAAAATATATAAAACATATAGTTTTTGAAAATGT
1 ATATAATATATAGTTT-T-TAAAAATATTTTAAAAATATATATAATATATAGTTTTTGAAAATAT
*
175128 TTTGAAAATATAT
64 TTTGAAAACATAT
* * * *
175141 ATATAATATATAGTTTTTGAAAACATTTTAAAAATATATATAATATACAGGTTTTGAAAATATTT
1 ATATAATATATAGTTTTTAAAAATATTTTAAAAATATATATAATATATAGTTTTTGAAAATATTT
*
175206 TTAAAACAT
66 TGAAAACAT
175215 TTTGAAAATA
Statistics
Matches: 200, Mismatches: 21, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
74 5 0.03
75 2 0.01
76 125 0.62
77 5 0.03
78 17 0.09
79 25 0.12
80 8 0.04
81 13 0.06
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.43
Consensus pattern (76 bp):
ATATAATATATAGTTTTTAAAAATATTTTAAAAATATATATAATATATAGTTTTTGAAAATATTT
TGAAAACATAT
Found at i:175211 original size:11 final size:11
Alignment explanation
Indices: 175192--175225 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
175182 AATATACAGG
175192 TTTTGAAAATA
1 TTTTGAAAATA
* *
175203 TTTTTAAAACA
1 TTTTGAAAATA
175214 TTTTGAAAATA
1 TTTTGAAAATA
175225 T
1 T
175226 ATATTATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:175267 original size:17 final size:18
Alignment explanation
Indices: 175242--175282 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
175232 TATAAAATAT
*
175242 TTATGTATTATATT-TTA
1 TTATTTATTATATTATTA
175259 TTATTTATTATATTATTA
1 TTATTTATTATATTATTA
175277 TTATTT
1 TTATTT
175283 TCTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
TTATTTATTATATTATTA
Found at i:175267 original size:25 final size:24
Alignment explanation
Indices: 175239--175318 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 24
175229 TTATATAAAA
175239 TATTTATGTATTA-TATTTTATTATT
1 TATTTAT-TATTATTATTTTATT-TT
*
175264 TATTATATTATTATTATTTTCTTTT
1 TATT-TATTATTATTATTTTATTTT
*
175289 TATTTATT-TTACTTATTTTCTTTTT
1 TATTTATTATTA-TTATTTT-ATTTT
175314 TATTT
1 TATTT
175319 TGGTCAACCT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
23 3 0.06
24 11 0.22
25 24 0.49
26 11 0.22
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (24 bp):
TATTTATTATTATTATTTTATTTT
Found at i:175319 original size:21 final size:22
Alignment explanation
Indices: 175262--175319 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 22
175252 TATTTTATTA
175262 TTTATTATATTATTATTATTTTCTT
1 TTTATT-TATT-TTATTATTTTC-T
175287 TTTATTTATTTTACTTATTTTC-
1 TTTATTTATTTTA-TTATTTTCT
175309 TTT-TTTATTTT
1 TTTATTTATTTT
175320 GGTCAACCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.25
22 3 0.09
23 3 0.09
24 12 0.38
25 6 0.19
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTATTTTATTATTTTCT
Found at i:182091 original size:17 final size:17
Alignment explanation
Indices: 182071--182129 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
182061 TCTTATTTCA
*
182071 TTTCTTTTGAACTCAAT
1 TTTCTTTTGAATTCAAT
*
182088 TTTC-TTT-CATTCAGTACT
1 TTTCTTTTGAATTCA--A-T
182106 TTTCTTTTGAATTCAAT
1 TTTCTTTTGAATTCAAT
182123 TTTCTTT
1 TTTCTTT
182130 CGTTCGGTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 13 0.38
18 6 0.18
19 3 0.09
20 5 0.15
ACGTcount: A:0.19, C:0.17, G:0.05, T:0.59
Consensus pattern (17 bp):
TTTCTTTTGAATTCAAT
Found at i:182122 original size:35 final size:35
Alignment explanation
Indices: 182071--182141 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
182061 TCTTATTTCA
182071 TTTCTTTTGAACTCAATTTTCTTTCATTCAGTACT
1 TTTCTTTTGAACTCAATTTTCTTTCATTCAGTACT
* * *
182106 TTTCTTTTGAATTCAATTTTCTTTCGTTCGGTACT
1 TTTCTTTTGAACTCAATTTTCTTTCATTCAGTACT
182141 T
1 T
182142 CATTTCATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.17, C:0.18, G:0.08, T:0.56
Consensus pattern (35 bp):
TTTCTTTTGAACTCAATTTTCTTTCATTCAGTACT
Found at i:184107 original size:26 final size:26
Alignment explanation
Indices: 184071--184134 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
184061 TAAATATCAG
* **
184071 ATGACACTCATTTATGATGTGCGTTT
1 ATGACACTCATTTATGACGCACGTTT
184097 ATGACACTCATTTATGACGCACGTTT
1 ATGACACTCATTTATGACGCACGTTT
*
184123 ATGACGCTCATT
1 ATGACACTCATT
184135 GCGCATCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (26 bp):
ATGACACTCATTTATGACGCACGTTT
Found at i:191204 original size:30 final size:30
Alignment explanation
Indices: 191163--191220 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
191153 GGTTGAGAAT
*
191163 TTCAAGGACCAATAGGGTAATTTTCAAAAG
1 TTCAAGGACCAAAAGGGTAATTTTCAAAAG
* **
191193 TTCAGGGACCAAAATTGTAATTTTCAAA
1 TTCAAGGACCAAAAGGGTAATTTTCAAA
191221 TGATGTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (30 bp):
TTCAAGGACCAAAAGGGTAATTTTCAAAAG
Found at i:202796 original size:59 final size:57
Alignment explanation
Indices: 202726--202861 Score: 184
Period size: 59 Copynumber: 2.4 Consensus size: 57
202716 TCGAGTAACA
* * *
202726 ATTTTGTAACTTTTAATAGTCGGGGATTCAACAAAACAATGCCTTATAGTCAATGGAA-C
1 ATTTCGTAACTTTTAATAGTCAGGGACTCAACAAAACAATGCCTTA-A-TCAA-GGAACC
**
202785 ATTTCGTAACTTTTAATAGTCAGGGACTCAACAAAACAATTTCTTAATCAAGGAACC
1 ATTTCGTAACTTTTAATAGTCAGGGACTCAACAAAACAATGCCTTAATCAAGGAACC
*
202842 ATTTCGTAACTTTTGATAGT
1 ATTTCGTAACTTTTAATAGT
202862 AGTGGGACTC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
56 4 0.06
57 24 0.34
58 1 0.01
59 41 0.59
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (57 bp):
ATTTCGTAACTTTTAATAGTCAGGGACTCAACAAAACAATGCCTTAATCAAGGAACC
Found at i:207381 original size:213 final size:214
Alignment explanation
Indices: 207013--207440 Score: 698
Period size: 213 Copynumber: 2.0 Consensus size: 214
207003 ACTGAAACAT
* *
207013 ATATTTACGTCATTATTTGTATTTTATGACGTAAAAATTGATGTCACAGTGAACGTCACGCTAAG
1 ATATTTACGTCATTATTTATATTTTATGACGTAAAAATTGATGTCACAGTGAACGTCACACTAAG
* * *
207078 TGTGTCACTAAATGTCAAATGTGACAATGTTTATGTTTTCGTCACATATTGTTAAATATATGGTG
66 TGTGTCACTAAATGTCAAATGTGACAATGTCTATATTTTCGTCACATATTGTTAAATATATGGCG
* *
207143 ACGTTAATGCATAATGTCACCTTATATTAATGCCACCATATATTTTACATTCAATAACAATTAGT
131 ACGTTAATGCATAATGTCACCTTATATTAATGCCACCACATATTTTACATTCAATAACAATTAAT
207208 TACTTT-ATCAAATAATCTA
196 TA-TTTCATCAAATAATCTA
*
207227 ATATTTACGTCATTATTTATATTTTATGACGTAAAAATTGA-GTCATAGTGAACGTCACACTAAG
1 ATATTTACGTCATTATTTATATTTTATGACGTAAAAATTGATGTCACAGTGAACGTCACACTAAG
* *** *
207291 TGTGTCATTAAATGTCAAATGTGGTGATGTCTATATTTTCGTCACGTATTGTTAAATATATGGCG
66 TGTGTCACTAAATGTCAAATGTGACAATGTCTATATTTTCGTCACATATTGTTAAATATATGGCG
* *
207356 ACGTTAATTCATAATGTCACCTTATATTAATGTCACCACATATTTTACATTCAATAACAATTAAT
131 ACGTTAATGCATAATGTCACCTTATATTAATGCCACCACATATTTTACATTCAATAACAATTAAT
207421 TATTTCATCAAATAATCTA
196 TATTTCATCAAATAATCTA
207440 A
1 A
207441 AAGTTCACCG
Statistics
Matches: 198, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
212 3 0.02
213 155 0.78
214 40 0.20
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (214 bp):
ATATTTACGTCATTATTTATATTTTATGACGTAAAAATTGATGTCACAGTGAACGTCACACTAAG
TGTGTCACTAAATGTCAAATGTGACAATGTCTATATTTTCGTCACATATTGTTAAATATATGGCG
ACGTTAATGCATAATGTCACCTTATATTAATGCCACCACATATTTTACATTCAATAACAATTAAT
TATTTCATCAAATAATCTA
Found at i:207707 original size:29 final size:28
Alignment explanation
Indices: 207650--207779 Score: 86
Period size: 29 Copynumber: 4.5 Consensus size: 28
207640 GTATTAATGA
**
207650 TGAAATTTACAATACAAG-ACAATTTTTTT
1 TGAAATTTACAATA-AAGAACAA-AATTTT
* *
207679 TGAAATTTGCAATAAAGAATAAAACTTTT
1 TGAAATTTACAATAAAGAACAAAA-TTTT
* * *
207708 TGGAATATACAATAAAGTACAAAATTTT
1 TGAAATTTACAATAAAGAACAAAATTTT
* * *
207736 TGTAAA-TTACAATGATGTACAAAACTTTT
1 TG-AAATTTACAATAAAGAACAAAA-TTTT
*
207765 T-ATAAATTACAATAA
1 TGA-AATTTACAATAA
207780 TGATATTTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.01
28 26 0.32
29 54 0.67
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.36
Consensus pattern (28 bp):
TGAAATTTACAATAAAGAACAAAATTTT
Found at i:207746 original size:28 final size:28
Alignment explanation
Indices: 207675--207779 Score: 104
Period size: 29 Copynumber: 3.6 Consensus size: 28
207665 AAGACAATTT
* * *
207675 TTTTTGAAATTTGCAATAAAGAATAAAAC
1 TTTTTGAAA-TTACAATAAAGTACAAAAC
*
207704 TTTTTGGAATATACAATAAAGTACAAAA-
1 TTTTTGAAAT-TACAATAAAGTACAAAAC
* *
207732 TTTTTGTAAATTACAATGATGTACAAAAC
1 TTTTTG-AAATTACAATAAAGTACAAAAC
*
207761 TTTTTATAAATTACAATAA
1 TTTTT-GAAATTACAATAA
207780 TGATATTTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
28 22 0.35
29 41 0.65
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.37
Consensus pattern (28 bp):
TTTTTGAAATTACAATAAAGTACAAAAC
Found at i:215121 original size:20 final size:20
Alignment explanation
Indices: 215093--215142 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
215083 GAATGTGACC
* *
215093 TTTGATGAAAAGACACAACT
1 TTTGGTGAAAAGACACAACA
* *
215113 TTTGGTGAAGAGTCACAACA
1 TTTGGTGAAAAGACACAACA
215133 TTTGGTGAAA
1 TTTGGTGAAA
215143 GGGTATGACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (20 bp):
TTTGGTGAAAAGACACAACA
Found at i:216578 original size:23 final size:23
Alignment explanation
Indices: 216549--216594 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
216539 TCAATATAAG
*
216549 ACAAGATTCTATAAGATTTATGT
1 ACAAGATTATATAAGATTTATGT
216572 ACAAGATTATATAAGATTTATGT
1 ACAAGATTATATAAGATTTATGT
216595 CTTATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (23 bp):
ACAAGATTATATAAGATTTATGT
Found at i:227060 original size:22 final size:21
Alignment explanation
Indices: 227017--227070 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
227007 CGGATGGTGT
*
227017 AACCGGTTTTGGTTTGAAAAA
1 AACCGGTTTTTGTTTGAAAAA
227038 AACCGGTTTTTGTTTGAATAAA
1 AACCGGTTTTTGTTTGAA-AAA
227060 AACCGGTTTTT
1 AACCGGTTTTT
227071 TAAAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (21 bp):
AACCGGTTTTTGTTTGAAAAA
Found at i:229258 original size:20 final size:19
Alignment explanation
Indices: 229212--229259 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
229202 ATGACCAACA
* * *
229212 AAATCTCAATGCGATCTCT
1 AAATCGCAACGCGATCTCC
229231 AAATCGCAACGCGATCTCC
1 AAATCGCAACGCGATCTCC
229250 AATATCGCAA
1 AA-ATCGCAA
229260 ATCAGTTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.23
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCC
Found at i:230229 original size:23 final size:24
Alignment explanation
Indices: 230189--230241 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
230179 GTATTCGAAA
230189 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
230213 TTTGATCTT-GTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
230236 TTTGAT
1 TTTGAT
230242 AATGTTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:230460 original size:14 final size:14
Alignment explanation
Indices: 230431--230467 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
230421 AGAAAAAGAA
230431 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
230446 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
230460 GAAGAAAA
1 GAAGAAAA
230468 TACCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:236851 original size:17 final size:17
Alignment explanation
Indices: 236831--236870 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
236821 AATGTTGAAA
* *
236831 AAAAAACTAGCAGTTCG
1 AAAAAACAAACAGTTCG
*
236848 AAAAAACAAACTGTTCG
1 AAAAAACAAACAGTTCG
236865 AAAAAA
1 AAAAAA
236871 AAAGACATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.15, G:0.12, T:0.15
Consensus pattern (17 bp):
AAAAAACAAACAGTTCG
Found at i:239662 original size:20 final size:20
Alignment explanation
Indices: 239637--239731 Score: 154
Period size: 20 Copynumber: 4.8 Consensus size: 20
239627 TTATACATTC
*
239637 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
239657 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
239677 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
239697 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
239717 ATTTGACTATCGCAA
1 ATTTGACTATCGCAA
239732 TGAGAAAATC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:239801 original size:20 final size:20
Alignment explanation
Indices: 239772--239835 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
239762 GCAATGCGAA
*
239772 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
* **
239792 TTGGCTTTCGCATTATGATT
1 TTGACTTTCGCATTGCGATT
239812 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
239832 TTGA
1 TTGA
239836 GTTTAGCGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.14, C:0.17, G:0.22, T:0.47
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:239965 original size:36 final size:36
Alignment explanation
Indices: 239924--240046 Score: 122
Period size: 36 Copynumber: 3.3 Consensus size: 36
239914 TTACATTTCA
239924 ATCAATTAAATAAACACAAATAAGAATTATTTACAC
1 ATCAATTAAATAAACACAAATAAGAATTATTTACAC
*** * *
239960 ATCAATTAAATAAATCAACTTTTACA-AATCAACTTTTACAA
1 ATCAATTAAATAAA-C-ACAAATA-AGAAT-TA--TTTACAC
* *
240001 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAATAAACACAAATAAGAATTATTTACAC
240037 ATCAATTAAA
1 ATCAATTAAA
240047 CAAATCAACT
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
36 30 0.44
37 1 0.01
38 9 0.13
39 9 0.13
40 1 0.01
41 18 0.26
ACGTcount: A:0.53, C:0.15, G:0.02, T:0.29
Consensus pattern (36 bp):
ATCAATTAAATAAACACAAATAAGAATTATTTACAC
Found at i:239990 original size:14 final size:14
Alignment explanation
Indices: 239971--240005 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
239961 TCAATTAAAT
239971 AAATCAACTTTTAC
1 AAATCAACTTTTAC
239985 AAATCAACTTTTAC
1 AAATCAACTTTTAC
239999 AAATCAA
1 AAATCAA
240006 TTAAACAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:240025 original size:77 final size:78
Alignment explanation
Indices: 239902--240068 Score: 273
Period size: 77 Copynumber: 2.1 Consensus size: 78
239892 ATTTAAATCA
*
239902 ACAAATCAACTTTTACATTTCAATCAATTAAATAAACACAAATAAGAATTATTTACACATCAATT
1 ACAAATCAACTTTTACA--T-AATCAATTAAACAAACACAAATAAGAATTATTTACACATCAATT
*
239967 AAATAAATCAACTTTT
63 AAACAAATCAACTTTT
*
239983 ACAAATCAACTTTTACA-AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTAAA
1 ACAAATCAACTTTTACATAATCAATTAAACAAACACAAATAAGAATTATTTACACATCAATTAAA
240047 CAAATCAACTTTT
66 CAAATCAACTTTT
240060 ACAAATCAA
1 ACAAATCAA
240069 TTAAACAAGC
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
77 66 0.80
81 17 0.20
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (78 bp):
ACAAATCAACTTTTACATAATCAATTAAACAAACACAAATAAGAATTATTTACACATCAATTAAA
CAAATCAACTTTT
Found at i:241481 original size:21 final size:21
Alignment explanation
Indices: 241457--241537 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 21
241447 GAATGGTGGG
*
241457 AGGGACCTCTTCAACGATGAT
1 AGGGACCTCTTGAACGATGAT
* * **
241478 AGGGGCCTCTTGAACGGTGGG
1 AGGGACCTCTTGAACGATGAT
**
241499 AGGGGA-CTCTTGAGGGATGAT
1 A-GGGACCTCTTGAACGATGAT
*
241520 AGGGGCCTCTTGAACGAT
1 AGGGACCTCTTGAACGAT
241538 AGGAGAGGCC
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (21 bp):
AGGGACCTCTTGAACGATGAT
Found at i:241501 original size:42 final size:42
Alignment explanation
Indices: 241442--241535 Score: 136
Period size: 42 Copynumber: 2.2 Consensus size: 42
241432 ATGAATCGGG
*
241442 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTCAACGATGATAGGGGC
* **
241484 CTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGATAGGGGC
241526 CTCTTGAACG
1 CTCTTGAACG
241536 ATAGGAGAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
42 43 0.91
43 4 0.09
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGATAGGGGC
Found at i:241551 original size:42 final size:42
Alignment explanation
Indices: 241472--241553 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
241462 CCTCTTCAAC
* * *
241472 GATGATAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGATAGGGGCCTCTTGAACGATAGGAGAGGACTCTTGAGG
*
241514 GATGATAGGGGCCTCTTGAACGATAGGAGAGGCCTCTTGA
1 GATGATAGGGGCCTCTTGAACGATAGGAGAGGACTCTTGA
241554 ACAATGACAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.16, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGATAGGGGCCTCTTGAACGATAGGAGAGGACTCTTGAGG
Done.