Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 76 of 206
Found at i:21601748 original size:134 final size:134
Alignment explanation
Indices: 21601407--21601824 Score: 615
Period size: 138 Copynumber: 3.1 Consensus size: 134
21601397 GAGAACATAG
* ***
21601407 ATATAATTAATATATGAATTTGATTCATACAAAATATTAGTTGTATATATTTTACCAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAATGAATTTATT
* * *
21601472 AATATAAATATTTATATTAATTAATTTCGGTCAAAATATAAAA-ACATGAAAATTAATATTCTTT
66 AATATAAATAGTTATATTAA-T--TTT-GGTCAAAATATAAAAGAAATGAGAATTAATATTCTTT
21601536 TGGAAAGA
127 TGGAAAGA
21601544 ATATAATTAATATATGAATTTGATTCATACAAAATATTTAATTGTATATATTTTAATGAATTTAT
1 ATATAATTAATATATGAATTTGATTCATACAAAATA-TTAATTGTATATATTTTAATGAATTTAT
*
21601609 TAATATAAAAAGTTATATTAATTTTGGTCAAAATATAAAAGAAATGAGAATTAATATTCTTTTGG
65 TAATATAAATAGTTATATTAATTTTGGTCAAAATATAAAAGAAATGAGAATTAATATTCTTTTGG
21601674 AAAGA
130 AAAGA
* * *
21601679 ATATAATTAATATATCAATTTGAGTCATACAAAATATTAATTGTATATATTTTATTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAATGAATTTATT
* *
21601744 AATATAAATAGTTATATTAATTAATTTTTGTCAAAATATAAAAGATATG-GAAATTAATATTCTT
66 AATATAAATAG-T-TA-T-ATTAATTTTGGTCAAAATATAAAAGAAATGAG-AATTAATATTCTT
21601808 TTGGAAAGA
126 TTGGAAAGA
21601817 ATATAATT
1 ATATAATT
21601825 CATTTTTCTA
Statistics
Matches: 260, Mismatches: 14, Indels: 13
0.91 0.05 0.05
Matches are distributed among these distances:
134 53 0.20
135 65 0.25
136 2 0.01
137 39 0.15
138 101 0.39
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (134 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAATGAATTTATT
AATATAAATAGTTATATTAATTTTGGTCAAAATATAAAAGAAATGAGAATTAATATTCTTTTGGA
AAGA
Found at i:21602238 original size:4 final size:4
Alignment explanation
Indices: 21602229--21602396 Score: 327
Period size: 4 Copynumber: 42.0 Consensus size: 4
21602219 TAACAAGACA
21602229 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
21602277 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
21602325 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAC GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
21602373 GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT
21602397 ATATTAAGAA
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 162 1.00
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:21612167 original size:17 final size:19
Alignment explanation
Indices: 21612127--21612168 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
21612117 TTGATCTAAC
21612127 ATACAATGTTATATAAATT
1 ATACAATGTTATATAAATT
*
21612146 TTACAAT-TTATAT-AATT
1 ATACAATGTTATATAAATT
21612163 ATACAA
1 ATACAA
21612169 ATACAACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 9 0.43
18 6 0.29
19 6 0.29
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (19 bp):
ATACAATGTTATATAAATT
Found at i:21614935 original size:25 final size:26
Alignment explanation
Indices: 21614899--21614951 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
21614889 TAATGTCCCT
*
21614899 TTTCTTTCTCATGTTTTTTCTTT-GC
1 TTTCTTTCTCATGTTTTTCCTTTAGC
*
21614924 TTTCTTTTTCATGTTTTTCCTTTAGC
1 TTTCTTTCTCATGTTTTTCCTTTAGC
21614950 TT
1 TT
21614952 CCTAGACTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.06, C:0.19, G:0.08, T:0.68
Consensus pattern (26 bp):
TTTCTTTCTCATGTTTTTCCTTTAGC
Found at i:21615744 original size:42 final size:41
Alignment explanation
Indices: 21615567--21615908 Score: 447
Period size: 41 Copynumber: 8.4 Consensus size: 41
21615557 ATTCGGTGGC
* * * *
21615567 TTTAGTGGCGTTTATGAGAAAGCGCCGCTAATGGTCTGGGT
1 TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGGTCTGGGT
* * *
21615608 TTTAGCAGCGTTTTTT--AAAGCGCCACTAATGCTCTGGGT
1 TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGGTCTGGGT
* * * * *
21615647 TTTAGCAGCGTGTTTTAAAAAGCACCACTAATGGTCTTGGT
1 TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGGTCTGGGT
* * *
21615688 TTTAGCGGCGTTTTTTTAAAAGCACCGCTAATGGTCTGAGT
1 TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGGTCTGGGT
* *
21615729 TTTAGCGGCGTTTTTTTAAAAAGCGTCGCTAATGGTCTGAGT
1 TTTAGCGGCG-TTTTTTAAAAAGCGCCGCTAATGGTCTGGGT
21615771 TTTAGCGGCGTTTTTTTAAAAAGCGCCGCTAATGGTCTGGGT
1 TTTAGCGGCG-TTTTTTAAAAAGCGCCGCTAATGGTCTGGGT
* * *
21615813 TTTACCGGCGTCTTTTAAAAAGCGCCGCTAATGGTCTTGGT
1 TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGGTCTGGGT
* *
21615854 TTTAGCTGCATTTTTT-AAAAGCGCCGCTAATGGTCTGGGT
1 TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGGTCTGGGT
21615894 TTTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
21615909 GTTAAAGTGC
Statistics
Matches: 267, Mismatches: 31, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
39 36 0.13
40 36 0.13
41 118 0.44
42 77 0.29
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.36
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGGTCTGGGT
Found at i:21615914 original size:83 final size:82
Alignment explanation
Indices: 21615567--21615908 Score: 458
Period size: 83 Copynumber: 4.2 Consensus size: 82
21615557 ATTCGGTGGC
* * * * * *
21615567 TTTAGTGGCGTTTATGAGAAAGCGCCGCTAATGGTCTGGGTTTTAGCAGCG-TTTTTT-AAAGCG
1 TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGGTCTTGGTTTTAGCGGCGTTTTTTTAAAAGCG
* *
21615630 CCACTAATGCTCTGGGT
66 CCGCTAATGGTCTGGGT
* * * * *
21615647 TTTAGCAGCGTGTTTTAAAAAGCACCACTAATGGTCTTGGTTTTAGCGGCGTTTTTTTAAAAGCA
1 TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGGTCTTGGTTTTAGCGGCGTTTTTTTAAAAGCG
*
21615712 CCGCTAATGGTCTGAGT
66 CCGCTAATGGTCTGGGT
*
21615729 TTTAGCGGCGTTTTTTTAAAAAGCGTCGCTAATGGTC-TGAGTTTTAGCGGCGTTTTTTTAAAAA
1 TTTAGCGGCG-TTTTTTAAAAAGCGCCGCTAATGGTCTTG-GTTTTAGCGGCGTTTTTTT-AAAA
21615793 GCGCCGCTAATGGTCTGGGT
63 GCGCCGCTAATGGTCTGGGT
* * * *
21615813 TTTACCGGCGTCTTTTAAAAAGCGCCGCTAATGGTCTTGGTTTTAGCTGC-ATTTTTTAAAAGCG
1 TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGGTCTTGGTTTTAGCGGCGTTTTTTTAAAAGCG
21615877 CCGCTAATGGTCTGGGT
66 CCGCTAATGGTCTGGGT
21615894 TTTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
21615909 GTTAAAGTGC
Statistics
Matches: 228, Mismatches: 28, Indels: 11
0.85 0.10 0.04
Matches are distributed among these distances:
80 41 0.18
81 43 0.19
82 36 0.16
83 75 0.33
84 33 0.14
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.36
Consensus pattern (82 bp):
TTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGGTCTTGGTTTTAGCGGCGTTTTTTTAAAAGCG
CCGCTAATGGTCTGGGT
Found at i:21616370 original size:22 final size:22
Alignment explanation
Indices: 21616335--21616389 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
21616325 GTTTAATTAA
* * *
21616335 GGGTT-GGGATTTAATGTTTAG
1 GGGTTAGGGGTTTAAGGGTTAG
21616356 GGGTTAGGGGTTTAAGGGTTAG
1 GGGTTAGGGGTTTAAGGGTTAG
**
21616378 ACGTTAGGGGTT
1 GGGTTAGGGGTT
21616390 AATAGTTAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.18, C:0.02, G:0.44, T:0.36
Consensus pattern (22 bp):
GGGTTAGGGGTTTAAGGGTTAG
Found at i:21616819 original size:22 final size:22
Alignment explanation
Indices: 21616777--21616819 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
21616767 GTTTAGATAA
* *
21616777 ATTTTTTATTTATATTTTAAAT
1 ATTTTTTATGTATATTGTAAAT
21616799 ATTTTCTTATGTA-ATTGTAAA
1 ATTTT-TTATGTATATTGTAAA
21616820 AGATGTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (22 bp):
ATTTTTTATGTATATTGTAAAT
Found at i:21617153 original size:19 final size:18
Alignment explanation
Indices: 21617120--21617158 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
21617110 AAATTATACG
*
21617120 AAATAAAATTAAAATACAA
1 AAATAAAAATAAAATA-AA
*
21617139 AAATAAAAATGAAATAAA
1 AAATAAAAATAAAATAAA
21617157 AA
1 AA
21617159 CTCTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATAAAAATAAAATAAA
Found at i:21617222 original size:47 final size:47
Alignment explanation
Indices: 21617161--21617251 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
21617151 AATAAAAACT
** * * *
21617161 CTAAAATTTTTAATTTTGTCTAATTTTTATAAATATTACTTAAAAAA
1 CTAAAATTGATAATTTTATCTAAATTTTATAAATATTACCTAAAAAA
21617208 CTAAAATTGATAATTTTATCTAAATTTTATAAATATTACCTAAA
1 CTAAAATTGATAATTTTATCTAAATTTTATAAATATTACCTAAA
21617252 CAAAAGTATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (47 bp):
CTAAAATTGATAATTTTATCTAAATTTTATAAATATTACCTAAAAAA
Found at i:21617635 original size:16 final size:15
Alignment explanation
Indices: 21617614--21617652 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
21617604 ACGATGTCGT
*
21617614 TTTATTCCCGTCCAAA
1 TTTATTCCCCTCC-AA
21617630 TTTATTCCCCTCCAA
1 TTTATTCCCCTCCAA
21617645 TTT-TTCCC
1 TTTATTCCC
21617653 ATACCCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 5 0.23
15 5 0.23
16 12 0.55
ACGTcount: A:0.18, C:0.36, G:0.03, T:0.44
Consensus pattern (15 bp):
TTTATTCCCCTCCAA
Found at i:21617784 original size:16 final size:16
Alignment explanation
Indices: 21617763--21617824 Score: 79
Period size: 16 Copynumber: 3.9 Consensus size: 16
21617753 TCTGCCATCG
*
21617763 CTCGTCCACCGTCGCA
1 CTCGTCTACCGTCGCA
*
21617779 CTCGTCGACCGTCGCA
1 CTCGTCTACCGTCGCA
**
21617795 GGCGTCTACCGTCGCA
1 CTCGTCTACCGTCGCA
*
21617811 CTCCTCTACCGTCG
1 CTCGTCTACCGTCG
21617825 GAGAAATCGG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.11, C:0.45, G:0.23, T:0.21
Consensus pattern (16 bp):
CTCGTCTACCGTCGCA
Found at i:21620684 original size:66 final size:66
Alignment explanation
Indices: 21620578--21620709 Score: 185
Period size: 66 Copynumber: 2.0 Consensus size: 66
21620568 AGAAAATTAC
* * *
21620578 ACAACTTAAAGCGGAGGGAGCATCGAGAGAAGCTGAGGTTCAAA-AAAGATATGAAGAACTCCAG
1 ACAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAG-TATGAAGAACTCCAG
21620642 CT
65 CT
* * * *
21620644 ACAACTTAAAGTAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGGAAGTATGAAGATCTCCAGC
1 ACAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCAGC
21620709 T
66 T
21620710 GTAGCTTAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 55 0.95
67 3 0.05
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (66 bp):
ACAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCAGC
T
Found at i:21620718 original size:66 final size:66
Alignment explanation
Indices: 21620578--21620747 Score: 180
Period size: 66 Copynumber: 2.6 Consensus size: 66
21620568 AGAAAATTAC
* * * * *
21620578 ACAACTTAAAGCGGAGGGAGCATCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
1 ACAACTTAAAACAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
21620643 T
66 T
** * *
21620644 ACAACTTAAAGTAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGGAAG-TATGAAGATCTCCAG
1 ACAACTTAAAACAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAA-AAAGATATGAAGAACTCCAG
21620708 CT
65 CT
** * * * * *
21620710 GTAGCTTAAAACAGATGCGGTAGCGAGGGAAGCAGAGG
1 ACAACTTAAAACAGATGCAGCAGCGAGAGAAGCTGAGG
21620748 CAGCAGCGAG
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
66 84 0.97
67 3 0.03
ACGTcount: A:0.38, C:0.16, G:0.30, T:0.16
Consensus pattern (66 bp):
ACAACTTAAAACAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGC
T
Found at i:21621265 original size:43 final size:44
Alignment explanation
Indices: 21621089--21621280 Score: 184
Period size: 43 Copynumber: 4.5 Consensus size: 44
21621079 CGTTTTTAAA
* * *
21621089 AAAAGCGTCGCTAAA-AGTCATGG-CTTTTAGCGGCATTTT-TTGG
1 AAAAGCGCCGCTAAAGAGTCATGGTC-TATAGCGGC-TTTTGTGGG
** * * *
21621132 AAAAGCGCCATTAAA-AGTCATGGTATATAGTGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGAGTCATGGTCTATAGCGGCTTTTGTGGG
* *
21621175 AAAAGCACCGCTAAAG-GTCATGGTCTATAGCGG-TGATTGTGGG
1 AAAAGCGCCGCTAAAGAGTCATGGTCTATAGCGGCT-TTTGTGGG
* **
21621218 AAAAGCGCCGCTAAAGA-TCATGGTCTATAGCGGCTTTTCTGTA
1 AAAAGCGCCGCTAAAGAGTCATGGTCTATAGCGGCTTTTGTGGG
21621261 AAAAGCGCCGCTAAAG-GTCA
1 AAAAGCGCCGCTAAAGAGTCA
21621281 AGTGCACCTT
Statistics
Matches: 122, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
42 3 0.02
43 118 0.97
44 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (44 bp):
AAAAGCGCCGCTAAAGAGTCATGGTCTATAGCGGCTTTTGTGGG
Found at i:21624403 original size:34 final size:34
Alignment explanation
Indices: 21624352--21624418 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
21624342 TCAGTTTAAT
* *
21624352 TGGGCCTTAACCTATTATAGTGACAGTATCAGTG
1 TGGGCCTTAACCCATTATAGTGACAGTAACAGTG
*
21624386 TGGGCCTTAGCCCATTATAGTGACAGTAACAGT
1 TGGGCCTTAACCCATTATAGTGACAGTAACAGT
21624419 TCAGACATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (34 bp):
TGGGCCTTAACCCATTATAGTGACAGTAACAGTG
Found at i:21624729 original size:27 final size:27
Alignment explanation
Indices: 21624687--21624895 Score: 260
Period size: 27 Copynumber: 7.8 Consensus size: 27
21624677 ATAACATTAA
*
21624687 GCAT-ATAGCCATTTTATAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
*
21624713 GCATAATAATCATTTTATAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
* *
21624740 GCATAATAGTTATTTTATAACATAAGG
1 GCATAATAGTCATTTTATAACATAGGG
** **
21624767 GCATAACCGTCATTTTATAACATAAAG
1 GCATAATAGTCATTTTATAACATAGGG
**
21624794 GCATAACCGTCATTTTATAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
* *
21624821 ACATGATAGTCATTTTATAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
* **
21624848 GCATAATAGTTATTTTACCACAT-GAGG
1 GCATAATAGTCATTTTATAACATAG-GG
21624875 GCATAATAGTCATTTTATAAC
1 GCATAATAGTCATTTTATAAC
21624896 CGTTTAAAGG
Statistics
Matches: 158, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
26 5 0.03
27 153 0.97
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (27 bp):
GCATAATAGTCATTTTATAACATAGGG
Found at i:21629981 original size:15 final size:15
Alignment explanation
Indices: 21629961--21629993 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
21629951 AATTTTTTAA
21629961 AAATTA-TAAAAATAT
1 AAATTATTAAAAAT-T
21629976 AAATTATTAAAAATT
1 AAATTATTAAAAATT
21629991 AAA
1 AAA
21629994 ATTTTATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTATTAAAAATT
Found at i:21635695 original size:22 final size:22
Alignment explanation
Indices: 21635667--21635776 Score: 148
Period size: 22 Copynumber: 5.0 Consensus size: 22
21635657 TTTATTGTTC
*
21635667 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
21635689 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
21635711 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
21635733 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
21635755 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
21635777 TCTAAAGAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 77 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:21636847 original size:27 final size:26
Alignment explanation
Indices: 21636816--21636884 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
21636806 AAACTTAAAG
*
21636816 GAATGATATTCATGTCGAACTTTGAAT
1 GAATGATATTCATG-AGAACTTTGAAT
*
21636843 GAATGATATTTATAGAGAACTTTGAAT
1 GAATGATATTCAT-GAGAACTTTGAAT
* *
21636870 GAACGATATGCATGA
1 GAATGATATTCATGA
21636885 CAAACTATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.06
27 33 0.92
28 1 0.03
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (26 bp):
GAATGATATTCATGAGAACTTTGAAT
Found at i:21636890 original size:27 final size:27
Alignment explanation
Indices: 21636833--21636895 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
21636823 ATTCATGTCG
* ** *
21636833 AACTTTGAATGAATGATATTTATAGAG
1 AACTTTGAATGAACGATATGCATAGAA
21636860 AACTTTGAATGAACGATATGCAT-GACA
1 AACTTTGAATGAACGATATGCATAGA-A
*
21636887 AACTATGAA
1 AACTTTGAA
21636896 GGAAATATCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 2 0.07
27 28 0.93
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (27 bp):
AACTTTGAATGAACGATATGCATAGAA
Found at i:21638415 original size:6 final size:6
Alignment explanation
Indices: 21638404--21638431 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
21638394 ATTTTGTTTC
21638404 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
21638432 TGAATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:21645657 original size:23 final size:23
Alignment explanation
Indices: 21645602--21645657 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
21645592 AATTTGATGA
*
21645602 TTGAATTATTTTAAAGTTTTTAT
1 TTGAATTATTTAAAAGTTTTTAT
*
21645625 TTGAACTATTTAAAAGTTTTTAT
1 TTGAATTATTTAAAAGTTTTTAT
21645648 TT-AAGTTATT
1 TTGAA-TTATT
21645658 AAGTTTTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 2 0.07
23 27 0.93
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (23 bp):
TTGAATTATTTAAAAGTTTTTAT
Found at i:21653353 original size:45 final size:45
Alignment explanation
Indices: 21653257--21653456 Score: 172
Period size: 45 Copynumber: 4.5 Consensus size: 45
21653247 TTGGAAATAT
* * * * ** **
21653257 AGGTGGATGCTATGTGCTTATTCCACCCAATATTAATGAAAATAA
1 AGGTGGTTGCTATGTGCTGATTTCACCCAGTACCAATGAGTATAA
* * ** *
21653302 ATGTGGTTGCTATGTACTGATTTCA-CTGGATACCAATG-GTTATAT
1 AGGTGGTTGCTATGTGCTGATTTCACCCAG-TACCAATGAG-TATAA
*
21653347 AGGTGGTTGCTATGTGCTGATTTCACCCAGTACCATTGAGTATAA
1 AGGTGGTTGCTATGTGCTGATTTCACCCAGTACCAATGAGTATAA
* * * * *
21653392 AGGTAGTTGCTATGTGCTGATTTCACCAAGTACTATTGACTATAA
1 AGGTGGTTGCTATGTGCTGATTTCACCCAGTACCAATGAGTATAA
* *
21653437 GGGTGG-TGCTGTGTGCTGAT
1 AGGTGGTTGCTATGTGCTGAT
21653457 CCACCGTGTA
Statistics
Matches: 125, Mismatches: 26, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
44 14 0.11
45 108 0.86
46 3 0.02
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (45 bp):
AGGTGGTTGCTATGTGCTGATTTCACCCAGTACCAATGAGTATAA
Found at i:21653392 original size:90 final size:90
Alignment explanation
Indices: 21653253--21653417 Score: 222
Period size: 90 Copynumber: 1.8 Consensus size: 90
21653243 ATCATTGGAA
* ** * *
21653253 ATATAGGTGGATGCTATGTGCTTATTCCACCCAATATTAATGAAAATAAATGTGGTTGCTATGTA
1 ATATAGGTGGATGCTATGTGCTGATTCCACCCAATACCAATGAAAATAAAGGTAGTTGCTATGTA
21653318 CTGATTTCACTGGATACCAATGGTT
66 CTGATTTCACTGGATACCAATGGTT
* * * * ** *
21653343 ATATAGGTGGTTGCTATGTGCTGATTTCACCCAGTACCATTGAGTATAAAGGTAGTTGCTATGTG
1 ATATAGGTGGATGCTATGTGCTGATTCCACCCAATACCAATGAAAATAAAGGTAGTTGCTATGTA
21653408 CTGATTTCAC
66 CTGATTTCAC
21653418 CAAGTACTAT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
90 63 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (90 bp):
ATATAGGTGGATGCTATGTGCTGATTCCACCCAATACCAATGAAAATAAAGGTAGTTGCTATGTA
CTGATTTCACTGGATACCAATGGTT
Found at i:21657574 original size:43 final size:43
Alignment explanation
Indices: 21657504--21657625 Score: 167
Period size: 43 Copynumber: 2.8 Consensus size: 43
21657494 GGCTTGTACA
* * * * *
21657504 ATGCCAACGTCCCAGACGTGGTTTTACATGTAACCACAGATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACAAATCG
21657547 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAAACACAAATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAAACACAAATCG
21657590 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACA
21657626 GTTTTCGAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
42 3 0.04
43 64 0.91
44 3 0.04
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.19
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAAACACAAATCG
Found at i:21662224 original size:37 final size:38
Alignment explanation
Indices: 21662183--21662265 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 38
21662173 ACCCTATACC
21662183 TCAAAATTTT-CAATTTTTA-GAAAATAGTCCCTAAAAT
1 TCAAAATTTTACAATTTTTATG-AAATAGTCCCTAAAAT
** *
21662220 TC-AAATTTTACAATTTTTATGATTTTGTCCCTAAAAT
1 TCAAAATTTTACAATTTTTATGAAATAGTCCCTAAAAT
*
21662257 CCAAAATTT
1 TCAAAATTT
21662266 ACACTATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
36 7 0.18
37 25 0.64
38 7 0.18
ACGTcount: A:0.39, C:0.14, G:0.05, T:0.42
Consensus pattern (38 bp):
TCAAAATTTTACAATTTTTATGAAATAGTCCCTAAAAT
Found at i:21664371 original size:41 final size:41
Alignment explanation
Indices: 21664309--21664417 Score: 128
Period size: 41 Copynumber: 2.7 Consensus size: 41
21664299 TGATCGAATG
* *
21664309 TAATACAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
* * *
21664350 TAATTCAGACTTTACGTCTAGCAGGTTTAATGTCGGTGATA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
* * * * *
21664391 CATTTCGGACTATAGGTCTAGCAGGCT
1 TAATTCAGACTTTACGTCTAGCAGGCT
21664418 AAAAGCCAGT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (41 bp):
TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
Found at i:21669046 original size:26 final size:24
Alignment explanation
Indices: 21669016--21669067 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
21669006 AAATTTTTAT
21669016 CAAATTAATCACTTAAAATCATCCAC
1 CAAATTAATCA--TAAAATCATCCAC
* *
21669042 CAAATTATTCATAAAATCATTCAC
1 CAAATTAATCATAAAATCATCCAC
21669066 CA
1 CA
21669068 GTCATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.58
26 10 0.42
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (24 bp):
CAAATTAATCATAAAATCATCCAC
Found at i:21673368 original size:43 final size:43
Alignment explanation
Indices: 21673320--21673407 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
21673310 ATTGAAACGT
*
21673320 AATTTAAAATTTATGCAAAATGCTATATACCCCCTTTAAAGGG
1 AATTTAAAATTTATGCAAAATGCCATATACCCCCTTTAAAGGG
21673363 AATTTAAAATTTATGCAAAATGCCATATACCCCCTTTAAAGGG
1 AATTTAAAATTTATGCAAAATGCCATATACCCCCTTTAAAGGG
21673406 AA
1 AA
21673408 ACAATATACT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (43 bp):
AATTTAAAATTTATGCAAAATGCCATATACCCCCTTTAAAGGG
Found at i:21674765 original size:50 final size:50
Alignment explanation
Indices: 21674648--21674874 Score: 158
Period size: 50 Copynumber: 4.4 Consensus size: 50
21674638 GAGATCCAAT
* * ** * *
21674648 GTAAGACCATGTCCGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCGAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-A--ATGAGAACTCCCAC
* *
21674704 GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAAATGAGAGA-TCCCCC
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAAATGAGA-ACTCCCAC
* * * * * *
21674754 GTAAGACCATGTCTAGGACCTGACATGGGCACCGATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCGAAATGAGAACTCCCAC
* * * *
21674804 GTAAGACCATATCTGGGATATGGCATTGGTA--GTACAA-GA-AACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCACCG-A-AATGAGAAC-TCCCAC
*
21674853 GTAAGACCATGTTTGGGACATG
1 GTAAGACCATGTCTGGGACATG
21674875 AATTTGGCAT
Statistics
Matches: 140, Mismatches: 26, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
48 4 0.03
49 29 0.21
50 74 0.53
52 1 0.01
53 2 0.01
55 1 0.01
56 29 0.21
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.22
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACCGAAATGAGAACTCCCAC
Found at i:21677209 original size:9 final size:9
Alignment explanation
Indices: 21677195--21677258 Score: 92
Period size: 9 Copynumber: 7.1 Consensus size: 9
21677185 TATAGTTTGA
*
21677195 TATTCGAGT
1 TATTCGAAT
21677204 TATTCGAAT
1 TATTCGAAT
21677213 TATTCGAAT
1 TATTCGAAT
*
21677222 TATTCGACT
1 TATTCGAAT
21677231 TATTCGAAT
1 TATTCGAAT
*
21677240 TATTCGAGT
1 TATTCGAAT
*
21677249 TATTCAAAT
1 TATTCGAAT
21677258 T
1 T
21677259 CGAAAACTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (9 bp):
TATTCGAAT
Found at i:21692574 original size:24 final size:23
Alignment explanation
Indices: 21692542--21692587 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
21692532 TAGGGGTAGG
* *
21692542 ATCTTTTTATGCATTCGTATCTGT
1 ATCTATTTATGAATT-GTATCTGT
21692566 ATCTATTTATGAATTGTATCTG
1 ATCTATTTATGAATTGTATCTG
21692588 ATTCTGTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.52
Consensus pattern (23 bp):
ATCTATTTATGAATTGTATCTGT
Found at i:21695407 original size:27 final size:26
Alignment explanation
Indices: 21695354--21695410 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
21695344 TAGGTTAGTT
* * *
21695354 TTAAAATAAGTAATATATAAAATAAC
1 TTAAAATAAATAATATACAAAACAAC
*
21695380 TTAAAATAAAATAATATACAAAGCAAC
1 TTAAAAT-AAATAATATACAAAACAAC
21695407 TTAA
1 TTAA
21695411 TGTAAATACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (26 bp):
TTAAAATAAATAATATACAAAACAAC
Found at i:21701539 original size:43 final size:42
Alignment explanation
Indices: 21701456--21701541 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 42
21701446 TTTTATCCTA
** * *
21701456 TAAAAAAATATTTTGAACAAGGAGAAGATAATCTTGGGTTGT
1 TAAAAAAATATTTAAAAAAAGGAGAAGATAAACTTGGGTTGT
21701498 TAAAAAAATAATTTAAAAAAAGGAGAAGATAAACATT-GGTTGT
1 TAAAAAAAT-ATTTAAAAAAAGGAGAAGATAAAC-TTGGGTTGT
21701541 T
1 T
21701542 GGATTTACCC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 9 0.24
43 27 0.71
44 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.29
Consensus pattern (42 bp):
TAAAAAAATATTTAAAAAAAGGAGAAGATAAACTTGGGTTGT
Found at i:21702651 original size:33 final size:33
Alignment explanation
Indices: 21702614--21702682 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
21702604 GATTTGACGT
21702614 GTATACTTGCAGAATTCGTATATCATTTCACAC
1 GTATACTTGCAGAATTCGTATATCATTTCACAC
21702647 GTATACTTGCAGAATTCGTATATCATTTCACAC
1 GTATACTTGCAGAATTCGTATATCATTTCACAC
21702680 GTA
1 GTA
21702683 ACAAGTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.36
Consensus pattern (33 bp):
GTATACTTGCAGAATTCGTATATCATTTCACAC
Found at i:21702668 original size:17 final size:17
Alignment explanation
Indices: 21702614--21702668 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
21702604 GATTTGACGT
21702614 GTATACTTGCAGAATTC
1 GTATACTTGCAGAATTC
* *
21702631 GTATATCATTTCA-CA--C
1 GTATA-C-TTGCAGAATTC
21702647 GTATACTTGCAGAATTC
1 GTATACTTGCAGAATTC
21702664 GTATA
1 GTATA
21702669 TCATTTCACA
Statistics
Matches: 29, Mismatches: 4, Indels: 10
0.67 0.09 0.23
Matches are distributed among these distances:
14 4 0.14
15 2 0.07
16 6 0.21
17 11 0.38
18 2 0.07
19 4 0.14
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (17 bp):
GTATACTTGCAGAATTC
Found at i:21712638 original size:9 final size:9
Alignment explanation
Indices: 21712624--21712648 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21712614 TTGCTCCCTA
21712624 TCTTCCTCC
1 TCTTCCTCC
21712633 TCTTCCTCC
1 TCTTCCTCC
21712642 TCTTCCT
1 TCTTCCT
21712649 TGTAATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (9 bp):
TCTTCCTCC
Found at i:21724600 original size:26 final size:26
Alignment explanation
Indices: 21724557--21724617 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
21724547 TATCCGAAGC
* * * *
21724557 TCCTAATTAAAGGCTCTTCGTGAGCT
1 TCCTGATTAAAAGCTCTTCGTAAACT
* *
21724583 TCCTGATTAAAAGTTCTTTGTAAACT
1 TCCTGATTAAAAGCTCTTCGTAAACT
21724609 TCCTGATTA
1 TCCTGATTA
21724618 TGGCTTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (26 bp):
TCCTGATTAAAAGCTCTTCGTAAACT
Found at i:21730416 original size:75 final size:76
Alignment explanation
Indices: 21730289--21730543 Score: 282
Period size: 75 Copynumber: 3.4 Consensus size: 76
21730279 ACAAATTATT
* *
21730289 GTCGGTTTATCCGACTAGCGCTGGGTGCAACTTTCATCAATTTAACTGACTAGTGCTGGGCACAT
1 GTCGGTTTATCCGACTAGAGCTGGGTGCAACTTTCATCAGTTTAACTGACTAGTGCTGGGCACAT
* *
21730354 CTTTATACTCA
66 CATTATACTAA
* * * * *
21730365 -TCGGTTTACCCGACTAGAGCTGGTTGCAACTTTCATTAGTTTAACTAACTAGTGTTGGGCACAT
1 GTCGGTTTATCCGACTAGAGCTGGGTGCAACTTTCATCAGTTTAACTGACTAGTGCTGGGCACAT
*
21730429 CATTAT-GTAA
66 CATTATACTAA
* * * * * **
21730439 GTCGGTCTATTCGACTAGTGTTGGGCGCAACCATCATCAGTTTAACTGACTAGTGCTGGGCACAT
1 GTCGGTTTATCCGACTAGAGCTGGGTGCAACTTTCATCAGTTTAACTGACTAGTGCTGGGCACAT
*
21730504 CATTATA-TAT
66 CATTATACTAA
* * * * *
21730514 GTCAGTCTATCCAACTAGCGCTGGGCGCAA
1 GTCGGTTTATCCGACTAGAGCTGGGTGCAA
21730544 AACTTGATTA
Statistics
Matches: 149, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
74 2 0.01
75 147 0.99
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (76 bp):
GTCGGTTTATCCGACTAGAGCTGGGTGCAACTTTCATCAGTTTAACTGACTAGTGCTGGGCACAT
CATTATACTAA
Found at i:21731654 original size:54 final size:54
Alignment explanation
Indices: 21731578--21731701 Score: 167
Period size: 54 Copynumber: 2.3 Consensus size: 54
21731568 CTCAGCCTGC
* * *
21731578 GACACGGCCATGTGACTCAAGTCAGTAAGTTACACGGAAAGAGACACGGGCTGA
1 GACACGGCCGTGTGTCTCAAGTCAGTAAGTTACACAGAAAGAGACACGGGCTGA
* * ** * *
21731632 GACACGGCCGTGTGTCTGAAGTCAGTGAGTTTTACAGATAGAGACACGGGTTGA
1 GACACGGCCGTGTGTCTCAAGTCAGTAAGTTACACAGAAAGAGACACGGGCTGA
21731686 GACACGGCCGTGTGTC
1 GACACGGCCGTGTGTC
21731702 CCAATTTCGA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.27, C:0.21, G:0.32, T:0.19
Consensus pattern (54 bp):
GACACGGCCGTGTGTCTCAAGTCAGTAAGTTACACAGAAAGAGACACGGGCTGA
Found at i:21733545 original size:19 final size:19
Alignment explanation
Indices: 21733521--21733559 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
21733511 ACTCATTAGG
*
21733521 TTAGTGGAAAATCGAGAGA
1 TTAGTGGAAAATCAAGAGA
*
21733540 TTAGTGGAACATCAAGAGA
1 TTAGTGGAAAATCAAGAGA
21733559 T
1 T
21733560 CTCGCTAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.28, T:0.23
Consensus pattern (19 bp):
TTAGTGGAAAATCAAGAGA
Found at i:21738258 original size:16 final size:16
Alignment explanation
Indices: 21738239--21738281 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
21738229 CATTAATTAA
*
21738239 TTAATTAATTATTGTT
1 TTAATTAATTATTATT
*
21738255 TTAAATAA-TATTATT
1 TTAATTAATTATTATT
21738270 TTACATTAATTA
1 TTA-ATTAATTA
21738282 CATAAAGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 9 0.41
16 11 0.50
17 2 0.09
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
TTAATTAATTATTATT
Found at i:21738462 original size:26 final size:26
Alignment explanation
Indices: 21738433--21738483 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
21738423 TCTAATTATT
*
21738433 ATAATTAAA-AATATAATATTTAAAAA
1 ATAATTAAATAATA-AATATGTAAAAA
21738459 ATAATTAAATAATAAATATGTAAAA
1 ATAATTAAATAATAAATATGTAAAA
21738484 TCAAAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
ATAATTAAATAATAAATATGTAAAAA
Found at i:21744379 original size:30 final size:30
Alignment explanation
Indices: 21744345--21744403 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 30
21744335 GCATCACAAA
21744345 ATGTTAAAATT-T-ATTAATAATATATTTTTT
1 ATGTT-AAATTATAATTAA-AATATATTTTTT
21744375 ATGTTAAATTATAAATTAAAATATATTTT
1 ATGTTAAATTAT-AATTAAAATATATTTT
21744404 AAAAACATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 5 0.19
30 6 0.23
31 10 0.38
32 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (30 bp):
ATGTTAAATTATAATTAAAATATATTTTTT
Found at i:21745304 original size:2 final size:2
Alignment explanation
Indices: 21745297--21745345 Score: 82
Period size: 2 Copynumber: 24.5 Consensus size: 2
21745287 ATTTATCTAC
21745297 TA TA TA TA TA T- TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21745339 TA TA TA T
1 TA TA TA T
21745346 TTTCCTCCTC
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 43 0.96
3 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21746693 original size:23 final size:23
Alignment explanation
Indices: 21746661--21746704 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
21746651 GCTACCATTT
21746661 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
21746684 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
21746705 ATAATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:21746697 original size:13 final size:11
Alignment explanation
Indices: 21746665--21746707 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
21746655 CCATTTTCTA
*
21746665 AATAAAATAAT
1 AATAAAATATT
21746676 AAT-AAATATCT
1 AATAAAATAT-T
21746687 AAGTAAAATATT
1 AA-TAAAATATT
21746699 AATAAAATA
1 AATAAAATA
21746708 ATTTTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:21750956 original size:50 final size:50
Alignment explanation
Indices: 21750894--21751063 Score: 241
Period size: 50 Copynumber: 3.4 Consensus size: 50
21750884 CAATATCATA
* ** * * *
21750894 TCCCAGATATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATG
** *
21750944 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATG
* *
21750994 TCCCTGACATGGTCTTACATGGGACCTCTTATCTTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATG
21751044 TCCCAGACATGGTCTTACAT
1 TCCCAGACATGGTCTTACAT
21751064 ACCTCTTTAC
Statistics
Matches: 105, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 105 1.00
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.28
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATCTTGGTGCCAACGCCATG
Found at i:21753978 original size:37 final size:37
Alignment explanation
Indices: 21753928--21754029 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 37
21753918 CGTATTGAGA
* * *
21753928 TCTGATTTGCATGTTAAACATGCCATATTTTTTATAT
1 TCTGATTCGCATGTTAAACATGCCATATTTCTGATAT
* *
21753965 TCTGATTCGCATGTAAAACATGTCATATTTCTGATAT
1 TCTGATTCGCATGTTAAACATGCCATATTTCTGATAT
*
21754002 TCTGATTCGCTTG-TAAAGCATGCC-TATT
1 TCTGATTCGCATGTTAAA-CATGCCATATT
21754030 GAAAATCTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
36 7 0.12
37 49 0.88
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (37 bp):
TCTGATTCGCATGTTAAACATGCCATATTTCTGATAT
Found at i:21754612 original size:19 final size:19
Alignment explanation
Indices: 21754588--21754638 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
21754578 TTAATTATTT
*
21754588 TGGACTTTGGTTTTGGACA
1 TGGACTTTGGATTTGGACA
21754607 TGGACTTTGGATTTGGACA
1 TGGACTTTGGATTTGGACA
21754626 TGGACTTTGGATT
1 TGGACTTTGGATT
21754639 ATTTTTGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.18, C:0.10, G:0.31, T:0.41
Consensus pattern (19 bp):
TGGACTTTGGATTTGGACA
Found at i:21755442 original size:57 final size:55
Alignment explanation
Indices: 21755379--21755484 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 55
21755369 TGTCCCAGCT
*
21755379 TGTGTGTATACTGAAATTAAGGTCACACGGCCGTGTCGCAGGGCGTGTGCCTGCCCG
1 TGTGTGTATAC-GAAATT-AGGTCACACGGCCGTGTCGCAGGCCGTGTGCCTGCCCG
* * * *
21755436 TGTGTGTATTCGAAGTTTGGTCACACGGTCGTGTCGCAGGCCGTGTGCC
1 TGTGTGTATACGAAATTAGGTCACACGGCCGTGTCGCAGGCCGTGTGCC
21755485 AGATCATGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
55 29 0.66
56 5 0.11
57 10 0.23
ACGTcount: A:0.15, C:0.24, G:0.34, T:0.27
Consensus pattern (55 bp):
TGTGTGTATACGAAATTAGGTCACACGGCCGTGTCGCAGGCCGTGTGCCTGCCCG
Found at i:21756825 original size:75 final size:74
Alignment explanation
Indices: 21756594--21756842 Score: 272
Period size: 75 Copynumber: 3.3 Consensus size: 74
21756584 AAATCAATAG
* * * * * * * *
21756594 ATATAATGATGTTCCCAGCACTAGTAAGAAAAACTGACGAAAGTTGCACCTAGCGCTAGTTAG-A
1 ATATAATGGTGTGCCCAGCACTAGTAAGATAAACTGATGAAAGTTTCGCC-AGCACTAG-TCGTA
*
21756658 TAAATCGAAAA
64 TAAACCGAAAA
* *
21756669 ATATAATGGTGTGCCCAGCACTAGTAAGAT-AATTGATGAAA-TTTGCGCTCAGCAGTAGTCGTA
1 ATATAATGGTGTGCCCAGCACTAGTAAGATAAACTGATGAAAGTTT-CGC-CAGCACTAGTCGTA
*
21756732 AAAACC-AAAA
64 TAAACCGAAAA
* *
21756742 ACTATAATGGTGTGCCCAGCACTAGTCAGATAAACTGATGAAAGTTTCGCCAAACACTAGTCGTA
1 A-TATAATGGTGTGCCCAGCACTAGTAAGATAAACTGATGAAAGTTTCGCC-AGCACTAGTCGTA
*
21756807 TAAACCGACAA
64 TAAACCGAAAA
*
21756818 ATATAATGGTGTGTCCAGCACTAGT
1 ATATAATGGTGTGCCCAGCACTAGT
21756843 TGCATAAATC
Statistics
Matches: 147, Mismatches: 19, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
73 9 0.06
74 51 0.35
75 80 0.54
76 7 0.05
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (74 bp):
ATATAATGGTGTGCCCAGCACTAGTAAGATAAACTGATGAAAGTTTCGCCAGCACTAGTCGTATA
AACCGAAAA
Found at i:21758211 original size:38 final size:38
Alignment explanation
Indices: 21758165--21758241 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
21758155 CAGTAACTTG
*
21758165 ATCAATGGCTTATTTGCCTAATAAACCCCTTGTTTGAT
1 ATCAATGGCTTATTTGCCTAATAAACACCTTGTTTGAT
*
21758203 ATCAATGGCTTATTTGCCTAATAAGCACCTTGTTTGAT
1 ATCAATGGCTTATTTGCCTAATAAACACCTTGTTTGAT
21758241 A
1 A
21758242 GTCACTTATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (38 bp):
ATCAATGGCTTATTTGCCTAATAAACACCTTGTTTGAT
Found at i:21763553 original size:75 final size:74
Alignment explanation
Indices: 21763473--21763709 Score: 270
Period size: 75 Copynumber: 3.3 Consensus size: 74
21763463 TAATTTGACG
* * * * * *
21763473 AATATAATGATGTGCCTATCACTAGTTAGATAAACTGACAAAAGTTACACCCAGCGCTAGTTAGA
1 AATATAATGGTGTGCCCAGCACTAGTAAGATAAACTGAC-AAAGTTACGCCCAGCGCTAGTTGGA
21763538 TAAACCGAAA
65 TAAACCGAAA
*
21763548 AATATAATGGTGTGCCCAGCACTAGTAAGATAAACTGAC---G-T--GCCTAGCGCTAGTTGGAT
1 AATATAATGGTGTGCCCAGCACTAGTAAGATAAACTGACAAAGTTACGCCCAGCGCTAGTTGGAT
**
21763607 AAACCGAGC
66 AAACCGAAA
* * **
21763616 AATATAATGGTGTGCCCAGCACTAGTCAGATAAACTAACGAAAGTTACGCCCAATGCTAGTTGGA
1 AATATAATGGTGTGCCCAGCACTAGTAAGATAAACTGAC-AAAGTTACGCCCAGCGCTAGTTGGA
** *
21763681 TAAACATATA
65 TAAACCGAAA
21763691 AATATAATGGTGTGCCCAG
1 AATATAATGGTGTGCCCAG
21763710 AGTAGTTGAA
Statistics
Matches: 137, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
68 59 0.43
70 1 0.01
71 1 0.01
72 1 0.01
73 1 0.01
75 74 0.54
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (74 bp):
AATATAATGGTGTGCCCAGCACTAGTAAGATAAACTGACAAAGTTACGCCCAGCGCTAGTTGGAT
AAACCGAAA
Found at i:21763634 original size:68 final size:68
Alignment explanation
Indices: 21763525--21763651 Score: 218
Period size: 68 Copynumber: 1.9 Consensus size: 68
21763515 AGTTACACCC
21763525 AGCGCTAGTTAGATAAACCGAAAAATATAATGGTGTGCCCAGCACTAGTAAGATAAACTGACGTG
1 AGCGCTAGTTAGATAAACCGAAAAATATAATGGTGTGCCCAGCACTAGTAAGATAAACTGACGTG
21763590 CCT
66 CCT
* ** *
21763593 AGCGCTAGTTGGATAAACCGAGCAATATAATGGTGTGCCCAGCACTAGTCAGATAAACT
1 AGCGCTAGTTAGATAAACCGAAAAATATAATGGTGTGCCCAGCACTAGTAAGATAAACT
21763652 AACGAAAGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 55 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (68 bp):
AGCGCTAGTTAGATAAACCGAAAAATATAATGGTGTGCCCAGCACTAGTAAGATAAACTGACGTG
CCT
Found at i:21766818 original size:36 final size:36
Alignment explanation
Indices: 21766770--21766840 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
21766760 ATCAAAGGCT
*
21766770 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
*
21766806 ATAATTAGAAGCTGTATACAATTAAAACTCTAAGA
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGA
21766841 TTAAATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (36 bp):
ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
Found at i:21771919 original size:36 final size:36
Alignment explanation
Indices: 21771871--21771941 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
21771861 ATCAAAGGCT
*
21771871 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
*
21771907 ATAATTAGAAGCTGTATACAATTAAAACTCTAAGA
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGA
21771942 TTAAATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (36 bp):
ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
Found at i:21781522 original size:60 final size:60
Alignment explanation
Indices: 21781337--21781523 Score: 216
Period size: 60 Copynumber: 3.1 Consensus size: 60
21781327 AAAATGAAGA
* * * * * ** * *
21781337 GGTGCTCCTGTATACCCTTCGATGTCCCTGTTTGCATGACTGTGCCTTTGTTCGCACTTC
1 GGTGCCCCTATATACACTTCGGTGTCACTGTTTGCACAATTGTGCCCTTGTTCGCACTTC
* * *
21781397 GGTACCCCTGTATACACTTCGGTGTCCCTGTTTGCACAATTGTGCCCTTGTTCGCACTTC
1 GGTGCCCCTATATACACTTCGGTGTCACTGTTTGCACAATTGTGCCCTTGTTCGCACTTC
* *
21781457 AGTGCCCCTATATACACTTCGGTGTCACTGTTTGCA-AGTTTGTTGCCC-TGTTCGCACTTC
1 GGTGCCCCTATATACACTTCGGTGTCACTGTTTGCACA-ATTG-TGCCCTTGTTCGCACTTC
21781517 GGTGCCC
1 GGTGCCC
21781524 TTGACTGCAC
Statistics
Matches: 111, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
59 1 0.01
60 105 0.95
61 5 0.05
ACGTcount: A:0.12, C:0.30, G:0.21, T:0.36
Consensus pattern (60 bp):
GGTGCCCCTATATACACTTCGGTGTCACTGTTTGCACAATTGTGCCCTTGTTCGCACTTC
Found at i:21784965 original size:50 final size:50
Alignment explanation
Indices: 21784859--21785037 Score: 196
Period size: 50 Copynumber: 3.5 Consensus size: 50
21784849 GGGAATGAGA
*
21784859 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ATCGA-G--ATGAGAGG
* *
21784915 TCCCATGTAAGACCATGCCTGGGACATGGCGTTGGCATCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGG
* * * * * * **
21784965 TCCCATGTAAGACCATGTTTGGGACATAGTATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGG
*
21785015 TCCCATGTAAGACCATATCTGGG
1 TCCCATGTAAGACCATGTCTGGG
21785038 GTATGACATT
Statistics
Matches: 108, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
50 69 0.64
52 1 0.01
53 4 0.04
56 34 0.31
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGG
Found at i:21785317 original size:20 final size:20
Alignment explanation
Indices: 21785292--21785330 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
21785282 TGAGTTATTT
21785292 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
21785312 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
21785331 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:21790860 original size:27 final size:27
Alignment explanation
Indices: 21790839--21790892 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
21790829 TTAGAGATTG
* *
21790839 CTTGAAAGTAGCTTTAGATAGATAGAA
1 CTTGAAAGTAGCTTCAGATAGAGAGAA
*
21790866 CTTGAAAGTAGCTTCAGATAGACAGAA
1 CTTGAAAGTAGCTTCAGATAGAGAGAA
21790893 ATCCTATGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (27 bp):
CTTGAAAGTAGCTTCAGATAGAGAGAA
Found at i:21792764 original size:50 final size:50
Alignment explanation
Indices: 21792654--21792764 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 50
21792644 TTATGATAGG
* * **
21792654 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * *
21792704 TCCTC-CGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCC-CATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
21792754 TCCCATGTAAG
1 TCCCATGTAAG
21792765 CCCGTTTCTA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.02
50 49 0.96
51 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
Found at i:21793015 original size:20 final size:20
Alignment explanation
Indices: 21792990--21793028 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
21792980 TGAGTTATTT
21792990 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
21793010 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
21793029 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:21794298 original size:14 final size:14
Alignment explanation
Indices: 21794279--21794317 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
21794269 TTGTTTCACT
21794279 GGAAATGACTTCCG
1 GGAAATGACTTCCG
* *
21794293 GGAAATGATTTCTG
1 GGAAATGACTTCCG
*
21794307 GAAAATGACTT
1 GGAAATGACTT
21794318 ACTTTTCTGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (14 bp):
GGAAATGACTTCCG
Found at i:21796159 original size:20 final size:18
Alignment explanation
Indices: 21796125--21796186 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 18
21796115 AACATTCATT
21796125 TAAAAAATATGTATACATA
1 TAAAAAATATGTATA-ATA
* *
21796144 TAAAATAATATCTATATTA
1 TAAAA-AATATGTATAATA
21796163 TAAAAATATATGTATATATA
1 TAAAAA-ATATGTATA-ATA
21796183 TAAA
1 TAAA
21796187 TATGAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 1 0.03
19 20 0.56
20 15 0.42
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (18 bp):
TAAAAAATATGTATAATA
Found at i:21796164 original size:19 final size:20
Alignment explanation
Indices: 21796125--21796186 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
21796115 AACATTCATT
* *
21796125 TAAAAA-ATATGTATACATA
1 TAAAAATATATCTATATATA
21796144 T-AAAATAATATCTATAT-TA
1 TAAAAAT-ATATCTATATATA
*
21796163 TAAAAATATATGTATATATA
1 TAAAAATATATCTATATATA
21796183 TAAA
1 TAAA
21796187 TATGAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 4 0.11
19 13 0.36
20 19 0.53
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (20 bp):
TAAAAATATATCTATATATA
Found at i:21797954 original size:44 final size:44
Alignment explanation
Indices: 21797904--21798007 Score: 120
Period size: 44 Copynumber: 2.4 Consensus size: 44
21797894 TACTCTCTGC
* * *
21797904 AACTTCAGAGAGATAAAATCTAT-GGTTTTAATCCGCTCCACTGT
1 AACTTCAGGGAGATAAAAT-TATCAGCTTTAATCCGCTCCACTGT
** * * *
21797948 AACTTCAGGGAGATAGGATTATCAGCTTTGATCTGCTCTACTGT
1 AACTTCAGGGAGATAAAATTATCAGCTTTAATCCGCTCCACTGT
21797992 AACTTCAGGGAGATAA
1 AACTTCAGGGAGATAA
21798008 GATTTGCCAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 3 0.06
44 47 0.94
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (44 bp):
AACTTCAGGGAGATAAAATTATCAGCTTTAATCCGCTCCACTGT
Found at i:21798542 original size:45 final size:45
Alignment explanation
Indices: 21798478--21798609 Score: 169
Period size: 45 Copynumber: 3.0 Consensus size: 45
21798468 AAGGCTGGAG
21798478 TTTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCTA
1 TTTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCTA
* * * * * * * *
21798523 TTTTTGACCTGCTCCGCTGCAGCT-CAGGGAGGCAAG-GCTGGTG
1 TTTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCTA
*
21798566 TCTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCT
1 TTTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCT
21798610 GTCTTCATTG
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
43 23 0.33
44 22 0.32
45 24 0.35
ACGTcount: A:0.17, C:0.24, G:0.30, T:0.29
Consensus pattern (45 bp):
TTTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCTA
Found at i:21798549 original size:88 final size:88
Alignment explanation
Indices: 21798390--21798609 Score: 316
Period size: 88 Copynumber: 2.5 Consensus size: 88
21798380 AAAACTGATA
* * * * *
21798390 TCTTCGATCTGCTTCACTGCCAGTACAAGAAGGCAAGATCTGCTATTTTCAACCTACTCTACTGC
1 TCTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTGC
21798455 TACTCAGGGAGACAAGGCTGGAG
66 TACTCAGGGAGACAAGGCTGGAG
* ** * *
21798478 TTTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCTATTTTTGACCTGCTCCGCTGC
1 TCTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTGC
* *
21798543 -AGCTCAGGGAGGCAAGGCTGGTG
66 TA-CTCAGGGAGACAAGGCTGGAG
21798566 TCTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCT
1 TCTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCT
21798610 GTCTTCATTG
Statistics
Matches: 118, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
87 1 0.01
88 117 0.99
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (88 bp):
TCTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTGC
TACTCAGGGAGACAAGGCTGGAG
Found at i:21798600 original size:44 final size:44
Alignment explanation
Indices: 21798467--21798602 Score: 166
Period size: 44 Copynumber: 3.1 Consensus size: 44
21798457 CTCAGGGAGA
*
21798467 CAAGGCTGGAGTTTTTGATCTGCTTCGCTGCCGGTACAGGAAGG
1 CAAGGCTGGTGTTTTTGATCTGCTTCGCTGCCGGTACAGGAAGG
* * * * * * * *
21798511 CAAGATCTGCTATTTTTGACCTGCTCCGCTGCAGCT-CAGGGAGG
1 CAAG-GCTGGTGTTTTTGATCTGCTTCGCTGCCGGTACAGGAAGG
*
21798555 CAAGGCTGGTGTCTTTGATCTGCTTCGCTGCCGGTACAGGAAGG
1 CAAGGCTGGTGTTTTTGATCTGCTTCGCTGCCGGTACAGGAAGG
21798599 CAAG
1 CAAG
21798603 ATCTGCTGTC
Statistics
Matches: 72, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
43 23 0.32
44 26 0.36
45 23 0.32
ACGTcount: A:0.18, C:0.24, G:0.32, T:0.26
Consensus pattern (44 bp):
CAAGGCTGGTGTTTTTGATCTGCTTCGCTGCCGGTACAGGAAGG
Found at i:21799850 original size:12 final size:12
Alignment explanation
Indices: 21799818--21799852 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
21799808 GGCCTCTCCA
*
21799818 TTTTCTTTCTTC
1 TTTTCTTTTTTC
21799830 TTTTCTTTTTTC
1 TTTTCTTTTTTC
21799842 TTTTCTTTTTT
1 TTTTCTTTTTT
21799853 TTTGAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:21808014 original size:50 final size:50
Alignment explanation
Indices: 21807935--21808035 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
21807925 CTACGTACTC
21807935 TACACGCAATTATTCTATTATAAAATATTTAATAATTCAATTCATTAAAT
1 TACACGCAATTATTCTATTATAAAATATTTAATAATTCAATTCATTAAAT
* *
21807985 TACACGCTATTATTCTATTATAAATTATTTAATAATTCAATTCATTAAAT
1 TACACGCAATTATTCTATTATAAAATATTTAATAATTCAATTCATTAAAT
21808035 T
1 T
21808036 CGGTTCAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.45
Consensus pattern (50 bp):
TACACGCAATTATTCTATTATAAAATATTTAATAATTCAATTCATTAAAT
Found at i:21808033 original size:25 final size:25
Alignment explanation
Indices: 21807955--21808035 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
21807945 TATTCTATTA
*
21807955 TAAAATATTTAATAATTCAATTCAT
1 TAAATTATTTAATAATTCAATTCAT
** * *
21807980 TAAATTACACGCT-ATTATTCTATT-A-
1 TAAATT--A-TTTAATAATTCAATTCAT
21808005 TAAATTATTTAATAATTCAATTCAT
1 TAAATTATTTAATAATTCAATTCAT
21808030 TAAATT
1 TAAATT
21808036 CGGTTCAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 12
0.66 0.15 0.19
Matches are distributed among these distances:
22 1 0.02
23 10 0.24
24 1 0.02
25 17 0.41
26 1 0.02
27 10 0.24
28 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.46
Consensus pattern (25 bp):
TAAATTATTTAATAATTCAATTCAT
Found at i:21809079 original size:42 final size:42
Alignment explanation
Indices: 21809027--21809117 Score: 173
Period size: 42 Copynumber: 2.2 Consensus size: 42
21809017 GAAAACACTC
*
21809027 AAATACCGATTTGAATATCAAAGCCAATACTAAATTGGGAAA
1 AAATCCCGATTTGAATATCAAAGCCAATACTAAATTGGGAAA
21809069 AAATCCCGATTTGAATATCAAAGCCAATACTAAATTGGGAAA
1 AAATCCCGATTTGAATATCAAAGCCAATACTAAATTGGGAAA
21809111 AAATCCC
1 AAATCCC
21809118 CTAATTATCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (42 bp):
AAATCCCGATTTGAATATCAAAGCCAATACTAAATTGGGAAA
Found at i:21810253 original size:143 final size:143
Alignment explanation
Indices: 21810004--21810288 Score: 482
Period size: 143 Copynumber: 2.0 Consensus size: 143
21809994 CAATTTTGGG
* * *
21810004 CCTAGTCGGAACAGTGGTTTTGGGACTACAAATCCGATGAGAAAAAAATTATTTTTATTATATTT
1 CCTAGTCGGAACAGTGGTTTCGGGACCACAAATCCGATGAGAAAAAAATTATTTTTATTATATAT
21810069 TTATGGTCTACGATTTCACGGAATGATTTTGTGAAAATTTCGTTCAAAAATTTCGACGTTTAGGC
66 TTATGGTCTACGATTTCACGGAATGATTTTGTGAAAATTTCGTTCAAAAATTTCGACGTTTAGGC
21810134 ACTCAATTTAGTT
131 ACTCAATTTAGTT
* *
21810147 CCTAGTCGGAACAGTGGTTTCGGGACCACAAATCCGTTGAGAAAAAAATTATTTTTCTTATATAT
1 CCTAGTCGGAACAGTGGTTTCGGGACCACAAATCCGATGAGAAAAAAATTATTTTTATTATATAT
* *
21810212 TTATGGTCTACGATTTCACGGAATGATTTT-TTAAAATTTTCGTTCAAAAATTTCGACGTTTGGG
66 TTATGGTCTACGATTTCACGGAATGATTTTGTGAAAA-TTTCGTTCAAAAATTTCGACGTTTAGG
*
21810276 CACTTAATTTAGT
130 CACTCAATTTAGT
21810289 CAAAAGGACT
Statistics
Matches: 133, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
142 5 0.04
143 128 0.96
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (143 bp):
CCTAGTCGGAACAGTGGTTTCGGGACCACAAATCCGATGAGAAAAAAATTATTTTTATTATATAT
TTATGGTCTACGATTTCACGGAATGATTTTGTGAAAATTTCGTTCAAAAATTTCGACGTTTAGGC
ACTCAATTTAGTT
Found at i:21811372 original size:24 final size:24
Alignment explanation
Indices: 21811345--21811392 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
21811335 AGAGGTCCCA
*
21811345 TGTAAGACAATGTTTGCGACATGG
1 TGTAAGACAATGTCTGCGACATGG
* *
21811369 TGTAAGACCATGTCTGGGACATGG
1 TGTAAGACAATGTCTGCGACATGG
21811393 CGTTGGCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (24 bp):
TGTAAGACAATGTCTGCGACATGG
Found at i:21811447 original size:50 final size:50
Alignment explanation
Indices: 21811369--21811550 Score: 238
Period size: 50 Copynumber: 3.6 Consensus size: 50
21811359 TGCGACATGG
* *
21811369 TGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATAAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * * *
21811419 TGCAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATGAGAGGTCCCC
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * * * **
21811469 CGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAACTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* *
21811519 TGTAAGACCATATCTGGGATATGGCATTGGCA
1 TGTAAGACCATGTCTGGGACATGGCATTGGCA
21811551 GTACAAAAAA
Statistics
Matches: 114, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 114 1.00
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
Found at i:21811543 original size:100 final size:100
Alignment explanation
Indices: 21811370--21811550 Score: 263
Period size: 100 Copynumber: 1.8 Consensus size: 100
21811360 GCGACATGGT
* * ** *
21811370 GTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATAAGAGGTCCCATGCAAGACCATGTCTG
1 GTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATAAGAACTCCCATGCAAGACCATATCTG
*
21811435 GGACATGGCGTTGGCACTGAGATGAGAGGTCCCCC
66 GGACATGGCATTGGCACTGAGATGAGAGGTCCCCC
* * * *
21811470 GTAAGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAACTCCCATGTAAGACCATATCTG
1 GTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATAAGAACTCCCATGCAAGACCATATCTG
*
21811535 GGATATGGCATTGGCA
66 GGACATGGCATTGGCA
21811551 GTACAAAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
100 70 1.00
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (100 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATAAGAACTCCCATGCAAGACCATATCTG
GGACATGGCATTGGCACTGAGATGAGAGGTCCCCC
Found at i:21815291 original size:28 final size:28
Alignment explanation
Indices: 21815256--21815311 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
21815246 GATTGATCCG
21815256 ATGGGTACTTTTACTCTAAGAATTTGAT
1 ATGGGTACTTTTACTCTAAGAATTTGAT
21815284 ATGGGTACTTTTACTCTAAGAATTTGAT
1 ATGGGTACTTTTACTCTAAGAATTTGAT
21815312 CTAGAAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.43
Consensus pattern (28 bp):
ATGGGTACTTTTACTCTAAGAATTTGAT
Found at i:21827541 original size:16 final size:17
Alignment explanation
Indices: 21827520--21827551 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21827510 TGGTGGAATA
21827520 TAGCAAA-GAAAATGAG
1 TAGCAAATGAAAATGAG
21827536 TAGCAAATGAAAATGA
1 TAGCAAATGAAAATGA
21827552 TTCAAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.56, C:0.06, G:0.22, T:0.16
Consensus pattern (17 bp):
TAGCAAATGAAAATGAG
Found at i:21829824 original size:46 final size:46
Alignment explanation
Indices: 21829660--21829835 Score: 154
Period size: 46 Copynumber: 3.8 Consensus size: 46
21829650 TGGGCTTAAA
* * *** *
21829660 ATTCATGTATGCTCGAGTCCGCAACATATGCAGAAGCTTAAAACCC
1 ATTCATGTATTCTCGAGTCCGCAACATATGCAGGAGCTCGGAACCT
** * * * * * *
21829706 AAACCTGTATTATGGTGTCCGCAACATATACAAGAGCTCGGAACCT
1 ATTCATGTATTCTCGAGTCCGCAACATATGCAGGAGCTCGGAACCT
* * * * ** *
21829752 ATTCTTGTCTTCTTGAGTTCATAACATATGTAGGAGCTCGGAACCT
1 ATTCATGTATTCTCGAGTCCGCAACATATGCAGGAGCTCGGAACCT
*
21829798 ATTCATGTATTCTCGAGTCCGCAACATATGTAGGAGCT
1 ATTCATGTATTCTCGAGTCCGCAACATATGCAGGAGCT
21829836 TAAAACCTGG
Statistics
Matches: 97, Mismatches: 33, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
46 97 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (46 bp):
ATTCATGTATTCTCGAGTCCGCAACATATGCAGGAGCTCGGAACCT
Found at i:21830726 original size:16 final size:17
Alignment explanation
Indices: 21830701--21830732 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
21830691 TTGTTTTTAT
21830701 TTTTATTTATTTTAACC
1 TTTTATTTATTTTAACC
21830718 TTTTA-TTATTTTAAC
1 TTTTATTTATTTTAAC
21830733 TTAGTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTTATTTTAACC
Found at i:21832372 original size:13 final size:13
Alignment explanation
Indices: 21832330--21832385 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
21832320 TAGATTCTTC
21832330 CTAAATATTATCA
1 CTAAATATTATCA
*
21832343 C-AAA-ATAATC-
1 CTAAATATTATCA
21832353 CTAAATATTATCA
1 CTAAATATTATCA
*
21832366 TTAAATATTATCA
1 CTAAATATTATCA
21832379 CTAAATA
1 CTAAATA
21832386 ATTTAAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 1 0.03
11 8 0.22
12 8 0.22
13 19 0.53
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:21839715 original size:27 final size:27
Alignment explanation
Indices: 21839684--21840164 Score: 497
Period size: 27 Copynumber: 17.8 Consensus size: 27
21839674 TAAGCCCAAC
*
21839684 ATACCCCCGAAGGGTAAAATGATCAAA
1 ATACCCCCGAAGGGTAAAATGATCGAA
* *
21839711 ATACCCCCGAAGGGTAACATGA-CTAAA
1 ATACCCCCGAAGGGTAAAATGATC-GAA
* * * *
21839738 ATAACCTCGAAGGGTAAAATAACCGAA
1 ATACCCCCGAAGGGTAAAATGATCGAA
* *
21839765 ATACCCCCGAAGGTTAAAATGATTGAA
1 ATACCCCCGAAGGGTAAAATGATCGAA
* * * *
21839792 ATACCCCCAAAAGGTAAAAT-AACTAAA
1 ATACCCCCGAAGGGTAAAATGATC-GAA
* * *
21839819 ATACCCTCAAAGGGTAAAATGA-CCAA
1 ATACCCCCGAAGGGTAAAATGATCGAA
* *
21839845 ACTACTCCCGAATGGTAAAATGA-CTGAA
1 A-TACCCCCGAAGGGTAAAATGATC-GAA
*
21839873 ATACCCCCGAAAGGTAAAATGATCGAA
1 ATACCCCCGAAGGGTAAAATGATCGAA
** * *
21839900 ATACCTTCTAAGGGTAAAATGACCGAA
1 ATACCCCCGAAGGGTAAAATGATCGAA
** * *
21839927 ATACCCTTGAAGGGTAAAATGACCAAA
1 ATACCCCCGAAGGGTAAAATGATCGAA
21839954 ATACCCCCGAAGGGTAAAATGATCGAA
1 ATACCCCCGAAGGGTAAAATGATCGAA
* * *
21839981 ATACCCCCGAAAGGTAAAATAATTGAA
1 ATACCCCCGAAGGGTAAAATGATCGAA
* * *
21840008 ATACCCTCGAAAGATAAAATGATCGAA
1 ATACCCCCGAAGGGTAAAATGATCGAA
*
21840035 ATACCCCCAAAGGGTAAAATGATCGAA
1 ATACCCCCGAAGGGTAAAATGATCGAA
* *
21840062 ATACCCCCAAAGGTTAAAATGA-CTGAA
1 ATACCCCCGAAGGGTAAAATGATC-GAA
* *
21840089 ATACCCCCAAAGGGTAAAATGACCGAA
1 ATACCCCCGAAGGGTAAAATGATCGAA
* * *
21840116 ATACCCCTGAAAGGTAAAATGACCGAA
1 ATACCCCCGAAGGGTAAAATGATCGAA
21840143 ATACCCCC-ATAGGGTAAAATGA
1 ATACCCCCGA-AGGGTAAAATGA
21840165 CTGTTATACC
Statistics
Matches: 385, Mismatches: 59, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
26 7 0.02
27 371 0.96
28 7 0.02
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.17
Consensus pattern (27 bp):
ATACCCCCGAAGGGTAAAATGATCGAA
Found at i:21840382 original size:26 final size:26
Alignment explanation
Indices: 21840353--21840407 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
21840343 TTTGCCACAT
*
21840353 ATACTTTTACTGGCAGCTTCGTTGCG
1 ATACTTTTACTGGCAGCTTCGCTGCG
*
21840379 ATACTTTTACTGGCAGCTTTGCTGCG
1 ATACTTTTACTGGCAGCTTCGCTGCG
21840405 ATA
1 ATA
21840408 TTGGTGTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (26 bp):
ATACTTTTACTGGCAGCTTCGCTGCG
Found at i:21840538 original size:28 final size:28
Alignment explanation
Indices: 21840507--21840574 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
21840497 GTAATATTAT
* ** *
21840507 CACACTGTTATTGTATTGGGCTAAGGAC
1 CACACTGTTACTGTATCAGGCTAACGAC
*
21840535 CACACTGTTACTGTATCAGGCTAACGCC
1 CACACTGTTACTGTATCAGGCTAACGAC
21840563 CACACTG-TACTG
1 CACACTGTTACTG
21840575 ATACTAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 5 0.14
28 30 0.86
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (28 bp):
CACACTGTTACTGTATCAGGCTAACGAC
Found at i:21843301 original size:52 final size:52
Alignment explanation
Indices: 21843223--21843325 Score: 206
Period size: 52 Copynumber: 2.0 Consensus size: 52
21843213 CGTTGAGCTA
21843223 CATTGGAATAATAAGGATACTCGGGTCTCTTCTGATAATAACATGCCAAAGT
1 CATTGGAATAATAAGGATACTCGGGTCTCTTCTGATAATAACATGCCAAAGT
21843275 CATTGGAATAATAAGGATACTCGGGTCTCTTCTGATAATAACATGCCAAAG
1 CATTGGAATAATAAGGATACTCGGGTCTCTTCTGATAATAACATGCCAAAG
21843326 CCATGTCCCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (52 bp):
CATTGGAATAATAAGGATACTCGGGTCTCTTCTGATAATAACATGCCAAAGT
Found at i:21843511 original size:50 final size:50
Alignment explanation
Indices: 21843318--21843510 Score: 323
Period size: 50 Copynumber: 3.8 Consensus size: 50
21843308 GATAATAACA
* ** *
21843318 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
*
21843369 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
21843419 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
21843469 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
21843511 TTACCCAAAT
Statistics
Matches: 136, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
50 100 0.74
51 36 0.26
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:21843626 original size:13 final size:13
Alignment explanation
Indices: 21843605--21843635 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
21843595 GCTTAGATCA
*
21843605 TCATCAAATAAAT
1 TCATAAAATAAAT
21843618 TCATAAAATAAAT
1 TCATAAAATAAAT
21843631 TCATA
1 TCATA
21843636 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:21847091 original size:50 final size:50
Alignment explanation
Indices: 21847016--21847136 Score: 143
Period size: 50 Copynumber: 2.4 Consensus size: 50
21847006 TCATATATTA
* ** * * *
21847016 TCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATAG
1 TCTTACAGGGGACCTCTCATATCGGTGCCAACGCCACGTCCCAGACATAG
* * * *
21847066 TCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCACGTCCTAGACATGG
1 TCTTACAGGGGACCTCTCATATCGGTGCCAACGCCACGTCCCAGACATAG
*
21847116 TCTTACATGGGACCTCTCATA
1 TCTTACAGGGGACCTCTCATA
21847137 ACCTCAATGA
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 58 1.00
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TCTTACAGGGGACCTCTCATATCGGTGCCAACGCCACGTCCCAGACATAG
Found at i:21847560 original size:30 final size:30
Alignment explanation
Indices: 21847526--21847583 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
21847516 CCTCGACTCT
*
21847526 AACTTAGGCAAAATTATGATTTTGCCCCTA
1 AACTTAGACAAAATTATGATTTTGCCCCTA
** * *
21847556 AACTTTTACATAATTATGCTTTTGCCCC
1 AACTTAGACAAAATTATGATTTTGCCCC
21847584 AAAGCTCGGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38
Consensus pattern (30 bp):
AACTTAGACAAAATTATGATTTTGCCCCTA
Found at i:21850147 original size:26 final size:26
Alignment explanation
Indices: 21850113--21850174 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
21850103 CCTGTAAGTG
*
21850113 TTCTAAAACTGATACATGCTATGATA
1 TTCTGAAACTGATACATGCTATGATA
* *
21850139 TTCTGAAACTGATATATGTTATGATA
1 TTCTGAAACTGATACATGCTATGATA
21850165 TTCTGAAACT
1 TTCTGAAACT
21850175 ACTGTAGGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (26 bp):
TTCTGAAACTGATACATGCTATGATA
Found at i:21859161 original size:189 final size:188
Alignment explanation
Indices: 21858818--21859194 Score: 646
Period size: 189 Copynumber: 2.0 Consensus size: 188
21858808 ACCCGAAATG
*
21858818 CAAAAAATGGGATCGACGAAAAACCAAAATTGCTTGCTATCGAACAATAAGAGAAATAAGAGAAA
1 CAAAAAATGGGATCGACGAAAAACCAAAATTGCTTGCTATCGAAAAATAAGAGAAATAAGAGAAA
*
21858883 ATGATGCAAAAAATTGTAGAGAAAAGAAATAAGGGTGTTATAATCTTGGAAATCAACAATCTGCA
66 ATGATGCAAAAAATTGTAGAGAAAAGAAATAAGGGTGTTATAATCTTGGAAATCAACAATCTACA
* * *
21858948 CTAAAATAGTTTTGGACAGCAGCAGTAGCCTAACTTTGAAAAATCATCTAAAATAGTA
131 CTAAAATAGTTTTAGACAGCAGCAGTAGCCTAAATTTAAAAAATCATCTAAAATAGTA
* * * *
21859006 CAAAAAATGGGATTCGGCGAAAAGCCAAAATTTCTTGCTGTCGAAAAATAAGAGAAATAAGAGAA
1 CAAAAAATGGGA-TCGACGAAAAACCAAAATTGCTTGCTATCGAAAAATAAGAGAAATAAGAGAA
*
21859071 AATGATGCAAAAAATTGTAGAGAAAGGAAATAAGGGTGTTATAATCTTGGAAATCAACAATCTAC
65 AATGATGCAAAAAATTGTAGAGAAAAGAAATAAGGGTGTTATAATCTTGGAAATCAACAATCTAC
*
21859136 ACTAAAATAGTTTTAGACAGCAGCAGTAGTCTAAATTTAAAAAATCATCTAAAATAGTA
130 ACTAAAATAGTTTTAGACAGCAGCAGTAGCCTAAATTTAAAAAATCATCTAAAATAGTA
21859195 GAAATTGAGT
Statistics
Matches: 177, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
188 12 0.07
189 165 0.93
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (188 bp):
CAAAAAATGGGATCGACGAAAAACCAAAATTGCTTGCTATCGAAAAATAAGAGAAATAAGAGAAA
ATGATGCAAAAAATTGTAGAGAAAAGAAATAAGGGTGTTATAATCTTGGAAATCAACAATCTACA
CTAAAATAGTTTTAGACAGCAGCAGTAGCCTAAATTTAAAAAATCATCTAAAATAGTA
Found at i:21860340 original size:34 final size:34
Alignment explanation
Indices: 21860288--21860355 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
21860278 GCATTTTTGA
* *
21860288 CACTATACTGAGATGGGCTAAGGCCCAA-ACTGT
1 CACTATACTGAAAAGGGCTAAGGCCCAAGACTGT
* *
21860321 CACTGATACTGAAAAGGGCTTAGGTCCAAGACTGT
1 CACT-ATACTGAAAAGGGCTAAGGCCCAAGACTGT
21860356 TCAACTATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 4 0.14
34 20 0.69
35 5 0.17
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (34 bp):
CACTATACTGAAAAGGGCTAAGGCCCAAGACTGT
Found at i:21861334 original size:178 final size:178
Alignment explanation
Indices: 21861035--21861393 Score: 691
Period size: 178 Copynumber: 2.0 Consensus size: 178
21861025 AAGTCTTCCT
21861035 CTTTGACTTTTGTTTCAATTTAACCCATTTTTGTAAAAGTTTGAATTCAGCACACCAACTTCATT
1 CTTTGACTTTTGTTTCAATTTAACCCATTTTTGTAAAAGTTTGAATTCAGCACACCAACTTCATT
*
21861100 CCTAATAAGAAAAATCCAAATTTAATAGCATTTTATCCGATAATTAGCCAAAAATAAATACATTA
66 CCTAATAAGAAAAATCCAAATTAAATAGCATTTTATCCGATAATTAGCCAAAAATAAATACATTA
21861165 AAATACAAATTTATCTTGCTATCAGGGGTTGTTACACCTTAAGTCACC
131 AAATACAAATTTATCTTGCTATCAGGGGTTGTTACACCTTAAGTCACC
*
21861213 CTTTGACTTTTGTTTCAATTTAACCCCTTTTTGTAAAAGTTTGAATTCAGCACACCAACTTCATT
1 CTTTGACTTTTGTTTCAATTTAACCCATTTTTGTAAAAGTTTGAATTCAGCACACCAACTTCATT
21861278 CCTAATAAGAAAAATCCAAATTAAATAGCATTTTATCCGATAATTAGCCAAAAATAAATACATTA
66 CCTAATAAGAAAAATCCAAATTAAATAGCATTTTATCCGATAATTAGCCAAAAATAAATACATTA
*
21861343 AAATACAAATTTATCTTGCTATCAGGGGTTGTTACACCTTAAGTCATC
131 AAATACAAATTTATCTTGCTATCAGGGGTTGTTACACCTTAAGTCACC
21861391 CTT
1 CTT
21861394 GTTAGGGAGT
Statistics
Matches: 178, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
178 178 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (178 bp):
CTTTGACTTTTGTTTCAATTTAACCCATTTTTGTAAAAGTTTGAATTCAGCACACCAACTTCATT
CCTAATAAGAAAAATCCAAATTAAATAGCATTTTATCCGATAATTAGCCAAAAATAAATACATTA
AAATACAAATTTATCTTGCTATCAGGGGTTGTTACACCTTAAGTCACC
Found at i:21864397 original size:2 final size:2
Alignment explanation
Indices: 21864385--21864415 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
21864375 AAGAACATAG
21864385 AT AT CAT 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
21864416 GTATTATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21875486 original size:25 final size:25
Alignment explanation
Indices: 21875469--21875528 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
21875459 CAGCTCGAGA
* *
21875469 GAGCTTACTGATATTCAGTTTGCAT
1 GAGCTTACTGATATTCAGCTCGCAT
*
21875494 GAGCTTA-TCGATATTCAGCTCGTAT
1 GAGCTTACT-GATATTCAGCTCGCAT
21875519 GAGCTTACTG
1 GAGCTTACTG
21875529 TTTACAGCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 1 0.03
25 28 0.93
26 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (25 bp):
GAGCTTACTGATATTCAGCTCGCAT
Found at i:21878721 original size:43 final size:43
Alignment explanation
Indices: 21878673--21878819 Score: 185
Period size: 43 Copynumber: 3.4 Consensus size: 43
21878663 TGTGATTTCG
21878673 TGTAAGACCATGTCTAGGACATTGGCATCGATATGAGATTACA
1 TGTAAGACCATGTCTAGGACATTGGCATCGATATGAGATTACA
*
21878716 TGTAAGACCATGTCTAGGACATTGGCATCG-TAT-ATGATTTCA
1 TGTAAGACCATGTCTAGGACATTGGCATCGATATGA-GATTACA
* * * *
21878758 TATAAGA-CACTGTCT-GAGACAGTGGCATCGATATGTGATAACA
1 TGTAAGACCA-TGTCTAG-GACATTGGCATCGATATGAGATTACA
*
21878801 TGTAAGACCATATCTAGGA
1 TGTAAGACCATGTCTAGGA
21878820 TATGGATTTG
Statistics
Matches: 89, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
41 4 0.04
42 32 0.36
43 50 0.56
44 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACATTGGCATCGATATGAGATTACA
Found at i:21886300 original size:43 final size:43
Alignment explanation
Indices: 21886252--21886395 Score: 186
Period size: 43 Copynumber: 3.4 Consensus size: 43
21886242 GATTTCGTAG
21886252 AAGACCATGTCTAGGACATTGGCATCGATATGAGATTACATGT
1 AAGACCATGTCTAGGACATTGGCATCGATATGAGATTACATGT
* *
21886295 AAGACCATGTCTAGGACATTGGCATCG-TAT-ATGATTTCATAT
1 AAGACCATGTCTAGGACATTGGCATCGATATGA-GATTACATGT
* * * *
21886337 AAGA-CACTGTCTGGGACAATGGCATCGATATGTGATAACATGT
1 AAGACCA-TGTCTAGGACATTGGCATCGATATGAGATTACATGT
*
21886380 AAGACCATATCTAGGA
1 AAGACCATGTCTAGGA
21886396 TATGGCTTTG
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
41 3 0.03
42 33 0.38
43 48 0.56
44 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (43 bp):
AAGACCATGTCTAGGACATTGGCATCGATATGAGATTACATGT
Found at i:21886401 original size:42 final size:42
Alignment explanation
Indices: 21886252--21886414 Score: 177
Period size: 43 Copynumber: 3.9 Consensus size: 42
21886242 GATTTCGTAG
* *
21886252 AAGACCATGTCTAGGACATTGGCATCGATATGAGATTACATGT
1 AAGACCATGTCTAGGACATTGGCATCG-TATGTGATAACATGT
* ** *
21886295 AAGACCATGTCTAGGACATTGGCATCGTATATGATTTCATAT
1 AAGACCATGTCTAGGACATTGGCATCGTATGTGATAACATGT
* *
21886337 AAGA-CACTGTCTGGGACAATGGCATCGATATGTGATAACATGT
1 AAGACCA-TGTCTAGGACATTGGCATCG-TATGTGATAACATGT
* * * *
21886380 AAGACCATATCTAGGATA-TGGCTTTGTATGTGATA
1 AAGACCATGTCTAGGACATTGGCATCGTATGTGATA
21886415 TATGTGTTTC
Statistics
Matches: 102, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
41 11 0.11
42 39 0.38
43 50 0.49
44 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (42 bp):
AAGACCATGTCTAGGACATTGGCATCGTATGTGATAACATGT
Found at i:21891594 original size:16 final size:16
Alignment explanation
Indices: 21891573--21891629 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
21891563 ATTTACTTCG
21891573 TTTTTATTTAGTTTTA
1 TTTTTATTTAGTTTTA
* ** **
21891589 TTTTTATATTCGCGCTCG
1 TTTTTAT-TTAG-TTTTA
21891607 TTTTTATTTAGTTTTA
1 TTTTTATTTAGTTTTA
21891623 TTTTTAT
1 TTTTTAT
21891630 ATTCGCGTAT
Statistics
Matches: 29, Mismatches: 10, Indels: 4
0.67 0.23 0.09
Matches are distributed among these distances:
16 15 0.52
17 6 0.21
18 8 0.28
ACGTcount: A:0.16, C:0.07, G:0.09, T:0.68
Consensus pattern (16 bp):
TTTTTATTTAGTTTTA
Found at i:21891609 original size:34 final size:34
Alignment explanation
Indices: 21891570--21891636 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
21891560 TTTATTTACT
21891570 TCGTTTTTATTTAGTTTTATTTTTATATTCGCGC
1 TCGTTTTTATTTAGTTTTATTTTTATATTCGCGC
21891604 TCGTTTTTATTTAGTTTTATTTTTATATTCGCG
1 TCGTTTTTATTTAGTTTTATTTTTATATTCGCG
21891637 TATTTGAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.15, C:0.10, G:0.12, T:0.63
Consensus pattern (34 bp):
TCGTTTTTATTTAGTTTTATTTTTATATTCGCGC
Found at i:21892242 original size:29 final size:28
Alignment explanation
Indices: 21892194--21892260 Score: 98
Period size: 29 Copynumber: 2.4 Consensus size: 28
21892184 AAGAATAAGA
* *
21892194 AATTTCATTAGGTTACTTTAGGTTAATT
1 AATTTCATTAGATTAATTTAGGTTAATT
21892222 AATTTCCATTAGATTAATTTAGGTTAATT
1 AATTT-CATTAGATTAATTTAGGTTAATT
*
21892251 AATTTAATTA
1 AATTTCATTA
21892261 CGTTGTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 9 0.26
29 26 0.74
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.49
Consensus pattern (28 bp):
AATTTCATTAGATTAATTTAGGTTAATT
Found at i:21892253 original size:14 final size:14
Alignment explanation
Indices: 21892210--21892256 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
21892200 ATTAGGTTAC
21892210 TTTAGGTTAATTAA
1 TTTAGGTTAATTAA
***
21892224 TTTCCATTAGATTAA
1 TTTAGGTTA-ATTAA
21892239 TTTAGGTTAATTAA
1 TTTAGGTTAATTAA
21892253 TTTA
1 TTTA
21892257 ATTACGTTGT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (14 bp):
TTTAGGTTAATTAA
Found at i:21892982 original size:16 final size:17
Alignment explanation
Indices: 21892955--21893003 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
21892945 CAGAATTGAT
*
21892955 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
21892972 TTGAG-AAATTAATTAA
1 TTGAGAAAATTAATTAA
* *
21892988 TTAATTAAAATTAATT
1 TTGA-GAAAATTAATT
21893004 TATAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 13 0.48
17 5 0.19
18 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:21894220 original size:53 final size:53
Alignment explanation
Indices: 21894110--21894222 Score: 120
Period size: 53 Copynumber: 2.1 Consensus size: 53
21894100 GTAGACTGAC
* * * * * ** *
21894110 GGTGGTCTGACGATGATGAACGATGGCAAGGGTTGGTAGTGGAGGTTGATGAT
1 GGTGGTCTAACGATGATGAACGATGGCAAAGGTCGGTAGTAGAGGCTGACAAA
* *
21894163 GGTGGTCTAAC-AGTGATGAATGATGGTAAAGGTCGGTAGTAGAGGCTGACAAA
1 GGTGGTCTAACGA-TGATGAACGATGGCAAAGGTCGGTAGTAGAGGCTGACAAA
21894216 GGTGGTC
1 GGTGGTC
21894223 GGTAAGGTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
52 1 0.02
53 48 0.98
ACGTcount: A:0.26, C:0.09, G:0.41, T:0.25
Consensus pattern (53 bp):
GGTGGTCTAACGATGATGAACGATGGCAAAGGTCGGTAGTAGAGGCTGACAAA
Found at i:21917823 original size:30 final size:31
Alignment explanation
Indices: 21917787--21917848 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
21917777 TATTAGTATA
*
21917787 GTGTGGGCCTTAGCCCATTACAGTAA-CAGT
1 GTGTGGGCCTTAGCCCAATACAGTAATCAGT
21917817 GTGTGGGCCTTAGCCCAATACAGTAATCAGT
1 GTGTGGGCCTTAGCCCAATACAGTAATCAGT
21917848 G
1 G
21917849 CAATGTAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (31 bp):
GTGTGGGCCTTAGCCCAATACAGTAATCAGT
Found at i:21918194 original size:27 final size:26
Alignment explanation
Indices: 21918164--21918225 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 26
21918154 TTTCAACTCC
21918164 TAGGGGTATAACAGTCATTTTACCCT
1 TAGGGGTATAACAGTCATTTTACCCT
**
21918190 ATAGGGGTATTTCAGTCATTTTACCCT
1 -TAGGGGTATAACAGTCATTTTACCCT
21918217 TAGGGGTAT
1 TAGGGGTAT
21918226 TTCGCTCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
26 9 0.27
27 24 0.73
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (26 bp):
TAGGGGTATAACAGTCATTTTACCCT
Found at i:21918261 original size:27 final size:27
Alignment explanation
Indices: 21918177--21918372 Score: 270
Period size: 27 Copynumber: 7.3 Consensus size: 27
21918167 GGGTATAACA
* *
21918177 GTCATTTTACCCTAT-AGGGGTATTTCA
1 GTCATTTTACCCT-TCAAGGGTATTTCG
*
21918204 GTCATTTTACCCTT-AGGGGTATTTCG
1 GTCATTTTACCCTTCAAGGGTATTTCG
* * *
21918230 CTCATTTTACCTTTCAAGGGTATTTTG
1 GTCATTTTACCCTTCAAGGGTATTTCG
*
21918257 GTCATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTCAAGGGTATTTCG
*
21918284 ATCATTTTACCCTTCAAGGGTATTTCG
1 GTCATTTTACCCTTCAAGGGTATTTCG
* * *
21918311 ATCATTTTACCCTTCAAAGGTATTTTG
1 GTCATTTTACCCTTCAAGGGTATTTCG
21918338 GTCATTTTACCCTTCAAGGGTATTTCG
1 GTCATTTTACCCTTCAAGGGTATTTCG
21918365 GTCATTTT
1 GTCATTTT
21918373 CCCATGAATC
Statistics
Matches: 152, Mismatches: 16, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
26 24 0.16
27 128 0.84
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTTCAAGGGTATTTCG
Found at i:21927338 original size:20 final size:21
Alignment explanation
Indices: 21927300--21927339 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21927290 TAACCTTCAA
21927300 AAAAATTCAAGATAGTTTTCC
1 AAAAATTCAAGATAGTTTTCC
*
21927321 AAAAATTCCAGATA-TTTTC
1 AAAAATTCAAGATAGTTTTC
21927340 AAACCCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (21 bp):
AAAAATTCAAGATAGTTTTCC
Found at i:21928474 original size:15 final size:15
Alignment explanation
Indices: 21928436--21928475 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
21928426 AGAGATGAGT
21928436 AAAGAAGAGA-AAAG
1 AAAGAAGAGAGAAAG
*
21928450 AAAAAAGAGAGAAAG
1 AAAGAAGAGAGAAAG
*
21928465 AAAGATGAGAG
1 AAAGAAGAGAG
21928476 GATTCAACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (15 bp):
AAAGAAGAGAGAAAG
Found at i:21935673 original size:137 final size:138
Alignment explanation
Indices: 21935435--21935700 Score: 360
Period size: 137 Copynumber: 1.9 Consensus size: 138
21935425 ATGGGTTTGC
* ** *
21935435 TCACACAAGTTGTCAGTCGAAATGTAAGCTACACAATACTACTCACACAAGATGTCGAGTATCTG
1 TCACACAAGCTGTCAGTCGAAACATAAGCTACACAATACTACTCACACAAGATGTCAAGTATCTG
* *
21935500 CAACTAATATCGAACCTCAGCCATCGGTAGGACATTCAAGACCAACAATTGAAACATGGTAACCT
66 CAACTAATACCGAACCTCAGCCATCGGTAGGACATTCAAGACCAACAATCGAAACATGGTAACCT
21935565 GGGTCTAA
131 GGGTCTAA
* ** * *
21935573 TCACACAAGCTGTCAGTCGGAACAT-AGCTACACGGTGCTACTCACACAAGCTGTCAAGTATCTG
1 TCACACAAGCTGTCAGTCGAAACATAAGCTACACAATACTACTCACACAAGATGTCAAGTATCTG
* *
21935637 CAACTAATGCCGGAA-CTCTA-CCAAT-GGTAGGACATTCAAGACCAACACTCGAAACATGGTAA
66 CAACTAATACC-GAACCTC-AGCC-ATCGGTAGGACATTCAAGACCAACAATCGAAACATGGTAA
21935699 CC
128 CC
21935701 CTAATGACAA
Statistics
Matches: 112, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
137 85 0.76
138 27 0.24
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (138 bp):
TCACACAAGCTGTCAGTCGAAACATAAGCTACACAATACTACTCACACAAGATGTCAAGTATCTG
CAACTAATACCGAACCTCAGCCATCGGTAGGACATTCAAGACCAACAATCGAAACATGGTAACCT
GGGTCTAA
Found at i:21939807 original size:13 final size:12
Alignment explanation
Indices: 21939790--21939819 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
21939780 TAATAATAGT
21939790 AAAAGAAAAGAA
1 AAAAGAAAAGAA
21939802 AGAAAGAAAAGAA
1 A-AAAGAAAAGAA
21939815 AAAAG
1 AAAAG
21939820 GAGAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:21945658 original size:19 final size:22
Alignment explanation
Indices: 21945620--21945661 Score: 63
Period size: 19 Copynumber: 2.0 Consensus size: 22
21945610 GTTAGTGTAA
21945620 TTAAATTGTACATATATATGTT
1 TTAAATTGTACATATATATGTT
21945642 TTAAATTG-A-AT-TATATGTT
1 TTAAATTGTACATATATATGTT
21945661 T
1 T
21945662 CTGAAGTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 1 0.05
22 8 0.40
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (22 bp):
TTAAATTGTACATATATATGTT
Found at i:21953968 original size:26 final size:26
Alignment explanation
Indices: 21953939--21953991 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
21953929 TTTCGACAAA
21953939 TTGAGTTTGGATATGCTTTGTGTGCT
1 TTGAGTTTGGATATGCTTTGTGTGCT
21953965 TTGAGTTTGGATATGCTTTGTGTGCT
1 TTGAGTTTGGATATGCTTTGTGTGCT
21953991 T
1 T
21953992 ACCTTAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.11, C:0.08, G:0.30, T:0.51
Consensus pattern (26 bp):
TTGAGTTTGGATATGCTTTGTGTGCT
Found at i:21957819 original size:7 final size:7
Alignment explanation
Indices: 21957807--21957839 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
21957797 TAAAAACATA
21957807 AATTTGG
1 AATTTGG
21957814 AATTTGG
1 AATTTGG
21957821 AATTTGG
1 AATTTGG
21957828 AATTTGG
1 AATTTGG
21957835 AATTT
1 AATTT
21957840 TGGGTATTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (7 bp):
AATTTGG
Found at i:21966483 original size:41 final size:41
Alignment explanation
Indices: 21966449--21966568 Score: 127
Period size: 41 Copynumber: 2.9 Consensus size: 41
21966439 GGGGCATGTG
*
21966449 TATGCAATTCAAGGGTATC-ATAGTACAAATAGGGGCACATA
1 TATGCAATTCAAGGGTACCGA-AGTACAAATAGGGGCACATA
* * * *
21966490 TGTGCAATTTAGGGGTACCGAAGTACAAATAGGGGCACTTA
1 TATGCAATTCAAGGGTACCGAAGTACAAATAGGGGCACATA
* * * *
21966531 TGTACAATT-TAGGGATACCGAAGTACAAACAGGGGCAC
1 TATGCAATTCAAGGG-TACCGAAGTACAAATAGGGGCAC
21966569 GAATGTGTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 3 0.04
41 64 0.94
42 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.23
Consensus pattern (41 bp):
TATGCAATTCAAGGGTACCGAAGTACAAATAGGGGCACATA
Found at i:21966502 original size:21 final size:21
Alignment explanation
Indices: 21966478--21966544 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
21966468 ATAGTACAAA
*
21966478 TAGGGGCACATATGTGCAATT
1 TAGGGGCACATATGTACAATT
* ** * *
21966499 TAGGGGTACCGAAGTACAA-A
1 TAGGGGCACATATGTACAATT
*
21966519 TAGGGGCACTTATGTACAATT
1 TAGGGGCACATATGTACAATT
21966540 TAGGG
1 TAGGG
21966545 ATACCGAAGT
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.25
Consensus pattern (21 bp):
TAGGGGCACATATGTACAATT
Found at i:21966524 original size:20 final size:20
Alignment explanation
Indices: 21966499--21966565 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
21966489 ATGTGCAATT
21966499 TAGGGGTACCGAAGTACAAA
1 TAGGGGTACCGAAGTACAAA
* ** * *
21966519 TAGGGGCACTTATGTACAATT
1 TAGGGGTACCGAAGTACAA-A
*
21966540 TAGGGATACCGAAGTACAAA
1 TAGGGGTACCGAAGTACAAA
*
21966560 CAGGGG
1 TAGGGG
21966566 CACGAATGTG
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.19
Consensus pattern (20 bp):
TAGGGGTACCGAAGTACAAA
Done.