Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008124.1 Hibiscus syriacus cultivar Beakdansim tig00110678_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: 3296903
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 19
Found at i:2619309 original size:26 final size:26
Alignment explanation
Indices: 2619266--2619345 Score: 115
Period size: 26 Copynumber: 3.0 Consensus size: 26
2619256 TTGTAATACA
2619266 ATGGATATGTGAAATGACCAAAATATCC
1 ATGG-TATG-GAAATGACCAAAATATCC
*
2619294 ATGGTATGGAAATGACCAAAATACCC
1 ATGGTATGGAAATGACCAAAATATCC
*
2619320 CTGGTATGGAAATGACCAAGAATATC
1 ATGGTATGGAAATGACCAA-AATATC
2619346 ACCAAACTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
26 35 0.73
27 9 0.19
28 4 0.08
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (26 bp):
ATGGTATGGAAATGACCAAAATATCC
Found at i:2620354 original size:26 final size:26
Alignment explanation
Indices: 2620325--2620379 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2620315 TTTTATATGG
*
2620325 TTTTCGATTTGAAATATGTTCTGATT
1 TTTTCGATTCGAAATATGTTCTGATT
** * *
2620351 TTTTTTATTCGAATTCTGTTCTGATT
1 TTTTCGATTCGAAATATGTTCTGATT
2620377 TTT
1 TTT
2620380 GATATGGATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.09, G:0.13, T:0.60
Consensus pattern (26 bp):
TTTTCGATTCGAAATATGTTCTGATT
Found at i:2620784 original size:12 final size:13
Alignment explanation
Indices: 2620767--2620795 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2620757 TGATTTCTGA
2620767 ATGTTT-AAAAAT
1 ATGTTTAAAAAAT
2620779 ATGTTTAAAAAAT
1 ATGTTTAAAAAAT
2620792 ATGT
1 ATGT
2620796 ATCTTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (13 bp):
ATGTTTAAAAAAT
Found at i:2624014 original size:30 final size:30
Alignment explanation
Indices: 2623975--2624041 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
2623965 TCGGGACATA
*
2623975 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
2624005 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
2624035 TGGATAG
1 TGGATAG
2624042 GTCATTCGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:2627688 original size:21 final size:21
Alignment explanation
Indices: 2627627--2627681 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
2627617 TCTGGGTTGC
2627627 GTGCATCGATGCATCTTCAAT
1 GTGCATCGATGCATCTTCAAT
*
2627648 GTGCATCGATGTATCTTCAAT
1 GTGCATCGATGCATCTTCAAT
*
2627669 GTGCATTGATGCA
1 GTGCATCGATGCA
2627682 CTCTCAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (21 bp):
GTGCATCGATGCATCTTCAAT
Found at i:2628071 original size:21 final size:21
Alignment explanation
Indices: 2628010--2628090 Score: 108
Period size: 21 Copynumber: 3.7 Consensus size: 21
2628000 TCAAATCAAA
2628010 GCAAACAAGCCTAAGGTGAGT
1 GCAAACAAGCCTAAGGTGAGT
* **
2628031 GCATAATATAAGTATAAGGTGAGT
1 GC--AA-ACAAGCCTAAGGTGAGT
2628055 GCAAACAAGCCTAAGGTGAGT
1 GCAAACAAGCCTAAGGTGAGT
2628076 GCAAACAAGCCTAAG
1 GCAAACAAGCCTAAG
2628091 TGTAAGTTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 31 0.61
22 2 0.04
23 2 0.04
24 16 0.31
ACGTcount: A:0.41, C:0.16, G:0.26, T:0.17
Consensus pattern (21 bp):
GCAAACAAGCCTAAGGTGAGT
Found at i:2629300 original size:105 final size:105
Alignment explanation
Indices: 2629093--2629315 Score: 286
Period size: 105 Copynumber: 2.1 Consensus size: 105
2629083 GATTATCCAT
* * * * *
2629093 AAGGACCACATA-TAAATTCCTTAAGAACCATATATATATACCAAGGATCAAGTAAGTGTCTCAA
1 AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAA
2629157 AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
66 AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
* * * *
2629197 AAGGACCACGTAGAAAATTCCTTAAGAATCATATACATATGCTAAGGACCAAATACGTGTCTCAA
1 AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAA
* * * * * * *
2629262 AGGACCTCATAGATGTTCCATAGGATACCTATATGTCCCG
66 AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
*
2629302 AAGGACCTCGTAGA
1 AAGGACCACGTAGA
2629316 CCCTCGACTC
Statistics
Matches: 101, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
104 11 0.11
105 90 0.89
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (105 bp):
AAGGACCACGTAGAAAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAA
AAGACCTCATACATGCTCCAAAGAATACATATACGTCCCG
Found at i:2629590 original size:106 final size:106
Alignment explanation
Indices: 2629456--2629666 Score: 343
Period size: 106 Copynumber: 2.0 Consensus size: 106
2629446 CACATACATG
* *
2629456 TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTTATATGA-TCACGTAATTCACTTA
1 TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATAT-ATTCACGTAATACACTTA
* *
2629520 CACATAGCACATTTTCATGTAATTCATAGATATCCCTTAGCT
65 CACATAGCACATTTTCAAGTAATTCACAGATATCCCTTAGCT
* *
2629562 TAATTACGTAGTTCATGTCAATTCTCATATGATTTCATATTCATATATTCACGTAATACACTTAC
1 TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATATTCACGTAATACACTTAC
*
2629627 ACATAGCACATTTTCAAGTAATTCACATATATCCCTTAGC
66 ACATAGCACATTTTCAAGTAATTCACAGATATCCCTTAGC
2629667 GTATATCTCT
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
105 1 0.01
106 96 0.99
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (106 bp):
TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATATTCACGTAATACACTTAC
ACATAGCACATTTTCAAGTAATTCACAGATATCCCTTAGCT
Found at i:2630915 original size:22 final size:22
Alignment explanation
Indices: 2630898--2630970 Score: 137
Period size: 22 Copynumber: 3.3 Consensus size: 22
2630888 GGGGGTATCG
*
2630898 ATTCCCCTTTGAATGGGTACCA
1 ATTCCCCCTTGAATGGGTACCA
2630920 ATTCCCCCTTGAATGGGTACCA
1 ATTCCCCCTTGAATGGGTACCA
2630942 ATTCCCCCTTGAATGGGTACCA
1 ATTCCCCCTTGAATGGGTACCA
2630964 ATTCCCC
1 ATTCCCC
2630971 TAGCCCAGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (22 bp):
ATTCCCCCTTGAATGGGTACCA
Found at i:2634771 original size:106 final size:106
Alignment explanation
Indices: 2634637--2634847 Score: 413
Period size: 106 Copynumber: 2.0 Consensus size: 106
2634627 CACATACATG
2634637 TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
1 TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
2634702 ACATAGCACATATTCATGTAATTCACAGATATCCCTTAGCT
66 ACATAGCACATATTCATGTAATTCACAGATATCCCTTAGCT
2634743 TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
1 TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
*
2634808 ACATAGCACATTTTCATGTAATTCACAGATATCCCTTAGC
66 ACATAGCACATATTCATGTAATTCACAGATATCCCTTAGC
2634848 GTATATCTTT
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.37
Consensus pattern (106 bp):
TAATCACGTAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
ACATAGCACATATTCATGTAATTCACAGATATCCCTTAGCT
Found at i:2636095 original size:22 final size:22
Alignment explanation
Indices: 2636078--2636129 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
2636068 GAGGGTATCG
2636078 ATTCCCCTTTGAATGGGTACCA
1 ATTCCCCTTTGAATGGGTACCA
*
2636100 ATTCCCCCTTGAATGGGTACCA
1 ATTCCCCTTTGAATGGGTACCA
2636122 ATTCCCCT
1 ATTCCCCT
2636130 AGCCCAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (22 bp):
ATTCCCCTTTGAATGGGTACCA
Found at i:2636882 original size:31 final size:31
Alignment explanation
Indices: 2636841--2636901 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
2636831 GGATGTTACA
* * *
2636841 ACCTATGTTCTACGGGACATATGGATAGTTT
1 ACCTAGGTTCTACGAGACATATGGACAGTTT
* *
2636872 ACCTAGGTTCTTCGAGACCTATGGACAGTT
1 ACCTAGGTTCTACGAGACATATGGACAGTT
2636902 ACCGAGGATC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (31 bp):
ACCTAGGTTCTACGAGACATATGGACAGTTT
Found at i:2636957 original size:30 final size:30
Alignment explanation
Indices: 2636887--2636959 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
2636877 GGTTCTTCGA
* *
2636887 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2636917 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
2636947 GACCTCTGGATAG
1 GACCTCTGGATAG
2636960 GTGCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:2637909 original size:17 final size:18
Alignment explanation
Indices: 2637876--2637911 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2637866 AGAAAACGAT
2637876 ACAACTCAAACAATAAAA
1 ACAACTCAAACAATAAAA
*
2637894 ACAACT-AAATAATAAAA
1 ACAACTCAAACAATAAAA
2637911 A
1 A
2637912 TAATTCTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.69, C:0.17, G:0.00, T:0.14
Consensus pattern (18 bp):
ACAACTCAAACAATAAAA
Found at i:2638666 original size:13 final size:13
Alignment explanation
Indices: 2638648--2638675 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2638638 ATACCTCCAC
2638648 CTCAGTATCGATA
1 CTCAGTATCGATA
2638661 CTCAGTATCGATA
1 CTCAGTATCGATA
2638674 CT
1 CT
2638676 TCTTCAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (13 bp):
CTCAGTATCGATA
Found at i:2639733 original size:18 final size:18
Alignment explanation
Indices: 2639712--2639776 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 18
2639702 TTGTCCCGAC
2639712 GGACCACTATGTCACGAA
1 GGACCACTATGTCACGAA
*
2639730 GGACCACTGATATGTCCCGAA
1 GGACCAC---TATGTCACGAA
*
2639751 GGACCACTATGTCTCGAA
1 GGACCACTATGTCACGAA
*
2639769 TGACCACT
1 GGACCACT
2639777 GATAATCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 24 0.59
21 17 0.41
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (18 bp):
GGACCACTATGTCACGAA
Found at i:2639745 original size:21 final size:21
Alignment explanation
Indices: 2639719--2639780 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
2639709 GACGGACCAC
2639719 TATGTCACGAAGGACCACTGA
1 TATGTCACGAAGGACCACTGA
*
2639740 TATGTCCCGAAGGACCAC---
1 TATGTCACGAAGGACCACTGA
* *
2639758 TATGTCTCGAATGACCACTGA
1 TATGTCACGAAGGACCACTGA
2639779 TA
1 TA
2639781 ATCCCTCGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 16 0.46
21 19 0.54
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (21 bp):
TATGTCACGAAGGACCACTGA
Found at i:2639755 original size:39 final size:39
Alignment explanation
Indices: 2639703--2639780 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
2639693 ACTGAATATT
*
2639703 TGTCCCGACGGACCACTATGTCACGAAGGACCACTGATA
1 TGTCCCGAAGGACCACTATGTCACGAAGGACCACTGATA
* *
2639742 TGTCCCGAAGGACCACTATGTCTCGAATGACCACTGATA
1 TGTCCCGAAGGACCACTATGTCACGAAGGACCACTGATA
2639781 ATCCCTCGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (39 bp):
TGTCCCGAAGGACCACTATGTCACGAAGGACCACTGATA
Found at i:2641230 original size:18 final size:17
Alignment explanation
Indices: 2641203--2641240 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
2641193 CAAACATGTT
2641203 CTTAATCCTTTCTAATA
1 CTTAATCCTTTCTAATA
2641220 CTTATATCCTTTCTAATA
1 CTTA-ATCCTTTCTAATA
2641238 CTT
1 CTT
2641241 CTAACTGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (17 bp):
CTTAATCCTTTCTAATA
Found at i:2644137 original size:12 final size:12
Alignment explanation
Indices: 2644122--2644164 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
2644112 CCGGTTTTTT
*
2644122 AACCGGATAAAA
1 AACCGGTTAAAA
2644134 AACCGGTTTGAAAAA
1 AACCGG-TT--AAAA
2644149 AACCGGTTAAAA
1 AACCGGTTAAAA
2644161 AACC
1 AACC
2644165 AGTTTTTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 14 0.52
13 1 0.04
14 2 0.07
15 10 0.37
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
AACCGGTTAAAA
Found at i:2645231 original size:229 final size:231
Alignment explanation
Indices: 2644829--2645288 Score: 906
Period size: 229 Copynumber: 2.0 Consensus size: 231
2644819 GTGGCGTACG
2644829 GCGAGGGAAAAAATGATTTTAGGATTCCAAGAACACCGTTATGGTGTGTCGCTTACATGTGACGT
1 GCGAGGGAAAAAATGATTTTAGGATTCCAAGAACACCGTTATGGTGTGTCGCTTACATGTGACGT
2644894 TTGGAGTTCCCCTCATAATACCGGAAATTCTTTTTAGCCGTTACGTCACATTGGTTAGATCAAGA
66 TTGGAGTTCCCCTCATAATACCGGAAATTCTTTTTAGCCGTTACGTCACATTGGTTAGATCAAGA
2644959 TAATTGGCAAATGATGAAAAGAACAATCGCGTTTGAATTATTCGGTGAGCCGCATACCGGTGCTA
131 TAATTGGCAAATGATGAAAAGAACAATCGCGTTTGAATTATTCGGTGAGCCGCATACCGGTGCTA
2645024 ATTTATTTACACTTTTAAAACGGGTAA-TTGTCTTT
196 ATTTATTTACACTTTTAAAACGGGTAATTTGTCTTT
2645059 GCGAGGGAAAAAATGATTTTAGGATTCCAAGAACACCGTTATGGTGTGTCGCTTACATGTGACGT
1 GCGAGGGAAAAAATGATTTTAGGATTCCAAGAACACCGTTATGGTGTGTCGCTTACATGTGACGT
2645124 TTGGAG-TCCCCTCATAATACCGGAAATTCTTTTTAGCCGTTACGTCACATTGGTTAGATCAAGA
66 TTGGAGTTCCCCTCATAATACCGGAAATTCTTTTTAGCCGTTACGTCACATTGGTTAGATCAAGA
2645188 TAATTGGCAAATGATGAAAAGAACAATCGCGTTTGAATTATTCGGTGAGCCGCATACCGGTGCTA
131 TAATTGGCAAATGATGAAAAGAACAATCGCGTTTGAATTATTCGGTGAGCCGCATACCGGTGCTA
2645253 ATTTATTTACACTTTTAAAACGGGTAATTTGTCTTT
196 ATTTATTTACACTTTTAAAACGGGTAATTTGTCTTT
2645289 ATAAATTAGA
Statistics
Matches: 229, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
229 150 0.66
230 79 0.34
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (231 bp):
GCGAGGGAAAAAATGATTTTAGGATTCCAAGAACACCGTTATGGTGTGTCGCTTACATGTGACGT
TTGGAGTTCCCCTCATAATACCGGAAATTCTTTTTAGCCGTTACGTCACATTGGTTAGATCAAGA
TAATTGGCAAATGATGAAAAGAACAATCGCGTTTGAATTATTCGGTGAGCCGCATACCGGTGCTA
ATTTATTTACACTTTTAAAACGGGTAATTTGTCTTT
Found at i:2646702 original size:21 final size:21
Alignment explanation
Indices: 2646678--2646717 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2646668 TTTATTTTAT
2646678 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
2646699 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
2646718 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:2646765 original size:33 final size:33
Alignment explanation
Indices: 2646712--2646810 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
2646702 TTTGTTTCAA
*
2646712 TTATCGAACTT-GAAGTTTTTAAATATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2646744 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
2646777 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2646810 T
1 T
2646811 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 11 0.18
33 51 0.82
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:2646839 original size:13 final size:13
Alignment explanation
Indices: 2646796--2646850 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2646786 TTGGAAGTAT
2646796 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
2646809 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
2646823 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
2646836 TTAAGTATTTGAA
1 TTAAGTATTTCAA
2646849 TT
1 TT
2646851 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:2647272 original size:15 final size:15
Alignment explanation
Indices: 2647247--2647302 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
2647237 ATCTGGAATA
*
2647247 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
2647262 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
2647277 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
2647294 TTAAAACCG
1 TTAAAACCG
2647303 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:2647311 original size:21 final size:18
Alignment explanation
Indices: 2647266--2647299 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2647256 GTTTTTTTAT
2647266 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
2647283 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
2647300 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:2651013 original size:14 final size:14
Alignment explanation
Indices: 2650994--2651021 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2650984 ATCTCTAACT
2650994 TAAACCTTAAATTA
1 TAAACCTTAAATTA
2651008 TAAACCTTAAATTA
1 TAAACCTTAAATTA
2651022 AGGTTTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAACCTTAAATTA
Found at i:2652442 original size:22 final size:22
Alignment explanation
Indices: 2652417--2652463 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2652407 TATATTATTT
2652417 AAATTATTTACGTTTATGTGTA
1 AAATTATTTACGTTTATGTGTA
2652439 AAATTATTTACGTTTATGTGTA
1 AAATTATTTACGTTTATGTGTA
2652461 AAA
1 AAA
2652464 ATGTTATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (22 bp):
AAATTATTTACGTTTATGTGTA
Found at i:2656657 original size:12 final size:12
Alignment explanation
Indices: 2656640--2656700 Score: 81
Period size: 12 Copynumber: 5.1 Consensus size: 12
2656630 AAAAAAATTA
2656640 ATTAAATAAAAT
1 ATTAAATAAAAT
2656652 ATTAAA-ATAAAT
1 ATTAAATA-AAAT
2656664 AATTAAATAAAAT
1 -ATTAAATAAAAT
*
2656677 ACT-AATAAAAT
1 ATTAAATAAAAT
2656688 ATTAAATAAAAT
1 ATTAAATAAAAT
2656700 A
1 A
2656701 AAATATACCT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
11 11 0.26
12 21 0.49
13 10 0.23
14 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:2656662 original size:17 final size:17
Alignment explanation
Indices: 2656642--2656706 Score: 64
Period size: 17 Copynumber: 3.7 Consensus size: 17
2656632 AAAAATTAAT
2656642 TAAATAAAATATTAAAA
1 TAAATAAAATATTAAAA
2656659 TAAATAATTAA-A-TAAAA
1 TAAATAA--AATATTAAAA
2656676 TACTAATAAAATATT-AAA
1 TA--AATAAAATATTAAAA
2656694 TAAAATAAAATAT
1 T-AAATAAAATAT
2656707 ACCTTAAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
17 26 0.63
18 6 0.15
19 9 0.22
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAATAAAATATTAAAA
Found at i:2656666 original size:25 final size:24
Alignment explanation
Indices: 2656630--2656700 Score: 99
Period size: 25 Copynumber: 2.9 Consensus size: 24
2656620 TATAACTGCA
*
2656630 AAAAAAATTAATTAAATAAAATATT
1 AAAAAAA-TAATTAAATAAAATACT
2656655 AAAATAAATAATTAAATAAAATACT
1 AAAA-AAATAATTAAATAAAATACT
*
2656680 AATAAAAT-ATTAAATAAAATA
1 AAAAAAATAATTAAATAAAATA
2656701 AAATATACCT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.30
24 4 0.09
25 23 0.53
26 3 0.07
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAAAAATAATTAAATAAAATACT
Found at i:2659883 original size:20 final size:21
Alignment explanation
Indices: 2659858--2659896 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2659848 TGGTCCCAAA
2659858 TCAT-CCAGTATCGATACTGT
1 TCATCCCAGTATCGATACTGT
2659878 TCATCCCAGTATCGATACT
1 TCATCCCAGTATCGATACT
2659897 CAAACCCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (21 bp):
TCATCCCAGTATCGATACTGT
Found at i:2660685 original size:18 final size:18
Alignment explanation
Indices: 2660662--2660704 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2660652 GACAACATAA
2660662 TATGTTATTCTATTTAAT
1 TATGTTATTCTATTTAAT
*
2660680 TATGTTGTTCTATTTAAT
1 TATGTTATTCTATTTAAT
2660698 TATGTTA
1 TATGTTA
2660705 AATTTGATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (18 bp):
TATGTTATTCTATTTAAT
Found at i:2662746 original size:65 final size:60
Alignment explanation
Indices: 2662625--2662747 Score: 149
Period size: 65 Copynumber: 2.0 Consensus size: 60
2662615 TAAATATAAT
* * *
2662625 TATATACTTTTGAATATTTCAAATTAAAATAATATATTTTGAGTTTGAATAGTAAAAGTG
1 TATATACTTTTAAATATTTCAAATTAAAATAATATATTTTAAATTTGAATAGTAAAAGTG
*
2662685 TATATA-TTTTAAATATTTCAAATTAAAATATATTAATATATGTTTAAATTTGAATATTAAAAG
1 TATATACTTTTAAATATTTCAAATT--AA-A-A-TAATATAT-TTTAAATTTGAATAGTAAAAG
2662748 ATATATGATT
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
59 17 0.32
60 6 0.11
61 2 0.04
62 1 0.02
63 1 0.02
64 8 0.15
65 18 0.34
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (60 bp):
TATATACTTTTAAATATTTCAAATTAAAATAATATATTTTAAATTTGAATAGTAAAAGTG
Found at i:2671395 original size:30 final size:31
Alignment explanation
Indices: 2671371--2671430 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2671361 GAAAATAATA
*
2671371 AAATATATTGATTTTCAAACGAAAATGACCT
1 AAATATATTGATTTTCAAACGAAAATGACAT
* * *
2671402 CAATGTATTGATTTTCACACGAAAATGAC
1 AAATATATTGATTTTCAAACGAAAATGAC
2671431 CTCTCAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.32
Consensus pattern (31 bp):
AAATATATTGATTTTCAAACGAAAATGACAT
Found at i:2672203 original size:31 final size:31
Alignment explanation
Indices: 2672168--2672243 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
2672158 ACATGTTATT
*
2672168 GTTTTGGTCACTTGCGTTATTGTTTTATTAA
1 GTTTTGGTCACTTGCGTTATCGTTTTATTAA
* **
2672199 GTTTTTGTCACTTATGTTATCGTTTTATTAA
1 GTTTTGGTCACTTGCGTTATCGTTTTATTAA
*
2672230 ATTTTGGTCACTTG
1 GTTTTGGTCACTTG
2672244 GACGTTGAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.55
Consensus pattern (31 bp):
GTTTTGGTCACTTGCGTTATCGTTTTATTAA
Found at i:2673586 original size:31 final size:31
Alignment explanation
Indices: 2673551--2673629 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 31
2673541 ATTTAATGTC
2673551 TAAGTGACCAAAACTTAATAAAACGA-TATA-G
1 TAAGTGACCAAAACTTAATAAAAC-ATTA-ACG
*
2673582 TAAGTGACCAAAACTTAATAAATCATTAACG
1 TAAGTGACCAAAACTTAATAAAACATTAACG
*
2673613 TAAGTGAACAAAACTTA
1 TAAGTGACCAAAACTTA
2673630 TGTTTTTCTG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 2 0.05
31 42 0.95
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24
Consensus pattern (31 bp):
TAAGTGACCAAAACTTAATAAAACATTAACG
Found at i:2673885 original size:59 final size:58
Alignment explanation
Indices: 2673789--2673930 Score: 205
Period size: 59 Copynumber: 2.4 Consensus size: 58
2673779 AAAACGAAAC
*
2673789 GAAAGTGACCAAATCTTATGTTTTTTGAATTCAATGAGAAAAAGTTTACAAAA-CTCAATT
1 GAAAGTGA-CAAATCTTATG-GTTTTGAATTCAATGAGAAAAAGTTTACAAAATC-CAATT
*
2673849 GAAAGTGATCAAATCTTATGGTTTTGAATTCGATGAGAAAAAGTTTACAAAATCCAATT
1 GAAAGTGA-CAAATCTTATGGTTTTGAATTCAATGAGAAAAAGTTTACAAAATCCAATT
* *
2673908 GAAAGTGACAATTTTTATGGTTT
1 GAAAGTGACAAATCTTATGGTTT
2673931 ACCCTTAATA
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
58 13 0.17
59 43 0.57
60 20 0.26
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (58 bp):
GAAAGTGACAAATCTTATGGTTTTGAATTCAATGAGAAAAAGTTTACAAAATCCAATT
Found at i:2673967 original size:17 final size:17
Alignment explanation
Indices: 2673938--2673976 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2673928 TTTACCCTTA
2673938 ATAT-TTTAATGAACAT
1 ATATATTTAATGAACAT
*
2673954 ATATATTTAGTGAACAT
1 ATATATTTAATGAACAT
*
2673971 GTATAT
1 ATATAT
2673977 CCATATGACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (17 bp):
ATATATTTAATGAACAT
Found at i:2676080 original size:24 final size:24
Alignment explanation
Indices: 2676048--2676120 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
2676038 TGCCACATAG
2676048 ATTTGTCCCGAATGACCGCGTAGA
1 ATTTGTCCCGAATGACCGCGTAGA
* * *
2676072 ATTTATCCCGAATGACCACGTAAA
1 ATTTGTCCCGAATGACCGCGTAGA
* * *
2676096 AATTGTCCCGAAGGACCGCATAGA
1 ATTTGTCCCGAATGACCGCGTAGA
2676120 A
1 A
2676121 CCTTCGACTC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.22
Consensus pattern (24 bp):
ATTTGTCCCGAATGACCGCGTAGA
Found at i:2676299 original size:15 final size:15
Alignment explanation
Indices: 2676278--2676332 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
2676268 TTCACTTGGC
2676278 ACATTTTCACATAAA
1 ACATTTTCACATAAA
* *
2676293 ACTTTTTCATATAAA
1 ACATTTTCACATAAA
* * *
2676308 ACATATTCGCATATA
1 ACATTTTCACATAAA
2676323 ACATTTTCAC
1 ACATTTTCAC
2676333 GTACCAATAA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:2676831 original size:20 final size:20
Alignment explanation
Indices: 2676808--2676877 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
2676798 CTTACTCCAG
2676808 GTATCGATACCTCCATATCA
1 GTATCGATACCTCCATATCA
2676828 GTATCGATACCTCCATATCA
1 GTATCGATACCTCCATATCA
*
2676848 GTATCGATACTACTTCA-ATCA
1 GTATCGATAC--CTCCATATCA
2676869 GTATCGATA
1 GTATCGATA
2676878 TTGTTAATCC
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
20 30 0.64
21 13 0.28
22 4 0.09
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.31
Consensus pattern (20 bp):
GTATCGATACCTCCATATCA
Found at i:2679328 original size:65 final size:65
Alignment explanation
Indices: 2679130--2679339 Score: 216
Period size: 65 Copynumber: 3.2 Consensus size: 65
2679120 TGCACTAAGA
* * * * *
2679130 GTGCATCGATGCATCAAGTGCATTTGATGTTTCAA-AATAGC-CAGAGTGCATCGATGCAT-GAC
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAAAATCTC--AGTGCATCGATGCATGGAT
2679192 TG
64 TG
* * *
2679194 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATAAAATCCTCAGTGCATCGGTGCATGG-TA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAAAAT-CTCAGTGCATCGATGCATGGATT
*
2679258 A
65 G
* **
2679259 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAAAATCTCA--GTGCATCGATGCATGGAT
2679322 TG
64 TG
*
2679324 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
2679340 CTTTGAAAAA
Statistics
Matches: 121, Mismatches: 18, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
62 3 0.02
64 55 0.45
65 60 0.50
66 2 0.02
67 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATAAAATCTCAGTGCATCGATGCATGGATTG
Found at i:2686636 original size:12 final size:12
Alignment explanation
Indices: 2686619--2686654 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2686609 TATCATGTTC
2686619 TCATATCACATG
1 TCATATCACATG
*
2686631 TCATATCACATA
1 TCATATCACATG
2686643 TCATATCACATG
1 TCATATCACATG
2686655 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:2687159 original size:64 final size:64
Alignment explanation
Indices: 2687025--2687178 Score: 179
Period size: 64 Copynumber: 2.4 Consensus size: 64
2687015 TTATTGCTGG
* * * *
2687025 GATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTAATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAAAGA
* *
2687089 GATGCATCGATGCACTACTAATGCATCGATGCA-CGAATTGCATTCGATGTCTTTA-TTTTAAA-
1 GATGCATCGATGCACTACTAATGCATCGATGCACCG-ATTGCATTCGATGT-TTCACTATTAAAG
2687151 A
64 A
* * *
2687152 GAGTGCATTGATGCATTACCAATGCAT
1 GA-TGCATCGATGCACTACTAATGCAT
2687179 TGGTGCACAT
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 4 0.05
64 71 0.91
65 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (64 bp):
GATGCATCGATGCACTACTAATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAAAGA
Found at i:2693310 original size:12 final size:12
Alignment explanation
Indices: 2693293--2693328 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2693283 TATCATGTTC
2693293 TCATATCACATG
1 TCATATCACATG
*
2693305 TCATATCACATA
1 TCATATCACATG
2693317 TCATATCACATG
1 TCATATCACATG
2693329 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:2693833 original size:64 final size:64
Alignment explanation
Indices: 2693699--2693840 Score: 164
Period size: 64 Copynumber: 2.2 Consensus size: 64
2693689 TTATTGCTGG
* * * * * *
2693699 GATGCATTGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATACATCGATGCACCGATTACATTCGATGTTTCACTATTAAAGA
* *
2693763 GATGCATCGATGCACTACTTATACATCGATGCA-CGAATTACATTCGATGTCTTTA-TTTTAAA-
1 GATGCATCGATGCACTACTTATACATCGATGCACCG-ATTACATTCGATGT-TTCACTATTAAAG
2693825 A
64 A
2693826 GAGTGCATCGATGCA
1 GA-TGCATCGATGCA
2693841 TTACCAATGC
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 4 0.06
64 60 0.90
65 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (64 bp):
GATGCATCGATGCACTACTTATACATCGATGCACCGATTACATTCGATGTTTCACTATTAAAGA
Found at i:2696811 original size:18 final size:17
Alignment explanation
Indices: 2696757--2696805 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2696747 TTAGACCCTT
* *
2696757 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
2696775 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
2696793 AGTGCATTCGATG
1 AGTGCA-TCGATG
2696806 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:2696975 original size:65 final size:64
Alignment explanation
Indices: 2696777--2696986 Score: 196
Period size: 65 Copynumber: 3.2 Consensus size: 64
2696767 TGCACTAAGA
* * * * * *
2696777 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAA-AATAGC-CAAAGTACATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCAATGTTTCAATAAAATCTC--AGTGCATCGATGCATGGTT
2696840 G
64 G
* * *
2696841 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATAAAATCCTCAGTGCATC-AGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCAATGTTTCAATAAAAT-CTCAGTGCATCGA-TGCATGGTT
*
2696905 A
64 G
* **
2696906 GTGCATCGATGCATGAAATGCATTCAATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCAATGTTTCAATAAAATCTCA--GTGCATCGATGCATGG-T
2696969 TG
63 TG
*
2696971 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
2696987 CTCTGAAAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
62 3 0.02
64 56 0.46
65 60 0.50
66 1 0.01
67 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCAATGTTTCAATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:2701089 original size:23 final size:23
Alignment explanation
Indices: 2701059--2701110 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
2701049 ATCTGACATA
* *
2701059 GTATCAATAAATGATCATTACGC
1 GTATCAATAAATGATCATGACAC
*
2701082 GTATCAATATATGATCATGACAC
1 GTATCAATAAATGATCATGACAC
2701105 GTATCA
1 GTATCA
2701111 TTAGTGACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (23 bp):
GTATCAATAAATGATCATGACAC
Found at i:2701661 original size:6 final size:6
Alignment explanation
Indices: 2701650--2701694 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
2701640 ATTTGTCTAG
* * *
2701650 ATTTTA ATTTTA ATTTTA ATTATA A-TTTC ATTTTA GTTTTA ATTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTT
2701695 CTTTTACCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 3 0.09
6 29 0.91
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (6 bp):
ATTTTA
Found at i:2701684 original size:17 final size:17
Alignment explanation
Indices: 2701662--2701700 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2701652 TTTAATTTTA
2701662 ATTTTAATTATAATTTC
1 ATTTTAATTATAATTTC
* *
2701679 ATTTTAGTTTTAATTTC
1 ATTTTAATTATAATTTC
2701696 -TTTTA
1 ATTTTA
2701701 CCATTAGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (17 bp):
ATTTTAATTATAATTTC
Found at i:2702249 original size:34 final size:34
Alignment explanation
Indices: 2702211--2702279 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
2702201 TAAATAGTTA
2702211 AGTGATCATATAATTTACCCATAATAAAAATACT
1 AGTGATCATATAATTTACCCATAATAAAAATACT
2702245 AGTGATCATATAATTTACCCATAATAAAAATACT
1 AGTGATCATATAATTTACCCATAATAAAAATACT
2702279 A
1 A
2702280 CTCCTCTCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (34 bp):
AGTGATCATATAATTTACCCATAATAAAAATACT
Found at i:2703463 original size:2 final size:2
Alignment explanation
Indices: 2703458--2703499 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2703448 ACACACTCCA
2703458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2703500 GTTTTCCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2705814 original size:2 final size:2
Alignment explanation
Indices: 2705801--2705848 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
2705791 ATGTTAATAG
*
2705801 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2705843 AT AT AT
1 AT AT AT
2705849 TAATTATTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2706710 original size:18 final size:18
Alignment explanation
Indices: 2706655--2706704 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
2706645 AAACAAGATT
*
2706655 AAGACAATGAAGATTAAATA
1 AAGACAA-GAATA-TAAATA
*
2706675 AAGTCAAGAATATAAATA
1 AAGACAAGAATATAAATA
2706693 AAGACAATGAAT
1 AAGACAA-GAAT
2706705 GTAATAGGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 12 0.46
19 8 0.31
20 6 0.23
ACGTcount: A:0.60, C:0.06, G:0.14, T:0.20
Consensus pattern (18 bp):
AAGACAAGAATATAAATA
Found at i:2707470 original size:29 final size:29
Alignment explanation
Indices: 2707415--2707471 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2707405 GCGACCTCCT
*
2707415 AGGTCGCCATGCACTCCGGACGACCAAGG
1 AGGTCGCCATGCACCCCGGACGACCAAGG
* *
2707444 AGGTCGCTATGCACGCCCGG-CGGCCAAG
1 AGGTCGCCATGCAC-CCCGGACGACCAAG
2707472 CTTTTAACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.21, C:0.35, G:0.33, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACCCCGGACGACCAAGG
Found at i:2708995 original size:43 final size:43
Alignment explanation
Indices: 2708938--2709029 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 43
2708928 TTTTTTAGAG
*
2708938 AAATTTCAATCGATCAAAGATAATCATTCGAATCGAACATTTT
1 AAATTTCAATCGATCAAAGATAATCATTCGAATCAAACATTTT
* * * *
2708981 AAATTTCAATCGATCAAAGGTAATTATTTGAATCAAACGTTTT
1 AAATTTCAATCGATCAAAGATAATCATTCGAATCAAACATTTT
2709024 AAATTT
1 AAATTT
2709030 TAATTTTTGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (43 bp):
AAATTTCAATCGATCAAAGATAATCATTCGAATCAAACATTTT
Found at i:2709873 original size:15 final size:15
Alignment explanation
Indices: 2709855--2709901 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 15
2709845 TAACCGGTTT
2709855 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
2709870 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
2709887 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
2709902 TGATTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 13 0.48
17 14 0.52
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:2709883 original size:17 final size:17
Alignment explanation
Indices: 2709858--2709891 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2709848 CCGGTTTCGG
2709858 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
2709875 TTTTTAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
2709892 ATAAAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:2710320 original size:13 final size:13
Alignment explanation
Indices: 2710304--2710333 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2710294 AAGTTCAATA
2710304 AATTCAAATACTT
1 AATTCAAATACTT
*
2710317 AATTGAAATACTT
1 AATTCAAATACTT
2710330 AATT
1 AATT
2710334 AACTCAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (13 bp):
AATTCAAATACTT
Found at i:2710440 original size:32 final size:33
Alignment explanation
Indices: 2710344--2710442 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
2710334 AACTCAACAT
* * *
2710344 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2710377 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2710410 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2710442 A
1 A
2710443 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:2710461 original size:21 final size:21
Alignment explanation
Indices: 2710437--2710476 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2710427 ACTTCAAGTT
2710437 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
2710458 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
2710477 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:2712790 original size:12 final size:12
Alignment explanation
Indices: 2712769--2712813 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
2712759 TTCGGATAAA
2712769 AACCGGTTTTTT
1 AACCGGTTTTTT
*
2712781 AACCGATTTTTT
1 AACCGGTTTTTT
2712793 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
2712807 ATCCGGT
1 AACCGGT
2712814 AAAAAAACCG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 17 0.61
14 11 0.39
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:2712798 original size:14 final size:13
Alignment explanation
Indices: 2712768--2712807 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
2712758 TTTCGGATAA
2712768 AAACCGGTTTTTT
1 AAACCGGTTTTTT
*
2712781 -AACCGATTTTTT
1 AAACCGGTTTTTT
2712793 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
2712807 A
1 A
2712808 TCCGGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 11 0.48
13 1 0.04
14 11 0.48
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (13 bp):
AAACCGGTTTTTT
Found at i:2716209 original size:110 final size:110
Alignment explanation
Indices: 2715962--2717045 Score: 1484
Period size: 110 Copynumber: 10.0 Consensus size: 110
2715952 TGATGGTGGT
* *
2715962 AGCTCAACTTCACAGCGAAGGAGCGACTGACTGTCAAGAAACAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* *
2716027 CAATTTCAAGTTCACA--G--TGA-A--GGACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * *
2716065 AGCTCAACTTCACAGTGAAGGGGCGGCTGACTGTCAACAAATAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* *
2716130 CAATTTCAACTTCACGGCGAAGGATATTGAACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * * *
2716175 AGCTCAACTTCACAGCTAAGGGGCAACTAACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
*
2716240 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGATAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * *
2716285 AGCTCAACTTCACAGCGAATGAGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * *
2716350 CAATTTCAACTTCACAACGAATGATATTGGACTCGAGACAACAAA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * * * * *
2716395 AGCTCAACTTCACAGCGAAGGGGCGACTGACTATCAATAAATAACTTCTCAGTTTAATTTAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* *
2716460 CAATTTCAACTTCAAAGCGAAGGATATTGGACTCGAGGCAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
*
2716505 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAAAAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* *
2716570 CAATTTTAACTTCACAGCGAAGGATATTAGACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * * * *
2716615 AGATTAACTTTACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTTATTCAGATT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * *
2716680 CAATTTCAATTTCACAGCGAATGATATTTGACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * * *
2716725 AGCTCAACTTCACAGCGAAGGGGTGACTGACTGTCAAAAAACAACTTTTTAGTTTCATTTAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * * *
2716790 CAATTTCAATTTCACAGCGAATGATATTAGACTCGAGATAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* *
2716835 AGCTCAACTTCACAACGAAGGGGCGACTGACTGTC-ACAAACAACTTTTCAATTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * *
2716899 CAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCG
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * ** *
2716944 AGCTCAACTTTACAG-G--GGCG-GA-TGGTTGTCAACAAACAACTTTCCAG--T--TTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * * *
2717000 CAATTTCAACTTCA-TGACGAAGGATATTGGCCTCGAAACATCACA
66 CAATTTCAACTTCACAG-CGAAGGATATTGGACTCGAGACAACACA
2717045 A
1 A
2717046 ATATTTGGAT
Statistics
Matches: 874, Mismatches: 98, Indels: 20
0.88 0.10 0.02
Matches are distributed among these distances:
101 46 0.05
103 75 0.09
104 6 0.01
105 17 0.02
106 3 0.00
107 2 0.00
108 2 0.00
109 76 0.09
110 647 0.74
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (110 bp):
AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
Found at i:2717387 original size:83 final size:81
Alignment explanation
Indices: 2717154--2717433 Score: 348
Period size: 84 Copynumber: 3.4 Consensus size: 81
2717144 TCATGCCCAC
* * * *
2717154 CAAAGGCCTTCGAGTTCGAGTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTTAAGTCG
1 CAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
*
2717219 AGAAGGGCTATCTGC-
66 AGAAGGGTTATCTGCA
* * * * * * *
2717234 CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGATTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
*
2717299 TAGAAGGGTTATCTGTCA
65 GAGAAGGGTTATCTG-CA
* *
2717317 CTAAAGACCTTCGATTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
1 C-AAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
2717382 GAGAAGGGTTATCTGC-
65 GAGAAGGGTTATCTGCA
2717398 CAACCGATGACCTTCGAGTTCGATTACACTCAGCTC
1 CAA---A-GACCTTCGAGTTCGATTACACTCAGCTC
2717434 AGAGGCAAAC
Statistics
Matches: 167, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
80 28 0.17
81 41 0.25
82 2 0.01
83 44 0.26
84 52 0.31
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (81 bp):
CAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
AGAAGGGTTATCTGCA
Found at i:2718116 original size:15 final size:15
Alignment explanation
Indices: 2718098--2718132 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2718088 CACTATATAG
2718098 TATTATATTAAATAA
1 TATTATATTAAATAA
**
2718113 TATTATATTTTATAA
1 TATTATATTAAATAA
2718128 TATTA
1 TATTA
2718133 AAACTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTATATTAAATAA
Found at i:2725328 original size:21 final size:20
Alignment explanation
Indices: 2725242--2725399 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
2725232 AAATGACCAA
**
2725242 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
2725261 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2725281 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2725301 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
2725322 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2725343 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2725363 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2725384 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2725400 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2725415 original size:40 final size:40
Alignment explanation
Indices: 2725366--2725520 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
2725356 CGATTTTCCA
* ** *
2725366 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
2725406 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
2725446 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
2725486 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
2725521 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:2725428 original size:20 final size:20
Alignment explanation
Indices: 2725366--2725519 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
2725356 CGATTTTCCA
* ** *
2725366 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
2725386 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2725406 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2725426 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2725446 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
2725466 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
2725486 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
2725507 AAATCGCAACGCG
1 AAATCGCAACGCG
2725520 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2725940 original size:33 final size:33
Alignment explanation
Indices: 2725901--2725971 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2725891 TTCACTTAGA
*
2725901 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2725934 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2725967 TTTCA
1 TTTCA
2725972 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2726095 original size:20 final size:20
Alignment explanation
Indices: 2726051--2726160 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
2726041 TGCAGAAGAG
*
2726051 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
2726072 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
2726092 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
2726113 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
2726127 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
2726146 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
2726161 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:2726108 original size:41 final size:38
Alignment explanation
Indices: 2726044--2726160 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
2726034 TTCAATTTGC
* *
2726044 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
2726082 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
2726123 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
2726156 AGAAT
1 AGAAT
2726161 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:2726130 original size:14 final size:14
Alignment explanation
Indices: 2726111--2726167 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2726101 GAGAAATGAA
2726111 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2726125 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2726144 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2726158 AATCGCAACG
1 AATCGCAACG
2726168 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2726143 original size:33 final size:33
Alignment explanation
Indices: 2726103--2726183 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
2726093 CGCAACGAGA
2726103 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2726136 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
2726169 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
2726184 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2726201 original size:19 final size:19
Alignment explanation
Indices: 2726179--2726276 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
2726169 GAAACCAAAA
*
2726179 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2726198 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2726212 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2726231 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
2726245 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2726264 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2726277 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
16 6 0.10
17 6 0.10
19 31 0.50
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2726220 original size:14 final size:14
Alignment explanation
Indices: 2726201--2726290 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
2726191 TTTCATTTCG
2726201 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2726215 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2726234 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
2726248 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2726267 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2726281 CGTTGCGATT
1 CGTTGCGATT
2726291 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 29 0.48
16 6 0.10
17 6 0.10
19 19 0.32
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2726226 original size:33 final size:33
Alignment explanation
Indices: 2726184--2726298 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
2726174 CAAAATCGCA
2726184 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
2726217 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2726250 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2726283 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2726299 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2728150 original size:93 final size:93
Alignment explanation
Indices: 2727991--2728645 Score: 1294
Period size: 93 Copynumber: 7.1 Consensus size: 93
2727981 TAGATTGCTT
*
2727991 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2728056 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2728084 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2728149 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2728177 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2728242 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2728270 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2728335 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2728363 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2728428 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2728456 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2728521 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2728549 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2728614 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2728641 AGTAA
1 AGTAA
2728646 TGCAATCCAT
Statistics
Matches: 561, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
92 6 0.01
93 555 0.99
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2728733 original size:19 final size:19
Alignment explanation
Indices: 2728693--2728821 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2728683 TAGTTTACTT
* *
2728693 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2728713 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2728732 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2728751 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2728765 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2728784 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2728798 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2728817 TCGCA
1 TCGCA
2728822 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2728772 original size:33 final size:32
Alignment explanation
Indices: 2728729--2728821 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
2728719 CGCGAAACCA
**
2728729 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2728761 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2728794 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2728822 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2728819 original size:52 final size:52
Alignment explanation
Indices: 2728693--2728821 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
2728683 TAGTTTACTT
**
2728693 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
2728745 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
2728798 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2728822 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:2728839 original size:19 final size:19
Alignment explanation
Indices: 2728817--2728950 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
2728807 GAAACCAAAA
*
2728817 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2728836 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2728852 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2728869 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2728885 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2728902 TCGCGTTGCGA-TTTGGTT
1 TCGCGTTGCGATTTTCATT
*
2728920 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2728940 TCGTGTTGCGA
1 TCGCGTTGCGA
2728951 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
18 16 0.17
19 28 0.30
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2728858 original size:14 final size:14
Alignment explanation
Indices: 2728839--2728895 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2728829 TTTCATTTCG
2728839 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2728853 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
2728870 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2728886 CGTTGCGATT
1 CGTTGCGATT
2728896 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2728864 original size:33 final size:33
Alignment explanation
Indices: 2728822--2728950 Score: 168
Period size: 33 Copynumber: 3.8 Consensus size: 33
2728812 CAAAATCGCA
2728822 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
* *
2728855 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
2728888 TTGCGATTTTCATTTCGCGTTGCGATTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA-TT-CTTT--CG
* *
2728925 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTTCA-TTTCGCGTTGCGA
2728951 AAGTAAACTA
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 55 0.65
34 2 0.02
35 2 0.02
37 13 0.15
38 12 0.14
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:2730892 original size:14 final size:14
Alignment explanation
Indices: 2730873--2730908 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2730863 ATTGTTTAAT
2730873 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2730887 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2730901 TGATTTGT
1 TGATTTGT
2730909 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2731039 original size:19 final size:19
Alignment explanation
Indices: 2731015--2731112 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
2731005 AAAATTGACT
2731015 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2731034 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2731053 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2731067 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2731086 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2731106 ATCGCAA
1 ATCGCAA
2731113 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2731144 original size:53 final size:53
Alignment explanation
Indices: 2731015--2731131 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
2731005 AAAATTGACT
2731015 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
2731067 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
2731120 ATCGCAATGCGA
1 ATCGCAATGCGA
2731132 TTTTAATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:2731149 original size:19 final size:19
Alignment explanation
Indices: 2731121--2731309 Score: 219
Period size: 19 Copynumber: 10.7 Consensus size: 19
2731111 AACGGGAGAA
* *
2731121 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
2731140 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
2731156 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2731173 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2731192 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
2731208 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2731225 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2731244 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2731263 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
2731281 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
2731297 TCGCATTGCGATT
1 TCGCATTGCGATT
2731310 CTCTCGTTGC
Statistics
Matches: 146, Mismatches: 8, Indels: 32
0.78 0.04 0.17
Matches are distributed among these distances:
14 23 0.16
16 16 0.11
17 14 0.10
18 1 0.01
19 76 0.52
20 16 0.11
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2731184 original size:52 final size:52
Alignment explanation
Indices: 2731121--2731323 Score: 281
Period size: 52 Copynumber: 3.9 Consensus size: 52
2731111 AACGGGAGAA
* *
2731121 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
2731173 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
2731225 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
*
2731281 T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
2731324 GTAATTTCCG
Statistics
Matches: 140, Mismatches: 5, Indels: 17
0.86 0.03 0.10
Matches are distributed among these distances:
47 8 0.06
49 2 0.01
50 2 0.01
51 3 0.02
52 80 0.57
53 24 0.17
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.09
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:2731331 original size:33 final size:33
Alignment explanation
Indices: 2731178--2731323 Score: 195
Period size: 33 Copynumber: 4.2 Consensus size: 33
2731168 TCATTTCGCA
2731178 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
2731211 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
2731247 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
2731283 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
2731316 TTGCGATT
1 TTGCGATT
2731324 GTAATTTCCG
Statistics
Matches: 99, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
32 1 0.01
33 47 0.47
34 14 0.14
35 3 0.03
36 6 0.06
37 3 0.03
38 15 0.15
39 10 0.10
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:2733783 original size:24 final size:24
Alignment explanation
Indices: 2733749--2733795 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2733739 CTGAAACATC
2733749 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2733773 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2733796 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2734506 original size:20 final size:20
Alignment explanation
Indices: 2734478--2734727 Score: 261
Period size: 20 Copynumber: 12.5 Consensus size: 20
2734468 AAATTTCAGT
* * *
2734478 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2734498 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
2734518 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2734538 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
2734558 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
2734578 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2734598 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
2734618 ATTGCGATTTACGGATAT-GC
1 GTTGCGATTTACGGAT-TCGC
* * *
2734638 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
2734658 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
2734678 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
2734698 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
2734718 GTTGCGATTT
1 GTTGCGATTT
2734728 TGGAAAATCG
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:2734744 original size:21 final size:21
Alignment explanation
Indices: 2734714--2734796 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
2734704 ATTTTCATAT
*
2734714 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
2734735 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
2734756 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
2734777 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
2734797 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:2734787 original size:42 final size:43
Alignment explanation
Indices: 2734694--2734792 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
2734684 ATTTATGTGT
* *
2734694 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
2734735 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
2734777 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
2734793 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:2736735 original size:24 final size:23
Alignment explanation
Indices: 2736680--2736738 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
2736670 AATAGATGTC
*
2736680 ATTTTAATAAAAAATAAAAATATT
1 ATTTAAAT-AAAAATAAAAATATT
***
2736704 AAAAAAATAAAAATAAAAATATTT
1 ATTTAAATAAAAATAAAAATA-TT
2736728 ATTTAAATAAA
1 ATTTAAATAAA
2736739 TGTTGGAGAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
ATTTAAATAAAAATAAAAATATT
Found at i:2737123 original size:2 final size:2
Alignment explanation
Indices: 2737116--2737153 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2737106 CTGTTCTTAC
2737116 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2737154 TGTTTTTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2739480 original size:27 final size:29
Alignment explanation
Indices: 2739424--2739481 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 29
2739414 CCAGTCTATG
*
2739424 TAAGTACCTAAAATATTTTTTAATCAAAA
1 TAAGTACCTAAAATATTATTTAATCAAAA
2739453 TAAGTACCT-AAA-ATTATTTAATCAAAA
1 TAAGTACCTAAAATATTATTTAATCAAAA
2739480 TA
1 TA
2739482 GGTGTATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 16 0.57
28 3 0.11
29 9 0.32
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.36
Consensus pattern (29 bp):
TAAGTACCTAAAATATTATTTAATCAAAA
Found at i:2739587 original size:22 final size:21
Alignment explanation
Indices: 2739562--2739605 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
2739552 TTTATTATCA
*
2739562 TTATTATATTTATATAATA-AAT
1 TTATAATA-TTAT-TAATATAAT
2739584 TTATAATATTATTAATATAAT
1 TTATAATATTATTAATATAAT
2739605 T
1 T
2739606 ACTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 8 0.40
22 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTATAATATTATTAATATAAT
Found at i:2740230 original size:17 final size:15
Alignment explanation
Indices: 2740210--2740238 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2740200 AAGAGAGAAT
2740210 AAGAA-AGAGTGAAG
1 AAGAAGAGAGTGAAG
2740224 AAGAAGAGAGTGAAG
1 AAGAAGAGAGTGAAG
2740239 CGGCGGGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (15 bp):
AAGAAGAGAGTGAAG
Found at i:2740235 original size:15 final size:14
Alignment explanation
Indices: 2740199--2740238 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
2740189 ATTTGGGTTA
* *
2740199 AAAGAGAGAATAAG
1 AAAGAGTGAAGAAG
2740213 AAAGAGTGAAGAAG
1 AAAGAGTGAAGAAG
2740227 AAGAGAGTGAAG
1 AA-AGAGTGAAG
2740239 CGGCGGGGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.35, T:0.07
Consensus pattern (14 bp):
AAAGAGTGAAGAAG
Found at i:2742715 original size:28 final size:28
Alignment explanation
Indices: 2742684--2742745 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
2742674 TAAACCTTTT
* *
2742684 TATATTTTTAATTTTGTAAAAAAAATTA
1 TATATATTTAATTTTGTAAAAAAAATAA
* * *
2742712 TATAAATTTAATTTTTTTAAAAAAATAA
1 TATATATTTAATTTTGTAAAAAAAATAA
2742740 TATATA
1 TATATA
2742746 AATATTTTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
TATATATTTAATTTTGTAAAAAAAATAA
Found at i:2742744 original size:30 final size:28
Alignment explanation
Indices: 2742690--2742748 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
2742680 TTTTTATATT
*
2742690 TTTAATTTTGTAAAAAAAATTATATAAA
1 TTTAATTTTGTAAAAAAAAATATATAAA
*
2742718 TTTAATTTTTTTAAAAAAATAATATATAAA
1 TTTAA-TTTTGTAAAAAAA-AATATATAAA
2742748 T
1 T
2742749 ATTTTCTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 5 0.19
29 12 0.44
30 10 0.37
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
TTTAATTTTGTAAAAAAAAATATATAAA
Found at i:2742872 original size:35 final size:35
Alignment explanation
Indices: 2742830--2742911 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 35
2742820 TTATTTCTTT
* *
2742830 AACCAAACACAATAATTTTACATTCCTGCTAAACC
1 AACCAAACACAATAATCTTACATTCATGCTAAACC
**
2742865 AACCAAACACGGTAATCTTACATTCATGCTAAACC
1 AACCAAACACAATAATCTTACATTCATGCTAAACC
2742900 AACCAAACACAA
1 AACCAAACACAA
2742912 AATACAACAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.45, C:0.29, G:0.05, T:0.21
Consensus pattern (35 bp):
AACCAAACACAATAATCTTACATTCATGCTAAACC
Found at i:2742957 original size:18 final size:18
Alignment explanation
Indices: 2742934--2742990 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 18
2742924 CCAGTAATTC
2742934 TATTCTCTGATAATCTTT
1 TATTCTCTGATAATCTTT
* *
2742952 TATTCTCACGGGTAATCTTT
1 TATTCT--CTGATAATCTTT
*
2742972 TATTCACACTGATAATCTT
1 TATT--CTCTGATAATCTT
2742991 ACATTCCGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 6 0.20
20 23 0.77
22 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (18 bp):
TATTCTCTGATAATCTTT
Found at i:2742996 original size:20 final size:20
Alignment explanation
Indices: 2742940--2742990 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2742930 ATTCTATTCT
*
2742940 CTGATAATCTTTTATTCTCA
1 CTGATAATCTTTTATTCACA
* *
2742960 CGGGTAATCTTTTATTCACA
1 CTGATAATCTTTTATTCACA
2742980 CTGATAATCTT
1 CTGATAATCTT
2742991 ACATTCCGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (20 bp):
CTGATAATCTTTTATTCACA
Found at i:2745004 original size:24 final size:24
Alignment explanation
Indices: 2744972--2745020 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2744962 GATCCAACTG
2744972 TACCATTTCTCTCCAAAATTCGTT
1 TACCATTTCTCTCCAAAATTCGTT
2744996 TACCATTTCTCTCCAAAATTCGTT
1 TACCATTTCTCTCCAAAATTCGTT
2745020 T
1 T
2745021 TCTTCATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.29, G:0.04, T:0.43
Consensus pattern (24 bp):
TACCATTTCTCTCCAAAATTCGTT
Found at i:2745033 original size:26 final size:24
Alignment explanation
Indices: 2744980--2745034 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2744970 TGTACCATTT
**
2744980 CTCTCCAAAATTCGTTTACCATTT
1 CTCTCCAAAATTCGTTTACCATCA
*
2745004 CTCTCCAAAATTCGTTTTCTTCATCA
1 CTCTCCAAAATTCGTTTAC--CATCA
2745030 CTCTC
1 CTCTC
2745035 AGAAGATCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 18 0.69
26 8 0.31
ACGTcount: A:0.22, C:0.33, G:0.04, T:0.42
Consensus pattern (24 bp):
CTCTCCAAAATTCGTTTACCATCA
Found at i:2745222 original size:73 final size:73
Alignment explanation
Indices: 2745133--2745275 Score: 232
Period size: 73 Copynumber: 2.0 Consensus size: 73
2745123 ACTCATGGCT
* * **
2745133 ATAAAAGAACAATCCAAAATTTGACATCCCAGAATAAAATTAAATTGAGTCTTGCTTATAATAAT
1 ATAAAAGAACAATCCAAAATTTGACATCCCAAAACAAAAACAAATTGAGTCTTGCTTATAATAAT
2745198 ATCTGTGC
66 ATCTGTGC
* *
2745206 ATAAAAGAACAATCCAAAATTTGACATCCCAAAACAAAAACAAATTGAGTCTTTCTTATAATAGT
1 ATAAAAGAACAATCCAAAATTTGACATCCCAAAACAAAAACAAATTGAGTCTTGCTTATAATAAT
2745271 ATCTG
66 ATCTG
2745276 AACATTAGTG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (73 bp):
ATAAAAGAACAATCCAAAATTTGACATCCCAAAACAAAAACAAATTGAGTCTTGCTTATAATAAT
ATCTGTGC
Found at i:2745579 original size:19 final size:19
Alignment explanation
Indices: 2745555--2745594 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2745545 TAATAATAGT
* *
2745555 AATAATATTAAGATTAATA
1 AATAATAGTAAGAATAATA
*
2745574 AATAATAGTAATAATAATA
1 AATAATAGTAAGAATAATA
2745593 AA
1 AA
2745595 AACGTTAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
AATAATAGTAAGAATAATA
Found at i:2745718 original size:17 final size:17
Alignment explanation
Indices: 2745673--2745720 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
2745663 CATATAGCAA
2745673 ATACTATATAATAATAAG
1 ATACTA-ATAATAATAAG
* *
2745691 ATAATAGTAATAAGTAAG
1 ATACTAATAATAA-TAAG
2745709 -TACTAATAATAA
1 ATACTAATAATAA
2745721 CATAAAATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.31
Consensus pattern (17 bp):
ATACTAATAATAATAAG
Found at i:2753196 original size:28 final size:27
Alignment explanation
Indices: 2753157--2753221 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 27
2753147 ATTATTCAAG
*
2753157 ATAATCTTAAGATAGTCATTGATTGAC
1 ATAATCTTAAGATAGCCATTGATTGAC
*
2753184 ATAATTCTTAAGATAGCCGTTGATTGAC
1 ATAA-TCTTAAGATAGCCATTGATTGAC
*
2753212 AGAAGTCTTA
1 ATAA-TCTTA
2753222 CTCAGACTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 4 0.12
28 29 0.88
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (27 bp):
ATAATCTTAAGATAGCCATTGATTGAC
Found at i:2755971 original size:5 final size:6
Alignment explanation
Indices: 2755955--2756044 Score: 58
Period size: 6 Copynumber: 14.7 Consensus size: 6
2755945 AGTTAGATTG
** * * *
2755955 TAAAAA TAAAAA TAAAAA TAAAAA TATGAA TAATAAA -AAAAT TTAATA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAA-AAA TAAAAA TAAAAA
* * *
2756003 TAATAA TAATAA TAAATAA -ATAAA TAAATAA GTAAAAA TAAA
1 TAAAAA TAAAAA TAAA-AA TAAAAA TAAA-AA -TAAAAA TAAA
2756045 TAAAAGTGAG
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
5 4 0.06
6 48 0.75
7 8 0.12
8 4 0.06
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (6 bp):
TAAAAA
Found at i:2755991 original size:21 final size:20
Alignment explanation
Indices: 2755955--2756047 Score: 65
Period size: 21 Copynumber: 4.7 Consensus size: 20
2755945 AGTTAGATTG
2755955 TAAAAATA-AA-AATAAAAA
1 TAAAAATATAATAATAAAAA
2755973 TAAAAATATGAATAATAAAAA
1 TAAAAATAT-AATAATAAAAA
* *
2755994 -AATTTAATATAATAATAATAA
1 TAA--AAATATAATAATAAAAA
2756015 T--AAATA-AATAAATAAATAA
1 TAAAAATATAAT-AATAAA-AA
2756034 GTAAAAATA-AATAA
1 -TAAAAATATAATAA
2756048 AAGTGAGTAG
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
17 3 0.05
18 17 0.28
19 2 0.03
20 5 0.08
21 20 0.33
22 13 0.22
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAAAATATAATAATAAAAA
Found at i:2756208 original size:17 final size:19
Alignment explanation
Indices: 2756172--2756214 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2756162 ATGACAGTAG
2756172 AAATAATAAAATGAATCAAA
1 AAATAATAAAA-GAATCAAA
2756192 AAATAATAAAA-AA-CAAA
1 AAATAATAAAAGAATCAAA
*
2756209 ACATAA
1 AAATAA
2756215 ATGCCCAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 2 0.09
20 11 0.50
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (19 bp):
AAATAATAAAAGAATCAAA
Found at i:2757915 original size:34 final size:36
Alignment explanation
Indices: 2757838--2757927 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 36
2757828 CTCGAGGGTC
* * *
2757838 TTTGGGTTTCAAGAGAAACATTTTCAAAGGCTTTTT
1 TTTGTGTTTCAAGAGAAACAATTTCAAAGGCGTTTT
*
2757874 TTGTGTGTTTCAAGAGAAACAATTTC-GAGG-GTTTT
1 TT-TGTGTTTCAAGAGAAACAATTTCAAAGGCGTTTT
2757909 TTTGTGTTTCAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
2757928 TGGACAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
34 17 0.35
35 6 0.12
36 5 0.10
37 21 0.43
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (36 bp):
TTTGTGTTTCAAGAGAAACAATTTCAAAGGCGTTTT
Found at i:2758084 original size:36 final size:36
Alignment explanation
Indices: 2758037--2758141 Score: 174
Period size: 37 Copynumber: 2.9 Consensus size: 36
2758027 AAAGATTTTA
*
2758037 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
*
2758073 TTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAA-AATTTG
*
2758110 ATTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
2758142 CTTGGAAATT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 30 0.47
37 34 0.53
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:2759327 original size:32 final size:32
Alignment explanation
Indices: 2759291--2759351 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
2759281 CCAAAGATGT
* * *
2759291 CCCAATAATCGGTGTTGAATCTCAAAAAATGC
1 CCCAACAATCGATGTTAAATCTCAAAAAATGC
* *
2759323 CCCAACATTTGATGTTAAATCTCAAAAAA
1 CCCAACAATCGATGTTAAATCTCAAAAAA
2759352 ATGCTCCAGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.26
Consensus pattern (32 bp):
CCCAACAATCGATGTTAAATCTCAAAAAATGC
Found at i:2759382 original size:34 final size:33
Alignment explanation
Indices: 2759303--2759371 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
2759293 CAATAATCGG
*
2759303 TGTTGAATCTC-AAAAAATGCCCCAACATTTGA
1 TGTTAAATCTCAAAAAAATGCCCCAACATTTGA
* *
2759335 TGTTAAATCTCAAAAAAATGCTCCAGCATTTGA
1 TGTTAAATCTCAAAAAAATGCCCCAACATTTGA
2759368 TGTT
1 TGTT
2759372 GAATATTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 10 0.30
33 23 0.70
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (33 bp):
TGTTAAATCTCAAAAAAATGCCCCAACATTTGA
Done.