Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_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: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 37
Found at i:2963113 original size:149 final size:148
Alignment explanation
Indices: 2962859--2963171 Score: 486
Period size: 149 Copynumber: 2.1 Consensus size: 148
2962849 GAGTCGAGGG
* * * * * * *
2962859 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAATATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* *
2962924 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGGGACATTATTAT
2962989 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
* *
2963007 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
*
2963072 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGGGACATTATTA
2963137 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
2963156 T-TACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
2963172 TGCAATTATA
Statistics
Matches: 151, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
147 1 0.01
148 60 0.40
149 90 0.60
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGGGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:2967876 original size:22 final size:21
Alignment explanation
Indices: 2967824--2967883 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
2967814 GATTTTTGGG
2967824 CAAGGGGAATCGATACCCATT
1 CAAGGGGAATCGATACCCATT
*
2967845 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
2967865 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGATACCC
2967884 CTCAAGCGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 19 0.54
21 3 0.09
22 13 0.37
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:2968898 original size:31 final size:31
Alignment explanation
Indices: 2968860--2968984 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
2968850 AGGGTCGAGG
*
2968860 GTTTACCTATATTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2968891 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
2968922 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
2968953 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
2968984 G
1 G
2968985 GTCCTTCGGG
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2969490 original size:21 final size:21
Alignment explanation
Indices: 2969465--2969507 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2969455 AAAGAATATA
2969465 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
2969486 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
2969507 T
1 T
2969508 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:2970497 original size:20 final size:20
Alignment explanation
Indices: 2970472--2970513 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2970462 GTTTTATGAG
*
2970472 ATGTAGTAT-ATATATTGTTC
1 ATGTAGTATCA-ATATAGTTC
2970492 ATGTAGTATCAATATAGTTC
1 ATGTAGTATCAATATAGTTC
2970512 AT
1 AT
2970514 ATTCTGGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (20 bp):
ATGTAGTATCAATATAGTTC
Found at i:2991275 original size:16 final size:17
Alignment explanation
Indices: 2991241--2991296 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
2991231 TACTATTATC
2991241 AATAAATTTATTATTTT
1 AATAAATTTATTATTTT
2991258 AATAAATTT-TGT-TTTT
1 AATAAATTTAT-TATTTT
2991274 AATATACA-TTATTATGTTT
1 AATA-A-ATTTATTAT-TTT
2991293 AATA
1 AATA
2991297 TAATAGAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 9 0.27
17 14 0.42
18 3 0.09
19 7 0.21
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
AATAAATTTATTATTTT
Found at i:2995318 original size:20 final size:20
Alignment explanation
Indices: 2995293--2995334 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2995283 TATATGCAAC
*
2995293 ATAACAATGCCAGTAATGGT
1 ATAACAATCCCAGTAATGGT
*
2995313 ATAACACTCCCAGTAATGGT
1 ATAACAATCCCAGTAATGGT
2995333 AT
1 AT
2995335 GCCACATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (20 bp):
ATAACAATCCCAGTAATGGT
Found at i:2995561 original size:19 final size:19
Alignment explanation
Indices: 2995508--2995561 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
2995498 AGTGTCGAAT
* * *
2995508 AATGCACACATAGTGACAT
1 AATGCACATATAGTGCCAG
* *
2995527 ATTGCACATAAAGTGCCAG
1 AATGCACATATAGTGCCAG
2995546 AATGCACATATAGTGC
1 AATGCACATATAGTGC
2995562 ATGACAAATG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (19 bp):
AATGCACATATAGTGCCAG
Found at i:3001831 original size:32 final size:31
Alignment explanation
Indices: 3001793--3001869 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
3001783 CGGGACCGTG
*
3001793 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
3001825 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
3001856 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
3001870 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:3002751 original size:7 final size:7
Alignment explanation
Indices: 3002739--3002783 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
3002729 GTCAAAGAAA
3002739 GTCAACG
1 GTCAACG
3002746 GTCAACG
1 GTCAACG
3002753 GTCAACG
1 GTCAACG
*
3002760 GTCAACA
1 GTCAACG
3002767 GTCAACG
1 GTCAACG
3002774 GTCAACG
1 GTCAACG
3002781 GTC
1 GTC
3002784 GGGTCGGGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:3002790 original size:5 final size:5
Alignment explanation
Indices: 3002780--3002836 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
3002770 AACGGTCAAC
* *
3002780 GGTCG GGTCG GGTC- GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
3002828 GGTCG GGTC
1 GGTCG GGTC
3002837 AGACCGGTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 32 0.73
7 8 0.18
ACGTcount: A:0.07, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:3002796 original size:21 final size:21
Alignment explanation
Indices: 3002772--3002836 Score: 121
Period size: 21 Copynumber: 3.0 Consensus size: 21
3002762 CAACAGTCAA
3002772 CGGTCAACGGTCGGGTCGGGT
1 CGGTCAACGGTCGGGTCGGGT
3002793 CGGTCAACGGTCGGGTCGGGT
1 CGGTCAACGGTCGGGTCGGGT
3002814 CGGGTCAACGGTCGGGTCGGGT
1 C-GGTCAACGGTCGGGTCGGGT
3002836 C
1 C
3002837 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 22 0.51
22 21 0.49
ACGTcount: A:0.09, C:0.25, G:0.48, T:0.18
Consensus pattern (21 bp):
CGGTCAACGGTCGGGTCGGGT
Found at i:3002856 original size:19 final size:18
Alignment explanation
Indices: 3002833--3002911 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 18
3002823 GGTCGGGTCG
3002833 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
3002851 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
3002870 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
3002890 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
3002909 GGT
1 GGT
3002912 TGAAAACCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
18 5 0.10
19 39 0.75
20 8 0.15
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:3002890 original size:29 final size:31
Alignment explanation
Indices: 3002858--3002932 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
3002848 ACCGAGTCAG
3002858 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
3002887 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
3002917 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
3002933 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:3002932 original size:9 final size:9
Alignment explanation
Indices: 3002833--3002931 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
3002823 GGTCGGGTCG
*
3002833 GGTCAGACC
1 GGTCAAACC
3002842 GGTCAAACC
1 GGTCAAACC
*
3002851 GAGTCAGACC
1 G-GTCAAACC
3002861 GGTCAAACC
1 GGTCAAACC
*
3002870 GGTTCGAACC
1 GG-TCAAACC
*
3002880 GGTTGAAACC
1 GG-TCAAACC
3002890 GGTCAAACC
1 GGTCAAACC
3002899 GGTCAGAACC
1 GGTCA-AACC
*
3002909 GGTTGAAAACC
1 GG-T-CAAACC
*
3002920 GGTTAAACC
1 GGTCAAACC
3002929 GGT
1 GGT
3002932 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:3009091 original size:32 final size:31
Alignment explanation
Indices: 3009055--3009131 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
3009045 CGGGGCCGTG
*
3009055 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
3009087 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
3009118 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
3009132 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:3009114 original size:63 final size:63
Alignment explanation
Indices: 3009008--3009131 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
3008998 CCCTAAGGGA
* * ** *
3009008 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
3009071 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
3009132 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:3010008 original size:7 final size:7
Alignment explanation
Indices: 3009992--3010022 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3009982 GTCAAAGAAA
3009992 GTCAACG
1 GTCAACG
*
3009999 GTCAATG
1 GTCAACG
3010006 GTCAACG
1 GTCAACG
3010013 GTCAACG
1 GTCAACG
3010020 GTC
1 GTC
3010023 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:3010040 original size:22 final size:22
Alignment explanation
Indices: 3010012--3010054 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3010002 AATGGTCAAC
3010012 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
3010034 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
3010055 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:3010074 original size:19 final size:18
Alignment explanation
Indices: 3010051--3010129 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 18
3010041 GGTCGGGTCG
3010051 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
3010069 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
3010088 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
3010108 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
3010127 GGT
1 GGT
3010130 TGAAAACCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
18 5 0.10
19 39 0.75
20 8 0.15
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:3010108 original size:29 final size:31
Alignment explanation
Indices: 3010076--3010150 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
3010066 ACCGAGTCAG
3010076 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
3010105 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
3010135 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
3010151 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:3010150 original size:9 final size:9
Alignment explanation
Indices: 3010051--3010149 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
3010041 GGTCGGGTCG
*
3010051 GGTCAGACC
1 GGTCAAACC
3010060 GGTCAAACC
1 GGTCAAACC
*
3010069 GAGTCAGACC
1 G-GTCAAACC
3010079 GGTCAAACC
1 GGTCAAACC
*
3010088 GGTTCGAACC
1 GG-TCAAACC
*
3010098 GGTTGAAACC
1 GG-TCAAACC
3010108 GGTCAAACC
1 GGTCAAACC
3010117 GGTCAGAACC
1 GGTCA-AACC
*
3010127 GGTTGAAAACC
1 GG-T-CAAACC
*
3010138 GGTTAAACC
1 GGTCAAACC
3010147 GGT
1 GGT
3010150 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:3012237 original size:6 final size:6
Alignment explanation
Indices: 3012226--3012253 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3012216 CATTAATTGA
3012226 TGAATT TGAATT TGAATT TGAATT TGAA
1 TGAATT TGAATT TGAATT TGAATT TGAA
3012254 CAATCATTGC
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:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (6 bp):
TGAATT
Found at i:3018258 original size:13 final size:13
Alignment explanation
Indices: 3018240--3018273 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3018230 ATGTTATTTT
3018240 CTTGATATGATCA
1 CTTGATATGATCA
3018253 CTTGATATGATCA
1 CTTGATATGATCA
*
3018266 CTTTATAT
1 CTTGATAT
3018274 CCACTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (13 bp):
CTTGATATGATCA
Found at i:3019126 original size:30 final size:30
Alignment explanation
Indices: 3019091--3019425 Score: 240
Period size: 30 Copynumber: 11.2 Consensus size: 30
3019081 GTGGTTGTTA
3019091 TGAAAGTGGTGGTGTAGAAGTGGATAATGC
1 TGAAAGTGGTGGTGTAGAAGTGGATAATGC
* *
3019121 TGAAAGTGGTGGTGTGGAAATGGATAATGC
1 TGAAAGTGGTGGTGTAGAAGTGGATAATGC
* * * *
3019151 TGAAAGTAGTGGTGCAGAAATGGATACTGC
1 TGAAAGTGGTGGTGTAGAAGTGGATAATGC
* * * *
3019181 TGAAA-TGGGTAGTGTAAAAAG-GGACAATAC
1 TGAAAGT-GGTGGTGT-AGAAGTGGATAATGC
* * * *
3019211 TGAAA-TGGGTAGTGTTGAAAG-GGACAATGT
1 TGAAAGT-GGTGGTGTAG-AAGTGGATAATGC
* * *
3019241 TGAAAGTGCTGGTGTAGAAATGGATAGTGC
1 TGAAAGTGGTGGTGTAGAAGTGGATAATGC
* *
3019271 TGAAAGTGCTGGTGTAGAAATGGATAATGC
1 TGAAAGTGGTGGTGTAGAAGTGGATAATGC
* *
3019301 TGAAA-TGGGTAGTGTAGAAAG-GGACAATGC
1 TGAAAGT-GGTGGTGTAG-AAGTGGATAATGC
* * *
3019331 TGAAA-TGGGTAGTGTGGAAAG-GGACAATGC
1 TGAAAGT-GGTGGTGTAG-AAGTGGATAATGC
* * * *
3019361 TGAAA-TGGGTAGTGTTGAAAG-GGACAATGT
1 TGAAAGT-GGTGGTGTAG-AAGTGGATAATGC
* *
3019391 TGAAAGTGTTGGTGTAGAAATGGATAATGC
1 TGAAAGTGGTGGTGTAGAAGTGGATAATGC
3019421 TGAAA
1 TGAAA
3019426 TGAGTAATGT
Statistics
Matches: 257, Mismatches: 39, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
29 6 0.02
30 244 0.95
31 7 0.03
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (30 bp):
TGAAAGTGGTGGTGTAGAAGTGGATAATGC
Found at i:3019129 original size:16 final size:16
Alignment explanation
Indices: 3019108--3019157 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
3019098 GGTGGTGTAG
3019108 AAGTGGATAATGCTGA
1 AAGTGGATAATGCTGA
**
3019124 AAGTGG-TGGTG-TGGA
1 AAGTGGATAATGCT-GA
3019139 AA-TGGATAATGCTGA
1 AAGTGGATAATGCTGA
3019154 AAGT
1 AAGT
3019158 AGTGGTGCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
14 4 0.15
15 14 0.54
16 8 0.31
ACGTcount: A:0.34, C:0.04, G:0.36, T:0.26
Consensus pattern (16 bp):
AAGTGGATAATGCTGA
Found at i:3019284 original size:120 final size:119
Alignment explanation
Indices: 3019116--3019427 Score: 455
Period size: 120 Copynumber: 2.6 Consensus size: 119
3019106 AGAAGTGGAT
* * *
3019116 AATGCTGAAAGTGGTGGTGTGGAAATGGATAATGCTGAAAGTAGTGGTGCAGAAATGGATACTGC
1 AATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAAGT-GTGGTGTAGAAATGGATAATGC
*
3019181 TGAAATGGGTAGTGTAAAAAGGGACAATACTGAAATGGGTAGTGTTGAAAGGGAC
65 TGAAATGGGTAGTGTAAAAAGGGACAATACTGAAATGGGTAGTGTGGAAAGGGAC
* * *
3019236 AATGTTGAAAGTGCTGGTGTAGAAATGGATAGTGCTGAAAGTGCTGGTGTAGAAATGGATAATGC
1 AATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAAGTG-TGGTGTAGAAATGGATAATGC
* *
3019301 TGAAATGGGTAGTGTAGAAAGGGACAATGCTGAAATGGGTAGTGTGGAAAGGGAC
65 TGAAATGGGTAGTGTAAAAAGGGACAATACTGAAATGGGTAGTGTGGAAAGGGAC
* * * * *
3019356 AATGCTGAAA-TGGGTAGTGTTGAAAGGGACAATGTTGAAAGTGTTGGTGTAGAAATGGATAATG
1 AATGCTGAAAGT-GGTGGTGTAGAAATGGATAATGCTGAAAGTG-TGGTGTAGAAATGGATAATG
3019420 CTGAAATG
64 CTGAAATG
3019428 AGTAATGTTG
Statistics
Matches: 172, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
119 2 0.01
120 170 0.99
ACGTcount: A:0.34, C:0.06, G:0.35, T:0.25
Consensus pattern (119 bp):
AATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAAGTGTGGTGTAGAAATGGATAATGCT
GAAATGGGTAGTGTAAAAAGGGACAATACTGAAATGGGTAGTGTGGAAAGGGAC
Found at i:3019305 original size:15 final size:15
Alignment explanation
Indices: 3019287--3019440 Score: 66
Period size: 15 Copynumber: 10.3 Consensus size: 15
3019277 TGCTGGTGTA
3019287 GAAATGGATAATGCT
1 GAAATGGATAATGCT
* *
3019302 GAAATGGGTAGTG-T
1 GAAATGGATAATGCT
* *
3019316 AGAAAGGGACAATGCT
1 -GAAATGGATAATGCT
* *
3019332 GAAATGGGTAGTG-T
1 GAAATGGATAATGCT
* *
3019346 GGAAAGGGACAATGCT
1 -GAAATGGATAATGCT
* * *
3019362 GAAATGGGTAGTGTT
1 GAAATGGATAATGCT
* * *
3019377 GAAAGGGACAATGTT
1 GAAATGGATAATGCT
* **
3019392 GAAA-GTGTTGGTG-T
1 GAAATG-GATAATGCT
3019406 AGAAATGGATAATGCT
1 -GAAATGGATAATGCT
*
3019422 GAAAT-GAGTAATGTT
1 GAAATGGA-TAATGCT
3019437 GAAA
1 GAAA
3019441 AGGACAATGA
Statistics
Matches: 99, Mismatches: 31, Indels: 18
0.67 0.21 0.12
Matches are distributed among these distances:
14 6 0.06
15 89 0.90
16 4 0.04
ACGTcount: A:0.36, C:0.05, G:0.34, T:0.25
Consensus pattern (15 bp):
GAAATGGATAATGCT
Found at i:3019338 original size:150 final size:150
Alignment explanation
Indices: 3019091--3019425 Score: 519
Period size: 150 Copynumber: 2.2 Consensus size: 150
3019081 GTGGTTGTTA
* * * *
3019091 TGAAAGTGGTGGTGTAGAAGTGGATAATGCTGAAAGTGGTGGTGTGGAAATGGATAATGCTGAAA
1 TGAAAGTGCTGGTGTAGAAATGGATAATGCTGAAAGTGCTGGTGTAGAAATGGATAATGCTGAAA
* * * *
3019156 GTAGTGGTGCAGAAATGGATACTGCTGAAATGGGTAGTGTAAAAAGGGACAATACTGAAATGGGT
66 GTAGTAGTGCAGAAAGGGACAATGCTGAAATGGGTAGTGTAAAAAGGGACAATACTGAAATGGGT
3019221 AGTGTTGAAAGGGACAATGT
131 AGTGTTGAAAGGGACAATGT
*
3019241 TGAAAGTGCTGGTGTAGAAATGGATAGTGCTGAAAGTGCTGGTGTAGAAATGGATAATGCTGAAA
1 TGAAAGTGCTGGTGTAGAAATGGATAATGCTGAAAGTGCTGGTGTAGAAATGGATAATGCTGAAA
* * ** *
3019306 -TGGGTAGTGTAGAAAGGGACAATGCTGAAATGGGTAGTGTGGAAAGGGACAATGCTGAAATGGG
66 GT-AGTAGTGCAGAAAGGGACAATGCTGAAATGGGTAGTGTAAAAAGGGACAATACTGAAATGGG
3019370 TAGTGTTGAAAGGGACAATGT
130 TAGTGTTGAAAGGGACAATGT
*
3019391 TGAAAGTGTTGGTGTAGAAATGGATAATGCTGAAA
1 TGAAAGTGCTGGTGTAGAAATGGATAATGCTGAAA
3019426 TGAGTAATGT
Statistics
Matches: 168, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
149 1 0.01
150 167 0.99
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (150 bp):
TGAAAGTGCTGGTGTAGAAATGGATAATGCTGAAAGTGCTGGTGTAGAAATGGATAATGCTGAAA
GTAGTAGTGCAGAAAGGGACAATGCTGAAATGGGTAGTGTAAAAAGGGACAATACTGAAATGGGT
AGTGTTGAAAGGGACAATGT
Found at i:3019426 original size:60 final size:61
Alignment explanation
Indices: 3019091--3019449 Score: 356
Period size: 60 Copynumber: 6.0 Consensus size: 61
3019081 GTGGTTGTTA
* * * * *
3019091 TGAAAGT-GGTGGTGTAGAAGTGGATAATGCTGAAA-GTGGTGGTGTGGAAATGGATAATGC
1 TGAAAGTGGGTGGTGTAGAAATGGATAATGCTGAAATG-GGTAGTGTAGAAAGGGACAATGC
* * * * *
3019151 TGAAAGT-AGTGGTGCAGAAATGGATACTGCTGAAATGGGTAGTGTAAAAAGGGACAATAC
1 TGAAAGTGGGTGGTGTAGAAATGGATAATGCTGAAATGGGTAGTGTAGAAAGGGACAATGC
* * * * * * * * * *
3019211 TGAAA-TGGGTAGTGTTGAAAGGGACAATGTTGAAA-GTGCTGGTGTAGAAATGGATAGTGC
1 TGAAAGTGGGTGGTGTAGAAATGGATAATGCTGAAATG-GGTAGTGTAGAAAGGGACAATGC
*
3019271 TGAAAGT-GCTGGTGTAGAAATGGATAATGCTGAAATGGGTAGTGTAGAAAGGGACAATGC
1 TGAAAGTGGGTGGTGTAGAAATGGATAATGCTGAAATGGGTAGTGTAGAAAGGGACAATGC
* * * * * *
3019331 TGAAA-TGGGTAGTGTGGAAAGGGACAATGCTGAAATGGGTAGTGTTGAAAGGGACAATGT
1 TGAAAGTGGGTGGTGTAGAAATGGATAATGCTGAAATGGGTAGTGTAGAAAGGGACAATGC
* * * * *
3019391 TGAAAGT-GTTGGTGTAGAAATGGATAATGCTGAAATGAGTAATGTTGAAAAGGACAATG
1 TGAAAGTGGGTGGTGTAGAAATGGATAATGCTGAAATGGGTAGTGTAGAAAGGGACAATG
3019450 AGAAAGACAA
Statistics
Matches: 241, Mismatches: 51, Indels: 14
0.79 0.17 0.05
Matches are distributed among these distances:
59 3 0.01
60 234 0.97
61 4 0.02
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.25
Consensus pattern (61 bp):
TGAAAGTGGGTGGTGTAGAAATGGATAATGCTGAAATGGGTAGTGTAGAAAGGGACAATGC
Found at i:3022383 original size:22 final size:21
Alignment explanation
Indices: 3022351--3022391 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3022341 CTTGCAGTTC
3022351 AATGCAAAATGAAGAAAAATTA
1 AATGCAAAATGAA-AAAAATTA
* *
3022373 AATGCACAATGCAAAAAAT
1 AATGCAAAATGAAAAAAAT
3022392 CAAAGTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.61, C:0.10, G:0.12, T:0.17
Consensus pattern (21 bp):
AATGCAAAATGAAAAAAATTA
Found at i:3022490 original size:15 final size:15
Alignment explanation
Indices: 3022470--3022500 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3022460 AAACATATAC
3022470 AAACTTCCATTACAA
1 AAACTTCCATTACAA
3022485 AAACTTCCATTACAA
1 AAACTTCCATTACAA
3022500 A
1 A
3022501 GCTTTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
AAACTTCCATTACAA
Found at i:3024995 original size:31 final size:31
Alignment explanation
Indices: 3024959--3025017 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
3024949 AACTTAAAAG
3024959 AGTTTTACAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
3024990 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
3025018 CCATACAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:3025069 original size:22 final size:22
Alignment explanation
Indices: 3025041--3025381 Score: 459
Period size: 22 Copynumber: 15.5 Consensus size: 22
3025031 ATAATAATTT
3025041 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
3025063 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
3025085 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
*
3025107 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
3025129 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
3025151 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
* ***
3025173 TTTTAAAATAATTTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
3025195 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
***
3025217 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
3025239 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** *
3025261 TTTTAAAATAAATTTTTTTCATA
1 TTTTAAAATAAA-TCAATCCATA
*** *
3025284 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
*
3025306 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
3025328 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
3025350 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
3025372 TTTTAAAATA
1 TTTTAAAATA
3025382 GATTTAAATA
Statistics
Matches: 283, Mismatches: 33, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
21 4 0.01
22 257 0.91
23 22 0.08
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:3026656 original size:25 final size:27
Alignment explanation
Indices: 3026601--3026654 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
3026591 TTGTCCTATT
3026601 CAAAACATTTCATTAAAAAAATCAACA
1 CAAAACATTTCATTAAAAAAATCAACA
* *
3026628 CAAAACATTTTATTAAAAATATCAACA
1 CAAAACATTTCATTAAAAAAATCAACA
3026655 AATAATAATA
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:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (27 bp):
CAAAACATTTCATTAAAAAAATCAACA
Found at i:3028568 original size:189 final size:189
Alignment explanation
Indices: 3028248--3028626 Score: 742
Period size: 189 Copynumber: 2.0 Consensus size: 189
3028238 AGCATTCATA
3028248 TTAGAGTGTAAAACCCTCAATTCCCACAAAATGAAACCATAACAGAAGCAGGAAGGAAAAGGGAG
1 TTAGAGTGTAAAACCCTCAATTCCCACAAAATGAAACCATAACAGAAGCAGGAAGGAAAAGGGAG
3028313 CTAATAAGCATTAGTATTAAAGATTTGCAGTTAGATCAGAAGAAAATATAATAATTTAACCATTT
66 CTAATAAGCATTAGTATTAAAGATTTGCAGTTAGATCAGAAGAAAATATAATAATTTAACCATTT
3028378 CTCTAATGATCTTTCTATGTTCTTAGGAC-GGGAGCAATGTTTATATGGGAAAAGGACTT
131 CTCTAATGATC-TTCTATGTTCTTAGGACTGGGAGCAATGTTTATATGGGAAAAGGACTT
3028437 TTAGAGTGTAAAACCCTCAATTCCCACAAAATGAAACCATAACAGAAGCAGGAAGGAAAAGGGAG
1 TTAGAGTGTAAAACCCTCAATTCCCACAAAATGAAACCATAACAGAAGCAGGAAGGAAAAGGGAG
3028502 CTAATAAGCATTAGTATTAAAGATTTGCAGTTAGATCAGAAGAAAATATAATAATTTAACCATTT
66 CTAATAAGCATTAGTATTAAAGATTTGCAGTTAGATCAGAAGAAAATATAATAATTTAACCATTT
3028567 CTCTAATGATCTTCTATGTTCTTAGGACTGGGAGCAATGTTTATATGGGAAAAGGACTT
131 CTCTAATGATCTTCTATGTTCTTAGGACTGGGAGCAATGTTTATATGGGAAAAGGACTT
3028626 T
1 T
3028627 AACAAATTCA
Statistics
Matches: 189, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
188 17 0.09
189 172 0.91
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (189 bp):
TTAGAGTGTAAAACCCTCAATTCCCACAAAATGAAACCATAACAGAAGCAGGAAGGAAAAGGGAG
CTAATAAGCATTAGTATTAAAGATTTGCAGTTAGATCAGAAGAAAATATAATAATTTAACCATTT
CTCTAATGATCTTCTATGTTCTTAGGACTGGGAGCAATGTTTATATGGGAAAAGGACTT
Found at i:3030060 original size:20 final size:20
Alignment explanation
Indices: 3029966--3030334 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
3029956 GATTTTCCAT
* ** *
3029966 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
3029986 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
3030006 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3030026 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
3030046 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
3030066 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3030086 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3030106 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
3030126 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3030146 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3030166 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3030186 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3030206 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
3030226 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3030246 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3030266 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3030286 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3030306 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3030326 AATCACAAC
1 AATCGCAAC
3030335 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:3031243 original size:12 final size:12
Alignment explanation
Indices: 3031226--3031250 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3031216 ATATAATCCT
3031226 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3031238 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3031250 G
1 G
3031251 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3033399 original size:19 final size:19
Alignment explanation
Indices: 3033377--3033702 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
3033367 CGGAAAATAC
*
3033377 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3033396 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
3033410 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
3033430 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3033444 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3033463 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3033482 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3033496 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3033515 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3033534 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3033548 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3033567 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
3033586 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
3033605 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3033624 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3033643 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
3033657 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3033676 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3033695 AATCGCAA
1 AATCGCAA
3033703 CGAGATAATC
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 50 0.19
15 3 0.01
16 13 0.05
17 12 0.04
18 4 0.01
19 174 0.65
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3033464 original size:33 final size:34
Alignment explanation
Indices: 3033377--3033702 Score: 321
Period size: 33 Copynumber: 9.2 Consensus size: 34
3033367 CGGAAAATAC
* *
3033377 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
3033410 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
3033444 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
3033482 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
3033515 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
3033548 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
3033586 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
3033624 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
3033656 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
3033695 AATCGCAA
1 AATCGCAA
3033703 CGAGATAATC
Statistics
Matches: 257, Mismatches: 12, Indels: 43
0.82 0.04 0.14
Matches are distributed among these distances:
32 2 0.01
33 111 0.43
34 32 0.12
35 9 0.04
36 6 0.02
37 4 0.02
38 91 0.35
39 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:3033638 original size:161 final size:157
Alignment explanation
Indices: 3033405--3033724 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
3033395 AAATCCCAAC
*
3033405 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
3033470 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
66 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
3033535 ATCGCAACGAGAGAATCGCAATGCGAA
131 ATCGCAACGAGAGAATCGCAATGCGAA
*
3033562 ATGAAAATCGCAATGC-GAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGC-A-ACG--A-GAAAATCGCAATGCGAAATGAAAA
3033626 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
61 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
*
3033691 TGAAAATCGCAACGAGATAATCGCAATGCGAA
126 TGAAAATCGCAACGAGAGAATCGCAATGCGAA
3033723 AT
1 AT
3033725 TATAAACGCA
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 13 0.08
157 17 0.11
158 3 0.02
160 1 0.01
161 120 0.78
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (157 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
ATCGCAACGAGAGAATCGCAATGCGAA
Found at i:3033740 original size:52 final size:52
Alignment explanation
Indices: 3033405--3033724 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
3033395 AAATCCCAAC
3033405 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3033458 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3033510 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
3033562 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
3033619 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
3033671 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3033723 AT
1 AT
3033725 TATAAACGCA
Statistics
Matches: 255, Mismatches: 7, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
52 184 0.72
53 18 0.07
54 3 0.01
55 3 0.01
56 2 0.01
57 45 0.18
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:3033840 original size:19 final size:19
Alignment explanation
Indices: 3033731--3033832 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
3033721 AAATTATAAA
3033731 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3033750 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
3033770 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
3033786 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3033803 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
3033822 CGCATTGCGAT
1 CGCATTGCGAT
3033833 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:3033957 original size:14 final size:14
Alignment explanation
Indices: 3033938--3033974 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3033928 CATCAATTAC
3033938 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3033952 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3033966 ACAAATCAA
1 ACAAATCAA
3033975 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3034002 original size:37 final size:37
Alignment explanation
Indices: 3033955--3034025 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
3033945 AACTTTTACA
*
3033955 AATCATCTTTTACAAATCAATTAAACAATCAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAATTG
3033992 AATCAACTTTTACAAATCAATTAAACAATCAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAA
3034026 AACAATCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.52, C:0.17, G:0.01, T:0.30
Consensus pattern (37 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAATTG
Found at i:3034033 original size:37 final size:37
Alignment explanation
Indices: 3033955--3034034 Score: 124
Period size: 37 Copynumber: 2.2 Consensus size: 37
3033945 AACTTTTACA
* ***
3033955 AATCATCTTTTACAAATCAATTAAACAATCAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
3033992 AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
3034029 AATCAA
1 AATCAA
3034035 TTAAACTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.28
Consensus pattern (37 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAAAC
Found at i:3035902 original size:14 final size:14
Alignment explanation
Indices: 3035883--3035939 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3035873 GCGAAATGAA
*
3035883 AATCGCAACGACAG
1 AATCGCAACGAAAG
3035897 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
3035914 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
3035930 AATCGCAACG
1 AATCGCAACG
3035940 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3035910 original size:33 final size:33
Alignment explanation
Indices: 3035864--3035956 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3035854 GCGAAACCAA
*
3035864 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
3035897 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3035930 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3035957 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3035921 original size:19 final size:19
Alignment explanation
Indices: 3035827--3035961 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3035817 TAGTTTACTT
* *
3035827 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3035847 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3035866 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3035885 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
3035899 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
3035918 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
3035932 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3035951 TCGCAATGCGA
1 TCGCAACGCGA
3035962 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3035979 original size:19 final size:19
Alignment explanation
Indices: 3035957--3036085 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3035947 AAAATCGCAA
3035957 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3035976 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3035990 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3036009 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
3036023 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3036042 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3036061 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3036081 TGCGA
1 TGCGA
3036086 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3035999 original size:33 final size:33
Alignment explanation
Indices: 3035957--3036048 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
3035947 AAAATCGCAA
3035957 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
3035990 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
3036023 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
3036049 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3036513 original size:92 final size:93
Alignment explanation
Indices: 3036129--3036599 Score: 903
Period size: 93 Copynumber: 5.1 Consensus size: 93
3036119 TTGAATGGAT
3036129 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3036194 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3036222 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3036287 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3036315 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3036378 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3036406 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3036470 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3036498 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
* *
3036563 AGTTTAGCAGAATTGGTAGCAACCAAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3036591 AAATTTACT
1 AAATTTACT
3036600 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
91 91 0.24
92 91 0.24
93 192 0.51
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3038323 original size:14 final size:14
Alignment explanation
Indices: 3038304--3038393 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3038294 TTGAAATGAA
3038304 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3038318 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
3038335 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
3038351 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3038370 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3038384 AATCGCAACG
1 AATCGCAACG
3038394 CGAAACCAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3038341 original size:33 final size:33
Alignment explanation
Indices: 3038296--3038410 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
3038286 TCTTTTGGTT
3038296 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
3038329 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3038362 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
3038395 GAAACCAAAATCGCAA
1 GAAATGAAAATCGCAA
3038411 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3038446 original size:14 final size:14
Alignment explanation
Indices: 3038427--3038481 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3038417 TTTGGTTTCG
3038427 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3038441 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3038460 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3038474 CGTTGCGA
1 CGTTGCGA
3038482 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3038459 original size:33 final size:33
Alignment explanation
Indices: 3038411--3038481 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3038401 AAAATCGCAA
**
3038411 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3038444 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3038477 TGCGA
1 TGCGA
3038482 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:3038489 original size:33 final size:33
Alignment explanation
Indices: 3038422--3038503 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
3038412 GCGATTTTGG
***
3038422 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
3038455 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
3038488 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
3038504 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:3038508 original size:20 final size:20
Alignment explanation
Indices: 3038434--3038522 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
3038424 TCGCGTTGCG
3038434 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
3038454 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
3038467 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
3038487 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
3038507 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
3038523 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:3038644 original size:33 final size:33
Alignment explanation
Indices: 3038602--3038672 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3038592 AATACTAACT
*
3038602 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
3038635 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
3038668 TGAAA
1 TGAAA
3038673 TCTAAGTGAA
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:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3038906 original size:22 final size:22
Alignment explanation
Indices: 3038854--3038908 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3038844 TGGTTGTGAG
**
3038854 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3038876 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3038898 GGATTTCTTCG
1 GGATTTCTTCG
3038909 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3039079 original size:20 final size:20
Alignment explanation
Indices: 3039054--3039247 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
3039044 CTTTAAATAT
3039054 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3039074 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3039096 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3039115 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3039135 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3039155 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3039175 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3039195 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3039215 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3039235 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3039248 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3039241 original size:60 final size:60
Alignment explanation
Indices: 3039054--3039247 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
3039044 CTTTAAATAT
**
3039054 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
3039115 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
3039175 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
3039235 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3039248 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:3039264 original size:21 final size:20
Alignment explanation
Indices: 3039240--3039316 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
3039230 ATATTCGCGT
3039240 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
3039261 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
3039281 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
3039303 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
3039317 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:3039327 original size:20 final size:20
Alignment explanation
Indices: 3039302--3039353 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3039292 AAGAATCGCG
*
3039302 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3039322 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
3039342 TTGCGATTCTGG
1 TTGCGATTCTGG
3039354 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:3040126 original size:14 final size:14
Alignment explanation
Indices: 3040107--3040140 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
3040097 TCGAGATATG
3040107 TTGAAGGACGGACA
1 TTGAAGGACGGACA
3040121 TTGAAGGACGGACA
1 TTGAAGGACGGACA
3040135 TTGAAG
1 TTGAAG
3040141 AACCAACTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.18
Consensus pattern (14 bp):
TTGAAGGACGGACA
Found at i:3041858 original size:5 final size:5
Alignment explanation
Indices: 3041848--3041874 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3041838 CGGTCAGCGT
3041848 TCGGG TCGGG TCGGG TCGGG TCGGG TC
1 TCGGG TCGGG TCGGG TCGGG TCGGG TC
3041875 AGACCGGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.22, G:0.56, T:0.22
Consensus pattern (5 bp):
TCGGG
Found at i:3041917 original size:11 final size:10
Alignment explanation
Indices: 3041895--3041931 Score: 58
Period size: 11 Copynumber: 3.7 Consensus size: 10
3041885 GACTGGTTCG
3041895 AACCGGTCAA
1 AACCGGTCAA
3041905 AACCGGTTCAA
1 AACCGG-TCAA
3041916 AACCGGTC-A
1 AACCGGTCAA
3041925 AACCGGT
1 AACCGGT
3041932 TTTCCAGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 8 0.31
10 8 0.31
11 10 0.38
ACGTcount: A:0.35, C:0.30, G:0.22, T:0.14
Consensus pattern (10 bp):
AACCGGTCAA
Found at i:3041927 original size:20 final size:19
Alignment explanation
Indices: 3041877--3041932 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
3041867 GTCGGGTCAG
* * *
3041877 ACCGGTCAGACTGGTTCGA
1 ACCGGTCAAACCGGTTCAA
3041896 ACCGGTCAAAACCGGTTCAAA
1 ACCGGTC-AAACCGGTTC-AA
3041917 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
3041933 TTCCAGCTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.22
20 17 0.53
21 8 0.25
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.18
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAA
Found at i:3041929 original size:9 final size:9
Alignment explanation
Indices: 3041871--3041931 Score: 50
Period size: 9 Copynumber: 6.3 Consensus size: 9
3041861 GGTCGGGTCG
*
3041871 GGTCAGACC
1 GGTCAAACC
* *
3041880 GGTCAGACT
1 GGTCAAACC
*
3041889 GGTTCGAACC
1 GG-TCAAACC
3041899 GGTCAAAACC
1 GGTC-AAACC
3041909 GGTTCAAAACC
1 GG-TC-AAACC
3041920 GGTCAAACC
1 GGTCAAACC
3041929 GGT
1 GGT
3041932 TTTCCAGCTG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 20 0.45
10 14 0.32
11 10 0.23
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:3049083 original size:5 final size:5
Alignment explanation
Indices: 3049073--3049111 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
3049063 CGGTCAACGT
*
3049073 TCGGG TCGGG TCAACGG TCGGG TCGGG TCGGG TCGGG TC
1 TCGGG TCGGG TC--GGG TCGGG TCGGG TCGGG TCGGG TC
3049112 AGACCGGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 26 0.87
7 4 0.13
ACGTcount: A:0.05, C:0.23, G:0.51, T:0.21
Consensus pattern (5 bp):
TCGGG
Found at i:3049086 original size:17 final size:17
Alignment explanation
Indices: 3049064--3049101 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
3049054 AACGGTCAAC
*
3049064 GGTCAACGTTCGGGTCG
1 GGTCAACGGTCGGGTCG
3049081 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
3049098 GGTC
1 GGTC
3049102 GGGTCGGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.24, G:0.45, T:0.21
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:3049126 original size:9 final size:9
Alignment explanation
Indices: 3049108--3049147 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
3049098 GGTCGGGTCG
*
3049108 GGTCAGACC
1 GGTCAAACC
3049117 GGTCAAACC
1 GGTCAAACC
*
3049126 GATCGAAACC
1 GGTC-AAACC
3049136 GGTCAAACC
1 GGTCAAACC
3049145 GGT
1 GGT
3049148 TTTCCAGCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.30, C:0.30, G:0.28, T:0.12
Consensus pattern (9 bp):
GGTCAAACC
Found at i:3052394 original size:12 final size:13
Alignment explanation
Indices: 3052360--3052402 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
3052350 ATTTTCTATA
3052360 TTAATTATAATCC
1 TTAATTATAATCC
*
3052373 TTATATTATAAT-T
1 TTA-ATTATAATCC
*
3052386 TTAATTATAATCA
1 TTAATTATAATCC
3052399 TTAA
1 TTAA
3052403 ATTAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 8 0.31
13 10 0.38
14 8 0.31
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAATTATAATCC
Found at i:3052874 original size:21 final size:21
Alignment explanation
Indices: 3052823--3052875 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3052813 ATTCTGACTA
*
3052823 TCGCATTGCAATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
3052844 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
3052865 TCGCAATGCGA
1 TCGCATTGCGA
3052876 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:3052893 original size:20 final size:20
Alignment explanation
Indices: 3052868--3052906 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3052858 TCCTAATTCG
*
3052868 CAATGCGAATACGTAAATCA
1 CAATGCGAATACATAAATCA
3052888 CAATGCGAATACATAAATC
1 CAATGCGAATACATAAATC
3052907 GCAACACGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.21
Consensus pattern (20 bp):
CAATGCGAATACATAAATCA
Found at i:3052916 original size:20 final size:20
Alignment explanation
Indices: 3052873--3052917 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3052863 ATTCGCAATG
* **
3052873 CGAATACGTAAATCACAATG
1 CGAATACATAAATCACAACA
*
3052893 CGAATACATAAATCGCAACA
1 CGAATACATAAATCACAACA
3052913 CGAAT
1 CGAAT
3052918 CTGACTATCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.22, G:0.13, T:0.18
Consensus pattern (20 bp):
CGAATACATAAATCACAACA
Found at i:3053139 original size:22 final size:22
Alignment explanation
Indices: 3053114--3053179 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
3053104 GGCGACATCC
3053114 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
3053136 GTCCCCATCTCCAACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
3053158 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
3053180 TTCACAGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.26, C:0.39, G:0.14, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:3053558 original size:20 final size:20
Alignment explanation
Indices: 3053516--3053585 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
3053506 CGATTCTGTC
*
3053516 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
**
3053535 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
3053555 GTTGCGGTTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
3053575 GTTGTGATTTT
1 GTTGCGATTTT
3053586 AAGTTTCAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 11 0.26
20 31 0.74
ACGTcount: A:0.10, C:0.14, G:0.24, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:3055479 original size:20 final size:20
Alignment explanation
Indices: 3055454--3055610 Score: 90
Period size: 20 Copynumber: 8.5 Consensus size: 20
3055444 AGAATAGTTT
3055454 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
3055474 ACTATCGCAAAGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
3055494 ACTATCGC-A-GCG--AGGG
1 ACTATCGCAATGCGAAAATG
3055510 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
** *
3055527 AAAATCGC-AT--TAACAA--
1 ACTATCGCAATGCGAA-AATG
*
3055543 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* **
3055561 ACTATCGCAATGTGAATTTG
1 ACTATCGCAATGCGAAAATG
**
3055581 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
*
3055601 ACTACCGCAA
1 ACTATCGCAA
3055611 CGAAAGAATC
Statistics
Matches: 109, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
14 10 0.09
15 2 0.02
16 9 0.08
17 6 0.06
18 8 0.07
19 6 0.06
20 68 0.62
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:3055523 original size:34 final size:34
Alignment explanation
Indices: 3055477--3055569 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 34
3055467 GAAAATGACT
* ***
3055477 ATCGCAAAGCGAAAATGACTATCGCAGCGAGGGA
1 ATCGCAAAGCGAAAATGACTATCGCAGCAACAAA
* ** **
3055511 ATCGCAATGCG-AAATGAAAATCGCATTAACAAA
1 ATCGCAAAGCGAAAATGACTATCGCAGCAACAAA
*
3055544 ATCGCAACGCGAAAATGACTATCGCA
1 ATCGCAAAGCGAAAATGACTATCGCA
3055570 ATGTGAATTT
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
33 24 0.52
34 22 0.48
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.15
Consensus pattern (34 bp):
ATCGCAAAGCGAAAATGACTATCGCAGCAACAAA
Found at i:3055739 original size:20 final size:20
Alignment explanation
Indices: 3055677--3055743 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
3055667 CAAATTCACA
*
3055677 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCG
**
3055697 TTATGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
*
3055717 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCATTTTCGCG
3055737 TTGCGAT
1 TTGCGAT
3055744 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.43
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:3057735 original size:14 final size:14
Alignment explanation
Indices: 3057716--3057751 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3057706 ATTGTTTAAT
3057716 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3057730 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3057744 TGATTTGT
1 TGATTTGT
3057752 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3057907 original size:33 final size:33
Alignment explanation
Indices: 3057857--3057952 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
3057847 AAAACAGACT
* **
3057857 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
3057891 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3057924 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
3057953 CGAATTTAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 31 0.55
34 25 0.45
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3058024 original size:33 final size:33
Alignment explanation
Indices: 3057967--3058062 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
3057957 TTTAGTTTCG
*
3057967 CGTTGCGATTTTCATTTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
3058001 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
3058034 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
3058063 AGTCATATTC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 33 0.58
34 24 0.42
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:3058059 original size:20 final size:20
Alignment explanation
Indices: 3058034--3058082 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
3058024 GCGATTCTCT
*
3058034 CGTTGCGATAGTCAT-TTCCG
1 CGTTGCGATAGTCATATT-CA
3058054 CGTTGCGATAGTCATATTCA
1 CGTTGCGATAGTCATATTCA
3058074 CGTTGCGAT
1 CGTTGCGAT
3058083 TTCCGCGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATATTCA
Found at i:3060546 original size:24 final size:24
Alignment explanation
Indices: 3060512--3060565 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3060502 CTGAAAAATC
3060512 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* * *
3060536 ATCAAAGTCTGGGTATTGACTAAG
1 ATCAAAATCTGAGTATTGACCAAG
3060560 ATCAAA
1 ATCAAA
3060566 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:3061433 original size:20 final size:20
Alignment explanation
Indices: 3061408--3061454 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
3061398 AAATTCAATA
*
3061408 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
3061428 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
3061448 TTGCGAT
1 TTGCGAT
3061455 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:3061494 original size:21 final size:21
Alignment explanation
Indices: 3061470--3061515 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3061460 TATTCGCATT
*
3061470 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCACAAC
* *
3061491 GCGAATTTGGAAAATCACAAT
1 GCGAATTAGGAAAATCACAAC
3061512 GCGA
1 GCGA
3061516 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCACAAC
Found at i:3061797 original size:12 final size:12
Alignment explanation
Indices: 3061766--3061800 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3061756 ATTTCAAGCG
* *
3061766 TAAATTTCAATG
1 TAAATTTTAATA
3061778 TAAATTTTAATA
1 TAAATTTTAATA
3061790 TAAATTTTAAT
1 TAAATTTTAAT
3061801 TTTATCTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (12 bp):
TAAATTTTAATA
Found at i:3061824 original size:23 final size:23
Alignment explanation
Indices: 3061786--3061839 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
3061776 TGTAAATTTT
* *
3061786 AATATAAATTTTAATTTTATCTCA
1 AATAT-AATTTAAATTTTAGCTCA
3061810 AATATAATTTAAATTTTAGCTCA
1 AATATAATTTAAATTTTAGCTCA
*
3061833 AGTATAA
1 AATATAA
3061840 ATAAGAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (23 bp):
AATATAATTTAAATTTTAGCTCA
Found at i:3061907 original size:29 final size:29
Alignment explanation
Indices: 3061870--3061927 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
3061860 TACTTTAATA
*
3061870 TTTAAATTTATAA-ATTTATTTATATATAT
1 TTTAAATTTATAATATAT-TTTATATATAT
* *
3061899 TTTATATTTATACTATATTTTATATATAT
1 TTTAAATTTATAATATATTTTATATATAT
3061928 GTGTGTATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTAAATTTATAATATATTTTATATATAT
Found at i:3061917 original size:18 final size:17
Alignment explanation
Indices: 3061886--3061923 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
3061876 TTTATAAATT
3061886 TATTTATATATATTTTA
1 TATTTATATATATTTTA
3061903 TATTTATACTATATTTTA
1 TATTTATA-TATATTTTA
3061921 TAT
1 TAT
3061924 ATATGTGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTATATATATTTTA
Found at i:3065875 original size:21 final size:20
Alignment explanation
Indices: 3065837--3065875 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3065827 ATGTCATATA
3065837 AAGGATAGGATTTTGAGTTT
1 AAGGATAGGATTTTGAGTTT
3065857 AAGGA-AGTGATTATTGAGT
1 AAGGATAG-GATT-TTGAGT
3065876 AGGAATGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 9 0.53
21 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (20 bp):
AAGGATAGGATTTTGAGTTT
Found at i:3073474 original size:21 final size:21
Alignment explanation
Indices: 3073448--3073510 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
3073438 GTCGAGGGTT
3073448 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
*
3073469 TCATAGGTCCTTCAGGACATAC
1 TCATAGGTCCTTCGGGACA-AC
* *
3073491 TCACAGGTCCTTCGAGACAA
1 TCATAGGTCCTTCGGGACAA
3073511 TTTCATATGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:3073509 original size:22 final size:21
Alignment explanation
Indices: 3073452--3073510 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
3073442 AGGGTTTCAT
* *
3073452 AGGTCCTTCGGGACAACTCAT
1 AGGTCCTTCGAGACAACTCAC
3073473 AGGTCCTTC-AGGACATACTCAC
1 AGGTCCTTCGA-GACA-ACTCAC
3073495 AGGTCCTTCGAGACAA
1 AGGTCCTTCGAGACAA
3073511 TTTCATATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 14 0.42
22 18 0.55
23 1 0.03
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (21 bp):
AGGTCCTTCGAGACAACTCAC
Found at i:3074826 original size:63 final size:63
Alignment explanation
Indices: 3074733--3074851 Score: 166
Period size: 63 Copynumber: 1.9 Consensus size: 63
3074723 CCAAGACCAA
* * ** * *
3074733 CAGCATCAACTACATTTTTAGTAACCCTCTCAGCAGCGTAATCACCAGCACCCTCATCAAGAC
1 CAGCAGCAACTACATTTTTAGCAACCCTCTCAGCAGCACAATCAACAACACCCTCATCAAGAC
* *
3074796 CAGCAGCAATTACATTTTTAGCAACCCTCTCAGTAGCACAATCAACAACACCCTCA
1 CAGCAGCAACTACATTTTTAGCAACCCTCTCAGCAGCACAATCAACAACACCCTCA
3074852 CCAACACCCT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.34, C:0.34, G:0.10, T:0.22
Consensus pattern (63 bp):
CAGCAGCAACTACATTTTTAGCAACCCTCTCAGCAGCACAATCAACAACACCCTCATCAAGAC
Found at i:3076365 original size:2 final size:2
Alignment explanation
Indices: 3076352--3076409 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
3076342 TTTGATACTT
3076352 TA TA TA -A T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3076392 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
3076410 AGTTTATAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3076526 original size:22 final size:22
Alignment explanation
Indices: 3076501--3076550 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
3076491 TAATACTTCA
* *
3076501 ATTTATTAATTTATTTTTATAT
1 ATTTATTAATTTATATTCATAT
* *
3076523 ATTTAATACTTTATATTCATAT
1 ATTTATTAATTTATATTCATAT
*
3076545 ACTTAT
1 ATTTAT
3076551 ACTTAAATAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTATTAATTTATATTCATAT
Found at i:3076586 original size:2 final size:2
Alignment explanation
Indices: 3076581--3076685 Score: 64
Period size: 2 Copynumber: 53.5 Consensus size: 2
3076571 TTATATACTT
*
3076581 TA TA TA TA TA TA TA T- TG TA TA CT- TA TA CTA TA TA CT- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA
* * *
3076621 TT TA -A TA AA TA TA T- TA TA CT- TA TA CTT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA
3076662 TA TA TA TA TA TA CT- TA TA -A TA TA T
1 TA TA TA TA TA TA -TA TA TA TA TA TA T
3076686 GCATAAGTAT
Statistics
Matches: 82, Mismatches: 7, Indels: 28
0.70 0.06 0.24
Matches are distributed among these distances:
1 8 0.10
2 67 0.82
3 7 0.09
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3076592 original size:24 final size:24
Alignment explanation
Indices: 3076518--3076667 Score: 76
Period size: 24 Copynumber: 6.6 Consensus size: 24
3076508 AATTTATTTT
3076518 TATATA-TTTA-ATACTTTATAT-
1 TATATACTTTATATACTTTATATA
*
3076539 TCATATAC--T-TATACTTAAATATA
1 T-ATATACTTTATATACTT-TATATA
*
3076562 TTTTATACTTTATATACTTTATATA
1 -TATATACTTTATATACTTTATATA
* *
3076587 TATATA-TATTGTATAC-TTATA-C
1 TATATACT-TTATATACTTTATATA
* * **
3076609 TATATACTTATATTTAATAAATATA
1 TATATACTT-TATATACTTTATATA
3076634 T-TATAC--T-TATACTTTATATA
1 TATATACTTTATATACTTTATATA
*
3076654 TATATA-TATATATA
1 TATATACTTTATATA
3076668 TATATACTTA
Statistics
Matches: 95, Mismatches: 16, Indels: 34
0.66 0.11 0.23
Matches are distributed among these distances:
20 10 0.11
21 13 0.14
22 17 0.18
23 20 0.21
24 21 0.22
25 7 0.07
26 7 0.07
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (24 bp):
TATATACTTTATATACTTTATATA
Found at i:3076664 original size:69 final size:70
Alignment explanation
Indices: 3076518--3076662 Score: 183
Period size: 69 Copynumber: 2.1 Consensus size: 70
3076508 AATTTATTTT
* * *
3076518 TATATATTTAATACTTTATATTCATATACTTATACTTAAATATATTTTATACTTTATATACTTTA
1 TATATATTTAATACTTTATACTCATATACTTATACTTAAAAATATATTATACTTTATATA-TTTA
3076583 TATATA
65 TATATA
* *
3076589 TATATATTGT-ATAC-TTATACT-ATATACTTATATTTAATAAATATATTATAC-TTATA-CTTT
1 TATATATT-TAATACTTTATACTCATATACTTATACTTAA-AAATATATTATACTTTATATATTT
3076649 ATATATA
64 ATATATA
3076656 TATATAT
1 TATATAT
3076663 ATATATATAT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
67 17 0.25
69 20 0.30
70 17 0.25
71 12 0.18
72 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (70 bp):
TATATATTTAATACTTTATACTCATATACTTATACTTAAAAATATATTATACTTTATATATTTAT
ATATA
Found at i:3076685 original size:13 final size:13
Alignment explanation
Indices: 3076572--3076685 Score: 56
Period size: 13 Copynumber: 9.4 Consensus size: 13
3076562 TTTTATACTT
3076572 TATATACTT-T-A
1 TATATACTTATAA
*
3076583 TATATA-TATATAT
1 TATATACT-TATAA
* *
3076596 TGTATACTTATAC
1 TATATACTTATAA
3076609 TATATACTTAT-A
1 TATATACTTATAA
3076621 T-T-TA---ATAA
1 TATATACTTATAA
*
3076629 -ATATA-TTATAC
1 TATATACTTATAA
3076640 T-TATACTTTATATA
1 TATATAC-TTATA-A
3076654 TATATA-TATATATA
1 TATATACT-TATA-A
3076668 TATATACTTATAA
1 TATATACTTATAA
3076681 TATAT
1 TATAT
3076686 GCATAAGTAT
Statistics
Matches: 80, Mismatches: 7, Indels: 30
0.68 0.06 0.26
Matches are distributed among these distances:
7 2 0.03
8 2 0.03
9 2 0.03
10 3 0.04
11 15 0.19
12 2 0.03
13 31 0.39
14 18 0.22
15 5 0.06
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (13 bp):
TATATACTTATAA
Found at i:3076761 original size:2 final size:2
Alignment explanation
Indices: 3076745--3076780 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
3076735 TTCATCATAC
3076745 AT AT -T AT AT AT -T AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3076781 ATTGTTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3077772 original size:41 final size:41
Alignment explanation
Indices: 3077656--3077774 Score: 136
Period size: 41 Copynumber: 2.9 Consensus size: 41
3077646 CAACAAAGTA
* * *
3077656 GTACTTTAGTGGT-GTTTTTATCCAAACGTCGCTAAAGACTC
1 GTACTTTAGT-GTCGTTTTTATACAAACGCCGCTATAGACTC
* * *
3077697 GTACTTTAGCAG-CATTTGTATACAAACGCCGCTATAGAC-C
1 GTACTTTAG-TGTCGTTTTTATACAAACGCCGCTATAGACTC
3077737 TGTACTTTAGTGTCGTTTTTATACAAACGCCGCTATAG
1 -GTACTTTAGTGTCGTTTTTATACAAACGCCGCTATAG
3077775 TTTATAATTT
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
40 2 0.03
41 63 0.97
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (41 bp):
GTACTTTAGTGTCGTTTTTATACAAACGCCGCTATAGACTC
Found at i:3080901 original size:43 final size:41
Alignment explanation
Indices: 3080854--3081099 Score: 222
Period size: 43 Copynumber: 5.8 Consensus size: 41
3080844 TAATGAGCCT
* *
3080854 TTTTGCGGTGTTTGTATCAAAAAACGCCACTATAGATATGATC
1 TTTTGCGGTGTTTGT-TCCAAAAACGCCGCTATAGATATGA-C
* * ** *
3080897 TTTTGCGGAGTTTGTTTCAAAAAATACCGCTATAGATCTGAC
1 TTTTGCGGTGTTTG-TTCCAAAAACGCCGCTATAGATATGAC
* * * *
3080939 ATTTTGCGTTGTTTGTTCCAAAAATGCCGCTATAAATCTGACC
1 -TTTTGCGGTGTTTGTTCCAAAAACGCCGCTATAGATATGA-C
* * * * *
3080982 TTTTGCGATATTTATTCCAAAAACGTCGTTATAGATATTGAC
1 TTTTGCGGTGTTTGTTCCAAAAACGCCGCTATAGATA-TGAC
* * * *
3081024 TTTTTACGGCGTTTATTCCAAAAACGCCACTATAGATATCGATC
1 -TTTTGCGGTGTTTGTTCCAAAAACGCCGCTATAGATAT-GA-C
*
3081068 TTTTGCGGCGTTTGTTCCAAAAACGCCGCTAT
1 TTTTGCGGTGTTTGTTCCAAAAACGCCGCTAT
3081100 GATCTTGACC
Statistics
Matches: 168, Mismatches: 28, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
42 55 0.33
43 111 0.66
44 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (41 bp):
TTTTGCGGTGTTTGTTCCAAAAACGCCGCTATAGATATGAC
Found at i:3081120 original size:85 final size:86
Alignment explanation
Indices: 3080854--3081122 Score: 253
Period size: 85 Copynumber: 3.2 Consensus size: 86
3080844 TAATGAGCCT
* * * *
3080854 TTTTGCGGTGTTTGTATCAAAAAACGCCACTATAGATAT-GATCTTTTGCGGAGTTTGTTTCAAA
1 TTTTGCGGCGTTTAT-TCCAAAAACGCCACTATAGATATCGATCTTTTGCGGAGTTTG-TTCCAA
**
3080918 AAATACCGCTATAGATC-TGACA
64 AAACGCCGCTATAGATCTTGACA
** * * * * * *
3080940 TTTTGCGTTGTTTGTTCCAAAAATGCCGCTATA-A-ATCTGACCTTTTGC-GATATTTATTCCAA
1 TTTTGCGGCGTTTATTCCAAAAACGCCACTATAGATATC-GATCTTTTGCGGA-GTTTGTTCCAA
* * * *
3081002 AAACGTCGTTATAGATATTGACT
64 AAACGCCGCTATAGATCTTGACA
* *
3081025 TTTTACGGCGTTTATTCCAAAAACGCCACTATAGATATCGATCTTTTGCGGCGTTTGTTCCAAAA
1 TTTTGCGGCGTTTATTCCAAAAACGCCACTATAGATATCGATCTTTTGCGGAGTTTGTTCCAAAA
*
3081090 ACGCCGCTAT-GATCTTGACC
66 ACGCCGCTATAGATCTTGACA
* *
3081110 TATTGTGGCGTTT
1 TTTTGCGGCGTTT
3081123 TTTGTTCTCA
Statistics
Matches: 145, Mismatches: 31, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
83 2 0.01
84 20 0.14
85 76 0.52
86 43 0.30
87 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (86 bp):
TTTTGCGGCGTTTATTCCAAAAACGCCACTATAGATATCGATCTTTTGCGGAGTTTGTTCCAAAA
ACGCCGCTATAGATCTTGACA
Found at i:3085862 original size:32 final size:32
Alignment explanation
Indices: 3085808--3085873 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 32
3085798 AAATTTTAAG
3085808 ATTTTAAAATAATAATTCTTAAATTTTATTAAATT
1 ATTTTAAAATAATAA-T-TTAAA-TTTATTAAATT
*
3085843 ATTTTAAAATAATCA-TTAAATTTATTAAATT
1 ATTTTAAAATAATAATTTAAATTTATTAAATT
3085874 TTACACTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 11 0.37
32 5 0.17
35 14 0.47
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
ATTTTAAAATAATAATTTAAATTTATTAAATT
Found at i:3090818 original size:13 final size:13
Alignment explanation
Indices: 3090800--3090830 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3090790 AAGTTTGCAC
3090800 TCCTAGCATAAAT
1 TCCTAGCATAAAT
3090813 TCCTAGCATAAAT
1 TCCTAGCATAAAT
3090826 TCCTA
1 TCCTA
3090831 CATCGGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (13 bp):
TCCTAGCATAAAT
Found at i:3106240 original size:13 final size:13
Alignment explanation
Indices: 3106222--3106246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3106212 TACAGACGTG
3106222 CATATGAAGATTA
1 CATATGAAGATTA
3106235 CATATGAAGATT
1 CATATGAAGATT
3106247 GTTCAACTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
CATATGAAGATTA
Found at i:3111167 original size:14 final size:14
Alignment explanation
Indices: 3111134--3111168 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3111124 CTATCAACAT
3111134 AAATGAATTTAAAC
1 AAATGAATTTAAAC
* *
3111148 AGATGAATTTAAAG
1 AAATGAATTTAAAC
3111162 AAATGAA
1 AAATGAA
3111169 CAAAAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.14, T:0.26
Consensus pattern (14 bp):
AAATGAATTTAAAC
Found at i:3113616 original size:21 final size:21
Alignment explanation
Indices: 3113525--3113616 Score: 51
Period size: 21 Copynumber: 4.2 Consensus size: 21
3113515 TAGTTTATAA
3113525 TTAGAATTTATATTAGAAATG
1 TTAGAATTTATATTAGAAATG
** * * * *
3113546 TTAGGGTTAATTATTCGTAAGG
1 TTAGAATTTA-TATTAGAAATG
** *
3113568 TCTAGTATATTTAGCTTAGTATAT-
1 T-TAG-A-ATTTATATTAG-AAATG
3113592 TTAGAATTTATATTAGAAATG
1 TTAGAATTTATATTAGAAATG
3113613 TTAG
1 TTAG
3113617 GGTTAATTAT
Statistics
Matches: 47, Mismatches: 18, Indels: 12
0.61 0.23 0.16
Matches are distributed among these distances:
20 3 0.06
21 20 0.43
22 10 0.21
23 6 0.13
24 4 0.09
25 4 0.09
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (21 bp):
TTAGAATTTATATTAGAAATG
Found at i:3113655 original size:67 final size:67
Alignment explanation
Indices: 3113520--3113662 Score: 173
Period size: 67 Copynumber: 2.1 Consensus size: 67
3113510 AGGTTTAGTT
* * * * *
3113520 TATAATTAGAATTTATATTAGAAATGTTAGGGTTAATTATTCGTAAGGTCTAGTATATTTAGCTT
1 TATATTTAGAATTTATATTAGAAATGTTAGGGTTAATTATTCGTAAAGTCTAGTAGAGTGAGCTT
3113585 AG
66 AG
* * * *
3113587 TATATTTAGAATTTATATTAGAAATGTTAGGGTTAATTATT-TTAGAAGT-TATTAGCGTGAGGT
1 TATATTTAGAATTTATATTAGAAATGTTAGGGTTAATTATTCGTA-AAGTCTAGTAGAGTGAGCT
3113650 CTAG
65 -TAG
3113654 TATATTTAG
1 TATATTTAG
3113663 CTTAGTATAT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
66 10 0.15
67 55 0.85
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (67 bp):
TATATTTAGAATTTATATTAGAAATGTTAGGGTTAATTATTCGTAAAGTCTAGTAGAGTGAGCTT
AG
Found at i:3118436 original size:19 final size:19
Alignment explanation
Indices: 3118412--3118448 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3118402 TGACTAAATT
3118412 AGCCG-CCCATTAATGTTGA
1 AGCCGCCCCATT-ATGTTGA
3118431 AGCCGCCCCATTATGTTG
1 AGCCGCCCCATTATGTTG
3118449 CTTTGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (19 bp):
AGCCGCCCCATTATGTTGA
Found at i:3123813 original size:7 final size:7
Alignment explanation
Indices: 3123801--3123827 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3123791 ACTTTTTTAA
3123801 AAAATTT
1 AAAATTT
3123808 AAAATTT
1 AAAATTT
3123815 AAAATTT
1 AAAATTT
3123822 AAAATT
1 AAAATT
3123828 GTTTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAAATTT
Found at i:3126592 original size:45 final size:45
Alignment explanation
Indices: 3126542--3126637 Score: 174
Period size: 45 Copynumber: 2.1 Consensus size: 45
3126532 TGAGATTTGC
*
3126542 ATGTTAATTGAATTGGATTATATGATTTTGATTCATTATAACCTT
1 ATGTTAATTGAATTGGATTATATGATTTTCATTCATTATAACCTT
3126587 ATGTTAATTGAATTGGATTATATGATTTTCATTCATTATAACCTT
1 ATGTTAATTGAATTGGATTATATGATTTTCATTCATTATAACCTT
3126632 ACTGTT
1 A-TGTT
3126638 TTTTCGGGTC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 45 0.92
46 4 0.08
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.49
Consensus pattern (45 bp):
ATGTTAATTGAATTGGATTATATGATTTTCATTCATTATAACCTT
Found at i:3131122 original size:9 final size:9
Alignment explanation
Indices: 3131094--3131124 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3131084 GAGACTTAAA
3131094 TTAAAATTT
1 TTAAAATTT
*
3131103 TCAAAATTT
1 TTAAAATTT
3131112 TTAAAATTT
1 TTAAAATTT
3131121 TTAA
1 TTAA
3131125 TTTTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (9 bp):
TTAAAATTT
Found at i:3131901 original size:14 final size:15
Alignment explanation
Indices: 3131862--3131913 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
3131852 TTGTTTTTAA
*
3131862 AATTAAATATAAGAATT
1 AATTAAATA-AACAA-T
*
3131879 AAATAAATAAA-AAT
1 AATTAAATAAACAAT
3131893 AATTAAATAAACAA-
1 AATTAAATAAACAAT
3131907 AATTAAA
1 AATTAAA
3131914 GAGATTGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 18 0.56
15 4 0.12
16 2 0.06
17 8 0.25
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (15 bp):
AATTAAATAAACAAT
Found at i:3132593 original size:65 final size:67
Alignment explanation
Indices: 3132496--3132684 Score: 188
Period size: 76 Copynumber: 2.7 Consensus size: 67
3132486 TAAAACATCT
* * *
3132496 TAAATTCTAATTAAAACACTTAAAA-CTGTTTAAACTAAAATACATAAAAAA-AT-CAT-ATAAT
1 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATAC-TAAAAAAGATACATAATAAT
3132557 ATTC
64 ATTC
* *
3132561 TAAATCCTAATTAAAATACAAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATA-CT-AAA-AAAGAT---ACAT--
3132626 AAATAATATTC
58 -AATAATATTC
* *
3132637 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACTAAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACTAAAA
3132685 CCTATTTAAA
Statistics
Matches: 103, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
64 4 0.04
65 34 0.33
66 4 0.04
67 3 0.03
68 2 0.02
72 2 0.02
73 1 0.01
74 3 0.03
75 2 0.02
76 48 0.47
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (67 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACTAAAAAAGATACATAATAATAT
TC
Found at i:3132669 original size:19 final size:19
Alignment explanation
Indices: 3132636--3132694 Score: 55
Period size: 24 Copynumber: 2.8 Consensus size: 19
3132626 AAATAATATT
* *
3132636 CTAAAACTTAATTAAAATA
1 CTAAAACCTATTTAAAATA
3132655 CTAAAACCTATTTAAACTAAAATA
1 CTAAAACCTA-TT----TAAAATA
3132679 CTAAAACCTATTTAAA
1 CTAAAACCTATTTAAA
3132695 TTGAAATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
19 13 0.39
20 1 0.03
23 2 0.06
24 17 0.52
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (19 bp):
CTAAAACCTATTTAAAATA
Found at i:3132675 original size:24 final size:24
Alignment explanation
Indices: 3132648--3132703 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
3132638 AAAACTTAAT
3132648 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
*
3132672 TAAAATACTAAAACCTATTTAAAT
1 TAAAATACTAAAACCTATTTAAAC
*
3132696 TGAAATAC
1 TAAAATAC
3132704 AAAGATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (24 bp):
TAAAATACTAAAACCTATTTAAAC
Done.