Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007832.1 Hibiscus syriacus cultivar Beakdansim tig00110174_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: 4020056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 21
Found at i:2902914 original size:21 final size:23
Alignment explanation
Indices: 2902862--2902914 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
2902852 ATTTACTTAT
2902862 TCGC-ATTGCG-AATTGGGAAAA
1 TCGCTATTGCGAAATTGGGAAAA
*
2902883 TCGCTA-CGCGAAATT-GGAAAA
1 TCGCTATTGCGAAATTGGGAAAA
2902904 TCG-TATTGCGA
1 TCGCTATTGCGA
2902915 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 2 0.07
21 20 0.74
22 5 0.19
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (23 bp):
TCGCTATTGCGAAATTGGGAAAA
Found at i:2913367 original size:3 final size:3
Alignment explanation
Indices: 2913359--2913421 Score: 51
Period size: 3 Copynumber: 21.3 Consensus size: 3
2913349 AAATATTAGT
* * *
2913359 ATA ATA ATA ATA ATA ATA ATA A-A ATAA ATA AAA ATTA GTA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA A-TA ATA ATA ATA
*
2913405 ATA A-A GTA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA A
2913422 AATTAAAGGA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
2 5 0.11
3 38 0.81
4 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:2914847 original size:14 final size:14
Alignment explanation
Indices: 2914828--2914856 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2914818 CTGTCCCTTT
2914828 TTGCACATTTTTCG
1 TTGCACATTTTTCG
2914842 TTGCACATTTTTCG
1 TTGCACATTTTTCG
2914856 T
1 T
2914857 AGAACGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.52
Consensus pattern (14 bp):
TTGCACATTTTTCG
Found at i:2915305 original size:84 final size:85
Alignment explanation
Indices: 2915159--2915352 Score: 257
Period size: 84 Copynumber: 2.3 Consensus size: 85
2915149 AACTGAATGA
* * * * *
2915159 AGTCAAACTCGAAAGGTC-TTCGTTGACAGATAACCCTTTTAGCCTTGGGTTATGCTGTAAATGA
1 AGTCGAACTC-AAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA
* * * *
2915223 TGTG-CCTTGGAGTTGAGTGT
65 TGTGCCCTCGAAGCTAAGTGT
*
2915243 AGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
1 AGTCGAACTCAAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
2915308 GTGCCCTCGAAGCTAAGTGT
66 GTGCCCTCGAAGCTAAGTGT
*
2915328 AGTCGAACTCGAAGGTCTTTGTGTT
1 AGTCGAACTCAAAGGTCTTT-TGTT
2915353 TCAAGAAAAC
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
83 7 0.07
84 54 0.56
85 31 0.32
86 4 0.04
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (85 bp):
AGTCGAACTCAAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
GTGCCCTCGAAGCTAAGTGT
Found at i:2915383 original size:34 final size:34
Alignment explanation
Indices: 2915345--2915462 Score: 190
Period size: 33 Copynumber: 3.6 Consensus size: 34
2915335 CTCGAAGGTC
2915345 TTTGTGTTTCAAGA-AAAC-ATTTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACGA-TTTCAAAGGTTTT
2915378 TTT-TGTTTCAAGAGAAACGATTTCAAAGG-TTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
*
2915410 TTTGTGCTTCAAGAGAAACGATTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
2915444 TTTGTGTTTCAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
2915463 TGTCTCCAAG
Statistics
Matches: 79, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
32 16 0.20
33 41 0.52
34 22 0.28
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.41
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:2915496 original size:37 final size:36
Alignment explanation
Indices: 2915448--2915800 Score: 309
Period size: 36 Copynumber: 10.1 Consensus size: 36
2915438 GGTTTTTTTG
*
2915448 TGTTTCAAGAGAAACTGTCTCCAAG-GAGGCAAAATTT
1 TGTTTCAAGAGAAACTGTCT-CAAGAGAGACAAAA-TT
*
2915485 TGTTTCAAGAGAAACAT-ACTCAA-AG-G------TT
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT
2915513 GGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 --TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
2915552 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC--AATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
**
2915586 TGTTTCAAGAGAATTTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
2915623 AGTTCCAAAAGAAATTGTCTC-AGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
2915658 TATTTCAAG-GAACACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAGAA-AC-TGTCTCAAGAGAGACAAAATT
*
2915687 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** *
2915723 TGTTTTTAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
2915759 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
2915796 TGTTT
1 TGTTT
2915801 TGAGTAAATT
Statistics
Matches: 260, Mismatches: 27, Indels: 58
0.75 0.08 0.17
Matches are distributed among these distances:
28 4 0.02
29 16 0.06
30 24 0.09
31 3 0.01
32 3 0.01
33 2 0.01
34 32 0.12
35 14 0.05
36 87 0.33
37 72 0.28
38 1 0.00
39 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:2915574 original size:67 final size:69
Alignment explanation
Indices: 2915445--2915636 Score: 207
Period size: 67 Copynumber: 2.8 Consensus size: 69
2915435 AAAGGTTTTT
* *
2915445 TTGTGTTTCAAGAGAAACTGTCTCCAAG-GAGGCAAAATTTTGTTTCAAGAGAAACATACTCAA-
1 TTGTGTTTCAAGAGAAACTGTCT-CAAGAGAGACAAAACTTTGTTTCAAGAGAAACATACTCAAG
2915508 AG-G-
65 AGAGA
* *
2915511 TTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAAC-TGTCTCAA
1 TT-GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAT-ACTCAA
2915575 GAGAGACAA
64 GAGAG---A
** * * *
2915584 TT-TGTTTCAAGAGAATTTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAA
1 TTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAA
2915637 TTGTCTCAGG
Statistics
Matches: 107, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
66 7 0.07
67 50 0.47
68 2 0.02
69 1 0.01
71 45 0.42
73 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (69 bp):
TTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACATACTCAAGA
GAGA
Found at i:2915602 original size:15 final size:15
Alignment explanation
Indices: 2915582--2915612 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2915572 CAAGAGAGAC
*
2915582 AATTTGTTTCAAGAG
1 AATTTGTCTCAAGAG
2915597 AATTTGTCTCAAGAG
1 AATTTGTCTCAAGAG
2915612 A
1 A
2915613 GACAAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (15 bp):
AATTTGTCTCAAGAG
Found at i:2915613 original size:71 final size:72
Alignment explanation
Indices: 2915515--2915800 Score: 292
Period size: 71 Copynumber: 4.1 Consensus size: 72
2915505 CAAAGGTTGG
*
2915515 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
2915580 AC-AATT
66 ACAAATT
** * * * * *
2915586 TGTTTCAAGAGAATTTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTC-AGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
2915650 ACAAAATT
66 AC-AAATT
* * * *
2915658 TATTTCAAG-GAACACATAT-TC-A-A-AG-----ATTTTGTTTCAAGGGAAACTGTCTCAAGAG
1 TGTTTCAAGAGAA-AC-TGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAG
2915713 AGACAAAATT
64 AGAC-AAATT
** *
2915723 TGTTTTTAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
2915787 ACAAAACTT
66 AC-AAA-TT
2915796 TGTTT
1 TGTTT
2915801 TGAGTAAATT
Statistics
Matches: 175, Mismatches: 24, Indels: 30
0.76 0.10 0.13
Matches are distributed among these distances:
64 21 0.12
65 23 0.13
66 4 0.02
67 1 0.01
68 2 0.01
69 2 0.01
70 8 0.05
71 55 0.31
72 49 0.28
73 10 0.06
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (72 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
ACAAATT
Found at i:2915759 original size:101 final size:105
Alignment explanation
Indices: 2915524--2915787 Score: 290
Period size: 101 Copynumber: 2.5 Consensus size: 105
2915514 GTGTTTCAAG
*
2915524 AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAATTTGT
1 AGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAA-GGAAACTATCTCAAGAGAGA-AATTTGT
**
2915589 TTCAAGAGAATTTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
63 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
* * * *
2915632 AGAAATTGTCTC-AGGGAGACAAAATTTATTTCAAGGAACACATAT-TC-A-A-AG-ATTTTGTT
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAA-AC-TATCTCAAGAGAGAAATTTGTT
* * *** *
2915691 TCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTTTAG
64 TCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
* *
2915732 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG-GAAACTATCTCAAGAGAGA
2915788 CAAAACTTTG
Statistics
Matches: 129, Mismatches: 18, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
100 18 0.14
101 59 0.46
102 4 0.03
103 3 0.02
104 3 0.02
105 5 0.04
106 13 0.10
107 13 0.10
108 11 0.09
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (105 bp):
AGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAACTATCTCAAGAGAGAAATTTGTTTC
AAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
Found at i:2915782 original size:173 final size:175
Alignment explanation
Indices: 2915457--2915795 Score: 508
Period size: 173 Copynumber: 1.9 Consensus size: 175
2915447 GTGTTTCAAG
* * *
2915457 AGAAACTGTCTCCAAGGAGGCAAAATTTTGTTTCAAGAGAAACATACTCAAAGGTTGGTGTTTCA
1 AGAAACTGTCTCCAAGGAGACAAAATTTTATTTCAAGAGAAACATACTCAAAGATTGGTGTTTCA
2915522 AGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAATTT
66 AGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAATTT
**
2915587 GTTTCAAGAGAATTTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
131 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
* * * *
2915632 AGAAATTGTCT-CAGGGAGACAAAA-TTTATTTCAAG-GAACACATATTCAAAGATT-TTGTTTC
1 AGAAACTGTCTCCAAGGAGACAAAATTTTATTTCAAGAGAA-ACATACTCAAAGATTGGTGTTTC
* **
2915693 AAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTTTAGGGAAACTGTCTCAAGAGAGACAAAA
65 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC--AA
2915757 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
128 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
2915796 TGTTTTGAGT
Statistics
Matches: 149, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
171 30 0.20
172 36 0.24
173 62 0.42
174 11 0.07
175 10 0.07
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (175 bp):
AGAAACTGTCTCCAAGGAGACAAAATTTTATTTCAAGAGAAACATACTCAAAGATTGGTGTTTCA
AGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAATTT
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
Found at i:2915816 original size:37 final size:34
Alignment explanation
Indices: 2915697--2915825 Score: 159
Period size: 36 Copynumber: 3.6 Consensus size: 34
2915687 TGTTTCAAGG
*
2915697 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTTAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTG-TTTT-GA
*
2915733 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTT--TGA
2915769 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTTGA
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTTGA
* *
2915804 GTAAATTAGTCTCAAGCGAGAC
1 G-AAACT-GTCTCAAGAGAGAC
2915826 GACCCCTTGT
Statistics
Matches: 83, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
35 6 0.07
36 57 0.69
37 20 0.24
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (34 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTTGA
Found at i:2924059 original size:22 final size:22
Alignment explanation
Indices: 2924023--2924105 Score: 112
Period size: 22 Copynumber: 3.7 Consensus size: 22
2924013 TTAGTGCAGA
2924023 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* * *
2924045 GAGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-TTGAAG
* *
2924068 GGGAATCGATTCCCCCTTGTAG
1 GGGAATCGATACCCCCTTGAAG
2924090 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
2924106 ATGGGGTTCT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
22 33 0.62
23 20 0.38
ACGTcount: A:0.24, C:0.30, G:0.25, T:0.20
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:2924065 original size:23 final size:23
Alignment explanation
Indices: 2924029--2924085 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
2924019 CAGAGGGAAT
*
2924029 CGATACCCCC-TTGAAGGAGAAC
1 CGATTCCCCCTTTGAAGGAGAAC
* *
2924051 CGATTCCCCCTTTGAAGGGGAAT
1 CGATTCCCCCTTTGAAGGAGAAC
2924074 CGATTCCCCCTT
1 CGATTCCCCCTT
2924086 GTAGGGGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 9 0.29
23 22 0.71
ACGTcount: A:0.23, C:0.33, G:0.21, T:0.23
Consensus pattern (23 bp):
CGATTCCCCCTTTGAAGGAGAAC
Found at i:2925701 original size:18 final size:18
Alignment explanation
Indices: 2925680--2925720 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2925670 AGAACAACAC
* *
2925680 GAGGAACAAGCACGAGCA
1 GAGGAACAAGCACAACCA
2925698 GAGGAACAAGCACAACCA
1 GAGGAACAAGCACAACCA
2925716 GAGGA
1 GAGGA
2925721 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.32, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGCACAACCA
Found at i:2929692 original size:29 final size:30
Alignment explanation
Indices: 2929651--2929714 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
2929641 AGATTATAAA
* *
2929651 ATAAAAAT-GAAAAATGAAA-AAATATTAGT
1 ATAAAAATAAAAAAAT-AAATAAAAATTAGT
*
2929680 ATAATAATAAAAAAATAAATAAAAATTAGT
1 ATAAAAATAAAAAAATAAATAAAAATTAGT
2929710 A-AAAA
1 ATAAAA
2929715 TGTTAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.23
Consensus pattern (30 bp):
ATAAAAATAAAAAAATAAATAAAAATTAGT
Found at i:2929704 original size:40 final size:42
Alignment explanation
Indices: 2929629--2929739 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 42
2929619 CTCTAAAGTC
* *
2929629 AAAAATATTAT-TAGATTATAAAATAA-AAATGAAAAA-T-GA
1 AAAAATATTATATA-ATAATAAAAAAATAAATGAAAAATTAGA
*
2929668 AAAAATATTAGTATAATAATAAAAAAATAAAT-AAAAATTAGT
1 AAAAATATTA-TATAATAATAAAAAAATAAATGAAAAATTAGA
*
2929710 AAAAATGTTA-ATAATAATAATAATAAATAA
1 AAAAATATTATATAATAATAA-AA-AAATAA
2929740 TAAAGTACTA
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
39 10 0.16
40 26 0.43
41 9 0.15
42 16 0.26
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (42 bp):
AAAAATATTATATAATAATAAAAAAATAAATGAAAAATTAGA
Found at i:2931112 original size:12 final size:14
Alignment explanation
Indices: 2931095--2931137 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
2931085 TTGACCTACA
2931095 AAAATAA-AA-AAT
1 AAAATAATAATAAT
2931107 AAAATAATAATAAT
1 AAAATAATAATAAT
2931121 AATAATAATAATAAT
1 AA-AATAATAATAAT
2931136 AA
1 AA
2931138 TTTGTAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.25
13 2 0.07
14 5 0.18
15 14 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:2931117 original size:3 final size:3
Alignment explanation
Indices: 2931104--2931138 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2931094 AAAAATAAAA
2931104 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2931139 TTGTAAATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2931310 original size:15 final size:15
Alignment explanation
Indices: 2931290--2931318 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2931280 TGTTTATGTA
2931290 TATGTTAATGGTGTT
1 TATGTTAATGGTGTT
2931305 TATGTTAATGGTGT
1 TATGTTAATGGTGT
2931319 ATATCTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.52
Consensus pattern (15 bp):
TATGTTAATGGTGTT
Found at i:2938524 original size:3 final size:3
Alignment explanation
Indices: 2938511--2938555 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
2938501 TATATATATA
2938511 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2938556 TTTAACGCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2942345 original size:94 final size:92
Alignment explanation
Indices: 2942180--2942362 Score: 260
Period size: 94 Copynumber: 2.0 Consensus size: 92
2942170 TATAATATTA
* * * *
2942180 TATATATACAATAAAGCTTGAGTTGTCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGGATA
1 TATATATACAATAAAGCTTGAGCTGTCCCTAAAGCAATTGGTTAAACGCCCCAGATTTATGGATA
* *
2942245 ATATTCAACTAGCCTGATAAAGGTAAT
66 AGATTCAACTAACCTGATAAAGGTAAT
2942272 TATACTATACAATAAAGCTTGAGCTGTCCCTATAAGGCAATTGGTTAAACGCCCCA-ATTTATGG
1 TATA-TATACAATAAAGCTTGAGCTGTCCCTA-AA-GCAATTGGTTAAACGCCCCAGATTTATGG
**
2942336 ATAAGATTCAGTTAACCTGATAAAGGT
63 ATAAGATTCAACTAACCTGATAAAGGT
2942363 GTTTATGTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
92 4 0.05
93 25 0.31
94 31 0.39
95 20 0.25
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (92 bp):
TATATATACAATAAAGCTTGAGCTGTCCCTAAAGCAATTGGTTAAACGCCCCAGATTTATGGATA
AGATTCAACTAACCTGATAAAGGTAAT
Found at i:2943697 original size:84 final size:82
Alignment explanation
Indices: 2943542--2945017 Score: 1371
Period size: 84 Copynumber: 17.9 Consensus size: 82
2943532 TTTAAGACAA
* * * * *
2943542 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAGACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-GCAACAAAGACCTTCGAGTTCGACTACA
2943607 CTCAGCTCCAAGGCACAT
65 CTCAGCTCCAAGGCACAT
* * * * * * * *
2943625 CATTTCCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAAC-AAAGACCTTCGAGTTCGACTAC
* *
2943690 ATTCAGCTCCAAGGCATAT
64 ACTCAGCTCCAAGGCACAT
** * *
2943709 CATTTATAGCATAACTTAAGACGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAA-CAAAGACCTTCGAGTTCGACTAC
* * *
2943774 GCTTAGCTCCAACGCACAT
64 ACTCAGCTCCAAGGCACAT
* * * * * * *
2943793 CATTTGCAGAATAACTTAAGTCGAGAAGGGCTATCTGC--CAAAGACCCTCGAATTCAATTACAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACAC
* * *
2943856 TTAGCTTCGAGGGCACAT
66 TCAGC-TCCAAGGCACAT
* * * * * * *
2943874 CATTTACAGCATAACTCAAGGCTAGAAGGGTTACCTGTGACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAAC-AAAGACCTTCGAGTTCGACTAC
* *
2943939 GCTCAGCTCCAAGGCATAT
64 ACTCAGCTCCAAGGCACAT
* *
2943958 CATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAA-CAAAGACCTTCGAGTTCGACTAC
* *
2944023 GCTCAGCTCCAAGGCATAT
64 ACTCAGCTCCAAGGCACAT
* * * * *
2944042 CATTTGCAACATAGCTTAAGTCGAGAAGGGTTATCTGC--CAAAGACCCTCAAGTTCGATTACAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACAC
** *
2944105 TCAGCTTTGAGGGCACAT
66 TCAGC-TCCAAGGCACAT
* * * * * * * *
2944123 TATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTTGAGTTCAACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAAC-AAAGACCTTCGAGTTCGACTAC
* *
2944188 ACTCAGCTCTAAGGCATAT
64 ACTCAGCTCCAAGGCACAT
*
2944207 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAA-CAAAGACCTTCGAGTTCGACTAC
* *
2944272 GCTCAGCTCCAAGGCATAT
64 ACTCAGCTCCAAGGCACAT
* * * * *
2944291 CATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCT--ACCAAAGACCTTCGAGTTCGACTACGC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACAC
* *
2944354 TTAGCTTCAAGGCACAT
66 TCAGCTCCAAGGCACAT
* * * * *
2944371 CATTTGCAGCATAGCTTAAGTTGAGAAGGGCTATCTGC--CAAAGACCCTCGAGTTCGATTACAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACAC
** *
2944434 TCAGCTTTGAGGGCACAT
66 TCAGC-TCCAAGGCACAT
* * * * * *
2944452 CATTTACAGCATAACTTAAGGCTATAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAAC-AAAGACCTTCGAGTTCGACTAC
* * * *
2944517 GCTTAGCTCTAAGGCATAT
64 ACTCAGCTCCAAGGCACAT
* * *
2944536 CATTTGCAGCATAACTTAAGTCAAAAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CAA-CAAAGACCTTCGAGTTCGACTAC
* * *
2944601 GCTTAGCTCCAAGGCATAT
64 ACTCAGCTCCAAGGCACAT
* * * *
2944620 CATTTGCAGCA-AGCTTAAGTCAAGAAGGGATATCTGC--CAAAGACCTTCGAGTTCGACTACGC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACAC
* *
2944682 TCAACTTCAAGGCACAT
66 TCAGCTCCAAGGCACAT
* * * *
2944699 CCTTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGC--CAAAGACCCTCGAGTTCAATTACAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACAC
** *
2944762 TCAGCTTTGAGGGCACAT
66 TCAGC-TCCAAGGCACAT
* * * * * * *
2944780 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCACCAAAATACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-GCAAC-AAAGACCTTCGAGTTCGACTAC
* * * *
2944845 GCTTAGCTCTAAGGCATAT
64 ACTCAGCTCCAAGGCACAT
* ** * *
2944864 CATTTGCAGCACAACTTAAGTAAAAAAGGGTTATCTGC--CAAAGACCTTCGAGTTCGACTACGC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACAC
* *
2944927 TCAGCTCCTAGGCATAT
66 TCAGCTCCAAGGCACAT
* * * * * * * * * *
2944944 CATTTGCAGTATAGCTTAAATCGAGAAAGGCTATCTCCCAACCGAAGACCTCCGAGTTCAATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-GCAA-CAAAGACCTTCGAGTTCGACTAC
*
2945009 ATTCAGCTC
64 ACTCAGCTC
2945018 AGAGGCAAAC
Statistics
Matches: 1148, Mismatches: 212, Indels: 65
0.81 0.15 0.05
Matches are distributed among these distances:
79 47 0.04
80 259 0.23
81 161 0.14
82 4 0.00
83 59 0.05
84 521 0.45
85 97 0.08
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (82 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCAACAAAGACCTTCGAGTTCGACTACAC
TCAGCTCCAAGGCACAT
Found at i:2943934 original size:165 final size:161
Alignment explanation
Indices: 2943542--2944984 Score: 1399
Period size: 165 Copynumber: 8.8 Consensus size: 161
2943532 TTTAAGACAA
* * *
2943542 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCT-ACCAACAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGA-C--CAAAGACCTTCGAGTTCGACTAC
* * * * * *
2943606 GCTCAGCTCCAAGGCACATCATTTCCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAA
63 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTG-C--C-AAA
** *
2943671 GACCTTCGAGTTCGACTACATTCAGCTCCAAGGCATAT
124 GACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCATAT
** * *
2943709 CATTTATAGCATAACTTAAGACGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTCGACTAC
* * * *
2943774 GCTTAGCTCCAACGCACATCATTTGCAGAATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
63 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAAAGACC
* * * * ** * * * *
2943839 CTCGAATTCAATTACATTTAGCTTCGAGGGCACAT
128 TTCGAGTTCGACTACGCTCAGC-TCTAAGGCATAT
* * * * *
2943874 CATTTACAGCATAACTCAAGGCTAGAAGGGTTACCTGTGACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTA--TCTGACC-AAAGACCTTCGAGTTCGACTAC
* ** *
2943939 GCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAA
63 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTG----CCAAA
* *
2944004 GACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATAT
124 GACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCATAT
* * * * * *
2944042 CATTTGCAACATAGCTTAAGTCGAGAAGGGTTATCTG-CCAAAGACCCTCAAGTTCGATTACACT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACGCT
** * * * * * * *
2944106 CAGCTTTGAGGGCACATTATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGA
66 CAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTG---CC-AAAGA
* * *
2944171 CCTTTGAGTTCAACTACACTCAGCTCTAAGGCATAT
126 CCTTCGAGTTCGACTACGCTCAGCTCTAAGGCATAT
*
2944207 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTCGACTAC
* * *
2944272 GCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTACCAAAGACC
63 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAAAGACC
* *
2944337 TTCGAGTTCGACTACGCTTAGCT-TCAAGGCACAT
128 TTCGAGTTCGACTACGCTCAGCTCT-AAGGCATAT
* * * * * *
2944371 CATTTGCAGCATAGCTTAAGTTGAGAAGGGCTATCTG-CCAAAGACCCTCGAGTTCGATTACACT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACGCT
** * * * * * *
2944435 CAGCTTTGAGGGCACATCATTTACAGCATAACTTAAGGCTATAAGGGTTATCTGTCACCAAAAGA
66 CAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTG---CC-AAAGA
* *
2944500 CCTTCGAGTTTGACTACGCTTAGCTCTAAGGCATAT
126 CCTTCGAGTTCGACTACGCTCAGCTCTAAGGCATAT
* * *
2944536 CATTTGCAGCATAACTTAAGTCAAAAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTCGACTAC
* * * *
2944601 GCTTAGCTCCAAGGCATATCATTTGCAGCA-AGCTTAAGTCAAGAAGGGATATCTGCCAAAGACC
63 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAAAGACC
* *
2944665 TTCGAGTTCGACTACGCTCAACT-TCAAGGCACAT
128 TTCGAGTTCGACTACGCTCAGCTCT-AAGGCATAT
* * * * *
2944699 CCTTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CCAAAGACCCTCGAGTTCAATTACACT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACGCT
** * * * * * * * *
2944763 CAGCTTTGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCACCAAAATA
66 CAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATC--T-GCC-AAAGA
*
2944828 CCTTCGAGTTCGACTACGCTTAGCTCTAAGGCATAT
126 CCTTCGAGTTCGACTACGCTCAGCTCTAAGGCATAT
* ** *
2944864 CATTTGCAGCACAACTTAAGTAAAAAAGGGTTATCTG-CCAAAGACCTTCGAGTTCGACTACGCT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACGCT
* * * * * * * *
2944928 CAGCTCCTAGGCATATCATTTGCAGTATAGCTTAAATCGAGAAAGGCTATCTCCCAA
66 CAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAA
2944985 CCGAAGACCT
Statistics
Matches: 1050, Mismatches: 189, Indels: 81
0.80 0.14 0.06
Matches are distributed among these distances:
159 25 0.02
160 48 0.05
161 58 0.06
162 2 0.00
163 71 0.07
164 161 0.15
165 388 0.37
166 5 0.00
167 55 0.05
168 159 0.15
169 76 0.07
170 1 0.00
171 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (161 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACGCT
CAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAAAGACCTTC
GAGTTCGACTACGCTCAGCTCTAAGGCATAT
Found at i:2944062 original size:249 final size:245
Alignment explanation
Indices: 2943542--2945002 Score: 1515
Period size: 249 Copynumber: 5.9 Consensus size: 245
2943532 TTTAAGACAA
* * * * *
2943542 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAGACCTTCGAGTTCGACTACG
1 CATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCT-GC--CAAAGACCTTCGAATTCGACTACG
* * * * * * *
2943607 CTCAGC-TCCAAGGCACATCATTTCCAACATAGCTCAAGGCAAGAAGGGCTATTTGCCAACAAAA
63 CTTAGCTTCGAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTG-C--C-AAA
* ** *
2943671 GACCTTCGAGTTCGACTACATTCAGCTCCAAGGCATATCATTTATAGCATAACTTAAGACGAGAA
124 GACCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAA
* * * *
2943736 GGGTTATCTGCCAACCAAAGACCTTCAAGTTCGACTACGCTTAGCTCCAACGCACAT
189 GGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
* * * * * * **
2943793 CATTTGCAGAATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAATTCAATTACATTT
1 CATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAAAGACCTTCGAATTCGACTACGCTT
* * * *
2943858 AGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTACCTGTGACCAAAAGAC
66 AGCTTCGAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTA--TCTG-CC-AAAGAC
* *
2943923 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTTGAGAAGGG
127 CTTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
*
2943988 TTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCATAT
192 TTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
* * * * * *
2944042 CATTTGCAACATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTC-AAGTTCGATTACACT
1 CATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAAAGACCTTCGAA-TTCGACTACGCT
* * * * * *
2944106 CAGCTTTGAGGGCACATTATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGA
65 TAGCTTCGAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTG---CC-AAAGA
* * * *
2944171 CCTTTGAGTTCAACTACACTCAGCTCTAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGG
126 CCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGG
2944236 GTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
191 GTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
* * * *
2944291 CATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTACCAAAGACCTTCGAGTTCGACTACGCTT
1 CATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAAAGACCTTCGAATTCGACTACGCTT
* * *** * *
2944356 AGCTTC-AAGGCACATCATTTGCAGCATAGCTTAAGTTGAGAAGGGCTATCTGCCAAAGACCCTC
66 AGCTTCGAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAAAGACCTTC
* ** * * * * * *
2944420 GAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAGCATAACTTAAGGCTATAAGGGTTA
131 GAGTTCGACTACACTCAGC-TCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTA
* * * *
2944485 TCTGTC-ACCAAAAGACCTTCGAGTTTGACTACGCTTAGCTCTAAGGCATAT
195 TCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
*
2944536 CATTTGCAGCATAACTTAAGTCAAAAAGGGTTATCTGCCAACCAAAGACCTTC-AAGTTCGACTA
1 CATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTG----CCAAAGACCTTCGAA-TTCGACTA
* * * * * *
2944600 CGCTTAGC-TCCAAGGCATATCATTTGCAGCA-AGCTTAAGTCAAGAAGGGATATCTGCCAAAGA
61 CGCTTAGCTTCGAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAAAGA
* * * * *
2944663 CCTTCGAGTTCGACTACGCTCAACTTCAAGGCACATCCTTTGCAGCATAACTTAAGTCGAGAAGG
126 CCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGG
* * * * ** * *
2944728 GTTATCTG----CCAAAGACCCTCGAGTTCAATTACACTCAGCTTTGAGGGCACAT
191 GTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATAT
* * * * * * *
2944780 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATCACCAAAATACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCAAGAAGGGTTATC--T-GCC-AAAGACCTTCGAATTCGACTAC
* * * * ** *
2944845 GCTTAGC-TCTAAGGCATATCATTTGCAGCACAACTTAAGTAAAAAAGGGTTATCTGCCAAAGAC
62 GCTTAGCTTCGAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAAAGAC
* * * * * *
2944909 CTTCGAGTTCGACTACGCTCAGCTCCTAGGCATATCATTTGCAGTATAGCTTAAATCGAGAAAGG
127 CTTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* * * *
2944974 CTATCTCCCAACCGAAGACCTCCGAGTTC
192 TTATCTGCCAACCAAAGACCTTCGAGTTC
2945003 AATTACATTC
Statistics
Matches: 1041, Mismatches: 143, Indels: 54
0.84 0.12 0.04
Matches are distributed among these distances:
243 25 0.02
244 115 0.11
245 205 0.20
246 1 0.00
247 45 0.04
248 114 0.11
249 499 0.48
250 2 0.00
251 35 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (245 bp):
CATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAAAGACCTTCGAATTCGACTACGCTT
AGCTTCGAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAAAGACCTTC
GAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTAT
CTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
Found at i:2945763 original size:35 final size:35
Alignment explanation
Indices: 2945706--2946009 Score: 308
Period size: 37 Copynumber: 8.7 Consensus size: 35
2945696 AATACGTATT
2945706 TAATATATAATTTTTAAAATCATTTTGAAAATTATA
1 TAATATATAA-TTTTAAAATCATTTTGAAAATTATA
2945742 TAATATATAATTTTAAAATCATTTTGAAAATTATA
1 TAATATATAATTTTAAAATCATTTTGAAAATTATA
*
2945777 TAATATATAATTTTAAAATCTTTTTTGAAAAATTATA
1 TAATATATAATTTTAAAATC-ATTTTG-AAAATTATA
*
2945814 TAATATATAATTCTAAAATCATTTTTGAAAAATTATA
1 TAATATATAATTTTAAAATCA-TTTTG-AAAATTATA
*
2945851 TAATATATAGTTTTAAAAAT-ATTTTTGAAAAATTATA
1 TAATATATAATTTT-AAAATCA-TTTTG-AAAATTATA
* * *
2945888 TAATATATAGTTTTAAAAACATTTTTAAAAACTTATA
1 TAATATATAATTTTAAAATCA-TTTTGAAAA-TTATA
* *
2945925 T-A-ATAT--TTTT-AAACCATTTTTGAAAACTATA
1 TAATATATAATTTTAAAATCA-TTTTGAAAATTATA
* * *
2945956 TAATGTATAGTTTTGAAAT--TTTT-AAAA--ATA
1 TAATATATAATTTTAAAATCATTTTGAAAATTATA
* *
2945986 TAATATATAGTTTAAAAAT-ATTTT
1 TAATATATAATTTTAAAATCATTTT
2946010 TTTTGAAATA
Statistics
Matches: 241, Mismatches: 15, Indels: 29
0.85 0.05 0.10
Matches are distributed among these distances:
30 19 0.08
31 9 0.04
32 19 0.08
33 11 0.05
35 53 0.22
36 27 0.11
37 98 0.41
38 5 0.02
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (35 bp):
TAATATATAATTTTAAAATCATTTTGAAAATTATA
Found at i:2945809 original size:37 final size:37
Alignment explanation
Indices: 2945688--2945974 Score: 337
Period size: 37 Copynumber: 7.9 Consensus size: 37
2945678 TTGCAAACAG
* *
2945688 TTTTTGAAAATACGTATTTAATATATAATTTTTAAAATCA
1 TTTTTGAAAA-A-TTATATAATATATAA-TTTTAAAATCA
2945728 -TTTTG-AAAATTATATAATATATAATTTTAAAATCA
1 TTTTTGAAAAATTATATAATATATAATTTTAAAATCA
*
2945763 -TTTTG-AAAATTATATAATATATAATTTTAAAATCT
1 TTTTTGAAAAATTATATAATATATAATTTTAAAATCA
*
2945798 TTTTTGAAAAATTATATAATATATAATTCTAAAATCA
1 TTTTTGAAAAATTATATAATATATAATTTTAAAATCA
*
2945835 TTTTTGAAAAATTATATAATATATAGTTTTAAAAAT-A
1 TTTTTGAAAAATTATATAATATATAATTTT-AAAATCA
* *
2945872 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
1 TTTTTGAAAAATTATATAATATATAATTTTAAAATCA
*
2945909 TTTTT-AAAAACTTATAT-A-ATAT--TTTT-AAACCA
1 TTTTTGAAAAA-TTATATAATATATAATTTTAAAATCA
* * * *
2945941 TTTTTG-AAAACTATATAATGTATAGTTTTGAAAT
1 TTTTTGAAAAATTATATAATATATAATTTTAAAAT
2945975 TTTTAAAAAT
Statistics
Matches: 224, Mismatches: 12, Indels: 26
0.85 0.05 0.10
Matches are distributed among these distances:
31 5 0.02
32 15 0.07
33 7 0.03
35 53 0.24
36 31 0.14
37 100 0.45
38 8 0.04
39 5 0.02
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (37 bp):
TTTTTGAAAAATTATATAATATATAATTTTAAAATCA
Found at i:2946058 original size:11 final size:10
Alignment explanation
Indices: 2946017--2946071 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 10
2946007 TTTTTTTGAA
2946017 ATATATATATT
1 ATATAT-TATT
2946028 ATATAGTT-TAT
1 ATATA-TTAT-T
2946039 ATCATATTATT
1 AT-ATATTATT
2946050 AGTATATTATT
1 A-TATATTATT
2946061 AT-TATTATT
1 ATATATTATT
2946070 AT
1 AT
2946072 TTTTATTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
9 9 0.23
10 2 0.05
11 22 0.56
12 6 0.15
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (10 bp):
ATATATTATT
Found at i:2947327 original size:21 final size:21
Alignment explanation
Indices: 2947284--2947331 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2947274 TTCCTTTTTG
*
2947284 ATATATTTTTTTAATTCTCAT
1 ATATATTTTTTTAATTATCAT
*
2947305 ATATATTTTTTTTATATAT-AT
1 ATATATTTTTTTAAT-TATCAT
2947326 ATATAT
1 ATATAT
2947332 ATTAATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATATTTTTTTAATTATCAT
Found at i:2949166 original size:45 final size:45
Alignment explanation
Indices: 2949116--2949338 Score: 307
Period size: 45 Copynumber: 5.1 Consensus size: 45
2949106 TACGTACAGT
* * *
2949116 TGGCTTGGGAGTTTGATTCAGCAATTCTTGTTGTTGCACTGTCTG
1 TGGCTTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
* * *
2949161 TGGCTTGAGAGTTTGATTCAGCACTCCTTTTTGTTGCACAGCCTG
1 TGGCTTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
*
2949206 TGGAC-TGGGAGTTTGATTCAGCACTCC---TTGTTGCACAGCCTG
1 TGG-CTTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
*
2949248 TGGCGTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
1 TGGCTTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
*
2949293 TGGCCTGGGAGTTTGATTCAGCAATCC---TTGTTGCACAGCCTG
1 TGGCTTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
2949335 TGGC
1 TGGC
2949339 CTGTACGTAC
Statistics
Matches: 164, Mismatches: 9, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
41 1 0.01
42 58 0.35
45 104 0.63
46 1 0.01
ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35
Consensus pattern (45 bp):
TGGCTTGGGAGTTTGATTCAGCAATCCTTGTTGTTGCACAGCCTG
Found at i:2949270 original size:87 final size:87
Alignment explanation
Indices: 2949121--2949338 Score: 319
Period size: 87 Copynumber: 2.5 Consensus size: 87
2949111 ACAGTTGGCT
** * * * *
2949121 TGGGAGTTTGATTCAGCAATTCTTGTTGTTGCACTGTCTGTGGCTTGAGAGTTTGATTCAGCACT
1 TGGGAGTTTGATTCAGC-A--CTCCTTGTTGCACAGCCTGTGGCGTGAGAGTTTGATTCAGCAAT
*
2949186 CCTTTTTGTTGCACAGCCTGTGGAC
63 CCTTGTTGTTGCACAGCCTGTGGAC
*
2949211 TGGGAGTTTGATTCAGCACTCCTTGTTGCACAGCCTGTGGCGTGGGAGTTTGATTCAGCAATCCT
1 TGGGAGTTTGATTCAGCACTCCTTGTTGCACAGCCTGTGGCGTGAGAGTTTGATTCAGCAATCCT
*
2949276 TGTTGTTGCACAGCCTGTGGCC
66 TGTTGTTGCACAGCCTGTGGAC
*
2949298 TGGGAGTTTGATTCAGCAATCCTTGTTGCACAGCCTGTGGC
1 TGGGAGTTTGATTCAGCACTCCTTGTTGCACAGCCTGTGGC
2949339 CTGTACGTAC
Statistics
Matches: 118, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
87 100 0.85
89 1 0.01
90 17 0.14
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.35
Consensus pattern (87 bp):
TGGGAGTTTGATTCAGCACTCCTTGTTGCACAGCCTGTGGCGTGAGAGTTTGATTCAGCAATCCT
TGTTGTTGCACAGCCTGTGGAC
Found at i:2953885 original size:18 final size:19
Alignment explanation
Indices: 2953854--2953891 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2953844 GAGACGGTTT
*
2953854 AAATAGTGGTTTGTTATTA
1 AAATAGTGGTTTGTCATTA
2953873 AAATAGTGG-TTGTCATTA
1 AAATAGTGGTTTGTCATTA
2953891 A
1 A
2953892 TAGTATTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.34, C:0.03, G:0.21, T:0.42
Consensus pattern (19 bp):
AAATAGTGGTTTGTCATTA
Found at i:2954929 original size:13 final size:13
Alignment explanation
Indices: 2954911--2954938 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2954901 AAATGTGCAT
2954911 AGGGTACCAAATA
1 AGGGTACCAAATA
2954924 AGGGTACCAAATA
1 AGGGTACCAAATA
2954937 AG
1 AG
2954939 CTTGTGCCAT
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:0.46, C:0.14, G:0.25, T:0.14
Consensus pattern (13 bp):
AGGGTACCAAATA
Found at i:2956632 original size:17 final size:16
Alignment explanation
Indices: 2956612--2956646 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2956602 TTTGGATAAA
*
2956612 TATTTCATCTTTTACTT
1 TATTTCAT-TTCTACTT
2956629 TATTTCATTTCTACTT
1 TATTTCATTTCTACTT
2956645 TA
1 TA
2956647 CTTTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTCATTTCTACTT
Found at i:2956729 original size:21 final size:21
Alignment explanation
Indices: 2956704--2956764 Score: 74
Period size: 19 Copynumber: 3.0 Consensus size: 21
2956694 ATATATTAAG
*
2956704 TAGTTTCGAAAATAGTATATA
1 TAGTTTAGAAAATAGTATATA
*
2956725 TAGTTTAGAAAACA--ATATA
1 TAGTTTAGAAAATAGTATATA
*
2956744 TAGTTTTG-AAATAGTATATA
1 TAGTTTAGAAAATAGTATATA
2956764 T
1 T
2956765 TATATATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
18 4 0.12
19 12 0.35
20 6 0.18
21 12 0.35
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.39
Consensus pattern (21 bp):
TAGTTTAGAAAATAGTATATA
Found at i:2956772 original size:46 final size:45
Alignment explanation
Indices: 2956719--2956830 Score: 129
Period size: 46 Copynumber: 2.4 Consensus size: 45
2956709 TCGAAAATAG
* *
2956719 TATATATAGTTTAGAAAACAATA-TATAGTTTTG-AAATAGTATATAT
1 TATATATAGTTT--AAAA-AATAGTATAGTTTTGAAAATAATACATAT
*
2956765 TATATATAGTTTTAAAAATAGTATAGTTTTGAAAAATAATACATAT
1 TATATATAGTTTAAAAAATAGTATAGTTTTG-AAAATAATACATAT
* *
2956811 TATACATAGTTTCAAAAATA
1 TATATATAGTTTAAAAAATA
2956831 ACATAAAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
43 4 0.07
44 13 0.22
46 41 0.71
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (45 bp):
TATATATAGTTTAAAAAATAGTATAGTTTTGAAAATAATACATAT
Found at i:2956791 original size:17 final size:18
Alignment explanation
Indices: 2956769--2956802 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2956759 ATATATTATA
2956769 TATAGTTTT-AAAAATAG
1 TATAGTTTTGAAAAATAG
2956786 TATAGTTTTGAAAAATA
1 TATAGTTTTGAAAAATA
2956803 ATACATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (18 bp):
TATAGTTTTGAAAAATAG
Found at i:2956914 original size:3 final size:3
Alignment explanation
Indices: 2956888--2956935 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
2956878 GGTATCACTT
* *
2956888 TTA TTT TTA TTT TTA CTT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2956933 TTA
1 TTA
2956936 ATATAATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:2959178 original size:31 final size:31
Alignment explanation
Indices: 2959068--2959179 Score: 161
Period size: 31 Copynumber: 3.6 Consensus size: 31
2959058 TCTATAGATT
* * *
2959068 CCGAAGAACCTAGGTAATCAGTCCATATGTT
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
* *
2959099 CCGAAGAACATAGATAAATAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
* *
2959130 CCGAAGAACATAGGTAAACAGTTCATATATC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
2959161 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
2959180 CCTCGACCCT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:2962543 original size:22 final size:22
Alignment explanation
Indices: 2962503--2962545 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2962493 GAAATATAGT
*
2962503 ATGAACAGTACCGTAAACAATA
1 ATGAACAGTACCATAAACAATA
* *
2962525 ATGAACAGTGCCATGAACAAT
1 ATGAACAGTACCATAAACAAT
2962546 GCTATAGTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.19
Consensus pattern (22 bp):
ATGAACAGTACCATAAACAATA
Found at i:2963366 original size:31 final size:31
Alignment explanation
Indices: 2963328--2963513 Score: 248
Period size: 31 Copynumber: 6.0 Consensus size: 31
2963318 CCCGAAGGAC
* * * *
2963328 CAGTCCATAGGTTCCGAAGAACCTAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2963359 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
2963390 CAATCCATATGTCCCGAAAAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
2963421 TAGT-CATATGTCCCGAAGAACATATGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
2963451 CAGTGCATATGTCCCGAAGAACATATGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
2963482 CAGTCCATATGTCCCAAAGAACATAGATAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2963513 C
1 C
2963514 CGTTAACCTT
Statistics
Matches: 139, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
30 27 0.19
31 112 0.81
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2963443 original size:61 final size:62
Alignment explanation
Indices: 2963331--2963513 Score: 235
Period size: 61 Copynumber: 3.0 Consensus size: 62
2963321 GAAGGACCAG
* * * *
2963331 TCCATAGGTTCCGAAGAACCTAGGT-AATCAGTCCATATGTTCCGAAGAACATAGGTAAACAA
1 TCCATATGTCCCGAAGAACATAGGTAAAT-AGTCCATATGTCCCGAAGAACATAGGTAAACAA
* * *
2963393 TCCATATGTCCCGAAAAACATAGGTAAATAGT-CATATGTCCCGAAGAACATATGTAAACAG
1 TCCATATGTCCCGAAGAACATAGGTAAATAGTCCATATGTCCCGAAGAACATAGGTAAACAA
* * * * *
2963454 TGCATATGTCCCGAAGAACATATGTAAACAGTCCATATGTCCCAAAGAACATAGATAAAC
1 TCCATATGTCCCGAAGAACATAGGTAAATAGTCCATATGTCCCGAAGAACATAGGTAAAC
2963514 CGTTAACCTT
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
61 54 0.51
62 48 0.46
63 3 0.03
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (62 bp):
TCCATATGTCCCGAAGAACATAGGTAAATAGTCCATATGTCCCGAAGAACATAGGTAAACAA
Found at i:2963505 original size:92 final size:92
Alignment explanation
Indices: 2963341--2963512 Score: 256
Period size: 92 Copynumber: 1.9 Consensus size: 92
2963331 TCCATAGGTT
* * *
2963341 CCGAAGAACCTAGGTAATCAGTCCATATGTTCCGAAGAACATAGGTAAACAATCCATATGTCCCG
1 CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATGTCCCG
*
2963406 AAAAACATAGGTAAATAGTCATATGTC
66 AAAAACATAGATAAATAGTCATATGTC
* * * *
2963433 CCGAAGAACATATGTAAACAGTGCATATGTCCCGAAGAACATATGTAAACAGTCCATATGTCCC-
1 CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATGTCCCG
2963497 AAAGAACATAGATAAA
66 AAA-AACATAGATAAA
2963513 CCGTTAACCT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
91 3 0.04
92 68 0.96
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (92 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAATCCATATGTCCCG
AAAAACATAGATAAATAGTCATATGTC
Found at i:2965057 original size:31 final size:31
Alignment explanation
Indices: 2965009--2965141 Score: 212
Period size: 31 Copynumber: 4.3 Consensus size: 31
2964999 CCAAAGAGCC
** **
2965009 TAGGTAATGAGTCCATATGTTTCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
*
2965040 TAGGTAAACAGTACATATGTCCCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
2965071 TAGGTAAACAGTCCATATGTCCCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
*
2965102 TATGTAAACAGTCCATATGTCCCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
2965133 TAGGTAAAC
1 TAGGTAAAC
2965142 CCTCGACCTT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 94 1.00
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.23
Consensus pattern (31 bp):
TAGGTAAACAGTCCATATGTCCCGAAGAACA
Found at i:2966672 original size:31 final size:31
Alignment explanation
Indices: 2966637--2966769 Score: 185
Period size: 31 Copynumber: 4.3 Consensus size: 31
2966627 CCAAAGAGCC
* **
2966637 TAGGTAATCAGTCCATATGTTTCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
* *
2966668 TAGGTAAACAGTACATATGTCCCAAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
*
2966699 TAGGTAAACAGTCCATATGTCTCGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
* * *
2966730 TATGTAAACAGTTCATATGTCCTGAAGAACA
1 TAGGTAAACAGTCCATATGTCCCGAAGAACA
2966761 TAGGTAAAC
1 TAGGTAAAC
2966770 CCTCGACCTT
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 89 1.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (31 bp):
TAGGTAAACAGTCCATATGTCCCGAAGAACA
Found at i:2966724 original size:62 final size:62
Alignment explanation
Indices: 2966627--2966769 Score: 214
Period size: 62 Copynumber: 2.3 Consensus size: 62
2966617 ACCATAGGTT
* * * *
2966627 CCAAAGAGCCTAGGTAATCAGTCCATATGTTTCGAAGAACATAGGTAAACAGTACATATGTC
1 CCAAAGAACATAGGTAAACAGTCCATATGTCTCGAAGAACATAGGTAAACAGTACATATGTC
* *
2966689 CCAAAGAACATAGGTAAACAGTCCATATGTCTCGAAGAACATATGTAAACAGTTCATATGTC
1 CCAAAGAACATAGGTAAACAGTCCATATGTCTCGAAGAACATAGGTAAACAGTACATATGTC
**
2966751 CTGAAGAACATAGGTAAAC
1 CCAAAGAACATAGGTAAAC
2966770 CCTCGACCTT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 73 1.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (62 bp):
CCAAAGAACATAGGTAAACAGTCCATATGTCTCGAAGAACATAGGTAAACAGTACATATGTC
Found at i:2967913 original size:18 final size:17
Alignment explanation
Indices: 2967890--2967928 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
2967880 TACATATATG
*
2967890 ATTATCCTCTTCCTTATC
1 ATTATCCTCTT-ATTATC
2967908 ATTATCCTCTTATTATC
1 ATTATCCTCTTATTATC
2967925 ATTA
1 ATTA
2967929 ATACCTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATCCTCTTATTATC
Found at i:2968291 original size:31 final size:31
Alignment explanation
Indices: 2968241--2968395 Score: 154
Period size: 31 Copynumber: 5.0 Consensus size: 31
2968231 CCCGAAGGAC
* * *
2968241 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCTGAAGAACATAGGTAAA
*
2968272 CATTCCATATGTTCTGAAGAACATAGGTAAA
1 CAGTCCATATGTTCTGAAGAACATAGGTAAA
* *
2968303 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCTGAAGAACATAGGTAAA
* *
2968334 CAGTCCATATG-TCTTGTAGAACATATGTAAA
1 CAGTCCATATGTTC-TGAAGAACATAGGTAAA
* * * **
2968365 CATTCTATATGTCCCAAAGAACATA-GTAAA
1 CAGTCCATATGTTCTGAAGAACATAGGTAAA
2968395 C
1 C
2968396 CCTCGACTCT
Statistics
Matches: 104, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
30 7 0.07
31 95 0.91
32 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (31 bp):
CAGTCCATATGTTCTGAAGAACATAGGTAAA
Found at i:2968341 original size:62 final size:62
Alignment explanation
Indices: 2968241--2968395 Score: 190
Period size: 62 Copynumber: 2.5 Consensus size: 62
2968231 CCCGAAGGAC
* * * *
2968241 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCATTCCATATGT-TCTGAAGAACATAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAACAGTCCATATGTCT-TGAAGAACATAGGTAAA
* *
2968303 CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCTTGTAGAACATATGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCTTGAAGAACATAGGTAAA
* * *
2968365 CATTCTATATGTCCCAAAGAACATA-GTAAAC
1 CAGTCCATATGTCCCGAAGAACATAGGTAAAC
2968396 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
61 6 0.07
62 74 0.90
63 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (62 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCTTGAAGAACATAGGTAAA
Found at i:2968653 original size:16 final size:17
Alignment explanation
Indices: 2968632--2968669 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2968622 TATAACACGT
*
2968632 ATCACA-AGTGCATGTA
1 ATCACATAGTACATGTA
*
2968648 ATCACATATTACATGTA
1 ATCACATAGTACATGTA
2968665 ATCAC
1 ATCAC
2968670 GTAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (17 bp):
ATCACATAGTACATGTA
Found at i:2975015 original size:13 final size:13
Alignment explanation
Indices: 2974999--2975028 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2974989 TAATTAGAGC
*
2974999 TTTAAATTTTAGG
1 TTTAAACTTTAGG
2975012 TTTAAACTTTAGG
1 TTTAAACTTTAGG
2975025 TTTA
1 TTTA
2975029 TTTTCACTTT
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:0.30, C:0.03, G:0.13, T:0.53
Consensus pattern (13 bp):
TTTAAACTTTAGG
Found at i:2982731 original size:22 final size:22
Alignment explanation
Indices: 2982705--2982784 Score: 85
Period size: 23 Copynumber: 3.7 Consensus size: 22
2982695 ATAGGGCAGA
*
2982705 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
* *
2982727 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATACCCCC-TTGAAG
*
2982750 GGGAACCGATTCCCCC-T--AG
1 GGGAACCGATACCCCCTTGAAG
*
2982769 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
2982785 CTGGGGTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 15 0.29
21 1 0.02
22 14 0.27
23 21 0.41
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.19
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:2982747 original size:23 final size:23
Alignment explanation
Indices: 2982705--2982766 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2982695 ATAGGGCAGA
* *
2982705 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
2982727 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCTTTGAAG
2982750 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
2982767 AGGGGAATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:2987997 original size:12 final size:12
Alignment explanation
Indices: 2987982--2988018 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2987972 AAAGAAAAAT
*
2987982 AAAAAGATTTCA
1 AAAAAGATTTAA
2987994 AAAAAGATTTAA
1 AAAAAGATTTAA
2988006 AAAAAG-TTTAA
1 AAAAAGATTTAA
2988017 AA
1 AA
2988019 GAAAATTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.29
12 17 0.71
ACGTcount: A:0.65, C:0.03, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAAAGATTTAA
Found at i:2988561 original size:16 final size:16
Alignment explanation
Indices: 2988540--2988573 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2988530 CCTCGGCTTG
*
2988540 AAAGAAAATTAAAGAA
1 AAAGAAAATAAAAGAA
2988556 AAAGAAAATAAAAGAA
1 AAAGAAAATAAAAGAA
2988572 AA
1 AA
2988574 GAATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (16 bp):
AAAGAAAATAAAAGAA
Found at i:2992196 original size:15 final size:15
Alignment explanation
Indices: 2992160--2992197 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2992150 TTTGATATCA
* *
2992160 TTTCTTATCATTTCT
1 TTTCTTCTCATTTCC
2992175 TTTCTTCTCATTTCC
1 TTTCTTCTCATTTCC
2992190 TTTCTTCT
1 TTTCTTCT
2992198 TCCATATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTCTTCTCATTTCC
Found at i:2995977 original size:13 final size:13
Alignment explanation
Indices: 2995949--2995997 Score: 80
Period size: 13 Copynumber: 3.7 Consensus size: 13
2995939 CTACTATTTT
*
2995949 CATCACCATCTTTC
1 CATCACCATC-CTC
2995963 CATCACCATCCTC
1 CATCACCATCCTC
2995976 CATCACCATCCTC
1 CATCACCATCCTC
2995989 CATCACCAT
1 CATCACCAT
2995998 TCACGCCCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 24 0.71
14 10 0.29
ACGTcount: A:0.24, C:0.49, G:0.00, T:0.27
Consensus pattern (13 bp):
CATCACCATCCTC
Found at i:2996258 original size:7 final size:6
Alignment explanation
Indices: 2996239--2996286 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
2996229 GTGTTGCAAC
* *
2996239 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG CAAAAAG CAAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG -AAAAAG AAAAAG AAAA
2996287 GACTCCTACA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 24 0.67
7 12 0.33
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2996260 original size:13 final size:12
Alignment explanation
Indices: 2996239--2996286 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
2996229 GTGTTGCAAC
2996239 AAAAAGAAAAAG
1 AAAAAGAAAAAG
*
2996251 AAAGAAGAAAAAC
1 AAA-AAGAAAAAG
2996264 AAAAAGCAAAAAG
1 AAAAAG-AAAAAG
*
2996277 CAAAAGAAAA
1 AAAAAGAAAA
2996287 GACTCCTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:2996264 original size:25 final size:25
Alignment explanation
Indices: 2996236--2996286 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
2996226 CAAGTGTTGC
2996236 AACAAAAAG-AAAAAGAAAGAAGAAA
1 AACAAAAAGCAAAAAGAAA-AAGAAA
*
2996261 AACAAAAAGCAAAAAGCAAAAGAAA
1 AACAAAAAGCAAAAAGAAAAAGAAA
2996286 A
1 A
2996287 GACTCCTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (25 bp):
AACAAAAAGCAAAAAGAAAAAGAAA
Found at i:2996281 original size:19 final size:19
Alignment explanation
Indices: 2996239--2996286 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
2996229 GTGTTGCAAC
2996239 AAAAAGAAAAAGAAAGAAG
1 AAAAAGAAAAAGAAAGAAG
*
2996258 AAAAACAAAAAGCAAA-AAG
1 AAAAAGAAAAAG-AAAGAAG
*
2996277 CAAAAGAAAA
1 AAAAAGAAAA
2996287 GACTCCTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 22 0.88
20 3 0.12
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAGAAAGAAG
Found at i:2999261 original size:13 final size:13
Alignment explanation
Indices: 2999243--2999292 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
2999233 TCTTCTTAGT
2999243 TCCATCACCATCC
1 TCCATCACCATCC
*
2999256 TCCATCACCATCT
1 TCCATCACCATCC
*
2999269 TTCATCACCATCC
1 TCCATCACCATCC
2999282 TCCATCACCAT
1 TCCATCACCAT
2999293 TCACGCCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.28
Consensus pattern (13 bp):
TCCATCACCATCC
Found at i:3001477 original size:2 final size:2
Alignment explanation
Indices: 3001470--3001513 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3001460 TCCGTTACAT
3001470 TA TA TA TA TA 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
3001512 TA
1 TA
3001514 AACAATTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3002152 original size:19 final size:19
Alignment explanation
Indices: 3002130--3002181 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
3002120 AAAAAATCAG
*
3002130 AAAAATAAAATTGAA-AAT
1 AAAAATAAAATTGAACAAC
3002148 AAAAATAAAAATTGAACAAAC
1 AAAAAT-AAAATTGAAC-AAC
3002169 GAAAAATAAAATT
1 -AAAAATAAAATT
3002182 AATAATGGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.21
19 9 0.31
21 8 0.28
22 6 0.21
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (19 bp):
AAAAATAAAATTGAACAAC
Found at i:3003146 original size:16 final size:16
Alignment explanation
Indices: 3003125--3003158 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3003115 CCTCGGCTTG
*
3003125 AAAGAAAATTAAAGAA
1 AAAGAAAATAAAAGAA
3003141 AAAGAAAATAAAAGAA
1 AAAGAAAATAAAAGAA
3003157 AA
1 AA
3003159 GATTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (16 bp):
AAAGAAAATAAAAGAA
Found at i:3011761 original size:27 final size:27
Alignment explanation
Indices: 3011723--3011778 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
3011713 AGCGTTCACA
3011723 CTGGATATGGTAAGAATCCTCCAATTT
1 CTGGATATGGTAAGAATCCTCCAATTT
3011750 CTGGATATGGTAAGAATCCTCCAATTT
1 CTGGATATGGTAAGAATCCTCCAATTT
3011777 CT
1 CT
3011779 CTATTGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (27 bp):
CTGGATATGGTAAGAATCCTCCAATTT
Found at i:3018006 original size:10 final size:10
Alignment explanation
Indices: 3017978--3018011 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3017968 TCCACCACAC
3017978 CAAATCCTCT
1 CAAATCCTCT
* *
3017988 TAAAACCTCT
1 CAAATCCTCT
3017998 CAAATCCTCT
1 CAAATCCTCT
3018008 CAAA
1 CAAA
3018012 CCATATCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (10 bp):
CAAATCCTCT
Found at i:3018020 original size:20 final size:20
Alignment explanation
Indices: 3017978--3018021 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3017968 TCCACCACAC
*
3017978 CAAATCCTCTTAAAACCTCT
1 CAAATCCTCTTAAAACCTAT
*
3017998 CAAATCCTC-TCAAACCATAT
1 CAAATCCTCTTAAAACC-TAT
3018018 CAAA
1 CAAA
3018022 AATCAAACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.41, C:0.34, G:0.00, T:0.25
Consensus pattern (20 bp):
CAAATCCTCTTAAAACCTAT
Found at i:3038917 original size:20 final size:20
Alignment explanation
Indices: 3038892--3038941 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
3038882 ATGACCAACA
3038892 AATTCGCAACTCGATTTCTG
1 AATTCGCAACTCGATTTCTG
3038912 AATTCGCAACTCGATTTCTG
1 AATTCGCAACTCGATTTCTG
3038932 AATTCGCAAC
1 AATTCGCAAC
3038942 GCGAATTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (20 bp):
AATTCGCAACTCGATTTCTG
Found at i:3039907 original size:24 final size:24
Alignment explanation
Indices: 3039890--3039935 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3039880 GTCAATATTC
3039890 GAAATTTGATCTTGGTCAATACCT
1 GAAATTTGATCTTGGTCAATACCT
*
3039914 GAACTTTGATCTTGGTCAATAC
1 GAAATTTGATCTTGGTCAATAC
3039936 TCGGATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.37
Consensus pattern (24 bp):
GAAATTTGATCTTGGTCAATACCT
Found at i:3042229 original size:18 final size:18
Alignment explanation
Indices: 3042206--3042241 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3042196 AAGTAAAAGG
*
3042206 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
3042224 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
3042242 CAACCGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:3042526 original size:29 final size:29
Alignment explanation
Indices: 3042484--3042539 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
3042474 CGATTTTTTG
*
3042484 TTGCGATTGTTGCGAAAGTCAAATTCGCA
1 TTGCGATTGTTGCGAAAATCAAATTCGCA
3042513 TTGCGATTGTTGCGAAAATCAAATTCG
1 TTGCGATTGTTGCGAAAATCAAATTCG
3042540 AAACGTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (29 bp):
TTGCGATTGTTGCGAAAATCAAATTCGCA
Found at i:3042605 original size:20 final size:20
Alignment explanation
Indices: 3042582--3042642 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
3042572 CGCAATGTGC
3042582 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* ***
3042602 ATTTTACTTTCGCAACGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
3042622 ATTTGACTTTTGCGTTACGA
1 ATTTGACTTTCGCGTTGCGA
3042642 A
1 A
3042643 AGTGTACTTT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:3044593 original size:21 final size:21
Alignment explanation
Indices: 3044569--3044616 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3044559 ATCATTGTCT
** *
3044569 TCACGTAAAGTACCGACCTCC
1 TCACGTAAAACACCGACCTCA
*
3044590 TCACGTAAAACACTGACCTCA
1 TCACGTAAAACACCGACCTCA
3044611 TCACGT
1 TCACGT
3044617 TACTCCCCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.21
Consensus pattern (21 bp):
TCACGTAAAACACCGACCTCA
Found at i:3046296 original size:19 final size:19
Alignment explanation
Indices: 3046272--3046314 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
3046262 TCTGAAACTT
**
3046272 AAAATCGCAACGTGAAATG
1 AAAATCGCAACACGAAATG
3046291 AAAATCGCAACACGAAATG
1 AAAATCGCAACACGAAATG
3046310 AAAAT
1 AAAAT
3046315 TACAACGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACACGAAATG
Found at i:3046332 original size:19 final size:19
Alignment explanation
Indices: 3046305--3046352 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
3046295 TCGCAACACG
*
3046305 AAATGAAAATTACAACGCAA
1 AAATAAAAATT-CAACGCAA
3046325 AAATAAAAATCTCAACGCAA
1 AAATAAAAAT-TCAACGCAA
*
3046345 AACTAAAA
1 AAATAAAA
3046353 TTGCGTTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.62, C:0.17, G:0.06, T:0.15
Consensus pattern (19 bp):
AAATAAAAATTCAACGCAA
Found at i:3046908 original size:19 final size:20
Alignment explanation
Indices: 3046886--3046923 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3046876 AATATTGTGT
3046886 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
3046905 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
3046924 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:3046955 original size:20 final size:20
Alignment explanation
Indices: 3046930--3046975 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
3046920 TAAACGCGCT
*
3046930 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTATGTG
3046950 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
3046970 TTGCGA
1 TTGCGA
3046976 TTTACAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.13, G:0.26, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:3047619 original size:21 final size:20
Alignment explanation
Indices: 3047592--3047690 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
3047582 AATCAGTTTC
3047592 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
3047613 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3047634 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
3047654 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3047675 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
3047691 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 15 0.25
21 44 0.75
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3047705 original size:40 final size:39
Alignment explanation
Indices: 3047658--3047851 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
3047648 GATTTTCCAG
* ** *
3047658 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
3047698 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* * *
3047738 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
3047778 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
* *
3047819 AATCGCAACGAGAATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
3047852 TATTTAAAGC
Statistics
Matches: 130, Mismatches: 21, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 98 0.75
41 31 0.24
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:3047741 original size:60 final size:60
Alignment explanation
Indices: 3047658--3047850 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
3047648 GATTTTCCAG
* ** *
3047658 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
* * * *
3047718 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTA
* ** * * *
3047778 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGAGAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT-AAATCGCAACGCGTATCCGTA
3047839 AATCGCAACGCG
1 AATCGCAACGCG
3047851 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.01
60 79 0.71
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
Found at i:3047823 original size:21 final size:20
Alignment explanation
Indices: 3047658--3047848 Score: 96
Period size: 20 Copynumber: 9.5 Consensus size: 20
3047648 GATTTTCCAG
* *
3047658 AATCGCAACGCGAATATGA-A
1 AATCGCAACGAGAATA-CATA
* *
3047678 AATCGCAACGCGAACACATA
1 AATCGCAACGAGAATACATA
* * * *
3047698 AATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACATA
* * * *
3047718 AATCGCAACGTGTATCCGTA
1 AATCGCAACGAGAATACATA
* * * *
3047738 AATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACATA
* * * * *
3047758 AATCGCAATGCGTATCCGTA
1 AATCGCAACGAGAATACATA
* * * * *
3047778 TATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACATA
*
3047798 AATCGCAACGATAATACATAA
1 AATCGCAACGAGAATACAT-A
* *
3047819 AATCGCAACGAGAATCCGTA
1 AATCGCAACGAGAATACATA
3047839 AATCGCAACG
1 AATCGCAACG
3047849 CGATATTTAA
Statistics
Matches: 149, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
19 1 0.01
20 131 0.88
21 17 0.11
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGAGAATACATA
Found at i:3048269 original size:33 final size:33
Alignment explanation
Indices: 3048230--3048300 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3048220 TTCACTTAGA
3048230 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
3048263 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
3048296 TTTCA
1 TTTCA
3048301 AGTTAGTATT
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:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:3048406 original size:21 final size:20
Alignment explanation
Indices: 3048380--3048487 Score: 95
Period size: 21 Copynumber: 5.7 Consensus size: 20
3048370 TGCAGAAGAG
3048380 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
3048401 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
3048421 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
3048442 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
3048456 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
*
3048475 TCGCAACGCGAAA
1 TCGCAACGAGAAA
3048488 CCAAAATCGC
Statistics
Matches: 71, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
14 11 0.15
16 2 0.03
17 2 0.03
19 12 0.17
20 18 0.25
21 26 0.37
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:3048424 original size:20 final size:20
Alignment explanation
Indices: 3048380--3048456 Score: 100
Period size: 21 Copynumber: 3.8 Consensus size: 20
3048370 TGCAGAAGAG
*
3048380 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
3048401 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
3048421 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
3048442 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
3048457 CGCAACGCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 20 0.42
21 28 0.58
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:3048437 original size:41 final size:41
Alignment explanation
Indices: 3048379--3048456 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
3048369 TTGCAGAAGA
*
3048379 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
3048420 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
3048457 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:3048478 original size:19 final size:19
Alignment explanation
Indices: 3048392--3048498 Score: 80
Period size: 19 Copynumber: 5.7 Consensus size: 19
3048382 GCAACGAGAT
*
3048392 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
*** *
3048411 AGAATGACTGTCGCAACGAGAG
1 A-AATGAAAATCGCAAC--GCG
3048433 AAATGAAAATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
3048450 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
3048466 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
**
3048485 AAACCAAAATCGCA
1 AAATGAAAATCGCA
3048499 TTGCGATTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 1 0.01
18 1 0.01
19 27 0.39
20 12 0.17
21 11 0.16
22 4 0.06
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:3048516 original size:19 final size:19
Alignment explanation
Indices: 3048494--3048607 Score: 94
Period size: 19 Copynumber: 6.1 Consensus size: 19
3048484 GAAACCAAAA
*
3048494 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3048513 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3048527 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3048546 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
3048566 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
* *
3048586 CTCTCGTTGCGATTTTTATT
1 -TCGCGTTGCGATTTTCATT
3048606 TC
1 TC
3048608 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
14 10 0.13
16 3 0.04
17 3 0.04
19 28 0.36
20 20 0.26
21 13 0.17
ACGTcount: A:0.11, C:0.24, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3048589 original size:20 final size:20
Alignment explanation
Indices: 3048523--3048601 Score: 106
Period size: 20 Copynumber: 4.0 Consensus size: 20
3048513 TCGCGTTGCG
3048523 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
3048543 ATT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
3048562 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
3048583 ATTCTCTCGTTGCGATTTT
1 ATTCTCTCGTTGCGATTTT
3048602 TATTTCAACC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 16 0.33
20 20 0.41
21 13 0.27
ACGTcount: A:0.11, C:0.24, G:0.18, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:3050465 original size:93 final size:92
Alignment explanation
Indices: 3050306--3050495 Score: 344
Period size: 93 Copynumber: 2.1 Consensus size: 92
3050296 TAGATTGCTT
3050306 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
* *
3050371 TTTGTGTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGATTG-A
*
3050399 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3050464 TTTGTCTTTGTTTTGTCTTTTGATTGA
66 TTTGTCTTTGTTTTGTCTTTTGATTGA
3050491 AGTAA
1 AGTAA
3050496 TGCAATCCAT
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 6 0.06
93 88 0.94
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (92 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGATTGA
Found at i:3050580 original size:19 final size:19
Alignment explanation
Indices: 3050540--3050668 Score: 134
Period size: 19 Copynumber: 7.3 Consensus size: 19
3050530 TAGTTTACTT
* *
3050540 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
3050560 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3050579 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3050598 TCGCAA--C-AAA--AGAA
1 TCGCAACGCGAAACCAAAA
3050612 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3050631 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAACCAAAA
3050645 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3050664 TCGCA
1 TCGCA
3050669 TTGCGATTTT
Statistics
Matches: 93, Mismatches: 6, Indels: 21
0.77 0.05 0.17
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.06
17 6 0.06
18 1 0.01
19 46 0.49
20 13 0.14
ACGTcount: A:0.48, C:0.28, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:3050614 original size:33 final size:33
Alignment explanation
Indices: 3050575--3050668 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
3050565 ACGCGAAACC
**
3050575 AAAATCGCAACGCGAAATGAAAATCGCAAC-AA
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAA
*
3050607 AAGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AA-AATCGCAACGCGAAACCAAAATCGCAACGAA
3050641 AAAATCGCAACGCGAAACCAAAATCGCA
1 AAAATCGCAACGCGAAACCAAAATCGCA
3050669 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 52 0.91
34 3 0.05
ACGTcount: A:0.50, C:0.27, G:0.16, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGAA
Found at i:3050645 original size:14 final size:14
Alignment explanation
Indices: 3050626--3050652 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3050616 AACGCGAAAC
3050626 CAAAATCGCAACGA
1 CAAAATCGCAACGA
3050640 CAAAATCGCAACG
1 CAAAATCGCAACG
3050653 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:3050666 original size:52 final size:52
Alignment explanation
Indices: 3050540--3050668 Score: 147
Period size: 52 Copynumber: 2.5 Consensus size: 52
3050530 TAGTTTACTT
** *
3050540 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACAAAAAATCGCAACGCGAAACCAAAATCGCAACGCAAAA
* *
3050592 T-G-AAAATCGCAACAAAAGAATCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACA-CGAAACAAAA-AATCGCAACGCGAAACCAAAATCGCAACG-CAAAA
* *
3050645 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACAAAAAATCGCA
3050669 TTGCGATTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
50 3 0.05
51 8 0.13
52 37 0.59
53 7 0.11
54 6 0.10
55 2 0.03
ACGTcount: A:0.48, C:0.28, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACAAAAAATCGCAACGCGAAACCAAAATCGCAACGCAAAA
Found at i:3050686 original size:19 final size:19
Alignment explanation
Indices: 3050664--3050836 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
3050654 GAAACCAAAA
*
3050664 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3050683 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
*
3050699 T--CGTTGGGATTTTCATT
1 TCGCGTTGCGATTTTCATT
** *
3050716 TCGTATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3050732 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3050749 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
3050768 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
3050787 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
3050806 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3050826 TCGTGTTGCGA
1 TCGCGTTGCGA
3050837 AAGTAAACTA
Statistics
Matches: 124, Mismatches: 19, Indels: 21
0.76 0.12 0.13
Matches are distributed among these distances:
14 13 0.10
16 11 0.09
17 11 0.09
19 77 0.62
20 12 0.10
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3050794 original size:38 final size:38
Alignment explanation
Indices: 3050664--3050836 Score: 150
Period size: 33 Copynumber: 4.8 Consensus size: 38
3050654 GAAACCAAAA
*
3050664 TCGCATTGCGATTTTCATTTCGCGTTGCGA-T-TC-TT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* ** *
3050699 T--CGTTGGGATTTTCATTTCGTATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* **
3050732 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
** *
3050768 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
* *
3050806 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
3050837 AAGTAAACTA
Statistics
Matches: 112, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
33 52 0.46
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.39
39 11 0.10
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTATCATT
Found at i:3052780 original size:14 final size:14
Alignment explanation
Indices: 3052761--3052796 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3052751 ATTGTTTAAT
3052761 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3052775 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3052789 TGATTTGT
1 TGATTTGT
3052797 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:3052919 original size:19 final size:19
Alignment explanation
Indices: 3052903--3052996 Score: 126
Period size: 19 Copynumber: 5.2 Consensus size: 19
3052893 AAAAATGACT
3052903 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3052922 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3052941 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
3052955 ATCGCAATGCGAAATTAAA
1 ATCGCAATGCGAAATGAAA
3052974 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3052994 ATC
1 ATC
3052997 ACAACGAGAG
Statistics
Matches: 65, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 38 0.58
20 11 0.17
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3053032 original size:53 final size:53
Alignment explanation
Indices: 3052903--3053019 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
3052893 AAAAATGACT
* *
3052903 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATTAAAATCGCAATGCGGAAATGAAAATCACAACGAGAGA
3052955 ATCGCAATGCGAAATTAAAATCGCAATGCGGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATTAAAATCGCAATGCGGAAATGAAAATCACAACGAGAGA
3053008 ATCGCAATGCGA
1 ATCGCAATGCGA
3053020 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 28 0.45
53 34 0.55
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATTAAAATCGCAATGCGGAAATGAAAATCACAACGAGAGA
Found at i:3053062 original size:33 final size:33
Alignment explanation
Indices: 3053015--3053178 Score: 163
Period size: 33 Copynumber: 4.8 Consensus size: 33
3053005 AGAATCGCAA
*
3053015 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
3053048 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
3053086 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
3053119 TGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
3053153 TGCGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
3053179 TTCATTTCCG
Statistics
Matches: 106, Mismatches: 13, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
31 4 0.04
32 6 0.06
33 47 0.44
34 18 0.17
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.08
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:3053176 original size:86 final size:84
Alignment explanation
Indices: 3053066--3053245 Score: 242
Period size: 86 Copynumber: 2.1 Consensus size: 84
3053056 TCATTTCGCA
3053066 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-TTGCGATTTTCATTTCGCATTGCGATTT
1 TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTCA--T-G--TTGCGATTT
3053127 TCATTTCCGCATTGCGATTCTCTCG
61 TCATTT-CGCATTGCGATTCTCTCG
* *
3053152 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-ATTGCGATTTTCATGTTGCGATTTTCA
3053217 TTTCGCATTGCGATTCTCTCG
64 TTTCGCATTGCGATTCTCTCG
3053238 TTGCGATT
1 TTGCGATT
3053246 GTAATTTCCG
Statistics
Matches: 86, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
86 51 0.59
87 14 0.16
88 3 0.03
89 3 0.03
90 3 0.03
92 12 0.14
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (84 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTCATGTTGCGATTTTCATT
TCGCATTGCGATTCTCTCG
Found at i:3053229 original size:33 final size:34
Alignment explanation
Indices: 3053047--3053245 Score: 185
Period size: 33 Copynumber: 5.7 Consensus size: 34
3053037 GATTCTCTCG
3053047 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCA--TCG--TTGCGATTTTCATTTCGCA
*
3053085 TTGCGATTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
* * * *
3053118 TTGCGATTTTCAT--TTCCGCA-TTGCGATTCTCTCG
1 TTGCGATTTTCATCGTTGCG-ATTTTC-ATT-TCGCA
3053152 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCA--TCG--TTGCGATTTTCATTT-CGCA
*
3053191 TTGCGATTTTCAT-GTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
*
3053224 TTGCGATTCTC-TCGTTGCGATT
1 TTGCGATTTTCATCGTTGCGATT
3053246 GTAATTTCCG
Statistics
Matches: 135, Mismatches: 13, Indels: 31
0.75 0.07 0.17
Matches are distributed among these distances:
32 8 0.06
33 55 0.41
34 30 0.22
35 3 0.02
36 2 0.01
37 1 0.01
38 11 0.08
39 18 0.13
40 7 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (34 bp):
TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
Found at i:3053231 original size:19 final size:19
Alignment explanation
Indices: 3053009--3053231 Score: 234
Period size: 19 Copynumber: 12.7 Consensus size: 19
3052999 AACGAGAGAA
* *
3053009 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
3053028 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
3053044 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3053061 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
3053080 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
3053096 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3053113 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
3053132 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
3053149 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3053166 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3053185 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
3053203 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
3053219 TCGCATTGCGATT
1 TCGCATTGCGATT
3053232 CTCTCGTTGC
Statistics
Matches: 172, Mismatches: 10, Indels: 44
0.76 0.04 0.19
Matches are distributed among these distances:
14 29 0.17
16 21 0.12
17 20 0.12
18 4 0.02
19 72 0.42
20 26 0.15
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3053260 original size:53 final size:53
Alignment explanation
Indices: 3053009--3053231 Score: 380
Period size: 53 Copynumber: 4.2 Consensus size: 53
3052999 AACGAGAGAA
* *
3053009 TCGCAATGCGATTTTAATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
3053061 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
3053113 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* *
3053166 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGATTTTCATT
3053219 TCGCATTGCGATT
1 TCGCATTGCGATT
3053232 CTCTCGTTGC
Statistics
Matches: 165, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
52 70 0.42
53 94 0.57
54 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:3055760 original size:24 final size:24
Alignment explanation
Indices: 3055726--3055772 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3055716 CTGAAACATC
3055726 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3055750 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3055773 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:3056493 original size:20 final size:20
Alignment explanation
Indices: 3056465--3056673 Score: 231
Period size: 20 Copynumber: 10.4 Consensus size: 20
3056455 AAATTTCAGT
* * *
3056465 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
3056485 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
3056505 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
3056525 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
3056545 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
3056565 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
3056585 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
3056605 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
3056625 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
3056645 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
3056665 GTTGCGATT
1 GTTGCGATT
3056674 CTGGAAAATC
Statistics
Matches: 167, Mismatches: 20, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
20 166 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:3058044 original size:12 final size:12
Alignment explanation
Indices: 3058027--3058054 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3058017 ATCGTTAAAA
3058027 AATTAAATTTAT
1 AATTAAATTTAT
3058039 AATTAAATTTAT
1 AATTAAATTTAT
3058051 AATT
1 AATT
3058055 TATTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTAAATTTAT
Found at i:3058412 original size:51 final size:50
Alignment explanation
Indices: 3058256--3058420 Score: 228
Period size: 51 Copynumber: 3.3 Consensus size: 50
3058246 AGATGTACAT
**
3058256 ACTTACATCGGTGTAAGTATGCATTAAGTGCTACACTTTTTTATTTTATTC
1 ACTTACATCGGTGTAAGTATGTGTTAAGTGCTACAC-TTTTTATTTTATTC
* *
3058307 ACTTACA-CTAGTGT-AGTATGTGTTAAGTGTTACAC-TTTTATTTTATTC
1 ACTTACATC-GGTGTAAGTATGTGTTAAGTGCTACACTTTTTATTTTATTC
*
3058355 ACTTACATCGGTGTAAGAATGTGTTAAGTGCTACACTTGTTTATTTTATTC
1 ACTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTT-TTTATTTTATTC
*
3058406 ACTTACACCGGTGTA
1 ACTTACATCGGTGTA
3058421 GTGTTAAGTG
Statistics
Matches: 101, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
48 24 0.24
49 20 0.20
50 20 0.20
51 37 0.37
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (50 bp):
ACTTACATCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTATTTTATTC
Found at i:3066160 original size:17 final size:19
Alignment explanation
Indices: 3066119--3066161 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
3066109 TATATTAACT
3066119 TTAAGAAATATTTTTATCATA
1 TTAA-AAATATTTTTAT-ATA
3066140 TTAAAAATA-TTTTAT-TA
1 TTAAAAATATTTTTATATA
3066157 TTAAA
1 TTAAA
3066162 TCATTTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.32
19 6 0.27
20 5 0.23
21 4 0.18
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
TTAAAAATATTTTTATATA
Found at i:3073127 original size:25 final size:25
Alignment explanation
Indices: 3073099--3073161 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
3073089 TTTTAAACAA
*
3073099 CACTTTTAAAAGTTTTTTTCTACCG
1 CACTTTTAAAAGTTCTTTTCTACCG
3073124 CACTTTTAAAAGTTCTTTTCTACCG
1 CACTTTTAAAAGTTCTTTTCTACCG
*
3073149 CATTTTTAAAAGT
1 CACTTTTAAAAGT
3073162 CAATTTCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (25 bp):
CACTTTTAAAAGTTCTTTTCTACCG
Found at i:3073489 original size:28 final size:28
Alignment explanation
Indices: 3073457--3073521 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 28
3073447 AATTTTCGAT
*
3073457 TGCCTTTCCTTTTAAATTTGTATCAGTA
1 TGCCTTTCCTTTTAAACTTGTATCAGTA
*
3073485 TGCCTTTCCTTTTAAACTTGTATTAGTA
1 TGCCTTTCCTTTTAAACTTGTATCAGTA
3073513 TG-CTTTCCT
1 TGCCTTTCCT
3073522 AGACATTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 7 0.20
28 28 0.80
ACGTcount: A:0.18, C:0.20, G:0.11, T:0.51
Consensus pattern (28 bp):
TGCCTTTCCTTTTAAACTTGTATCAGTA
Found at i:3074799 original size:15 final size:15
Alignment explanation
Indices: 3074778--3074815 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
3074768 TAGAAGGTAA
3074778 AATTATTTTTTA-TT
1 AATTATTTTTTATTT
3074792 ATATTATTTTTTATTT
1 A-ATTATTTTTTATTT
3074808 AATTATTT
1 AATTATTT
3074816 AATCAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 18 0.82
16 3 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
AATTATTTTTTATTT
Found at i:3077288 original size:16 final size:17
Alignment explanation
Indices: 3077267--3077299 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3077257 ACACACTAAA
*
3077267 TCGGTT-TCGGTTTTTT
1 TCGGTTATCGATTTTTT
3077283 TCGGTTATCGATTTTTT
1 TCGGTTATCGATTTTTT
3077300 GGATCGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.06, C:0.12, G:0.21, T:0.61
Consensus pattern (17 bp):
TCGGTTATCGATTTTTT
Found at i:3085809 original size:29 final size:29
Alignment explanation
Indices: 3085767--3085831 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
3085757 GGAAGAGAGA
* *
3085767 GAAAGAAACGTTAGGCACCAAACTATAAC
1 GAAATAAACGTTAGGCACCAAACTAGAAC
* *
3085796 GAAATAAACGTTAGGCGCCAAACTGGAAC
1 GAAATAAACGTTAGGCACCAAACTAGAAC
3085825 GAAATAA
1 GAAATAA
3085832 TTTTTTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (29 bp):
GAAATAAACGTTAGGCACCAAACTAGAAC
Found at i:3085855 original size:21 final size:21
Alignment explanation
Indices: 3085825--3085878 Score: 92
Period size: 20 Copynumber: 2.6 Consensus size: 21
3085815 AAACTGGAAC
*
3085825 GAAATAATTTTTTTATTTTCA
1 GAAATCATTTTTTTATTTTCA
3085846 GAAATCA-TTTTTTATTTTCA
1 GAAATCATTTTTTTATTTTCA
3085866 GAAATCATTTTTT
1 GAAATCATTTTTT
3085879 AATATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.56
Consensus pattern (21 bp):
GAAATCATTTTTTTATTTTCA
Found at i:3085876 original size:19 final size:20
Alignment explanation
Indices: 3085833--3085879 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
3085823 ACGAAATAAT
3085833 TTTTTTATTTTCAGAAATCA
1 TTTTTTATTTTCAGAAATCA
3085853 TTTTTTATTTTCAGAAATCA
1 TTTTTTATTTTCAGAAATCA
3085873 TTTTTTA
1 TTTTTTA
3085880 ATATTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTTTATTTTCAGAAATCA
Found at i:3085891 original size:21 final size:20
Alignment explanation
Indices: 3085833--3085891 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
3085823 ACGAAATAAT
* * *
3085833 TTTTTTATTTTCAGAAATCA
1 TTTTTTATATTAAAAAATCA
* * *
3085853 TTTTTTATTTTCAGAAATCA
1 TTTTTTATATTAAAAAATCA
3085873 TTTTTTAATATTAAAAAAT
1 TTTTTT-ATATTAAAAAAT
3085892 ATGTCAGGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 26 0.74
21 9 0.26
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTTTTATATTAAAAAATCA
Found at i:3086566 original size:36 final size:35
Alignment explanation
Indices: 3086478--3086866 Score: 421
Period size: 36 Copynumber: 10.8 Consensus size: 35
3086468 AGTTAGAAGT
3086478 CATTTTG-AAATTATATAATATATAGTCTTTTAAAAAA
1 CATTTTGAAAATTATATAATATATAGT-TTTT--AAAA
* *
3086515 CATTTTG-AAAGTATATAATATATGGTTTTTAAAA
1 CATTTTGAAAATTATATAATATATAGTTTTTAAAA
* * *
3086549 CATTTTGAAAACTTATATAATGTATAGTTTTGAAAT
1 CATTTTGAAAA-TTATATAATATATAGTTTTTAAAA
3086585 CATTTTGAAAATATATATAATATATAGTTTTTAAAA
1 CATTTTGAAAAT-TATATAATATATAGTTTTTAAAA
* * *
3086621 CTTTTTTGAAAACTTATATAATATATAGTTTTGAAAT
1 C-ATTTTGAAAA-TTATATAATATATAGTTTTTAAAA
*
3086658 CATTTTGAAAATATATATAATATATTGTTTTTAAAA
1 CATTTTGAAAAT-TATATAATATATAGTTTTTAAAA
**
3086694 CATTTTTGAAAACTTATATAATATATAGCTTTAAAAAAA
1 CA-TTTTGAAAA-TTATATAATATATAG-TTT-TTAAAA
* *
3086733 AATTTTGAAAAATTATATAATATATAGTTTTAAAAA
1 CATTTTG-AAAATTATATAATATATAGTTTTTAAAA
*
3086769 CATTTTTGAAAAAT-TAT-ATATATAG-TTTTAAAA
1 CA-TTTTGAAAATTATATAATATATAGTTTTTAAAA
* *
3086802 TCATTTTGAAAACTTATACAATATATAGTTTTGAAAA
1 -CATTTTGAAAA-TTATATAATATATAGTTTTTAAAA
* * *
3086839 CTTTTTTAAAA-AATATAATATATAGTTT
1 CATTTTGAAAATTATATAATATATAGTTT
3086867 AAAAAAAATA
Statistics
Matches: 303, Mismatches: 32, Indels: 37
0.81 0.09 0.10
Matches are distributed among these distances:
33 16 0.05
34 37 0.12
35 10 0.03
36 114 0.38
37 92 0.30
38 25 0.08
39 9 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (35 bp):
CATTTTGAAAATTATATAATATATAGTTTTTAAAA
Found at i:3086575 original size:73 final size:72
Alignment explanation
Indices: 3086478--3086904 Score: 455
Period size: 73 Copynumber: 5.9 Consensus size: 72
3086468 AGTTAGAAGT
* *
3086478 CATTTTG-AAA-TTATATAATATATAGTCTTTTAAAAAACATTTTG-AAA-GTATATAATATATG
1 CATTTTGAAAACTTATATAATATATAG--TTTT-AAAAACATTTTGAAAATATATATAATATATA
3086539 GTTTTTAAAA
63 GTTTTTAAAA
* * *
3086549 CATTTTGAAAACTTATATAATGTATAGTTTTGAAATCATTTTGAAAATATATATAATATATAGTT
1 CATTTTGAAAACTTATATAATATATAGTTTTAAAAACATTTTGAAAATATATATAATATATAGTT
3086614 TTTAAAA
66 TTTAAAA
* * * *
3086621 CTTTTTTGAAAACTTATATAATATATAGTTTTGAAATCATTTTGAAAATATATATAATATATTGT
1 C-ATTTTGAAAACTTATATAATATATAGTTTTAAAAACATTTTGAAAATATATATAATATATAGT
3086686 TTTTAAAA
65 TTTTAAAA
* *
3086694 CATTTTTGAAAACTTATATAATATATAGCTTTAAAAAAAAATTTTGAAAA-ATTATATAATATAT
1 CA-TTTTGAAAACTTATATAATATATAG-TTT-TAAAAACATTTTGAAAATA-TATATAATATAT
*
3086758 AGTTTTAAAAA
62 AGTTTTTAAAA
* * *
3086769 CATTTTTGAAAA-AT-TAT-ATATATAGTTTTAAAATCATTTTGAAAACT-TATACAATATATAG
1 CA-TTTTGAAAACTTATATAATATATAGTTTTAAAAACATTTTGAAAA-TATATATAATATATAG
*
3086830 TTTTGAAAA
64 TTTTTAAAA
* * * * * *
3086839 CTTTTTTAAAA--AATATAATATATAGTTTAAAAAAAATATTTTTG-AAATATATATAATTTATA
1 CATTTTGAAAACTTATATAATATATAGTTT--TAAAAACA-TTTTGAAAATATATATAATATATA
3086901 GTTT
63 GTTT
3086905 ATATTATTTT
Statistics
Matches: 310, Mismatches: 29, Indels: 33
0.83 0.08 0.09
Matches are distributed among these distances:
69 11 0.04
70 57 0.18
71 18 0.06
72 57 0.18
73 116 0.37
74 5 0.02
75 46 0.15
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (72 bp):
CATTTTGAAAACTTATATAATATATAGTTTTAAAAACATTTTGAAAATATATATAATATATAGTT
TTTAAAA
Found at i:3086881 original size:36 final size:36
Alignment explanation
Indices: 3086479--3086905 Score: 188
Period size: 37 Copynumber: 11.8 Consensus size: 36
3086469 GTTAGAAGTC
** ** *
3086479 ATTTTGAAATTATATAATATATAGTCTTTTAAAAAAC
1 ATTTTGAAAAAATATAATATATAGT-TTAAAAAAAAT
** * ** *
3086516 ATTTTGAAAGTATATAATATATGGTTT--TTAAAAC
1 ATTTTGAAAAAATATAATATATAGTTTAAAAAAAAT
* * **
3086550 ATTTTGAAAACTTATATAATGTATAGTTT---TGAAAT
1 ATTTTGAAAA--AATATAATATATAGTTTAAAAAAAAT
** *
3086585 CATTTTGAAAATATATATAATATATAGTTT-TTAAAACT
1 -ATTTTGAAAA-A-ATATAATATATAGTTTAAAAAAAAT
* * **
3086623 TTTTTGAAAACTTATATAATATATAGTTT---TGAAAT
1 ATTTTGAAAA--AATATAATATATAGTTTAAAAAAAAT
* ** *
3086658 CATTTTGAAAATATATATAATATATTGTTTTTAAAACAT
1 -ATTTTGAAAA-A-ATATAATATATAGTTTAAAAAAAAT
*
3086697 -TTTTGAAAACTTATATAATATATAGCTTTAAAAAAAA-
1 ATTTTGAAAA--AATATAATATATAG-TTTAAAAAAAAT
* *
3086734 ATTTTGAAAAATTATATAATATATAGTTTTAAAAACAT
1 ATTTTGAAAAA--ATATAATATATAGTTTAAAAAAAAT
* *
3086772 -TTTTGAAAAATTAT-ATATATAGTTT---TAAAAT
1 ATTTTGAAAAAATATAATATATAGTTTAAAAAAAAT
* * ** *
3086803 CATTTTGAAAACTTATACAATATATAGTTT-TGAAAACT
1 -ATTTTGAAAA--AATATAATATATAGTTTAAAAAAAAT
*
3086841 -TTTTTAAAAAATATAATATATAGTTTAAAAAAAAT
1 ATTTTGAAAAAATATAATATATAGTTTAAAAAAAAT
* *
3086876 ATTTTTGAAATATATATAATTTATAGTTTA
1 A-TTTTGAAA-AAATATAATATATAGTTTA
3086906 TATTATTTTA
Statistics
Matches: 311, Mismatches: 50, Indels: 57
0.74 0.12 0.14
Matches are distributed among these distances:
31 4 0.01
33 9 0.03
34 40 0.13
35 19 0.06
36 85 0.27
37 95 0.31
38 56 0.18
39 3 0.01
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
ATTTTGAAAAAATATAATATATAGTTTAAAAAAAAT
Done.