Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 86 of 109
Found at i:27598147 original size:23 final size:22
Alignment explanation
Indices: 27598117--27598160 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
27598107 AATATAAGAA
*
27598117 ATCTAGATGTATGAATGTACTT
1 ATCTAGATGCATGAATGTACTT
*
27598139 ATCTAAGATGCATGTATGTACT
1 ATCT-AGATGCATGAATGTACT
27598161 AAAGTCACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (22 bp):
ATCTAGATGCATGAATGTACTT
Found at i:27602681 original size:42 final size:42
Alignment explanation
Indices: 27602633--27602729 Score: 167
Period size: 42 Copynumber: 2.3 Consensus size: 42
27602623 CTCGGTATCA
* **
27602633 CACACTTAGTGCCCGTTATTCAACATCATTATTTTAATTTCG
1 CACACTTAGTGCCCATTACCCAACATCATTATTTTAATTTCG
27602675 CACACTTAGTGCCCATTACCCAACATCATTATTTTAATTTCG
1 CACACTTAGTGCCCATTACCCAACATCATTATTTTAATTTCG
27602717 CACACTTAGTGCC
1 CACACTTAGTGCC
27602730 GTTCATATAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.27, C:0.28, G:0.09, T:0.36
Consensus pattern (42 bp):
CACACTTAGTGCCCATTACCCAACATCATTATTTTAATTTCG
Found at i:27603631 original size:16 final size:17
Alignment explanation
Indices: 27603598--27603631 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27603588 TATAAAGTTA
*
27603598 ATATTTACCTTATTACT
1 ATATTAACCTTATTACT
27603615 ATATTAACCTT-TTACT
1 ATATTAACCTTATTACT
27603631 A
1 A
27603632 ATAATTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTAACCTTATTACT
Found at i:27604591 original size:114 final size:114
Alignment explanation
Indices: 27604439--27604647 Score: 328
Period size: 114 Copynumber: 1.8 Consensus size: 114
27604429 CTTCTCTTTT
* * * *
27604439 TTTTTCTTTTCTTAAGAATATATTGAACATTTTTACGCGAATAGAGATGACAACCAAGCACCCCA
1 TTTTTCTTTTCTTAAGAATATATTCAACATTTTGACGCGAAGAGAGATGACAACCAAACACCCCA
* * *
27604504 CCTCGGTTACTCAGCCCAACGCACTCCTAATTTATTATATTTATATATG
66 CCCCGGGTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATG
* *
27604553 TTTTTCTTTTCTTTAGAATATATTCAACCTTTTGACGCGAAGAGAGATGACAACCAAACACCCCA
1 TTTTTCTTTTCTTAAGAATATATTCAACATTTTGACGCGAAGAGAGATGACAACCAAACACCCCA
*
27604618 CCCCGGGTACTCAGCCCAACACATTCCTAA
66 CCCCGGGTACTCAGCCCAACACACTCCTAA
27604648 AAAATTTTTG
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 85 1.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (114 bp):
TTTTTCTTTTCTTAAGAATATATTCAACATTTTGACGCGAAGAGAGATGACAACCAAACACCCCA
CCCCGGGTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATG
Found at i:27605073 original size:18 final size:18
Alignment explanation
Indices: 27605020--27605073 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
27605010 ATTCACCTAA
* *
27605020 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAATT
*
27605039 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAATT
27605057 ACCCAACCCAACCCAAT
1 ACCCAACCCAACCCAAT
27605074 CATAAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 26 0.84
19 5 0.16
ACGTcount: A:0.41, C:0.46, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAATT
Found at i:27607894 original size:33 final size:33
Alignment explanation
Indices: 27607857--27607930 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
27607847 TTATTTCTTT
* *
27607857 TTGGAAATAAAGAGTTTGCCGTTGTATTTGCTG
1 TTGGAAATAAACAGTTTGCCGTTGTATCTGCTG
* ** *
27607890 TTGGAAATTAACAGTTTGTTGTTGTATCTGTTG
1 TTGGAAATAAACAGTTTGCCGTTGTATCTGCTG
27607923 TTGGAAAT
1 TTGGAAAT
27607931 CAAGCATATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.24, C:0.07, G:0.26, T:0.43
Consensus pattern (33 bp):
TTGGAAATAAACAGTTTGCCGTTGTATCTGCTG
Found at i:27610196 original size:20 final size:20
Alignment explanation
Indices: 27610151--27610197 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
27610141 TACATTTTGA
27610151 ATAATTCCATTAATGGTAAT
1 ATAATTCCATTAATGGTAAT
*
27610171 -TCAATTCGATTAATGG-AAT
1 AT-AATTCCATTAATGGTAAT
27610190 GATAATTC
1 -ATAATTC
27610198 AATTTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 4 0.17
20 18 0.78
21 1 0.04
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (20 bp):
ATAATTCCATTAATGGTAAT
Found at i:27610571 original size:85 final size:86
Alignment explanation
Indices: 27610482--27610652 Score: 195
Period size: 86 Copynumber: 2.0 Consensus size: 86
27610472 TAAGGTTTTT
* * * * * * *
27610482 TTTTTTTTGCATTTAAGTGAGCACTTAAA-TTTTAGAATG-TATTAAAAAGGCTCTCAAACTTTT
1 TTTTTTTTGCACTTAAGTGAGCACTTAAACTTTCAAAATGCT-TCAAAAAGACACTCAAAATTTT
27610545 TCAAAAGAA-AATTAAGCCCCTG
65 TCAAAA-AACAATTAAGCCCCTG
* * * *
27610567 TTTTTTTTTCACTTAATTGGGTACTTAAACTTTCAAAATGCTTCAAAAAGACACTCAAAATTTTT
1 TTTTTTTTGCACTTAAGTGAGCACTTAAACTTTCAAAATGCTTCAAAAAGACACTCAAAATTTTT
27610632 CAAAAAAGCAATTAAGCCCCT
66 CAAAAAA-CAATTAAGCCCCT
27610653 ACTCTTATTA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
85 26 0.37
86 32 0.45
87 13 0.18
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (86 bp):
TTTTTTTTGCACTTAAGTGAGCACTTAAACTTTCAAAATGCTTCAAAAAGACACTCAAAATTTTT
CAAAAAACAATTAAGCCCCTG
Found at i:27610768 original size:46 final size:45
Alignment explanation
Indices: 27610681--27610770 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 45
27610671 AAAAAAAATT
*
27610681 ATAAAAAATAAAAAATAAAAAATTTTAGAAAATTATTAAATTTTA
1 ATAAAAAATAAAAAATAAAAAATTTTAGAAAATTATGAAATTTTA
* *
27610726 ATAAAAATATAAAAAATTTAAAAGTTATTA-AAAATTA-GAAATTTT
1 ATAAAAA-ATAAAAAA-TAAAAAATT-TTAGAAAATTATGAAATTTT
27610771 TTTATAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
45 7 0.18
46 15 0.38
47 14 0.36
48 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (45 bp):
ATAAAAAATAAAAAATAAAAAATTTTAGAAAATTATGAAATTTTA
Found at i:27611217 original size:16 final size:16
Alignment explanation
Indices: 27611180--27611221 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
27611170 TTAATCATAT
*
27611180 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
27611196 TT-AAATATATTATAA
1 TTAAAATATATTATAA
27611211 TTAAAATATAT
1 TTAAAATATAT
27611222 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:27611228 original size:14 final size:15
Alignment explanation
Indices: 27611189--27611230 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
27611179 TTTAAACATA
*
27611189 ATTATTATTAAATAT
1 ATTATAATTAAATAT
27611204 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
27611218 A-TATAATTTAATA
1 ATTATAATTAAATA
27611231 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:27616864 original size:29 final size:29
Alignment explanation
Indices: 27616831--27616928 Score: 96
Period size: 29 Copynumber: 3.4 Consensus size: 29
27616821 TTACATTTTG
* *
27616831 TATAATTTTCTTATGACTTTATAAAATTT
1 TATAATTTTTTTATGAATTTATAAAATTT
*
27616860 TATAATTTTTTTAT-AATTCTAT-ATATTT
1 TATAATTTTTTTATGAATT-TATAAAATTT
* *
27616888 TAT-ATTTTTTTACGATTTTTATAAAATTT
1 TATAATTTTTTTATGA-ATTTATAAAATTT
*
27616917 TA-CATTTTTTTA
1 TATAATTTTTTTA
27616929 CTATTTTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
27 9 0.16
28 15 0.26
29 34 0.59
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (29 bp):
TATAATTTTTTTATGAATTTATAAAATTT
Found at i:27616926 original size:19 final size:19
Alignment explanation
Indices: 27616848--27616926 Score: 54
Period size: 19 Copynumber: 4.2 Consensus size: 19
27616838 TTCTTATGAC
*
27616848 TTTATAAAATTTTATAATTT
1 TTTATAAAATTTTA-CATTT
* * * *
27616868 TTT-TATAATTCTATATAT
1 TTTATAAAATTTTACATTT
***
27616886 TTTATATTTTTTTACGA-TT
1 TTTATAAAATTTTAC-ATTT
27616905 TTTATAAAATTTTACATTT
1 TTTATAAAATTTTACATTT
27616924 TTT
1 TTT
27616927 TACTATTTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
18 7 0.16
19 33 0.75
20 4 0.09
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (19 bp):
TTTATAAAATTTTACATTT
Found at i:27616934 original size:11 final size:10
Alignment explanation
Indices: 27616920--27616965 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
27616910 AAAATTTTAC
27616920 ATTTTTTTACT
1 ATTTTTTT-CT
27616931 A-TTTTTT-T
1 ATTTTTTTCT
27616939 ATTTTTTTCT
1 ATTTTTTTCT
27616949 ATTTTTTTCT
1 ATTTTTTTCT
27616959 AATTTTT
1 -ATTTTT
27616966 AATTTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 2 0.06
9 6 0.19
10 17 0.53
11 7 0.22
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (10 bp):
ATTTTTTTCT
Found at i:27616946 original size:29 final size:29
Alignment explanation
Indices: 27616885--27616973 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
27616875 ATTCTATATA
* * * ***
27616885 TTTTATATTTTTTTACGATTTTTATAAAA
1 TTTTACATTTTTTTACTATTTTTTTATTT
27616914 TTTTACATTTTTTTACTATTTTTTTATTT
1 TTTTACATTTTTTTACTATTTTTTTATTT
* *
27616943 TTTT-CTATTTTTTT-CTAATTTTTAATTT
1 TTTTAC-ATTTTTTTACTATTTTTTTATTT
27616971 TTT
1 TTT
27616974 AATTAAAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
28 16 0.31
29 35 0.69
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.72
Consensus pattern (29 bp):
TTTTACATTTTTTTACTATTTTTTTATTT
Found at i:27616954 original size:18 final size:19
Alignment explanation
Indices: 27616920--27616956 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
27616910 AAAATTTTAC
27616920 ATTTTTTTACTATTTTTTT
1 ATTTTTTTACTATTTTTTT
27616939 ATTTTTTT-CTATTTTTTT
1 ATTTTTTTACTATTTTTTT
27616957 CTAATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (19 bp):
ATTTTTTTACTATTTTTTT
Found at i:27616964 original size:18 final size:18
Alignment explanation
Indices: 27616924--27616974 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
27616914 TTTTACATTT
**
27616924 TTTTACTATTTTTTTATTT
1 TTTT-CTATTTTTTTATAA
*
27616943 TTTTCTATTTTTTTCTAA
1 TTTTCTATTTTTTTATAA
*
27616961 TTTT-TAATTTTTTA
1 TTTTCTATTTTTTTA
27616975 ATTAAAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 8 0.30
18 15 0.56
19 4 0.15
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTCTATTTTTTTATAA
Found at i:27617906 original size:33 final size:33
Alignment explanation
Indices: 27617850--27617912 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
27617840 AATAATTCAA
*
27617850 AAAATTATATAAAAATAATTTTTAATAAAATTCT
1 AAAATTATATAAAAATAAATTTTAA-AAAATTCT
27617884 AAAA-TATA-AAAATATAAATTTTAAAAAAT
1 AAAATTATATAAAA-ATAAATTTTAAAAAAT
27617913 CAAAATNNNN
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 9 0.33
33 14 0.52
34 4 0.15
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (33 bp):
AAAATTATATAAAAATAAATTTTAAAAAATTCT
Found at i:27617908 original size:22 final size:21
Alignment explanation
Indices: 27617873--27617918 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
27617863 AATAATTTTT
*
27617873 AATAAAATTCTAAAATATAAA
1 AATAAAATTCTAAAAAATAAA
* *
27617894 AATATAAATTTTAAAAAATCAA
1 AATA-AAATTCTAAAAAATAAA
27617916 AAT
1 AAT
27617919 NNNNNNNNNN
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (21 bp):
AATAAAATTCTAAAAAATAAA
Found at i:27622845 original size:21 final size:21
Alignment explanation
Indices: 27622819--27622858 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
27622809 AATTCTGTTT
*
27622819 ATTTTTACAATTTCAATTTCA
1 ATTTTTACAATCTCAATTTCA
27622840 ATTTTTACAATCTCAATTT
1 ATTTTTACAATCTCAATTT
27622859 GTCCATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTTTACAATCTCAATTTCA
Found at i:27629219 original size:72 final size:71
Alignment explanation
Indices: 27629134--27629277 Score: 243
Period size: 72 Copynumber: 2.0 Consensus size: 71
27629124 AATTTGAAGG
* * *
27629134 AAGTGACGAAAATAACTTAACTATCTAACGTGACGTGAGTGCTTAAATTATGAATTTTTTTTTAT
1 AAGTGACGAAAATAACATAACTATCTAACGTCACGTGAATGCTTAAATTAT-AATTTTTTTTTAT
27629199 TTTTAGT
65 TTTTAGT
*
27629206 AAGTGACGAAAATAACATAACTATCTATCGTCACGTGAATGCTTAAATTATAATTTTTTTTTATT
1 AAGTGACGAAAATAACATAACTATCTAACGTCACGTGAATGCTTAAATTATAATTTTTTTTTATT
27629271 TTTAGT
66 TTTAGT
27629277 A
1 A
27629278 TCTAAAATAA
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
71 21 0.31
72 47 0.69
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (71 bp):
AAGTGACGAAAATAACATAACTATCTAACGTCACGTGAATGCTTAAATTATAATTTTTTTTTATT
TTTAGT
Found at i:27629637 original size:6 final size:6
Alignment explanation
Indices: 27629628--27629652 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27629618 TTTATTTTAT
27629628 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
27629653 ATTGACACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:27630091 original size:17 final size:18
Alignment explanation
Indices: 27630069--27630103 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
27630059 TTGAGTGGTA
27630069 AAATTTAATTA-AAAATT
1 AAATTTAATTACAAAATT
27630086 AAATTTAATTACAAAATT
1 AAATTTAATTACAAAATT
27630104 TAATAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTTAATTACAAAATT
Found at i:27630102 original size:30 final size:30
Alignment explanation
Indices: 27630068--27630124 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
27630058 ATTGAGTGGT
27630068 AAAATTTAATTAAAAATT-AAA-TTTAATTAC
1 AAAATTTAA-T-AAAATTCAAAGTTTAATTAC
27630098 AAAATTTAATAAAATTCAAAGTTTAAT
1 AAAATTTAATAAAATTCAAAGTTTAAT
27630125 AGTAACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 6 0.24
29 4 0.16
30 15 0.60
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAATTTAATAAAATTCAAAGTTTAATTAC
Found at i:27630122 original size:17 final size:18
Alignment explanation
Indices: 27630092--27630125 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
27630082 AATTAAATTT
27630092 AATTACAAAATTTAATAA
1 AATTACAAAATTTAATAA
*
27630110 AATT-CAAAGTTTAATA
1 AATTACAAAATTTAATA
27630126 GTAACATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (18 bp):
AATTACAAAATTTAATAA
Found at i:27630932 original size:17 final size:18
Alignment explanation
Indices: 27630910--27630944 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
27630900 TTGAGTGGTA
27630910 AAATTTAATTA-AAAATT
1 AAATTTAATTACAAAATT
27630927 AAATTTAATTACAAAATT
1 AAATTTAATTACAAAATT
27630945 TAATAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTTAATTACAAAATT
Found at i:27630943 original size:30 final size:30
Alignment explanation
Indices: 27630909--27630965 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
27630899 ATTGAGTGGT
27630909 AAAATTTAATTAAAAATT-AAA-TTTAATTAC
1 AAAATTTAA-T-AAAATTCAAAGTTTAATTAC
27630939 AAAATTTAATAAAATTCAAAGTTTAAT
1 AAAATTTAATAAAATTCAAAGTTTAAT
27630966 AGTAACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 6 0.24
29 4 0.16
30 15 0.60
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (30 bp):
AAAATTTAATAAAATTCAAAGTTTAATTAC
Found at i:27630963 original size:17 final size:18
Alignment explanation
Indices: 27630933--27630966 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
27630923 AATTAAATTT
27630933 AATTACAAAATTTAATAA
1 AATTACAAAATTTAATAA
*
27630951 AATT-CAAAGTTTAATA
1 AATTACAAAATTTAATA
27630967 GTAACATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (18 bp):
AATTACAAAATTTAATAA
Found at i:27632427 original size:296 final size:297
Alignment explanation
Indices: 27631882--27632474 Score: 1179
Period size: 296 Copynumber: 2.0 Consensus size: 297
27631872 ATGATAAATA
27631882 TTTTCAAAATAATTTAAAATTATTATAAAAATATTAATAAAATAATAAACATCTAAAATTGCCTC
1 TTTTCAAAATAATTTAAAATTATTATAAAAATATTAATAAAATAATAAACATCTAAAATTGCCTC
27631947 TATATTGTATCAAACCCAAAACATGGGCAATAAAATAAACACTTATAATCATTAGTATTCAACAA
66 TATATTGTATCAAACCCAAAACATGGGCAATAAAATAAACACTTATAATCATTAGTATTCAACAA
27632012 TTAGAAGGTTAATATTATTGTATTTATTTGTAGAGGAGCCTAATTGTGTAATTAAATTGAGAAAT
131 TTAGAAGGTTAATATTATTGTATTTATTTGTAGAGGAGCCTAATTGTGTAATTAAATTGAGAAAT
27632077 AAATTCAGTATCTACCAATCCTCCCTAGTTTACAAGGGAACAAACATGTTATTATATAATAAATC
196 AAATTCAGTATCTACCAATCCTCCCTAGTTTACAAGGGAACAAACATGTTATTATATAATAAATC
27632142 AATTAATTTCTAATGCTACTTGTTTCGTTGAATGTAC
261 AATTAATTTCTAATGCTACTTGTTTCGTTGAATGTAC
27632179 TTTTCAAAAT-ATTTAAAATTATTATAAAAATATTAATAAAATAATAAACATCTAAAATTGCCTC
1 TTTTCAAAATAATTTAAAATTATTATAAAAATATTAATAAAATAATAAACATCTAAAATTGCCTC
27632243 TATATTGTATCAAACCCAAAACATGGGCAATAAAATAAACACTTATAATCATTAGTATTCAACAA
66 TATATTGTATCAAACCCAAAACATGGGCAATAAAATAAACACTTATAATCATTAGTATTCAACAA
27632308 TTAGAAGGTTAATATTATTGTATTTATTTGTAGAGGAGCCTAATTGTGTAATTAAATTGAGAAAT
131 TTAGAAGGTTAATATTATTGTATTTATTTGTAGAGGAGCCTAATTGTGTAATTAAATTGAGAAAT
27632373 AAATTCAGTATCTACCAATCCTCCCTAGTTTACAAGGGAACAAACATGTTATTATATAATAAATC
196 AAATTCAGTATCTACCAATCCTCCCTAGTTTACAAGGGAACAAACATGTTATTATATAATAAATC
27632438 AATTAATTTCTAATGCTACTTGTTTCGTTGAATGTAC
261 AATTAATTTCTAATGCTACTTGTTTCGTTGAATGTAC
27632475 GGAATCACAT
Statistics
Matches: 296, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
296 286 0.97
297 10 0.03
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (297 bp):
TTTTCAAAATAATTTAAAATTATTATAAAAATATTAATAAAATAATAAACATCTAAAATTGCCTC
TATATTGTATCAAACCCAAAACATGGGCAATAAAATAAACACTTATAATCATTAGTATTCAACAA
TTAGAAGGTTAATATTATTGTATTTATTTGTAGAGGAGCCTAATTGTGTAATTAAATTGAGAAAT
AAATTCAGTATCTACCAATCCTCCCTAGTTTACAAGGGAACAAACATGTTATTATATAATAAATC
AATTAATTTCTAATGCTACTTGTTTCGTTGAATGTAC
Found at i:27637152 original size:293 final size:293
Alignment explanation
Indices: 27636625--27637211 Score: 1138
Period size: 293 Copynumber: 2.0 Consensus size: 293
27636615 AGGGCAACCT
*
27636625 ATGTGGTTTCCTTTTTTGACAAGCAACACAAACATTATCAAGACATTTTTTATTTGAAACAATTC
1 ATGTGGTTTCCTTTTTTGACAAGCAACACAAACATTATCAAGACATTTTTTATTTGAAACAATTA
27636690 TACACTTGGTAAGTACAAGTTTAACAATTTCAAAAGAAGGATGAACAAGCCTTTTATGCCATATG
66 TACACTTGGTAAGTACAAGTTTAACAATTTCAAAAGAAGGATGAACAAGCCTTTTATGCCATATG
*
27636755 GAGAATACATTAGCATCATTCACTCGACAATCTGTAACCTCAGTGTTGTGAACAGAGGGACTTGG
131 GAGAATACATTAGCATCATTCACTCGACAATCTGTAACCCCAGTGTTGTGAACAGAGGGACTTGG
27636820 ATCAGAAACAACAGACGAACCAGCCGAAAATTGATAGAGACCATCACGAACTTGGCCTCGCAGTA
196 ATCAGAAACAACAGACGAACCAGCCGAAAATTGATAGAGACCATCACGAACTTGGCCTCGCAGTA
*
27636885 AAATTTCCTGTGTTTGGATGTCCTTAACAACAC
261 AAATTTACTGTGTTTGGATGTCCTTAACAACAC
27636918 ATGTGGTTTCCTTTTTTGACAAGCAACACAAACATTATCAAGACATTTTTTATTTGAAACAATTA
1 ATGTGGTTTCCTTTTTTGACAAGCAACACAAACATTATCAAGACATTTTTTATTTGAAACAATTA
27636983 TACACTTGGTAAGTACAAGTTTAACAATTTCAAAAGAAGGATGAACAAGCCTTTTATGCCATATG
66 TACACTTGGTAAGTACAAGTTTAACAATTTCAAAAGAAGGATGAACAAGCCTTTTATGCCATATG
27637048 GAGAATACATTAGCATCATTCACTCGACAATCTGTAACCCCAGTGTTGTGAACAGAGGGACTTGG
131 GAGAATACATTAGCATCATTCACTCGACAATCTGTAACCCCAGTGTTGTGAACAGAGGGACTTGG
*
27637113 ATCAGAAACAATAGACGAACCAGCCGAAAATTGATAGAGACCATCACGAACTTGGCCTCGCAGTA
196 ATCAGAAACAACAGACGAACCAGCCGAAAATTGATAGAGACCATCACGAACTTGGCCTCGCAGTA
27637178 AAATTTACTGTGTTTGGATGTCCTTAACAACAC
261 AAATTTACTGTGTTTGGATGTCCTTAACAACAC
27637211 A
1 A
27637212 ATAAGAGGGG
Statistics
Matches: 290, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
293 290 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (293 bp):
ATGTGGTTTCCTTTTTTGACAAGCAACACAAACATTATCAAGACATTTTTTATTTGAAACAATTA
TACACTTGGTAAGTACAAGTTTAACAATTTCAAAAGAAGGATGAACAAGCCTTTTATGCCATATG
GAGAATACATTAGCATCATTCACTCGACAATCTGTAACCCCAGTGTTGTGAACAGAGGGACTTGG
ATCAGAAACAACAGACGAACCAGCCGAAAATTGATAGAGACCATCACGAACTTGGCCTCGCAGTA
AAATTTACTGTGTTTGGATGTCCTTAACAACAC
Found at i:27643509 original size:23 final size:23
Alignment explanation
Indices: 27643479--27643531 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
27643469 GAAGATGGAG
*
27643479 GAAAGAAAAATTAATACCAAAAT
1 GAAAGAAAAAGTAATACCAAAAT
*
27643502 GAAAGAAAAAGTAATACCATAAT
1 GAAAGAAAAAGTAATACCAAAAT
27643525 GAAAGAA
1 GAAAGAA
27643532 CCCTTCCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.64, C:0.08, G:0.13, T:0.15
Consensus pattern (23 bp):
GAAAGAAAAAGTAATACCAAAAT
Found at i:27647174 original size:5 final size:5
Alignment explanation
Indices: 27647164--27647192 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
27647154 TTGTTTCTTT
27647164 TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATA
27647193 TAAACTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:27651052 original size:46 final size:46
Alignment explanation
Indices: 27650984--27651160 Score: 291
Period size: 46 Copynumber: 3.8 Consensus size: 46
27650974 ACAATGCTAT
*
27650984 AACTCAGTATGGTTTTCTTTACTGAAATACTATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
* * *
27651030 AACTCAGTATGGTTTTCGTTACTGAAATATCATACCTACTTCTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
* *
27651076 AACTCAATATGATTTTCTTTACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
*
27651122 AACTGAGTATGGTTTTCTTTACTGAAATACCATACCTAC
1 AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTAC
27651161 GTTCCACACT
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 119 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACTGAAATACCATACCTACTTTTCAC
Found at i:27652088 original size:41 final size:41
Alignment explanation
Indices: 27652035--27652112 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
27652025 TTTATCATTG
*
27652035 TTTTATATATTTAATTTGTAAAATTTCCAATTTTGCCTTGT
1 TTTTATATATTTAATTTGCAAAATTTCCAATTTTGCCTTGT
27652076 TTTTATATATTTAATTTGCAAAATTTCCAATTTTGCC
1 TTTTATATATTTAATTTGCAAAATTTCCAATTTTGCC
27652113 CTTAATTTTC
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:0.28, C:0.12, G:0.06, T:0.54
Consensus pattern (41 bp):
TTTTATATATTTAATTTGCAAAATTTCCAATTTTGCCTTGT
Found at i:27659374 original size:27 final size:27
Alignment explanation
Indices: 27659336--27659389 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
27659326 AATAAACAAC
27659336 GACATGAACTGGACATTGAAATTCTAT
1 GACATGAACTGGACATTGAAATTCTAT
27659363 GACATGAACTGGACATTGAAATTCTAT
1 GACATGAACTGGACATTGAAATTCTAT
27659390 CACTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (27 bp):
GACATGAACTGGACATTGAAATTCTAT
Found at i:27661769 original size:34 final size:35
Alignment explanation
Indices: 27661711--27661777 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
27661701 CAAACACCAG
27661711 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
27661746 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
27661778 TATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:27662064 original size:13 final size:13
Alignment explanation
Indices: 27662046--27662072 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
27662036 CCTAAAATAC
27662046 CCTTCTTCTTCTT
1 CCTTCTTCTTCTT
27662059 CCTTCTTCTTCTT
1 CCTTCTTCTTCTT
27662072 C
1 C
27662073 TTAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (13 bp):
CCTTCTTCTTCTT
Found at i:27662231 original size:19 final size:19
Alignment explanation
Indices: 27662209--27662270 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
27662199 ATTTTTGAAT
*
27662209 TATTGAATGATTTTAGCTC
1 TATTGAATGATTTTCGCTC
* *
27662228 TATTTGCAT-CTGTTTCGCTC
1 TA-TTGAATGAT-TTTCGCTC
27662248 TATTGAATGATTTTCGCTC
1 TATTGAATGATTTTCGCTC
27662267 TATT
1 TATT
27662271 TTCCTTCTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 20 0.57
20 15 0.43
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.50
Consensus pattern (19 bp):
TATTGAATGATTTTCGCTC
Found at i:27662626 original size:17 final size:17
Alignment explanation
Indices: 27662604--27662655 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
27662594 AATTTCCCAA
27662604 AGTAATAATGTAATATT
1 AGTAATAATGTAATATT
*
27662621 AGTAATAATATAATATT
1 AGTAATAATGTAATATT
*
27662638 AGTAATAACGTAATATT
1 AGTAATAATGTAATATT
27662655 A
1 A
27662656 ATAGAGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (17 bp):
AGTAATAATGTAATATT
Found at i:27663214 original size:95 final size:90
Alignment explanation
Indices: 27663018--27663369 Score: 476
Period size: 91 Copynumber: 3.8 Consensus size: 90
27663008 AATTTTAACT
*
27663018 CTAACTTTAAAGTTTAAACTGTGGTTTAACAGACTTTTTTTTTGTTTAATTTATGCTATTGTACT
1 CTAACTTTAAAGTTTAAACTGTAGTTTAACAGAC-TTTTTTTTGTTTAATTTATGCTATTGTACT
*
27663083 ATTATATTAATTTAGGTTTCAATTAA
65 ATTATATTAATTTAGGCTTCAATTAA
* **
27663109 CTAACTTTAAAGTTTAAACTGTAGTTTAACATA-AATTTTTTGTTTAATTTATGCTGTTGTACTT
1 CTAACTTTAAAGTTTAAACTGTAGTTTAACAGACTTTTTTTTGTTTAATTTATGC-----TA-TT
*
27663173 GTACTATTATATTAATTTATGCTTCAATTAA
60 GTACTATTATATTAATTTAGGCTTCAATTAA
*
27663204 CTAACTTTAAAGTTTAAAC-GATAGCTTAACAGACTTTTTTTTTGTTTAATTTATGCTATTGTAC
1 CTAACTTTAAAGTTTAAACTG-TAGTTTAACAGAC-TTTTTTTTGTTTAATTTATGCTATTGTAC
27663268 TATTATATTAATTTAGGCTTCAATTAA
64 TATTATATTAATTTAGGCTTCAATTAA
* * * * * * *
27663295 CTAAATTTAAAGTTTAAAATGTAGTTCAATATAC-TTTTTTTGTTTAATTTATGCTGTTGTAATA
1 CTAACTTTAAAGTTTAAACTGTAGTTTAACAGACTTTTTTTTGTTTAATTTATGCTATTGTACTA
27663359 TTATATTAATT
66 TTATATTAATT
27663370 AATTAATTTT
Statistics
Matches: 232, Mismatches: 19, Indels: 22
0.85 0.07 0.08
Matches are distributed among these distances:
89 58 0.25
91 89 0.38
92 3 0.01
94 3 0.01
95 60 0.26
97 19 0.08
ACGTcount: A:0.32, C:0.09, G:0.10, T:0.50
Consensus pattern (90 bp):
CTAACTTTAAAGTTTAAACTGTAGTTTAACAGACTTTTTTTTGTTTAATTTATGCTATTGTACTA
TTATATTAATTTAGGCTTCAATTAA
Found at i:27663244 original size:186 final size:186
Alignment explanation
Indices: 27663018--27663355 Score: 579
Period size: 186 Copynumber: 1.8 Consensus size: 186
27663008 AATTTTAACT
* *
27663018 CTAACTTTAAAGTTTAAACTGTGGTTTAACAGACTTTTTTTTTGTTTAATTTATGCTATTGTACT
1 CTAACTTTAAAGTTTAAACTGTAGCTTAACAGACTTTTTTTTTGTTTAATTTATGCTATTGTACT
* * * *
27663083 ATTATATTAATTTAGGTTTCAATTAACTAACTTTAAAGTTTAAACTGTAGTTTAACATAAATTTT
66 ATTATATTAATTTAGGCTTCAATTAACTAAATTTAAAGTTTAAAATGTAGTTCAACATAAATTTT
27663148 TTGTTTAATTTATGCTGTTGTACTTGTACTATTATATTAATTTATGCTTCAATTAA
131 TTGTTTAATTTATGCTGTTGTACTTGTACTATTATATTAATTTATGCTTCAATTAA
27663204 CTAACTTTAAAGTTTAAAC-GATAGCTTAACAGACTTTTTTTTTGTTTAATTTATGCTATTGTAC
1 CTAACTTTAAAGTTTAAACTG-TAGCTTAACAGACTTTTTTTTTGTTTAATTTATGCTATTGTAC
* **
27663268 TATTATATTAATTTAGGCTTCAATTAACTAAATTTAAAGTTTAAAATGTAGTTCAATATACTTTT
65 TATTATATTAATTTAGGCTTCAATTAACTAAATTTAAAGTTTAAAATGTAGTTCAACATAAATTT
27663333 TTTGTTTAATTTATGCTGTTGTA
130 TTTGTTTAATTTATGCTGTTGTA
27663356 ATATTATATT
Statistics
Matches: 142, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
185 1 0.01
186 141 0.99
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.49
Consensus pattern (186 bp):
CTAACTTTAAAGTTTAAACTGTAGCTTAACAGACTTTTTTTTTGTTTAATTTATGCTATTGTACT
ATTATATTAATTTAGGCTTCAATTAACTAAATTTAAAGTTTAAAATGTAGTTCAACATAAATTTT
TTGTTTAATTTATGCTGTTGTACTTGTACTATTATATTAATTTATGCTTCAATTAA
Found at i:27682000 original size:12 final size:12
Alignment explanation
Indices: 27681985--27682016 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
27681975 TAATGAAAAT
27681985 ATAAATAAAGAA
1 ATAAATAAAGAA
27681997 ATAAATAAAGAA
1 ATAAATAAAGAA
*
27682009 ATGAATAA
1 ATAAATAA
27682017 GGCTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (12 bp):
ATAAATAAAGAA
Found at i:27682091 original size:16 final size:16
Alignment explanation
Indices: 27682070--27682108 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
27682060 AATTATGGAG
*
27682070 ATATATGAAAGCATGT
1 ATATATAAAAGCATGT
*
27682086 ATATATAAAAGTATGT
1 ATATATAAAAGCATGT
27682102 ATATATA
1 ATATATA
27682109 TGTATACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (16 bp):
ATATATAAAAGCATGT
Found at i:27682363 original size:13 final size:13
Alignment explanation
Indices: 27682345--27682378 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
27682335 GAATCATAAA
27682345 ATATAAAATACAT
1 ATATAAAATACAT
27682358 ATATAAAATACAT
1 ATATAAAATACAT
*
27682371 ATTTAAAA
1 ATATAAAA
27682379 AAAATGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (13 bp):
ATATAAAATACAT
Found at i:27683918 original size:57 final size:57
Alignment explanation
Indices: 27683827--27683959 Score: 180
Period size: 57 Copynumber: 2.3 Consensus size: 57
27683817 TTATATTATG
* * *
27683827 TAAGACCATAGCTAAAAGATGTTATGGCATCAAGTAATGATTTGAC-GATAGAATGAA
1 TAAGACCATAGATAAAAGAAGTTATGGCAACAAGTAATGATTTGACAG-TAGAATGAA
*
27683884 TAAGACCATAGATGAAAA-AAGTTATGGCAACAAGTAATGATTTGACAGTAGAATGAG
1 TAAGACCATAGAT-AAAAGAAGTTATGGCAACAAGTAATGATTTGACAGTAGAATGAA
* *
27683941 TAAGACTATAGCTAAAAGA
1 TAAGACCATAGATAAAAGA
27683960 CGGTATGACA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
56 4 0.06
57 58 0.87
58 5 0.07
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (57 bp):
TAAGACCATAGATAAAAGAAGTTATGGCAACAAGTAATGATTTGACAGTAGAATGAA
Found at i:27686611 original size:21 final size:22
Alignment explanation
Indices: 27686562--27686616 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
27686552 CTAGATACAT
27686562 GTCTCGAGACATAAGACACAAA
1 GTCTCGAGACATAAGACACAAA
* *
27686584 ATCTCGAGACATAAGGA-TC-AA
1 GTCTCGAGACATAA-GACACAAA
27686605 GTCTCGAGACAT
1 GTCTCGAGACAT
27686617 TATTTCACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.45
22 14 0.48
23 2 0.07
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (22 bp):
GTCTCGAGACATAAGACACAAA
Found at i:27697734 original size:28 final size:27
Alignment explanation
Indices: 27697682--27697734 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
27697672 TATTTCGTGC
* *
27697682 TTTTGGAATTTAGTCCCATGTTTTTAT
1 TTTTGGAATTTAATCCCATCTTTTTAT
27697709 TTTTAGGAATTTAATCCC-TCTATTTT
1 TTTT-GGAATTTAATCCCATCT-TTTT
27697735 TCATATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (27 bp):
TTTTGGAATTTAATCCCATCTTTTTAT
Found at i:27698277 original size:14 final size:14
Alignment explanation
Indices: 27698258--27698293 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
27698248 AATTATATTA
27698258 AAAATTAAAATATC
1 AAAATTAAAATATC
27698272 AAAATT-AAATATC
1 AAAATTAAAATATC
*
27698285 AAATTTAAA
1 AAAATTAAA
27698294 CATAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATTAAAATATC
Found at i:27705108 original size:15 final size:15
Alignment explanation
Indices: 27705090--27705128 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
27705080 CCTCCGTTGG
27705090 CTTCTCGGCAGGCTT
1 CTTCTCGGCAGGCTT
* *
27705105 CTTCTCAGCGGGCTT
1 CTTCTCGGCAGGCTT
*
27705120 TTTCTCGGC
1 CTTCTCGGC
27705129 TTTCGGCGCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.33, G:0.26, T:0.36
Consensus pattern (15 bp):
CTTCTCGGCAGGCTT
Found at i:27705559 original size:18 final size:18
Alignment explanation
Indices: 27705536--27705572 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
27705526 TCTTCATCAA
* *
27705536 TAAAATTAGCACACTTTT
1 TAAAATTAACACAATTTT
27705554 TAAAATTAACACAATTTT
1 TAAAATTAACACAATTTT
27705572 T
1 T
27705573 TTACCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.41
Consensus pattern (18 bp):
TAAAATTAACACAATTTT
Found at i:27705801 original size:17 final size:17
Alignment explanation
Indices: 27705716--27705807 Score: 70
Period size: 17 Copynumber: 5.6 Consensus size: 17
27705706 TATTCTAAAA
*
27705716 TTAATATTAAATTTAAT
1 TTAATATTTAATTTAAT
*
27705733 TTAATATTT-ATCTTGA-
1 TTAATATTTAAT-TTAAT
* *
27705749 -TAGTATTTTA-TTAAT
1 TTAATATTTAATTTAAT
*
27705764 TTAATAAATTAA-TT-AT
1 TTAAT-ATTTAATTTAAT
27705780 CTTAATATTTAATTTAAT
1 -TTAATATTTAATTTAAT
27705798 TTAATATTTA
1 TTAATATTTA
27705808 TCTTGATAAG
Statistics
Matches: 59, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
14 3 0.05
15 7 0.12
16 13 0.22
17 34 0.58
18 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAATATTTAATTTAAT
Found at i:27706483 original size:22 final size:22
Alignment explanation
Indices: 27706434--27706499 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
27706424 TACACAGCAC
*
27706434 CAAAGAGCATCGAA-TGCTAAA
1 CAAAGAGCATCTAAGTGCTAAA
*
27706455 CAAAGAGCATCTAAGTGCTAAG
1 CAAAGAGCATCTAAGTGCTAAA
* *
27706477 CATAGAGCA-CTGAAGTGTTAAA
1 CAAAGAGCATCT-AAGTGCTAAA
27706499 C
1 C
27706500 TCATACAAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
21 15 0.39
22 23 0.61
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.18
Consensus pattern (22 bp):
CAAAGAGCATCTAAGTGCTAAA
Found at i:27714495 original size:16 final size:18
Alignment explanation
Indices: 27714474--27714507 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27714464 TTAAACACAC
27714474 AATTAA-AC-AAATTCAT
1 AATTAACACTAAATTCAT
27714490 AATTAACACTAAATTCAT
1 AATTAACACTAAATTCAT
27714508 TCTATTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTAACACTAAATTCAT
Found at i:27716317 original size:10 final size:9
Alignment explanation
Indices: 27716300--27716341 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
27716290 TCTTTTTCTT
27716300 TTTTATTTA
1 TTTTATTTA
27716309 TTTTGATTTA
1 TTTT-ATTTA
27716319 TATTTATTTA
1 T-TTTATTTA
27716329 TTTT-TTATA
1 TTTTATT-TA
27716338 TTTT
1 TTTT
27716342 TTATGCTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 2 0.07
9 13 0.43
10 12 0.40
11 3 0.10
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTTATTTA
Found at i:27716344 original size:20 final size:20
Alignment explanation
Indices: 27716298--27716345 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
27716288 GTTCTTTTTC
27716298 TTTTTTATTTATTTTGATTTA
1 TTTTTTATTTATTTT-ATTTA
*
27716319 -TATTTATTTATTTT-TTATA
1 TTTTTTATTTATTTTATT-TA
27716338 TTTTTTAT
1 TTTTTTAT
27716346 GCTTTAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 2 0.09
19 2 0.09
20 19 0.83
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTTTATTTATTTTATTTA
Found at i:27724099 original size:21 final size:22
Alignment explanation
Indices: 27724063--27724106 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
27724053 ATTTAGTCCC
27724063 TATTAGATAAAAGATCATAAATA
1 TATTAGAT-AAAGATCATAAATA
27724086 TATTAGAT-AAGATCATAAATA
1 TATTAGATAAAGATCATAAATA
27724107 GCTCAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 13 0.62
23 8 0.38
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.32
Consensus pattern (22 bp):
TATTAGATAAAGATCATAAATA
Found at i:27729015 original size:16 final size:18
Alignment explanation
Indices: 27728994--27729027 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
27728984 TTAAACACAC
27728994 AATTAA-AC-AAATTCAT
1 AATTAACACTAAATTCAT
27729010 AATTAACACTAAATTCAT
1 AATTAACACTAAATTCAT
27729028 TCTATTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTAACACTAAATTCAT
Found at i:27730101 original size:8 final size:8
Alignment explanation
Indices: 27730084--27730120 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
27730074 TGTTGGTTGG
27730084 ATCCGCAT
1 ATCCGCAT
*
27730092 ATCCGTAT
1 ATCCGCAT
27730100 ATCCGCAT
1 ATCCGCAT
27730108 ATCCGCAT
1 ATCCGCAT
27730116 ATCCG
1 ATCCG
27730121 AGTCTGAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.24, C:0.35, G:0.14, T:0.27
Consensus pattern (8 bp):
ATCCGCAT
Found at i:27731693 original size:17 final size:17
Alignment explanation
Indices: 27731661--27731693 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27731651 CTTCCATTCT
27731661 TTTAGATTTTAATTTAC
1 TTTAGATTTTAATTTAC
27731678 TTTAG-TTTTAACTTTA
1 TTTAGATTTTAA-TTTA
27731694 GTTTCACCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTAGATTTTAATTTAC
Found at i:27740348 original size:23 final size:24
Alignment explanation
Indices: 27740317--27740362 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
27740307 TATGTGATAT
*
27740317 AAATTATATAT-AAAAGTAAAATA
1 AAATGATATATAAAAAGTAAAATA
27740340 AAATGATATATACAAAAGTAAAA
1 AAATGATATATA-AAAAGTAAAA
27740363 AATAGATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
25 10 0.50
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATGATATATAAAAAGTAAAATA
Found at i:27745120 original size:45 final size:45
Alignment explanation
Indices: 27745006--27745129 Score: 149
Period size: 45 Copynumber: 2.8 Consensus size: 45
27744996 ACCTCCGTCT
* * *
27745006 CATCACTGACTGTATCTTTGCCTTCTGATTCAGGATCTATTGTTC
1 CATCACCGACTGTATCTTTGCCTTCTGGTTCAGGATCTACTGTTC
* * *
27745051 CATCACTGACTGTATCTTTGCCTTCTGGTTCAGGATCTGCTGTTT
1 CATCACCGACTGTATCTTTGCCTTCTGGTTCAGGATCTACTGTTC
* ** * *
27745096 CATTACCGGTTGTACCTTTCCCTTCTGGTTCAGG
1 CATCACCGACTGTATCTTTGCCTTCTGGTTCAGG
27745130 TTACAATTCT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.41
Consensus pattern (45 bp):
CATCACCGACTGTATCTTTGCCTTCTGGTTCAGGATCTACTGTTC
Found at i:27748572 original size:29 final size:28
Alignment explanation
Indices: 27748509--27748604 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 28
27748499 AGCCTTTCAT
*
27748509 AATTTTTAAAATTTTTAATTAGCCCTCAA
1 AATTTTTAAAA-TTCTAATTAGCCCTCAA
* * * *
27748538 ATTTTTTAAAATTCTCATTAGCTTCTTAA
1 AATTTTTAAAATTCTAATTAGC-CCTCAA
* *
27748567 AATTTTTGAAAATTTTAATCAGACCCTCCAA
1 AATTTTT-AAAATTCTAATTAG-CCCT-CAA
27748598 AATTTTT
1 AATTTTT
27748605 GGATGTTCTC
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
28 9 0.17
29 20 0.38
30 13 0.25
31 10 0.19
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (28 bp):
AATTTTTAAAATTCTAATTAGCCCTCAA
Found at i:27750319 original size:32 final size:32
Alignment explanation
Indices: 27750233--27750319 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
27750223 TTCTGGAAAA
*
27750233 ATGATTTACTAGAAAATATTTTCTGGTGTTTGG
1 ATGATTTCCT-GAAAATATTTTCTGGTGTTTGG
* * *
27750266 ATGA-ATCTGTGTAAAATATTTTCTGTTGTTTGG
1 ATGATTTC-CTG-AAAATATTTTCTGGTGTTTGG
27750299 CA-GATTTCCTGAAAATATTTT
1 -ATGATTTCCTGAAAATATTTT
27750320 TCGGAAAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
32 12 0.27
33 29 0.66
34 3 0.07
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (32 bp):
ATGATTTCCTGAAAATATTTTCTGGTGTTTGG
Found at i:27753222 original size:18 final size:18
Alignment explanation
Indices: 27753201--27753251 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
27753191 AGGAATGAAG
27753201 GAAGGGAGAAGAATGGAT
1 GAAGGGAGAAGAATGGAT
* *** *
27753219 GAAGGTAGCTTACTGGAT
1 GAAGGGAGAAGAATGGAT
27753237 GAAGGGAGAAGAATG
1 GAAGGGAGAAGAATG
27753252 ACTGAGAGCT
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.04, G:0.41, T:0.16
Consensus pattern (18 bp):
GAAGGGAGAAGAATGGAT
Found at i:27754768 original size:22 final size:22
Alignment explanation
Indices: 27754727--27754768 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
27754717 TAGTATTTTT
*
27754727 AAAAATAAAAATTAATTAAAGA
1 AAAAATAAAAATTAAATAAAGA
27754749 AAAAATAATAAA-TAAATAAA
1 AAAAATAA-AAATTAAATAAA
27754769 ATTAAGTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAAATAAAAATTAAATAAAGA
Found at i:27755496 original size:12 final size:12
Alignment explanation
Indices: 27755479--27755521 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
27755469 TTTCAACAAT
27755479 TCATCTCATCCA
1 TCATCTCATCCA
27755491 TCATCTC-TCCA
1 TCATCTCATCCA
*
27755502 CTTATCTCATCCA
1 -TCATCTCATCCA
27755515 TCATCTC
1 TCATCTC
27755522 TCAACTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 19 0.70
13 4 0.15
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (12 bp):
TCATCTCATCCA
Found at i:27755513 original size:24 final size:24
Alignment explanation
Indices: 27755481--27755528 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
27755471 TCAACAATTC
*
27755481 ATCTCATCCATCATCTCTCCACTT
1 ATCTCATCCATCATCTCTCAACTT
27755505 ATCTCATCCATCATCTCTCAACTT
1 ATCTCATCCATCATCTCTCAACTT
27755529 TTGAATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.40, G:0.00, T:0.38
Consensus pattern (24 bp):
ATCTCATCCATCATCTCTCAACTT
Found at i:27758123 original size:30 final size:31
Alignment explanation
Indices: 27758075--27758133 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
27758065 TGAATTTATT
*
27758075 CACTAAACTTTGAATTTTAA-TTAATTTTGG
1 CACTAAACTTTGAATTTTAACTAAATTTTGG
*
27758105 CACT-AACTTTGATTTTTTAACTAAATTTT
1 CACTAAACTTTGA-ATTTTAACTAAATTTT
27758134 TACTATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.32
30 10 0.40
31 7 0.28
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (31 bp):
CACTAAACTTTGAATTTTAACTAAATTTTGG
Found at i:27764104 original size:26 final size:26
Alignment explanation
Indices: 27764039--27764098 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
27764029 GTAGATTTGG
**
27764039 GTGTGAAATGGAGAAGAGAAGAGCAA
1 GTGTGAAATGGAGAAGAGAAGAAAAA
27764065 GTGTGAAATGGAGAAGAGAAGAAAATA
1 GTGTGAAATGGAGAAGAGAAGAAAA-A
27764092 GT-TGAAA
1 GTGTGAAA
27764099 ATGAGAGTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 28 0.90
27 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.35, T:0.15
Consensus pattern (26 bp):
GTGTGAAATGGAGAAGAGAAGAAAAA
Found at i:27765329 original size:21 final size:20
Alignment explanation
Indices: 27765296--27765383 Score: 65
Period size: 20 Copynumber: 4.2 Consensus size: 20
27765286 AAGAAATATA
* **
27765296 TAAAAATACATAAATATTTT
1 TAAAAATATATAAATAAATT
27765316 TAAAAAT-TATATAATAAATT
1 TAAAAATATATA-AATAAATT
27765336 TAAAAATATA-AAATGATTAATT
1 TAAAAATATATAAAT-A--AATT
27765358 TCAAAGAATATA-ATAATAAATT
1 T-AAA-AATATATA-AATAAATT
27765380 TAAA
1 TAAA
27765384 TATTATATTA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
19 6 0.11
20 22 0.39
21 5 0.09
22 10 0.18
23 3 0.05
24 8 0.14
25 3 0.05
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAAAATATATAAATAAATT
Found at i:27765379 original size:22 final size:20
Alignment explanation
Indices: 27765314--27765383 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 20
27765304 CATAAATATT
27765314 TTTAAAAAT-TATATAATAAA
1 TTTAAAAATATA-ATAATAAA
27765334 TTTAAAAATATAA-AATGATTAA
1 TTTAAAAATATAATAAT-A--AA
27765356 TTTCAAAGAATATAATAATAAA
1 TTT-AAA-AATATAATAATAAA
27765378 TTTAAA
1 TTTAAA
27765384 TATTATATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
19 3 0.07
20 11 0.26
21 5 0.12
22 10 0.23
23 3 0.07
24 8 0.19
25 3 0.07
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (20 bp):
TTTAAAAATATAATAATAAA
Found at i:27771619 original size:15 final size:15
Alignment explanation
Indices: 27771599--27771634 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
27771589 TTATTCAAAC
27771599 ATTTATTTTTTGAAA
1 ATTTATTTTTTGAAA
27771614 ATTTATTTTTTGAAA
1 ATTTATTTTTTGAAA
27771629 ATTTAT
1 ATTTAT
27771635 AAAACAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
ATTTATTTTTTGAAA
Found at i:27775026 original size:3 final size:3
Alignment explanation
Indices: 27775020--27775103 Score: 87
Period size: 3 Copynumber: 28.0 Consensus size: 3
27775010 ACTAATTAGG
* * * * *
27775020 TTA TTA TTA TTA CTA TTA TTA TCA TCA TCA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
27775068 TTA GTA TTA TTA TTA ATA TTA CTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27775104 CATTTCCATT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.35, C:0.08, G:0.01, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:27787503 original size:45 final size:45
Alignment explanation
Indices: 27787331--27787731 Score: 251
Period size: 45 Copynumber: 9.0 Consensus size: 45
27787321 ATGGATTGAA
* * ** *
27787331 GAAGATTGTAGATCTTGTCTTCCTGTATTGATAGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * * * *** * * * *
27787376 GAAAACA-CAAACCTTATCTCCCTG-AGCAGCAGTGGAGTAGGTT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
27787419 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAACGAAGTAAATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
27787464 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * * *** * * * *
27787509 GAA-AAAACTAG-CCTCGTCTTCTTG-AGCAGCAGTGGAGTAGGTA
1 GAAGATAGC-AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
27787552 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * * *** * * * *
27787597 GAAAACA-CAAACCTTATCTTCCTG-AGCAGCAGTGGAGTAGGTT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * *
27787640 GAAAATAGCATG-TCTCGTTTTCTTGTATTGGCAGCGAAGTAGATC
1 GAAGATAGCA-GATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
27787685 GAAGAAAGTAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
1 GAAG--A-TAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
27787732 AAAAAACATC
Statistics
Matches: 256, Mismatches: 87, Indels: 23
0.70 0.24 0.06
Matches are distributed among these distances:
43 52 0.20
44 75 0.29
45 93 0.36
47 2 0.01
48 34 0.13
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
Found at i:27787567 original size:88 final size:88
Alignment explanation
Indices: 27787464--27787696 Score: 324
Period size: 88 Copynumber: 2.6 Consensus size: 88
27787454 GAAGTAAATT
* *
27787464 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAAAAACTAGCCTCGTCTT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAAAAACTAGCCTCATCTT
*
27787529 CTTGAGCAGCAGTGGAGTAGGTA
66 CCTGAGCAGCAGTGGAGTAGGTA
* * * *
27787552 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAAACACAAACCTTATCTT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAAAAACTAGCCTCATCTT
*
27787617 CCTGAGCAGCAGTGGAGTAGGTT
66 CCTGAGCAGCAGTGGAGTAGGTA
* * * * * *
27787640 GAAAATAGCATG-TCTCGTTTTCTTGTATTGGCAGCGAAGTAGATCGAAGAAAGTAGC
1 GAAGATAGCA-GATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAAAAACTAGC
27787697 AGATCTTGTC
Statistics
Matches: 127, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
88 126 0.99
89 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (88 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAAAAACTAGCCTCATCTT
CCTGAGCAGCAGTGGAGTAGGTA
Found at i:27787569 original size:133 final size:133
Alignment explanation
Indices: 27787331--27787592 Score: 407
Period size: 133 Copynumber: 2.0 Consensus size: 133
27787321 ATGGATTGAA
* * * * *
27787331 GAAGATTGTAGATCTTGTCTTCCTGTATTGATAGTGAAGTAGATCGAAAACACAAACCTTATCTC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGACAGTGAAGTAGATCGAAAAAACAAACCTCATCTC
*
27787396 CCTGAGCAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAACGAAGTAA
66 CCTGAGCAGCAGTGGAGTAGGTAGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAACGAAGTAA
27787461 ATT
131 ATT
* * * * *
27787464 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGTGAAGTAGATCGAAAAAACTAGCCTCGTCTT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGACAGTGAAGTAGATCGAAAAAACAAACCTCATCTC
* *
27787529 CTTGAGCAGCAGTGGAGTAGGTAGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTA
66 CCTGAGCAGCAGTGGAGTAGGTAGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAACGAAGTA
27787593 GATCGAAAAC
Statistics
Matches: 116, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
133 116 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (133 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTGACAGTGAAGTAGATCGAAAAAACAAACCTCATCTC
CCTGAGCAGCAGTGGAGTAGGTAGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAACGAAGTAA
ATT
Found at i:27787842 original size:224 final size:220
Alignment explanation
Indices: 27787366--27787805 Score: 580
Period size: 221 Copynumber: 2.0 Consensus size: 220
27787356 TATTGATAGT
* *
27787366 GAAGTAGATCGAAAACACAAACCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATAGCAGA
1 GAAGTAGATCGAAAACACAAACCTTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGA
* *
27787431 TCTTGTCTTCCTGTATTGGCAACGAAGTAAATTGAAGATAGCAGATCTTGTCTTCCTGTATTGGC
66 TCTCGTCTTCCTGTATTGGCAACGAAGTAAATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGC
* * * * *
27787496 AGTGAAGTAGATCGAAAAAACTAGCCTCGTCTTCTTGAGCAGCAGTGGAGTAGGTAGAAGATAGC
131 AGCGAAGTAGATC-AAAAAACTAGCCTCATCTCCCTGAGCAGCAGTGAAGTAGGTAGAAGATAGC
* * * ***
27787561 AGATCTTGTCTTCCTGTATTGGCAGC
195 AGATCCTGTCTCCCTGAAGCAGCAGC
27787587 GAAGTAGATCGAAAACACAAACCTTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCATG
1 GAAGTAGATCGAAAACACAAACCTTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCA-G
* * * *
27787652 -TCTCGTTTTCTTGTATTGGCAGCGAAGTAGATCGAAGAAAGTAGCAGATCTTGTCTTCCTGTAT
65 ATCTCGTCTTCCTGTATTGGCAACGAAGTAAATCGAAG--A-TAGCAGATCTTGTCTTCCTGTAT
* * *
27787716 TGGCAGCGAAGTAGAT-AAAAAACATCAGCCTTATCTCCCTGAGCAGTAGTGAAGTAGGTTGAAG
127 TGGCAGCGAAGTAGATCAAAAAAC-T-AGCCTCATCTCCCTGAGCAGCAGTGAAGTAGGTAGAAG
* *
27787780 ATTGTAGATCCTGTCTCCCT-AAGCAG
190 ATAGCAGATCCTGTCTCCCTGAAGCAG
27787806 TAGTGGAGTA
Statistics
Matches: 189, Mismatches: 24, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
221 92 0.49
222 8 0.04
223 4 0.02
224 85 0.45
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (220 bp):
GAAGTAGATCGAAAACACAAACCTTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGA
TCTCGTCTTCCTGTATTGGCAACGAAGTAAATCGAAGATAGCAGATCTTGTCTTCCTGTATTGGC
AGCGAAGTAGATCAAAAAACTAGCCTCATCTCCCTGAGCAGCAGTGAAGTAGGTAGAAGATAGCA
GATCCTGTCTCCCTGAAGCAGCAGC
Found at i:27787995 original size:132 final size:132
Alignment explanation
Indices: 27787747--27787996 Score: 306
Period size: 132 Copynumber: 1.9 Consensus size: 132
27787737 ACATCAGCCT
** * *
27787747 TATCTCCCTGAGCAGTAGTGAAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAACAGTGAAGTAGGATAAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
** * ** * **
27787812 AGTAGATTAAAGATGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGTAGATTTAAGCCCCCAGT
66 AACAGATCAAAGACAGCGAATCTTATCTTCCCAACATAGTAGGGAAGTAGATTTAAGCCCCCAGT
27787877 CC
131 CC
* * *
27787879 TATCTCCCTGAGCAACAGTGGAGTAGGATAAAGATTGTAGATCCTGTTTCTCTAAGCAGTAGTGG
1 TATCTCCCTGAGCAACAGTGAAGTAGGATAAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
* * *
27787944 AACAGATCAATGACAGCGAATCTTAT-TTCCCTGACATTGTAGTGGAA-TAGATT
66 AACAGATCAAAGACAGCGAATCTTATCTTCCC-AACATAGTAG-GGAAGTAGATT
27787997 AAAGTTGAAG
Statistics
Matches: 98, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
131 5 0.05
132 89 0.91
133 4 0.04
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (132 bp):
TATCTCCCTGAGCAACAGTGAAGTAGGATAAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGG
AACAGATCAAAGACAGCGAATCTTATCTTCCCAACATAGTAGGGAAGTAGATTTAAGCCCCCAGT
CC
Found at i:27788010 original size:21 final size:21
Alignment explanation
Indices: 27787984--27788027 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
27787974 CTGACATTGT
* *
27787984 AGTGGAATAGATTAAAGTTGA
1 AGTGGAACAGATTAAAGCTGA
27788005 AGTGGAACAGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
27788026 AG
1 AG
27788028 GCAGCGAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.05, G:0.30, T:0.23
Consensus pattern (21 bp):
AGTGGAACAGATTAAAGCTGA
Found at i:27789804 original size:3 final size:3
Alignment explanation
Indices: 27789798--27789881 Score: 87
Period size: 3 Copynumber: 28.0 Consensus size: 3
27789788 ACTAATTAGG
* * * * *
27789798 TTA TTA TTA TTA CTA TTA TTA TCA TCA TCA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
27789846 TTA GTA TTA TTA TTA ATA TTA CTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27789882 CATTTCCATT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.35, C:0.08, G:0.01, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:27790909 original size:2 final size:2
Alignment explanation
Indices: 27790902--27790940 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
27790892 TGTATATGAT
27790902 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
27790941 ACATTATAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:27806564 original size:46 final size:46
Alignment explanation
Indices: 27806455--27806545 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
27806445 AGTGTTATTT
* *
27806455 AAGTCTACATATTTTTTAAAATTTATTTTCAATTTTTTGGGAAATG
1 AAGTATACATATTTTTTAAAATTTATTTTCAATTTGTTGGGAAATG
*
27806501 AAGTATACATATTTTTTAAAATTTATTTTCAGTTTGTTGGGAAAT
1 AAGTATACATATTTTTTAAAATTTATTTTCAATTTGTTGGGAAAT
27806546 ATTTATTTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.49
Consensus pattern (46 bp):
AAGTATACATATTTTTTAAAATTTATTTTCAATTTGTTGGGAAATG
Found at i:27810726 original size:25 final size:24
Alignment explanation
Indices: 27810692--27810742 Score: 93
Period size: 25 Copynumber: 2.1 Consensus size: 24
27810682 ACTTTGGAAG
27810692 TTAGTTTCTTTGTGCAAAATTATTT
1 TTAGTTTCTTTGTGCAAAATT-TTT
27810717 TTAGTTTCTTTGTGCAAAATTTTT
1 TTAGTTTCTTTGTGCAAAATTTTT
27810741 TT
1 TT
27810743 CTTGTGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.22, C:0.08, G:0.12, T:0.59
Consensus pattern (24 bp):
TTAGTTTCTTTGTGCAAAATTTTT
Found at i:27811015 original size:31 final size:32
Alignment explanation
Indices: 27810971--27811030 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
27810961 ATTTATTATT
* *
27810971 TTTTCTTTGTTCTTAAATTTCTTCTTTTAGTG
1 TTTTCGTTGTTCTTAAATTTCTTATTTTAGTG
*
27811003 TTTTCGTT-TTCTTTAATTTCTTATTTTA
1 TTTTCGTTGTTCTTAAATTTCTTATTTTA
27811031 TTTGGTGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.13, C:0.12, G:0.07, T:0.68
Consensus pattern (32 bp):
TTTTCGTTGTTCTTAAATTTCTTATTTTAGTG
Found at i:27812682 original size:21 final size:21
Alignment explanation
Indices: 27812650--27812692 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
27812640 ATTATATTAT
* *
27812650 AATAAAACAAAATAAATAAAG
1 AATAAAACAAAAGAAAGAAAG
27812671 AATAAATA-AAAAGAAAGAAAG
1 AATAAA-ACAAAAGAAAGAAAG
27812692 A
1 A
27812693 TAGAAATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.12
Consensus pattern (21 bp):
AATAAAACAAAAGAAAGAAAG
Found at i:27812687 original size:4 final size:4
Alignment explanation
Indices: 27812680--27812748 Score: 63
Period size: 4 Copynumber: 17.0 Consensus size: 4
27812670 GAATAAATAA
*
27812680 AAAG AAAG AAAG ATAG AAATG AAACAG AAAG -AA- AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAA-G -AA-AG AAAG AAAG AAAG AAAG AAAG AAAG
*
27812729 AAAAG AAA- AAGG AAAG AAAG
1 -AAAG AAAG AAAG AAAG AAAG
27812749 GAAGGAGAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
3 6 0.11
4 37 0.69
5 7 0.13
6 3 0.06
7 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.23, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:27812720 original size:33 final size:34
Alignment explanation
Indices: 27812678--27812747 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 34
27812668 AAGAATAAAT
* * *
27812678 AAAAAGAAAGAAAGATAGAAATGAAACA-GAAAG
1 AAAAAGAAAGAAAGAAAGAAAAGAAAAAGGAAAG
27812711 AAAAAGAAAGAAAGAAAGAAAAGAAAAAGGAAAG
1 AAAAAGAAAGAAAGAAAGAAAAGAAAAAGGAAAG
27812745 AAA
1 AAA
27812748 GGAAGGAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 25 0.76
34 8 0.24
ACGTcount: A:0.74, C:0.01, G:0.21, T:0.03
Consensus pattern (34 bp):
AAAAAGAAAGAAAGAAAGAAAAGAAAAAGGAAAG
Found at i:27812739 original size:29 final size:28
Alignment explanation
Indices: 27812667--27812748 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 28
27812657 CAAAATAAAT
* *
27812667 AAAGAATAAATAAAAAGAAAGAAAGATAG
1 AAAGAA-AAAGAAAAAGAAAGAAAGAAAG
*
27812696 AAATGAAACAGAAAGAA-AAAGAAAGAAAG
1 AAA-GAAAAAGAAA-AAGAAAGAAAGAAAG
27812725 AAAG-AAAAGAAAAAGGAAAGAAAG
1 AAAGAAAAAGAAAAA-GAAAGAAAG
27812749 GAAGGAGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
26 2 0.04
27 7 0.16
28 9 0.20
29 22 0.49
30 5 0.11
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.05
Consensus pattern (28 bp):
AAAGAAAAAGAAAAAGAAAGAAAGAAAG
Found at i:27812759 original size:20 final size:20
Alignment explanation
Indices: 27812680--27812759 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
27812670 GAATAAATAA
* *
27812680 AAAGAAAGAAAGATAGAAATGA
1 AAAGAAAGAAA-AGAGAAA-GG
27812702 AACAGAAAGAAAA-AGAAA-G
1 AA-AGAAAGAAAAGAGAAAGG
*
27812721 AAAGAAAGAAAAGAAAAAGG
1 AAAGAAAGAAAAGAGAAAGG
* *
27812741 AAAGAAAGGAAGGAGAAAG
1 AAAGAAAGAAAAGAGAAAG
27812760 CCATGGCCTT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 10 0.20
19 6 0.12
20 17 0.34
21 5 0.10
22 3 0.06
23 9 0.18
ACGTcount: A:0.70, C:0.01, G:0.26, T:0.03
Consensus pattern (20 bp):
AAAGAAAGAAAAGAGAAAGG
Found at i:27816373 original size:12 final size:12
Alignment explanation
Indices: 27816356--27816381 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27816346 AACACCAACT
27816356 TAAAAAAATAAA
1 TAAAAAAATAAA
27816368 TAAAAAAATAAA
1 TAAAAAAATAAA
27816380 TA
1 TA
27816382 CGTAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
TAAAAAAATAAA
Found at i:27816536 original size:15 final size:15
Alignment explanation
Indices: 27816513--27816550 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
27816503 TAAAAAAATC
*
27816513 ATAAAAATAACAATA
1 ATAACAATAACAATA
*
27816528 ATAACAATAATAATA
1 ATAACAATAACAATA
27816543 ATAACAAT
1 ATAACAAT
27816551 GAAAGTCAAG
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAACAATAACAATA
Found at i:27824115 original size:12 final size:12
Alignment explanation
Indices: 27824086--27824118 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
27824076 AAAATAGACA
*
27824086 TAAAAA-ATAAT
1 TAAAAATATAAG
27824097 TAAAAATATAAG
1 TAAAAATATAAG
27824109 TAAAAATATA
1 TAAAAATATA
27824119 TATTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (12 bp):
TAAAAATATAAG
Found at i:27831793 original size:18 final size:18
Alignment explanation
Indices: 27831770--27831808 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
27831760 AGAACTTTTT
*
27831770 CAATCCTGTTAAGTCAAG
1 CAATCCCGTTAAGTCAAG
*
27831788 CAATCCCGTTAAGTCGAG
1 CAATCCCGTTAAGTCAAG
27831806 CAA
1 CAA
27831809 GCAGGCGGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (18 bp):
CAATCCCGTTAAGTCAAG
Found at i:27841804 original size:59 final size:60
Alignment explanation
Indices: 27841707--27841831 Score: 236
Period size: 59 Copynumber: 2.1 Consensus size: 60
27841697 TGAGAGGGTT
27841707 CGGG-TAAAAATATAGGCCTAAAATATGAGCTTTGGTAAAAAAGAGGCCCATTTAGAAAA
1 CGGGCTAAAAATATAGGCCTAAAATATGAGCTTTGGTAAAAAAGAGGCCCATTTAGAAAA
27841766 CGGGCTAAAAATATA-GCCTAAAATATGAGCTTTGGTAAAAAAGAGGCCCATTTAGAAAA
1 CGGGCTAAAAATATAGGCCTAAAATATGAGCTTTGGTAAAAAAGAGGCCCATTTAGAAAA
27841825 CGGGCTA
1 CGGGCTA
27841832 GGCCTCGGGC
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 55 0.85
60 10 0.15
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.22
Consensus pattern (60 bp):
CGGGCTAAAAATATAGGCCTAAAATATGAGCTTTGGTAAAAAAGAGGCCCATTTAGAAAA
Found at i:27841934 original size:19 final size:21
Alignment explanation
Indices: 27841910--27841956 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
27841900 TAAAATATAC
27841910 TAGTTTAAG-TTTTTA-GTTT
1 TAGTTTAAGTTTTTTATGTTT
27841929 TAGTTTAAGTTTTTTATGTTT
1 TAGTTTAAGTTTTTTATGTTT
27841950 TAAGTTT
1 T-AGTTT
27841957 TTTATGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.36
20 6 0.24
21 5 0.20
22 5 0.20
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (21 bp):
TAGTTTAAGTTTTTTATGTTT
Found at i:27841966 original size:15 final size:15
Alignment explanation
Indices: 27841926--27841967 Score: 68
Period size: 16 Copynumber: 2.8 Consensus size: 15
27841916 AAGTTTTTAG
27841926 TTTTA-GTTTAAGTT
1 TTTTATGTTTAAGTT
27841940 TTTTATGTTTTAAGTT
1 TTTTATG-TTTAAGTT
27841956 TTTTATGTTTAA
1 TTTTATGTTTAA
27841968 AATATATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.19
15 6 0.23
16 15 0.58
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (15 bp):
TTTTATGTTTAAGTT
Found at i:27842000 original size:13 final size:14
Alignment explanation
Indices: 27841977--27842007 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
27841967 AAATATATAT
27841977 TTTTTATGTTTTAG
1 TTTTTATGTTTTAG
27841991 TTTTTA-GTTTTAG
1 TTTTTATGTTTTAG
27842004 TTTT
1 TTTT
27842008 GACTTCCCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (14 bp):
TTTTTATGTTTTAG
Found at i:27842001 original size:22 final size:22
Alignment explanation
Indices: 27841940--27842001 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
27841930 AGTTTAAGTT
*
27841940 TTTTATGTTTTAAGTTTTTTATG
1 TTTTA-GTTTTTAGTTTTTTATG
* * * *
27841963 TTTAAAATATATA-TTTTTTATG
1 TTT-TAGTTTTTAGTTTTTTATG
27841985 TTTTAGTTTTTAGTTTT
1 TTTTAGTTTTTAGTTTT
27842002 AGTTTTGACT
Statistics
Matches: 28, Mismatches: 9, Indels: 5
0.67 0.21 0.12
Matches are distributed among these distances:
21 5 0.18
22 16 0.57
23 6 0.21
24 1 0.04
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (22 bp):
TTTTAGTTTTTAGTTTTTTATG
Found at i:27852411 original size:19 final size:21
Alignment explanation
Indices: 27852387--27852433 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
27852377 TAAAATATAC
27852387 TAGTTTAAG-TTTTTA-GTTT
1 TAGTTTAAGTTTTTTATGTTT
27852406 TAGTTTAAGTTTTTTATGTTT
1 TAGTTTAAGTTTTTTATGTTT
27852427 TAAGTTT
1 T-AGTTT
27852434 TTTATGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.36
20 6 0.24
21 5 0.20
22 5 0.20
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (21 bp):
TAGTTTAAGTTTTTTATGTTT
Found at i:27852443 original size:15 final size:15
Alignment explanation
Indices: 27852403--27852444 Score: 68
Period size: 16 Copynumber: 2.8 Consensus size: 15
27852393 AAGTTTTTAG
27852403 TTTTA-GTTTAAGTT
1 TTTTATGTTTAAGTT
27852417 TTTTATGTTTTAAGTT
1 TTTTATG-TTTAAGTT
27852433 TTTTATGTTTAA
1 TTTTATGTTTAA
27852445 AATATATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.19
15 6 0.23
16 15 0.58
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (15 bp):
TTTTATGTTTAAGTT
Found at i:27852477 original size:13 final size:14
Alignment explanation
Indices: 27852454--27852484 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
27852444 AAATATATAT
27852454 TTTTTATGTTTTAG
1 TTTTTATGTTTTAG
27852468 TTTTTA-GTTTTAG
1 TTTTTATGTTTTAG
27852481 TTTT
1 TTTT
27852485 GACTTCCCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (14 bp):
TTTTTATGTTTTAG
Found at i:27852478 original size:22 final size:22
Alignment explanation
Indices: 27852417--27852478 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
27852407 AGTTTAAGTT
*
27852417 TTTTATGTTTTAAGTTTTTTATG
1 TTTTA-GTTTTTAGTTTTTTATG
* * * *
27852440 TTTAAAATATATA-TTTTTTATG
1 TTT-TAGTTTTTAGTTTTTTATG
27852462 TTTTAGTTTTTAGTTTT
1 TTTTAGTTTTTAGTTTT
27852479 AGTTTTGACT
Statistics
Matches: 28, Mismatches: 9, Indels: 5
0.67 0.21 0.12
Matches are distributed among these distances:
21 5 0.18
22 16 0.57
23 6 0.21
24 1 0.04
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (22 bp):
TTTTAGTTTTTAGTTTTTTATG
Found at i:27857573 original size:23 final size:24
Alignment explanation
Indices: 27857531--27857578 Score: 57
Period size: 23 Copynumber: 2.0 Consensus size: 24
27857521 ACATGAAATG
27857531 ATTTAAATAGTATTTATTAT-TAT
1 ATTTAAATAGTATTTATTATGTAT
27857554 ATTTAAA-ATGTATGTT-TTATGTAT
1 ATTTAAATA-GTAT-TTATTATGTAT
27857578 A
1 A
27857579 ATGATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
22 1 0.05
23 15 0.68
24 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAAATAGTATTTATTATGTAT
Found at i:27857667 original size:13 final size:13
Alignment explanation
Indices: 27857649--27857674 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27857639 ATATTTTAAC
27857649 TTTTGACCGCAAT
1 TTTTGACCGCAAT
27857662 TTTTGACCGCAAT
1 TTTTGACCGCAAT
27857675 GTTAAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
TTTTGACCGCAAT
Found at i:27858760 original size:111 final size:110
Alignment explanation
Indices: 27858631--27858834 Score: 354
Period size: 111 Copynumber: 1.8 Consensus size: 110
27858621 TAAATTGCCC
* *
27858631 TTAATACAATTAATAATTAATAATTTTACTAACAAAATGTTAGATTTTACAAAATGTTTTGACTG
1 TTAATACAATTAACAATTAATAATTTTACTAACAAAATGTTAGATTTTAAAAAATGTTTTGACTG
* * *
27858696 GTGTAACAATTAATAATTTGATATAATTTGATAATTTTACTAACAA
66 GTGAAAAAAAT-ATAATTTGATATAATTTGATAATTTTACTAACAA
27858742 TTAATACAATTAACAATTAATAATTTTACTAACAAAATGTTAGATTTTAAAAAATGTTTTGACTG
1 TTAATACAATTAACAATTAATAATTTTACTAACAAAATGTTAGATTTTAAAAAATGTTTTGACTG
27858807 GTGAAAAAAATATAATTTGATATAATTT
66 GTGAAAAAAATATAATTTGATATAATTT
27858835 TAATAACAAT
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 17 0.19
111 71 0.81
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (110 bp):
TTAATACAATTAACAATTAATAATTTTACTAACAAAATGTTAGATTTTAAAAAATGTTTTGACTG
GTGAAAAAAATATAATTTGATATAATTTGATAATTTTACTAACAA
Found at i:27858848 original size:16 final size:16
Alignment explanation
Indices: 27858829--27858870 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
27858819 TAATTTGATA
27858829 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
27858845 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
27858861 TAGTTTTAAT
1 TAATTTTAAT
27858871 TTTAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:27858854 original size:22 final size:23
Alignment explanation
Indices: 27858844--27858905 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
27858834 TTAATAACAA
* *
27858844 TTAATTTTAATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
27858866 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
27858889 TTAATTTTAATCAAAAA
1 TTAATTTTAAT-AAAAA
27858906 ATGGGTCGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 15 0.42
24 5 0.14
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:27861372 original size:30 final size:31
Alignment explanation
Indices: 27861315--27861375 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
27861305 AAAATGGTCG
27861315 CTAAACTATTCAAAAGTTTTCATTTAAGTCA
1 CTAAACTATTCAAAAGTTTTCATTTAAGTCA
* * *
27861346 CTAAACTATTTAGAA-TTTTTATTTAAGTCA
1 CTAAACTATTCAAAAGTTTTCATTTAAGTCA
27861376 TTGAGCTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.43
Consensus pattern (31 bp):
CTAAACTATTCAAAAGTTTTCATTTAAGTCA
Found at i:27864539 original size:16 final size:18
Alignment explanation
Indices: 27864508--27864540 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
27864498 ATTTACTTTA
27864508 ATGTATTTAGTATTTTTG
1 ATGTATTTAGTATTTTTG
27864526 ATGTA-TTA-TATTTTT
1 ATGTATTTAGTATTTTT
27864541 TTAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (18 bp):
ATGTATTTAGTATTTTTG
Found at i:27867083 original size:24 final size:24
Alignment explanation
Indices: 27867023--27867084 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
27867013 GATAAGAATA
27867023 ATAAT-ATATAAATATTTAAAAAT
1 ATAATAATATAAATATTTAAAAAT
*
27867046 ACATATAA-ATAAATATTTAAAAATT
1 ATA-ATAATATAAATATTTAAAAA-T
27867071 ATAATAATA-AAATA
1 ATAATAATATAAATA
27867085 ATAATTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
23 2 0.06
24 26 0.79
25 5 0.15
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAATAATATAAATATTTAAAAAT
Found at i:27867097 original size:6 final size:6
Alignment explanation
Indices: 27867083--27867125 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
27867073 AATAATAAAA
*
27867083 TAATAAT TAATAT TAAT-T TTATAT TAATAT TAATAT TAATAT T
1 TAAT-AT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT T
27867126 TATAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 4 0.12
6 25 0.76
7 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TAATAT
Found at i:27867118 original size:23 final size:25
Alignment explanation
Indices: 27867083--27867129 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 25
27867073 AATAATAAAA
27867083 TAATAATTAATATTAAT-TTTATAT
1 TAATAATTAATATTAATATTTATAT
27867107 TAAT-ATTAATATTAATATTTATA
1 TAATAATTAATATTAATATTTATA
27867130 AATATAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TAATAATTAATATTAATATTTATAT
Found at i:27874405 original size:49 final size:50
Alignment explanation
Indices: 27874341--27874439 Score: 155
Period size: 49 Copynumber: 2.0 Consensus size: 50
27874331 ACCTCAGGTC
* *
27874341 TCTGTTCGAAACAATAGAAATAGGTACACCATGCAACCTCACAATCTGAG
1 TCTGTCCGAAACAATAGAAATAGGCACACCATGCAACCTCACAATCTGAG
* *
27874391 TCTGTCCG-AACAATAGAAATAGGCACACCATGCAACTTCACAATTTGAG
1 TCTGTCCGAAACAATAGAAATAGGCACACCATGCAACCTCACAATCTGAG
27874440 CAACATATAG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 38 0.84
50 7 0.16
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.22
Consensus pattern (50 bp):
TCTGTCCGAAACAATAGAAATAGGCACACCATGCAACCTCACAATCTGAG
Found at i:27880134 original size:28 final size:27
Alignment explanation
Indices: 27880102--27880200 Score: 112
Period size: 28 Copynumber: 3.6 Consensus size: 27
27880092 TTAATAAGTA
* *
27880102 CGCACACTTAGTGCTTAATAATCACACT
1 CGCACACTTAGTGCTT-ATAATTAAACT
*
27880130 CGCACACTTAGTGCTT-TACCATTATACT
1 CGCACACTTAGTGCTTATA--ATTAAACT
27880158 CGCACACTTAGTGCATT-TCAATTAAACT
1 CGCACACTTAGTGC-TTAT-AATTAAACT
27880186 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
27880201 AATCTCATTA
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
26 2 0.03
27 1 0.02
28 57 0.89
29 3 0.05
30 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTATAATTAAACT
Found at i:27885117 original size:190 final size:190
Alignment explanation
Indices: 27884788--27885173 Score: 738
Period size: 190 Copynumber: 2.0 Consensus size: 190
27884778 ATTCTCATAA
*
27884788 TTTATGTGGTTTCCCCACTAAGAATGTGGGCTGTTTGGTGGCTTAGAACGTAATTTTTTAAAATT
1 TTTATCTGGTTTCCCCACTAAGAATGTGGGCTGTTTGGTGGCTTAGAACGTAATTTTTTAAAATT
27884853 TTAATTTATTTATATTTTAGATTTAACTATATAAATTCAATTATTAATATTTAAAATATTTTTAT
66 TTAATTTATTTATATTTTAGATTTAACTATATAAATTCAATTATTAATATTTAAAATATTTTTAT
27884918 TAAATTTTAGTTTATTATATTATTA-TTTTTTTATTATATAGTCATTAAATGAGTAACATT
131 TAAATTTTAGTTTATTATATTATTATTTTTTTTATTATATAG-CATTAAATGAGTAACATT
27884978 TTTATCTGGTTTCCCCACTAAGAATGTGGGCTGTTTGGTGGCTTAGAACGTAATTTTTTAAAATT
1 TTTATCTGGTTTCCCCACTAAGAATGTGGGCTGTTTGGTGGCTTAGAACGTAATTTTTTAAAATT
27885043 TTAATTTATTTATATTTTAGATTTAACTATATAAATTCAATTATTAATATTTAAAATATTTTTAT
66 TTAATTTATTTATATTTTAGATTTAACTATATAAATTCAATTATTAATATTTAAAATATTTTTAT
*
27885108 TAAATTTTAGTTTATTATATTATTATTTTTTTTATTATATAGCATTAAATGAGTATCATT
131 TAAATTTTAGTTTATTATATTATTATTTTTTTTATTATATAGCATTAAATGAGTAACATT
27885168 TTTATC
1 TTTATC
27885174 CGTAAACATT
Statistics
Matches: 193, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
190 177 0.92
191 16 0.08
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (190 bp):
TTTATCTGGTTTCCCCACTAAGAATGTGGGCTGTTTGGTGGCTTAGAACGTAATTTTTTAAAATT
TTAATTTATTTATATTTTAGATTTAACTATATAAATTCAATTATTAATATTTAAAATATTTTTAT
TAAATTTTAGTTTATTATATTATTATTTTTTTTATTATATAGCATTAAATGAGTAACATT
Found at i:27885128 original size:20 final size:20
Alignment explanation
Indices: 27885105--27885147 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
27885095 AAAATATTTT
27885105 TATTA-AATTTTAGTTTATTA
1 TATTATAATTTT-GTTTATTA
* *
27885125 TATTATTATTTTTTTTATTA
1 TATTATAATTTTGTTTATTA
27885145 TAT
1 TAT
27885148 AGCATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTATAATTTTGTTTATTA
Found at i:27893409 original size:26 final size:27
Alignment explanation
Indices: 27893342--27893410 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
27893332 GGTGGAGGGC
27893342 TTGCCAAAGGCGGCACCAGAGGTGTCA
1 TTGCCAAAGGCGGCACCAGAGGTGTCA
* * * *
27893369 GTGGCAGAGGTGGCACCA-AGGTG-CTA
1 TTGCCAAAGGCGGCACCAGAGGTGTC-A
*
27893395 TTGCCACAGGCGGCAC
1 TTGCCAAAGGCGGCAC
27893411 TAGCCCGTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
25 1 0.03
26 18 0.55
27 14 0.42
ACGTcount: A:0.23, C:0.26, G:0.36, T:0.14
Consensus pattern (27 bp):
TTGCCAAAGGCGGCACCAGAGGTGTCA
Found at i:27893460 original size:10 final size:10
Alignment explanation
Indices: 27893445--27893564 Score: 83
Period size: 10 Copynumber: 12.1 Consensus size: 10
27893435 CATTCGGCTG
27893445 AAGGAGAAGA
1 AAGGAGAAGA
27893455 AAGGAGAAGA
1 AAGGAGAAGA
* *
27893465 AAGAAAAAAGA
1 AAG-GAGAAGA
*
27893476 AA-GAAAAGGA
1 AAGGAGAA-GA
27893486 AAGGAGAAGA
1 AAGGAGAAGA
27893496 AAGGA-AAGGA
1 AAGGAGAA-GA
27893506 AAGGAGAAG-
1 AAGGAGAAGA
* *
27893515 AAGAAAAAG-
1 AAGGAGAAGA
27893524 AAGGAGAAGA
1 AAGGAGAAGA
*
27893534 CACGG-GAA-A
1 -AAGGAGAAGA
27893543 AA-GAGAAAGA
1 AAGGAG-AAGA
27893553 GAAGGAGAAGA
1 -AAGGAGAAGA
27893564 A
1 A
27893565 GAAGGTATTT
Statistics
Matches: 88, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
7 1 0.01
8 2 0.02
9 23 0.26
10 37 0.42
11 22 0.25
12 3 0.03
ACGTcount: A:0.63, C:0.02, G:0.35, T:0.00
Consensus pattern (10 bp):
AAGGAGAAGA
Found at i:27893497 original size:20 final size:20
Alignment explanation
Indices: 27893445--27893533 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
27893435 CATTCGGCTG
*
27893445 AAGGAGAAGAAAGGAGAA-GA
1 AAGGAGAAGAAA-GAAAAGGA
* *
27893465 AAGAAAAAAGAAAGAAAAGGA
1 AAG-GAGAAGAAAGAAAAGGA
*
27893486 AAGGAGAAGAAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAGGA
*
27893506 AAGGAGAAG-AAGAAAAAG-
1 AAGGAGAAGAAAGAAAAGGA
27893524 AAGGAGAAGA
1 AAGGAGAAGA
27893534 CACGGGAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
18 9 0.16
19 7 0.12
20 30 0.52
21 12 0.21
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
AAGGAGAAGAAAGAAAAGGA
Found at i:27893498 original size:15 final size:15
Alignment explanation
Indices: 27893453--27893505 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
27893443 TGAAGGAGAA
27893453 GAAAGGAGAAGAAA-
1 GAAAGGAGAAGAAAG
**
27893467 GAAAAAAGAAAGAAAAG
1 GAAAGGAG-AAG-AAAG
27893484 GAAAGGAGAAGAAAG
1 GAAAGGAGAAGAAAG
27893499 GAAAGGA
1 GAAAGGA
27893506 AAGGAGAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
14 6 0.19
15 14 0.44
16 6 0.19
17 6 0.19
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
GAAAGGAGAAGAAAG
Done.