Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 10 of 141
Found at i:2689761 original size:25 final size:25
Alignment explanation
Indices: 2689701--2689761 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
2689691 CTCCTAAATT
*
2689701 TTAATTTAATTATCTAATTTTTCAA
1 TTAATTAAATTATCTAATTTTTCAA
* *
2689726 TTTATTGAATTAT-TAATATTTT-ATA
1 TTAATTAAATTATCTAAT-TTTTCA-A
2689751 TTAATTAAATT
1 TTAATTAAATT
2689762 TTTGAGAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATCTAATTTTTCAA
Found at i:2690697 original size:55 final size:55
Alignment explanation
Indices: 2690636--2690746 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
2690626 AGTTGAAGAA
2690636 AGTGAGGATCCTGAAAAAGAAGAAGAAAAAGATCCCACAGAGATCGAGCCAGTGC
1 AGTGAGGATCCTGAAAAAGAAGAAGAAAAAGATCCCACAGAGATCGAGCCAGTGC
* *
2690691 AGTGAGGATCCTGAAAAAGAAGAAGAAGAAGATCCTACAGAGATCGAGCCAGTGC
1 AGTGAGGATCCTGAAAAAGAAGAAGAAAAAGATCCCACAGAGATCGAGCCAGTGC
2690746 A
1 A
2690747 ATCGGTTGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.43, C:0.17, G:0.28, T:0.12
Consensus pattern (55 bp):
AGTGAGGATCCTGAAAAAGAAGAAGAAAAAGATCCCACAGAGATCGAGCCAGTGC
Found at i:2696178 original size:22 final size:21
Alignment explanation
Indices: 2696148--2696198 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2696138 AAGTCATCAA
*
2696148 TTCCCTTCTTTCTCTTCTCTTT
1 TTCCTTTCTTT-TCTTCTCTTT
*
2696170 TTCCTTTCTTTTTTTCTCTTT
1 TTCCTTTCTTTTCTTCTCTTT
*
2696191 TTTCTTTC
1 TTCCTTTC
2696199 CGAAAGAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
TTCCTTTCTTTTCTTCTCTTT
Found at i:2710903 original size:22 final size:20
Alignment explanation
Indices: 2710877--2710916 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2710867 TAACGTGTCA
2710877 TTGGAGAAAGCTGGAAGAAATC
1 TTGGAG-AAG-TGGAAGAAATC
*
2710899 TTGGAGTAGTGGAAGAAA
1 TTGGAGAAGTGGAAGAAA
2710917 AGAAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.40, C:0.05, G:0.35, T:0.20
Consensus pattern (20 bp):
TTGGAGAAGTGGAAGAAATC
Found at i:2732709 original size:46 final size:46
Alignment explanation
Indices: 2732642--2732734 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
2732632 GATTTTTTGA
2732642 AAGACTATGATTGTGCGATCAAGTATCAGCACAAAAAGACTAATGT
1 AAGACTATGATTGTGCGATCAAGTATCAGCACAAAAAGACTAATGT
*
2732688 AAGACTATGATTGTGCGATCAAGTATCAGCACGAAAAGACTAATGT
1 AAGACTATGATTGTGCGATCAAGTATCAGCACAAAAAGACTAATGT
2732734 A
1 A
2732735 GTGGTCGATG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (46 bp):
AAGACTATGATTGTGCGATCAAGTATCAGCACAAAAAGACTAATGT
Found at i:2734661 original size:28 final size:28
Alignment explanation
Indices: 2734629--2734711 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 28
2734619 ATTTGCATAT
2734629 GTGGTGGCCTGTCCATAAAGTATTATCA
1 GTGGTGGCCTGTCCATAAAGTATTATCA
* ** * *
2734657 GTGGTAG-CT-T--AT-CTGCA-AATCA
1 GTGGTGGCCTGTCCATAAAGTATTATCA
*
2734679 GTGGTGGCTTGTCCATAAAGTATTATCA
1 GTGGTGGCCTGTCCATAAAGTATTATCA
2734707 GTGGT
1 GTGGT
2734712 AGTTTATCTG
Statistics
Matches: 38, Mismatches: 11, Indels: 12
0.62 0.18 0.20
Matches are distributed among these distances:
22 10 0.26
23 3 0.08
24 3 0.08
26 3 0.08
27 4 0.11
28 15 0.39
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.34
Consensus pattern (28 bp):
GTGGTGGCCTGTCCATAAAGTATTATCA
Found at i:2734692 original size:50 final size:48
Alignment explanation
Indices: 2734570--2734743 Score: 214
Period size: 50 Copynumber: 3.6 Consensus size: 48
2734560 GTGGAGATTC
* * *
2734570 ATCTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTT-TCAGTGGAAGTGT
1 ATCTGCAAAT-AGTGGTGGCTTGTCCATAAAGTATTATCAGTGGTAGT-T
* * *
2734619 ATTTGCATAT-GTGGTGGCCTGTCCATAAAGTATTATCAGTGGTAGCTT
1 ATCTGCAAATAGTGGTGGCTTGTCCATAAAGTATTATCAGTGGTAG-TT
2734667 ATCTGCAAATCAGTGGTGGCTTGTCCATAAAGTATTATCAGTGGTAGTTT
1 ATCTGCAAAT-AGTGGTGGCTTGTCCATAAAGTATTATCAGTGGTAG-TT
2734717 ATCTGC--A-AGTGGTGGCTTGTCCATAAA
1 ATCTGCAAATAGTGGTGGCTTGTCCATAAA
2734744 TGATACTTTA
Statistics
Matches: 111, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
46 20 0.18
47 21 0.19
48 19 0.17
49 9 0.08
50 42 0.38
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (48 bp):
ATCTGCAAATAGTGGTGGCTTGTCCATAAAGTATTATCAGTGGTAGTT
Found at i:2737057 original size:15 final size:15
Alignment explanation
Indices: 2737037--2737070 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2737027 TGGTCCCACT
2737037 ACATATTAAAAATTA
1 ACATATTAAAAATTA
*
2737052 ACATATTAATAATTA
1 ACATATTAAAAATTA
2737067 ACAT
1 ACAT
2737071 GAAAGTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (15 bp):
ACATATTAAAAATTA
Found at i:2747087 original size:25 final size:25
Alignment explanation
Indices: 2747058--2747115 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
2747048 CTGTTTAAAA
*
2747058 ACTGAAAATGCTATAGATAGTA-TAT
1 ACTGAAAATACTATAGATAG-ACTAT
* * *
2747083 ACTGAGACTACTATAGATAGACTGT
1 ACTGAAAATACTATAGATAGACTAT
2747108 ACTGAAAA
1 ACTGAAAA
2747116 CACTCAAGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (25 bp):
ACTGAAAATACTATAGATAGACTAT
Found at i:2750649 original size:246 final size:246
Alignment explanation
Indices: 2750215--2750706 Score: 975
Period size: 246 Copynumber: 2.0 Consensus size: 246
2750205 AGTTTGGAAC
2750215 GCATTTGTCAGGCCTTTGATCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACGTTCTTGG
1 GCATTTGTCAGGCCTTTGATCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACGTTCTTGG
2750280 GCTTGGGTTAGGCCTTTGTGACTCGTATAATTAGGCCAGGCTTTTAAATGACTCCTTAAATTGGC
66 GCTTGGGTTAGGCCTTTGTGACTCGTATAATTAGGCCAGGCTTTTAAATGACTCCTTAAATTGGC
2750345 ACTTGTTGGCTAAAAATATAGAAGCATTGAAGAGAGTCTTTGAACAGCCACACAAGTGTGAAAAG
131 ACTTGTTGGCTAAAAATATAGAAGCATTGAAGAGAGTCTTTGAACAGCCACACAAGTGTGAAAAG
2750410 TCAATTTTGGAGAGTCACTTGTGTGAACATCATCAGCTGAAAAGTCCTTAG
196 TCAATTTTGGAGAGTCACTTGTGTGAACATCATCAGCTGAAAAGTCCTTAG
*
2750461 GCATTTGTCGGGCCTTTGATCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACGTTCTTGG
1 GCATTTGTCAGGCCTTTGATCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACGTTCTTGG
2750526 GCTTGGGTTAGGCCTTTGTGACTCGTATAATTAGGCCAGGCTTTTAAATGACTCCTTAAATTGGC
66 GCTTGGGTTAGGCCTTTGTGACTCGTATAATTAGGCCAGGCTTTTAAATGACTCCTTAAATTGGC
2750591 ACTTGTTGGCTAAAAATATAGAAGCATTGAAGAGAGTCTTTGAACAGCCACACAAGTGTGAAAAG
131 ACTTGTTGGCTAAAAATATAGAAGCATTGAAGAGAGTCTTTGAACAGCCACACAAGTGTGAAAAG
2750656 TCAATTTTGGAGAGTCACTTGTGTGAACATCATCAGCTGAAAAGTCCTTAG
196 TCAATTTTGGAGAGTCACTTGTGTGAACATCATCAGCTGAAAAGTCCTTAG
2750707 TGTGAATGCT
Statistics
Matches: 245, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
246 245 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (246 bp):
GCATTTGTCAGGCCTTTGATCTCGTTATTGGGCCTTGTGGTAATTTGAGCCCATCACGTTCTTGG
GCTTGGGTTAGGCCTTTGTGACTCGTATAATTAGGCCAGGCTTTTAAATGACTCCTTAAATTGGC
ACTTGTTGGCTAAAAATATAGAAGCATTGAAGAGAGTCTTTGAACAGCCACACAAGTGTGAAAAG
TCAATTTTGGAGAGTCACTTGTGTGAACATCATCAGCTGAAAAGTCCTTAG
Found at i:2751173 original size:20 final size:20
Alignment explanation
Indices: 2751111--2751177 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
2751101 GCAAGTTAAG
* *
2751111 ATGAGCTGAAGTTGAGCTGA
1 ATGAGCTAAAGTTGAACTGA
* * * *
2751131 ATAAGCTAAGGAT-AAGCTCA
1 ATGAGCTAAAGTTGAA-CTGA
2751151 ATGAGCTAAAGTTGAACTGA
1 ATGAGCTAAAGTTGAACTGA
2751171 ATGAGCT
1 ATGAGCT
2751178 TGAGGTAGAG
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
19 1 0.03
20 32 0.91
21 2 0.06
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (20 bp):
ATGAGCTAAAGTTGAACTGA
Found at i:2770131 original size:27 final size:27
Alignment explanation
Indices: 2770101--2770152 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
2770091 TCTCCTACCG
2770101 AAATTGGCTCGTTGATGCTCGTAACGT
1 AAATTGGCTCGTTGATGCTCGTAACGT
*
2770128 AAATTGGTTCGTTGATGCTCGTAAC
1 AAATTGGCTCGTTGATGCTCGTAAC
2770153 AGAGATCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (27 bp):
AAATTGGCTCGTTGATGCTCGTAACGT
Found at i:2772190 original size:18 final size:18
Alignment explanation
Indices: 2772167--2772202 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2772157 AAATTAAAAA
2772167 AATCAGA-TCACAAAGAAT
1 AATCAGATTCA-AAAGAAT
2772185 AATCAGATTCAAAAGAAT
1 AATCAGATTCAAAAGAAT
2772203 TCTAGGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.56, C:0.14, G:0.11, T:0.19
Consensus pattern (18 bp):
AATCAGATTCAAAAGAAT
Found at i:2780362 original size:22 final size:22
Alignment explanation
Indices: 2780332--2780373 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2780322 ATTTGGAGAT
*
2780332 TTTTTGAAGGAAATTGAGAGGA
1 TTTTGGAAGGAAATTGAGAGGA
*
2780354 TTTTGGAAGGAATTTGAGAG
1 TTTTGGAAGGAAATTGAGAG
2780374 TTTGAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (22 bp):
TTTTGGAAGGAAATTGAGAGGA
Found at i:2780400 original size:22 final size:23
Alignment explanation
Indices: 2780375--2780466 Score: 104
Period size: 22 Copynumber: 4.2 Consensus size: 23
2780365 ATTTGAGAGT
2780375 TTGAGAG-AATTTTGGAAGGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
*
2780397 TTGATG-GAAATTTT-GAAGGGAA
1 TTGA-GAGAAATTTTGGAAGGAAA
*
2780419 TTGAGAGAAATTTTGAAAGG-AA
1 TTGAGAGAAATTTTGGAAGGAAA
* *
2780441 TTGAGAG-AATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGGAAGGAAA
2780463 TTGA
1 TTGA
2780467 TATTGAATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
21 10 0.17
22 39 0.65
23 11 0.18
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.30
Consensus pattern (23 bp):
TTGAGAGAAATTTTGGAAGGAAA
Found at i:2780415 original size:52 final size:51
Alignment explanation
Indices: 2780323--2780425 Score: 122
Period size: 52 Copynumber: 2.0 Consensus size: 51
2780313 TTAATATGGA
* * *
2780323 TTTGGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAA-GGAATTTGAGAG
1 TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGGAA-TTGAGAG
2780374 TTTGAGAGAATTTTGGAAGGAAATTGATG-GAAATTTT-GAAGGGAATTGAGAG
1 TTTG-GAGAATTTTGGAAGGAAATTGA-GAG-AATTTTGGAAGGGAATTGAGAG
2780426 AAATTTTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
51 4 0.09
52 31 0.69
53 10 0.22
ACGTcount: A:0.34, C:0.00, G:0.33, T:0.33
Consensus pattern (51 bp):
TTTGGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGGAATTGAGAG
Found at i:2780423 original size:44 final size:44
Alignment explanation
Indices: 2780375--2780466 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
2780365 ATTTGAGAGT
* * *
2780375 TTGAGAG-AATTTTGGAAGGAAATTGATG-GAAATTTTGAAGGGAA
1 TTGAGAGAAATTTTGAAAGG-AATTGA-GAGAAATTTTGAAAGAAA
*
2780419 TTGAGAGAAATTTTGAAAGGAATTGAGAGAATTTTTGAAAGAAA
1 TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
2780463 TTGA
1 TTGA
2780467 TATTGAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 30 0.71
45 11 0.26
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.30
Consensus pattern (44 bp):
TTGAGAGAAATTTTGAAAGGAATTGAGAGAAATTTTGAAAGAAA
Found at i:2781678 original size:20 final size:20
Alignment explanation
Indices: 2781655--2781694 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2781645 TTTGGTGTAA
*
2781655 GAATTTTAAGAACAGGTTTC
1 GAATTTTAAGAACAGATTTC
2781675 GAATTTTAAGAACAGATTTC
1 GAATTTTAAGAACAGATTTC
2781695 TTTAATACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (20 bp):
GAATTTTAAGAACAGATTTC
Found at i:2781876 original size:11 final size:11
Alignment explanation
Indices: 2781860--2781907 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
2781850 GATGATGATG
2781860 ATTTTAAAATC
1 ATTTTAAAATC
2781871 ATTTTAATAAT-
1 ATTTTAA-AATC
*
2781882 -TTTTAAAAATA
1 ATTTT-AAAATC
2781893 ATTTTAAAATC
1 ATTTTAAAATC
2781904 ATTT
1 ATTT
2781908 GTTGATATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
10 7 0.22
11 18 0.56
12 7 0.22
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (11 bp):
ATTTTAAAATC
Found at i:2786031 original size:16 final size:16
Alignment explanation
Indices: 2786010--2786043 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2786000 AAGAACATAG
2786010 AAAATGAAACAAAGGA
1 AAAATGAAACAAAGGA
*
2786026 AAAATGAAATAAAGGA
1 AAAATGAAACAAAGGA
2786042 AA
1 AA
2786044 TTTAAAAAAA
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:0.71, C:0.03, G:0.18, T:0.09
Consensus pattern (16 bp):
AAAATGAAACAAAGGA
Found at i:2787267 original size:34 final size:35
Alignment explanation
Indices: 2787212--2787278 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
2787202 CAAACACCAG
*
2787212 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
2787247 AAAACATTTTCCTG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
2787279 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2790067 original size:5 final size:5
Alignment explanation
Indices: 2790057--2790081 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2790047 GGGGTAGGAC
2790057 ATGAT ATGAT ATGAT ATGAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT
2790082 TCGTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
ATGAT
Found at i:2798719 original size:17 final size:18
Alignment explanation
Indices: 2798692--2798727 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2798682 AGGAAGCAAT
2798692 AGAAGAAAAACATGGAGA
1 AGAAGAAAAACATGGAGA
*
2798710 AGAA-AAAAACATTGAGA
1 AGAAGAAAAACATGGAGA
2798727 A
1 A
2798728 AATGAGTGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.64, C:0.06, G:0.22, T:0.08
Consensus pattern (18 bp):
AGAAGAAAAACATGGAGA
Found at i:2811382 original size:25 final size:25
Alignment explanation
Indices: 2811349--2811397 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
2811339 TAACCAAACC
2811349 GAAATTTTTTCGGTTAATTCGGTTT
1 GAAATTTTTTCGGTTAATTCGGTTT
*
2811374 GAAATTTTTTTGGTTAATTCGGTT
1 GAAATTTTTTCGGTTAATTCGGTT
2811398 GGTTAACCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.20, C:0.06, G:0.20, T:0.53
Consensus pattern (25 bp):
GAAATTTTTTCGGTTAATTCGGTTT
Found at i:2811460 original size:9 final size:9
Alignment explanation
Indices: 2811446--2811503 Score: 75
Period size: 9 Copynumber: 6.4 Consensus size: 9
2811436 TTTGGTTAAA
2811446 AATTAACCG
1 AATTAACCG
*
2811455 AATTAACCT
1 AATTAACCG
2811464 AATT-ACCTG
1 AATTAACC-G
2811473 AATTAACCG
1 AATTAACCG
2811482 AATT-ACTCG
1 AATTAAC-CG
2811491 AATTAACCG
1 AATTAACCG
2811500 AATT
1 AATT
2811504 GAATCACTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
8 5 0.12
9 33 0.77
10 5 0.12
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:2811646 original size:18 final size:18
Alignment explanation
Indices: 2811606--2811649 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2811596 AATTTTTATG
**
2811606 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
2811624 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
2811642 GTTGGGTT
1 ATTGGGTT
2811650 TAGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.45, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:2812724 original size:36 final size:36
Alignment explanation
Indices: 2812656--2812726 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
2812646 CAAAAGTTAA
*
2812656 TAATTTAATCTACACATTTTTAACATACAATTTTTC
1 TAATTTAATCTACACATTTTTAACATAAAATTTTTC
* * *
2812692 TAATTTTATCTTCACCTTTTTAA-ATGAAAATTTTT
1 TAATTTAATCTACACATTTTTAACAT-AAAATTTTT
2812727 AATGTTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 2 0.07
36 28 0.93
ACGTcount: A:0.34, C:0.14, G:0.01, T:0.51
Consensus pattern (36 bp):
TAATTTAATCTACACATTTTTAACATAAAATTTTTC
Found at i:2813469 original size:24 final size:24
Alignment explanation
Indices: 2813420--2813470 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
2813410 TCATTGTTCT
*
2813420 AAATATTAAAAAATTATAATTATA
1 AAATATTAAAAAATTATAATAATA
*
2813444 AAATATTCAAAAATTATAA-AAGTA
1 AAATATTAAAAAATTATAATAA-TA
2813468 AAA
1 AAA
2813471 CAAATCAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (24 bp):
AAATATTAAAAAATTATAATAATA
Found at i:2819446 original size:15 final size:15
Alignment explanation
Indices: 2819418--2819478 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 15
2819408 ACTATATTAT
*
2819418 AATAAATCATAAAAG
1 AATAAATAATAAAAG
*
2819433 AGATAAAT-ATAAAAT
1 A-ATAAATAATAAAAG
2819448 AACTAAATAACTAAAAG
1 AA-TAAATAA-TAAAAG
2819465 AAATAAA-AATAAAA
1 -AATAAATAATAAAA
2819479 TAAACAAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 1 0.03
15 18 0.46
16 9 0.23
17 9 0.23
18 2 0.05
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (15 bp):
AATAAATAATAAAAG
Found at i:2819471 original size:32 final size:32
Alignment explanation
Indices: 2819427--2819494 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
2819417 TAATAAATCA
* * *
2819427 TAAAAGAGATAAATATAAAAT-AACTAAATAAC
1 TAAAAGAAATAAAAATAAAATAAAC-AAACAAC
2819459 TAAAAGAAATAAAAATAAAATAAACAAACAAC
1 TAAAAGAAATAAAAATAAAATAAACAAACAAC
2819491 TAAA
1 TAAA
2819495 CCAATTAGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 29 0.91
33 3 0.09
ACGTcount: A:0.71, C:0.07, G:0.04, T:0.18
Consensus pattern (32 bp):
TAAAAGAAATAAAAATAAAATAAACAAACAAC
Found at i:2823306 original size:39 final size:38
Alignment explanation
Indices: 2823251--2823324 Score: 94
Period size: 39 Copynumber: 1.9 Consensus size: 38
2823241 ACTTTGGAAT
* * *
2823251 TTTCTTTTAACTGTTGGGATGAAATGGATATGTTGAAAA
1 TTTCTTTTAACCGTTGGGAT-AAACGCATATGTTGAAAA
* *
2823290 TTTCTTTTAGCCGTTGGGGTAAACGCATATGTTGA
1 TTTCTTTTAACCGTTGGGATAAACGCATATGTTGA
2823325 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
38 13 0.43
39 17 0.57
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (38 bp):
TTTCTTTTAACCGTTGGGATAAACGCATATGTTGAAAA
Found at i:2826414 original size:790 final size:790
Alignment explanation
Indices: 2824893--2826472 Score: 3151
Period size: 790 Copynumber: 2.0 Consensus size: 790
2824883 TCCTCTATCT
2824893 CAAGACACAACACTGAAATTTGATAATTGAGTTTGGATTTGAGTCTAAACTCAAAGCTTAACCTA
1 CAAGACACAACACTGAAATTTGATAATTGAGTTTGGATTTGAGTCTAAACTCAAAGCTTAACCTA
2824958 GCATAACCCCATAACATGATCTAATTGAATCATAAAATCTATGGATGCATATGTGTGAGTATGAT
66 GCATAACCCCATAACATGATCTAATTGAATCATAAAATCTATGGATGCATATGTGTGAGTATGAT
2825023 TGATGATTAAGTTGATTTGAATGATAATTATGACATAAATTTTATGATTATGTAATGAGATAGCT
131 TGATGATTAAGTTGATTTGAATGATAATTATGACATAAATTTTATGATTATGTAATGAGATAGCT
2825088 GGAGTTACTTTAGCAACGTAATGCGTTATCATGCATTCAGATTCGATAATCAGGTTGGGTGTTGG
196 GGAGTTACTTTAGCAACGTAATGCGTTATCATGCATTCAGATTCGATAATCAGGTTGGGTGTTGG
2825153 GTGTTACACGAATACTAAGGAAGAGTGTGTAAGGTGTCATATTAGAGATGATCCTTTTTGCGAGT
261 GTGTTACACGAATACTAAGGAAGAGTGTGTAAGGTGTCATATTAGAGATGATCCTTTTTGCGAGT
2825218 TTTGTAGAAATGTTGTAAAAGATGTAAATAATATACTATGTTAGTGCTTTACGGCAGGGTCCATC
326 TTTGTAGAAATGTTGTAAAAGATGTAAATAATATACTATGTTAGTGCTTTACGGCAGGGTCCATC
2825283 TTGACAACATTAAATTAGGAATAAATGGTGAGTGAGTTTTTGTCTATGGAGATTTTAGAATGGAT
391 TTGACAACATTAAATTAGGAATAAATGGTGAGTGAGTTTTTGTCTATGGAGATTTTAGAATGGAT
2825348 TAACTTGAACATTCAAGATATTGTCTATTTCCCTAGAGAAGTTGCAAATTGAGAACTGCTCTTTG
456 TAACTTGAACATTCAAGATATTGTCTATTTCCCTAGAGAAGTTGCAAATTGAGAACTGCTCTTTG
2825413 GGTGTGTATGTTGGAACTTGTGGGTGGACAGAATAAAAGGATGTTTGCTCAGGAGTACGAGGAAA
521 GGTGTGTATGTTGGAACTTGTGGGTGGACAGAATAAAAGGATGTTTGCTCAGGAGTACGAGGAAA
2825478 TAGAAGGGGTCTTGGAAAGATTTTTGGTTTATGTTGTCAACAAGATAGAGGAAATCAACATATCA
586 TAGAAGGGGTCTTGGAAAGATTTTTGGTTTATGTTGTCAACAAGATAGAGGAAATCAACATATCA
2825543 GTTAGTTATATGATGGGGAAACCCTCCGGTAGATTGGTATAAAGTAAACATGGATGGGCATTGAA
651 GTTAGTTATATGATGGGGAAACCCTCCGGTAGATTGGTATAAAGTAAACATGGATGGGCATTGAA
2825608 TATGAGTATGGGAAGGGCTGCATCAGCAGGAGTTGTATTGTACTCTAGTGGAAGGTGGATGAAAG
716 TATGAGTATGGGAAGGGCTGCATCAGCAGGAGTTGTATTGTACTCTAGTGGAAGGTGGATGAAAG
*
2825673 GTTTTTTCCG
781 GGTTTTTCCG
2825683 CAAGACACAACACTGAAATTTGATAATTGAGTTTGGATTTGAGTCTAAACTCAAAGCTTAACCTA
1 CAAGACACAACACTGAAATTTGATAATTGAGTTTGGATTTGAGTCTAAACTCAAAGCTTAACCTA
2825748 GCATAACCCCATAACATGATCTAATTGAATCATAAAATCTATGGATGCATATGTGTGAGTATGAT
66 GCATAACCCCATAACATGATCTAATTGAATCATAAAATCTATGGATGCATATGTGTGAGTATGAT
2825813 TGATGATTAAGTTGATTTGAATGATAATTATGACATAAATTTTATGATTATGTAATGAGATAGCT
131 TGATGATTAAGTTGATTTGAATGATAATTATGACATAAATTTTATGATTATGTAATGAGATAGCT
2825878 GGAGTTACTTTAGCAACGTAATGCGTTATCATGCATTCAGATTCGATAATCAGGTTGGGTGTTGG
196 GGAGTTACTTTAGCAACGTAATGCGTTATCATGCATTCAGATTCGATAATCAGGTTGGGTGTTGG
2825943 GTGTTACACGAATACTAAGGAAGAGTGTGTAAGGTGTCATATTAGAGATGATCCTTTTTGCGAGT
261 GTGTTACACGAATACTAAGGAAGAGTGTGTAAGGTGTCATATTAGAGATGATCCTTTTTGCGAGT
2826008 TTTGTAGAAATGTTGTAAAAGATGTAAATAATATACTATGTTAGTGCTTTACGGCAGGGTCCATC
326 TTTGTAGAAATGTTGTAAAAGATGTAAATAATATACTATGTTAGTGCTTTACGGCAGGGTCCATC
2826073 TTGACAACATTAAATTAGGAATAAATGGTGAGTGAGTTTTTGTCTATGGAGATTTTAGAATGGAT
391 TTGACAACATTAAATTAGGAATAAATGGTGAGTGAGTTTTTGTCTATGGAGATTTTAGAATGGAT
2826138 TAACTTGAACATTCAAGATATTGTCTATTTCCCTAGAGAAGTTGCAAATTGAGAACTGCTCTTTG
456 TAACTTGAACATTCAAGATATTGTCTATTTCCCTAGAGAAGTTGCAAATTGAGAACTGCTCTTTG
2826203 GGTGTGTATGTTGGAACTTGTGGGTGGACAGAATAAAAGGATGTTTGCTCAGGAGTACGAGGAAA
521 GGTGTGTATGTTGGAACTTGTGGGTGGACAGAATAAAAGGATGTTTGCTCAGGAGTACGAGGAAA
2826268 TAGAAGGGGTCTTGGAAAGATTTTTGGTTTATGTTGTCAACAAGATAGAGGAAATCAACATATCA
586 TAGAAGGGGTCTTGGAAAGATTTTTGGTTTATGTTGTCAACAAGATAGAGGAAATCAACATATCA
2826333 GTTAGTTATATGATGGGGAAACCCTCCGGTAGATTGGTATAAAGTAAACATGGATGGGCATTGAA
651 GTTAGTTATATGATGGGGAAACCCTCCGGTAGATTGGTATAAAGTAAACATGGATGGGCATTGAA
2826398 TATGAGTATGGGAAGGGCTGCATCAGCAGGAGTTGTATTGTACTCTAGTGGAAGGTGGATGAAAG
716 TATGAGTATGGGAAGGGCTGCATCAGCAGGAGTTGTATTGTACTCTAGTGGAAGGTGGATGAAAG
2826463 GGTTTTTCCG
781 GGTTTTTCCG
2826473 GGGTTTTGGA
Statistics
Matches: 789, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
790 789 1.00
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (790 bp):
CAAGACACAACACTGAAATTTGATAATTGAGTTTGGATTTGAGTCTAAACTCAAAGCTTAACCTA
GCATAACCCCATAACATGATCTAATTGAATCATAAAATCTATGGATGCATATGTGTGAGTATGAT
TGATGATTAAGTTGATTTGAATGATAATTATGACATAAATTTTATGATTATGTAATGAGATAGCT
GGAGTTACTTTAGCAACGTAATGCGTTATCATGCATTCAGATTCGATAATCAGGTTGGGTGTTGG
GTGTTACACGAATACTAAGGAAGAGTGTGTAAGGTGTCATATTAGAGATGATCCTTTTTGCGAGT
TTTGTAGAAATGTTGTAAAAGATGTAAATAATATACTATGTTAGTGCTTTACGGCAGGGTCCATC
TTGACAACATTAAATTAGGAATAAATGGTGAGTGAGTTTTTGTCTATGGAGATTTTAGAATGGAT
TAACTTGAACATTCAAGATATTGTCTATTTCCCTAGAGAAGTTGCAAATTGAGAACTGCTCTTTG
GGTGTGTATGTTGGAACTTGTGGGTGGACAGAATAAAAGGATGTTTGCTCAGGAGTACGAGGAAA
TAGAAGGGGTCTTGGAAAGATTTTTGGTTTATGTTGTCAACAAGATAGAGGAAATCAACATATCA
GTTAGTTATATGATGGGGAAACCCTCCGGTAGATTGGTATAAAGTAAACATGGATGGGCATTGAA
TATGAGTATGGGAAGGGCTGCATCAGCAGGAGTTGTATTGTACTCTAGTGGAAGGTGGATGAAAG
GGTTTTTCCG
Found at i:2829093 original size:55 final size:55
Alignment explanation
Indices: 2829006--2829115 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
2828996 GTATTCGTTG
* *
2829006 GATGATAAATCATCACTTTTAATTTGATTAGTGCTTATGAATAATTAATTTGCAA
1 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTGCAA
*
2829061 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATTAATAATTAATTTGCAA
1 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTGCAA
2829116 TCTGTAATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (55 bp):
GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTGCAA
Found at i:2830759 original size:16 final size:17
Alignment explanation
Indices: 2830735--2830781 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
2830725 TGAGGATTAA
2830735 ATATAATTAATATTTTT
1 ATATAATTAATATTTTT
*
2830752 AT-TAATTAACATTTTT
1 ATATAATTAATATTTTT
*
2830768 TTATAATTGAATAT
1 ATATAATT-AATAT
2830782 GGTAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 14 0.56
17 7 0.28
18 4 0.16
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
ATATAATTAATATTTTT
Found at i:2833970 original size:55 final size:55
Alignment explanation
Indices: 2833875--2833984 Score: 175
Period size: 55 Copynumber: 2.0 Consensus size: 55
2833865 GTATTCATTG
* * * * *
2833875 GATGATAAATCATCACTTTTAATTTTATTATTGCTTATGAATAATTAATTTGCAA
1 GATGATAAATCATCACTTTTAACTTGAATAGTGCTCATGAATAATTAATTTGCAA
2833930 GATGATAAATCATCACTTTTAACTTGAATAGTGCTCATGAATAATTAATTTGCAA
1 GATGATAAATCATCACTTTTAACTTGAATAGTGCTCATGAATAATTAATTTGCAA
2833985 TCTATAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (55 bp):
GATGATAAATCATCACTTTTAACTTGAATAGTGCTCATGAATAATTAATTTGCAA
Found at i:2837753 original size:46 final size:46
Alignment explanation
Indices: 2837686--2838053 Score: 263
Period size: 46 Copynumber: 8.5 Consensus size: 46
2837676 TTTGAGTACT
2837686 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
2837732 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * ** *
2837778 TTTGATCAAGTGAAAAAGTGATAAGTGGTAGC-CAAG-TGA-A--AA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCT-ACACTTA
** ** ** * * * * *
2837820 AGTGAT-AAGTG--GTAG-CCT-A--GCTA-CACTTATCT-GA-TCA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTTAGCTACACTTA
** * * ** *
2837857 AGTGA-CAAAGTGA-TAAGTGGT-AG-CCTAGC-TA--C-AC--TTA
1 TCTGATC-AAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
2837894 TCTGATCAAGTGACAAAGTAATAAGAT-TTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAG-TGGTAGCTTTAGCTACACTTA
2837940 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
2837986 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
2838031 TCTGATCAAG-GAC-AAGTGATAAG
1 TCTGATCAAGTGACAAAGTGATAAG
2838054 AGGTCATATG
Statistics
Matches: 263, Mismatches: 34, Indels: 53
0.75 0.10 0.15
Matches are distributed among these distances:
34 1 0.00
35 3 0.01
36 2 0.01
37 19 0.07
38 13 0.05
39 6 0.02
40 7 0.03
41 9 0.03
42 6 0.02
43 11 0.04
44 7 0.03
45 26 0.10
46 153 0.58
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:2837820 original size:26 final size:26
Alignment explanation
Indices: 2837784--2837836 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2837774 CTTATTTGAT
2837784 CAAGTGAAAAAGTGATAAGTGGTAGC
1 CAAGTGAAAAAGTGATAAGTGGTAGC
2837810 CAAGTGAAAAAGTGATAAGTGGTAGC
1 CAAGTGAAAAAGTGATAAGTGGTAGC
2837836 C
1 C
2837837 TAGCTACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.42, C:0.09, G:0.30, T:0.19
Consensus pattern (26 bp):
CAAGTGAAAAAGTGATAAGTGGTAGC
Found at i:2837861 original size:45 final size:45
Alignment explanation
Indices: 2837810--2838053 Score: 395
Period size: 45 Copynumber: 5.4 Consensus size: 45
2837800 AAGTGGTAGC
*
2837810 CAAGTGAAAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGAT
2837855 CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGAT
* * *
2837900 CAAGTGACAAAGTAATAAGAT-TTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAG-TGGTAGC-CTAGCTACACTTATCTGAT
*
2837946 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
2837992 CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGAT
2838037 CAAG-GAC-AAGTGATAAG
1 CAAGTGACAAAGTGATAAG
2838054 AGGTCATATG
Statistics
Matches: 189, Mismatches: 7, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
43 10 0.05
44 3 0.02
45 89 0.47
46 87 0.46
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (45 bp):
CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGAT
Found at i:2837867 original size:71 final size:72
Alignment explanation
Indices: 2837738--2837881 Score: 245
Period size: 71 Copynumber: 2.0 Consensus size: 72
2837728 CTTATCTGAT
* * *
2837738 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATTTGATCAAGTGAAAAAGTGATAAG
1 CAAGTGAAAAAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAG
2837803 TGGTAGC
66 TGGTAGC
*
2837810 CAAGTGAAAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
1 CAAGTGAAAAAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAG
2837874 TGGTAGC
66 TGGTAGC
2837881 C
1 C
2837882 TAGCTACACT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
71 43 0.63
72 25 0.37
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (72 bp):
CAAGTGAAAAAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAG
TGGTAGC
Found at i:2837944 original size:91 final size:91
Alignment explanation
Indices: 2837810--2838053 Score: 388
Period size: 91 Copynumber: 2.7 Consensus size: 91
2837800 AAGTGGTAGC
* *
2837810 CAAGTGAAAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
1 CAAGTGACAAAGTAATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
2837875 GGTAGC-CTAGCTACACTTATCTGAT
66 GGTAGCTCTAGCTACACTTATCTGAT
* *
2837900 CAAGTGACAAAGTAATAAGAT-TTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAA
1 CAAGTGACAAAGTAATAAG-TGGTAGC-CTAGCTACACTTATCTGATCAAGTGACAAAGTGATAA
*
2837964 GTGGTAGCTTTAGCTACACTTATCTGAT
64 GTGGTAGCTCTAGCTACACTTATCTGAT
*
2837992 CAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 CAAGTGACAAAGTAATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAG
2838054 AGGTCATATG
Statistics
Matches: 142, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
89 10 0.07
90 24 0.17
91 68 0.48
92 40 0.28
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (91 bp):
CAAGTGACAAAGTAATAAGTGGTAGCCTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
GGTAGCTCTAGCTACACTTATCTGAT
Found at i:2838838 original size:23 final size:21
Alignment explanation
Indices: 2838802--2838850 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 21
2838792 ATAAATAAAA
2838802 TAAAATAAATATATTAAATA-T
1 TAAAATAAATATA-TAAATATT
2838823 TAAAATAAAATGATATAAATATT
1 TAAAAT-AAAT-ATATAAATATT
2838846 TAAAA
1 TAAAA
2838851 AGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.24
22 10 0.40
23 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
TAAAATAAATATATAAATATT
Found at i:2838841 original size:22 final size:22
Alignment explanation
Indices: 2838802--2838850 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 22
2838792 ATAAATAAAA
2838802 TAAAATAAATATATTAAATA-T
1 TAAAATAAATATATTAAATATT
2838823 TAAAATAAA-ATGATATAAATATT
1 TAAAATAAATAT-AT-TAAATATT
2838846 TAAAA
1 TAAAA
2838851 AGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.08
21 11 0.44
22 6 0.24
23 6 0.24
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAAATAAATATATTAAATATT
Found at i:2850200 original size:27 final size:27
Alignment explanation
Indices: 2850170--2850242 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 27
2850160 TAGGATAAAA
*
2850170 ATATAAATTACTATCATATAATAATTT
1 ATATAAATTACTATCATATAATAATGT
2850197 ATATATAATATA-TAT-ATATAATAATGT
1 ATATA-AAT-TACTATCATATAATAATGT
2850224 ATGA-AAA-TACTATCATATA
1 AT-ATAAATTACTATCATATA
2850243 TTTCTTTAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
24 2 0.05
25 3 0.08
26 7 0.17
27 19 0.47
28 7 0.17
29 2 0.05
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (27 bp):
ATATAAATTACTATCATATAATAATGT
Found at i:2850404 original size:64 final size:63
Alignment explanation
Indices: 2850333--2850502 Score: 199
Period size: 61 Copynumber: 2.7 Consensus size: 63
2850323 TATATTAAAC
**
2850333 TTATATAAAAATATGCACTAATTAGATTTAAACATTAATTAGATAATACTAGA-TTAAACATTAA
1 TTATATAAAAATATGCACTAATTAGATTTAAACATTAATTA-ATAATACTAGACTTAAA-AAAAA
*
2850397 TTATATAAAAATATGCACTAATGAGA-TTAAACATT-A--AATAATACTAGATCTTAAAAAAAA
1 TTATATAAAAATATGCACTAATTAGATTTAAACATTAATTAATAATACTAGA-CTTAAAAAAAA
** *
2850457 CCATGTCAAAAATATGCACTAATTAGATTTAAA-ATTAAATTAATAA
1 TTATAT-AAAAATATGCACTAATTAGATTTAAACATT-AATTAATAA
2850503 AAAACTAAAT
Statistics
Matches: 91, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
59 11 0.12
60 7 0.08
61 27 0.30
62 6 0.07
63 10 0.11
64 25 0.27
65 5 0.05
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (63 bp):
TTATATAAAAATATGCACTAATTAGATTTAAACATTAATTAATAATACTAGACTTAAAAAAAA
Found at i:2852378 original size:117 final size:117
Alignment explanation
Indices: 2852184--2852399 Score: 360
Period size: 117 Copynumber: 1.8 Consensus size: 117
2852174 GGGGGATAAG
* ** *
2852184 ATTAGTGGCTTCAATATACTCCACTGTAACCTGAGGGAGGTAAAATCTGCCACCTTCGATCTACT
1 ATTACTGGCTTCAATATACTCCACTGTAACCACAGGGAGGTAAAATCCGCCACCTTCGATCTACT
*
2852249 CCACTACTGCTTAGGGAGATAAGATCTGTAATCTACTGACTAGGGAGGTAGA
66 CCACTACTGCTTAAGGAGATAAGATCTGTAATCTACTGACTAGGGAGGTAGA
* * *
2852301 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1 ATTACTGGCTTCAATATACTCCACTGTAACCACAGGGAGGTAAAATCCGCCACCTTCGATCTACT
2852366 CCACTACTGCTTAAGGAGATAAGATCTGTAATCT
66 CCACTACTGCTTAAGGAGATAAGATCTGTAATCT
2852400 TCAATCTATT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
117 91 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (117 bp):
ATTACTGGCTTCAATATACTCCACTGTAACCACAGGGAGGTAAAATCCGCCACCTTCGATCTACT
CCACTACTGCTTAAGGAGATAAGATCTGTAATCTACTGACTAGGGAGGTAGA
Found at i:2852525 original size:132 final size:132
Alignment explanation
Indices: 2852290--2852889 Score: 1015
Period size: 132 Copynumber: 4.6 Consensus size: 132
2852280 TCTACTGACT
*
2852290 AGGGAGGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
* * *
2852355 TTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGC
66 TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
*
2852420 CT
131 CC
* * * *
2852422 AGGGA-AGTAGAATTACTGACTTCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCTGCCCT
1 AGGGAGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCAT
* *
2852486 CTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGCTG
65 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTG
2852551 CCC
130 CCC
* * *
2852554 AGGGAGATAGAATTACTGGTTTCAATGTACTCCACTGTAACCACAGGGAGTTAAAATCTGCCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
* *
2852619 TTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGCTGC
66 TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
2852684 CC
131 CC
*
2852686 AGGGAGATAGAATTACTGGCTTCAA-GTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
2852750 TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
66 TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
2852815 CC
131 CC
*
2852817 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
2852882 TTCGATCT
66 TTCGATCT
2852890 GCTTCGCTGT
Statistics
Matches: 439, Mismatches: 26, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
131 126 0.29
132 312 0.71
133 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (132 bp):
AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
TTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
CC
Found at i:2852533 original size:44 final size:44
Alignment explanation
Indices: 2852485--2852825 Score: 214
Period size: 44 Copynumber: 7.8 Consensus size: 44
2852475 AAATCTGCCC
* **
2852485 TCTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAA
1 TCTTTAATCTACTCCACTACTGCCCAGGGAGATAAGATCTGTAA
* * * *
2852529 TCTTTAATCTATTCCACTGCTGCCCAGGGAGAT-AGA-AT-TAC
1 TCTTTAATCTACTCCACTACTGCCCAGGGAGATAAGATCTGTAA
* * * * * * **
2852570 TGGTTTCAATGTACTCCACT-GTAACCACAGGGAGTTAAAATCTGCCA
1 T-CTTT-AATCTACTCCACTACT-GCC-CAGGGAGATAAGATCTGTAA
* **
2852617 TCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAA
1 TCTTTAATCTACTCCACTACTGCCCAGGGAGATAAGATCTGTAA
* * * *
2852661 TCTTTAATCTATTCCACTGCTGCCCAGGGAGAT-AGA-AT-TAC
1 TCTTTAATCTACTCCACTACTGCCCAGGGAGATAAGATCTGTAA
* * * * * * **
2852702 TGGCTTCAA-GTACTCCACTA-TAACCACAGGGAGGTAAAATCCGCCA
1 T--CTTTAATCTACTCCACTACT-GCC-CAGGGAGATAAGATCTGTAA
** **
2852748 TCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAA
1 TCTTTAATCTACTCCACTACTGCCCAGGGAGATAAGATCTGTAA
* * *
2852792 TCTTCAATCTATTCCACTGCTGCCCAGGGAGATA
1 TCTTTAATCTACTCCACTACTGCCCAGGGAGATA
2852826 GAATTACTGG
Statistics
Matches: 217, Mismatches: 63, Indels: 34
0.69 0.20 0.11
Matches are distributed among these distances:
41 7 0.03
42 16 0.07
43 32 0.15
44 129 0.59
45 26 0.12
46 6 0.03
47 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
TCTTTAATCTACTCCACTACTGCCCAGGGAGATAAGATCTGTAA
Found at i:2852689 original size:88 final size:87
Alignment explanation
Indices: 2852333--2852691 Score: 214
Period size: 88 Copynumber: 4.1 Consensus size: 87
2852323 ACTGTAACCA
* * * *
2852333 CAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAAT
1 CAGGGA-GTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTCAAGGAGATAAGATCTGTAAT
* * *
2852398 CTTCAATCTATTCCACTGTTGCC
65 CTTTAATCTACTCCACTGCTGCC
* * * * * *
2852421 TAGGGAAGTAGAATTACTG--A-CTTCAATGTACTCCACTGTAAC--CACAAGGAGGTAAAATCT
1 CAGGG-AGTA-AAAT-CTGCCATCTTCAATCTACTCCAC--T-ACTGCTCAAGGAGATAAGATCT
*** * * *
2852481 GCCCTCTTTGATCTACTCCACTACTGCT
60 GTAATCTTTAATCTACTCCACTGCTGCC
* * ** * * * * * * *
2852509 TAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGCTGCCCAGGGAGAT-AGA-AT-TACT
1 CAGGGAG-TAAAATCTGCCATCTTCAATCTACTCCACTACTGCTCAAGGAGATAAGATCTGTAAT
* * *
2852571 GGTTTCAATGTACTCCACTG-TAACC
65 -CTTT-AATCTACTCCACTGCT-GCC
* *
2852596 ACAGGGAGTTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAA
1 -CAGGGAG-TAAAATCTGCCATCTTCAATCTACTCCACTACTGCTCAAGGAGATAAGATCTGTAA
*
2852661 TCTTTAATCTATTCCACTGCTGCC
64 TCTTTAATCTACTCCACTGCTGCC
2852685 CAGGGAG
1 CAGGGAG
2852692 ATAGAATTAC
Statistics
Matches: 197, Mismatches: 54, Indels: 40
0.68 0.19 0.14
Matches are distributed among these distances:
85 2 0.01
86 9 0.05
87 32 0.16
88 107 0.54
89 35 0.18
90 9 0.05
91 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (87 bp):
CAGGGAGTAAAATCTGCCATCTTCAATCTACTCCACTACTGCTCAAGGAGATAAGATCTGTAATC
TTTAATCTACTCCACTGCTGCC
Found at i:2852843 original size:263 final size:264
Alignment explanation
Indices: 2852290--2852889 Score: 1015
Period size: 263 Copynumber: 2.3 Consensus size: 264
2852280 TCTACTGACT
*
2852290 AGGGAGGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
* *
2852355 TTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGC
66 TTCGATCTACTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
* * * *
2852420 CTAGGGAAGTAGAATTACTGACTTCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCTGCCC
131 CCAGGGAAGTAGAATTACTGACTTCAATGTACTCCACTATAACCACAAGGAGGTAAAATCCGCCA
* *
2852485 TCTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGCT
196 TCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCT
2852550 GCCC
261 GCCC
* * *
2852554 AGGGAGATAGAATTACTGGTTTCAATGTACTCCACTGTAACCACAGGGAGTTAAAATCTGCCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
* * *
2852619 TTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGCTGC
66 TTCGATCTACTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
* *
2852684 CCAGGG-AGATAGAATTACTGGCTTCAA-GTACTCCACTATAACCACAGGGAGGTAAAATCCGCC
131 CCAGGGAAG-TAGAATTACTGACTTCAATGTACTCCACTATAACCACAAGGAGGTAAAATCCGCC
2852747 ATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGC
195 ATCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGC
2852812 TGCCC
260 TGCCC
*
2852817 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATC
1 AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
2852882 TTCGATCT
66 TTCGATCT
2852890 GCTTCGCTGT
Statistics
Matches: 313, Mismatches: 22, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
263 170 0.54
264 143 0.46
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (264 bp):
AGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATC
TTCGATCTACTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGC
CCAGGGAAGTAGAATTACTGACTTCAATGTACTCCACTATAACCACAAGGAGGTAAAATCCGCCA
TCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCT
GCCC
Found at i:2854158 original size:42 final size:42
Alignment explanation
Indices: 2854093--2854185 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 42
2854083 CACGCCTCGA
2854093 TCTGATCAAGATACAAGCTGCTCTAATCACTTCATGCCCCAT
1 TCTGATCAAGATACAAGCTGCTCTAATCACTTCATGCCCCAT
*
2854135 TTTGATCAAGATACAAG-TAGCTCTAATCACTTCATGCCCCAT
1 TCTGATCAAGATACAAGCT-GCTCTAATCACTTCATGCCCCAT
2854177 TCTGATCAA
1 TCTGATCAA
2854186 TATTTGAGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (42 bp):
TCTGATCAAGATACAAGCTGCTCTAATCACTTCATGCCCCAT
Found at i:2854288 original size:7 final size:7
Alignment explanation
Indices: 2854269--2854318 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
2854259 TTAGCCTCTC
2854269 CATTTTT
1 CATTTTT
2854276 -ACTTTTT
1 CA-TTTTT
2854283 CATTTTTT
1 CA-TTTTT
*
2854291 CACTTTT
1 CATTTTT
2854298 CA-TTTT
1 CATTTTT
2854304 CATTTTT
1 CATTTTT
2854311 CATCTTTT
1 CAT-TTTT
2854319 TTTTTTGGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
6 7 0.19
7 18 0.49
8 12 0.32
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (7 bp):
CATTTTT
Found at i:2854303 original size:21 final size:21
Alignment explanation
Indices: 2854279--2854318 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2854269 CATTTTTACT
2854279 TTTTCATTTTTTCA-CTTTTCA
1 TTTTCA-TTTTTCATCTTTTCA
2854300 TTTTCATTTTTCATCTTTT
1 TTTTCATTTTTCATCTTTT
2854319 TTTTTTGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCATTTTTCATCTTTTCA
Found at i:2854324 original size:21 final size:21
Alignment explanation
Indices: 2854272--2854324 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2854262 GCCTCTCCAT
2854272 TTTTACTTTTTCATTTTTTCAC
1 TTTT-CTTTTTCATTTTTTCAC
*
2854294 TTTTCATTTTCA-TTTTTCATC
1 TTTTCTTTTTCATTTTTTCA-C
*
2854315 TTTTTTTTTT
1 TTTTCTTTTT
2854325 GGAATTCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.26
21 16 0.59
22 4 0.15
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTCTTTTTCATTTTTTCAC
Found at i:2854765 original size:19 final size:20
Alignment explanation
Indices: 2854741--2854780 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2854731 TTTCTTTTTC
2854741 TTCTTTTT-GTCTTTGATTT
1 TTCTTTTTGGTCTTTGATTT
*
2854760 TTCTTTTTGGTTTTTGATTT
1 TTCTTTTTGGTCTTTGATTT
2854780 T
1 T
2854781 GATTTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.05, C:0.07, G:0.12, T:0.75
Consensus pattern (20 bp):
TTCTTTTTGGTCTTTGATTT
Found at i:2854792 original size:26 final size:26
Alignment explanation
Indices: 2854744--2854793 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2854734 CTTTTTCTTC
**
2854744 TTTTTGTCTTTGATTTTTCTTTTTGG
1 TTTTTGTCTTTGATTTTGATTTTTGG
2854770 TTTTTGAT-TTTGATTTTGATTTTT
1 TTTTTG-TCTTTGATTTTGATTTTT
2854794 TTTGGGATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.08, C:0.04, G:0.14, T:0.74
Consensus pattern (26 bp):
TTTTTGTCTTTGATTTTGATTTTTGG
Found at i:2859569 original size:13 final size:14
Alignment explanation
Indices: 2859539--2859579 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
2859529 AATTACTATC
2859539 ATATA-ATAATAAT
1 ATATATATAATAAT
*
2859552 TTATATATAA-AAT
1 ATATATATAATAAT
2859565 ATATATATAATAAT
1 ATATATATAATAAT
2859579 A
1 A
2859580 ATGTATGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATAATAAT
Found at i:2859823 original size:22 final size:21
Alignment explanation
Indices: 2859795--2859871 Score: 70
Period size: 22 Copynumber: 3.7 Consensus size: 21
2859785 AATTATGATA
2859795 TATGATAAATTTAAATAGTACT
1 TATGAT-AATTTAAATAGTACT
2859817 TATGATAATTTAAAATAGTA--
1 TATGATAATTT-AAATAGTACT
* **
2859837 TATGAT-ATTAAAATAAAACT
1 TATGATAATTTAAATAGTACT
*
2859857 AATGATAAATTTAAA
1 TATGAT-AATTTAAA
2859872 ACAATGTTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
18 6 0.13
19 3 0.07
20 11 0.24
21 5 0.11
22 20 0.44
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.38
Consensus pattern (21 bp):
TATGATAATTTAAATAGTACT
Found at i:2860387 original size:14 final size:15
Alignment explanation
Indices: 2860369--2860405 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
2860359 TTTTTCTCTG
2860369 CTCTTTTTTCTATTT
1 CTCTTTTTTCTATTT
*
2860384 -TC-TTTTTCTGTTT
1 CTCTTTTTTCTATTT
2860397 CTCTTTTTT
1 CTCTTTTTT
2860406 GTTTGTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 10 0.53
14 4 0.21
15 5 0.26
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.76
Consensus pattern (15 bp):
CTCTTTTTTCTATTT
Found at i:2862647 original size:7 final size:7
Alignment explanation
Indices: 2862635--2862679 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
2862625 AAAAAAAGAG
2862635 ATGAAAA
1 ATGAAAA
2862642 ATG-AAA
1 ATGAAAA
2862648 ATGAAAA
1 ATGAAAA
2862655 ATGAAAAA
1 ATG-AAAA
2862663 ATGAAAA
1 ATGAAAA
2862670 A-GTAAAA
1 ATG-AAAA
2862677 ATG
1 ATG
2862680 GAGAGGCTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
6 7 0.21
7 19 0.56
8 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (7 bp):
ATGAAAA
Found at i:2862651 original size:13 final size:13
Alignment explanation
Indices: 2862635--2862661 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2862625 AAAAAAAGAG
2862635 ATGAAAAATGAAA
1 ATGAAAAATGAAA
2862648 ATGAAAAATGAAA
1 ATGAAAAATGAAA
2862661 A
1 A
2862662 AATGAAAAAG
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:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:2862665 original size:15 final size:14
Alignment explanation
Indices: 2862635--2862679 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
2862625 AAAAAAAGAG
2862635 ATGAAAAATG-AAA
1 ATGAAAAATGAAAA
2862648 ATGAAAAATGAAAAA
1 ATGAAAAATG-AAAA
2862663 ATGAAAAA-GTAAAA
1 ATGAAAAATG-AAAA
2862677 ATG
1 ATG
2862680 GAGAGGCTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 10 0.34
14 8 0.28
15 11 0.38
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (14 bp):
ATGAAAAATGAAAA
Found at i:2864136 original size:128 final size:128
Alignment explanation
Indices: 2863928--2864610 Score: 1073
Period size: 128 Copynumber: 5.3 Consensus size: 128
2863918 GCTCATTGAC
2863928 CAGCAGTGGAATAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAA
1 CAGCAGTGGAATAGGTT-GGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATC-AA
** * *
2863993 AG-CGGCAAATCTTATCTTCAAAAGTAAGGAAGTAGATTTAACCCACAAGTCCTATATCCCTGAT
64 AGACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGAT
*
2864057 CAGCAGTGGAATAGGTTGGACATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAA
1 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATC-AAA
** * *
2864122 G-CGGCAAATCTTATCTTCAAAAGTAAGGAAGTAGATTTAACCCACAAGTCCTATATCCCTGAT
65 GACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGAT
* * * *
2864185 CAGCAGTGGAATAGGTTGGACATTACAGATCTTGTCTCCCTAAGCAATAACAGAGCAGATCAAAG
1 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAG
* *
2864250 ACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGAT
66 ACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGAT
* * *
2864313 TAGCAGTGGGATAGGTTGGAAATTACATATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAG
1 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAG
* * * *
2864378 ACGACAAATCTTATCTTCAAGTGTAACGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGGT
66 ACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGAT
2864441 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAG
1 CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAG
*
2864506 ACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGT
66 ACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGAT
* * * *
2864569 CAGTAGTGGAATAGGTTGGGAAACTACAGATCCTATCTCCCT
1 CAGCAGTGGAATAGGTT-GGAAATTACAGATCTTGTCTCCCT
2864611 GAAGTTGTAG
Statistics
Matches: 521, Mismatches: 31, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
127 4 0.01
128 479 0.92
129 38 0.07
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (128 bp):
CAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAG
ACGGCAAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGAT
Found at i:2864794 original size:44 final size:44
Alignment explanation
Indices: 2864746--2864843 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
2864736 AGGTTAAAGT
*
2864746 AGAGCAGATTGAAGCCAGAAATCTTATCTT-CCTGAGATTACAGC
1 AGAGCAGATTGAAGCCAGAAATCCTAT-TTCCCTGAGATTACAGC
* * * *
2864790 AGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGATATTATAGT
1 AGAGCAGATTGAAGCCAGAAATCCTATTTCCCTGAGATTACAGC
*
2864834 GGAGCAGATT
1 AGAGCAGATT
2864844 AAAATAAAGG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 2 0.04
44 45 0.96
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (44 bp):
AGAGCAGATTGAAGCCAGAAATCCTATTTCCCTGAGATTACAGC
Found at i:2871522 original size:60 final size:62
Alignment explanation
Indices: 2871376--2871575 Score: 186
Period size: 59 Copynumber: 3.3 Consensus size: 62
2871366 TCAAAGTGGA
* * * * *
2871376 AACAATTGTCTAGTTCAAAGAA-TAACTTGGACAAAA-A-AAAAGGTTCAAGCCCT-TATG-GA-
1 AACAATTGTCAAGTTC-AAGAACTAACTTAGATAAAAGAGAAAA-GTTTAA-CCCTCAATGTGAG
* * *
2871435 AACAATTGTCAAGTTCAGGAACTAACTTAGATAAAA-ATAATAA-TTTAACCCTTAATGTGAG
1 AACAATTGTCAAGTTCAAGAACTAACTTAGATAAAAGAGAA-AAGTTTAACCCTCAATGTGAG
* *
2871496 AACAATTG-CAAGTTCAAGAA-TAAACTTAGATAAAAGAGAAAAGTTTAGCCCTCCATGTGAG
1 AACAATTGTCAAGTTCAAGAACT-AACTTAGATAAAAGAGAAAAGTTTAACCCTCAATGTGAG
*
2871557 AACCATTGTCAAGTTCAAG
1 AACAATTGTCAAGTTCAAG
2871576 CCCCAAAAAG
Statistics
Matches: 119, Mismatches: 12, Indels: 17
0.80 0.08 0.11
Matches are distributed among these distances:
58 8 0.07
59 36 0.30
60 30 0.25
61 35 0.29
62 10 0.08
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (62 bp):
AACAATTGTCAAGTTCAAGAACTAACTTAGATAAAAGAGAAAAGTTTAACCCTCAATGTGAG
Found at i:2874859 original size:17 final size:17
Alignment explanation
Indices: 2874837--2874883 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
2874827 GTTCATATGA
*
2874837 AATAACAGTTTATACAT
1 AATAACAGTTCATACAT
2874854 AATAACAGTTCATACA-
1 AATAACAGTTCATACAT
*
2874870 ATTTAACAGTTCAT
1 A-ATAACAGTTCAT
2874884 TCAGTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 1 0.04
17 26 0.96
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (17 bp):
AATAACAGTTCATACAT
Found at i:2875428 original size:80 final size:80
Alignment explanation
Indices: 2875178--2875417 Score: 455
Period size: 80 Copynumber: 3.0 Consensus size: 80
2875168 ACACATCTCT
* *
2875178 AGGCCATAATGCTCATCACAG-AAAAAAGGGTGAGTACTCACAATCTTATGGCATGCCAACTATA
1 AGGCCATAATGCTCATTAGAGAAAAAAAGGGTGAGTACTCACAATCTTATGGCATGCCAACTATA
2875242 TCCAATGGTTCCATA
66 TCCAATGGTTCCATA
2875257 AGGCCATAATGCTCATTAGAGAAAAAAAGGGTGAGTACTCACAATCTTATGGCATGCCAACTATA
1 AGGCCATAATGCTCATTAGAGAAAAAAAGGGTGAGTACTCACAATCTTATGGCATGCCAACTATA
2875322 TCCAATGGTTCCATA
66 TCCAATGGTTCCATA
2875337 AGGCCATAATGCTCATTAGAGAAAAAAAGGGTGAGTACTCACAATCTTATGGCATGCCAACTATA
1 AGGCCATAATGCTCATTAGAGAAAAAAAGGGTGAGTACTCACAATCTTATGGCATGCCAACTATA
2875402 TCCAATGGTTCCATA
66 TCCAATGGTTCCATA
2875417 A
1 A
2875418 AGTCACAATG
Statistics
Matches: 158, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
79 19 0.12
80 139 0.88
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (80 bp):
AGGCCATAATGCTCATTAGAGAAAAAAAGGGTGAGTACTCACAATCTTATGGCATGCCAACTATA
TCCAATGGTTCCATA
Found at i:2875749 original size:36 final size:36
Alignment explanation
Indices: 2875709--2875783 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
2875699 ATTAATGCAA
*
2875709 TTCGCCATATTAATACAGATT-ACCAAATTAACATGG
1 TTCGCCATAATAATACA-ATTCACCAAATTAACATGG
* *
2875745 TTCGCCATAATAATATAATTCACCAAGTTAACATGG
1 TTCGCCATAATAATACAATTCACCAAATTAACATGG
2875781 TTC
1 TTC
2875784 AAAATATAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 3 0.09
36 32 0.91
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (36 bp):
TTCGCCATAATAATACAATTCACCAAATTAACATGG
Found at i:2879074 original size:87 final size:87
Alignment explanation
Indices: 2878928--2879367 Score: 619
Period size: 87 Copynumber: 5.0 Consensus size: 87
2878918 TTAGAGGTAT
* *
2878928 TGGTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCTG
1 TGGTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCCG
*
2878993 CTGTTGCTCAGGGAGATAGGGC
66 CTGCTGCTCAGGGAGATAGGGC
* * * *
2879015 TGGTGCCTTTGATCTACTCCACTACTACTTAGAGAGATAAGATCTACAATCTTCGACCTACTCCG
1 TGGTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCCG
*
2879080 CTGTTGCTCAGGGAGATAGGGC
66 CTGCTGCTCAGGGAGATAGGGC
* * **
2879102 TAGTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTATTTTG
1 TGGTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCCG
** * *
2879167 CTGCTATTCAAGAGAGATATGGC
66 CTGCTGCTC-AGGGAGATAGGGC
* *
2879190 TGGTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTTGACCTACTCCG
1 TGGTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCCG
*
2879255 CTGCTGATCAGGGAGATAGGGC
66 CTGCTGCTCAGGGAGATAGGGC
** * * * * *
2879277 TGGTGCCTTCGATCTGCTTTACTATTACTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCA
1 TGGTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCCG
* *
2879342 CTGCTGCTCATGGAGATAGGAC
66 CTGCTGCTCAGGGAGATAGGGC
2879364 TGGT
1 TGGT
2879368 TATGATGACT
Statistics
Matches: 311, Mismatches: 41, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
87 234 0.75
88 77 0.25
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (87 bp):
TGGTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCCG
CTGCTGCTCAGGGAGATAGGGC
Found at i:2879136 original size:43 final size:43
Alignment explanation
Indices: 2878930--2879140 Score: 134
Period size: 43 Copynumber: 4.9 Consensus size: 43
2878920 AGAGGTATTG
* * *
2878930 GTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTA
1 GTGCCTTCGATCTACTCCACTACTGCTTAGGGAGAT-AGAGCTA
**** * ** ** * * *
2878974 CAATCTTCGACCTACTCTGCTGTTGCTCAGGGAGATAGGGCTG
1 GTGCCTTCGATCTACTCCACTACTGCTTAGGGAGATAGAGCTA
* * * *
2879017 GTGCCTTTGATCTACTCCACTACTACTTAGAGAGATAAGATCTA
1 GTGCCTTCGATCTACTCCACTACTGCTTAGGGAGAT-AGAGCTA
**** * * ** * *
2879061 CAATCTTCGACCTACTCCGCTGTTGCTCAGGGAGATAGGGCTA
1 GTGCCTTCGATCTACTCCACTACTGCTTAGGGAGATAGAGCTA
*
2879104 GTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATA
1 GTGCCTTCGATCTACTCCACTACTGCTTAGGGAGATA
2879141 AGATCTACAA
Statistics
Matches: 111, Mismatches: 55, Indels: 3
0.66 0.33 0.02
Matches are distributed among these distances:
43 59 0.53
44 52 0.47
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.29
Consensus pattern (43 bp):
GTGCCTTCGATCTACTCCACTACTGCTTAGGGAGATAGAGCTA
Found at i:2879228 original size:43 final size:43
Alignment explanation
Indices: 2879180--2879317 Score: 105
Period size: 43 Copynumber: 3.2 Consensus size: 43
2879170 CTATTCAAGA
*
2879180 GAGATATGGCTGGTGCCTTCGATCTGCTCCACTACTGCTTAGG
1 GAGATAAGGCTGGTGCCTTCGATCTGCTCCACTACTGCTTAGG
* **** * * * * * * *
2879223 GAGATAAGATCTGCAATCTTTGACCTACTCCGCTGCTGATCAGG
1 GAGATAAG-GCTGGTGCCTTCGATCTGCTCCACTACTGCTTAGG
* ** * *
2879267 GAGATAGGGCTGGTGCCTTCGATCTGCTTTACTATTACTTAGG
1 GAGATAAGGCTGGTGCCTTCGATCTGCTCCACTACTGCTTAGG
2879310 GAGATAAG
1 GAGATAAG
2879318 ATCTACAATT
Statistics
Matches: 63, Mismatches: 31, Indels: 2
0.66 0.32 0.02
Matches are distributed among these distances:
43 33 0.52
44 30 0.48
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.30
Consensus pattern (43 bp):
GAGATAAGGCTGGTGCCTTCGATCTGCTCCACTACTGCTTAGG
Found at i:2879255 original size:175 final size:174
Alignment explanation
Indices: 2878930--2879367 Score: 608
Period size: 175 Copynumber: 2.5 Consensus size: 174
2878920 AGAGGTATTG
*
2878930 GTGCTTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCTGCT
1 GTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCTGCT
* * * *
2878995 GTTGCTCAGGGAGATAGGGCTGGTGCCTTTGATCTACTCCACTACTACTTAGAGAGATAAGATCT
66 GCTACTCAGAGAGATAGGGCTGGTGCCTTCGATCTACTCCACTACTACTTAGAGAGATAAGATCT
* *
2879060 ACAATCTTCGACCTACTCCGCTGTTGCTCAGGGAGATAGGGCTA
131 ACAATCTTCGACCTACTCCGCTGCTGATCAGGGAGATAGGGCTA
* *
2879104 GTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTATTTTGCT
1 GTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCTGCT
* * * * *
2879169 GCTATTCAAGAGAGATATGGCTGGTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATC
66 GCTACTC-AGAGAGATAGGGCTGGTGCCTTCGATCTACTCCACTACTACTTAGAGAGATAAGATC
* * *
2879234 TGCAATCTTTGACCTACTCCGCTGCTGATCAGGGAGATAGGGCTG
130 TACAATCTTCGACCTACTCCGCTGCTGATCAGGGAGATAGGGCTA
** * * * * **
2879279 GTGCCTTCGATCTGCTTTACTATTACTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCACT
1 GTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCTGCT
* *
2879344 GCTGCTCATG-GAGATAGGACTGGT
66 GCTACTCA-GAGAGATAGGGCTGGT
2879368 TATGATGACT
Statistics
Matches: 231, Mismatches: 31, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
174 79 0.34
175 152 0.66
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (174 bp):
GTGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCTGCT
GCTACTCAGAGAGATAGGGCTGGTGCCTTCGATCTACTCCACTACTACTTAGAGAGATAAGATCT
ACAATCTTCGACCTACTCCGCTGCTGATCAGGGAGATAGGGCTA
Found at i:2886730 original size:8 final size:7
Alignment explanation
Indices: 2886710--2886744 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
2886700 GGTATTCTAC
2886710 TTTTTCT
1 TTTTTCT
2886717 TTTTTCT
1 TTTTTCT
2886724 TTGTTTCTT
1 TT-TTTC-T
2886733 TTTTTCT
1 TTTTTCT
2886740 TTTTT
1 TTTTT
2886745 AGAATCTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 15 0.58
8 8 0.31
9 3 0.12
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (7 bp):
TTTTTCT
Found at i:2886732 original size:15 final size:16
Alignment explanation
Indices: 2886712--2886741 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2886702 TATTCTACTT
2886712 TTTC-TTTTTTCTTTG
1 TTTCTTTTTTTCTTTG
2886727 TTTCTTTTTTTCTTT
1 TTTCTTTTTTTCTTT
2886742 TTTAGAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (16 bp):
TTTCTTTTTTTCTTTG
Found at i:2889663 original size:59 final size:57
Alignment explanation
Indices: 2889597--2889785 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
2889587 ATTTTATTAA
2889597 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
2889656 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
2889717 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
2889776 ATCATATATT
1 ATCATATATT
2889786 ATTATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:2889694 original size:66 final size:64
Alignment explanation
Indices: 2889624--2889822 Score: 186
Period size: 66 Copynumber: 3.2 Consensus size: 64
2889614 AAATATATTT
*
2889624 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAA
2889689 G
64 G
* * * * **
2889690 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAAG
* *
2889744 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAA
2889809 G
64 G
*
2889810 AATATTGATTATT
1 AATATTAATTATT
2889823 AAGAATTTTA
Statistics
Matches: 102, Mismatches: 17, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 9 0.09
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.26
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAAG
Found at i:2889716 original size:120 final size:120
Alignment explanation
Indices: 2889586--2889883 Score: 483
Period size: 120 Copynumber: 2.5 Consensus size: 120
2889576 AATTATTTTA
* * *
2889586 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATCATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTATATTT
2889650 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
2889706 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATCATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
2889771 ATAGTATCATATATTATTATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
2889826 AATTTTATTAAATTC-TATATTTTAATTATAATATATCTAATAATAATTATGTTTAAAT
1 AATTTTATTAAA-TCATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
2889884 ATGATTAAAT
Statistics
Matches: 165, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
120 157 0.95
121 8 0.05
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:2889726 original size:61 final size:61
Alignment explanation
Indices: 2889659--2889846 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
2889649 TTATAGTATC
*
2889659 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * *
2889720 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATTATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
2889778 C
61 T
*
2889779 ATATATTATTATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
*
2889840 CTATATT
1 ATATATT
2889847 TTAATTATAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 17 0.18
61 24 0.25
62 7 0.07
63 11 0.11
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
ATATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:2889746 original size:15 final size:15
Alignment explanation
Indices: 2889711--2889762 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2889701 TTAAGAATTT
*
2889711 TATTAAATTAT-ATA
1 TATTTAATTATAATA
2889725 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
2889739 TATTTAATAATAAT-
1 TATTTAATTATAATA
2889753 TATGTTAATT
1 TAT-TTAATT
2889763 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:2890118 original size:16 final size:16
Alignment explanation
Indices: 2890097--2890164 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
2890087 GATTTGCTAT
2890097 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2890113 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
2890129 TACAACTCTAATCCAA
1 TACACCTCTAATCCAA
2890145 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2890161 TACA
1 TACA
2890165 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:2895161 original size:20 final size:20
Alignment explanation
Indices: 2895136--2895174 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2895126 AACAATAAAT
2895136 AAAATAAAT-AAAACTATACA
1 AAAATAAATGAAAA-TATACA
*
2895156 AAAATATATGAAAATATAC
1 AAAATAAATGAAAATATAC
2895175 GTATGTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAATAAATGAAAATATACA
Found at i:2895384 original size:25 final size:25
Alignment explanation
Indices: 2895356--2895406 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
2895346 ATTTTAACAT
2895356 TATA-AAGCATAAAAAAATATGTATA
1 TATATAAGCAT-AAAAAATATGTATA
** *
2895381 TATATAATTATAAAATATATGTATA
1 TATATAAGCATAAAAAATATGTATA
2895406 T
1 T
2895407 GTTATAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (25 bp):
TATATAAGCATAAAAAATATGTATA
Found at i:2896338 original size:12 final size:12
Alignment explanation
Indices: 2896321--2896353 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2896311 TGTTTGTAAG
2896321 GAAAATAAAAAT
1 GAAAATAAAAAT
2896333 GAAAATAAAAAT
1 GAAAATAAAAAT
2896345 -AAAGATAAA
1 GAAA-ATAAA
2896354 TAACGAAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 3 0.15
12 17 0.85
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (12 bp):
GAAAATAAAAAT
Found at i:2896822 original size:26 final size:25
Alignment explanation
Indices: 2896764--2896830 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
2896754 AATTGGGTCC
*
2896764 TACATATACTATGTAAAATAAAGCCA
1 TACATATA-TATATAAAATAAAGCCA
* * *
2896790 TATATATATTATATAAGATAAAGTCA
1 TACATATA-TATATAAAATAAAGCCA
*
2896816 TGCATATATATATAA
1 TACATATATATATAA
2896831 TATATGTATA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
25 7 0.21
26 27 0.79
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.34
Consensus pattern (25 bp):
TACATATATATATAAAATAAAGCCA
Found at i:2904005 original size:45 final size:45
Alignment explanation
Indices: 2903938--2904200 Score: 275
Period size: 45 Copynumber: 5.8 Consensus size: 45
2903928 TTTGACTTGA
* * *
2903938 GAAACGAGA-AAGACCATGGTTGAAAGATACCATGGCATTATATTC
1 GAAACGA-ATAAGACCATAGTTGAAAGATACTATGGCATTATATCC
* * *
2903983 GGAACGAGA-AAGACCATAGTTGAAAGATACTATGGTATTGT-TCC
1 GAAACGA-ATAAGACCATAGTTGAAAGATACTATGGCATTATATCC
* * * *
2904027 GGAGATGAATAAGACCATAGTTGAAAGATACTATGACACTATA-CC
1 -GAAACGAATAAGACCATAGTTGAAAGATACTATGGCATTATATCC
* * *
2904072 AGAAACGAATAAGACTATAGTTGAAAGATACCATGGCATTAAATCC
1 -GAAACGAATAAGACCATAGTTGAAAGATACTATGGCATTATATCC
* * *
2904118 GAAATGAATAAGACCATAGTTGAAAGATACTATAGCATTACAT-C
1 GAAACGAATAAGACCATAGTTGAAAGATACTATGGCATTATATCC
* * *
2904162 GATAACGAACAATACCATAGTGGAAAGATACTATGGCAT
1 GA-AACGAATAAGACCATAGTTGAAAGATACTATGGCAT
2904201 CACTTCGGGA
Statistics
Matches: 182, Mismatches: 31, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
44 6 0.03
45 174 0.96
46 2 0.01
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (45 bp):
GAAACGAATAAGACCATAGTTGAAAGATACTATGGCATTATATCC
Found at i:2904179 original size:135 final size:135
Alignment explanation
Indices: 2903937--2904196 Score: 321
Period size: 135 Copynumber: 1.9 Consensus size: 135
2903927 CTTTGACTTG
* * * *
2903937 AGAAACGAGAAAGACCATGGTTGAAAGATACCATGGCATTATATTCGGAACGAGAAAGACCATAG
1 AGAAACGAGAAAGACCATAGTTGAAAGATACCATGGCATTAAATCCGAAACGAGAAAGACCATAG
* * ** * * * *
2904002 TTGAAAGATACTATGGTATTGTTCCGGAGATGAATAAGACCATAGTTGAAAGATACTATGACACT
66 TTGAAAGATACTATAGCATTCATCCGGAAACGAACAAGACCATAGTGGAAAGATACTATGACACT
2904067 ATACC
131 ATACC
* *
2904072 AGAAACGA-ATAAGACTATAGTTGAAAGATACCATGGCATTAAATCCGAAATGA-ATAAGACCAT
1 AGAAACGAGA-AAGACCATAGTTGAAAGATACCATGGCATTAAATCCGAAACGAGA-AAGACCAT
*
2904135 AGTTGAAAGATACTATAGCATTACAT-C-GATAACGAACAATACCATAGTGGAAAGATACTATG
64 AGTTGAAAGATACTATAGCATT-CATCCGGA-AACGAACAAGACCATAGTGGAAAGATACTATG
2904197 GCATCACTTC
Statistics
Matches: 106, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
134 4 0.04
135 101 0.95
136 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.23
Consensus pattern (135 bp):
AGAAACGAGAAAGACCATAGTTGAAAGATACCATGGCATTAAATCCGAAACGAGAAAGACCATAG
TTGAAAGATACTATAGCATTCATCCGGAAACGAACAAGACCATAGTGGAAAGATACTATGACACT
ATACC
Found at i:2904219 original size:90 final size:86
Alignment explanation
Indices: 2903947--2904229 Score: 287
Period size: 90 Copynumber: 3.2 Consensus size: 86
2903937 AGAAACGAGA
* * *
2903947 AAGACCATGGTTGAAAGATACCATGGCATTATATTCGGAACGAGAAAGACCATAGTTGAAAGATA
1 AAGACCATAGTTGAAAGATACTAT-GCATTATA-TCGAAACGA-AAAGACCATAGTTGAAAGATA
* **
2904012 CTATGGTATTGTTCCGGAGATGAAT
63 CTATGGCATAATTCCGGA-ATGAAT
* * *
2904037 AAGACCATAGTTGAAAGATACTATGACACTATACCAGAAACGAATAAGACTATAGTTGAAAGATA
1 AAGACCATAGTTGAAAGATACTATG-CATTATATC-GAAACGAA-AAGACCATAGTTGAAAGATA
* * *
2904102 CCATGGCATTAAATCCGAAATGAAT
63 CTATGGCA-TAATTCCGGAATGAAT
* * *
2904127 AAGACCATAGTTGAAAGATACTATAGCATTACATCGATAACGAACAATACCATAGTGGAAAGATA
1 AAGACCATAGTTGAAAGATACTAT-GCATTATATCGA-AACGAA-AAGACCATAGTTGAAAGATA
* * *
2904192 CTATGGCATCACTTCGGGAATGTAT
63 CTATGGCAT-AATTCCGGAATGAAT
*
2904217 AAGACCATGGTTG
1 AAGACCATAGTTG
2904230 GAACATACCA
Statistics
Matches: 160, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
89 6 0.04
90 147 0.92
91 7 0.04
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.24
Consensus pattern (86 bp):
AAGACCATAGTTGAAAGATACTATGCATTATATCGAAACGAAAAGACCATAGTTGAAAGATACTA
TGGCATAATTCCGGAATGAAT
Found at i:2904224 original size:45 final size:45
Alignment explanation
Indices: 2903947--2904229 Score: 211
Period size: 45 Copynumber: 6.3 Consensus size: 45
2903937 AGAAACGAGA
* * * * * *
2903947 AAGACCATGGTTGAAAGATACCATGGCATTA-TATTCGGAACGAGA-
1 AAGACCATAGTTGAAAGATACTATGGCATCACT-TCCGAAATGA-AT
* ** *
2903992 AAGACCATAGTTGAAAGATACTATGGTAT-TGTTCCGGAGATGAAT
1 AAGACCATAGTTGAAAGATACTATGGCATCACTTCC-GAAATGAAT
*
2904037 AAGACCATAGTTGAAAGATACTAT-G-A-CACTATACCAGAAACGAAT
1 AAGACCATAGTTGAAAGATACTATGGCATCACT-T-CC-GAAATGAAT
* * * **
2904082 AAGACTATAGTTGAAAGATACCATGGCATTAAATCCGAAATGAAT
1 AAGACCATAGTTGAAAGATACTATGGCATCACTTCCGAAATGAAT
* * * * *
2904127 AAGACCATAGTTGAAAGATACTATAGCATTACAT-CGATAACGAAC
1 AAGACCATAGTTGAAAGATACTATGGCATCACTTCCGA-AATGAAT
* * * * *
2904172 AATACCATAGTGGAAAGATACTATGGCATCACTTCGGGAATGTAT
1 AAGACCATAGTTGAAAGATACTATGGCATCACTTCCGAAATGAAT
*
2904217 AAGACCATGGTTG
1 AAGACCATAGTTG
2904230 GAACATACCA
Statistics
Matches: 189, Mismatches: 38, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
43 2 0.01
44 8 0.04
45 172 0.91
46 4 0.02
47 2 0.01
48 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.24
Consensus pattern (45 bp):
AAGACCATAGTTGAAAGATACTATGGCATCACTTCCGAAATGAAT
Found at i:2911588 original size:21 final size:21
Alignment explanation
Indices: 2911562--2911613 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
2911552 CAACACATAA
2911562 GTGCCTGAAACAAAACATGAG
1 GTGCCTGAAACAAAACATGAG
* * *
2911583 GTGCCTGATACGACACATGAG
1 GTGCCTGAAACAAAACATGAG
2911604 GTGCCTGAAA
1 GTGCCTGAAA
2911614 TATGACACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (21 bp):
GTGCCTGAAACAAAACATGAG
Found at i:2911658 original size:23 final size:23
Alignment explanation
Indices: 2911548--2911658 Score: 106
Period size: 23 Copynumber: 5.0 Consensus size: 23
2911538 ACCTGATCCG
*
2911548 TATACAACACAT-AAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
* * * *
2911570 -A-ACAAAACATGAGGTGCCTG-
1 TATACGACACATAAAGTGCCTGA
* *
2911590 -ATACGACACATGAGGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
* *
2911612 AATATGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
2911635 TATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
2911658 T
1 T
2911659 CGGCAAAGTC
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
20 9 0.12
21 26 0.34
23 41 0.54
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (23 bp):
TATACGACACATAAAGTGCCTGA
Found at i:2914732 original size:17 final size:18
Alignment explanation
Indices: 2914699--2914738 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2914689 TTTACATTTT
2914699 ATAAAACTAAAAGAATAA
1 ATAAAACTAAAAGAATAA
2914717 ATAAAA-TAAATA-AATAA
1 ATAAAACTAAA-AGAATAA
2914734 ATAAA
1 ATAAA
2914739 CAAAACCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (18 bp):
ATAAAACTAAAAGAATAA
Found at i:2915795 original size:44 final size:43
Alignment explanation
Indices: 2915745--2916071 Score: 198
Period size: 44 Copynumber: 7.4 Consensus size: 43
2915735 CGATGTAGGA
*
2915745 AGGCAAGACATGCTATCTTCAACCTGCTCCACTACAACCGAGGG
1 AGGCAAGACTTG-TATCTTCAACCTGCTCCACTACAACCGAGGG
* * * * * * *
2915789 AGGCAAGGCTTGTATCTTCAATCTGCTTCACTGTCGA-TGCAGGA
1 AGGCAAGACTTGTATCTTCAACCTGCTCCACT-ACAACCG-AGGG
2915833 AGGCAAGA-TCTGCTATCTTCAACCTGCTCCACTACAACCGAGGG
1 AGGCAAGACT-TG-TATCTTCAACCTGCTCCACTACAACCGAGGG
* * * * * * * * *
2915877 AGGCAAGGCTTGTGTCTTCGATCTACTTCACCGT-CGA-TGCAGGA
1 AGGCAAGACTTGTATCTTCAACCTGCTCCA-C-TACAACCG-AGGG
* *
2915921 AGGCAAGATTTGTTATCTTCAACCTACTCCACTACAACCGAGGG
1 AGGCAAGACTTG-TATCTTCAACCTGCTCCACTACAACCGAGGG
* * * * * * * * * * *
2915965 AGGCAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCGA-TGCAAGA
1 AGGCAAGACTTGTATCTTCAACCTGCTCCACT-ACAACCG-AGGG
*
2916009 AGGCAAGA-TCTGCTATCTTCAACCTACTCCACTACAACCGAGGG
1 AGGCAAGACT-TG-TATCTTCAACCTGCTCCACTACAACCGAGGG
* *
2916053 AGGCAAGGCTTGTGTCTTC
1 AGGCAAGACTTGTATCTTC
2916072 GATCTACTTC
Statistics
Matches: 205, Mismatches: 60, Indels: 37
0.68 0.20 0.12
Matches are distributed among these distances:
43 57 0.28
44 96 0.47
45 52 0.25
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (43 bp):
AGGCAAGACTTGTATCTTCAACCTGCTCCACTACAACCGAGGG
Found at i:2916142 original size:88 final size:88
Alignment explanation
Indices: 2915716--2916129 Score: 677
Period size: 88 Copynumber: 4.7 Consensus size: 88
2915706 GGACCATTGG
*
2915716 CTTCGATCTGCTTCACTGTCGATGTAGGAAGGCAAGA-CATGCTATCTTCAACCTGCTCCACTAC
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATC-TGCTATCTTCAACCTGCTCCACTAC
*
2915780 AACCGAGGGAGGCAAGGCTTGTAT
65 AACCGAGGGAGGCAAGGCTTGTGT
*
2915804 CTTCAATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
2915869 ACCGAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* * * * *
2915892 CTTCGATCTACTTCACCGTCGATGCAGGAAGGCAAGATTTGTTATCTTCAACCTACTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
2915957 ACCGAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* * *
2915980 CTTCGATCTGCTTCGCTGTCGATGCAAGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
2916045 ACCGAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* * * *
2916068 CTTCGATCTACTTCGCTTTCGATGCAGGAAGGTAAGATCTGCTATCTTCAACCTGCTCCACT
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
2916130 GCTGCTCAGG
Statistics
Matches: 305, Mismatches: 20, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
88 304 1.00
89 1 0.00
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (88 bp):
CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
ACCGAGGGAGGCAAGGCTTGTGT
Found at i:2916174 original size:44 final size:44
Alignment explanation
Indices: 2916124--2916547 Score: 542
Period size: 44 Copynumber: 9.6 Consensus size: 44
2916114 TTCAACCTGC
* * * *
2916124 TCCACTGCTGCTCAGGGAGCTAGGACTTACAATCTTCTGCCCAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTATAATCTTCCGCCTAT
* * *
2916168 TCCACTGCTGTTCAGGGAGCTAGGACTTACATTCTTCCACCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTATAATCTTCCGCCTAT
* * *
2916212 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTATAATCTTCCGCCTAT
* * *
2916256 TCCACTGCTGTTCAGGGAGCTAGGAGTTATAGTCTTCCACCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTATAATCTTCCGCCTAT
* * * * *
2916300 TCCGCTGCTGGTCAGGGAGCTAGGATTTACAATCTTCTGCCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTATAATCTTCCGCCTAT
* * *
2916344 ACCACTGCTGTTCAGGGAGCTAGGACTTATAGTCTTCCACCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTATAATCTTCCGCCTAT
* * * *
2916388 TCCCCTGCTGGTCTGGGAGCTAGGATTTATAATCTTCCGCCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTATAATCTTCCGCCTAT
* * *
2916432 TCCACTGCTGTTCAGGGAGCTAGGACTTTTAGTCTTCCACCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTATAATCTTCCGCCTAT
* ** *
2916476 TCCACTACTGGCCAGGGAGCTAGGATTTATAATCTTCCGCCTAT
1 TCCACTGCTGTTCAGGGAGCTAGGACTTATAATCTTCCGCCTAT
* *
2916520 TTCACTGCTGTTCAGGGAGTTAGGACTT
1 TCCACTGCTGTTCAGGGAGCTAGGACTT
2916548 TCAGTCTTAC
Statistics
Matches: 324, Mismatches: 56, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 324 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (44 bp):
TCCACTGCTGTTCAGGGAGCTAGGACTTATAATCTTCCGCCTAT
Found at i:2916204 original size:88 final size:88
Alignment explanation
Indices: 2916124--2916555 Score: 677
Period size: 88 Copynumber: 4.9 Consensus size: 88
2916114 TTCAACCTGC
* * * *
2916124 TCCACTGCTGCTCAGGGAGCTAGGACTTACAATCTTCTGCCCATTCCACTGCTGTTCAGGGAGCT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGTTCAGGGAGCT
* *
2916189 AGGACTTACATTCTTCCACCTAT
66 AGGACTTATAGTCTTCCACCTAT
2916212 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGTTCAGGGAGCT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGTTCAGGGAGCT
*
2916277 AGGAGTTATAGTCTTCCACCTAT
66 AGGACTTATAGTCTTCCACCTAT
* * *
2916300 TCCGCTGCTGGTCAGGGAGCTAGGATTTACAATCTTCTGCCTATACCACTGCTGTTCAGGGAGCT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGTTCAGGGAGCT
2916365 AGGACTTATAGTCTTCCACCTAT
66 AGGACTTATAGTCTTCCACCTAT
* * *
2916388 TCCCCTGCTGGTCTGGGAGCTAGGATTTATAATCTTCCGCCTATTCCACTGCTGTTCAGGGAGCT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGTTCAGGGAGCT
*
2916453 AGGACTTTTAGTCTTCCACCTAT
66 AGGACTTATAGTCTTCCACCTAT
* * * * *
2916476 TCCACTACTGGCCAGGGAGCTAGGATTTATAATCTTCCGCCTATTTCACTGCTGTTCAGGGAGTT
1 TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGTTCAGGGAGCT
2916541 AGGACTT-TCAGTCTT
66 AGGACTTAT-AGTCTT
2916556 ACCGGTTTGT
Statistics
Matches: 320, Mismatches: 23, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
87 1 0.00
88 319 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (88 bp):
TCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCCGCCTATTCCACTGCTGTTCAGGGAGCT
AGGACTTATAGTCTTCCACCTAT
Found at i:2918847 original size:31 final size:31
Alignment explanation
Indices: 2918746--2918848 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 31
2918736 AACTACCTAA
* *
2918746 TTAGTCACCCAACTTTTAAGAAGCTTTTATT
1 TTAGTCACCCAACTTTTAAGACGCTTTCATT
* ** * * *
2918777 TTGGTCACCCAA-AATGAA-ATC-CTTACAAT
1 TTAGTCACCCAACTTTTAAGA-CGCTTTCATT
* *
2918806 TTCGTCACCCAACTTTTAAGGCGCTTTCATT
1 TTAGTCACCCAACTTTTAAGACGCTTTCATT
2918837 TTAGTCACCCAA
1 TTAGTCACCCAA
2918849 GCACTAAATC
Statistics
Matches: 52, Mismatches: 16, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
29 17 0.33
30 7 0.13
31 28 0.54
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (31 bp):
TTAGTCACCCAACTTTTAAGACGCTTTCATT
Found at i:2921110 original size:30 final size:30
Alignment explanation
Indices: 2921076--2921135 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
2921066 TGTTCTACCA
2921076 TCCTCAACAAGTCCGAAGATAAGCTACAAT
1 TCCTCAACAAGTCCGAAGATAAGCTACAAT
*
2921106 TCCTCAACAAGTCCGGAGATAAGCTACAAT
1 TCCTCAACAAGTCCGAAGATAAGCTACAAT
2921136 CTATGTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.20
Consensus pattern (30 bp):
TCCTCAACAAGTCCGAAGATAAGCTACAAT
Found at i:2925618 original size:257 final size:257
Alignment explanation
Indices: 2925162--2925676 Score: 1030
Period size: 257 Copynumber: 2.0 Consensus size: 257
2925152 AGCAACACAA
2925162 TACGCATAATAGCAATCGTCTCACATCATACAACATTCAAATATCAGAGGCATTATAATCAACAT
1 TACGCATAATAGCAATCGTCTCACATCATACAACATTCAAATATCAGAGGCATTATAATCAACAT
2925227 TAAAAGACATATTGAAAACAAGAGAAGAAATGATAGTCAATAAATTATAACCACTAAATTTTAAA
66 TAAAAGACATATTGAAAACAAGAGAAGAAATGATAGTCAATAAATTATAACCACTAAATTTTAAA
2925292 ATAAATATATATGAGTTCATGATAGATTCAAAATAAAGTTAATAAAATAAACACTATATAAATAA
131 ATAAATATATATGAGTTCATGATAGATTCAAAATAAAGTTAATAAAATAAACACTATATAAATAA
2925357 TAGAATTTAAATGCATTTTTTGGAAGAAAATCGAAATTCATAACATAATGTACACATATTAG
196 TAGAATTTAAATGCATTTTTTGGAAGAAAATCGAAATTCATAACATAATGTACACATATTAG
2925419 TACGCATAATAGCAATCGTCTCACATCATACAACATTCAAATATCAGAGGCATTATAATCAACAT
1 TACGCATAATAGCAATCGTCTCACATCATACAACATTCAAATATCAGAGGCATTATAATCAACAT
2925484 TAAAAGACATATTGAAAACAAGAGAAGAAATGATAGTCAATAAATTATAACCACTAAATTTTAAA
66 TAAAAGACATATTGAAAACAAGAGAAGAAATGATAGTCAATAAATTATAACCACTAAATTTTAAA
2925549 ATAAATATATATGAGTTCATGATAGATTCAAAATAAAGTTAATAAAATAAACACTATATAAATAA
131 ATAAATATATATGAGTTCATGATAGATTCAAAATAAAGTTAATAAAATAAACACTATATAAATAA
2925614 TAGAATTTAAATGCATTTTTTGGAAGAAAATCGAAATTCATAACATAATGTACACATATTAG
196 TAGAATTTAAATGCATTTTTTGGAAGAAAATCGAAATTCATAACATAATGTACACATATTAG
2925676 T
1 T
2925677 TTAAATAAGC
Statistics
Matches: 258, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
257 258 1.00
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (257 bp):
TACGCATAATAGCAATCGTCTCACATCATACAACATTCAAATATCAGAGGCATTATAATCAACAT
TAAAAGACATATTGAAAACAAGAGAAGAAATGATAGTCAATAAATTATAACCACTAAATTTTAAA
ATAAATATATATGAGTTCATGATAGATTCAAAATAAAGTTAATAAAATAAACACTATATAAATAA
TAGAATTTAAATGCATTTTTTGGAAGAAAATCGAAATTCATAACATAATGTACACATATTAG
Found at i:2928755 original size:9 final size:9
Alignment explanation
Indices: 2928741--2928771 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2928731 GTTAAATGAA
2928741 TCGAGTTAT
1 TCGAGTTAT
*
2928750 TCGAGTTAA
1 TCGAGTTAT
2928759 TCGAGTTAT
1 TCGAGTTAT
2928768 TCGA
1 TCGA
2928772 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:2928852 original size:9 final size:9
Alignment explanation
Indices: 2928823--2928859 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
2928813 TGAGTTTTCG
2928823 AATTCGAAT
1 AATTCGAAT
*
2928832 AACTCGAAT
1 AATTCGAAT
2928841 AATTCGAAT
1 AATTCGAAT
*
2928850 AATTCCAAT
1 AATTCGAAT
2928859 A
1 A
2928860 TTAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2929107 original size:30 final size:31
Alignment explanation
Indices: 2929073--2929132 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
2929063 AAACCTTTTA
*
2929073 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
2929103 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
2929133 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:2930795 original size:26 final size:26
Alignment explanation
Indices: 2930742--2930821 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 26
2930732 TGGAGGAAGT
* *
2930742 ATACTGTTACT-GCAGCTTTACTGTG
1 ATACTGTTACTGGCAGCTTTGCTGCG
* *
2930767 ATACTGTTATTGGCAGCTTCGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
* *
2930793 ATACTATTACTGGTAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
2930819 ATA
1 ATA
2930822 TTGGTGTGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
25 10 0.22
26 36 0.78
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTGCG
Found at i:2938288 original size:26 final size:26
Alignment explanation
Indices: 2938252--2938301 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
2938242 TGGAGGAAGT
2938252 ATACTGTTACAGGCAGCTTTGCTGAG
1 ATACTGTTACAGGCAGCTTTGCTGAG
2938278 ATACTGTTACAGGCAGCTTTGCTG
1 ATACTGTTACAGGCAGCTTTGCTG
2938302 CAATATTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (26 bp):
ATACTGTTACAGGCAGCTTTGCTGAG
Found at i:2943327 original size:23 final size:23
Alignment explanation
Indices: 2943301--2943346 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2943291 GGTGCCTAAA
*
2943301 ATACGACACATAAAGTGTCTGAT
1 ATACGACACATAAAGTGGCTGAT
2943324 ATACGACACATAAAGTGGCTGAT
1 ATACGACACATAAAGTGGCTGAT
2943347 TGGCAAAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (23 bp):
ATACGACACATAAAGTGGCTGAT
Found at i:2944395 original size:2 final size:2
Alignment explanation
Indices: 2944390--2944452 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
2944380 ATAGAGGGAC
** *
2944390 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA CT CA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2944432 GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA G
2944453 GGAAAGTCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.02
Consensus pattern (2 bp):
GA
Found at i:2944557 original size:84 final size:82
Alignment explanation
Indices: 2944459--2944676 Score: 292
Period size: 84 Copynumber: 2.6 Consensus size: 82
2944449 AGAGGGAAAG
* * * *
2944459 TCAAATATGGGAAATAAAAGAAAATAACAACTATGTAAAATAGAGATATGAAAGGGAATTGAATA
1 TCAAATATGGGAAATGAAAGAGAATAACAA-TATG-AAAATAGAGATATAAAAGAGAATTGAATA
*
2944524 TTTTATGAAAAATAGATAA
64 TTTTATGAAAAATAGAGAA
* *
2944543 TCAAATATGAGAAATGAAAGAGAATAACAAATATAGAAAATAGAGATATAAAAGAGAATTTAATA
1 TCAAATATGGGAAATGAAAGAGAATAAC-AATAT-GAAAATAGAGATATAAAAGAGAATTGAATA
*
2944608 TTTTATGGAAAATAGAGAA
64 TTTTATGAAAAATAGAGAA
* *
2944627 TCAAATATGGGAAAGGAAAGAGAATCACATATATGGAAAATAGAGATATA
1 TCAAATATGGGAAATGAAAGAGAATAACA-ATAT-GAAAATAGAGATATA
2944677 TTTTTCACAA
Statistics
Matches: 119, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
83 1 0.01
84 115 0.97
85 3 0.03
ACGTcount: A:0.55, C:0.04, G:0.18, T:0.23
Consensus pattern (82 bp):
TCAAATATGGGAAATGAAAGAGAATAACAATATGAAAATAGAGATATAAAAGAGAATTGAATATT
TTATGAAAAATAGAGAA
Found at i:2944816 original size:84 final size:84
Alignment explanation
Indices: 2944675--2944853 Score: 252
Period size: 84 Copynumber: 2.1 Consensus size: 84
2944665 AATAGAGATA
* * * *
2944675 TATTTTTCACAAAATATTAAATACCCTTTCATATCTCTATTTTTCAATTTTATTATTCTCTTTCT
1 TATTTTCCACAAAATATTAAATACCCTTTCATATCTCTATTTTCCAATTATATTATTCTCTTTCC
* *
2944740 TTTTTCATATTTGATTCTC
66 TTTCTCATATTTGATTATC
* ** *
2944759 TATTTTCCATAAAATATTAAATTTCTTTTCATATCTCTATTTTCC-ATATATATTATTCTCTTTC
1 TATTTTCCACAAAATATTAAATACCCTTTCATATCTCTATTTTCCAAT-TATATTATTCTCTTTC
2944823 CTTTCTCATATTTGATTATC
65 CTTTCTCATATTTGATTATC
2944843 TATTTTCCACA
1 TATTTTCCACA
2944854 TATTCTTTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
83 2 0.02
84 81 0.98
ACGTcount: A:0.26, C:0.18, G:0.01, T:0.55
Consensus pattern (84 bp):
TATTTTCCACAAAATATTAAATACCCTTTCATATCTCTATTTTCCAATTATATTATTCTCTTTCC
TTTCTCATATTTGATTATC
Found at i:2946184 original size:13 final size:13
Alignment explanation
Indices: 2946166--2946191 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2946156 TTTATAACTA
2946166 TCTCTGTTGATTT
1 TCTCTGTTGATTT
2946179 TCTCTGTTGATTT
1 TCTCTGTTGATTT
2946192 CCTTGAACTC
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:0.08, C:0.15, G:0.15, T:0.62
Consensus pattern (13 bp):
TCTCTGTTGATTT
Found at i:2949636 original size:9 final size:9
Alignment explanation
Indices: 2949622--2949676 Score: 83
Period size: 9 Copynumber: 6.1 Consensus size: 9
2949612 GTAGTGATTC
*
2949622 AATTCGATT
1 AATTCGGTT
2949631 AATTCGGTT
1 AATTCGGTT
2949640 AATTCGGTT
1 AATTCGGTT
*
2949649 AATTTGGTT
1 AATTCGGTT
*
2949658 AATTCGGCT
1 AATTCGGTT
2949667 AATTCGGTT
1 AATTCGGTT
2949676 A
1 A
2949677 TTTTTTAACC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (9 bp):
AATTCGGTT
Found at i:2950593 original size:86 final size:87
Alignment explanation
Indices: 2950426--2950597 Score: 220
Period size: 88 Copynumber: 2.0 Consensus size: 87
2950416 CCTGCTTTTT
* * ** *
2950426 TTTTTTTGCACTCAATTGTATATTTGAACTTTCAACATGCATAAAAAAAATGCCCTCAAACTTTT
1 TTTTTTTGCACTCAATTGGATACTTGAACTACCAAAATGCATAAAAAAAA-GCCCTCAAACTTTT
*
2950491 TCAAAAAAAAGTAATTAAGCCCC
65 TCAAAAAAAAGCAATTAAGCCCC
* * *
2950514 TTTTTTTGCACTCAATTGGGTACTTGAACTACCAAAATGCATTAAAAAGA-CCCTCAAACTTTTT
1 TTTTTTTGCACTCAATTGGATACTTGAACTACCAAAATGCATAAAAAAAAGCCCTCAAACTTTTT
***
2950578 TTCAAAAAAGCAATTAAGCC
66 CAAAAAAAAGCAATTAAGCC
2950598 ATTGCTTTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
86 30 0.42
88 42 0.58
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (87 bp):
TTTTTTTGCACTCAATTGGATACTTGAACTACCAAAATGCATAAAAAAAAGCCCTCAAACTTTTT
CAAAAAAAAGCAATTAAGCCCC
Found at i:2950781 original size:19 final size:19
Alignment explanation
Indices: 2950759--2950802 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2950749 ATAAAATAAA
*
2950759 ATAAAATTAG-AAAAAGATT
1 ATAAAAGTAGTAAAAA-ATT
*
2950778 ATAAAAGTCGTAAAAAATT
1 ATAAAAGTAGTAAAAAATT
2950797 ATAAAA
1 ATAAAA
2950803 AAATTGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (19 bp):
ATAAAAGTAGTAAAAAATT
Found at i:2950914 original size:19 final size:21
Alignment explanation
Indices: 2950892--2950937 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2950882 TAAGAAAATG
2950892 ATAAAAAAT-GT-AAAGAATT
1 ATAAAAAATCGTGAAAGAATT
*
2950911 AT-AAAATTCGTGAAAGAATT
1 ATAAAAAATCGTGAAAGAATT
2950931 ATAAAAA
1 ATAAAAA
2950938 TTATCATACT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 5 0.22
19 4 0.17
20 10 0.43
21 4 0.17
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.26
Consensus pattern (21 bp):
ATAAAAAATCGTGAAAGAATT
Found at i:2951151 original size:29 final size:28
Alignment explanation
Indices: 2951119--2951228 Score: 105
Period size: 28 Copynumber: 3.8 Consensus size: 28
2951109 TTTTTATGCA
* *
2951119 TTTTATAAAAGTTTTTTATTTTTTTTATT
1 TTTTATTAAA-TTTTATATTTTTTTTATT
** * *
2951148 TTTT-TTACGTTTTATATATATTTTTAAT
1 TTTTATTAAATTTTATAT-TTTTTTTATT
*
2951176 TTTTATTAAATTTTAAATATTTTTTATATT
1 TTTTATTAAATTTT--ATATTTTTTTTATT
*
2951206 TTTTATTAAATTTTAAATTTTTT
1 TTTTATTAAATTTTATATTTTTT
2951229 ATAACTTTTA
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
27 7 0.11
28 22 0.34
29 11 0.17
30 21 0.32
31 4 0.06
ACGTcount: A:0.28, C:0.01, G:0.02, T:0.69
Consensus pattern (28 bp):
TTTTATTAAATTTTATATTTTTTTTATT
Found at i:2951204 original size:9 final size:9
Alignment explanation
Indices: 2951130--2951260 Score: 66
Period size: 9 Copynumber: 13.7 Consensus size: 9
2951120 TTTATAAAAG
*
2951130 TTTTTTATT
1 TTTTTTATA
*
2951139 TTTTTTATT
1 TTTTTTATA
**
2951148 TTTTTTACG
1 TTTTTTATA
*
2951157 TTTTATATA
1 TTTTTTATA
2951166 TATTTTTA-A
1 T-TTTTTATA
*
2951175 TTTTTATTAAA
1 -TTTT-TTATA
**
2951186 TTTTAAATA
1 TTTTTTATA
2951195 TTTTTTATA
1 TTTTTTATA
2951204 TTTTTTATTA
1 TTTTTTA-TA
** *
2951214 AATTTTAAA
1 TTTTTTATA
2951223 TTTTTTATAA
1 TTTTTTAT-A
*
2951233 CTTTTATTGATT
1 -TTTT-TT-ATA
2951245 TTTTTTATAA
1 TTTTTTAT-A
2951255 TTTTTT
1 TTTTTT
2951261 TTGTCATATG
Statistics
Matches: 93, Mismatches: 19, Indels: 19
0.71 0.15 0.15
Matches are distributed among these distances:
9 51 0.55
10 29 0.31
11 9 0.10
12 2 0.02
13 2 0.02
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTTTATA
Found at i:2951211 original size:30 final size:30
Alignment explanation
Indices: 2951135--2951228 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
2951125 AAAAGTTTTT
* ** *
2951135 TATTTTTTTTATTTTTT-TTACGTTTTATA
1 TATTTTTTATATTTTTTATTAAATTTTAAA
2951164 TATATTTTTA-A-TTTTTATTAAATTTTAAA
1 TAT-TTTTTATATTTTTTATTAAATTTTAAA
2951193 TATTTTTTATATTTTTTATTAAATTTTAAA
1 TATTTTTTATATTTTTTATTAAATTTTAAA
2951223 T-TTTTT
1 TATTTTT
2951229 ATAACTTTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
28 11 0.19
29 22 0.39
30 24 0.42
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (30 bp):
TATTTTTTATATTTTTTATTAAATTTTAAA
Found at i:2951219 original size:19 final size:19
Alignment explanation
Indices: 2951197--2951258 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
2951187 TTTAAATATT
2951197 TTTTATATTTTTTATTAAA
1 TTTTATATTTTTTATTAAA
* *
2951216 TTTTAAATTTTTTA-TAAC
1 TTTTATATTTTTTATTAAA
2951234 TTTTATTGATTTTTT-TTATAA
1 TTTTA-T-ATTTTTTATTA-AA
2951255 TTTT
1 TTTT
2951259 TTTTGTCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 8 0.23
19 13 0.37
20 9 0.26
21 5 0.14
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTTATATTTTTTATTAAA
Found at i:2951258 original size:10 final size:10
Alignment explanation
Indices: 2951194--2951260 Score: 52
Period size: 10 Copynumber: 6.7 Consensus size: 10
2951184 AATTTTAAAT
2951194 ATTTTTTAT-
1 ATTTTTTATA
2951203 ATTTTTTATTA
1 ATTTTTTA-TA
*
2951214 A-ATTTTA-A
1 ATTTTTTATA
2951222 ATTTTTTATA
1 ATTTTTTATA
2951232 ACTTTTATTGAT-
1 A-TTTT-TT-ATA
*
2951244 TTTTTTTATA
1 ATTTTTTATA
2951254 ATTTTTT
1 ATTTTTT
2951261 TTGTCATATG
Statistics
Matches: 46, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
8 2 0.04
9 15 0.33
10 16 0.35
11 9 0.20
12 2 0.04
13 2 0.04
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.70
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:2953977 original size:33 final size:33
Alignment explanation
Indices: 2953940--2954058 Score: 152
Period size: 33 Copynumber: 3.6 Consensus size: 33
2953930 AAACGCGCGG
*
2953940 TTTTGTGAAATGATAACAAATATCAGCTTTTCA
1 TTTTGTAAAATGATAACAAATATCAGCTTTTCA
* * *
2953973 TTTTGTAAAATTATAACAAAT-TACAAC-TTTAA
1 TTTTGTAAAATGATAACAAATAT-CAGCTTTTCA
*
2954005 TTTTGTAAAATGATAACAAATATCAGATTTTCA
1 TTTTGTAAAATGATAACAAATATCAGCTTTTCA
* *
2954038 TTTTGTGAAATTATAACAAAT
1 TTTTGTAAAATGATAACAAAT
2954059 TACAACTGTC
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
32 27 0.37
33 46 0.63
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.40
Consensus pattern (33 bp):
TTTTGTAAAATGATAACAAATATCAGCTTTTCA
Found at i:2954021 original size:65 final size:65
Alignment explanation
Indices: 2953940--2954065 Score: 225
Period size: 65 Copynumber: 1.9 Consensus size: 65
2953930 AAACGCGCGG
* *
2953940 TTTTGTGAAATGATAACAAATATCAGCTTTTCATTTTGTAAAATTATAACAAATTACAACTTTAA
1 TTTTGTAAAATGATAACAAATATCAGATTTTCATTTTGTAAAATTATAACAAATTACAACTTTAA
*
2954005 TTTTGTAAAATGATAACAAATATCAGATTTTCATTTTGTGAAATTATAACAAATTACAACT
1 TTTTGTAAAATGATAACAAATATCAGATTTTCATTTTGTAAAATTATAACAAATTACAACT
2954066 GTCAAAACCA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (65 bp):
TTTTGTAAAATGATAACAAATATCAGATTTTCATTTTGTAAAATTATAACAAATTACAACTTTAA
Found at i:2954817 original size:12 final size:12
Alignment explanation
Indices: 2954800--2954824 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2954790 AAAATAAAAT
2954800 AAATAAATAATA
1 AAATAAATAATA
2954812 AAATAAATAATA
1 AAATAAATAATA
2954824 A
1 A
2954825 CGATGATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAAATAATA
Found at i:2956488 original size:14 final size:14
Alignment explanation
Indices: 2956469--2956498 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2956459 TAAAAGGGCT
2956469 GATTCTACCCGGCC
1 GATTCTACCCGGCC
2956483 GATTCTACCCGGCC
1 GATTCTACCCGGCC
2956497 GA
1 GA
2956499 GCCGAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.17, C:0.40, G:0.23, T:0.20
Consensus pattern (14 bp):
GATTCTACCCGGCC
Done.