Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 141 of 207
Found at i:43206673 original size:40 final size:40
Alignment explanation
Indices: 43206602--43206725 Score: 124
Period size: 40 Copynumber: 3.1 Consensus size: 40
43206592 TAATTATTGA
* * * *
43206602 TGAAAGCACATACATGCCCCTA-TTTGCACTTCGCTACCCC
1 TGAAAGCACACACGTGCCCC-AGTTTGTACTTCGATACCCC
* * * ** *
43206642 TGAAAGCAGATACGTTCCCTTGTTTGTACTTCAATACCCC
1 TGAAAGCACACACGTGCCCCAGTTTGTACTTCGATACCCC
* *
43206682 TGAATGCACACACGTGCCCCAGTTTATACTTCGATACCCC
1 TGAAAGCACACACGTGCCCCAGTTTGTACTTCGATACCCC
43206722 TGAA
1 TGAA
43206726 CGTACATACG
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (40 bp):
TGAAAGCACACACGTGCCCCAGTTTGTACTTCGATACCCC
Found at i:43208372 original size:35 final size:35
Alignment explanation
Indices: 43208319--43208435 Score: 135
Period size: 35 Copynumber: 3.3 Consensus size: 35
43208309 AATCCAACCA
* **
43208319 AAACATACCAAATGCTCATAAGAGCTACTCCATCCG
1 AAACAAACC-AATGCTCATAAGAGCTAAACCATCCG
* * *
43208355 AAATAAACCAATGCTCATATGAGCTAAACCATCTG
1 AAACAAACCAATGCTCATAAGAGCTAAACCATCCG
* * *
43208390 AAACATACCCATGCTCATACGAGCTAAACCATCCG
1 AAACAAACCAATGCTCATAAGAGCTAAACCATCCG
*
43208425 AAACACACCAA
1 AAACAAACCAA
43208436 AACAGAGAGT
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
35 61 0.90
36 7 0.10
ACGTcount: A:0.42, C:0.30, G:0.10, T:0.18
Consensus pattern (35 bp):
AAACAAACCAATGCTCATAAGAGCTAAACCATCCG
Found at i:43215832 original size:35 final size:35
Alignment explanation
Indices: 43215749--43215910 Score: 184
Period size: 35 Copynumber: 4.6 Consensus size: 35
43215739 GTACATCAAG
* *
43215749 AATCCAACCAAAACACACCAGATGCTCATAAGAGCT
1 AATCCATCCAAAACACACCA-ATGCTCATATGAGCT
* *
43215785 AATCCATTCAAAACACACCAATGCCCATATGAGCT
1 AATCCATCCAAAACACACCAATGCTCATATGAGCT
* *
43215820 AGA-CCATCCAAAACACACTAATGCTTATATGAGCT
1 A-ATCCATCCAAAACACACCAATGCTCATATGAGCT
* ** *
43215855 AAACCATCTGAAACACACCAATGCTCATCA-GATCT
1 AATCCATCCAAAACACACCAATGCTCAT-ATGAGCT
*
43215890 AATCCATCCGAAACACACCAA
1 AATCCATCCAAAACACACCAA
43215911 AACATAGAGT
Statistics
Matches: 108, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
34 1 0.01
35 87 0.81
36 20 0.19
ACGTcount: A:0.42, C:0.31, G:0.09, T:0.18
Consensus pattern (35 bp):
AATCCATCCAAAACACACCAATGCTCATATGAGCT
Found at i:43235938 original size:44 final size:44
Alignment explanation
Indices: 43235888--43236164 Score: 191
Period size: 44 Copynumber: 6.1 Consensus size: 44
43235878 AGTGTAAGGA
* * *
43235888 AGCAGATTTAAGCCACAAATCTTATCTCCCTGAGATTACAGCGG
1 AGCAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGG
* * * *
43235932 AGCAGATAGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGG
1 AGCAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGG
* *** * * *
43235976 AGCGGATT-AAAATA-AAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAG
1 AGCAGATTGAAGCCAGAA--ATCCTATCTCCCTGAGA-TTAC---AGCG--G
* * *
43236025 ATCGCATCAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTACAGCAG
1 A--G---CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGG
* * *
43236074 AGCAAATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGCGA
1 AGCAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGG
** * * *
43236118 AGCAGATAAAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGG
1 AGCAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGG
43236162 AGC
1 AGC
43236165 GAATTAAAAT
Statistics
Matches: 183, Mismatches: 34, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
42 1 0.01
43 5 0.03
44 137 0.75
47 4 0.02
49 4 0.02
51 3 0.02
54 23 0.13
55 4 0.02
56 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (44 bp):
AGCAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGG
Found at i:43236157 original size:142 final size:142
Alignment explanation
Indices: 43235890--43236159 Score: 373
Period size: 142 Copynumber: 1.9 Consensus size: 142
43235880 TGTAAGGAAG
* * * * *
43235890 CAGATTTAAGCCACAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATAGAAGCTAGTAATCCT
1 CAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTACAGCAGAGCAAATAGAAGCCAGTAATCCT
* * * * * * *
43235955 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGCGAAGCAGATTAAAAGAAAGAATCCTATCTCCCTGAAGTTACAGTAG
43236020 AGTAGATCGCAT
131 AGTAGATCGCAT
*
43236032 CAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTACAGCAGAGCAAATTGAAGCCAGTAATCCT
1 CAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTACAGCAGAGCAAATAGAAGCCAGTAATCCT
**
43236097 ATCTCCCTGAGATTACAGCGAAGCAGA-TAAAAGCTAGTAATCCTATCTCCCTG-AGATTACAGT
66 ATCTCCCTGAGATTACAGCGAAGCAGATTAAAAGAAAG-AATCCTATCTCCCTGAAG-TTACAGT
43236160 GGAGCGAATT
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
141 9 0.08
142 102 0.92
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (142 bp):
CAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTACAGCAGAGCAAATAGAAGCCAGTAATCCT
ATCTCCCTGAGATTACAGCGAAGCAGATTAAAAGAAAGAATCCTATCTCCCTGAAGTTACAGTAG
AGTAGATCGCAT
Found at i:43237942 original size:17 final size:15
Alignment explanation
Indices: 43237902--43237943 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
43237892 TTCCAAATTC
*
43237902 TTTTTAAATAAATCA
1 TTTTTTAATAAATCA
43237917 TTTTTTAATAAATCA
1 TTTTTTAATAAATCA
43237932 TTATTTTTAATA
1 -T-TTTTTAATA
43237944 TCTTTTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.58
16 1 0.04
17 9 0.38
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTTTAATAAATCA
Found at i:43239301 original size:13 final size:14
Alignment explanation
Indices: 43239283--43239312 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43239273 GCAAAATTGT
43239283 AATTT-AGTAATTA
1 AATTTAAGTAATTA
43239296 AATTTAAGTAATTA
1 AATTTAAGTAATTA
43239310 AAT
1 AAT
43239313 AGTTAGATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
AATTTAAGTAATTA
Found at i:43240929 original size:40 final size:40
Alignment explanation
Indices: 43240831--43241209 Score: 484
Period size: 40 Copynumber: 9.6 Consensus size: 40
43240821 TCCTCGTTCA
* * * * *
43240831 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
43240870 AATGCCTTCGGGACATAACCCGGATTTAACAACTCACACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
43240910 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
43240950 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
43240990 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
43241030 ACTGCCTTCGGGACTTAACCCGAATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
43241070 AATGCCTTCGGGACTTAACCCGGATTT-ATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
43241109 AATGCCTTC-GGA-TTAACCCGGA-TTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
43241146 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
43241186 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
43241210 CAGCATTCAA
Statistics
Matches: 305, Mismatches: 28, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
36 2 0.01
37 30 0.10
38 3 0.01
39 65 0.21
40 197 0.65
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:43248934 original size:40 final size:40
Alignment explanation
Indices: 43248886--43249186 Score: 302
Period size: 40 Copynumber: 7.6 Consensus size: 40
43248876 TCCTCGTTCA
* * *
43248886 AATGCCTTCGGGACATAGCCCGGTTTTAGTACAAT-GCCAC-
1 AATGCCTTCGGGACTTAACCCGGATTTA-TACAATCG-CACG
*
43248926 AATGCCTTCGGGACATAACCCGGATTTA-AC--TCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTATACAATCGCACG
*
43248963 AATGCCTTCGGGACTTAACCCGGATTTAATA-ACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTT-ATACAATCGCACG
*
43249003 AATGCCTTCGGGACTTAACCCGGATTTAATA-ACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTT-ATACAATCGCACG
43249043 AATGCCTTCGGGACTTAACCCGGATTTA-ACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTATACAA-TCGCACG
*
43249083 AATGCCTTCGGGACTTAACCCGGATTTAGTATC--TCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTA-TA-CAATCGCACG
* * * * * *
43249123 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTATACA-ATCGCACG
* *
43249163 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
43249187 CAGCATTCAA
Statistics
Matches: 232, Mismatches: 13, Indels: 32
0.84 0.05 0.12
Matches are distributed among these distances:
36 4 0.02
37 27 0.12
38 5 0.02
39 7 0.03
40 179 0.77
41 8 0.03
42 1 0.00
43 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTATACAATCGCACG
Found at i:43249062 original size:80 final size:78
Alignment explanation
Indices: 43248886--43249186 Score: 349
Period size: 80 Copynumber: 3.8 Consensus size: 78
43248876 TCCTCGTTCA
* * * * * *
43248886 AATGCCTTCGGGACATAGCCCGGTTTTAGTACAAT-GCCACAATGCCTTCGGGACATAACCCGGA
1 AATGCCTTCGGGACTTAACCCGGATTTAATA-ACTCG-CACAATGCCTTCGGGACTTAACCCGGA
43248950 -TT-TAACTCGCACG
64 TTTATAACTCGCACG
43248963 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC-AATGCCTTCGGGACTTAACCCGGAT
43249028 TTAATAACTCGCACG
65 TT-ATAACTCGCACG
*
43249043 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC-AATGCCTTCGGGACTTAACCCGGAT
* *
43249108 TTAGTATCTCGCACA
65 TTA-TAACTCGCACG
* * * * * * * *
43249123 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACAATGCCTTCGGGACTTAACCCGGA
43249187 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
76 5 0.03
77 51 0.26
78 2 0.01
79 4 0.02
80 131 0.66
81 5 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (78 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCGGATT
TATAACTCGCACG
Found at i:43249130 original size:120 final size:117
Alignment explanation
Indices: 43248923--43249186 Score: 361
Period size: 120 Copynumber: 2.2 Consensus size: 117
43248913 AGTACAATGC
*
43248923 CACAATGCCTTCGGGACATAACCCGGATTTAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 CACAATGCCTTCGGGACTTAACCCGGATTTAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
* * * *
43248988 TTAATAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCG
66 TTAATAACTCGCACAAAGGCCTTC-GGATCTTAACCCGGATATAATAACTTAG
43249039 CACGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCC
1 CAC-AATGCCTTCGGGACTTAACCCGGATTT---AACTCGCACGAATGCCTTCGGGACTTAACCC
* * * * *
43249104 GGATTTAGTATCTCGCACAAAGGCCTTCGGATCTTAATCCGGATATATTCACTTAG
62 GGATTTAATAACTCGCACAAAGGCCTTCGGATCTTAACCCGGATATAATAACTTAG
* *
43249160 CACAAAGCCTTCGGGACTTAGCCCGGA
1 CACAATGCCTTCGGGACTTAACCCGGA
43249187 CAGCATTCAA
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
116 3 0.02
117 26 0.20
119 3 0.02
120 93 0.72
121 5 0.04
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (117 bp):
CACAATGCCTTCGGGACTTAACCCGGATTTAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
TTAATAACTCGCACAAAGGCCTTCGGATCTTAACCCGGATATAATAACTTAG
Found at i:43251439 original size:40 final size:40
Alignment explanation
Indices: 43251395--43251570 Score: 210
Period size: 40 Copynumber: 4.4 Consensus size: 40
43251385 ATTATTTATG
* ** * *
43251395 AATGCACATACATGCCTTTATTTGTAGTTCGGTACCCCTA
1 AATGCACATACGTGCCCCTATTTGTACTTCGATACCCCTA
*
43251435 AATGCACATACGTGCCCCTGTTTGTACTTCGATACCCCTA
1 AATGCACATACGTGCCCCTATTTGTACTTCGATACCCCTA
*
43251475 AATGCACATACGTGCCCCTATTTGTACTTCGATACCCCTG
1 AATGCACATACGTGCCCCTATTTGTACTTCGATACCCCTA
* * * * * **
43251515 AATGCACAAATGTGCCCCTGTTTGTACTTGGGTACCCCCG
1 AATGCACATACGTGCCCCTATTTGTACTTCGATACCCCTA
*
43251555 AACGCACATAC-TGCCC
1 AATGCACATACGTGCCC
43251571 TGTTTATACT
Statistics
Matches: 119, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 5 0.04
40 114 0.96
ACGTcount: A:0.23, C:0.31, G:0.16, T:0.29
Consensus pattern (40 bp):
AATGCACATACGTGCCCCTATTTGTACTTCGATACCCCTA
Found at i:43251472 original size:20 final size:20
Alignment explanation
Indices: 43251449--43251513 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
43251439 CACATACGTG
*
43251449 CCCCTGTTTGTACTTCGATA
1 CCCCTATTTGTACTTCGATA
** * * *
43251469 CCCCTAAATGCACATACG-TG
1 CCCCTATTTGTAC-TTCGATA
43251489 CCCCTATTTGTACTTCGATA
1 CCCCTATTTGTACTTCGATA
43251509 CCCCT
1 CCCCT
43251514 GAATGCACAA
Statistics
Matches: 32, Mismatches: 11, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.32
Consensus pattern (20 bp):
CCCCTATTTGTACTTCGATA
Found at i:43253319 original size:12 final size:12
Alignment explanation
Indices: 43253302--43253326 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43253292 TCTCCATTTC
43253302 TTTTCTTCTTCT
1 TTTTCTTCTTCT
43253314 TTTTCTTCTTCT
1 TTTTCTTCTTCT
43253326 T
1 T
43253327 CTTCCAACAA
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTCTTCT
Found at i:43253386 original size:20 final size:20
Alignment explanation
Indices: 43253358--43253398 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
43253348 AAATTGGGTT
*
43253358 TCCACCGTGGCTAGTTAACG
1 TCCAACGTGGCTAGTTAACG
*
43253378 TCCAACGTGGGTAGTTAACG
1 TCCAACGTGGCTAGTTAACG
43253398 T
1 T
43253399 GCCACATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (20 bp):
TCCAACGTGGCTAGTTAACG
Found at i:43254711 original size:4 final size:4
Alignment explanation
Indices: 43254702--43254736 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
43254692 AAGTACGTAT
*
43254702 AATA AATA AATA AATA AATA AATA AA-A TATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA
43254737 GTAAATCTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 2 0.07
4 26 0.93
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:43256788 original size:94 final size:94
Alignment explanation
Indices: 43256625--43256814 Score: 335
Period size: 94 Copynumber: 2.0 Consensus size: 94
43256615 AAATTGCCAA
* * *
43256625 GTAATAGTGCTGTAACGTGTAGTTTATGTCTTTATGACATGTTTAATTTATGCATGAATACATAG
1 GTAATAGTGCAGTAACGTGTAGTGTATGTCTTTATGACATGTTTAATTTATGCATGAATACATAA
*
43256690 TCCTGTGAAATAGAATTCTGGTTAAACAG
66 TCCTGTGAAATAGAAATCTGGTTAAACAG
*
43256719 GTAATAGTGCAGTAACTTGTAGTGTATGTCTTTATGACATGTTTAATTTATGCATGAATACATAA
1 GTAATAGTGCAGTAACGTGTAGTGTATGTCTTTATGACATGTTTAATTTATGCATGAATACATAA
43256784 TCCTGTGAAATAGAAATCTGGTTAAACAG
66 TCCTGTGAAATAGAAATCTGGTTAAACAG
43256813 GT
1 GT
43256815 TTAAGAATGA
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 91 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (94 bp):
GTAATAGTGCAGTAACGTGTAGTGTATGTCTTTATGACATGTTTAATTTATGCATGAATACATAA
TCCTGTGAAATAGAAATCTGGTTAAACAG
Found at i:43258940 original size:129 final size:126
Alignment explanation
Indices: 43258693--43258952 Score: 321
Period size: 129 Copynumber: 2.0 Consensus size: 126
43258683 CAGACGGGGT
* * *
43258693 TGGTGACGAAAATGATTCTGAAGTGAATAGAGAATCCTTGGGTGTATCTGCTGCACTTAGTCCCT
1 TGGTGACGAAAATGATTCTGAAGTGAACAGAGAATCCTTGGGTGTATCTGCAGCACTTAGGCCCT
* * *
43258758 CAGAAAGGCTTCACTTGGGAGCAAGCGATATTCGCAGTCACACAGCACATGGCAGTTTGAG
66 CAGAAAGGCTTCACTTGGGAGCAAGCGACATGCGCAGTAACACAGCACATGGCAGTTTGAG
* * *
43258819 TGGTGATGAAAATGATTCTGAAGTTAACAGAGAATCCTTGGGCTTGT-T-TGCAGCTCTTAATGG
1 TGGTGACGAAAATGATTCTGAAGTGAACAGAGAATCCTTGGG--TGTATCTGCAGCACTT-A-GG
* * *
43258882 CCTCTCCGAAAGGCTTCA-TTGGGGAGCAGGCGGCATGCGCAGTAACACAAG-ACATGGCAGTTT
62 CC-CTCAGAAAGGCTTCACTT-GGGAGCAAGCGACATGCGCAGTAACAC-AGCACATGGCAGTTT
43258945 GAG
124 GAG
43258948 TGGTG
1 TGGTG
43258953 GAAATGGAAA
Statistics
Matches: 115, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
126 47 0.41
127 2 0.02
128 8 0.07
129 56 0.49
130 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.26
Consensus pattern (126 bp):
TGGTGACGAAAATGATTCTGAAGTGAACAGAGAATCCTTGGGTGTATCTGCAGCACTTAGGCCCT
CAGAAAGGCTTCACTTGGGAGCAAGCGACATGCGCAGTAACACAGCACATGGCAGTTTGAG
Found at i:43261081 original size:20 final size:20
Alignment explanation
Indices: 43261052--43261121 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
43261042 TTTGATTCGG
43261052 AAAA-AAATTTTAATGTTCA
1 AAAATAAATTTTAATGTTCA
43261071 AAAATAAATTTCTAGAAT-TTC-
1 AAAATAAATTT-T--AATGTTCA
** **
43261092 TTAATTTATTTTAATGTTCA
1 AAAATAAATTTTAATGTTCA
43261112 AAAATAAATT
1 AAAATAAATT
43261122 AATTTAATTA
Statistics
Matches: 37, Mismatches: 8, Indels: 11
0.66 0.14 0.20
Matches are distributed among these distances:
18 3 0.08
19 7 0.19
20 13 0.35
21 8 0.22
22 3 0.08
23 3 0.08
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (20 bp):
AAAATAAATTTTAATGTTCA
Found at i:43264647 original size:43 final size:43
Alignment explanation
Indices: 43264583--43264680 Score: 160
Period size: 43 Copynumber: 2.3 Consensus size: 43
43264573 TTATGTGGAA
* * *
43264583 AAACGCCACTATAGAATATGACCTTTAGCGGCGTTTTCCCCAC
1 AAACGCCACTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
*
43264626 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
1 AAACGCCACTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
43264669 AAACGCCACTAA
1 AAACGCCACTAA
43264681 CTTTAGCAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (43 bp):
AAACGCCACTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
Found at i:43270544 original size:50 final size:50
Alignment explanation
Indices: 43270471--43270782 Score: 273
Period size: 50 Copynumber: 5.9 Consensus size: 50
43270461 TCCTATACTA
* * * ** *
43270471 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * ** **
43270521 CCCATGCCATGTCCCATTCATGGTCTTACGGGGGACCTCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
*
43270571 CCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* *
43270621 CCAACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTC
1 CCAA-CGC-CA--T--GT-CCCA-G--A---------CATGGTCTTACATGGGACCTCTCATCTC
43270686 GGTG
47 GGTG
* *
43270690 CCAACGCCATGTCCCAGACATGGTCTTATATGGGATCTCTCATCTCGGTG
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * *
43270740 CCAAAGCCATGTTCCAGACATGGTCTTACATGAGACCTCTCAT
1 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
43270783 AATTTCAATA
Statistics
Matches: 214, Mismatches: 29, Indels: 38
0.76 0.10 0.14
Matches are distributed among these distances:
50 155 0.72
51 2 0.01
52 2 0.01
54 1 0.00
56 2 0.01
57 3 0.01
58 1 0.00
59 1 0.00
60 1 0.00
61 1 0.00
62 3 0.01
63 2 0.01
65 1 0.00
67 2 0.01
68 2 0.01
69 35 0.16
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.27
Consensus pattern (50 bp):
CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
Found at i:43270629 original size:19 final size:19
Alignment explanation
Indices: 43270605--43270644 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
43270595 CTTACATGAG
43270605 ACCTCTCATCTCGGTGCCA
1 ACCTCTCATCTCGGTGCCA
43270624 ACCTCTCATCTCGGTGCCA
1 ACCTCTCATCTCGGTGCCA
43270643 AC
1 AC
43270645 GCCATGTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.42, G:0.15, T:0.25
Consensus pattern (19 bp):
ACCTCTCATCTCGGTGCCA
Found at i:43270666 original size:69 final size:69
Alignment explanation
Indices: 43270555--43270694 Score: 271
Period size: 69 Copynumber: 2.0 Consensus size: 69
43270545 CTTACGGGGG
43270555 ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGT
1 ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGT
43270620 GCCA
66 GCCA
*
43270624 ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
1 ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGT
43270689 GCCA
66 GCCA
43270693 AC
1 AC
43270695 GCCATGTCCC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.20, C:0.36, G:0.19, T:0.24
Consensus pattern (69 bp):
ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGT
GCCA
Found at i:43270730 original size:119 final size:119
Alignment explanation
Indices: 43270508--43270743 Score: 382
Period size: 119 Copynumber: 2.0 Consensus size: 119
43270498 ACATGGGAGT
* * ** *
43270508 TCTCATATCGGTGCCCATGCCATGTCCCATTCATGGTCTTACGGGGGACCTCTCATCTCGGTGCC
1 TCTCATATCGGTGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCC
43270573 AACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACC
66 AACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACC
* *
43270627 TCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCC
1 TCTCATATCGGTGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCC
* * *
43270692 AACGCCATGTCCCAGACATGGTCTTATATGGGATCTCTCATCTCGGTGCCAA
66 AACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAA
43270744 AGCCATGTTC
Statistics
Matches: 107, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
119 107 1.00
ACGTcount: A:0.19, C:0.33, G:0.21, T:0.26
Consensus pattern (119 bp):
TCTCATATCGGTGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCC
AACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACC
Found at i:43270761 original size:169 final size:169
Alignment explanation
Indices: 43270471--43270782 Score: 480
Period size: 169 Copynumber: 1.8 Consensus size: 169
43270461 TCCTATACTA
* * ** * *
43270471 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCC
1 CCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCC
** * *
43270536 ATTCATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACA
66 AGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAAAGCCATGTCCCAGACATGGTCTTACA
43270601 TGAGACCTCTCATCTCGGTGCCAACCTCTCATCTCGGTG
131 TGAGACCTCTCATCTCGGTGCCAACCTCTCATCTCGGTG
* *
43270640 CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCC
1 CCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCC
* * * *
43270705 AGACATGGTCTTATATGGGATCTCTCATCTCGGTGCCAAAGCCATGTTCCAGACATGGTCTTACA
66 AGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAAAGCCATGTCCCAGACATGGTCTTACA
43270770 TGAGACCTCTCAT
131 TGAGACCTCTCAT
43270783 AATTTCAATA
Statistics
Matches: 127, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
169 127 1.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.27
Consensus pattern (169 bp):
CCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCC
AGACATGGTCTTACAGGGGACCTCTCATCTCGGTGCCAAAGCCATGTCCCAGACATGGTCTTACA
TGAGACCTCTCATCTCGGTGCCAACCTCTCATCTCGGTG
Found at i:43270909 original size:42 final size:41
Alignment explanation
Indices: 43270837--43270915 Score: 104
Period size: 42 Copynumber: 1.9 Consensus size: 41
43270827 TGGCTCACAT
* *
43270837 ATCGATGTCGATGCCATGTACCAAACATGGTCTTATATGAG
1 ATCGATGCCGATGCCATATACCAAACATGGTCTTATATGAG
* * *
43270878 ATCGCATGCCGATGCCATATCCCAGATATGGTCTTATA
1 ATCG-ATGCCGATGCCATATACCAAACATGGTCTTATA
43270916 CGTAAATCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
41 4 0.12
42 28 0.88
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (41 bp):
ATCGATGCCGATGCCATATACCAAACATGGTCTTATATGAG
Found at i:43292199 original size:40 final size:40
Alignment explanation
Indices: 43292101--43292363 Score: 298
Period size: 40 Copynumber: 6.6 Consensus size: 40
43292091 TCCTCGTTCA
* * * * *
43292101 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
43292140 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
43292180 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
43292220 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * *
43292260 AATGCCTTCGGGACTTAACCCGGATTTAGTGTCTCACACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
43292300 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
43292340 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
43292364 CAGCATTCAA
Statistics
Matches: 195, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
39 37 0.19
40 151 0.77
41 7 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:43294776 original size:53 final size:53
Alignment explanation
Indices: 43294699--43294858 Score: 221
Period size: 53 Copynumber: 3.0 Consensus size: 53
43294689 CCATGGCACT
* * * * *
43294699 GAAGAACCATATCATGTTAGACCGTAACTGGTGGGTTATGACATCGTATAAGAA
1 GAAG-ACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGAGAA
* *
43294753 GAAGACCATATCGTGTAAAACCGTAATTGGTGGGTTATGGCATCATATGAGAA
1 GAAGACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGAGAA
* * *
43294806 GAAGACCATATCGTGTAAGACTGTAACTAGTAGGTTATGGCATCATATGAGAA
1 GAAGACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGAGAA
43294859 ATTTAAGGAA
Statistics
Matches: 94, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
53 90 0.96
54 4 0.04
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (53 bp):
GAAGACCATATCGTGTAAGACCGTAACTGGTGGGTTATGGCATCATATGAGAA
Found at i:43295176 original size:31 final size:32
Alignment explanation
Indices: 43295103--43295178 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
43295093 TCTAGATACA
* * *
43295103 AAAGCTTTTGTGGTGAGTATTGGATATTAAGG
1 AAAGCTTTTGTGGTGAGTACTAGATATAAAGG
*
43295135 AAAGCTTTTGTGGTGAGTACTAGATGTAAAGG
1 AAAGCTTTTGTGGTGAGTACTAGATATAAAGG
*
43295167 -ATGCTTTTGTGG
1 AAAGCTTTTGTGG
43295179 AAAAACTCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 11 0.28
32 28 0.72
ACGTcount: A:0.26, C:0.05, G:0.32, T:0.37
Consensus pattern (32 bp):
AAAGCTTTTGTGGTGAGTACTAGATATAAAGG
Found at i:43303573 original size:12 final size:12
Alignment explanation
Indices: 43303558--43303585 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
43303548 ATTTCCCAAG
43303558 AAATTATTCCCT
1 AAATTATTCCCT
43303570 AAATTATTCCCT
1 AAATTATTCCCT
43303582 AAAT
1 AAAT
43303586 GACCTCTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATTATTCCCT
Found at i:43304463 original size:25 final size:25
Alignment explanation
Indices: 43304403--43304463 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
43304393 CTCCTAAATT
*
43304403 TTAATTTAATTATATAATTTTTAAA
1 TTAATTAAATTATATAATTTTTAAA
* * *
43304428 TTTATTGAATTAT-TAATATTTTATA
1 TTAATTAAATTATATAAT-TTTTAAA
43304453 TTAATTAAATT
1 TTAATTAAATT
43304464 TTTGAGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATATAATTTTTAAA
Found at i:43312205 original size:21 final size:20
Alignment explanation
Indices: 43312160--43312205 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
43312150 TTGTTGGAAT
43312160 GGTT-AATTTAATCAATTTA
1 GGTTGAATTTAATCAATTTA
*
43312179 GCTTGAATTTAATTC-ATGTTA
1 GGTTGAATTTAA-TCAAT-TTA
43312200 GGTTGA
1 GGTTGA
43312206 TTGCATTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (20 bp):
GGTTGAATTTAATCAATTTA
Found at i:43316454 original size:39 final size:39
Alignment explanation
Indices: 43316409--43316492 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
43316399 ATGTCATCAT
*
43316409 GACATCATGACATCACAAAGTTAGGTTTCTCCATGTCAC
1 GACATCATGACATCAAAAAGTTAGGTTTCTCCATGTCAC
**
43316448 GACATCATGATGTCAAAAAGTTAGGTTTCTCCATGTCAC
1 GACATCATGACATCAAAAAGTTAGGTTTCTCCATGTCAC
43316487 GACATC
1 GACATC
43316493 GACCCTATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (39 bp):
GACATCATGACATCAAAAAGTTAGGTTTCTCCATGTCAC
Found at i:43334852 original size:32 final size:33
Alignment explanation
Indices: 43334787--43334857 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
43334777 CATTTTCTAA
* * *
43334787 GGCACCACCAGGGTGGGTCATCCCATTCTCTAT
1 GGCACCACCAGGGTGGGCCATCACATTCACTAT
43334820 GGCACCACCAGGGT-GGCCA-CGACATTCACTAT
1 GGCACCACCAGGGTGGGCCATC-ACATTCACTAT
43334852 GGCACC
1 GGCACC
43334858 CCACCAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 1 0.03
32 19 0.56
33 14 0.41
ACGTcount: A:0.21, C:0.35, G:0.25, T:0.18
Consensus pattern (33 bp):
GGCACCACCAGGGTGGGCCATCACATTCACTAT
Found at i:43336927 original size:50 final size:50
Alignment explanation
Indices: 43336814--43337007 Score: 271
Period size: 50 Copynumber: 3.9 Consensus size: 50
43336804 TAATAATAAC
* * ** *
43336814 ATGCCAAAGCCATGTCCCAGACATGGTATTACATGGGATGTTCTCATATCG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCG
* * **
43336865 ATGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
*
43336915 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* *
43336965 GTGCCAACGTCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
43337008 TTACCCAAAT
Statistics
Matches: 128, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 95 0.74
51 33 0.26
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:43338949 original size:29 final size:29
Alignment explanation
Indices: 43338893--43338949 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
43338883 AACAAGATGG
* *
43338893 GTTCTGAAAAAATAAATTTGATGTGATAT
1 GTTCTGAAAAAATAAATTTGACGAGATAT
* * *
43338922 GTTCTGAAAAAATTATTTTTACGAGATA
1 GTTCTGAAAAAATAAATTTGACGAGATA
43338950 GATTTGTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (29 bp):
GTTCTGAAAAAATAAATTTGACGAGATAT
Found at i:43342744 original size:7 final size:7
Alignment explanation
Indices: 43342730--43342758 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
43342720 CATAATCGAT
43342730 TTTA-TA
1 TTTAGTA
43342736 TTTAGTA
1 TTTAGTA
43342743 TTTAGTA
1 TTTAGTA
43342750 TTTAGTA
1 TTTAGTA
43342757 TT
1 TT
43342759 ATATATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (7 bp):
TTTAGTA
Found at i:43342751 original size:14 final size:13
Alignment explanation
Indices: 43342730--43342764 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
43342720 CATAATCGAT
43342730 TTTATATTTAGTA
1 TTTATATTTAGTA
43342743 TTTAGTATTTAGTA
1 TTTA-TATTTAGTA
43342757 TTATATAT
1 TT-TATAT
43342765 ATAACTAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 14 0.70
15 2 0.10
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (13 bp):
TTTATATTTAGTA
Found at i:43344461 original size:19 final size:20
Alignment explanation
Indices: 43344420--43344461 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
43344410 ATTTCTATGC
* *
43344420 CATTGTGATATTTATTATTG
1 CATTGTGATATTTAATATAG
*
43344440 CATTGT-ATATTTAATGTAG
1 CATTGTGATATTTAATATAG
43344459 CAT
1 CAT
43344462 CACATCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (20 bp):
CATTGTGATATTTAATATAG
Found at i:43350532 original size:44 final size:44
Alignment explanation
Indices: 43350442--43351016 Score: 422
Period size: 44 Copynumber: 13.1 Consensus size: 44
43350432 GTAGATCAGT
* * *
43350442 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* * * *
43350486 GAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGGAGTATATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* * * *
43350530 GAAGAAAGCAGATCTTGTCTT-C---ATTGG-CGTGAAATAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* *
43350570 GAAGATAGCAGGTCTTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* *
43350614 GAAGATGCAGATCTTGTCTTCCCATATTGGTGGC-AGAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTAGCGA-AGTAGATC
* * * * **
43350658 GAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTTAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* * * * *
43350702 GAAGATAACAGATCCTCTCTTCCTATATTTGTAGCGAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* * *
43350747 GAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* ** * * *
43350791 GAAGAAAGCAGATCTTGTCTTTATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* * *
43350835 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* * * * * *
43350879 GAAGATGCAGATCATG-CATTCCCATACTGGTGGTGAAGTGGATC
1 GAAGATGCAGATCTTGTC-TTCCTATATTGGTAGCGAAGTAGATC
* * ** * * *
43350923 GAAGAAAGCAAATCTTGTCTTTATGTATTGG-CGTGAAGTAGATC
1 GAAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
* * * * * * *
43350967 AAAGATAGCAAATCTTGACTTCTTACA-TGGACAGCGAAGCAGATC
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGG-TAGCGAAGTAGATC
43351012 GAAGA
1 GAAGA
43351017 CACCAGCCTT
Statistics
Matches: 418, Mismatches: 89, Indels: 47
0.75 0.16 0.08
Matches are distributed among these distances:
39 1 0.00
40 25 0.06
41 6 0.01
42 1 0.00
43 74 0.18
44 205 0.49
45 105 0.25
46 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (44 bp):
GAAGATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATC
Found at i:43350951 original size:265 final size:260
Alignment explanation
Indices: 43350442--43350973 Score: 825
Period size: 265 Copynumber: 2.0 Consensus size: 260
43350432 GTAGATCAGT
* * *
43350442 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 GAAGATAACAGATCCTCTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* * *
43350507 CCATATTGGTGGCGGAGTATATCGAAGAAAGCAGATCTTGTCTTCATTGGCGTGAAATAGATCGA
66 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATTGGCGTGAAATAGATCGA
* *
43350572 AGATAGCAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCC
131 AGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCATGTCTTCCC
* * *
43350637 ATATTGGTGGCAGAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTTAAGTAGATC
196 ATACTGGTGGCAGAGTAGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATC
*
43350702 GAAGATAACAGATCCTCTCTTCCTATATTTGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTT
1 GAAGATAACAGATCCTCTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTT
* *
43350767 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTTATGTATTGGCGTGAAGTAG
65 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTC--T-T-CATTGGCGTGAAATAG
43350832 ATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCATG-C
126 ATCGAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCATGTC
* * *
43350896 ATTCCCATACTGGTGG-TGAAGTGGATCGAAGAAAGCAAATCTTGTCTTTATGTATTGGCGTGAA
191 -TTCCCATACTGGTGGCAG-AGTAGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAA
43350960 GTAGATC
254 GTAGATC
*
43350967 AAAGATA
1 GAAGATA
43350974 GCAAATCTTG
Statistics
Matches: 247, Mismatches: 18, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
260 30 0.12
261 70 0.28
263 1 0.00
264 3 0.01
265 143 0.58
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (260 bp):
GAAGATAACAGATCCTCTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTC
CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATTGGCGTGAAATAGATCGA
AGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCATGTCTTCCC
ATACTGGTGGCAGAGTAGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATC
Found at i:43351094 original size:88 final size:88
Alignment explanation
Indices: 43350996--43351277 Score: 429
Period size: 88 Copynumber: 3.2 Consensus size: 88
43350986 TTCTTACATG
* *
43350996 GACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGTAGGCTAAAAAT
1 GACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAAT
*
43351061 AGCATATCTTGCCTTCCTGCACC
66 AGCAGATCTTGCCTTCCTGCACC
* * *
43351084 GACAGTGAAGCAGATCAAAGACACCAACCTTGCCTCCCTGGGTTGCAGCGGAACAGGCTAAAAAT
1 GACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAAT
* *
43351149 AGCAGATCTTACCTTCCTGCACT
66 AGCAGATCTTGCCTTCCTGCACC
* * * * *
43351172 GACAGCGAAGCGGATCTAAGACACCAACCTTGCCTCTCTGGGTTACAGCGGAGCAGGTTAAAAAT
1 GACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAAT
* *
43351237 AGTAGATCTTGCCTTCCTGCATC
66 AGCAGATCTTGCCTTCCTGCACC
43351260 GACAGCGAAGCAGATCGA
1 GACAGCGAAGCAGATCGA
43351278 TGACCCCAGC
Statistics
Matches: 173, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 173 1.00
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.20
Consensus pattern (88 bp):
GACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAAT
AGCAGATCTTGCCTTCCTGCACC
Found at i:43351351 original size:44 final size:44
Alignment explanation
Indices: 43351288--43351453 Score: 217
Period size: 44 Copynumber: 3.8 Consensus size: 44
43351278 TGACCCCAGC
43351288 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * * *
43351332 CCTATCTTCCTGGTCAGCAGTGGAAGAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * * * * *
43351376 TCTATCTCCTTGGGCAACAGTGGAATAGATTGAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
*
43351420 CCTATCTCCCTGAG-CAGCAGTGGAGTAGGTTAAA
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGTTAAA
43351454 AATAACAGAT
Statistics
Matches: 103, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
44 102 0.99
45 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
Found at i:43351578 original size:88 final size:88
Alignment explanation
Indices: 43351424--43351586 Score: 211
Period size: 88 Copynumber: 1.9 Consensus size: 88
43351414 GTGAATCCTA
* * *
43351424 TCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAACAGATCTTGCCTTCCTGTACCGACAGCGAA
1 TCTCCCTGAGCAGCAGTAGAGTAGGTTAAAAATAACAGATCTTGCCTTCCTGTACAGACAACGAA
*
43351489 GCAGATCGAAAACTCCAGCCTTG
66 GCAAATCGAAAACTCCAGCCTTG
* * * * * * *
43351512 TCTCCCTGAGCAGTAGTAGATTAGGTTGAAAATAGCAGGTCTTGTCTTCCTGTACTAG-CAATGA
1 TCTCCCTGAGCAGCAGTAGAGTAGGTTAAAAATAACAGATCTTGCCTTCCTGTAC-AGACAACGA
43351576 AGCAAATCGAA
65 AGCAAATCGAA
43351587 GACATCAGTT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
88 62 0.98
89 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (88 bp):
TCTCCCTGAGCAGCAGTAGAGTAGGTTAAAAATAACAGATCTTGCCTTCCTGTACAGACAACGAA
GCAAATCGAAAACTCCAGCCTTG
Found at i:43352175 original size:44 final size:43
Alignment explanation
Indices: 43352106--43352392 Score: 232
Period size: 44 Copynumber: 6.6 Consensus size: 43
43352096 TGCAATGGCG
43352106 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAAT
* * * * **
43352150 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACTTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
* * * * *
43352193 GGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CGCATCT
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCA-AT
* * * *
43352234 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAA-T
* *
43352277 AAGTCTTATC-CTCCAGAAGTTGCAGT-GAGGCAGACTAAAG--AT
1 AA-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATTAAAGCAAT
43352319 GGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 ----AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAAT
* *
43352367 AATCCTATCTCCCTGAAGTTACAGTG
1 AATCTTATCTCCCTGAAGTTGCAGTG
43352393 AGGCGGATAA
Statistics
Matches: 193, Mismatches: 31, Indels: 38
0.74 0.12 0.15
Matches are distributed among these distances:
40 22 0.11
41 8 0.04
42 2 0.01
43 15 0.08
44 106 0.55
45 33 0.17
46 5 0.03
48 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
Found at i:43352357 original size:217 final size:215
Alignment explanation
Indices: 43352099--43352567 Score: 697
Period size: 217 Copynumber: 2.2 Consensus size: 215
43352089 TTAACATTGC
*
43352099 AATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCT
1 AATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCT
* ****
43352164 GAAGTTACAGTG-GAGCGGATTAAAACTTTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATC
66 GAAGTTACAGTGAG-GCGGATAAAAACCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATC
* * *
43352228 GCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCAG
130 GCATCTAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGAAAGTCTTATCCCCCAG
*
43352293 AAGTTGCAGTGAGGCAGACTAA
195 AAATTGCAGTGAGGCAGACT-A
43352315 AGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCC
1 A-ATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCC
*
43352380 TGAAGTTACAGTGAGGCGGATAAAAACCACAGATCTTATCTCTCTGAAGTTGTAGAGAGCAGATC
65 TGAAGTTACAGTGAGGCGGATAAAAACCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATC
* * * *
43352445 GCATCTGGTCTTATCTTCCTGAAGTTACAGTGGGGCAGACTGAGTAAGAAAGTCTTATCCCCCAG
130 GCATCTAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGAAAGTCTTATCCCCCAG
* * *
43352510 AAATTGCAGTGGGGCGGACTG
195 AAATTGCAGTGAGGCAGACTA
* * * *
43352531 AATGAACAAATCCTATCTCCCTAAAGTTGTAGTGGAG
1 AATG-GCAAATCTTATCTCCCTGAAGTTGCAGTGGAG
43352568 TGGATTAGAA
Statistics
Matches: 228, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
215 3 0.01
216 30 0.13
217 194 0.85
218 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (215 bp):
AATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCT
GAAGTTACAGTGAGGCGGATAAAAACCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCG
CATCTAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGAAAGTCTTATCCCCCAGA
AATTGCAGTGAGGCAGACTA
Found at i:43352392 original size:89 final size:88
Alignment explanation
Indices: 43352236--43352431 Score: 218
Period size: 89 Copynumber: 2.2 Consensus size: 88
43352226 TCGCATCTAG
* * *
43352236 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCAGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCCTATCCTCCAGAAGTTACA
* ***
43352301 GTGAGGCAGACTAAAGATGGCAAA
66 GTGAGGCAGA-TAAAAACCACAAA
* * *
43352325 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA-TAA-TCCTAT-CTCCCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-CAAGCAAGTCCTATCCT-CCAGAAGTT
* *
43352387 ACAGTGAGGCGGATAAAAACCACAGA
63 ACAGTGAGGCAGATAAAAACCACAAA
*
43352413 TCTTATCTCTCTGAAGTTG
1 TCTTATCTCCCTGAAGTTG
43352432 TAGAGAGCAG
Statistics
Matches: 91, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
88 28 0.31
89 56 0.62
90 5 0.05
91 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCCTATCCTCCAGAAGTTACA
GTGAGGCAGATAAAAACCACAAA
Found at i:43352420 original size:44 final size:44
Alignment explanation
Indices: 43352106--43352430 Score: 181
Period size: 44 Copynumber: 7.5 Consensus size: 44
43352096 TGCAATGGCG
* * *
43352106 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATAAAAACCAAT
* * * **
43352150 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAA-CTTT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATAAAAACCAAT
* * * * *** *
43352193 GGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGAT-CGCATC--T
1 -AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATAAAAACCAAT
* * * *
43352234 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-A-
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TAA-AAACCAAT
* * * **
43352278 AGTCTTATC-CTCCAGAAGTTGCAGT-GAGGCAGACTAAAGATGGC-A-
1 AATCTTATCTC-CCTGAAGTTACAGTGGA-GCAGA-TAAA-A-ACCAAT
* * *
43352323 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATAAAAACCAAT
* *
43352367 AATCCTATCTCCCTGAAGTTACAGT-GAGGCGGATAAAAACCACA-
1 AATCTTATCTCCCTGAAGTTACAGTGGA-GCAGATAAAAACCA-AT
* *
43352411 GATCTTATCTCTCTGAAGTT
1 AATCTTATCTCCCTGAAGTT
43352431 GTAGAGAGCA
Statistics
Matches: 226, Mismatches: 38, Indels: 34
0.76 0.13 0.11
Matches are distributed among these distances:
40 21 0.09
41 8 0.04
42 4 0.02
43 17 0.08
44 143 0.63
45 30 0.13
46 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATAAAAACCAAT
Found at i:43364093 original size:19 final size:19
Alignment explanation
Indices: 43364066--43364103 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
43364056 TCCTGACCTC
*
43364066 TCGTCACTAAAATTCAATT
1 TCGTAACTAAAATTCAATT
*
43364085 TCGTAACTAAAATTGAATT
1 TCGTAACTAAAATTCAATT
43364104 ATCTCATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
TCGTAACTAAAATTCAATT
Found at i:43365148 original size:50 final size:50
Alignment explanation
Indices: 43365031--43365370 Score: 380
Period size: 50 Copynumber: 6.8 Consensus size: 50
43365021 GAATATAACA
* * * ** * * * *
43365031 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * * * ** *
43365080 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
* * * *
43365130 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
43365179 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCA-G
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-AGG
* *
43365229 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
** * * * * *
43365279 TGCCAATTCCATATCCCAAACATGGTCTTACATGGGACCCCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
*
43365329 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
43365371 TTACCCAAAT
Statistics
Matches: 249, Mismatches: 38, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
49 78 0.31
50 171 0.69
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTAGG
Found at i:43365742 original size:29 final size:30
Alignment explanation
Indices: 43365709--43365765 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
43365699 CCTTGACTCT
43365709 AACTTTGACA-AAATATGA-TTTTGCCCCTA
1 AACTTTGACATAAATAT-ACTTTTGCCCCTA
* *
43365738 AACTTTTACATAATTATACTTTTGCCCC
1 AACTTTGACATAAATATACTTTTGCCCC
43365766 AAAGCTCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
AACTTTGACATAAATATACTTTTGCCCCTA
Found at i:43367725 original size:122 final size:122
Alignment explanation
Indices: 43367508--43367746 Score: 478
Period size: 122 Copynumber: 2.0 Consensus size: 122
43367498 AATAAACCCC
43367508 TTTTCTTGTAAAATGACTTACCCTTTTGAAAGTGTAAGTCATTTTTCGGAAAAGAGCTCATCTAT
1 TTTTCTTGTAAAATGACTTACCCTTTTGAAAGTGTAAGTCATTTTTCGGAAAAGAGCTCATCTAT
43367573 AGGTATTTTTATTTTTATATAAAAATTAACTTAAATCAAGCTTAATATTATTTTTAT
66 AGGTATTTTTATTTTTATATAAAAATTAACTTAAATCAAGCTTAATATTATTTTTAT
43367630 TTTTCTTGTAAAATGACTTACCCTTTTGAAAGTGTAAGTCATTTTTCGGAAAAGAGCTCATCTAT
1 TTTTCTTGTAAAATGACTTACCCTTTTGAAAGTGTAAGTCATTTTTCGGAAAAGAGCTCATCTAT
43367695 AGGTATTTTTATTTTTATATAAAAATTAACTTAAATCAAGCTTAATATTATT
66 AGGTATTTTTATTTTTATATAAAAATTAACTTAAATCAAGCTTAATATTATT
43367747 ATATTGATAA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 117 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (122 bp):
TTTTCTTGTAAAATGACTTACCCTTTTGAAAGTGTAAGTCATTTTTCGGAAAAGAGCTCATCTAT
AGGTATTTTTATTTTTATATAAAAATTAACTTAAATCAAGCTTAATATTATTTTTAT
Found at i:43367940 original size:13 final size:14
Alignment explanation
Indices: 43367924--43367965 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
43367914 TTTCAATTTT
43367924 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
43367937 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
43367952 ATTTTAAATAATAT
1 ATTTT-AATAATAT
43367966 TCTTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:43367950 original size:16 final size:16
Alignment explanation
Indices: 43367928--43367964 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
43367918 AATTTTATTT
43367928 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
43367945 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
43367960 TAATA
1 TAATA
43367965 TTCTTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:43369901 original size:43 final size:43
Alignment explanation
Indices: 43369853--43369975 Score: 165
Period size: 43 Copynumber: 2.9 Consensus size: 43
43369843 GTCGCTAACT
* *
43369853 TTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCA
1 TTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACAAGACCA
* * * * *
43369896 TTAGCGGCGCTTTTCGCACAAACGCCGCTATAGAACATGAGCT
1 TTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACAAGACCA
**
43369939 TTAGTAGCGCTTTTCCCACAAACGCCGCTAAAGAACA
1 TTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACA
43369976 TTATATTTAG
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (43 bp):
TTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAACAAGACCA
Found at i:43369985 original size:43 final size:43
Alignment explanation
Indices: 43369852--43370005 Score: 152
Period size: 43 Copynumber: 3.6 Consensus size: 43
43369842 CGTCGCTAAC
* * * *
43369852 TTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGACCA
1 TTTAGCAGCGCTTTTCCCACAAACGCCGCTAAAGAACATGA-CA
* * *
43369896 -TTAGCGGCGCTTTTCGCACAAACGCCGCTATAGAACATGAGC-
1 TTTAGCAGCGCTTTTCCCACAAACGCCGCTAAAGAACATGA-CA
* * *
43369938 TTTAGTAGCGCTTTTCCCACAAACGCCGCTAAAGAACATTATA
1 TTTAGCAGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACA
**
43369981 TTTAGC-GACGCTTTTATCACAAACG
1 TTTAGCAG-CGCTTTTCCCACAAACG
43370006 TCACTAAAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
42 1 0.01
43 92 0.99
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
TTTAGCAGCGCTTTTCCCACAAACGCCGCTAAAGAACATGACA
Found at i:43372148 original size:40 final size:40
Alignment explanation
Indices: 43372093--43372169 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
43372083 ACATCAGCAC
* * *
43372093 TTCAATATTTAATATGTAAGGAATTATCAAAAATCAACAT
1 TTCAATATTTAATATGCAAGAAATTAACAAAAATCAACAT
*
43372133 TTCAATAATTT-ATATGCAAGAAATTAACACAAATCAA
1 TTCAAT-ATTTAATATGCAAGAAATTAACAAAAATCAA
43372170 TCTTACAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 28 0.88
41 4 0.12
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.32
Consensus pattern (40 bp):
TTCAATATTTAATATGCAAGAAATTAACAAAAATCAACAT
Found at i:43372342 original size:86 final size:85
Alignment explanation
Indices: 43372245--43372432 Score: 268
Period size: 86 Copynumber: 2.2 Consensus size: 85
43372235 GGCATTAGGG
* * * *
43372245 CTAAATCTTCAATTTCTATAACGATTTATATGCAACAAATTAACAAAAATCAATGGTTCAAGTTC
1 CTAAATTTTCAATTT-TATAACAACTTATATGCAACAAATTAACAAAAATAAATGGTTCAAGTTC
** *
43372310 ATGTATTTACCAAAAATCAGA
65 ATCCATTTACCAAAAAGCAGA
* *
43372331 CTAATTTTTCAATATTTATAACAACTTATATGCAACAAATTAGCAAAAATAAATGGTTCAAGTTC
1 CTAAATTTTCAAT-TTTATAACAACTTATATGCAACAAATTAACAAAAATAAATGGTTCAAGTTC
*
43372396 ATCCATTTACCAACAAGCAGA
65 ATCCATTTACCAAAAAGCAGA
43372417 CTAAATTTTCAATTTT
1 CTAAATTTTCAATTTT
43372433 CAATTTTTAA
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
85 3 0.03
86 85 0.94
87 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.34
Consensus pattern (85 bp):
CTAAATTTTCAATTTTATAACAACTTATATGCAACAAATTAACAAAAATAAATGGTTCAAGTTCA
TCCATTTACCAAAAAGCAGA
Found at i:43372689 original size:86 final size:87
Alignment explanation
Indices: 43372535--43372697 Score: 211
Period size: 86 Copynumber: 1.9 Consensus size: 87
43372525 CAATTTACAA
* * * * * *
43372535 GCAAAAAATTAACAAAAATAAACAATTCATGTATAATGTATTTACCAAAAACCGGACCAACTTGT
1 GCAAAAAATTAACAAAAATAAACAATACAAGTATAATATATTCACCAAAAACCAGACCAAATTGT
43372600 CAATTTTTATAACATTTTAAAT
66 CAATTTTTATAACATTTTAAAT
* * * * * *
43372622 GCAACAAATTAACACAAATTAACAATACAAGT-TCATATATTCACCAAAAACCAGACTAAATTTT
1 GCAAAAAATTAACAAAAATAAACAATACAAGTATAATATATTCACCAAAAACCAGACCAAATTGT
43372686 CAATTTTTATAA
66 CAATTTTTATAA
43372698 AATAAGAGGA
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
86 37 0.58
87 27 0.42
ACGTcount: A:0.48, C:0.17, G:0.06, T:0.30
Consensus pattern (87 bp):
GCAAAAAATTAACAAAAATAAACAATACAAGTATAATATATTCACCAAAAACCAGACCAAATTGT
CAATTTTTATAACATTTTAAAT
Found at i:43374654 original size:21 final size:21
Alignment explanation
Indices: 43374630--43374675 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
43374620 TTTTGGATGT
43374630 GGGAAA-TTAGGGATTTTAGGG
1 GGGAAAGTTAGGGA-TTTAGGG
* *
43374651 GGGAAAGTTTGGGATTTCGGG
1 GGGAAAGTTAGGGATTTAGGG
43374672 GGGA
1 GGGA
43374676 GGGGGAGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.24, C:0.02, G:0.48, T:0.26
Consensus pattern (21 bp):
GGGAAAGTTAGGGATTTAGGG
Found at i:43375430 original size:7 final size:7
Alignment explanation
Indices: 43375420--43375449 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
43375410 CTTAACCTCA
43375420 AACCCCT
1 AACCCCT
43375427 AACCCCT
1 AACCCCT
*
43375434 AACCACT
1 AACCCCT
43375441 AACCCCT
1 AACCCCT
43375448 AA
1 AA
43375450 ACCTTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.37, C:0.50, G:0.00, T:0.13
Consensus pattern (7 bp):
AACCCCT
Found at i:43376549 original size:41 final size:41
Alignment explanation
Indices: 43376505--43376731 Score: 316
Period size: 41 Copynumber: 5.5 Consensus size: 41
43376495 TTTTATTATT
* *
43376505 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCTGAGT
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCTGAGC
* *
43376546 ATTAGCGACGCTTCTTCAAAAAATGCCGCTAAAGG-CTCGAGC
1 ATTAGCGGCGCTTCTTC-AAAAACGCCGCTAAAGGCCT-GAGC
*
43376588 ATTAGCGGCGCATT-TTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGC-TTCTTCAAAAACGCCGCTAAAGGCCTGAGC
* *
43376629 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCTGAGC
* *
43376670 ATTAGCAGCGCTTCTTCAAAAACGCCGCTAAAGG-CTAGATC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCT-GAGC
43376711 ATTAGCGGCGCTTCTTCAAAA
1 ATTAGCGGCGCTTCTTCAAAA
43376732 TTGCCGTTAA
Statistics
Matches: 167, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
40 3 0.02
41 129 0.77
42 33 0.20
43 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCTGAGC
Found at i:43389269 original size:27 final size:25
Alignment explanation
Indices: 43389239--43389335 Score: 79
Period size: 25 Copynumber: 3.8 Consensus size: 25
43389229 CGTTCCGACC
*
43389239 CACAACTTGTGTGAGCATGCCCATTTT
1 CACAACTTGTGTGAGCATACCCA--TT
* *
43389266 CAC-AGTTCGTGTGAGCATACCGATT
1 CACAACTT-GTGTGAGCATACCCATT
* * *
43389291 CACAGCTCGTGTGAGCATACCGATT
1 CACAACTTGTGTGAGCATACCCATT
* * *
43389316 CACAGCTCGTGTGAGTATAC
1 CACAACTTGTGTGAGCATAC
43389336 ATGTACAGGA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
25 41 0.67
26 4 0.07
27 16 0.26
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.28
Consensus pattern (25 bp):
CACAACTTGTGTGAGCATACCCATT
Found at i:43389300 original size:25 final size:25
Alignment explanation
Indices: 43389264--43389335 Score: 126
Period size: 25 Copynumber: 2.9 Consensus size: 25
43389254 CATGCCCATT
*
43389264 TTCACAGTTCGTGTGAGCATACCGA
1 TTCACAGCTCGTGTGAGCATACCGA
43389289 TTCACAGCTCGTGTGAGCATACCGA
1 TTCACAGCTCGTGTGAGCATACCGA
*
43389314 TTCACAGCTCGTGTGAGTATAC
1 TTCACAGCTCGTGTGAGCATAC
43389336 ATGTACAGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (25 bp):
TTCACAGCTCGTGTGAGCATACCGA
Found at i:43400587 original size:4 final size:4
Alignment explanation
Indices: 43400552--43400603 Score: 59
Period size: 4 Copynumber: 12.5 Consensus size: 4
43400542 ATTTTTTATA
* * *
43400552 ATTT CATTT ATTT GATTC ATTT ATTC ATTT ATTT ATTT ACTT ATTT ATTT
1 ATTT -ATTT ATTT -ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
43400602 AT
1 AT
43400604 CCATTATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
4 33 0.82
5 7 0.17
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (4 bp):
ATTT
Found at i:43400587 original size:12 final size:12
Alignment explanation
Indices: 43400554--43400613 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
43400544 TTTTTATAAT
43400554 TTCATTTATTTGA
1 TTCATTTATTT-A
*
43400567 TTCATTTATTCA
1 TTCATTTATTTA
*
43400579 TTTATTTATTTA
1 TTCATTTATTTA
43400591 CTT-ATTTATTTA
1 -TTCATTTATTTA
*
43400603 TCCATTATATT
1 TTCATT-TATT
43400614 CATTTTTACT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 1 0.03
12 23 0.57
13 16 0.40
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.63
Consensus pattern (12 bp):
TTCATTTATTTA
Found at i:43400587 original size:37 final size:35
Alignment explanation
Indices: 43400532--43400620 Score: 90
Period size: 37 Copynumber: 2.4 Consensus size: 35
43400522 TACATCCATA
* * *
43400532 CATTTCTTGCATTTTTTA-TAATTTCATTTATTTGATT
1 CATTTATT-CATTTTTTATTAACTT-ATTTATTT-ATC
*
43400569 CATTTATTCATTTATTTATTTACTTATTTATTTATC
1 CATTTATTCATTT-TTTATTAACTTATTTATTTATC
43400605 CATTATATTCATTTTT
1 CATT-TATTCATTTTT
43400621 ACTTAGATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
36 13 0.29
37 28 0.62
38 4 0.09
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (35 bp):
CATTTATTCATTTTTTATTAACTTATTTATTTATC
Found at i:43407426 original size:87 final size:88
Alignment explanation
Indices: 43407187--43407490 Score: 513
Period size: 88 Copynumber: 3.5 Consensus size: 88
43407177 ATGAAGTTGC
*
43407187 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
43407252 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
*
43407275 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTTGGTTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
*
43407340 TGATGGAGCTGGTTGAGGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
*
43407363 AGATCTTGCCTT-CTGTATTGATAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
*
43407427 TGATGGAGCTGGTTGAAGATAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * *
43407450 AGAACTTGCCTTCCTGTACT-AGCAGCGAAGCAGATCGAAGA
1 AGATCTTGCCTTCCTGTATTGA-CAGCGAAGCAGGTCGAAGA
43407491 TGGCAGATTT
Statistics
Matches: 203, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
87 83 0.41
88 120 0.59
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (88 bp):
AGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
TGATGGAGCTGGTTGAAGACAAA
Found at i:43409528 original size:4 final size:4
Alignment explanation
Indices: 43409493--43409544 Score: 59
Period size: 4 Copynumber: 12.5 Consensus size: 4
43409483 ATTTTTTATA
* * *
43409493 ATTT CATTT ATTT GATTC ATTT ATTC ATTT ATTT ATTT ACTT ATTT ATTT
1 ATTT -ATTT ATTT -ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
43409543 AT
1 AT
43409545 CCATTATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
4 33 0.82
5 7 0.17
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (4 bp):
ATTT
Found at i:43409528 original size:12 final size:12
Alignment explanation
Indices: 43409495--43409554 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
43409485 TTTTTATAAT
43409495 TTCATTTATTTGA
1 TTCATTTATTT-A
*
43409508 TTCATTTATTCA
1 TTCATTTATTTA
*
43409520 TTTATTTATTTA
1 TTCATTTATTTA
43409532 CTT-ATTTATTTA
1 -TTCATTTATTTA
*
43409544 TCCATTATATT
1 TTCATT-TATT
43409555 CATTTTTACT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 1 0.03
12 23 0.57
13 16 0.40
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.63
Consensus pattern (12 bp):
TTCATTTATTTA
Found at i:43409528 original size:37 final size:35
Alignment explanation
Indices: 43409473--43409561 Score: 90
Period size: 37 Copynumber: 2.4 Consensus size: 35
43409463 TACATCCATA
* * *
43409473 CATTTCTTGCATTTTTTA-TAATTTCATTTATTTGATT
1 CATTTATT-CATTTTTTATTAACTT-ATTTATTT-ATC
*
43409510 CATTTATTCATTTATTTATTTACTTATTTATTTATC
1 CATTTATTCATTT-TTTATTAACTTATTTATTTATC
43409546 CATTATATTCATTTTT
1 CATT-TATTCATTTTT
43409562 ACTTAGATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
36 13 0.29
37 28 0.62
38 4 0.09
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (35 bp):
CATTTATTCATTTTTTATTAACTTATTTATTTATC
Found at i:43416269 original size:69 final size:69
Alignment explanation
Indices: 43416130--43416592 Score: 252
Period size: 69 Copynumber: 6.7 Consensus size: 69
43416120 TAGCAGCAAC
* * * ** * * * * **
43416130 CTCCAAAACAGTTAGTGAGATCAAAGCTCCCAACTATCATATTAGGGTTCACAGGCGAAA-AACC
1 CTCCAAAACAGTTAGCGAGAGCAAAGCTCCTAGTTGTAATATTAAGGTTCATAGGC-AAAGAGTC
*
43416194 GCAAT
65 GTAAT
* * * * * **
43416199 CTCCAAAGCAATTAGCGAAAGCAAAGCTCTTAGTTGTCATATTAAGGTTCGCAGGCAAAGAGTCG
1 CTCCAAAACAGTTAGCGAGAGCAAAGCTCCTAGTTGTAATATTAAGGTTCATAGGCAAAGAGTCG
43416264 TAAT
66 TAAT
* * * * * * *
43416268 CTCCAAAATAGTTAGTGAGAG-AAAGCTCCTAGCTATTATATTAAGGTTCTTAGGTGAAA-AGTC
1 CTCCAAAACAGTTAGCGAGAGCAAAGCTCCTAGTTGTAATATTAAGGTTCATAGG-CAAAGAGTC
*
43416331 GTAAC
65 GTAAT
* * * * * * * *
43416336 CTCCAAAATAGTTAGCGATAGAAAAACTCCCAGTTGTAACATTAAGGTTCATAGGCGAAGAGCCG
1 CTCCAAAACAGTTAGCGAGAGCAAAGCTCCTAGTTGTAATATTAAGGTTCATAGGCAAAGAGTCG
43416401 TAA-
66 TAAT
* ** * * * * *
43416404 CTTCCAAAACAGTTAGCGAGAGCAAAGCTCCCAACTGTAACATTAAGGTTCACAGGTAAATATTC
1 C-TCCAAAACAGTTAGCGAGAGCAAAGCTCCTAGTTGTAATATTAAGGTTCATAGGCAAAGAGTC
** *
43416469 ACAAC
65 GTAAT
* * ** * * * * * * * * *
43416474 CTCTAAAATAGTTAATGAGGGCAAAGCTCCCAGCTGTAATAGTAAGGTTCACAGACGAAGAGCCA
1 CTCCAAAACAGTTAGCGAGAGCAAAGCTCCTAGTTGTAATATTAAGGTTCATAGGCAAAGAGTCG
*
43416539 TAAC
66 TAAT
* * * * * * *
43416543 CTCTAAAATAATTAGTGAGAGTAAAGCT-CTCAATTGTCATATTAAGGTTC
1 CTCCAAAACAGTTAGCGAGAGCAAAGCTCCT-AGTTGTAATATTAAGGTTC
43416593 GCAACCTCTA
Statistics
Matches: 309, Mismatches: 78, Indels: 14
0.77 0.19 0.03
Matches are distributed among these distances:
68 61 0.20
69 247 0.80
70 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (69 bp):
CTCCAAAACAGTTAGCGAGAGCAAAGCTCCTAGTTGTAATATTAAGGTTCATAGGCAAAGAGTCG
TAAT
Found at i:43416512 original size:138 final size:137
Alignment explanation
Indices: 43416131--43416592 Score: 361
Period size: 138 Copynumber: 3.4 Consensus size: 137
43416121 AGCAGCAACC
* * * * * * ** *
43416131 TCCAAAACAGTTAGTGAGATCAAAGCTCCCAACTATCATATTAGGGTTCACAGGCGAAAAACCGC
1 TCCAAAATAGTTAGTGAGA-GAAAGCTCCCAACTGTAATATTAAGGTTCACAGGTGAAAAGTCAC
* ** * * * * * ** * * * * *
43416196 AATCTCCAAAGCAATTAGCGAAAGCAAAGCTCTTAGTTGTCATATTAAGGTTCGCAGGCAAAGAG
65 AACCTCCAAAATAGTTAACGAGAGAAAAACTCCCAGCTGTAACATTAAGGTTCACAGGCGAAGAG
*
43416261 TCGTAA-T
130 CCGTAACT
* * * * ** **
43416268 CTCCAAAATAGTTAGTGAGAGAAAGCTCCTAGCTATTATATTAAGGTTCTTAGGTGAAAAGTCGT
1 -TCCAAAATAGTTAGTGAGAGAAAGCTCCCAACTGTAATATTAAGGTTCACAGGTGAAAAGTCAC
* * * *
43416333 AACCTCCAAAATAGTTAGCGATAGAAAAACTCCCAGTTGTAACATTAAGGTTCATAGGCGAAGAG
65 AACCTCCAAAATAGTTAACGAGAGAAAAACTCCCAGCTGTAACATTAAGGTTCACAGGCGAAGAG
43416398 CCGTAACT
130 CCGTAACT
* * * *
43416406 TCCAAAACAGTTAGCGAGAGCAAAGCTCCCAACTGTAACATTAAGGTTCACAGGT-AAATATTCA
1 TCCAAAATAGTTAGTGAGAG-AAAGCTCCCAACTGTAATATTAAGGTTCACAGGTGAAA-AGTCA
* * * * * * * *
43416470 CAACCTCTAAAATAGTTAATGAGGGCAAAGCTCCCAGCTGTAATAGTAAGGTTCACAGACGAAGA
64 CAACCTCCAAAATAGTTAACGAGAGAAAAACTCCCAGCTGTAACATTAAGGTTCACAGGCGAAGA
* *
43416535 GCCATAACC
129 GCCGTAACT
* * * * *
43416544 TCTAAAATAATTAGTGAGAGTAAAGCTCTCAATTGTCATATTAAGGTTC
1 TCCAAAATAGTTAGTGAGAG-AAAGCTCCCAACTGTAATATTAAGGTTC
43416593 GCAACCTCTA
Statistics
Matches: 259, Mismatches: 62, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
137 111 0.43
138 148 0.57
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (137 bp):
TCCAAAATAGTTAGTGAGAGAAAGCTCCCAACTGTAATATTAAGGTTCACAGGTGAAAAGTCACA
ACCTCCAAAATAGTTAACGAGAGAAAAACTCCCAGCTGTAACATTAAGGTTCACAGGCGAAGAGC
CGTAACT
Found at i:43416807 original size:70 final size:70
Alignment explanation
Indices: 43416607--43416812 Score: 208
Period size: 70 Copynumber: 3.0 Consensus size: 70
43416597 CCTCTAAAGT
* * * *
43416607 AGTTAGCGGGAGCAAAA-CTCCCCAGCTTTCATATTAAAGTTCGTAAAAGAAGAG-CCGCAACCT
1 AGTTAGCGAGAGCAAAAGCT-CCCAGCTATCATATTAAGGTTCGCAAAAGAAGAGTCC-CAACCT
*
43416670 CCAAAAT
64 CCAAAAC
* * * * ** **
43416677 AGTTAGTGAGAGC-AAAGCTCCTAG-TCATAATATTAAGG-CCAGCAGGCA-AAGAGTTGCAACC
1 AGTTAGCGAGAGCAAAAGCTCCCAGCT-ATCATATTAAGGTTC-GCA-AAAGAAGAGTCCCAACC
43416738 TCCAAAAC
63 TCCAAAAC
43416746 AGTTAGCGAGAGCAAAAGCTCCCAGCTATCATATTAAGGTTCGCAAAAGAAGAGTCCCAACCTCC
1 AGTTAGCGAGAGCAAAAGCTCCCAGCTATCATATTAAGGTTCGCAAAAGAAGAGTCCCAACCTCC
43416811 AA
66 AA
43416813 GTGTAACAGC
Statistics
Matches: 106, Mismatches: 21, Indels: 18
0.73 0.14 0.12
Matches are distributed among these distances:
68 2 0.02
69 48 0.45
70 54 0.51
71 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (70 bp):
AGTTAGCGAGAGCAAAAGCTCCCAGCTATCATATTAAGGTTCGCAAAAGAAGAGTCCCAACCTCC
AAAAC
Found at i:43425047 original size:25 final size:25
Alignment explanation
Indices: 43424983--43425070 Score: 88
Period size: 25 Copynumber: 3.5 Consensus size: 25
43424973 CAGGTATGCC
*
43424983 CATTCGAG-CATATAACCGGGAAGCT
1 CATTTGAGCCATATAA-CGGGAAGCT
*
43425008 CTTTTGAGCCATATAACGGGAAGCT
1 CATTTGAGCCATATAACGGGAAGCT
*** **
43425033 CATTTGAGTTGTATAATAGGAAGCT
1 CATTTGAGCCATATAACGGGAAGCT
*
43425058 CATTAGAGCCATA
1 CATTTGAGCCATA
43425071 ATCGGAAAGT
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
25 43 0.86
26 7 0.14
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (25 bp):
CATTTGAGCCATATAACGGGAAGCT
Found at i:43425187 original size:25 final size:25
Alignment explanation
Indices: 43425120--43425189 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
43425110 AGAGTCATTA
43425120 ATCAGGAAGCTCATAAGAGCCAGTT
1 ATCAGGAAGCTCATAAGAGCCAGTT
**
43425145 ATCAGGAAGCTCCGAAGAGCCTA-TT
1 ATCAGGAAGCTCATAAGAGCC-AGTT
** *
43425170 ATTGGGATGCTCATAAGAGC
1 ATCAGGAAGCTCATAAGAGC
43425190 TGCGGTGTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
25 36 0.97
26 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (25 bp):
ATCAGGAAGCTCATAAGAGCCAGTT
Found at i:43434246 original size:5 final size:5
Alignment explanation
Indices: 43434236--43434266 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
43434226 CTTTCCCTGT
43434236 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
43434267 GTAAAATCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:43436961 original size:59 final size:58
Alignment explanation
Indices: 43436896--43437071 Score: 150
Period size: 59 Copynumber: 3.0 Consensus size: 58
43436886 AATAATGTAG
43436896 ATTATATTTTATTTTCATAGTATTATATAATATGATTTTAGTAAATTCATATAAGAATA
1 ATTATATTTTATTTT-ATAGTATTATATAATATGATTTTAGTAAATTCATATAAGAATA
** * * * *
43436955 ATTATATTGAATTTTAT--TA--A-ATTATAT-ATTTTAACTAAATT-ATATTTAATATTA
1 ATTATATTTTATTTTATAGTATTATATAATATGATTTT-AGTAAATTCATA--TAAGAATA
* *
43437009 ATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATA
1 ATTA---T--ATTTTATTTTATAGTATTATATAATATGATTTTAGTAAATTCATATAAGAATA
43437072 TTGATTATTA
Statistics
Matches: 89, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
52 8 0.09
53 13 0.15
54 11 0.12
56 2 0.02
57 1 0.01
58 2 0.02
59 23 0.26
61 2 0.02
63 7 0.08
64 12 0.13
65 8 0.09
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (58 bp):
ATTATATTTTATTTTATAGTATTATATAATATGATTTTAGTAAATTCATATAAGAATA
Found at i:43437022 original size:14 final size:14
Alignment explanation
Indices: 43436971--43437022 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
43436961 TTGAATTTTA
43436971 TTAAATT-ATATATT
1 TTAAATTAAT-TATT
* *
43436985 TTAACTAAATTATAT
1 TTAAATTAATTAT-T
43437000 TTAATATTAATTATT
1 TTAA-ATTAATTATT
43437015 TTAAATTA
1 TTAAATTA
43437023 TATTTTATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 12 0.39
15 12 0.39
16 7 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
TTAAATTAATTATT
Found at i:43437051 original size:117 final size:120
Alignment explanation
Indices: 43436905--43437121 Score: 361
Period size: 117 Copynumber: 1.8 Consensus size: 120
43436895 GATTATATTT
43436905 TATTTTCATAGTATTATATAATATGATTTTAGTAAATTCATATAAGAATAATT-A-TATT-GAAT
1 TATTTTCATAGTATTATATAATATGATTTTAGTAAATTCATATAAGAAT-ATTGATTATTAGAAT
*
43436967 TTTATTAAATTATATATTTTAACTAAATTATATTTAATATTAATTATTTTAAATTA
65 TTTATTAAATTATATATTTTAACTAAAATATATTTAATATTAATTATTTTAAATTA
*
43437023 TATTTT-ATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAAT
1 TATTTTCATAGTATTATATAATATGATTTTAGTAAATTCATATAAGAATATTGATTATT-AGAAT
*
43437087 TTTATTAAATTATATATTTTAATTAAAATATATTT
65 TTTATTAAATTATATATTTTAACTAAAATATATTT
43437122 TATTAAATCA
Statistics
Matches: 92, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
116 3 0.03
117 42 0.46
118 10 0.11
120 37 0.40
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (120 bp):
TATTTTCATAGTATTATATAATATGATTTTAGTAAATTCATATAAGAATATTGATTATTAGAATT
TTATTAAATTATATATTTTAACTAAAATATATTTAATATTAATTATTTTAAATTA
Found at i:43437119 original size:16 final size:16
Alignment explanation
Indices: 43437085--43437129 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
43437075 ATTATTAAGA
43437085 ATTTTATTAAATTATAT
1 ATTTTATTAAA-TATAT
43437102 ATTTTAATTAAA-ATAT
1 ATTTT-ATTAAATATAT
43437118 ATTTTATTAAAT
1 ATTTTATTAAAT
43437130 CATTTATCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.23
16 9 0.35
17 5 0.19
18 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTATTAAATATAT
Found at i:43437300 original size:16 final size:16
Alignment explanation
Indices: 43437281--43437329 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
43437271 TTGCTATTAT
* *
43437281 ACCTCTATTCCATTAC
1 ACCTCTAATCCAATAC
43437297 ACCTCTAATCCAATAC
1 ACCTCTAATCCAATAC
43437313 ACCTCTAATCCAATAC
1 ACCTCTAATCCAATAC
43437329 A
1 A
43437330 ACAAACCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
ACCTCTAATCCAATAC
Found at i:43440663 original size:18 final size:18
Alignment explanation
Indices: 43440624--43440665 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
43440614 ATGACTTATG
*
43440624 AATTAATTTAATTTCTATT
1 AATT-ATTTAATTACTATT
43440643 AATTATTTAATTAACTA-T
1 AATTATTTAATT-ACTATT
43440661 AATTA
1 AATTA
43440666 AATAATTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTATTTAATTACTATT
Found at i:43444833 original size:41 final size:41
Alignment explanation
Indices: 43444735--43444896 Score: 234
Period size: 41 Copynumber: 3.9 Consensus size: 41
43444725 GTATATCCAA
* * *
43444735 GGGTACCGTAGTACAAACAGGGGCACGTATGTGCAATTTAGG
1 GGGTACCGAAGTACAAACAAGGGCACATATGTGCAATTTA-G
* *
43444777 GGGTACCAAAGTACAAAAAAGGGCACATATGTGCAATTTAG
1 GGGTACCGAAGTACAAACAAGGGCACATATGTGCAATTTAG
*
43444818 GGGTACCGAAGTACAAACAAGGGCACATATGTGCAATTCAG
1 GGGTACCGAAGTACAAACAAGGGCACATATGTGCAATTTAG
* * *
43444859 GGGTACCGAAGTACAAATAGGGGCACATATGTGTAATT
1 GGGTACCGAAGTACAAACAAGGGCACATATGTGCAATT
43444897 CAACATTATT
Statistics
Matches: 109, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 74 0.68
42 35 0.32
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.20
Consensus pattern (41 bp):
GGGTACCGAAGTACAAACAAGGGCACATATGTGCAATTTAG
Found at i:43450889 original size:23 final size:23
Alignment explanation
Indices: 43450863--43450906 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
43450853 AAAAAATTAT
*
43450863 AAATTCATAACGAAAAAATCTGG
1 AAATTCATAAAGAAAAAATCTGG
**
43450886 AAATTTTTAAAGAAAAAATCT
1 AAATTCATAAAGAAAAAATCT
43450907 TTTGACTTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (23 bp):
AAATTCATAAAGAAAAAATCTGG
Found at i:43452144 original size:25 final size:25
Alignment explanation
Indices: 43452114--43452164 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
43452104 ATTATTATTA
* *
43452114 ATGATTAGTTTAAGTTAA-TTAAATT
1 ATGATTAGGTT-ACTTAAGTTAAATT
43452139 ATGATTAGGTTACTTAAGTTAAATT
1 ATGATTAGGTTACTTAAGTTAAATT
43452164 A
1 A
43452165 ATTAAGCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (25 bp):
ATGATTAGGTTACTTAAGTTAAATT
Found at i:43453624 original size:28 final size:28
Alignment explanation
Indices: 43453576--43453707 Score: 149
Period size: 28 Copynumber: 4.7 Consensus size: 28
43453566 AACATGACAG
* *
43453576 GAAAGAATAAGCTTTTGTGGTGAACTAT
1 GAAAGAATAAACCTTTGTGGTGAACTAT
* *
43453604 GAAAGAATAAACATTTATGGTGAACTAT
1 GAAAGAATAAACCTTTGTGGTGAACTAT
* * *
43453632 GAAAGAATAAGCCTTTGGGGAGAA-TAAT
1 GAAAGAATAAACCTTTGTGGTGAACT-AT
* **
43453660 GAAAGAACAAACCTTTGTGGCAAACTAT
1 GAAAGAATAAACCTTTGTGGTGAACTAT
*
43453688 GAAAGAATAAGCCTTTGTGG
1 GAAAGAATAAACCTTTGTGG
43453708 CGGACTCCGT
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
27 1 0.01
28 85 0.98
29 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (28 bp):
GAAAGAATAAACCTTTGTGGTGAACTAT
Found at i:43453662 original size:56 final size:56
Alignment explanation
Indices: 43453576--43453704 Score: 170
Period size: 56 Copynumber: 2.3 Consensus size: 56
43453566 AACATGACAG
* * * * **
43453576 GAAAGAATAAGCTTTTGTGGTGAACTATGAAAGAATAAACATTTATGGTGAACTAT
1 GAAAGAATAAGCCTTTGGGGAGAACTATGAAAGAACAAACATTTATGGCAAACTAT
* *
43453632 GAAAGAATAAGCCTTTGGGGAGAA-TAATGAAAGAACAAACCTTTGTGGCAAACTAT
1 GAAAGAATAAGCCTTTGGGGAGAACT-ATGAAAGAACAAACATTTATGGCAAACTAT
43453688 GAAAGAATAAGCCTTTG
1 GAAAGAATAAGCCTTTG
43453705 TGGCGGACTC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
55 1 0.02
56 63 0.98
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.26
Consensus pattern (56 bp):
GAAAGAATAAGCCTTTGGGGAGAACTATGAAAGAACAAACATTTATGGCAAACTAT
Found at i:43455500 original size:25 final size:25
Alignment explanation
Indices: 43455472--43455531 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
43455462 TCACAGCTTG
*
43455472 TGTGAGCATTTAC-AGTTATAGCTCA
1 TGTGAGCATTT-CTAGTTATAACTCA
* **
43455497 TGTGAGCAATTCTAGTTATAACTTG
1 TGTGAGCATTTCTAGTTATAACTCA
43455522 TGTGAGCATT
1 TGTGAGCATT
43455532 ATTTCCGTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 1 0.03
25 28 0.97
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (25 bp):
TGTGAGCATTTCTAGTTATAACTCA
Found at i:43463480 original size:16 final size:16
Alignment explanation
Indices: 43463456--43463487 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
43463446 AATGTGTGGT
43463456 ACATCGAGTCTCCGGC
1 ACATCGAGTCTCCGGC
*
43463472 ACATTGAGTCTCCGGC
1 ACATCGAGTCTCCGGC
43463488 GCTGATCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.34, G:0.25, T:0.22
Consensus pattern (16 bp):
ACATCGAGTCTCCGGC
Found at i:43470512 original size:18 final size:18
Alignment explanation
Indices: 43470472--43470527 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
43470462 TTCTGTGATA
*
43470472 AATAACATTTTGAAAATT
1 AATAACATTTTGAAAATG
*
43470490 TATAACATTTTGAAAGA-G
1 AATAACATTTTGAAA-ATG
* *
43470508 AATAAC-TTATGAATATG
1 AATAACATTTTGAAAATG
43470525 AAT
1 AAT
43470528 CACGTTTGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 1 0.03
17 10 0.32
18 19 0.61
19 1 0.03
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (18 bp):
AATAACATTTTGAAAATG
Found at i:43473252 original size:37 final size:37
Alignment explanation
Indices: 43473202--43473280 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
43473192 TTATTACGAA
* * *
43473202 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
43473239 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
43473276 GTCTT
1 GTCTT
43473281 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:43473486 original size:47 final size:47
Alignment explanation
Indices: 43473399--43473715 Score: 501
Period size: 47 Copynumber: 6.7 Consensus size: 47
43473389 CCCTTCGGGA
* * * * * * *
43473399 CTTATCACATTTATACACTTTCACATCCACCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
43473446 CCTGTGACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43473493 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43473540 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43473587 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
43473634 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
43473681 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
43473716 AGAATCCTAA
Statistics
Matches: 253, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
46 1 0.00
47 252 1.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:43475697 original size:13 final size:13
Alignment explanation
Indices: 43475679--43475703 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43475669 TACTAAATTT
43475679 TCATGGATTCAAA
1 TCATGGATTCAAA
43475692 TCATGGATTCAA
1 TCATGGATTCAA
43475704 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAA
Found at i:43476825 original size:39 final size:39
Alignment explanation
Indices: 43476782--43477567 Score: 353
Period size: 39 Copynumber: 20.5 Consensus size: 39
43476772 AAAAACTAAT
* **
43476782 GGTCGTGATCGTAAATCAGTGGTTCGTAAAAAAGCCAAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* *
43476821 GGTCGTGATCGTAAATCAATGGACCGTAAGAAAGTCAAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* *** * * **
43476860 GGTCGTGATCGTAAATTAGCAGACAGTAAGAAAGCTGAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* *
43476899 GGTCTTGATC----AT-AA---ACCGTAAAAAGGCCAAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* * * * * *
43476930 GGCCGTGATCGTAAATCAATGGACCATGAGAAAGTCGAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* * * * ***
43476969 GGTCGTGACCATAAATAAATGGACCATAAGAAAA-TTGAA
1 GGTCGTGATCGTAAATCAATGGACCGTAA-AAAAGCCAAA
* * * * * **
43477008 GGTCATGATCGTAAATTAACGGACTGTAAGAAATTC---
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* * * * * * * * * *
43477044 GGTCATGATCATAAATTAGCT-TATCATAAGAAAGTCGAA
1 GGTCGTGATCGTAAATCA-ATGGACCGTAAAAAAGCCAAA
* * *
43477083 GGTCGTGATCGTAAATCAACGGACCGTAAGAAAGCCGAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* ** * *
43477122 GGTCGTGATTGTAAATCAATGGACCGTAGGAAACCCGAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* * * * * *
43477161 GGACATGATC-TCAAATCAATAGTCCGTAAGAAAGCCGAA
1 GGTCGTGATCGT-AAATCAATGGACCGTAAAAAAGCCAAA
* * * * * * * *
43477200 GATCATGATCGTAAATTAGTGGGCCATAAGAAAGCCGAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* * * *** * *
43477239 GGTCATGATCATAAATTAACATACCGTAAGAAAG-TAGAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCA-AA
* * * *
43477278 GGTCGTGATCATAAATCAGTGGACTGTAAGAAAGCCAAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* * * *** * **
43477317 GGTCGTGATCATAAATCAACGAATTTTAAGAAAGTTAAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* * * * * *
43477356 GGTCATGATCGTGATTCAGTGAACCGTAAGAAAGCCAAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* * * * * * *
43477395 GGTCATGATCATAAATCAACGAACTGTAAGAAAGTCAAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* * * ** * *
43477434 GGTTGTAATCGTGAATCAGCGGACCGTAAGAAATCCAAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* * *
43477473 GGTCATGATCGTAAATCAATGGACC-TAAGAAAGCCGAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* * * * * *
43477511 GGTCGTGATCGTGAATCAACGAATCGTAAGAAAGCTAAA
1 GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
* *
43477550 GGTCATGATCATAAATCA
1 GGTCGTGATCGTAAATCA
43477568 GCGAACCGTG
Statistics
Matches: 577, Mismatches: 150, Indels: 40
0.75 0.20 0.05
Matches are distributed among these distances:
31 20 0.03
34 1 0.00
35 4 0.01
36 29 0.05
38 35 0.06
39 483 0.84
40 5 0.01
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.21
Consensus pattern (39 bp):
GGTCGTGATCGTAAATCAATGGACCGTAAAAAAGCCAAA
Found at i:43476894 original size:78 final size:78
Alignment explanation
Indices: 43476807--43477567 Score: 510
Period size: 78 Copynumber: 9.9 Consensus size: 78
43476797 TCAGTGGTTC
* * * *
43476807 GTAAAAAAGCCAAAGGTCGTGATCGTAAATCAATGGACCGTAAGAAAGTCAAAGGTCGTGATCGT
1 GTAAGAAAGCCGAAGGTCGTGATCGTAAATCAATGGACCGTAAGAAAGCCAAAGGTCATGATCGT
* * *
43476872 AAATTAGCAGACA
66 AAATCAACGGACA
* * * *
43476885 GTAAGAAAGCTGAAGGTCTTGATC----AT-AA---ACCGTAA-AAAGGCCAAAGGCCGTGATCG
1 GTAAGAAAGCCGAAGGTCGTGATCGTAAATCAATGGACCGTAAGAAA-GCCAAAGGTCATGATCG
*
43476941 TAAATCAATGGACCA
65 TAAATCAACGGA-CA
* * * * * * ****
43476956 -TGAGAAAGTCGAAGGTCGTGACCATAAATAAATGGACCATAAGAAAATTGAAGGTCATGATCGT
1 GTAAGAAAGCCGAAGGTCGTGATCGTAAATCAATGGACCGTAAGAAAGCCAAAGGTCATGATCGT
* *
43477020 AAATTAACGGACT
66 AAATCAACGGACA
** * * * * * * * * * *
43477033 GTAAGAAATTC---GGTCATGATCATAAATTAGCT-TATCATAAGAAAGTCGAAGGTCGTGATCG
1 GTAAGAAAGCCGAAGGTCGTGATCGTAAATCA-ATGGACCGTAAGAAAGCCAAAGGTCATGATCG
*
43477094 TAAATCAACGGACC
65 TAAATCAACGGACA
* * * * *
43477108 GTAAGAAAGCCGAAGGTCGTGATTGTAAATCAATGGACCGTAGGAAACCCGAAGGACATGATC-T
1 GTAAGAAAGCCGAAGGTCGTGATCGTAAATCAATGGACCGTAAGAAAGCCAAAGGTCATGATCGT
** * *
43477172 CAAATCAATAGTCC
66 -AAATCAACGGACA
* * * * * * * *
43477186 GTAAGAAAGCCGAAGATCATGATCGTAAATTAGTGGGCCATAAGAAAGCCGAAGGTCATGATCAT
1 GTAAGAAAGCCGAAGGTCGTGATCGTAAATCAATGGACCGTAAGAAAGCCAAAGGTCATGATCGT
* ** *
43477251 AAATTAACATACC
66 AAATCAACGGACA
** * * * * *
43477264 GTAAGAAAGTAGAAGGTCGTGATCATAAATCAGTGGACTGTAAGAAAGCCAAAGGTCGTGATCAT
1 GTAAGAAAGCCGAAGGTCGTGATCGTAAATCAATGGACCGTAAGAAAGCCAAAGGTCATGATCGT
* **
43477329 AAATCAACGAATT
66 AAATCAACGGACA
* *** * * * * * *
43477342 TTAAGAAAGTTAAAGGTCATGATCGTGATTCAGTGAACCGTAAGAAAGCCAAAGGTCATGATCAT
1 GTAAGAAAGCCGAAGGTCGTGATCGTAAATCAATGGACCGTAAGAAAGCCAAAGGTCATGATCGT
* *
43477407 AAATCAACGAACT
66 AAATCAACGGACA
* * * * * ** *
43477420 GTAAGAAAGTCAAAGGTTGTAATCGTGAATCAGCGGACCGTAAGAAATCCAAAGGTCATGATCGT
1 GTAAGAAAGCCGAAGGTCGTGATCGTAAATCAATGGACCGTAAGAAAGCCAAAGGTCATGATCGT
*
43477485 AAATCAATGGAC-
66 AAATCAACGGACA
* * * * * * *
43477497 CTAAGAAAGCCGAAGGTCGTGATCGTGAATCAACGAATCGTAAGAAAGCTAAAGGTCATGATCAT
1 GTAAGAAAGCCGAAGGTCGTGATCGTAAATCAATGGACCGTAAGAAAGCCAAAGGTCATGATCGT
43477562 AAATCA
66 AAATCA
43477568 GCGAACCGTG
Statistics
Matches: 544, Mismatches: 120, Indels: 39
0.77 0.17 0.06
Matches are distributed among these distances:
69 3 0.01
70 48 0.09
71 2 0.00
73 2 0.00
74 4 0.01
75 62 0.11
76 1 0.00
77 63 0.12
78 355 0.65
79 4 0.01
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (78 bp):
GTAAGAAAGCCGAAGGTCGTGATCGTAAATCAATGGACCGTAAGAAAGCCAAAGGTCATGATCGT
AAATCAACGGACA
Found at i:43476999 original size:109 final size:109
Alignment explanation
Indices: 43476806--43477022 Score: 283
Period size: 109 Copynumber: 2.0 Consensus size: 109
43476796 ATCAGTGGTT
* * * *
43476806 CGTAAAAAAGCCAAAGGTCGTGATCGTAAATCAATGGACCGTAAGAAAGTCAAAGGTCGTGATCG
1 CGTAAAAAAGCCAAAGGCCGTGATCGTAAATCAATGGACCATAAGAAAGTCAAAGGTCGTGACCA
* * * *
43476871 TAAATTAGCAGACAGTAAGAAAGCTGAAGGTCTTGATCATAAAC
66 TAAATAAACAGACAGTAAGAAAACTGAAGGTCATGATCATAAAC
* * *
43476915 CGTAAAAAGGCCAAAGGCCGTGATCGTAAATCAATGGACCATGAGAAAGTCGAAGGTCGTGACCA
1 CGTAAAAAAGCCAAAGGCCGTGATCGTAAATCAATGGACCATAAGAAAGTCAAAGGTCGTGACCA
** * *
43476980 TAAATAAATGGACCA-TAAGAAAATTGAAGGTCATGATCGTAAA
66 TAAATAAACAGA-CAGTAAGAAAACTGAAGGTCATGATCATAAA
43477023 TTAACGGACT
Statistics
Matches: 92, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
109 90 0.98
110 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (109 bp):
CGTAAAAAAGCCAAAGGCCGTGATCGTAAATCAATGGACCATAAGAAAGTCAAAGGTCGTGACCA
TAAATAAACAGACAGTAAGAAAACTGAAGGTCATGATCATAAAC
Found at i:43483638 original size:13 final size:14
Alignment explanation
Indices: 43483612--43483640 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
43483602 TTAACTAATG
43483612 AATAAAAGGAATAA
1 AATAAAAGGAATAA
43483626 AATAAAA-GAATAA
1 AATAAAAGGAATAA
43483639 AA
1 AA
43483641 GAAACAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (14 bp):
AATAAAAGGAATAA
Found at i:43483651 original size:17 final size:17
Alignment explanation
Indices: 43483629--43483663 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
43483619 GGAATAAAAT
*
43483629 AAAAGAATAAAAGAAAC
1 AAAAGAAGAAAAGAAAC
43483646 AAAAGAAGAAAAGAAAC
1 AAAAGAAGAAAAGAAAC
43483663 A
1 A
43483664 GAGACCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.77, C:0.06, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAAGAAGAAAAGAAAC
Found at i:43484724 original size:23 final size:23
Alignment explanation
Indices: 43484698--43484852 Score: 178
Period size: 23 Copynumber: 7.0 Consensus size: 23
43484688 ACTTTGCCGA
* *
43484698 TCAGACACTTTATGTGTTGTA-C
1 TCAGGCACTTTATGTGTCGTATC
*
43484720 ATCAGGCACTTTATATGTCGTATC
1 -TCAGGCACTTTATGTGTCGTATC
43484744 TCAGGCACTTTATGTGTCGTATC
1 TCAGGCACTTTATGTGTCGTATC
*
43484767 TCAGGCACTTTATGTGTCCTATC
1 TCAGGCACTTTATGTGTCGTATC
43484790 TCAGGCACTTTATGTGTCGTA--
1 TCAGGCACTTTATGTGTCGTATC
** * **
43484811 TCATTCACCTCGTGTGTCGT-T-
1 TCAGGCACTTTATGTGTCGTATC
43484832 TCAGGCAC-TTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
43484853 ACTGATAAGG
Statistics
Matches: 114, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.08
21 22 0.19
23 82 0.72
24 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATC
Found at i:43487583 original size:22 final size:21
Alignment explanation
Indices: 43487558--43487600 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
43487548 GAGTTGGGAA
*
43487558 AGTTAAAATCTGAAATGTCTAG
1 AGTTAAAATAT-AAATGTCTAG
**
43487580 AGTTTTAATATAAATGTCTAG
1 AGTTAAAATATAAATGTCTAG
43487601 CCCTTTGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (21 bp):
AGTTAAAATATAAATGTCTAG
Found at i:43492462 original size:23 final size:23
Alignment explanation
Indices: 43492432--43492507 Score: 113
Period size: 23 Copynumber: 3.4 Consensus size: 23
43492422 GGAAGAGCCA
43492432 ATCAGGCACTTTATGTGTCGTAC
1 ATCAGGCACTTTATGTGTCGTAC
*
43492455 ATCAGGCACTTTATCTGTCGTATC
1 ATCAGGCACTTTATGTGTCGTA-C
43492479 -TCAGGCACTTTATGTGTCGT--
1 ATCAGGCACTTTATGTGTCGTAC
43492499 ATCAGGCAC
1 ATCAGGCAC
43492508 CTCGTGTGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.16
23 40 0.82
24 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAC
Found at i:43496867 original size:57 final size:57
Alignment explanation
Indices: 43496792--43496986 Score: 275
Period size: 57 Copynumber: 3.4 Consensus size: 57
43496782 TGAACACGTC
* *
43496792 AGAAAATGGAAGTCTTTGTGGCATATCTAAGAAAATGGAAGACTTTGTGGCAATCTA
1 AGAAAATGGAAGCCTTTGTGGCATATCTAAGAAAATGGAAGCCTTTGTGGCAATCTA
*
43496849 AGAAAATAGAAGCCTTTGTGGCATATCTAAGAAAATGGAAGCCTTTGTGGCATATCTA
1 AGAAAATGGAAGCCTTTGTGGCATATCTAAGAAAATGGAAGCCTTTGTGGCA-ATCTA
* * * * *
43496907 AGAAAATGGAAGCCTTTGTGGAAAAT-TAAGAAAATTGAAGCCTTTGTGGCGTATTTA
1 AGAAAATGGAAGCCTTTGTGGCATATCTAAGAAAATGGAAGCCTTTGTGGC-AATCTA
* *
43496964 TGAAAATGAAAGCCTTTGTGGCA
1 AGAAAATGGAAGCCTTTGTGGCA
43496987 AATTTTGTAA
Statistics
Matches: 124, Mismatches: 12, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
57 96 0.77
58 28 0.23
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (57 bp):
AGAAAATGGAAGCCTTTGTGGCATATCTAAGAAAATGGAAGCCTTTGTGGCAATCTA
Found at i:43496937 original size:86 final size:86
Alignment explanation
Indices: 43496792--43496986 Score: 302
Period size: 86 Copynumber: 2.3 Consensus size: 86
43496782 TGAACACGTC
* *
43496792 AGAAAATGGAAGTCTTTGTGGCATATCTAAGAAAATGGAAGACTTTGTGGCAATCTAAGAAAATA
1 AGAAAATGGAAGCCTTTGTGGCATATCTAAGAAAATGGAAGACTTTGTGGAAATCTAAGAAAATA
43496857 GAAGCCTTTGTGGCATATCTA
66 GAAGCCTTTGTGGCATATCTA
*
43496878 AGAAAATGGAAGCCTTTGTGGCATATCTAAGAAAATGGAAGCCTTTGTGGAAAAT-TAAGAAAAT
1 AGAAAATGGAAGCCTTTGTGGCATATCTAAGAAAATGGAAGACTTTGTGG-AAATCTAAGAAAAT
* * *
43496942 TGAAGCCTTTGTGGCGTATTTA
65 AGAAGCCTTTGTGGCATATCTA
* *
43496964 TGAAAATGAAAGCCTTTGTGGCA
1 AGAAAATGGAAGCCTTTGTGGCA
43496987 AATTTTGTAA
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
86 97 0.97
87 3 0.03
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (86 bp):
AGAAAATGGAAGCCTTTGTGGCATATCTAAGAAAATGGAAGACTTTGTGGAAATCTAAGAAAATA
GAAGCCTTTGTGGCATATCTA
Found at i:43496991 original size:29 final size:29
Alignment explanation
Indices: 43496792--43496986 Score: 286
Period size: 29 Copynumber: 6.8 Consensus size: 29
43496782 TGAACACGTC
*
43496792 AGAAAATGGAAGTCTTTGTGGCATATCTA
1 AGAAAATGGAAGCCTTTGTGGCATATCTA
*
43496821 AGAAAATGGAAGACTTTGTGGCA-ATCTA
1 AGAAAATGGAAGCCTTTGTGGCATATCTA
*
43496849 AGAAAATAGAAGCCTTTGTGGCATATCTA
1 AGAAAATGGAAGCCTTTGTGGCATATCTA
43496878 AGAAAATGGAAGCCTTTGTGGCATATCTA
1 AGAAAATGGAAGCCTTTGTGGCATATCTA
* *
43496907 AGAAAATGGAAGCCTTTGTGGAAAAT-TA
1 AGAAAATGGAAGCCTTTGTGGCATATCTA
* * *
43496935 AGAAAATTGAAGCCTTTGTGGCGTATTTA
1 AGAAAATGGAAGCCTTTGTGGCATATCTA
* *
43496964 TGAAAATGAAAGCCTTTGTGGCA
1 AGAAAATGGAAGCCTTTGTGGCA
43496987 AATTTTGTAA
Statistics
Matches: 150, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
28 50 0.33
29 100 0.67
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.28
Consensus pattern (29 bp):
AGAAAATGGAAGCCTTTGTGGCATATCTA
Found at i:43502109 original size:9 final size:10
Alignment explanation
Indices: 43502085--43502109 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
43502075 TTCCATAATT
43502085 ATTTTTTACA
1 ATTTTTTACA
43502095 ATTTTTTACA
1 ATTTTTTACA
43502105 ATTTT
1 ATTTT
43502110 CTAAAGTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTTTACA
Found at i:43502454 original size:23 final size:22
Alignment explanation
Indices: 43502411--43502454 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
43502401 TTCTAAGTCG
43502411 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
43502434 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
43502455 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:43502656 original size:51 final size:52
Alignment explanation
Indices: 43502598--43502733 Score: 206
Period size: 50 Copynumber: 2.7 Consensus size: 52
43502588 TTGGTTCACA
43502598 TAGTAGCCTACACATAGTACTACACATGTGACCATTACCATTC-GATACACG
1 TAGTAGCCTACACATAGTACTACACATGTGACCATTACCATTCTGATACACG
* * * *
43502649 TAGTAGCCTGCACATAGTACTACACATGCGACC--TATCATTCTGGTACACG
1 TAGTAGCCTACACATAGTACTACACATGTGACCATTACCATTCTGATACACG
*
43502699 TAGTAGCCTACACATAGTACTACACACGTGACCAT
1 TAGTAGCCTACACATAGTACTACACATGTGACCAT
43502734 CACTTTCACT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
49 7 0.09
50 37 0.49
51 31 0.41
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (52 bp):
TAGTAGCCTACACATAGTACTACACATGTGACCATTACCATTCTGATACACG
Found at i:43504484 original size:13 final size:13
Alignment explanation
Indices: 43504466--43504493 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
43504456 AAGTCAGTCA
43504466 TGTACCCACTCGT
1 TGTACCCACTCGT
43504479 TGTACCCACTCGT
1 TGTACCCACTCGT
43504492 TG
1 TG
43504494 ATAGACTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.36, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTACCCACTCGT
Found at i:43508916 original size:9 final size:9
Alignment explanation
Indices: 43508898--43508937 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
43508888 TTTAGTTAAA
43508898 AATTAACCG
1 AATTAACCG
*
43508907 AATTACCCG
1 AATTAACCG
*
43508916 AATTAACTG
1 AATTAACCG
43508925 AATTAACCG
1 AATTAACCG
43508934 AATT
1 AATT
43508938 GAATCACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:43509063 original size:18 final size:18
Alignment explanation
Indices: 43509040--43509093 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
43509030 AATTTTTATG
43509040 ATTGGGTTGGATTGGGTA
1 ATTGGGTTGGATTGGGTA
* **
43509058 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGATTGGGTA
*
43509076 CTTGGGTTTGGATTGGGT
1 ATTGGG-TTGGATTGGGT
43509094 TTAGGTGAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.15, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGATTGGGTA
Found at i:43515322 original size:30 final size:31
Alignment explanation
Indices: 43515283--43515342 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
43515273 GGAGGTGGGA
*
43515283 TGGGAAGGGAATAAAAGTTTTAGAGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGAGGAAAAG
* * *
43515314 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGAGGAAAA
43515343 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGAGGAAAAG
Found at i:43515545 original size:9 final size:9
Alignment explanation
Indices: 43515531--43515567 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
43515521 TATAATTTTA
43515531 TATTCGAAT
1 TATTCGAAT
43515540 TATTCGAAT
1 TATTCGAAT
*
43515549 TATTCGAGT
1 TATTCGAAT
43515558 TATTCGAAT
1 TATTCGAAT
43515567 T
1 T
43515568 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:43517121 original size:17 final size:19
Alignment explanation
Indices: 43517085--43517122 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
43517075 AATTCTTTAC
43517085 AATATTTTTTTAGTTATAT
1 AATATTTTTTTAGTTATAT
43517104 AATATTTTTTTAGTTATAT
1 AATATTTTTTTAGTTATAT
43517123 GACTACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
AATATTTTTTTAGTTATAT
Found at i:43517254 original size:15 final size:15
Alignment explanation
Indices: 43517234--43517279 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
43517224 TAAAAAATAA
43517234 AAAAATTAAATTACT
1 AAAAATTAAATTACT
* *
43517249 AAAAATAAAAATAC-
1 AAAAATTAAATTACT
*
43517263 AAACATTAAATT-CT
1 AAAAATTAAATTACT
43517277 AAA
1 AAA
43517280 TTTATGAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
13 1 0.04
14 12 0.48
15 12 0.48
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATTAAATTACT
Found at i:43521724 original size:51 final size:50
Alignment explanation
Indices: 43521565--43521755 Score: 181
Period size: 50 Copynumber: 3.8 Consensus size: 50
43521555 TTATTATCAT
* * * *
43521565 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCA-AACTTT
1 TCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATATC-TA
* * * * *
43521615 TCGGTTCACGTAGTAGCCTGCACATAGTAC-ACACACCTGACCAAAGCCT-
1 TCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATA-TCTA
* * * *
43521664 TCCGGTACACATAGTAGCCTGTACATAGTACTACACATGTGACCATTATCTA
1 T-CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TATCTA
* * *
43521716 TCGATACACGTTGTAGCCTGCACTTAGTACTTCACACGTG
1 TCGATACACGTAGTAGCCTGCACATAGTACTACACACGTG
43521756 TTTATAGGCA
Statistics
Matches: 115, Mismatches: 20, Indels: 11
0.79 0.14 0.08
Matches are distributed among these distances:
49 12 0.10
50 55 0.48
51 46 0.40
52 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.27
Consensus pattern (50 bp):
TCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATATCTA
Found at i:43525066 original size:24 final size:24
Alignment explanation
Indices: 43525039--43525084 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
43525029 GATATCCCTG
* *
43525039 TTTATTTATATTGAAAATATAATA
1 TTTAATTATATTAAAAATATAATA
*
43525063 TTTAATTATTTTAAAAATATAA
1 TTTAATTATATTAAAAATATAA
43525085 ATTATAACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTAATTATATTAAAAATATAATA
Found at i:43530886 original size:20 final size:20
Alignment explanation
Indices: 43530850--43530891 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
43530840 ATTTAATTTA
* *
43530850 ATAATAATTACA-TTTTTTT
1 ATAATAATTAAACTTTTATT
43530869 ATAACTAATTAAACTTTTATT
1 ATAA-TAATTAAACTTTTATT
43530890 AT
1 AT
43530892 TTTTAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
21 8 0.42
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATAATTAAACTTTTATT
Found at i:43531485 original size:20 final size:19
Alignment explanation
Indices: 43531446--43531643 Score: 98
Period size: 20 Copynumber: 10.6 Consensus size: 19
43531436 GACCAAACCA
*
43531446 AAAATATTGTAAAAATTATT
1 AAAA-ATTGTAAAAAATATT
*
43531466 AAAAATTGTAAGAAA-A-T
1 AAAAATTGTAAAAAATATT
43531483 ----ATT-TA-AAAATATT
1 AAAAATTGTAAAAAATATT
*
43531496 TAAAATTGTAAAAAA-A-T
1 AAAAATTGTAAAAAATATT
** *
43531513 AAACAATTG--AAAGTTAAT
1 AAA-AATTGTAAAAAATATT
43531531 AAAAATTGTAAAAGAATATT
1 AAAAATTGTAAAA-AATATT
* *
43531551 AAAAATGGTAAAAAGTATTT
1 AAAAATTGTAAAAAATA-TT
43531571 AAAAA-TGTAAAATAAATTATT
1 AAAAATTGT-AAA-AAA-TATT
* *
43531592 AAAAATTATAAAACATTATGT
1 AAAAATTGTAAAA-AATAT-T
* * *
43531613 AAAATTTGTAAGAATTATT
1 AAAAATTGTAAAAAATATT
*
43531632 AAAAATAGTAAA
1 AAAAATTGTAAA
43531644 TAATTAACAA
Statistics
Matches: 136, Mismatches: 21, Indels: 43
0.68 0.10 0.22
Matches are distributed among these distances:
11 3 0.02
12 3 0.02
13 4 0.03
16 3 0.02
17 13 0.10
18 13 0.10
19 31 0.23
20 38 0.28
21 24 0.18
22 4 0.03
ACGTcount: A:0.59, C:0.01, G:0.08, T:0.32
Consensus pattern (19 bp):
AAAAATTGTAAAAAATATT
Found at i:43531501 original size:9 final size:10
Alignment explanation
Indices: 43531445--43531500 Score: 53
Period size: 10 Copynumber: 5.4 Consensus size: 10
43531435 TGACCAAACC
43531445 AAAAATATTGT
1 AAAAATATT-T
43531456 AAAAAT-TATT
1 AAAAATAT-TT
*
43531466 AAAAAT-TGTA
1 AAAAATAT-TT
43531476 AGAAAATATTT
1 A-AAAATATTT
43531487 AAAAATATTT
1 AAAAATATTT
43531497 AAAA
1 AAAA
43531501 TTGTAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 24 0.62
11 14 0.36
12 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (10 bp):
AAAAATATTT
Done.