Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 182 of 438
Found at i:56140487 original size:26 final size:26
Alignment explanation
Indices: 56140458--56140520 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
56140448 AAAATTAACC
56140458 CTAGGGGTATAATGGTAATTTTGCAT-
1 CTAGGGGTATAATGGTAATTTT-CATA
*
56140484 CTAGGGGTAGAATGGTAATTTTCATA
1 CTAGGGGTATAATGGTAATTTTCATA
56140510 CTTAGGGGTAT
1 C-TAGGGGTAT
56140521 TTTAGTAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 3 0.09
26 22 0.67
27 8 0.24
ACGTcount: A:0.27, C:0.08, G:0.29, T:0.37
Consensus pattern (26 bp):
CTAGGGGTATAATGGTAATTTTCATA
Found at i:56147761 original size:40 final size:40
Alignment explanation
Indices: 56147669--56147818 Score: 132
Period size: 40 Copynumber: 3.8 Consensus size: 40
56147659 AATTGAATGA
* * * *
56147669 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAAT-T
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACATAC
* * *
56147708 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
56147749 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
56147788 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
56147819 ACATGGTTAT
Statistics
Matches: 91, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
38 3 0.03
39 31 0.34
40 54 0.59
41 3 0.03
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:56147832 original size:40 final size:40
Alignment explanation
Indices: 56147708--56147834 Score: 132
Period size: 40 Copynumber: 3.2 Consensus size: 40
56147698 GCTGGAAATT
* * * * *
56147708 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGGTTA
* * ** *
56147748 CATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CATTC
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGGTTA
56147788 TATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGGTTA
56147828 TATCCGG
1 TATCCGG
56147835 TTATTCCGAA
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 67 0.97
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGGTTA
Found at i:56152134 original size:39 final size:40
Alignment explanation
Indices: 56152076--56152176 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
56152066 AAATTGAATG
* *
56152076 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
56152115 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
56152155 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
56152177 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:56152169 original size:40 final size:40
Alignment explanation
Indices: 56152076--56152226 Score: 180
Period size: 40 Copynumber: 3.8 Consensus size: 40
56152066 AAATTGAATG
* * * * *
56152076 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
56152115 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
56152155 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* *
56152195 AAATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
56152227 AAATCGTGAT
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
39 32 0.33
40 62 0.65
41 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:56152241 original size:40 final size:38
Alignment explanation
Indices: 56152072--56152243 Score: 161
Period size: 40 Copynumber: 4.4 Consensus size: 38
56152062 TGAGAAATTG
* *
56152072 AATG-ATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-A
1 AATGTATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCA
* * *
56152111 AAT-TATATCCGGGTTAAGACCCGAAGGCAATTGTGCT
1 AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* *
56152148 AGTAGCTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA
1 AAT-G-TATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* *
56152188 AGTTGTTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCA
1 A-ATG-TATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
56152228 AATCGTGATATCCGGG
1 AAT-GT-ATATCCGGG
56152244 TAAAGTCCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
36 2 0.02
37 4 0.04
38 2 0.02
39 26 0.24
40 74 0.68
41 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (38 bp):
AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
Found at i:56160237 original size:40 final size:39
Alignment explanation
Indices: 56160069--56160239 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
56160059 AGAAATTGAA
* *
56160069 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
56160109 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
56160149 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
56160189 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
56160229 TGATATCCGGG
1 TGATATCCGGG
56160240 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:56165471 original size:50 final size:50
Alignment explanation
Indices: 56165406--56165634 Score: 259
Period size: 50 Copynumber: 4.6 Consensus size: 50
56165396 ATTGTGAGAA
*
56165406 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATGGTTAGGT
* * * * * *
56165456 CGCATGTGTAGTACTAACTGCAGGCTACTATGCGTACTCGATAGGTTCA-AT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGAT-GGTT-AGGT
*
56165507 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-TCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACT-AGATGGTTAGGT
** * * * * *
56165557 CATGTGTGTAGTACAAAGTGCAGGCTACTACATGTACCAAATTGTTAGG-
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATGGTTAGGT
*
56165606 -GCATGTGTAGTACTAAGTGCAGGCTACTA
1 CACATGTGTAGTACTAAGTGCAGGCTACTA
56165635 TACGTACCAG
Statistics
Matches: 150, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
48 25 0.17
49 1 0.01
50 85 0.57
51 38 0.25
52 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATGGTTAGGT
Found at i:56165680 original size:149 final size:150
Alignment explanation
Indices: 56165410--56165680 Score: 357
Period size: 149 Copynumber: 1.8 Consensus size: 150
56165400 TGAGAACACA
* * * *
56165410 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATTGTTAGGTCGCATGTGTAGTACTAACT
1 TGTGTAGTACAAAGTGCAGGCTACTACATGTACCAAATTGTTAGG-CGCATGTGTAGTACTAACT
* * * * * *
56165475 GCAGGCTACTATGCGTACTCGATAGGTTCAATCACGTGTGTAGTACTAAGTGCAGGCTACTACGT
65 GCAGGCTACTATACGTACTCGAGAGGTTCAATCACATGGGTAGTAATAAGTACAGGCTACTACGT
56165540 GTATCAGATGGTTAGGTCATG
130 GTATCAGATGGTTAGGTCATG
*
56165561 TGTGTAGTACAAAGTGCAGGCTACTACATGTACCAAATTGTTAGG-GCATGTGTAGTACTAAGTG
1 TGTGTAGTACAAAGTGCAGGCTACTACATGTACCAAATTGTTAGGCGCATGTGTAGTACTAACTG
* ** * * *
56165625 CAGGCTACTATACGTAC-CAGAGAGTTTCGGTTACATGGGTGGTAATATGTACAGGC
66 CAGGCTACTATACGTACTC-GAGAGGTTCAATCACATGGGTAGTAATAAGTACAGGC
56165681 CATCAGGTAT
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
148 1 0.01
149 60 0.59
151 41 0.40
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (150 bp):
TGTGTAGTACAAAGTGCAGGCTACTACATGTACCAAATTGTTAGGCGCATGTGTAGTACTAACTG
CAGGCTACTATACGTACTCGAGAGGTTCAATCACATGGGTAGTAATAAGTACAGGCTACTACGTG
TATCAGATGGTTAGGTCATG
Found at i:56167537 original size:30 final size:30
Alignment explanation
Indices: 56167482--56167641 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
56167472 ATAGTGAATC
56167482 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
56167511 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
56167541 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
* *
56167570 CGCACACTTAGTGCTGTATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
56167598 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
56167628 CGCACACTTAGTGC
1 CGCACACTTAGTGC
56167642 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 47 0.39
30 47 0.39
31 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:56167574 original size:59 final size:57
Alignment explanation
Indices: 56167482--56167641 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
56167472 ATAGTGAATC
*
56167482 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
*
56167541 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTGTATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
56167598 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
56167642 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 49 0.53
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:56175507 original size:30 final size:30
Alignment explanation
Indices: 56175452--56175611 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
56175442 ATAGTGAATC
56175452 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
56175481 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
56175511 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
*
56175540 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * * *
56175568 AGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
56175598 CGCACACTTAGTGC
1 CGCACACTTAGTGC
56175612 CAATCTTGTC
Statistics
Matches: 118, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 21 0.18
29 48 0.41
30 46 0.39
31 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:56182504 original size:40 final size:40
Alignment explanation
Indices: 56182455--56182662 Score: 231
Period size: 40 Copynumber: 5.2 Consensus size: 40
56182445 TCTTCGGAAT
* * *
56182455 TTAG-CCGGATATAACCACGAGGAC-AATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACGAA-TGCCTTCGGGTC
* * *** * * *
56182494 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCAGGTC
1 TTAGCCCGGATATAACAACTAGCACGAATGCCTTCGGGTC
* *
56182534 TTAGCCCAGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACGAATGCCTTCGGGTC
56182574 TTAGCCCGGATATAACAACTAGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACGAATGCCTTCGGGTC
* * ** *
56182614 TTAGCCCGGATATAATAATTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAACAACTAGCACGAATGCCTTCGGGTC
56182654 TTAGCCCGG
1 TTAGCCCGG
56182663 GTATCATTCA
Statistics
Matches: 141, Mismatches: 26, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.02
40 136 0.96
41 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTAGCACGAATGCCTTCGGGTC
Found at i:56189542 original size:21 final size:21
Alignment explanation
Indices: 56189516--56189558 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
56189506 AACCTAGAGT
56189516 TTCTCAATACTCAAATCTTAC
1 TTCTCAATACTCAAATCTTAC
*
56189537 TTCTCAGTACTCAAATCTTAC
1 TTCTCAATACTCAAATCTTAC
56189558 T
1 T
56189559 CTGAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.28, G:0.02, T:0.40
Consensus pattern (21 bp):
TTCTCAATACTCAAATCTTAC
Found at i:56189722 original size:29 final size:29
Alignment explanation
Indices: 56189666--56189723 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
56189656 CACATTTCTA
* *
56189666 TACTCTGGTCATCAACTGTTTAGAAACTT
1 TACTCTGGTCATCAACTATTTACAAACTT
*
56189695 TACTCTGGTCATCAACTATTTACCAACTT
1 TACTCTGGTCATCAACTATTTACAAACTT
56189724 CATAGATGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (29 bp):
TACTCTGGTCATCAACTATTTACAAACTT
Found at i:56190217 original size:32 final size:31
Alignment explanation
Indices: 56190147--56190221 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
56190137 CATTAAATTC
* * *
56190147 CAACCAAATACAACAAATATAGTATAAAATG
1 CAACCAAAAACAACAAATATAGCATAAAATA
* * *
56190178 CAGCCAAAAACAGCAAATTTAGCATAAAAATA
1 CAACCAAAAACAACAAATATAGCAT-AAAATA
56190210 CAACCAAAAACA
1 CAACCAAAAACA
56190222 TTAATTCTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 20 0.56
32 16 0.44
ACGTcount: A:0.59, C:0.20, G:0.07, T:0.15
Consensus pattern (31 bp):
CAACCAAAAACAACAAATATAGCATAAAATA
Found at i:56190534 original size:21 final size:21
Alignment explanation
Indices: 56190449--56190534 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
56190439 TGCTCTGCTG
* * *
56190449 CCCTTGCTACTACCTCTGCCT
1 CCCTCGCTACTGCCGCTGCCT
*
56190470 CCCTCGCT-CGTGCCTCTGCCT
1 CCCTCGCTAC-TGCCGCTGCCT
* * * *
56190491 CACTCACTGCTGTCGCTGCCT
1 CCCTCGCTACTGCCGCTGCCT
56190512 CCCTCGCTACTGCCGCTGCCT
1 CCCTCGCTACTGCCGCTGCCT
56190533 CC
1 CC
56190535 GTCTCTGCTG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
20 1 0.02
21 51 0.96
22 1 0.02
ACGTcount: A:0.06, C:0.50, G:0.16, T:0.28
Consensus pattern (21 bp):
CCCTCGCTACTGCCGCTGCCT
Found at i:56190545 original size:21 final size:20
Alignment explanation
Indices: 56190480--56190546 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
56190470 CCCTCGCTCG
*
56190480 TGCCTCTGCCTCACTCACTGC
1 TGCCGCTGCCTC-CTCACTGC
* * *
56190501 TGTCGCTGCCTCCCTCGCTAC
1 TGCCGCTGCCT-CCTCACTGC
*
56190522 TGCCGCTGCCTCCGTCTCTGC
1 TGCCGCTGCCTCC-TCACTGC
56190543 TGCC
1 TGCC
56190547 TCCGCTCTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.05
21 34 0.92
22 1 0.03
ACGTcount: A:0.04, C:0.48, G:0.19, T:0.28
Consensus pattern (20 bp):
TGCCGCTGCCTCCTCACTGC
Found at i:56196064 original size:9 final size:9
Alignment explanation
Indices: 56196050--56196294 Score: 76
Period size: 9 Copynumber: 27.0 Consensus size: 9
56196040 TAAGTATAAC
56196050 TAAGTTATG
1 TAAGTTATG
56196059 TAAGTTATG
1 TAAGTTATG
* * *
56196068 ATATGATATA
1 -TAAGTTATG
*
56196078 T-ATTTATG
1 TAAGTTATG
56196086 T-A-TTATG
1 TAAGTTATG
*
56196093 TAAGATATG
1 TAAGTTATG
*
56196102 TAAATTATG
1 TAAGTTATG
56196111 TAAGTTATCG
1 TAAGTTAT-G
*
56196121 GAA-TTATG
1 TAAGTTATG
*
56196129 TAAATTATG
1 TAAGTTATG
* *
56196138 TACGATATG
1 TAAGTTATG
*
56196147 ATATATATCTATG
1 -TA-A-GT-TATG
56196160 T-A-TTATG
1 TAAGTTATG
56196167 TAAGTTATG
1 TAAGTTATG
*
56196176 TAAATTATG
1 TAAGTTATG
* *
56196185 CAAGTTGT-
1 TAAGTTATG
**
56196193 TCATCTTATG
1 T-AAGTTATG
*
56196203 TAAATTATG
1 TAAGTTATG
*
56196212 TAAGATATGATA
1 TAAG-T-T-ATG
* *
56196224 TATACTTCTG
1 TA-AGTTATG
56196234 T-A-TTATG
1 TAAGTTATG
*
56196241 TAAGATATG
1 TAAGTTATG
*
56196250 TAAATTATG
1 TAAGTTATG
* *
56196259 TAAGTTGTT
1 TAAGTTATG
**
56196268 TATCTTATG
1 TAAGTTATG
*
56196277 TAAATTATG
1 TAAGTTATG
*
56196286 TAAGATATG
1 TAAGTTATG
56196295 ATATATATTT
Statistics
Matches: 168, Mismatches: 49, Indels: 38
0.66 0.19 0.15
Matches are distributed among these distances:
7 16 0.10
8 13 0.08
9 110 0.65
10 16 0.10
11 2 0.01
12 6 0.04
13 5 0.03
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:56196176 original size:74 final size:73
Alignment explanation
Indices: 56196067--56196308 Score: 335
Period size: 74 Copynumber: 3.3 Consensus size: 73
56196057 TGTAAGTTAT
* *
56196067 GATATGATATATATTTATGTATTATGTAAGATATGTAAATTATGTAAGTTATCGGA-ATTATGTA
1 GATATGATATATATCTATGTATTATGTAAGATATGTAAATTATGTAAGTTATC--ATCTTATGTA
*
56196131 AATTATGTAC
64 AATTATGTAA
* * *
56196141 GATATGATATATATCTATGTATTATGTAAGTTATGTAAATTATGCAAGTTGTTCATCTTATGTAA
1 GATATGATATATATCTATGTATTATGTAAGATATGTAAATTATGTAAGTT-ATCATCTTATGTAA
56196206 ATTATGTAA
65 ATTATGTAA
* * *
56196215 GATATGATATATA-CTTCTGTATTATGTAAGATATGTAAATTATGTAAGTTGTTTATCTTATGTA
1 GATATGATATATATC-TATGTATTATGTAAGATATGTAAATTATGTAAGTT-ATCATCTTATGTA
56196279 AATTATGTAA
64 AATTATGTAA
*
56196289 GATATGATATATATTTATGT
1 GATATGATATATATCTATGT
56196309 TGATGGGTTA
Statistics
Matches: 152, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
73 2 0.01
74 148 0.97
75 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (73 bp):
GATATGATATATATCTATGTATTATGTAAGATATGTAAATTATGTAAGTTATCATCTTATGTAAA
TTATGTAA
Found at i:56196184 original size:18 final size:18
Alignment explanation
Indices: 56196087--56196288 Score: 85
Period size: 18 Copynumber: 11.0 Consensus size: 18
56196077 ATATTTATGT
*
56196087 ATTATGTAAGATATGTAA
1 ATTATGTAAGTTATGTAA
*
56196105 ATTATGTAAGTTATCG-GA
1 ATTATGTAAGTTAT-GTAA
* *
56196123 ATTATGTAAATTATGTACG
1 ATTATGTAAGTTATGTA-A
*
56196142 A-TATGATATATATCTATGT--
1 ATTATG-TA-A-GT-TATGTAA
56196161 ATTATGTAAGTTATGTAA
1 ATTATGTAAGTTATGTAA
* * *
56196179 ATTATGCAAGTTGT-TCAT
1 ATTATGTAAGTTATGT-AA
* *
56196197 CTTATGTAAATTATGTAA
1 ATTATGTAAGTTATGTAA
* * *
56196215 GATATGATATATACTTCTGT--
1 -AT-T-ATGTA-AGTTATGTAA
*
56196235 ATTATGTAAGATATGTAA
1 ATTATGTAAGTTATGTAA
* * *
56196253 ATTATGTAAGTTGTTTAT
1 ATTATGTAAGTTATGTAA
* *
56196271 CTTATGTAAATTATGTAA
1 ATTATGTAAGTTATGTAA
56196289 GATATGATAT
Statistics
Matches: 135, Mismatches: 31, Indels: 36
0.67 0.15 0.18
Matches are distributed among these distances:
16 10 0.07
17 7 0.05
18 84 0.62
19 11 0.08
20 6 0.04
21 6 0.04
22 11 0.08
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.44
Consensus pattern (18 bp):
ATTATGTAAGTTATGTAA
Found at i:56196681 original size:106 final size:106
Alignment explanation
Indices: 56196562--56197332 Score: 1229
Period size: 106 Copynumber: 7.4 Consensus size: 106
56196552 TTTAAAAAAA
*
56196562 ACAATTTAATTTAATTAGATAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
1 ACAATTTAATTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
56196627 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
66 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
*
56196668 ACAATTTAATTTAATTAGGTAATTTAAAAA-TAAAATAAAAGTAGAC--AATATTTTTCGTGATT
1 ACAATTTAATTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
* * * *
56196730 AAAATAAAATAAAATAACATATTCAAAATAAAACTTTAAAT
66 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
* **
56196771 ACAATTTAGTTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGACAAAACGTTTTTAGTGATT
1 ACAATTTAATTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
56196836 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
66 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
* * * *
56196877 ACAATTTAATTTAATTAGATAATTCAAAAATTAAAATAAAAGTAGATAAAATATTTATAGTGATT
1 ACAATTTAATTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
56196942 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
66 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
* *
56196983 ACAATTTAATTTAATTAGGTAATTTAAAAATT-AAATAAAAGTAGAC--AATATTTTTTGTGATA
1 ACAATTTAATTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
* *
56197045 AAAATAAAATAAAATAAAATATTTAAAATAAAACTTTAAAT
66 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
* *
56197086 ACAATTTAATTTAATTAGATAATTTAAAAATTAAAATAAAAGTAGACAAAACA-TTTTAGTGATT
1 ACAATTTAATTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
56197150 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
66 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
* *
56197191 ATAATTTAATTTAATTAGGTAATTTAAAAA-TAAAATAAAAGTAGACAAAATATTTTTCGTGATT
1 ACAATTTAATTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
* * *
56197255 AAGA-TAAAATAAAATAACATATTCAAAATAAAACTTTAAAT
66 AA-ATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
* *
56197296 ATAATTTAGTTTAATTAGGTAATTTAAAAA-TAAAATA
1 ACAATTTAATTTAATTAGGTAATTTAAAAATTAAAATA
56197333 GAATATTTAA
Statistics
Matches: 614, Mismatches: 43, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
103 164 0.27
104 51 0.08
105 187 0.30
106 212 0.35
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (106 bp):
ACAATTTAATTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
Found at i:56197062 original size:209 final size:208
Alignment explanation
Indices: 56196562--56197332 Score: 1192
Period size: 209 Copynumber: 3.7 Consensus size: 208
56196552 TTTAAAAAAA
*
56196562 ACAATTTAATTTAATTAGATAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
1 ACAATTTAATTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGAC-AAATATTTTTAGTGATT
* * *
56196627 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATT
65 AAAATAAAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGATAATT
* * * * * *
56196692 TAAAAATAAAATAAAAGTAG-ACAATATTTTTCGTGATTAAAATAAAATAAAATAACATATTCAA
130 TAAAAATAAAATAAAAGTAGAAAAATA-TTTTAGTGATTAAATTAAAATCAAATAAAATATTTAA
56196756 AATAAAACTTTAAAT
194 AATAAAACTTTAAAT
*
56196771 ACAATTTAGTTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGACAAA-ACGTTTTTAGTGAT
1 ACAATTTAATTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGACAAATA--TTTTTAGTGAT
* *
56196835 TAAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGATAAT
64 TAAAATAAAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGATAAT
*
56196900 TCAAAAATTAAAATAAAAGTAGATAAAATATTTATAGTGATTAAATTAAAATCAAATAAAATATT
129 TTAAAAA-TAAAATAAAAGTAGA-AAAATATTT-TAGTGATTAAATTAAAATCAAATAAAATATT
56196965 TAAAATAAAACTTTAAAT
191 TAAAATAAAACTTTAAAT
* *
56196983 ACAATTTAATTTAATTAGGTAATTTAAAAATT-AAATAAAAGTAGAC-AATATTTTTTGTGATAA
1 ACAATTTAATTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGACAAATATTTTTAGTGATTA
56197046 AAATAAAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGATAATTT
66 AAATAAAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGATAATTT
*
56197111 AAAAATTAAAATAAAAGTAGACAAAACATTTTAGTGATTAAATTAAAATCAAATAAAATATTTAA
131 AAAAA-TAAAATAAAAGTAGA-AAAATATTTTAGTGATTAAATTAAAATCAAATAAAATATTTAA
56197176 AATAAAACTTTAAAT
194 AATAAAACTTTAAAT
* *
56197191 ATAATTTAATTTAATTAGGTAATTTAAAAA-TAAAATAAAAGTAGACAAAATATTTTTCGTGATT
1 ACAATTTAATTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGAC-AAATATTTTTAGTGATT
* * * * * *
56197255 AAGATAAAATAAAATAACATATTCAAAATAAAACTTTAAATATAATTTAGTTTAATTAGGTAATT
65 AAAATAAAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGATAATT
56197320 TAAAAATAAAATA
130 TAAAAATAAAATA
56197333 GAATATTTAA
Statistics
Matches: 525, Mismatches: 27, Indels: 20
0.92 0.05 0.03
Matches are distributed among these distances:
207 2 0.00
208 95 0.18
209 235 0.45
210 95 0.18
211 18 0.03
212 80 0.15
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (208 bp):
ACAATTTAATTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGACAAATATTTTTAGTGATTA
AAATAAAATAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGATAATTT
AAAAATAAAATAAAAGTAGAAAAATATTTTAGTGATTAAATTAAAATCAAATAAAATATTTAAAA
TAAAACTTTAAAT
Found at i:56197134 original size:315 final size:314
Alignment explanation
Indices: 56196562--56197332 Score: 1339
Period size: 315 Copynumber: 2.5 Consensus size: 314
56196552 TTTAAAAAAA
56196562 ACAATTTAATTTAATTAGATAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
1 ACAATTTAATTTAATTAGATAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
56196627 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATT
66 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATT
* *
56196692 TAAAAATAAAATAAAAGTAGACAATATTTTTCGTGATTAAAATAAAATAAAATAACATATTCAAA
131 TAAAAATAAAATAAAAGTAGACAATATTTTTCGTGATAAAAATAAAATAAAATAAAATATTCAAA
* *
56196757 ATAAAACTTTAAATACAATTTAGTTTAATTAGGTAATTTAAAAATTAAAATAAAAGTAGACAAAA
196 ATAAAACTTTAAATACAATTTAATTTAATTAGATAATTTAAAAATTAAAATAAAAGTAGACAAAA
*
56196822 CGTTTTTAGTGATTAAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
261 C-ATTTTAGTGATTAAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
* * *
56196877 ACAATTTAATTTAATTAGATAATTCAAAAATTAAAATAAAAGTAGATAAAATATTTATAGTGATT
1 ACAATTTAATTTAATTAGATAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
56196942 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATT
66 AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATT
* * *
56197007 TAAAAATTAAATAAAAGTAGACAATATTTTTTGTGATAAAAATAAAATAAAATAAAATATTTAAA
131 TAAAAATAAAATAAAAGTAGACAATATTTTTCGTGATAAAAATAAAATAAAATAAAATATTCAAA
56197072 ATAAAACTTTAAATACAATTTAATTTAATTAGATAATTTAAAAATTAAAATAAAAGTAGACAAAA
196 ATAAAACTTTAAATACAATTTAATTTAATTAGATAATTTAAAAATTAAAATAAAAGTAGACAAAA
56197137 CATTTTAGTGATTAAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
261 CATTTTAGTGATTAAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
* * *
56197191 ATAATTTAATTTAATTAGGTAATTTAAAAA-TAAAATAAAAGTAGACAAAATATTTTTCGTGATT
1 ACAATTTAATTTAATTAGATAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
* * * * *
56197255 AAGA-TAAAATAAAATAACATATTCAAAATAAAACTTTAAATATAATTTAGTTTAATTAGGTAAT
66 AA-ATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAAT
56197319 TTAAAAATAAAATA
130 TTAAAAATAAAATA
56197333 GAATATTTAA
Statistics
Matches: 432, Mismatches: 23, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
313 101 0.23
314 80 0.19
315 251 0.58
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (314 bp):
ACAATTTAATTTAATTAGATAATTTAAAAATTAAAATAAAAGTAGACAAAATATTTTTAGTGATT
AAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATT
TAAAAATAAAATAAAAGTAGACAATATTTTTCGTGATAAAAATAAAATAAAATAAAATATTCAAA
ATAAAACTTTAAATACAATTTAATTTAATTAGATAATTTAAAAATTAAAATAAAAGTAGACAAAA
CATTTTAGTGATTAAATTAAAATCAAATAAAATATTTAAAATAAAACTTTAAAT
Found at i:56202974 original size:25 final size:25
Alignment explanation
Indices: 56202945--56202992 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
56202935 TTATAATATG
* * *
56202945 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
56202970 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
56202993 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:56203061 original size:20 final size:20
Alignment explanation
Indices: 56203036--56203094 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
56203026 TAAATATGGT
56203036 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
*
56203056 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAA
56203076 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
56203095 GGTAATCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:56203076 original size:11 final size:11
Alignment explanation
Indices: 56203040--56203094 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
56203030 TATGGTATGT
56203040 ATGATATGCAC
1 ATGATATGCAC
* *
56203051 ATGAAATG--T
1 ATGATATGCAC
56203060 ATGATATGCAC
1 ATGATATGCAC
*
56203071 ATGATATG--T
1 ATGATATGCAC
56203080 ATGATATGCAC
1 ATGATATGCAC
56203091 ATGA
1 ATGA
56203095 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:56203172 original size:24 final size:24
Alignment explanation
Indices: 56203145--56203287 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
56203135 GAGGAAGTGA
56203145 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
56203169 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
56203193 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
56203216 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
56203240 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
56203264 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
56203288 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:56203238 original size:47 final size:47
Alignment explanation
Indices: 56203145--56203287 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
56203135 GAGGAAGTGA
56203145 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
56203193 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
56203240 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
56203288 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:56203261 original size:71 final size:72
Alignment explanation
Indices: 56203145--56203288 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
56203135 GAGGAAGTGA
*
56203145 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
56203208 CCAGTTAT
65 CCAGTTAT
** * *
56203216 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
56203281 CAGTTAT
66 CAGTTAT
56203288 A
1 A
56203289 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:56203514 original size:31 final size:31
Alignment explanation
Indices: 56203479--56203542 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
56203469 CGTTTACAGT
56203479 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
56203510 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
56203541 AA
1 AA
56203543 TATGAAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:56209576 original size:25 final size:25
Alignment explanation
Indices: 56209547--56209594 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
56209537 TTATAATATG
* * *
56209547 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
56209572 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
56209595 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:56209663 original size:20 final size:20
Alignment explanation
Indices: 56209638--56209696 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
56209628 TAAATATGGT
56209638 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
*
56209658 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAA
56209678 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
56209697 GGTAATCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:56209678 original size:11 final size:11
Alignment explanation
Indices: 56209642--56209696 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
56209632 TATGGTATGT
56209642 ATGATATGCAC
1 ATGATATGCAC
* *
56209653 ATGAAATG--T
1 ATGATATGCAC
56209662 ATGATATGCAC
1 ATGATATGCAC
*
56209673 ATGATATG--T
1 ATGATATGCAC
56209682 ATGATATGCAC
1 ATGATATGCAC
56209693 ATGA
1 ATGA
56209697 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:56209774 original size:24 final size:24
Alignment explanation
Indices: 56209747--56209888 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
56209737 GAGGAAGTGA
56209747 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
56209771 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
56209795 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
56209818 AAAAGGGCTTATG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
56209841 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
56209865 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
56209889 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
22 9 0.08
23 24 0.22
24 65 0.60
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:56209861 original size:70 final size:72
Alignment explanation
Indices: 56209747--56209889 Score: 211
Period size: 70 Copynumber: 2.0 Consensus size: 72
56209737 GAGGAAGTGA
*
56209747 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
56209810 CCAGTTAT
65 CCAGTTAT
** * *
56209818 AAAAGGGCTTATG-CCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
56209882 CAGTTAT
66 CAGTTAT
56209889 A
1 A
56209890 TGATAAAGCA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
70 40 0.62
71 25 0.38
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:56210145 original size:31 final size:31
Alignment explanation
Indices: 56210080--56210173 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
56210070 CGTTTACAGT
56210080 AAAGGCTTCGGCCCAGTAATATGAAAT-TGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
56210110 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
56210141 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
56210172 AA
1 AA
56210174 TATGAAAAGG
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
30 27 0.44
31 35 0.56
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:56210921 original size:8 final size:8
Alignment explanation
Indices: 56210908--56210939 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
56210898 ATTATACTTT
56210908 AAACCCTA
1 AAACCCTA
56210916 AAACCCTA
1 AAACCCTA
56210924 AAACCCT-
1 AAACCCTA
56210931 AAACCCTA
1 AAACCCTA
56210939 A
1 A
56210940 GCCCATCCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (8 bp):
AAACCCTA
Found at i:56210934 original size:15 final size:16
Alignment explanation
Indices: 56210908--56210939 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
56210898 ATTATACTTT
56210908 AAACCCTAAAACCCTA
1 AAACCCTAAAACCCTA
56210924 AAACCCT-AAACCCTA
1 AAACCCTAAAACCCTA
56210939 A
1 A
56210940 GCCCATCCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (16 bp):
AAACCCTAAAACCCTA
Found at i:56212351 original size:40 final size:40
Alignment explanation
Indices: 56212306--56212473 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
56212296 CGGAATATAA
56212306 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
56212346 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
56212386 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
56212426 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
56212466 CCGGATAT
1 CCGGATAT
56212474 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:56220348 original size:40 final size:40
Alignment explanation
Indices: 56220303--56220470 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
56220293 CGGAATATAA
56220303 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
56220343 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
56220383 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
56220423 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
56220463 CCGGATAT
1 CCGGATAT
56220471 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:56223048 original size:10 final size:9
Alignment explanation
Indices: 56223028--56223058 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
56223018 TACAAGAAGC
56223028 GCCGCTAAA
1 GCCGCTAAA
56223037 GCCGCTTAAA
1 GCCGC-TAAA
56223047 GCCGCTAAA
1 GCCGCTAAA
56223056 GCC
1 GCC
56223059 CTACAGACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (9 bp):
GCCGCTAAA
Found at i:56223324 original size:153 final size:153
Alignment explanation
Indices: 56223047--56223364 Score: 489
Period size: 153 Copynumber: 2.1 Consensus size: 153
56223037 GCCGCTTAAA
*
56223047 GCCGCTAAAGCC-CTACAGACTCACCAATGCACGACGTCGTATTTCTCAAAACTTTATGGCGTTT
1 GCCGCTAAAGCCTCTACAGACTCACCAATGCACGACGTAGTATTTCTCAAAACTTTATGGCGTTT
* *
56223111 TAGACAACCGCCGCTAATGCTTCACCTATTGTGGCATTTTATAAAAAACACCGTGAATTCTCGAT
66 TAGACAACCGCCACTAATGCTTCACCTATTGTGGCATTTTATAAAAAACACCCTGAATTCTCGAT
* *
56223176 ATATTGCGACGTTTACAGGAAGC
131 ATATTGAGACATTTACAGGAAGC
*
56223199 GCCGCTAAAGCCTCTACAG-CTCACCAATGCACGACGTAGTATTTCTCAAAACTTTTGTGGCGTT
1 GCCGCTAAAGCCTCTACAGACTCACCAATGCACGACGTAGTATTTCTCAAAAC-TTTATGGCGTT
* **
56223263 TTAGACAACCGCCACTAATGCTTCACCTATTGTGGCATTTTATAAAAAACGCCACT-AATTCTTT
65 TTAGACAACCGCCACTAATGCTTCACCTATTGTGGCATTTTATAAAAAACACC-CTGAATTCTCG
* *
56223327 ATATATTGAGGCATTTTCAGGAAGC
129 ATATATTGAGACATTTACAGGAAGC
*
56223352 GCCGCTAATGCCT
1 GCCGCTAAAGCCT
56223365 ATATAGCTGA
Statistics
Matches: 151, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
152 44 0.29
153 106 0.70
154 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (153 bp):
GCCGCTAAAGCCTCTACAGACTCACCAATGCACGACGTAGTATTTCTCAAAACTTTATGGCGTTT
TAGACAACCGCCACTAATGCTTCACCTATTGTGGCATTTTATAAAAAACACCCTGAATTCTCGAT
ATATTGAGACATTTACAGGAAGC
Found at i:56223400 original size:153 final size:152
Alignment explanation
Indices: 56223047--56223400 Score: 453
Period size: 153 Copynumber: 2.3 Consensus size: 152
56223037 GCCGCTTAAA
* * *
56223047 GCCGCTAAAGCC-CTACAGACTCACCAATGCACGACGTCGTATTTCTCAAAACTTTATGGCGTTT
1 GCCGCTAAAGCCTATACAG-CTCACCAATACACGACATCGTATTTCTCAAAACTTTATGGCGTTT
* *
56223111 TAGACAACCGCCGCTAATGCTTCACCTATTGTGGCATTTTATAAAAAACACCGTGAATTCTCGAT
65 TAGACAACCGCCACTAATGCTTCACCTATTGTGGCATTTTATAAAAAACACCCTGAATTCTCGAT
* *
56223176 ATATTGCGACGTTTACAGGAAGC
130 ATATTGAGACATTTACAGGAAGC
* * * * *
56223199 GCCGCTAAAGCCTCTACAGCTCACCAATGCACGACGTAGTATTTCTCAAAACTTTTGTGGCGTTT
1 GCCGCTAAAGCCTATACAGCTCACCAATACACGACATCGTATTTCTCAAAAC-TTTATGGCGTTT
* **
56223264 TAGACAACCGCCACTAATGCTTCACCTATTGTGGCATTTTATAAAAAACGCCACT-AATTCTTTA
65 TAGACAACCGCCACTAATGCTTCACCTATTGTGGCATTTTATAAAAAACACC-CTGAATTCTCGA
* *
56223328 TATATTGAGGCATTTTCAGGAAGC
129 TATATTGAGACATTTACAGGAAGC
* * * * *
56223352 GCCGCTAATGCCTATATAGCTGAGCAATACACGGCATCGT-TTTCCTCAA
1 GCCGCTAAAGCCTATACAGCTCACCAATACACGACATCGTATTT-CTCAA
56223401 CATTTTTGCG
Statistics
Matches: 178, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
152 47 0.26
153 130 0.73
154 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (152 bp):
GCCGCTAAAGCCTATACAGCTCACCAATACACGACATCGTATTTCTCAAAACTTTATGGCGTTTT
AGACAACCGCCACTAATGCTTCACCTATTGTGGCATTTTATAAAAAACACCCTGAATTCTCGATA
TATTGAGACATTTACAGGAAGC
Found at i:56228311 original size:40 final size:40
Alignment explanation
Indices: 56228226--56228376 Score: 132
Period size: 40 Copynumber: 3.8 Consensus size: 40
56228216 AATTGAATGA
* * * **
56228226 TATCCGGGCTAA-ATCCCGAAGACAATTATGCTG-GAAATTT
1 TATCCGGGCTAAGA-CCCGAAGGCAATTGTGC-GAGACATAC
* * *
56228266 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
56228307 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
56228346 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
56228377 ACATGGTTAT
Statistics
Matches: 91, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 77 0.85
41 5 0.05
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:56228390 original size:40 final size:40
Alignment explanation
Indices: 56228266--56228392 Score: 132
Period size: 40 Copynumber: 3.2 Consensus size: 40
56228256 CTGGAAATTT
* * * * *
56228266 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGGTTA
* * ** *
56228306 CATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CATTC
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGGTTA
56228346 TATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGGTTA
56228386 TATCCGG
1 TATCCGG
56228393 TTATGTTCCG
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 67 0.97
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGGTTA
Found at i:56230831 original size:47 final size:46
Alignment explanation
Indices: 56230768--56230891 Score: 135
Period size: 47 Copynumber: 2.7 Consensus size: 46
56230758 TCTCGTAGCT
*
56230768 AATGCATGTCCCAGACATGTCTTACACTAGATCTCGT-CTGAAT-GCC
1 AATGCATGTCCTAGACATGTCTTACACTAGATCTCGTACTG--TGGCC
* * * *
56230814 AATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCGTAGTGTGGTC
1 AATG-CATGTCCTAGACAT-GTCTTACACTAGATCTCGTACTGTGGCC
* *
56230862 GATGCATATCCTAGACATGTCTTACACTAG
1 AATGCATGTCCTAGACATGTCTTACACTAG
56230892 CACACACACA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
46 15 0.23
47 27 0.41
48 22 0.33
49 2 0.03
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (46 bp):
AATGCATGTCCTAGACATGTCTTACACTAGATCTCGTACTGTGGCC
Found at i:56232581 original size:45 final size:44
Alignment explanation
Indices: 56232517--56232622 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 44
56232507 TCTGAACTCA
* * * *
56232517 TTGAGTTGGT-CTAGGTTCATGATATATATGAG-GCATCCGAGCTAG
1 TTGAGTTGGTCCGA-GTTCAT--TATAGATGAGAGCATCCAAACTAG
* * *
56232562 TTGAGTTGGTCCGAGTTCATTATGGATGCGAGCATCCAAACTTG
1 TTGAGTTGGTCCGAGTTCATTATAGATGAGAGCATCCAAACTAG
56232606 TTGAGTTGGTCCGAGTT
1 TTGAGTTGGTCCGAGTT
56232623 TATAATGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
43 7 0.13
44 27 0.52
45 16 0.31
46 2 0.04
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (44 bp):
TTGAGTTGGTCCGAGTTCATTATAGATGAGAGCATCCAAACTAG
Found at i:56242837 original size:20 final size:20
Alignment explanation
Indices: 56242812--56242854 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
56242802 GAAATTTTTT
56242812 TTATTTATTTTAGGATAACC
1 TTATTTATTTTAGGATAACC
56242832 TTATTTATTTTAGGATAACC
1 TTATTTATTTTAGGATAACC
56242852 TTA
1 TTA
56242855 CTCTATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (20 bp):
TTATTTATTTTAGGATAACC
Found at i:56253070 original size:49 final size:49
Alignment explanation
Indices: 56253014--56253188 Score: 251
Period size: 49 Copynumber: 3.5 Consensus size: 49
56253004 CTAGTACGCA
*
56253014 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCCGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
* * * * * * *
56253063 TAGTAGCCTGCACTTAGTACTACATACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATCCGGTACACG
56253114 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
*
56253163 TAGTAGCCTGCACTTAGTATTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
56253189 CGTGACCTCA
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
49 64 0.59
50 6 0.06
51 38 0.35
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACG
Found at i:56253137 original size:100 final size:100
Alignment explanation
Indices: 56253007--56253193 Score: 347
Period size: 100 Copynumber: 1.9 Consensus size: 100
56252997 AGGCTATCTA
56253007 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCCGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCCGTACACGTAGTAGCCT
*
56253072 GCACTTAGTACTACATACGTGATCGAAGTTATCGG
66 GCACTTAGTACTACACACGTGATCGAAGTTATCGG
*
56253107 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCT
1 GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCCGTACACGTAGTAGCCT
*
56253172 GCACTTAGTATTACACACGTGA
66 GCACTTAGTACTACACACGTGA
56253194 CCTCACAATA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 84 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (100 bp):
GTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCCGTACACGTAGTAGCCT
GCACTTAGTACTACACACGTGATCGAAGTTATCGG
Found at i:56256447 original size:48 final size:48
Alignment explanation
Indices: 56256387--56256511 Score: 196
Period size: 48 Copynumber: 2.6 Consensus size: 48
56256377 ATATCCGGAT
* *
56256387 ATGGTCTTACATGGGATCACATGTCGATGCCAATGCCATGTCCTACAC
1 ATGGTCTTACATGGGATCATATGTCGATGCCAATGCCATGTCCCACAC
* * *
56256435 ATGGTCTTACATGGGATCATAAGTCGATGCCAATGCCATGTCCCAGAT
1 ATGGTCTTACATGGGATCATATGTCGATGCCAATGCCATGTCCCACAC
*
56256483 ATGGTCTTACATGGGATCATATATCGATG
1 ATGGTCTTACATGGGATCATATGTCGATG
56256512 TCGATAGCCC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (48 bp):
ATGGTCTTACATGGGATCATATGTCGATGCCAATGCCATGTCCCACAC
Found at i:56259718 original size:26 final size:23
Alignment explanation
Indices: 56259688--56259827 Score: 74
Period size: 23 Copynumber: 5.9 Consensus size: 23
56259678 GGACTCACCA
56259688 CAGCTCGTATGAGCTTACCGATATAT
1 CAGCTCGTATGAGCTTACCG-T-T-T
* * *
56259714 CAGCTCATAAGAGCTTACTGTTT
1 CAGCTCGTATGAGCTTACCGTTT
*
56259737 TAGCTCGTATGAGCTTA-C-TATT
1 CAGCTCGTATGAGCTTACCGT-TT
56259759 CAGCT--TAATAGAGCTTACCGTTT
1 CAGCTCGT-AT-GAGCTTACCGTTT
* * *
56259782 CATCTC-AATAGAGCTTACTGTTCAT
1 CAGCTCGTAT-GAGCTTACCGTT--T
* *
56259807 CAGCTCAGGAGGAGCTTACCG
1 CAGCTC-GTATGAGCTTACCG
56259828 ATTATGGCTC
Statistics
Matches: 89, Mismatches: 15, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
20 1 0.01
21 3 0.03
22 13 0.15
23 36 0.40
24 2 0.02
25 7 0.08
26 26 0.29
27 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (23 bp):
CAGCTCGTATGAGCTTACCGTTT
Found at i:56259750 original size:23 final size:26
Alignment explanation
Indices: 56259688--56259755 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 26
56259678 GGACTCACCA
*
56259688 CAGCTCGTATGAGCTTACCGATATAT
1 CAGCTCGTATGAGCTTACTGATATAT
* *
56259714 CAGCTCATAAGAGCTTACTG-T-T-T
1 CAGCTCGTATGAGCTTACTGATATAT
*
56259737 TAGCTCGTATGAGCTTACT
1 CAGCTCGTATGAGCTTACT
56259756 ATTCAGCTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 17 0.47
24 1 0.03
25 1 0.03
26 17 0.47
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (26 bp):
CAGCTCGTATGAGCTTACTGATATAT
Found at i:56261589 original size:120 final size:120
Alignment explanation
Indices: 56261381--56261597 Score: 283
Period size: 120 Copynumber: 1.8 Consensus size: 120
56261371 ATAACCACAC
* * * * *
56261381 GCACGAATGCCCTCGGGTCTTAGCCCGGATATAACGACTTGCACAAATGCCTTCGGGTATTAGCC
1 GCACAAATGCCCTCGGGTATTAGCCCGAATATAACGACTAGCACAAATGCCTTCGGGTATTAACC
**
56261446 CGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGACCGGATATTACAACTT
66 CGGATATAACAACTACCACAAATGCCTTCGGGTATTAGACCGGATATTACAACTT
* * * *
56261501 GCACAAATGCCTTCGGGTATTAGCCCGAATATAGTC-ACTAGCACAATTGCCTTCGGGTCTTAAC
1 GCACAAATGCCCTCGGGTATTAGCCCGAATATA-ACGACTAGCACAAATGCCTTCGGGTATTAAC
** * *
56261565 CCGGATATAATTACTACCATAAATGTCTTCGGG
65 CCGGATATAACAACTACCACAAATGCCTTCGGG
56261598 ACTTAGCCCG
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
120 80 0.99
121 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (120 bp):
GCACAAATGCCCTCGGGTATTAGCCCGAATATAACGACTAGCACAAATGCCTTCGGGTATTAACC
CGGATATAACAACTACCACAAATGCCTTCGGGTATTAGACCGGATATTACAACTT
Found at i:56261608 original size:40 final size:40
Alignment explanation
Indices: 56261365--56261574 Score: 269
Period size: 40 Copynumber: 5.2 Consensus size: 40
56261355 CGGAATACAA
* ** * * *
56261365 CCGGATATAACCACACGCACGAATGCCCTCGGGTCTTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
*
56261405 CCGGATATAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
*
56261445 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGA
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
*
56261485 CCGGATATTACAACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
* * * * * *
56261525 CCGAATATAGTC-ACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATA-ACAACTTGCACAAATGCCTTCGGGTATTAGC
56261565 CCGGATATAA
1 CCGGATATAA
56261575 TTACTACCAT
Statistics
Matches: 150, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
40 149 0.99
41 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
Found at i:56261801 original size:123 final size:123
Alignment explanation
Indices: 56261577--56262161 Score: 1053
Period size: 123 Copynumber: 4.8 Consensus size: 123
56261567 GGATATAATT
* * * * * * * *
56261577 ACTACCATAAATGTCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATAAATCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
*
56261642 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCGAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
*
56261700 ACTAGCATAATTGCCTTCGGGACTTAGCCTGGGTACCATTCAAATACTCATACACACATATATCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
56261765 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
*
56261823 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCAAACACACATATATCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
*
56261888 ATAATCATTACACATCCATATTTCATTTTCTTTACTAAGGCTCAAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
56261946 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
56262011 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
*
56262069 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATGTCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
56262134 ATAATCATTACACATCCATATTTCATTT
66 ATAATCATTACACATCCATATTTCATTT
56262162 CACATAATTC
Statistics
Matches: 446, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 446 1.00
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (123 bp):
ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
Found at i:56261822 original size:59 final size:59
Alignment explanation
Indices: 56261759--56261946 Score: 130
Period size: 59 Copynumber: 3.1 Consensus size: 59
56261749 ATACACACAT
56261759 ATATCAATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAAC
1 ATATCAATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAAC
* * * * *** * *** * ** *
56261818 ATATCACTAGCATAATTGC-CTTCGGGACTT-A-GCCCGGGTACCATTCAAATACTCAAACACAC
1 ATATCAATA--ATCATTACACATCCATATTTCATTTTC-GTTA-C--T--AAGGCTCAAACACAA
*
56261880 AT
58 AC
*
56261882 ATATCAATAATCATTACACATCCATATTTCATTTTCTTTACTAAGGCTCAAACACAAAC
1 ATATCAATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAAC
56261941 ATATCA
1 ATATCA
56261947 CTAGCATAAT
Statistics
Matches: 85, Mismatches: 33, Indels: 22
0.61 0.24 0.16
Matches are distributed among these distances:
58 1 0.01
59 31 0.36
60 7 0.08
61 7 0.08
62 7 0.08
63 7 0.08
64 24 0.28
65 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.30
Consensus pattern (59 bp):
ATATCAATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAAC
Found at i:56265378 original size:40 final size:40
Alignment explanation
Indices: 56265313--56265556 Score: 303
Period size: 40 Copynumber: 6.1 Consensus size: 40
56265303 CGGAATACAA
* ** * * *
56265313 CCGGATATAACCACACGCACGAATGCCCTCGGGTCTTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
*
56265353 CCGGATATAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
56265393 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
56265433 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
* * * * *
56265473 CCGGATATAGTC-ACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATA-ACAACTTGCACAAATGCCTTCGGGTATTAGC
** * * *
56265513 CCGGATATAATTACTAGCATAAATGTCTTCGGG-ACTTAGC
1 CCGGATATAACAACTTGCACAAATGCCTTCGGGTA-TTAGC
56265553 CCGG
1 CCGG
56265557 GTATCATTCA
Statistics
Matches: 182, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
40 181 0.99
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAACAACTTGCACAAATGCCTTCGGGTATTAGC
Found at i:56265711 original size:64 final size:64
Alignment explanation
Indices: 56265643--56265958 Score: 153
Period size: 64 Copynumber: 5.1 Consensus size: 64
56265633 GAACACAAAC
56265643 ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
1 ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
* * * * *** * *** * **
56265707 ATATCAATA--ATCATTACACATCCATATTTCATTTTC-GTTA-C--T--AAGGCTCGA-ACACA
1 ATATCACTAGCATAATTGC-CTTCGGGACTT-A-GCCCGGGTACCATTCAAATACTC-ATACACA
* *
56265763 AAC
62 CAT
56265766 ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
1 ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
* * * * *** * *** * ** * *
56265830 ATATCAATA--ATCATTACACATCCATATTTCATTTTC-GTTA-C--T--AAGGCTCAAACACAA
1 ATATCACTAGCATAATTGC-CTTCGGGACTT-A-GCCCGGGTACCATTCAAATACTCATACACAC
*
56265887 AC
63 AT
56265889 ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
1 ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
56265953 ATATCA
1 ATATCA
56265959 ATAATCATTA
Statistics
Matches: 162, Mismatches: 66, Indels: 48
0.59 0.24 0.17
Matches are distributed among these distances:
58 2 0.01
59 47 0.29
60 15 0.09
61 14 0.09
62 14 0.09
63 15 0.09
64 53 0.33
65 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (64 bp):
ATATCACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACAT
Found at i:56265744 original size:123 final size:123
Alignment explanation
Indices: 56265525--56266232 Score: 1308
Period size: 123 Copynumber: 5.8 Consensus size: 123
56265515 GGATATAATT
* * * * * * *
56265525 ACTAGCATAAATGTCTTCGGGACTTAGCCCGGGTATCATTCAATTGCTCATGCACACATAAATCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
*
56265590 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCGAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
56265648 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
*
56265713 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCGAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
56265771 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
56265836 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
56265894 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
56265959 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
* *
56266017 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGATACCATTCAAATACTCATACACACATATGTCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
56266082 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
66 ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
*
56266140 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATGTCA
1 ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
56266205 ATAATCATTACACATCCATATTTCATTT
66 ATAATCATTACACATCCATATTTCATTT
56266233 CACATAATTC
Statistics
Matches: 574, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 574 1.00
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (123 bp):
ACTAGCATAATTGCCTTCGGGACTTAGCCCGGGTACCATTCAAATACTCATACACACATATATCA
ATAATCATTACACATCCATATTTCATTTTCGTTACTAAGGCTCAAACACAAACATATC
Found at i:56273755 original size:10 final size:10
Alignment explanation
Indices: 56273742--56273772 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
56273732 TATAATTATT
56273742 TTATATTAAA
1 TTATATTAAA
56273752 TTATATTAAA
1 TTATATTAAA
*
56273762 ATATATTAAA
1 TTATATTAAA
56273772 T
1 T
56273773 ATTTTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TTATATTAAA
Found at i:56274260 original size:17 final size:18
Alignment explanation
Indices: 56274240--56274274 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
56274230 AAGTTTTTTC
56274240 CTAAATT-CTATTTTTAT
1 CTAAATTACTATTTTTAT
*
56274257 CTAAATTATTATTTTTAT
1 CTAAATTACTATTTTTAT
56274275 TATTATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (18 bp):
CTAAATTACTATTTTTAT
Found at i:56281408 original size:40 final size:40
Alignment explanation
Indices: 56281351--56281535 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 40
56281341 ATTAAATGAT
* * *
56281351 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAGTTAA
1 ATCCGGGCTAAGACCCGAAGGCATTTATGCAAGTAGTTAA
* * * *
56281391 ATCCGGGTTAAGACCCGAAGGCAATTATGCTAGT-GACTAA
1 ATCCGGGCTAAGACCCGAAGGCATTTATGCAAGTAG-TTAA
** *
56281431 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAA
1 ATCCGGGCTAAGACCCGAAGGCATTTATGCAAGTAGTTAA
* * **
56281471 ATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCA-TTCT
1 ATCCGGGCTAAGACCCGAAGGCATTTATGCAAGT-AGTTAA
56281511 ATCCGGGCTAAGACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATT
56281536 CGTGCATGTG
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
39 1 0.01
40 123 0.98
41 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTATGCAAGTAGTTAA
Found at i:56281487 original size:80 final size:80
Alignment explanation
Indices: 56281351--56281556 Score: 250
Period size: 80 Copynumber: 2.6 Consensus size: 80
56281341 ATTAAATGAT
* * ** * *
56281351 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAGTTAAATCCGGGTTAAGACCCGAAGGCAAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGGGCTAAGACCCGAAGGCAAT
* *
56281416 TATGCTAGTGACTAA
66 TATGCAAGTCACTAA
* * *
56281431 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGGGCTAAGACCCGAAGGCAAT
* * **
56281496 TGTGCAAGTCATTCT
66 TATGCAAGTCACTAA
* * *
56281511 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGG
56281557 TTGTATTCCG
Statistics
Matches: 108, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 108 1.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTAAATCCGGGCTAAGACCCGAAGGCAAT
TATGCAAGTCACTAA
Found at i:56281554 original size:40 final size:40
Alignment explanation
Indices: 56281351--56281556 Score: 193
Period size: 40 Copynumber: 5.2 Consensus size: 40
56281341 ATTAAATGAT
* * ** *
56281351 ATCCGGGCTAAGTCCCGAAGACATTTATGC-TAGTAGTTAA
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAT-GTGGTTAA
* * **
56281391 ATCCGGGTTAAGACCCGAAGGCAATT-ATGC-TAGTGACTAA
1 ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAT-GTGGTTAA
* *
56281431 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAA
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTAA
* * * ** **
56281471 ATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCATTCT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTAA
*
56281511 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTAA
56281551 ATCCGG
1 ATCCGG
56281557 TTGTATTCCG
Statistics
Matches: 139, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
39 3 0.02
40 133 0.96
41 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTAA
Found at i:56289197 original size:47 final size:47
Alignment explanation
Indices: 56289136--56289304 Score: 163
Period size: 47 Copynumber: 3.6 Consensus size: 47
56289126 TGTGTGCTAC
56289136 TGTAAGACATGTCTGGGACAT-GCATCAGCCACATTATG-AGAGCCAG
1 TGTAAGACATGTCTGGGACATGGCATC-GCCACATTATGAAGAGCCAG
* * *
56289182 TGTAAGACCATGTCTGGCACATGGCATCG--GCATTGA-GACAAGAGCTAG
1 TGTAAGA-CATGTCTGGGACATGGCATCGCCACATT-ATG--AAGAGCCAG
* * * *
56289230 TGTAAGACATGTCTGGGACAT-GCATCGGCCTCGTGATGTA-AGCCAG
1 TGTAAGACATGTCTGGGACATGGCATC-GCCACATTATGAAGAGCCAG
56289276 TGTAAGACCATGTCTGGGACATGGCATCG
1 TGTAAGA-CATGTCTGGGACATGGCATCG
56289305 ACATTACACC
Statistics
Matches: 102, Mismatches: 9, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
45 5 0.05
46 25 0.25
47 44 0.43
48 25 0.25
49 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.22
Consensus pattern (47 bp):
TGTAAGACATGTCTGGGACATGGCATCGCCACATTATGAAGAGCCAG
Found at i:56289232 original size:48 final size:49
Alignment explanation
Indices: 56289174--56289309 Score: 172
Period size: 47 Copynumber: 2.9 Consensus size: 49
56289164 CCACATTATG
*
56289174 AGAGCCAGTGTAAGACCATGTCTGGCACATGGCATCGGCATTGAGA-CA
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATCA
* * * * **
56289222 AGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGTGATGT
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATCA
*
56289269 A-AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGACATT
1 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATT
56289310 ACACCGTATG
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
46 24 0.32
47 28 0.38
48 22 0.30
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.22
Consensus pattern (49 bp):
AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATCA
Found at i:56289298 original size:94 final size:94
Alignment explanation
Indices: 56289131--56289309 Score: 279
Period size: 94 Copynumber: 1.9 Consensus size: 94
56289121 TTAATTGTGT
*
56289131 GCTACTGTAAGACATGTCTGGGACATGCATCAGCCACATTATGAGAGCCAGTGTAAGACCATGTC
1 GCTACTGTAAGACATGTCTGGGACATGCATCAGCCACATGATGAGAGCCAGTGTAAGACCATGTC
*
56289196 TGGCACATGGCATCGGCATTGAGACAAGA
66 TGGCACATGGCATCGACATTGAGACAAGA
* * * *
56289225 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTGATGTA-AGCCAGTGTAAGACCATGT
1 GCTACTGTAAGACATGTCTGGGACATGCATCAGCCACATGATG-AGAGCCAGTGTAAGACCATGT
*
56289289 CTGGGACATGGCATCGACATT
65 CTGGCACATGGCATCGACATT
56289310 ACACCGTATG
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 76 0.99
95 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (94 bp):
GCTACTGTAAGACATGTCTGGGACATGCATCAGCCACATGATGAGAGCCAGTGTAAGACCATGTC
TGGCACATGGCATCGACATTGAGACAAGA
Found at i:56298510 original size:43 final size:43
Alignment explanation
Indices: 56298449--56298531 Score: 157
Period size: 43 Copynumber: 1.9 Consensus size: 43
56298439 CCTCCTTCTA
56298449 TAACCAGTGTGGGTAGTGTCGGTAATCCCAAACCAAAATGCTG
1 TAACCAGTGTGGGTAGTGTCGGTAATCCCAAACCAAAATGCTG
*
56298492 TAACCAGTGTTGGTAGTGTCGGTAATCCCAAACCAAAATG
1 TAACCAGTGTGGGTAGTGTCGGTAATCCCAAACCAAAATG
56298532 TAAACATTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (43 bp):
TAACCAGTGTGGGTAGTGTCGGTAATCCCAAACCAAAATGCTG
Found at i:56308248 original size:20 final size:20
Alignment explanation
Indices: 56308219--56308260 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
56308209 CATATCTCAT
* *
56308219 ATAATGTTAGATACTCCGGA
1 ATAATATTAGATACTCCAGA
56308239 ATAATATTAGATACTCCAGA
1 ATAATATTAGATACTCCAGA
56308259 AT
1 AT
56308261 CTCGCACCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (20 bp):
ATAATATTAGATACTCCAGA
Found at i:56308304 original size:96 final size:96
Alignment explanation
Indices: 56308140--56308320 Score: 326
Period size: 96 Copynumber: 1.9 Consensus size: 96
56308130 TGAACCATTT
* * * *
56308140 GGAATAATATTAGATACTCCGGAATCTCTCACCCTAAGTGTCAATACAAGGCCGAAGCTATTTCA
1 GGAATAATATTAGATACTCCAGAATCTCGCACCCTAAGTGCCAATACAAGGCCAAAGCTATTTCA
56308205 ATCTCATATCTCATATAATGTTAGATACTCC
66 ATCTCATATCTCATATAATGTTAGATACTCC
56308236 GGAATAATATTAGATACTCCAGAATCTCGCACCCTAAGTGCCAATACAAGGCCAAAGCTATTTCA
1 GGAATAATATTAGATACTCCAGAATCTCGCACCCTAAGTGCCAATACAAGGCCAAAGCTATTTCA
56308301 ATCTCATATCTCATATAATG
66 ATCTCATATCTCATATAATG
56308321 CTCACTCTCG
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 81 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (96 bp):
GGAATAATATTAGATACTCCAGAATCTCGCACCCTAAGTGCCAATACAAGGCCAAAGCTATTTCA
ATCTCATATCTCATATAATGTTAGATACTCC
Found at i:56310336 original size:42 final size:42
Alignment explanation
Indices: 56310290--56310405 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 42
56310280 CGAGATTCTG
56310290 TATAAGACCATATCTAGGATATGGCATC-AGTATG-TGATTTCA
1 TATAAGACCATATCTAGGATATGGCATCGA-TATGAT-ATTTCA
* * *
56310332 TATAAGACCATGTCAAGGACATGGCATCGATATGATATTTCA
1 TATAAGACCATATCTAGGATATGGCATCGATATGATATTTCA
* * *
56310374 TGTAAGACCATAT-TCGGGATATGGCATTGATA
1 TATAAGACCATATCT-AGGATATGGCATCGATA
56310406 CGGTACTATG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
42 60 0.97
43 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.31
Consensus pattern (42 bp):
TATAAGACCATATCTAGGATATGGCATCGATATGATATTTCA
Found at i:56313491 original size:40 final size:40
Alignment explanation
Indices: 56313446--56313575 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
56313436 CGGAATACAA
56313446 CCGGATATAACCACGT-GCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACGAATGCCTTCGGGTCTTAGC
* ** *
56313486 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
* * *
56313526 CCGGATGTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACGAA-TGCCTTCGGGTCTTAGC
56313566 CCGGATATAA
1 CCGGATATAA
56313576 TTTCCAGCAT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.04
40 73 0.96
ACGTcount: A:0.24, C:0.28, G:0.25, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACGAATGCCTTCGGGTCTTAGC
Found at i:56318968 original size:40 final size:40
Alignment explanation
Indices: 56318860--56319069 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
56318850 CGGGATTTAA
* * * * *
56318860 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
56318900 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
56318940 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
56318980 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
56319020 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
56319060 CCGGATATAT
1 CCGGATATAT
56319070 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:56327116 original size:29 final size:29
Alignment explanation
Indices: 56327083--56327210 Score: 193
Period size: 29 Copynumber: 4.4 Consensus size: 29
56327073 CCTCCGAACT
** * * *
56327083 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
56327112 TGCACACTTAGTGCCAAATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
56327141 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
56327170 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
56327199 CGCACACTTAGT
1 CGCACACTTAGT
56327211 CCAATCTCGT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:56328488 original size:14 final size:14
Alignment explanation
Indices: 56328469--56328503 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
56328459 AAGATGAGCA
* *
56328469 TTCTTTTTTTTTTT
1 TTCTTTTCTTTTTC
56328483 TTCTTTTCTTTTTC
1 TTCTTTTCTTTTTC
56328497 TTCTTTT
1 TTCTTTT
56328504 ACTAACATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTCTTTTCTTTTTC
Found at i:56333252 original size:49 final size:48
Alignment explanation
Indices: 56333075--56333297 Score: 326
Period size: 47 Copynumber: 4.7 Consensus size: 48
56333065 CCCTTCGGGA
* * * *
56333075 CTTATCACAT-TTATACACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATTATACACTTTCACATTCATCACATCGGCCATTAGGC
*
56333122 CCTATCACATA-TATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATTATACACTTTCACATTCATCACATCGGCCATTAGGC
*
56333169 CTTATCACACA-TATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATTATACACTTTCACATTCATCACATCGGCCATTAGGC
*
56333216 CTTATCACATATGTATACACTTTCACATTCATCACATCGGCCTTTAGGC
1 CTTATCACATAT-TATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
56333265 CTTATCTCATATTTATACACATTCACATTCATC
1 CTTATCACATA-TTATACACTTTCACATTCATC
56333298 GCGTAGAATC
Statistics
Matches: 161, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
47 96 0.60
49 64 0.40
50 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (48 bp):
CTTATCACATATTATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:56336235 original size:30 final size:30
Alignment explanation
Indices: 56336201--56336258 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
56336191 TAGGCACTTC
*
56336201 CACACAGGT-GATCCACACGCCTGTGTGTGA
1 CACACAGGTAGA-CCACACGCCCGTGTGTGA
* *
56336231 CACACGGGTAGACCACATGCCCGTGTGT
1 CACACAGGTAGACCACACGCCCGTGTGT
56336259 CATGGCCGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.22, C:0.31, G:0.28, T:0.19
Consensus pattern (30 bp):
CACACAGGTAGACCACACGCCCGTGTGTGA
Found at i:56340290 original size:47 final size:47
Alignment explanation
Indices: 56340239--56340477 Score: 383
Period size: 47 Copynumber: 5.1 Consensus size: 47
56340229 TTAGGATTTT
*
56340239 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
*
56340286 ATGTGATAAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
56340333 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
*
56340380 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * *
56340427 ATGTGGTGAATATGAACATGC--ATATGTGGTAAAGCCGAATGGTCA
1 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
56340472 ATGTGA
1 ATGTGA
56340478 AATATATATG
Statistics
Matches: 180, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 25 0.14
47 155 0.86
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:56340292 original size:22 final size:22
Alignment explanation
Indices: 56340264--56340386 Score: 74
Period size: 22 Copynumber: 5.3 Consensus size: 22
56340254 ACATGCATAT
56340264 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * *
56340286 ATGTGATAAATGTG-AGCAT-GCATA
1 ATGTGAT-AA-G-GCCGAATGGC-CA
56340310 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
* * *
56340333 ATGTGATGAATGTG-AGCAT-GCATA
1 ATGTGAT-AA-G-GCCGAATGGC-CA
56340357 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
56340380 ATGTGAT
1 ATGTGAT
56340387 GAATGTGAGC
Statistics
Matches: 75, Mismatches: 12, Indels: 28
0.65 0.10 0.24
Matches are distributed among these distances:
22 23 0.31
23 18 0.24
24 18 0.24
25 16 0.21
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:56340343 original size:94 final size:94
Alignment explanation
Indices: 56340239--56340525 Score: 393
Period size: 94 Copynumber: 3.1 Consensus size: 94
56340229 TTAGGATTTT
56340239 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATAAATGTGAGCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATAAATGTGAGCA
56340304 TGCATATATGTGATAAGGCCGAATGGCCA
66 TGCATATATGTGATAAGGCCGAATGGCCA
* *
56340333 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAGCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATAAATGTGAGCA
*
56340398 TGCATATGTGTGATAAGGCCGAATGGCCA
66 TGCATATATGTGATAAGGCCGAATGGCCA
* * * * * * *
56340427 ATGTGGTGAATATGAACATGC--ATATGTGGTAAAGCCGAATGGTCAATGTGAAATATATATGAG
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTG--ATAAATGTGAG
* * * *
56340490 ATATGC--ATATGTGGTAAAGCCGAATGGTCA
64 -CATGCATATATGTGATAAGGCCGAATGGCCA
56340520 ATGTGA
1 ATGTGA
56340526 AATATATATA
Statistics
Matches: 172, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
92 26 0.15
93 25 0.15
94 117 0.68
95 4 0.02
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.26
Consensus pattern (94 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATAAATGTGAGCA
TGCATATATGTGATAAGGCCGAATGGCCA
Found at i:56340435 original size:25 final size:25
Alignment explanation
Indices: 56340360--56340435 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
56340350 ATGCATATAT
56340360 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
56340385 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
56340407 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
56340432 GTGA
1 GTGA
56340436 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:56340487 original size:47 final size:44
Alignment explanation
Indices: 56340239--56340581 Score: 283
Period size: 47 Copynumber: 7.3 Consensus size: 44
56340229 TTAGGATTTT
* *
56340239 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGAT-AATATGAACATGC--ATATGTGGTAAGGCCGAATGGCCA
* * *
56340286 ATGTGATAAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGAT-AATATGAACATGC--ATATGTGGTAAGGCCGAATGGCCA
* * *
56340333 ATGTGATGAATGTGAGCATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGAT-AATATGAACATGC--ATATGTGGTAAGGCCGAATGGCCA
* *
56340380 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGAT-AATATGAACATGCATATGTG-G-TAAGGCCGAATGGCCA
* * *
56340427 ATGTGGTGAATATGAACATGCATATGTGGTAAAGCCGAATGGTCA
1 ATGTGAT-AATATGAACATGCATATGTGGTAAGGCCGAATGGCCA
* * *
56340472 ATGTGAAATATATATGAGATATGCATATGTGGTAAAGCCGAATGGTCA
1 ATGTG--ATA-ATATGA-ACATGCATATGTGGTAAGGCCGAATGGCCA
* * * *
56340520 ATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTG----ATA-ATATGA-ACATGCATATGTGGTAAGGCCGAATGGCCA
*
56340570 GTGTGA-AATATG
1 ATGTGATAATATG
56340582 TAGGCGATGT
Statistics
Matches: 272, Mismatches: 16, Indels: 19
0.89 0.05 0.06
Matches are distributed among these distances:
44 5 0.02
45 27 0.10
46 3 0.01
47 160 0.59
48 34 0.12
50 43 0.16
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.27
Consensus pattern (44 bp):
ATGTGATAATATGAACATGCATATGTGGTAAGGCCGAATGGCCA
Found at i:56340554 original size:50 final size:50
Alignment explanation
Indices: 56340436--56340580 Score: 226
Period size: 50 Copynumber: 3.0 Consensus size: 50
56340426 AATGTGGTGA
*
56340436 ATATGA-ACATGCATATGTGGTAAAGCCGAATGGTCAATGTG-AA-ATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
56340483 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
* *
56340533 ATATGAGATATGTATATGTGGTAAAGCCGAATGG-CTAGTGTGAAATAT
1 ATATGAGATATGCATATGTGGTAAAGCCGAATGGTC-AATGTGAAATAT
56340581 GTAGGCGATG
Statistics
Matches: 91, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
47 6 0.07
48 34 0.37
49 3 0.03
50 48 0.53
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (50 bp):
ATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATATAT
Found at i:56340875 original size:37 final size:37
Alignment explanation
Indices: 56340730--56340874 Score: 254
Period size: 37 Copynumber: 3.9 Consensus size: 37
56340720 GGAAATATAT
*
56340730 TCCGGGTAAGACCCGATGACTACGTGTAGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
56340767 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
56340804 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
56340841 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
56340875 TCATCTGAGC
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:56344596 original size:93 final size:93
Alignment explanation
Indices: 56344467--56344637 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
56344457 CGCCCATAAG
* * * *
56344467 CGAACTCGGACTGAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
56344532 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
56344560 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
56344625 ACGAGTTCGGATG
66 ACGAGTTCGGATG
56344638 GTCAACCATC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:56344635 original size:46 final size:46
Alignment explanation
Indices: 56344460--56344635 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
56344450 TGTAACCCGC
* * * * *
56344460 CCATAAGCGAACTCGGACTGAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
56344506 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
56344556 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
56344599 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
56344636 TGGTCAACCA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:56352056 original size:46 final size:46
Alignment explanation
Indices: 56351989--56352117 Score: 186
Period size: 46 Copynumber: 2.8 Consensus size: 46
56351979 TGTAACCCGC
** * * * *
56351989 CCATAAGCAAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
*
56352035 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
*
56352081 CCATAAGTGAACTCAGACTCAACTCAATGAGTTCGGA
1 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
56352118 TGCTCAACCA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:56356146 original size:102 final size:101
Alignment explanation
Indices: 56356015--56356233 Score: 323
Period size: 102 Copynumber: 2.1 Consensus size: 101
56356005 ATACTGCCTG
* * *
56356015 GACACACGGGCATGTCCAAGGCCGTGTGAAAACTAGAGCTTAAATTTTAAATTTTAATTAAGTCA
1 GACACACAGGCATGTCCAAGGCCATGTGAAAACTAGAGCTTAAATTTCAAATTTTAATTAAGTCA
* * *
56356080 GAAAGCCACACGGGCAAGGCACACGGCTGTGTGTTC
66 GAAAGCCACACAGGCAAGGCACACAGCCGTGTGTTC
* *
56356116 AGACACACAGGCGTGTCCAAGGCCATGTGAAAAGTAGAGCTTAAATTTCAAATTTTAATTAAGTC
1 -GACACACAGGCATGTCCAAGGCCATGTGAAAACTAGAGCTTAAATTTCAAATTTTAATTAAGTC
*
56356181 AGGAAGCCACACAGGCAAGGCACACAGCCGTGTGTTC
65 AGAAAGCCACACAGGCAAGGCACACAGCCGTGTGTTC
56356218 GA-ACACACGAGCATGT
1 GACACACA-G-GCATGT
56356234 GAAGTACCAC
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
100 5 0.05
101 3 0.03
102 97 0.92
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (101 bp):
GACACACAGGCATGTCCAAGGCCATGTGAAAACTAGAGCTTAAATTTCAAATTTTAATTAAGTCA
GAAAGCCACACAGGCAAGGCACACAGCCGTGTGTTC
Found at i:56356819 original size:29 final size:30
Alignment explanation
Indices: 56356775--56356831 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
56356765 CCCCTCGAAC
56356775 TTCTTAGTTTTGATTTCATTT-TTTATTTTA
1 TTCTTAGTTTTGATTT-ATTTATTTATTTTA
*
56356805 TTCTT-GTTTTTATTTATTTATTTATTT
1 TTCTTAGTTTTGATTTATTTATTTATTT
56356832 ACAATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 16 0.64
30 5 0.20
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (30 bp):
TTCTTAGTTTTGATTTATTTATTTATTTTA
Found at i:56356843 original size:3 final size:3
Alignment explanation
Indices: 56356835--56356904 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
56356825 TTTATTTACA
* * **
56356835 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT AGT ATT ATT ATT AGG
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
56356883 CTT ATT TTT ATT ATT ACTT ATT
1 ATT ATT ATT ATT ATT A-TT ATT
56356905 TACTTTATCA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:56359712 original size:26 final size:26
Alignment explanation
Indices: 56359683--56359742 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
56359673 AAAGATTTGA
56359683 TTTTCATGCAAGCCTATGGTAATAAC
1 TTTTCATGCAAGCCTATGGTAATAAC
56359709 TTTTCATGCAAGCCTATGGTAATAAC
1 TTTTCATGCAAGCCTATGGTAATAAC
56359735 TTTTCATG
1 TTTTCATG
56359743 TTTGACTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (26 bp):
TTTTCATGCAAGCCTATGGTAATAAC
Found at i:56362590 original size:5 final size:5
Alignment explanation
Indices: 56362580--56362609 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
56362570 TGTGTTCTTC
56362580 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
56362610 TCACAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:56362903 original size:15 final size:16
Alignment explanation
Indices: 56362876--56362905 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
56362866 AAATTGAACC
56362876 ATAAAATTTCACTCAA
1 ATAAAATTTCACTCAA
56362892 ATAAAA-TTCACTCA
1 ATAAAATTTCACTCA
56362906 TATATATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAAATTTCACTCAA
Found at i:56384316 original size:85 final size:85
Alignment explanation
Indices: 56384168--56384618 Score: 670
Period size: 85 Copynumber: 5.3 Consensus size: 85
56384158 CTGAGACATT
* * * *
56384168 TGTAAGACCGTGTCTGGGACACATGCCTCGATTGAAATTTACGTATAAGACCATATCTAGGACAT
1 TGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAAATTTACATATAAGACCATGTCTGGGACAT
56384233 CGGCATCGTATCTGATTTCG
66 CGGCATCGTATCTGATTTCG
* * * *
56384253 TGTAAGACCGTGTCTGGGACACAGGCATCGATTGAAATTTTCATATAAAACCATGTTTGGGACAT
1 TGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAAATTTACATATAAGACCATGTCTGGGACAT
* *
56384318 CGGTATCGTATCTGATTTCA
66 CGGCATCGTATCTGATTTCG
* *
56384338 TGTAAGACCGTGTCTGGGACACAAGCCTCGATTCAAATTTACATATAAGACCATGTCTGGGACAT
1 TGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAAATTTACATATAAGACCATGTCTGGGACAT
* * *
56384403 CGACATCATATCTGATTTCA
66 CGGCATCGTATCTGATTTCG
*
56384423 TGTAAGACCATGTCTGGGACACAGGCCTCGATTGAAATTTA-AGTATAAGACCATGTCTGGGACA
1 TGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAAATTTACA-TATAAGACCATGTCTGGGACA
56384487 TCGGCATCGTATCTGATTTCG
65 TCGGCATCGTATCTGATTTCG
* * * *
56384508 TGTAAGACTGTATCTGGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTGGGACAT
1 TGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAAATTTACATATAAGACCATGTCTGGGACAT
*
56384573 CGGCATTGTATCTGATTTCG
66 CGGCATCGTATCTGATTTCG
* * *
56384593 TGTAAGACCCTGCCTGGGACAGAGGC
1 TGTAAGACCGTGTCTGGGACACAGGC
56384619 ATCAATATTG
Statistics
Matches: 328, Mismatches: 36, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
84 1 0.00
85 327 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (85 bp):
TGTAAGACCGTGTCTGGGACACAGGCCTCGATTGAAATTTACATATAAGACCATGTCTGGGACAT
CGGCATCGTATCTGATTTCG
Found at i:56384620 original size:42 final size:42
Alignment explanation
Indices: 56384168--56384621 Score: 324
Period size: 42 Copynumber: 10.7 Consensus size: 42
56384158 CTGAGACATT
* * *
56384168 TGTAAGACCGTGTCTGGGACACATGCCTCG-AT-TGAAATTTACG
1 TGTAAGACCATGTCTGGGACACAGGCATCGTATCTG--ATTT-CG
* * *
56384211 TATAAGACCATATCTAGGACATC-GGCATCGTATCTGATTTCG
1 TGTAAGACCATGTCTGGGACA-CAGGCATCGTATCTGATTTCG
* *
56384253 TGTAAGACCGTGTCTGGGACACAGGCATCG-AT-TGAAATTTTCA
1 TGTAAGACCATGTCTGGGACACAGGCATCGTATCTG--A-TTTCG
* * * * *
56384296 TATAAAACCATGTTTGGGACATC-GGTATCGTATCTGATTTCA
1 TGTAAGACCATGTCTGGGACA-CAGGCATCGTATCTGATTTCG
* * * ** *
56384338 TGTAAGACCGTGTCTGGGACACAAGCCTCG-ATTCAAATTTACA
1 TGTAAGACCATGTCTGGGACACAGGCATCGTA-TCTGATTT-CG
* * * *
56384381 TATAAGACCATGTCTGGGACATC-GACATCATATCTGATTTCA
1 TGTAAGACCATGTCTGGGACA-CAGGCATCGTATCTGATTTCG
* *
56384423 TGTAAGACCATGTCTGGGACACAGGCCTCG-AT-TGAAATTTAAG
1 TGTAAGACCATGTCTGGGACACAGGCATCGTATCTG--ATTT-CG
*
56384466 TATAAGACCATGTCTGGGACATC-GGCATCGTATCTGATTTCG
1 TGTAAGACCATGTCTGGGACA-CAGGCATCGTATCTGATTTCG
** * *
56384508 TGTAAGACTGTATCTGGGACACAGGCCTCG-AT-TGAGATTTACG
1 TGTAAGACCATGTCTGGGACACAGGCATCGTATCT--GATTT-CG
* *
56384551 TATAAGACCATGTCTGGGACATC-GGCATTGTATCTGATTTCG
1 TGTAAGACCATGTCTGGGACA-CAGGCATCGTATCTGATTTCG
* * *
56384593 TGTAAGACCCTGCCTGGGACAGAGGCATC
1 TGTAAGACCATGTCTGGGACACAGGCATC
56384622 AATATTGAAT
Statistics
Matches: 323, Mismatches: 58, Indels: 61
0.73 0.13 0.14
Matches are distributed among these distances:
40 5 0.02
41 11 0.03
42 143 0.44
43 143 0.44
44 14 0.04
45 7 0.02
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACACAGGCATCGTATCTGATTTCG
Found at i:56388488 original size:75 final size:75
Alignment explanation
Indices: 56388365--56388514 Score: 273
Period size: 75 Copynumber: 2.0 Consensus size: 75
56388355 ATCATAAAAT
*
56388365 AATTATTTATATCTCAGATTTTATGGTCCCGAAACCTCTGTTCCAACTAGACCCAATTTTGGGCT
1 AATTATTTATATCTCAGATTTTATGGTCCCGAAACCTCTATTCCAACTAGACCCAATTTTGGGCT
*
56388430 ATTACAACTA
66 ATTAAAACTA
*
56388440 AATTATTTATATCTCAGATTTTGTGGTCCCGAAACCTCTATTCCAACTAGACCCAATTTTGGGCT
1 AATTATTTATATCTCAGATTTTATGGTCCCGAAACCTCTATTCCAACTAGACCCAATTTTGGGCT
56388505 ATTAAAACTA
66 ATTAAAACTA
56388515 TTCTATGAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (75 bp):
AATTATTTATATCTCAGATTTTATGGTCCCGAAACCTCTATTCCAACTAGACCCAATTTTGGGCT
ATTAAAACTA
Found at i:56394131 original size:37 final size:37
Alignment explanation
Indices: 56394081--56394171 Score: 164
Period size: 37 Copynumber: 2.4 Consensus size: 37
56394071 TTATTACGAA
56394081 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
56394118 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
*
56394155 GTCTCACCCGGAACATA
1 GTCTTACCCGG-ACATA
56394172 TTTCCAAGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 47 0.90
38 5 0.10
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (37 bp):
GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
Found at i:56394368 original size:49 final size:49
Alignment explanation
Indices: 56394258--56394495 Score: 435
Period size: 49 Copynumber: 4.9 Consensus size: 49
56394248 CACACATATA
56394258 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT-T-TATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
*
56394305 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
*
56394354 TTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATATACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
*
56394403 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACAC
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
56394452 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
1 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
56394496 AATCTCATAC
Statistics
Matches: 186, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
47 38 0.20
48 1 0.01
49 147 0.79
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (49 bp):
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACAC
Found at i:56405197 original size:40 final size:40
Alignment explanation
Indices: 56405152--56405318 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
56405142 CGGAATATAA
56405152 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
56405192 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
56405232 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
56405272 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
56405311 CCGGATAT
1 CCGGATAT
56405319 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:56405302 original size:80 final size:79
Alignment explanation
Indices: 56405168--56405318 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
56405158 ATAATCACGT
*
56405168 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
56405233 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
56405248 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
56405311 CCGGATAT
64 CCGGATAT
56405319 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:56412003 original size:7 final size:7
Alignment explanation
Indices: 56411991--56412015 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56411981 GTTGTCTTCT
56411991 TGTTTGA
1 TGTTTGA
56411998 TGTTTGA
1 TGTTTGA
56412005 TGTTTGA
1 TGTTTGA
56412012 TGTT
1 TGTT
56412016 GTGGTGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (7 bp):
TGTTTGA
Found at i:56412945 original size:27 final size:28
Alignment explanation
Indices: 56412889--56412958 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
56412879 AAATTTGTAC
56412889 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
* *
56412917 AGCACTAGGTGTGCGAG-TTGATTTTAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
56412944 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
56412959 GACTCACTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:56419830 original size:7 final size:7
Alignment explanation
Indices: 56419818--56419842 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
56419808 GTTGTCTTCT
56419818 TGTTTGA
1 TGTTTGA
56419825 TGTTTGA
1 TGTTTGA
56419832 TGTTTGA
1 TGTTTGA
56419839 TGTT
1 TGTT
56419843 GTGGTGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (7 bp):
TGTTTGA
Found at i:56420773 original size:27 final size:28
Alignment explanation
Indices: 56420717--56420786 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
56420707 AAATTTGTAC
56420717 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
* *
56420745 AGCACTAGGTGTGCGAG-TTGATTTTAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
56420772 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
56420787 GACTCACTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:56424700 original size:25 final size:25
Alignment explanation
Indices: 56424672--56424719 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
56424662 TTATACCATG
* * *
56424672 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
56424697 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
56424720 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:56424788 original size:20 final size:20
Alignment explanation
Indices: 56424763--56424821 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
56424753 TAAATATGGT
56424763 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
*
56424783 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAA
56424803 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
56424822 GGTAATCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:56424803 original size:11 final size:11
Alignment explanation
Indices: 56424767--56424821 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
56424757 TATGGTATGT
56424767 ATGATATGCAC
1 ATGATATGCAC
* *
56424778 ATGAAATG--T
1 ATGATATGCAC
56424787 ATGATATGCAC
1 ATGATATGCAC
*
56424798 ATGATATG--T
1 ATGATATGCAC
56424807 ATGATATGCAC
1 ATGATATGCAC
56424818 ATGA
1 ATGA
56424822 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:56424899 original size:24 final size:24
Alignment explanation
Indices: 56424872--56424990 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
56424862 GAGGAAGTGA
*
56424872 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
56424896 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
56424919 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
56424943 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
56424967 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
56424991 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 22 0.26
24 53 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:56424941 original size:47 final size:48
Alignment explanation
Indices: 56424872--56424990 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
56424862 GAGGAAGTGA
56424872 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
56424919 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
56424967 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
56424991 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:56425217 original size:31 final size:31
Alignment explanation
Indices: 56425182--56425338 Score: 296
Period size: 31 Copynumber: 5.1 Consensus size: 31
56425172 CGTTTACAGT
56425182 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
56425213 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
56425244 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
56425275 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
* *
56425306 AAAGGCTTCGGCCCTGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
56425337 AA
1 AA
56425339 TATGAAAAGG
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 124 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:56432384 original size:11 final size:11
Alignment explanation
Indices: 56432368--56432393 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56432358 GCTCGTTTTG
56432368 TTATCAACTCA
1 TTATCAACTCA
56432379 TTATCAACTCA
1 TTATCAACTCA
56432390 TTAT
1 TTAT
56432394 TTAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (11 bp):
TTATCAACTCA
Found at i:56437833 original size:27 final size:27
Alignment explanation
Indices: 56437803--56437861 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
56437793 TTAACACCCT
56437803 AGGGGCAAAATGGTAATTCTACCCTAC
1 AGGGGCAAAATGGTAATTCTACCCTAC
* *** *
56437830 AGGGGTATTTTGGTAATTTTACCCTAC
1 AGGGGCAAAATGGTAATTCTACCCTAC
56437857 AGGGG
1 AGGGG
56437862 TATTTTAGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTCTACCCTAC
Found at i:56437862 original size:27 final size:27
Alignment explanation
Indices: 56437813--56437959 Score: 120
Period size: 27 Copynumber: 5.4 Consensus size: 27
56437803 AGGGGCAAAA
* *
56437813 TGGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTTTACCCAACAGGGGTATTT
*
56437840 TGGTAATTTTACCCTACAGGGGTATTT
1 TGGTAATTTTACCCAACAGGGGTATTT
* * * *
56437867 TAGTAATTTT-GCAAACCATGGGTATTT
1 TGGTAATTTTACCCAA-CAGGGGTATTT
*** *
56437894 TGGTAATTTT-GTAAACCAAGGGTATTT
1 TGGTAATTTTACCCAA-CAGGGGTATTT
* *
56437921 TAGTAATTTTA-CAAACCAGGGGTATTT
1 TGGTAATTTTACCCAA-CAGGGGTATTT
*
56437948 TGGTGATTTTAC
1 TGGTAATTTTAC
56437960 AAGTCGAGGG
Statistics
Matches: 103, Mismatches: 14, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
26 2 0.02
27 101 0.98
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (27 bp):
TGGTAATTTTACCCAACAGGGGTATTT
Found at i:56437960 original size:27 final size:27
Alignment explanation
Indices: 56437829--56437961 Score: 160
Period size: 27 Copynumber: 4.9 Consensus size: 27
56437819 TTCTACCCTA
**
56437829 CAGGGGTATTTTGGTAATTTTACCCTA-
1 CAGGGGTATTTTGGTAATTTTA-CAAAC
* *
56437856 CAGGGGTATTTTAGTAATTTTGCAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* **
56437883 CATGGGTATTTTGGTAATTTTGTAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* *
56437910 CAAGGGTATTTTAGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
*
56437937 CAGGGGTATTTTGGTGATTTTACAA
1 CAGGGGTATTTTGGTAATTTTACAA
56437962 GTCGAGGGCA
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 2 0.02
27 89 0.98
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.40
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTTACAAAC
Found at i:56437980 original size:54 final size:53
Alignment explanation
Indices: 56437829--56437982 Score: 166
Period size: 54 Copynumber: 2.8 Consensus size: 53
56437819 TTCTACCCTA
** *
56437829 CAGGGGTATTTTGGTAATTTTAC-CCTACAGGGGTATTTTAGTAATTTTGCAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAT-CA-GGGTATTTTAGTAATTTTACAAAC
* ** *
56437883 CATGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAATC-AGGGTATTTTAGTAATTTTACAAAC
* * * *
56437937 CAGGGGTATTTTGGTGATTTTACAAGTCGAGGGCATTTCAGTAATT
1 CAGGGGTATTTTGGTAATTTTACAAATC-AGGGTATTTTAGTAATT
56437983 GGTAAACTAA
Statistics
Matches: 82, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
54 81 0.99
55 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (53 bp):
CAGGGGTATTTTGGTAATTTTACAAATCAGGGTATTTTAGTAATTTTACAAAC
Found at i:56441478 original size:46 final size:46
Alignment explanation
Indices: 56441411--56441577 Score: 154
Period size: 46 Copynumber: 3.7 Consensus size: 46
56441401 AACCCGCCCC
* *
56441411 TAAGTGAACTCGGACCCAACTCAACGAGCTCGGGCTTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTTCGCATCCA
* *
56441457 TAAGTGAACTCGGACTCAACTCAACAAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-CT--TTCGCATCCA
* * * *
56441505 TCA-CGAACTCGG-----ACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTTCGCATCCA
56441545 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
56441578 ATGCTCAACC
Statistics
Matches: 95, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
37 2 0.02
38 3 0.03
39 2 0.02
40 2 0.02
41 8 0.08
42 14 0.15
46 45 0.47
47 8 0.08
48 3 0.03
49 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTTCGCATCCA
Found at i:56462371 original size:43 final size:43
Alignment explanation
Indices: 56462257--56462373 Score: 166
Period size: 42 Copynumber: 2.7 Consensus size: 43
56462247 CTGATATAAG
56462257 TTCGGTTTAATGTAA-TAGCACTAAGTGTGCGATACAATTATAGC
1 TTCGG-TTAAT-TAATTAGCACTAAGTGTGCGATACAATTATAGC
* * * *
56462301 TT-TGCTAATTAATTGGCACTAAATGTGCGATACAATTATAGC
1 TTCGGTTAATTAATTAGCACTAAGTGTGCGATACAATTATAGC
56462343 TTCGGTTAATTAATTAGCACTAAGTGTGCGA
1 TTCGGTTAATTAATTAGCACTAAGTGTGCGA
56462374 GTTCGTTGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
41 3 0.05
42 33 0.52
43 25 0.40
44 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (43 bp):
TTCGGTTAATTAATTAGCACTAAGTGTGCGATACAATTATAGC
Found at i:56465385 original size:20 final size:20
Alignment explanation
Indices: 56465369--56465405 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56465359 TGGTTTTACG
56465369 GTTGT-TTTAGGGGTTTTAA
1 GTTGTGTTTAGGGGTTTTAA
*
56465388 GTTTTGTTTAGGGGTTTT
1 GTTGTGTTTAGGGGTTTT
56465406 CGTGACCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.11, C:0.00, G:0.32, T:0.57
Consensus pattern (20 bp):
GTTGTGTTTAGGGGTTTTAA
Done.