Multiple sequence alignment - TraesCS3A01G428900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G428900 chr3A 100.000 4185 0 0 1 4185 672083629 672087813 0.000000e+00 7729.0
1 TraesCS3A01G428900 chr3A 100.000 493 0 0 4644 5136 672088272 672088764 0.000000e+00 911.0
2 TraesCS3A01G428900 chr3A 85.714 154 15 4 1378 1529 575152152 575152004 6.890000e-34 156.0
3 TraesCS3A01G428900 chr3A 93.902 82 5 0 2275 2356 360822472 360822553 1.940000e-24 124.0
4 TraesCS3A01G428900 chr3D 96.183 1834 65 5 2355 4185 536437105 536438936 0.000000e+00 2994.0
5 TraesCS3A01G428900 chr3D 90.192 2294 151 44 7 2268 536434847 536437098 0.000000e+00 2922.0
6 TraesCS3A01G428900 chr3D 93.538 650 38 4 3536 4185 536878808 536879453 0.000000e+00 965.0
7 TraesCS3A01G428900 chr3D 93.231 650 39 5 3536 4185 536588296 536588940 0.000000e+00 952.0
8 TraesCS3A01G428900 chr3D 92.769 650 42 5 3536 4185 536666650 536667294 0.000000e+00 935.0
9 TraesCS3A01G428900 chr3D 91.348 497 22 10 4644 5136 536439115 536439594 0.000000e+00 660.0
10 TraesCS3A01G428900 chr3D 89.546 507 32 11 4644 5136 536787360 536787859 1.570000e-174 623.0
11 TraesCS3A01G428900 chr3D 89.579 499 24 10 4644 5133 536879593 536880072 4.400000e-170 608.0
12 TraesCS3A01G428900 chr3D 88.363 507 27 9 4644 5136 536589080 536589568 9.590000e-162 580.0
13 TraesCS3A01G428900 chr3D 88.166 507 26 12 4644 5136 536667434 536667920 1.600000e-159 573.0
14 TraesCS3A01G428900 chr3D 91.509 212 16 2 3964 4174 536589527 536589737 1.810000e-74 291.0
15 TraesCS3A01G428900 chr3D 91.358 162 12 2 1875 2035 415924999 415925159 2.410000e-53 220.0
16 TraesCS3A01G428900 chr3D 93.814 97 5 1 5041 5136 536511256 536511352 1.490000e-30 145.0
17 TraesCS3A01G428900 chr3D 96.471 85 3 0 2275 2359 381989152 381989068 1.930000e-29 141.0
18 TraesCS3A01G428900 chr3D 93.827 81 5 0 2275 2355 429306248 429306328 6.980000e-24 122.0
19 TraesCS3A01G428900 chr3D 91.837 49 2 2 4648 4695 536439874 536439921 3.320000e-07 67.6
20 TraesCS3A01G428900 chr3D 91.837 49 2 2 4648 4695 536511632 536511679 3.320000e-07 67.6
21 TraesCS3A01G428900 chr3B 95.650 1839 71 9 2353 4185 708951833 708953668 0.000000e+00 2944.0
22 TraesCS3A01G428900 chr3B 87.682 1713 140 35 10 1700 708949643 708951306 0.000000e+00 1929.0
23 TraesCS3A01G428900 chr3B 93.415 653 40 3 3531 4183 709073628 709074277 0.000000e+00 965.0
24 TraesCS3A01G428900 chr3B 92.519 655 46 3 3531 4185 709267817 709268468 0.000000e+00 935.0
25 TraesCS3A01G428900 chr3B 93.837 503 27 3 1741 2240 708951307 708951808 0.000000e+00 754.0
26 TraesCS3A01G428900 chr3B 91.278 493 26 9 4644 5131 708953775 708954255 0.000000e+00 656.0
27 TraesCS3A01G428900 chr3B 89.592 490 31 8 4644 5131 709268614 709269085 5.690000e-169 604.0
28 TraesCS3A01G428900 chr3B 91.800 439 16 8 4644 5081 709074425 709074844 1.230000e-165 593.0
29 TraesCS3A01G428900 chr3B 84.677 496 50 15 1224 1696 231984100 231983608 6.020000e-129 472.0
30 TraesCS3A01G428900 chr3B 84.254 489 50 17 1232 1696 230929290 230928805 7.840000e-123 451.0
31 TraesCS3A01G428900 chr3B 88.618 123 13 1 1051 1173 231984448 231984327 1.150000e-31 148.0
32 TraesCS3A01G428900 chr3B 91.176 102 8 1 1051 1152 230929691 230929591 2.490000e-28 137.0
33 TraesCS3A01G428900 chrUn 91.038 212 17 2 3964 4174 359851766 359851976 8.420000e-73 285.0
34 TraesCS3A01G428900 chrUn 88.830 188 7 5 4963 5136 359851620 359851807 8.660000e-53 219.0
35 TraesCS3A01G428900 chrUn 88.830 188 7 5 4963 5136 404927894 404927707 8.660000e-53 219.0
36 TraesCS3A01G428900 chrUn 91.837 49 2 2 4648 4695 359852087 359852134 3.320000e-07 67.6
37 TraesCS3A01G428900 chrUn 91.837 49 2 2 4648 4695 404927427 404927380 3.320000e-07 67.6
38 TraesCS3A01G428900 chr5D 92.771 166 12 0 1878 2043 426994724 426994559 1.850000e-59 241.0
39 TraesCS3A01G428900 chr1A 91.124 169 15 0 1875 2043 75110915 75111083 4.000000e-56 230.0
40 TraesCS3A01G428900 chr2A 90.361 166 16 0 1878 2043 482751674 482751509 8.660000e-53 219.0
41 TraesCS3A01G428900 chr2A 93.258 89 5 1 2275 2362 78845856 78845768 4.170000e-26 130.0
42 TraesCS3A01G428900 chr7D 86.842 152 17 1 1378 1529 573300691 573300543 3.180000e-37 167.0
43 TraesCS3A01G428900 chr2B 85.211 142 14 3 1388 1529 73074833 73074699 6.930000e-29 139.0
44 TraesCS3A01G428900 chr2B 93.976 83 4 1 2275 2356 723392973 723392891 1.940000e-24 124.0
45 TraesCS3A01G428900 chr5B 95.062 81 4 0 2275 2355 364139424 364139504 1.500000e-25 128.0
46 TraesCS3A01G428900 chr7B 93.976 83 5 0 2275 2357 103891447 103891529 5.400000e-25 126.0
47 TraesCS3A01G428900 chr7B 94.937 79 4 0 1965 2043 153179514 153179592 1.940000e-24 124.0
48 TraesCS3A01G428900 chr7B 82.781 151 14 2 1379 1529 365873815 365873953 1.940000e-24 124.0
49 TraesCS3A01G428900 chr1D 93.976 83 5 0 2275 2357 120537695 120537613 5.400000e-25 126.0
50 TraesCS3A01G428900 chr4B 94.937 79 4 0 1965 2043 9819300 9819378 1.940000e-24 124.0
51 TraesCS3A01G428900 chr4B 93.671 79 5 0 1965 2043 619173298 619173376 9.030000e-23 119.0
52 TraesCS3A01G428900 chr2D 92.135 89 6 1 2275 2362 78563910 78563822 1.940000e-24 124.0
53 TraesCS3A01G428900 chr2D 94.595 37 2 0 1378 1414 524269039 524269075 2.000000e-04 58.4
54 TraesCS3A01G428900 chr4D 79.739 153 18 8 1378 1529 210024100 210024240 1.180000e-16 99.0
55 TraesCS3A01G428900 chr4D 97.561 41 1 0 1553 1593 210024238 210024278 2.570000e-08 71.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G428900 chr3A 672083629 672088764 5135 False 4320.000000 7729 100.000000 1 5136 2 chr3A.!!$F2 5135
1 TraesCS3A01G428900 chr3D 536434847 536439921 5074 False 1660.900000 2994 92.390000 7 5136 4 chr3D.!!$F4 5129
2 TraesCS3A01G428900 chr3D 536878808 536880072 1264 False 786.500000 965 91.558500 3536 5133 2 chr3D.!!$F8 1597
3 TraesCS3A01G428900 chr3D 536666650 536667920 1270 False 754.000000 935 90.467500 3536 5136 2 chr3D.!!$F7 1600
4 TraesCS3A01G428900 chr3D 536588296 536589737 1441 False 607.666667 952 91.034333 3536 5136 3 chr3D.!!$F6 1600
5 TraesCS3A01G428900 chr3B 708949643 708954255 4612 False 1570.750000 2944 92.111750 10 5131 4 chr3B.!!$F1 5121
6 TraesCS3A01G428900 chr3B 709073628 709074844 1216 False 779.000000 965 92.607500 3531 5081 2 chr3B.!!$F2 1550
7 TraesCS3A01G428900 chr3B 709267817 709269085 1268 False 769.500000 935 91.055500 3531 5131 2 chr3B.!!$F3 1600
8 TraesCS3A01G428900 chr3B 231983608 231984448 840 True 310.000000 472 86.647500 1051 1696 2 chr3B.!!$R2 645
9 TraesCS3A01G428900 chr3B 230928805 230929691 886 True 294.000000 451 87.715000 1051 1696 2 chr3B.!!$R1 645

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
257 261 0.108585 GAAGCTCGGCCATATTCCCA 59.891 55.000 2.24 0.00 0.00 4.37 F
258 262 0.179018 AAGCTCGGCCATATTCCCAC 60.179 55.000 2.24 0.00 0.00 4.61 F
273 277 0.250234 CCCACTTTCGGAGCTGATCA 59.750 55.000 0.00 0.00 0.00 2.92 F
935 955 0.393808 CCCCATAACCAACCACGGAG 60.394 60.000 0.00 0.00 0.00 4.63 F
2250 2539 0.034767 ATGGTGTGTGATGCTCCCTG 60.035 55.000 0.00 0.00 0.00 4.45 F
2252 2541 0.957395 GGTGTGTGATGCTCCCTGTG 60.957 60.000 0.00 0.00 0.00 3.66 F
2471 2760 1.930371 GCAATCAGGCAACGTTGGTTC 60.930 52.381 28.33 12.65 46.39 3.62 F
3960 4255 1.131638 GATATGGTGGCAGGTGAGGA 58.868 55.000 0.00 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 2005 0.179004 TTTGGCTGTTCGTGGATGGT 60.179 50.000 0.00 0.00 0.00 3.55 R
1895 2179 0.657840 CTGCGGCTAAATAGTGTGGC 59.342 55.000 0.00 0.00 0.00 5.01 R
2250 2539 4.454728 TCAATTAGCCCTCAAAATGCAC 57.545 40.909 0.00 0.00 0.00 4.57 R
2611 2902 0.397941 CAGGTCTTTGACTGGGAGCA 59.602 55.000 0.00 0.00 32.47 4.26 R
3728 4023 0.691078 AAGGGAGCTCAATCCGGCTA 60.691 55.000 17.19 0.00 40.56 3.93 R
3960 4255 1.270274 GTTAACCGCGGGGATTTTGTT 59.730 47.619 31.76 14.40 36.97 2.83 R
3974 4269 1.737793 CTGTGGATCGCAAGGTTAACC 59.262 52.381 17.41 17.41 38.47 2.85 R
4824 5128 1.005289 ATCCCAGCCACCCAGAGAT 59.995 57.895 0.00 0.00 0.00 2.75 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.390135 TCCAAAGCGTGACTTACAAGAG 58.610 45.455 0.00 0.00 37.75 2.85
35 36 4.704965 ACTTACAAGAGGGATTAATCGGC 58.295 43.478 9.32 1.63 0.00 5.54
109 110 4.530094 TCTACCGCATTTTTGCTTATCG 57.470 40.909 0.00 0.00 0.00 2.92
125 126 7.603963 TGCTTATCGAGTTATGCTTTAAACA 57.396 32.000 0.00 0.00 0.00 2.83
157 158 0.847373 TTTGAGGTGTGGTAAGGGCA 59.153 50.000 0.00 0.00 0.00 5.36
211 214 8.767478 AACATATTCAAGCCAATTCTCAAAAG 57.233 30.769 0.00 0.00 0.00 2.27
257 261 0.108585 GAAGCTCGGCCATATTCCCA 59.891 55.000 2.24 0.00 0.00 4.37
258 262 0.179018 AAGCTCGGCCATATTCCCAC 60.179 55.000 2.24 0.00 0.00 4.61
259 263 1.056700 AGCTCGGCCATATTCCCACT 61.057 55.000 2.24 0.00 0.00 4.00
261 265 1.750682 GCTCGGCCATATTCCCACTTT 60.751 52.381 2.24 0.00 0.00 2.66
268 272 2.158755 CCATATTCCCACTTTCGGAGCT 60.159 50.000 0.00 0.00 0.00 4.09
271 275 0.984230 TTCCCACTTTCGGAGCTGAT 59.016 50.000 0.00 0.00 0.00 2.90
272 276 0.537188 TCCCACTTTCGGAGCTGATC 59.463 55.000 0.00 0.00 0.00 2.92
273 277 0.250234 CCCACTTTCGGAGCTGATCA 59.750 55.000 0.00 0.00 0.00 2.92
278 282 4.635765 CCACTTTCGGAGCTGATCATTTTA 59.364 41.667 0.00 0.00 0.00 1.52
279 283 5.447818 CCACTTTCGGAGCTGATCATTTTAC 60.448 44.000 0.00 0.00 0.00 2.01
322 331 8.719645 AATAGCATAGAAGTTAGATGAGACCT 57.280 34.615 1.51 0.00 0.00 3.85
331 340 8.308207 AGAAGTTAGATGAGACCTTGTTAACTC 58.692 37.037 7.22 0.00 0.00 3.01
415 425 2.496470 ACTTCTACCAGGCTTTAGGACG 59.504 50.000 0.00 0.00 0.00 4.79
418 428 0.822164 TACCAGGCTTTAGGACGAGC 59.178 55.000 0.00 0.00 38.17 5.03
528 538 7.315890 CCAAAATCACCCTCTTGTATTTTCTC 58.684 38.462 0.00 0.00 29.66 2.87
537 547 4.323417 TCTTGTATTTTCTCGTGGTGCAT 58.677 39.130 0.00 0.00 0.00 3.96
539 549 3.669536 TGTATTTTCTCGTGGTGCATCA 58.330 40.909 0.00 0.00 0.00 3.07
540 550 4.068599 TGTATTTTCTCGTGGTGCATCAA 58.931 39.130 0.00 0.00 0.00 2.57
553 563 1.811266 CATCAAGACCTGGACCGCG 60.811 63.158 0.00 0.00 0.00 6.46
554 564 2.283529 ATCAAGACCTGGACCGCGT 61.284 57.895 4.92 0.00 0.00 6.01
555 565 2.227089 ATCAAGACCTGGACCGCGTC 62.227 60.000 4.92 2.44 0.00 5.19
560 570 4.351938 CCTGGACCGCGTCGACAA 62.352 66.667 17.16 0.00 32.65 3.18
562 572 3.553437 CTGGACCGCGTCGACAACT 62.553 63.158 17.16 0.00 32.65 3.16
604 616 8.841444 AAAAACTGCGATACATATGAACAATC 57.159 30.769 10.38 5.98 0.00 2.67
611 623 6.369890 GCGATACATATGAACAATCCATGTCT 59.630 38.462 10.38 0.00 42.99 3.41
613 625 9.423061 CGATACATATGAACAATCCATGTCTAA 57.577 33.333 10.38 0.00 42.99 2.10
623 635 7.566760 ACAATCCATGTCTAATATTTCGCAA 57.433 32.000 0.00 0.00 37.96 4.85
627 639 7.015226 TCCATGTCTAATATTTCGCAAACTG 57.985 36.000 0.00 0.00 0.00 3.16
642 654 4.557695 CGCAAACTGCAGTACCCAAATTTA 60.558 41.667 22.01 0.00 45.36 1.40
744 760 6.375455 AGTTGTGTCTGTCATTCTTGTTTCTT 59.625 34.615 0.00 0.00 0.00 2.52
748 764 7.012327 TGTGTCTGTCATTCTTGTTTCTTAAGG 59.988 37.037 1.85 0.00 0.00 2.69
754 770 8.352201 TGTCATTCTTGTTTCTTAAGGAATGTG 58.648 33.333 20.11 7.56 33.53 3.21
789 805 7.523293 AAATTTGTGGTGTGATAACTCATGA 57.477 32.000 0.00 0.00 32.98 3.07
860 880 6.385649 TGCTCAAAAAGGTAAAACCAGTAG 57.614 37.500 0.00 0.00 41.95 2.57
864 884 8.789762 GCTCAAAAAGGTAAAACCAGTAGATTA 58.210 33.333 0.00 0.00 41.95 1.75
933 953 1.379309 CCCCCATAACCAACCACGG 60.379 63.158 0.00 0.00 0.00 4.94
934 954 1.686416 CCCCATAACCAACCACGGA 59.314 57.895 0.00 0.00 0.00 4.69
935 955 0.393808 CCCCATAACCAACCACGGAG 60.394 60.000 0.00 0.00 0.00 4.63
936 956 1.029947 CCCATAACCAACCACGGAGC 61.030 60.000 0.00 0.00 0.00 4.70
1004 1028 3.226682 GGGTTGGTTAGTTGTTACCCA 57.773 47.619 0.00 0.00 43.73 4.51
1026 1050 4.024545 CGTACCCCCACCACACCC 62.025 72.222 0.00 0.00 0.00 4.61
1027 1051 3.654143 GTACCCCCACCACACCCC 61.654 72.222 0.00 0.00 0.00 4.95
1642 1922 2.046507 GCTCTGTCCTGTGGCCTG 60.047 66.667 3.32 0.00 0.00 4.85
1646 1926 1.302832 CTGTCCTGTGGCCTGGAAC 60.303 63.158 3.32 0.00 40.04 3.62
1654 1934 0.468226 GTGGCCTGGAACGGATCATA 59.532 55.000 3.32 0.00 36.31 2.15
1696 1976 1.717645 CTGCTCTGAATTGCGTTTTGC 59.282 47.619 0.00 0.00 46.70 3.68
1721 2001 1.198178 TGGAAAATCGTTTGCGTAGGC 59.802 47.619 0.00 0.00 37.86 3.93
1747 2027 2.598589 CATCCACGAACAGCCAAATTG 58.401 47.619 0.00 0.00 0.00 2.32
1765 2045 0.470766 TGCCCGGTGAAAACTGTACT 59.529 50.000 0.00 0.00 0.00 2.73
1798 2078 4.235360 CACACTAAACGGACGAAAGATCT 58.765 43.478 0.00 0.00 0.00 2.75
1851 2135 5.184892 AGCTCATCAAAGATAAACACCCT 57.815 39.130 0.00 0.00 0.00 4.34
1876 2160 2.203470 TGAACATTGCTCTCATGGCA 57.797 45.000 0.00 0.00 37.97 4.92
1895 2179 2.100631 GGTGTTCCATCGCTGTCGG 61.101 63.158 0.00 0.00 36.13 4.79
1910 2194 1.296727 GTCGGCCACACTATTTAGCC 58.703 55.000 2.24 0.00 40.33 3.93
1997 2282 5.525012 GCTTGCCTTGAAAGAAAAGAATGTT 59.475 36.000 8.17 0.00 0.00 2.71
2000 2285 6.638610 TGCCTTGAAAGAAAAGAATGTTTGA 58.361 32.000 0.00 0.00 0.00 2.69
2133 2422 5.598005 TGGATGTTCTTTGTGGAACTGAATT 59.402 36.000 8.47 0.00 44.02 2.17
2135 2424 7.451255 TGGATGTTCTTTGTGGAACTGAATTAT 59.549 33.333 8.47 0.00 44.02 1.28
2148 2437 7.284261 TGGAACTGAATTATAATTGCGGAATGA 59.716 33.333 15.39 0.00 0.00 2.57
2157 2446 3.872511 ATTGCGGAATGAAATGCTGAA 57.127 38.095 0.00 0.00 24.73 3.02
2185 2474 6.921914 ACCTATTGTCTACTACACTTGACAC 58.078 40.000 0.00 0.00 38.87 3.67
2189 2478 5.602458 TGTCTACTACACTTGACACTACG 57.398 43.478 0.00 0.00 34.94 3.51
2250 2539 0.034767 ATGGTGTGTGATGCTCCCTG 60.035 55.000 0.00 0.00 0.00 4.45
2252 2541 0.957395 GGTGTGTGATGCTCCCTGTG 60.957 60.000 0.00 0.00 0.00 3.66
2269 2558 3.196254 CCTGTGCATTTTGAGGGCTAATT 59.804 43.478 0.00 0.00 0.00 1.40
2272 2561 4.467082 TGTGCATTTTGAGGGCTAATTGAT 59.533 37.500 0.00 0.00 0.00 2.57
2273 2562 5.655974 TGTGCATTTTGAGGGCTAATTGATA 59.344 36.000 0.00 0.00 0.00 2.15
2274 2563 5.979517 GTGCATTTTGAGGGCTAATTGATAC 59.020 40.000 0.00 0.00 0.00 2.24
2275 2564 5.893255 TGCATTTTGAGGGCTAATTGATACT 59.107 36.000 0.00 0.00 0.00 2.12
2276 2565 6.039717 TGCATTTTGAGGGCTAATTGATACTC 59.960 38.462 0.00 0.00 0.00 2.59
2277 2566 6.264067 GCATTTTGAGGGCTAATTGATACTCT 59.736 38.462 0.00 0.00 0.00 3.24
2278 2567 7.646314 CATTTTGAGGGCTAATTGATACTCTG 58.354 38.462 0.00 0.00 0.00 3.35
2279 2568 5.957771 TTGAGGGCTAATTGATACTCTGT 57.042 39.130 0.00 0.00 0.00 3.41
2280 2569 5.537300 TGAGGGCTAATTGATACTCTGTC 57.463 43.478 0.00 0.00 0.00 3.51
2281 2570 4.345257 TGAGGGCTAATTGATACTCTGTCC 59.655 45.833 0.00 0.00 0.00 4.02
2282 2571 3.648545 AGGGCTAATTGATACTCTGTCCC 59.351 47.826 0.00 0.00 0.00 4.46
2283 2572 3.391296 GGGCTAATTGATACTCTGTCCCA 59.609 47.826 0.00 0.00 0.00 4.37
2284 2573 4.141482 GGGCTAATTGATACTCTGTCCCAA 60.141 45.833 0.00 0.00 0.00 4.12
2285 2574 5.437060 GGCTAATTGATACTCTGTCCCAAA 58.563 41.667 0.00 0.00 0.00 3.28
2286 2575 5.885912 GGCTAATTGATACTCTGTCCCAAAA 59.114 40.000 0.00 0.00 0.00 2.44
2287 2576 6.547510 GGCTAATTGATACTCTGTCCCAAAAT 59.452 38.462 0.00 0.00 0.00 1.82
2288 2577 7.719633 GGCTAATTGATACTCTGTCCCAAAATA 59.280 37.037 0.00 0.00 0.00 1.40
2289 2578 9.120538 GCTAATTGATACTCTGTCCCAAAATAA 57.879 33.333 0.00 0.00 0.00 1.40
2292 2581 7.921786 TTGATACTCTGTCCCAAAATAAGTG 57.078 36.000 0.00 0.00 0.00 3.16
2293 2582 7.016153 TGATACTCTGTCCCAAAATAAGTGT 57.984 36.000 0.00 0.00 0.00 3.55
2294 2583 7.103641 TGATACTCTGTCCCAAAATAAGTGTC 58.896 38.462 0.00 0.00 0.00 3.67
2295 2584 4.315803 ACTCTGTCCCAAAATAAGTGTCG 58.684 43.478 0.00 0.00 0.00 4.35
2296 2585 3.071479 TCTGTCCCAAAATAAGTGTCGC 58.929 45.455 0.00 0.00 0.00 5.19
2297 2586 3.074412 CTGTCCCAAAATAAGTGTCGCT 58.926 45.455 0.00 0.00 0.00 4.93
2298 2587 2.811431 TGTCCCAAAATAAGTGTCGCTG 59.189 45.455 0.00 0.00 0.00 5.18
2299 2588 3.071479 GTCCCAAAATAAGTGTCGCTGA 58.929 45.455 0.00 0.00 0.00 4.26
2300 2589 3.689649 GTCCCAAAATAAGTGTCGCTGAT 59.310 43.478 0.00 0.00 0.00 2.90
2301 2590 4.156008 GTCCCAAAATAAGTGTCGCTGATT 59.844 41.667 0.00 0.00 29.37 2.57
2302 2591 4.764823 TCCCAAAATAAGTGTCGCTGATTT 59.235 37.500 3.21 3.21 39.41 2.17
2303 2592 5.941058 TCCCAAAATAAGTGTCGCTGATTTA 59.059 36.000 8.84 0.00 37.29 1.40
2304 2593 6.093495 TCCCAAAATAAGTGTCGCTGATTTAG 59.907 38.462 8.84 4.74 37.29 1.85
2305 2594 6.128007 CCCAAAATAAGTGTCGCTGATTTAGT 60.128 38.462 8.84 0.00 37.29 2.24
2306 2595 7.065324 CCCAAAATAAGTGTCGCTGATTTAGTA 59.935 37.037 8.84 0.00 37.29 1.82
2307 2596 7.903431 CCAAAATAAGTGTCGCTGATTTAGTAC 59.097 37.037 8.84 0.00 37.29 2.73
2308 2597 8.440059 CAAAATAAGTGTCGCTGATTTAGTACA 58.560 33.333 8.84 0.00 37.29 2.90
2309 2598 8.542497 AAATAAGTGTCGCTGATTTAGTACAA 57.458 30.769 6.91 0.00 36.68 2.41
2310 2599 8.542497 AATAAGTGTCGCTGATTTAGTACAAA 57.458 30.769 0.00 0.00 0.00 2.83
2311 2600 6.467723 AAGTGTCGCTGATTTAGTACAAAG 57.532 37.500 0.00 0.00 0.00 2.77
2312 2601 5.539048 AGTGTCGCTGATTTAGTACAAAGT 58.461 37.500 0.00 0.00 0.00 2.66
2313 2602 5.989777 AGTGTCGCTGATTTAGTACAAAGTT 59.010 36.000 0.00 0.00 0.00 2.66
2314 2603 6.482308 AGTGTCGCTGATTTAGTACAAAGTTT 59.518 34.615 0.00 0.00 0.00 2.66
2315 2604 6.790825 GTGTCGCTGATTTAGTACAAAGTTTC 59.209 38.462 0.00 0.00 0.00 2.78
2316 2605 6.480651 TGTCGCTGATTTAGTACAAAGTTTCA 59.519 34.615 0.00 0.00 0.00 2.69
2317 2606 6.790825 GTCGCTGATTTAGTACAAAGTTTCAC 59.209 38.462 0.00 0.00 0.00 3.18
2318 2607 6.704493 TCGCTGATTTAGTACAAAGTTTCACT 59.296 34.615 0.00 5.08 0.00 3.41
2319 2608 7.868922 TCGCTGATTTAGTACAAAGTTTCACTA 59.131 33.333 0.00 3.49 0.00 2.74
2320 2609 8.492748 CGCTGATTTAGTACAAAGTTTCACTAA 58.507 33.333 12.32 12.32 32.97 2.24
2328 2617 8.428186 AGTACAAAGTTTCACTAAATCAACGA 57.572 30.769 0.00 0.00 0.00 3.85
2329 2618 8.333186 AGTACAAAGTTTCACTAAATCAACGAC 58.667 33.333 0.00 0.00 0.00 4.34
2330 2619 7.079182 ACAAAGTTTCACTAAATCAACGACA 57.921 32.000 0.00 0.00 0.00 4.35
2331 2620 6.964934 ACAAAGTTTCACTAAATCAACGACAC 59.035 34.615 0.00 0.00 0.00 3.67
2332 2621 6.920569 AAGTTTCACTAAATCAACGACACT 57.079 33.333 0.00 0.00 0.00 3.55
2333 2622 6.920569 AGTTTCACTAAATCAACGACACTT 57.079 33.333 0.00 0.00 0.00 3.16
2334 2623 8.428186 AAGTTTCACTAAATCAACGACACTTA 57.572 30.769 0.00 0.00 27.84 2.24
2335 2624 8.603242 AGTTTCACTAAATCAACGACACTTAT 57.397 30.769 0.00 0.00 0.00 1.73
2336 2625 9.052759 AGTTTCACTAAATCAACGACACTTATT 57.947 29.630 0.00 0.00 0.00 1.40
2337 2626 9.659830 GTTTCACTAAATCAACGACACTTATTT 57.340 29.630 0.00 0.00 0.00 1.40
2339 2628 9.658475 TTCACTAAATCAACGACACTTATTTTG 57.342 29.630 0.00 0.00 0.00 2.44
2340 2629 8.286800 TCACTAAATCAACGACACTTATTTTGG 58.713 33.333 0.00 0.00 0.00 3.28
2341 2630 7.537306 CACTAAATCAACGACACTTATTTTGGG 59.463 37.037 0.00 0.00 0.00 4.12
2342 2631 6.642707 AAATCAACGACACTTATTTTGGGA 57.357 33.333 0.00 0.00 0.00 4.37
2343 2632 5.622770 ATCAACGACACTTATTTTGGGAC 57.377 39.130 0.00 0.00 0.00 4.46
2344 2633 3.495377 TCAACGACACTTATTTTGGGACG 59.505 43.478 0.00 0.00 0.00 4.79
2345 2634 2.419667 ACGACACTTATTTTGGGACGG 58.580 47.619 0.00 0.00 0.00 4.79
2346 2635 2.037511 ACGACACTTATTTTGGGACGGA 59.962 45.455 0.00 0.00 0.00 4.69
2347 2636 2.671396 CGACACTTATTTTGGGACGGAG 59.329 50.000 0.00 0.00 0.00 4.63
2348 2637 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2349 2638 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2350 2639 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2351 2640 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2366 2655 4.989168 CGGAGGGAGTATTACTTATTGTGC 59.011 45.833 0.00 0.00 0.00 4.57
2402 2691 3.947868 AGCAGACTTGATGCACATAACT 58.052 40.909 0.00 0.00 46.31 2.24
2406 2695 5.582269 GCAGACTTGATGCACATAACTTCTA 59.418 40.000 0.00 0.00 43.31 2.10
2471 2760 1.930371 GCAATCAGGCAACGTTGGTTC 60.930 52.381 28.33 12.65 46.39 3.62
2513 2803 7.646548 TGATAACAGAGTAACTATGTGCTCT 57.353 36.000 0.00 0.00 36.00 4.09
2558 2849 6.017192 TGGATTACATGTTTCTGTGTTCAGTG 60.017 38.462 2.30 0.00 41.91 3.66
2619 2910 8.375506 TGTAATCCTAAGTAAATATGCTCCCAG 58.624 37.037 0.00 0.00 0.00 4.45
2654 2945 7.761409 TGTCATATAGTGAAACCAATCAAAGC 58.239 34.615 0.00 0.00 38.90 3.51
2689 2980 3.269178 TGCATCGCATGTCACTTGATTA 58.731 40.909 0.00 0.00 31.71 1.75
2816 3109 5.379732 AAGCTGTCTATAACTCTATCGGC 57.620 43.478 0.00 0.00 0.00 5.54
2855 3148 6.925610 TGTGTAATTCTGTCCTCATTATGC 57.074 37.500 0.00 0.00 0.00 3.14
3092 3385 3.868757 TCAGACTTTGGGAGATACACG 57.131 47.619 0.00 0.00 0.00 4.49
3245 3538 6.039047 CAGTCAGGAAAGATGTATGGAATTGG 59.961 42.308 0.00 0.00 0.00 3.16
3449 3744 5.604758 TCTCTGTCATTCATACCCTTCTG 57.395 43.478 0.00 0.00 0.00 3.02
3471 3766 9.959749 TTCTGTTTTTAGTGACATGGAATTAAC 57.040 29.630 0.00 0.00 0.00 2.01
3704 3999 2.602878 CTGTTTGATGCCATTGTCAGC 58.397 47.619 0.00 0.00 0.00 4.26
3728 4023 5.301045 CCATTGCATTCCTGTGATTATCAGT 59.699 40.000 0.00 0.00 0.00 3.41
3878 4173 3.559171 GGGTTGAGATGTGGTCAAAGCTA 60.559 47.826 0.00 0.00 35.71 3.32
3948 4243 2.708216 TGCCGTGAACATGATATGGT 57.292 45.000 0.00 0.00 33.60 3.55
3960 4255 1.131638 GATATGGTGGCAGGTGAGGA 58.868 55.000 0.00 0.00 0.00 3.71
3974 4269 0.958382 TGAGGAACAAAATCCCCGCG 60.958 55.000 0.00 0.00 40.59 6.46
4091 4386 2.744202 GACCGGCATCATTCATATGGTC 59.256 50.000 0.00 0.00 38.01 4.02
4126 4421 0.748005 GCGGTCCATACCTTGTGCAT 60.748 55.000 0.00 0.00 44.35 3.96
4164 4459 4.021981 CAGGAAGATGTACTGACAGACACA 60.022 45.833 10.08 12.66 39.50 3.72
4816 5120 9.513906 TTTGATATGTTCATTCTGTGTTTCCTA 57.486 29.630 0.00 0.00 33.34 2.94
4824 5128 8.567948 GTTCATTCTGTGTTTCCTATGAGAAAA 58.432 33.333 0.00 0.00 37.49 2.29
4849 5153 2.512515 GTGGCTGGGATCGACTGC 60.513 66.667 8.70 8.70 0.00 4.40
4960 5264 4.102524 AGGAACAAACTGACTATGGTGTGA 59.897 41.667 0.00 0.00 0.00 3.58
4961 5265 4.213482 GGAACAAACTGACTATGGTGTGAC 59.787 45.833 0.00 0.00 0.00 3.67
5022 5326 2.163818 TGTCATGTCGGTCCTGTTTC 57.836 50.000 0.00 0.00 0.00 2.78
5028 5332 0.321653 GTCGGTCCTGTTTCCAGCAT 60.322 55.000 0.00 0.00 37.38 3.79
5108 5425 3.822735 CTGACAAGAAAAATCCCTGCAGA 59.177 43.478 17.39 0.00 0.00 4.26
5110 5427 4.219070 TGACAAGAAAAATCCCTGCAGATG 59.781 41.667 17.39 6.04 0.00 2.90
5116 5433 6.666678 AGAAAAATCCCTGCAGATGATCTTA 58.333 36.000 17.39 0.00 0.00 2.10
5117 5434 7.296098 AGAAAAATCCCTGCAGATGATCTTAT 58.704 34.615 17.39 8.37 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.385825 TCTTGTAAGTCACGCTTTGGATT 58.614 39.130 0.00 0.00 38.57 3.01
1 2 3.997021 CTCTTGTAAGTCACGCTTTGGAT 59.003 43.478 0.00 0.00 38.57 3.41
2 3 3.390135 CTCTTGTAAGTCACGCTTTGGA 58.610 45.455 0.00 0.00 38.57 3.53
3 4 2.480419 CCTCTTGTAAGTCACGCTTTGG 59.520 50.000 0.00 0.00 38.57 3.28
4 5 2.480419 CCCTCTTGTAAGTCACGCTTTG 59.520 50.000 0.00 0.00 38.57 2.77
5 6 2.367567 TCCCTCTTGTAAGTCACGCTTT 59.632 45.455 0.00 0.00 38.57 3.51
11 12 5.684030 GCCGATTAATCCCTCTTGTAAGTCA 60.684 44.000 9.87 0.00 0.00 3.41
23 24 0.586802 GCTGAACGCCGATTAATCCC 59.413 55.000 9.87 0.79 0.00 3.85
49 50 9.251792 GGAAAACATAAAGTACAACCGAATTTT 57.748 29.630 0.00 0.00 0.00 1.82
132 133 4.315803 CCTTACCACACCTCAAAGTACAG 58.684 47.826 0.00 0.00 0.00 2.74
198 199 7.272244 ACTTGTTTTACCCTTTTGAGAATTGG 58.728 34.615 0.00 0.00 0.00 3.16
211 214 9.767228 AATGGTTTTGTATTACTTGTTTTACCC 57.233 29.630 0.00 0.00 0.00 3.69
228 232 1.669795 GGCCGAGCTTCAATGGTTTTG 60.670 52.381 0.00 0.00 0.00 2.44
257 261 4.636206 GGTAAAATGATCAGCTCCGAAAGT 59.364 41.667 0.09 0.00 0.00 2.66
258 262 4.878397 AGGTAAAATGATCAGCTCCGAAAG 59.122 41.667 0.09 0.00 0.00 2.62
259 263 4.843728 AGGTAAAATGATCAGCTCCGAAA 58.156 39.130 0.09 0.00 0.00 3.46
261 265 4.487714 AAGGTAAAATGATCAGCTCCGA 57.512 40.909 0.09 0.00 0.00 4.55
378 388 5.239087 GGTAGAAGTCCCTTAGATAGTGACG 59.761 48.000 0.00 0.00 36.49 4.35
385 395 3.051727 AGCCTGGTAGAAGTCCCTTAGAT 60.052 47.826 0.00 0.00 0.00 1.98
415 425 7.277098 TGTGTCCTCACTTTTATATTTACGCTC 59.723 37.037 0.00 0.00 44.14 5.03
418 428 9.916397 GATTGTGTCCTCACTTTTATATTTACG 57.084 33.333 0.00 0.00 44.14 3.18
490 500 4.359706 GTGATTTTGGCTTTGTCGACTTT 58.640 39.130 17.92 0.00 0.00 2.66
500 510 2.962859 ACAAGAGGGTGATTTTGGCTT 58.037 42.857 0.00 0.00 0.00 4.35
528 538 1.300971 CCAGGTCTTGATGCACCACG 61.301 60.000 0.00 0.00 34.80 4.94
537 547 2.915659 ACGCGGTCCAGGTCTTGA 60.916 61.111 12.47 0.00 0.00 3.02
539 549 4.052229 CGACGCGGTCCAGGTCTT 62.052 66.667 12.47 0.00 0.00 3.01
586 596 6.369890 AGACATGGATTGTTCATATGTATCGC 59.630 38.462 1.90 0.00 39.18 4.58
595 605 8.292448 GCGAAATATTAGACATGGATTGTTCAT 58.708 33.333 0.00 0.00 39.18 2.57
596 606 7.281999 TGCGAAATATTAGACATGGATTGTTCA 59.718 33.333 0.00 0.00 39.18 3.18
603 615 6.458206 GCAGTTTGCGAAATATTAGACATGGA 60.458 38.462 0.00 0.00 31.71 3.41
604 616 5.682862 GCAGTTTGCGAAATATTAGACATGG 59.317 40.000 0.00 0.00 31.71 3.66
623 635 6.759356 GTGTTTTAAATTTGGGTACTGCAGTT 59.241 34.615 27.06 9.41 0.00 3.16
627 639 5.176774 GCTGTGTTTTAAATTTGGGTACTGC 59.823 40.000 0.00 5.90 0.00 4.40
663 675 0.307760 CCGCTGAATGCCCGATAAAC 59.692 55.000 0.00 0.00 38.78 2.01
692 704 8.028938 AGTGTTCATAGTAATGATTGGCAAAAC 58.971 33.333 3.01 2.21 41.73 2.43
729 741 8.352942 ACACATTCCTTAAGAAACAAGAATGAC 58.647 33.333 24.51 0.00 38.21 3.06
735 751 5.534654 TGGGACACATTCCTTAAGAAACAAG 59.465 40.000 3.36 0.00 45.09 3.16
758 774 9.528018 AGTTATCACACCACAAATTTTTAAGTG 57.472 29.630 5.55 5.55 0.00 3.16
759 775 9.744468 GAGTTATCACACCACAAATTTTTAAGT 57.256 29.630 0.00 0.00 0.00 2.24
760 776 9.743057 TGAGTTATCACACCACAAATTTTTAAG 57.257 29.630 0.00 0.00 0.00 1.85
763 779 8.420222 TCATGAGTTATCACACCACAAATTTTT 58.580 29.630 0.00 0.00 38.57 1.94
818 835 7.320443 TGAGCATTGACTTGGATATGTTTAC 57.680 36.000 0.00 0.00 0.00 2.01
828 845 4.326504 ACCTTTTTGAGCATTGACTTGG 57.673 40.909 0.00 0.00 0.00 3.61
865 885 0.030603 TTGGGCCTCAAGGGGTTTTT 60.031 50.000 4.53 0.00 35.18 1.94
878 898 0.759060 GTGGGGAATATGGTTGGGCC 60.759 60.000 0.00 0.00 37.90 5.80
1598 1878 1.672881 CAAAAGCAGCGAGATAAGGGG 59.327 52.381 0.00 0.00 0.00 4.79
1624 1904 3.325753 AGGCCACAGGACAGAGCC 61.326 66.667 5.01 0.00 44.20 4.70
1642 1922 1.404315 GGAGCCGATATGATCCGTTCC 60.404 57.143 0.00 0.00 32.83 3.62
1696 1976 1.052287 GCAAACGATTTTCCACAGCG 58.948 50.000 0.00 0.00 0.00 5.18
1721 2001 1.626654 GCTGTTCGTGGATGGTCGTG 61.627 60.000 0.00 0.00 0.00 4.35
1722 2002 1.374252 GCTGTTCGTGGATGGTCGT 60.374 57.895 0.00 0.00 0.00 4.34
1723 2003 2.100631 GGCTGTTCGTGGATGGTCG 61.101 63.158 0.00 0.00 0.00 4.79
1724 2004 0.605319 TTGGCTGTTCGTGGATGGTC 60.605 55.000 0.00 0.00 0.00 4.02
1725 2005 0.179004 TTTGGCTGTTCGTGGATGGT 60.179 50.000 0.00 0.00 0.00 3.55
1747 2027 1.265905 CAAGTACAGTTTTCACCGGGC 59.734 52.381 6.32 0.00 0.00 6.13
1765 2045 4.634883 TCCGTTTAGTGTGTTTTGTAGCAA 59.365 37.500 0.00 0.00 0.00 3.91
1851 2135 2.585330 TGAGAGCAATGTTCAAAGCCA 58.415 42.857 0.00 0.00 0.00 4.75
1876 2160 2.507110 CCGACAGCGATGGAACACCT 62.507 60.000 5.32 0.00 40.82 4.00
1895 2179 0.657840 CTGCGGCTAAATAGTGTGGC 59.342 55.000 0.00 0.00 0.00 5.01
2000 2285 9.686683 ACCTCACAAATTATACTTGCTAATTCT 57.313 29.630 0.00 0.00 30.43 2.40
2133 2422 6.631971 TCAGCATTTCATTCCGCAATTATA 57.368 33.333 0.00 0.00 0.00 0.98
2135 2424 4.979943 TCAGCATTTCATTCCGCAATTA 57.020 36.364 0.00 0.00 0.00 1.40
2148 2437 8.322091 AGTAGACAATAGGTTACTTCAGCATTT 58.678 33.333 0.00 0.00 0.00 2.32
2157 2446 8.738106 GTCAAGTGTAGTAGACAATAGGTTACT 58.262 37.037 0.00 0.00 40.66 2.24
2185 2474 5.100259 AGATCAAACCATACGAACACGTAG 58.900 41.667 8.33 0.00 43.85 3.51
2189 2478 5.607119 ACAAGATCAAACCATACGAACAC 57.393 39.130 0.00 0.00 0.00 3.32
2194 2483 9.490663 GAATTTCTTACAAGATCAAACCATACG 57.509 33.333 0.00 0.00 34.49 3.06
2250 2539 4.454728 TCAATTAGCCCTCAAAATGCAC 57.545 40.909 0.00 0.00 0.00 4.57
2252 2541 6.264067 AGAGTATCAATTAGCCCTCAAAATGC 59.736 38.462 0.00 0.00 37.82 3.56
2269 2558 7.016153 ACACTTATTTTGGGACAGAGTATCA 57.984 36.000 0.00 0.00 42.39 2.15
2272 2561 5.475719 CGACACTTATTTTGGGACAGAGTA 58.524 41.667 0.00 0.00 42.39 2.59
2273 2562 4.315803 CGACACTTATTTTGGGACAGAGT 58.684 43.478 0.00 0.00 42.39 3.24
2274 2563 3.125316 GCGACACTTATTTTGGGACAGAG 59.875 47.826 0.00 0.00 42.39 3.35
2275 2564 3.071479 GCGACACTTATTTTGGGACAGA 58.929 45.455 0.00 0.00 42.39 3.41
2276 2565 3.074412 AGCGACACTTATTTTGGGACAG 58.926 45.455 0.00 0.00 42.39 3.51
2277 2566 2.811431 CAGCGACACTTATTTTGGGACA 59.189 45.455 0.00 0.00 0.00 4.02
2278 2567 3.071479 TCAGCGACACTTATTTTGGGAC 58.929 45.455 0.00 0.00 0.00 4.46
2279 2568 3.410631 TCAGCGACACTTATTTTGGGA 57.589 42.857 0.00 0.00 0.00 4.37
2280 2569 4.701956 AATCAGCGACACTTATTTTGGG 57.298 40.909 0.00 0.00 0.00 4.12
2281 2570 6.842163 ACTAAATCAGCGACACTTATTTTGG 58.158 36.000 0.00 0.00 34.69 3.28
2282 2571 8.440059 TGTACTAAATCAGCGACACTTATTTTG 58.560 33.333 0.00 0.00 34.69 2.44
2283 2572 8.542497 TGTACTAAATCAGCGACACTTATTTT 57.458 30.769 0.00 0.00 34.69 1.82
2284 2573 8.542497 TTGTACTAAATCAGCGACACTTATTT 57.458 30.769 0.00 0.00 36.43 1.40
2285 2574 8.542497 TTTGTACTAAATCAGCGACACTTATT 57.458 30.769 0.00 0.00 0.00 1.40
2286 2575 7.817962 ACTTTGTACTAAATCAGCGACACTTAT 59.182 33.333 0.00 0.00 0.00 1.73
2287 2576 7.149973 ACTTTGTACTAAATCAGCGACACTTA 58.850 34.615 0.00 0.00 0.00 2.24
2288 2577 5.989777 ACTTTGTACTAAATCAGCGACACTT 59.010 36.000 0.00 0.00 0.00 3.16
2289 2578 5.539048 ACTTTGTACTAAATCAGCGACACT 58.461 37.500 0.00 0.00 0.00 3.55
2290 2579 5.840940 ACTTTGTACTAAATCAGCGACAC 57.159 39.130 0.00 0.00 0.00 3.67
2291 2580 6.480651 TGAAACTTTGTACTAAATCAGCGACA 59.519 34.615 0.00 0.00 0.00 4.35
2292 2581 6.790825 GTGAAACTTTGTACTAAATCAGCGAC 59.209 38.462 0.00 0.00 0.00 5.19
2293 2582 6.884187 GTGAAACTTTGTACTAAATCAGCGA 58.116 36.000 0.00 0.00 0.00 4.93
2311 2600 9.659830 AAATAAGTGTCGTTGATTTAGTGAAAC 57.340 29.630 0.00 0.00 0.00 2.78
2313 2602 9.658475 CAAAATAAGTGTCGTTGATTTAGTGAA 57.342 29.630 0.00 0.00 0.00 3.18
2314 2603 8.286800 CCAAAATAAGTGTCGTTGATTTAGTGA 58.713 33.333 0.00 0.00 0.00 3.41
2315 2604 7.537306 CCCAAAATAAGTGTCGTTGATTTAGTG 59.463 37.037 0.00 0.00 0.00 2.74
2316 2605 7.446013 TCCCAAAATAAGTGTCGTTGATTTAGT 59.554 33.333 0.00 0.00 0.00 2.24
2317 2606 7.749126 GTCCCAAAATAAGTGTCGTTGATTTAG 59.251 37.037 0.00 0.00 0.00 1.85
2318 2607 7.571613 CGTCCCAAAATAAGTGTCGTTGATTTA 60.572 37.037 0.00 0.00 0.00 1.40
2319 2608 6.443792 GTCCCAAAATAAGTGTCGTTGATTT 58.556 36.000 0.00 0.00 0.00 2.17
2320 2609 5.334569 CGTCCCAAAATAAGTGTCGTTGATT 60.335 40.000 0.00 0.00 0.00 2.57
2321 2610 4.153475 CGTCCCAAAATAAGTGTCGTTGAT 59.847 41.667 0.00 0.00 0.00 2.57
2322 2611 3.495377 CGTCCCAAAATAAGTGTCGTTGA 59.505 43.478 0.00 0.00 0.00 3.18
2323 2612 3.364565 CCGTCCCAAAATAAGTGTCGTTG 60.365 47.826 0.00 0.00 0.00 4.10
2324 2613 2.809696 CCGTCCCAAAATAAGTGTCGTT 59.190 45.455 0.00 0.00 0.00 3.85
2325 2614 2.037511 TCCGTCCCAAAATAAGTGTCGT 59.962 45.455 0.00 0.00 0.00 4.34
2326 2615 2.671396 CTCCGTCCCAAAATAAGTGTCG 59.329 50.000 0.00 0.00 0.00 4.35
2327 2616 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2328 2617 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
2329 2618 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2330 2619 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2331 2620 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2332 2621 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2333 2622 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2334 2623 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2335 2624 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2336 2625 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
2337 2626 2.023695 AGTAATACTCCCTCCGTCCCAA 60.024 50.000 0.00 0.00 0.00 4.12
2338 2627 1.572415 AGTAATACTCCCTCCGTCCCA 59.428 52.381 0.00 0.00 0.00 4.37
2339 2628 2.378378 AGTAATACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
2340 2629 5.303845 ACAATAAGTAATACTCCCTCCGTCC 59.696 44.000 0.00 0.00 0.00 4.79
2341 2630 6.214399 CACAATAAGTAATACTCCCTCCGTC 58.786 44.000 0.00 0.00 0.00 4.79
2342 2631 5.452917 GCACAATAAGTAATACTCCCTCCGT 60.453 44.000 0.00 0.00 0.00 4.69
2343 2632 4.989168 GCACAATAAGTAATACTCCCTCCG 59.011 45.833 0.00 0.00 0.00 4.63
2344 2633 4.989168 CGCACAATAAGTAATACTCCCTCC 59.011 45.833 0.00 0.00 0.00 4.30
2345 2634 5.598769 ACGCACAATAAGTAATACTCCCTC 58.401 41.667 0.00 0.00 0.00 4.30
2346 2635 5.609533 ACGCACAATAAGTAATACTCCCT 57.390 39.130 0.00 0.00 0.00 4.20
2347 2636 6.510536 ACTACGCACAATAAGTAATACTCCC 58.489 40.000 0.00 0.00 0.00 4.30
2348 2637 9.125906 CATACTACGCACAATAAGTAATACTCC 57.874 37.037 0.00 0.00 0.00 3.85
2349 2638 9.125906 CCATACTACGCACAATAAGTAATACTC 57.874 37.037 0.00 0.00 0.00 2.59
2350 2639 7.597743 GCCATACTACGCACAATAAGTAATACT 59.402 37.037 0.00 0.00 0.00 2.12
2351 2640 7.148689 GGCCATACTACGCACAATAAGTAATAC 60.149 40.741 0.00 0.00 0.00 1.89
2366 2655 1.134818 TCTGCTTGTGGCCATACTACG 60.135 52.381 9.72 0.00 40.92 3.51
2402 2691 2.539688 GCACGACGAATGATGCATAGAA 59.460 45.455 0.00 0.00 38.00 2.10
2406 2695 1.372582 AAGCACGACGAATGATGCAT 58.627 45.000 0.00 0.00 40.63 3.96
2464 2753 8.665685 CATCCTAATACAGTTTACAGAACCAAC 58.334 37.037 0.00 0.00 0.00 3.77
2506 2796 0.673437 TGTCATCGTCACAGAGCACA 59.327 50.000 0.00 0.00 0.00 4.57
2513 2803 1.276138 AGCCTCATTGTCATCGTCACA 59.724 47.619 0.00 0.00 0.00 3.58
2514 2804 1.662629 CAGCCTCATTGTCATCGTCAC 59.337 52.381 0.00 0.00 0.00 3.67
2558 2849 2.159234 GCAGTGCACAATTCTGAGAGAC 59.841 50.000 21.04 0.00 0.00 3.36
2596 2887 7.072454 TGACTGGGAGCATATTTACTTAGGATT 59.928 37.037 0.00 0.00 0.00 3.01
2611 2902 0.397941 CAGGTCTTTGACTGGGAGCA 59.602 55.000 0.00 0.00 32.47 4.26
2619 2910 7.064728 GGTTTCACTATATGACAGGTCTTTGAC 59.935 40.741 0.65 0.00 36.92 3.18
2654 2945 3.613299 TGCGATGCAAGCAAAATAATGTG 59.387 39.130 16.37 0.00 42.18 3.21
2816 3109 2.726821 ACACATTTACAGGGGAGCATG 58.273 47.619 0.00 0.00 0.00 4.06
2901 3194 6.974965 AGATAGAAACAAGTTCAAAAGGCAG 58.025 36.000 0.00 0.00 38.86 4.85
3137 3430 6.456988 CGTTAAGGAAGGAATCTACAACATGC 60.457 42.308 0.00 0.00 0.00 4.06
3245 3538 6.763610 AGTAAATGCTAGGCTGAGACATAAAC 59.236 38.462 0.00 0.00 0.00 2.01
3449 3744 8.573035 TCCAGTTAATTCCATGTCACTAAAAAC 58.427 33.333 0.00 0.00 0.00 2.43
3471 3766 1.856539 ATGGTGAGGGGCAAGTCCAG 61.857 60.000 0.00 0.00 36.21 3.86
3704 3999 5.301045 ACTGATAATCACAGGAATGCAATGG 59.699 40.000 0.00 0.00 39.38 3.16
3728 4023 0.691078 AAGGGAGCTCAATCCGGCTA 60.691 55.000 17.19 0.00 40.56 3.93
3948 4243 2.238521 GATTTTGTTCCTCACCTGCCA 58.761 47.619 0.00 0.00 0.00 4.92
3960 4255 1.270274 GTTAACCGCGGGGATTTTGTT 59.730 47.619 31.76 14.40 36.97 2.83
3974 4269 1.737793 CTGTGGATCGCAAGGTTAACC 59.262 52.381 17.41 17.41 38.47 2.85
4070 4365 2.744202 GACCATATGAATGATGCCGGTC 59.256 50.000 3.65 0.00 34.84 4.79
4112 4407 3.065786 GTGTCATGATGCACAAGGTATGG 59.934 47.826 10.69 0.00 35.81 2.74
4126 4421 2.252535 TCCTGGATCCAGTGTCATGA 57.747 50.000 34.49 22.63 42.15 3.07
4684 4979 3.589495 AAGGGCTCAAGAAGTACGTAC 57.411 47.619 18.10 18.10 0.00 3.67
4685 4980 5.010922 TGTTAAAGGGCTCAAGAAGTACGTA 59.989 40.000 0.00 0.00 0.00 3.57
4686 4981 4.202284 TGTTAAAGGGCTCAAGAAGTACGT 60.202 41.667 0.00 0.00 0.00 3.57
4687 4982 4.312443 TGTTAAAGGGCTCAAGAAGTACG 58.688 43.478 0.00 0.00 0.00 3.67
4731 5032 7.362662 GTCAGCTATCTCAAAAACAATCAACA 58.637 34.615 0.00 0.00 0.00 3.33
4816 5120 2.579860 AGCCACCCAGAGATTTTCTCAT 59.420 45.455 7.24 0.00 45.73 2.90
4824 5128 1.005289 ATCCCAGCCACCCAGAGAT 59.995 57.895 0.00 0.00 0.00 2.75
4849 5153 2.877168 GTCAATGAGATAAGCAGGCCAG 59.123 50.000 5.01 0.00 0.00 4.85
4937 5241 4.102524 TCACACCATAGTCAGTTTGTTCCT 59.897 41.667 0.00 0.00 0.00 3.36
5034 5338 4.563140 TTACTTCTCCACAATACCCACC 57.437 45.455 0.00 0.00 0.00 4.61
5108 5425 9.253832 CTCCTACTCCTGTGAATATAAGATCAT 57.746 37.037 0.00 0.00 0.00 2.45
5110 5427 8.871629 TCTCCTACTCCTGTGAATATAAGATC 57.128 38.462 0.00 0.00 0.00 2.75


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.