Multiple sequence alignment - TraesCS2A01G156200

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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 TraesCS2A01G156200 chr2A 100.000 5510 0 0 1 5510 103106283 103100774 0.000000e+00 10176.0
1 TraesCS2A01G156200 chr2A 80.404 495 84 10 239 723 553049756 553049265 1.130000e-96 364.0
2 TraesCS2A01G156200 chr2A 93.023 129 6 1 5382 5510 251390719 251390844 9.430000e-43 185.0
3 TraesCS2A01G156200 chr2A 73.151 365 83 8 371 723 451014769 451014408 3.490000e-22 117.0
4 TraesCS2A01G156200 chr2A 94.828 58 2 1 4793 4850 103101460 103101404 7.600000e-14 89.8
5 TraesCS2A01G156200 chr2A 94.828 58 2 1 4824 4880 103101491 103101434 7.600000e-14 89.8
6 TraesCS2A01G156200 chr2A 80.247 81 15 1 640 720 36881500 36881579 5.960000e-05 60.2
7 TraesCS2A01G156200 chr2B 94.548 4072 141 34 779 4813 156597721 156593694 0.000000e+00 6215.0
8 TraesCS2A01G156200 chr2B 92.176 524 31 8 4992 5510 156593472 156592954 0.000000e+00 732.0
9 TraesCS2A01G156200 chr2B 82.745 765 106 14 13 754 156599316 156598555 0.000000e+00 658.0
10 TraesCS2A01G156200 chr2D 89.103 1193 74 20 755 1893 106632684 106631494 0.000000e+00 1432.0
11 TraesCS2A01G156200 chr2D 92.093 645 42 4 3124 3762 106630475 106629834 0.000000e+00 900.0
12 TraesCS2A01G156200 chr2D 85.235 745 88 16 16 746 106637914 106637178 0.000000e+00 747.0
13 TraesCS2A01G156200 chr2D 90.603 564 40 8 3756 4317 106629759 106629207 0.000000e+00 736.0
14 TraesCS2A01G156200 chr2D 91.506 518 29 6 4993 5510 106628382 106627880 0.000000e+00 699.0
15 TraesCS2A01G156200 chr2D 90.081 494 42 6 1919 2409 106631497 106631008 7.790000e-178 634.0
16 TraesCS2A01G156200 chr2D 87.530 417 39 7 2487 2895 106631010 106630599 2.320000e-128 470.0
17 TraesCS2A01G156200 chr2D 87.089 395 38 10 4369 4763 106629205 106628824 8.480000e-118 435.0
18 TraesCS2A01G156200 chr2D 92.366 131 5 3 5380 5510 622711270 622711395 1.220000e-41 182.0
19 TraesCS2A01G156200 chr2D 84.568 162 24 1 2965 3125 618204766 618204927 5.710000e-35 159.0
20 TraesCS2A01G156200 chr2D 73.446 354 75 14 382 723 61450442 61450788 1.250000e-21 115.0
21 TraesCS2A01G156200 chr2D 80.822 146 20 2 1140 1278 581247091 581246947 2.100000e-19 108.0
22 TraesCS2A01G156200 chr2D 94.737 57 3 0 4757 4813 106628660 106628604 7.600000e-14 89.8
23 TraesCS2A01G156200 chr1A 79.928 553 101 7 179 723 369999433 369998883 1.110000e-106 398.0
24 TraesCS2A01G156200 chr7D 82.353 442 74 4 179 619 25058611 25058173 1.120000e-101 381.0
25 TraesCS2A01G156200 chr7D 76.190 273 52 8 462 723 186395480 186395750 1.250000e-26 132.0
26 TraesCS2A01G156200 chr3D 79.348 552 102 8 179 723 529837915 529838461 1.450000e-100 377.0
27 TraesCS2A01G156200 chr7B 80.388 464 81 9 179 638 687549813 687549356 1.470000e-90 344.0
28 TraesCS2A01G156200 chr7B 74.706 170 34 5 557 717 57587419 57587588 3.560000e-07 67.6
29 TraesCS2A01G156200 chr3A 80.130 463 79 11 179 637 643213271 643213724 3.180000e-87 333.0
30 TraesCS2A01G156200 chr5D 76.937 555 107 14 179 719 285841012 285841559 4.170000e-76 296.0
31 TraesCS2A01G156200 chr5D 79.139 302 53 6 431 723 2134434 2134734 3.370000e-47 200.0
32 TraesCS2A01G156200 chr4D 76.350 537 111 11 198 723 63078551 63078020 1.960000e-69 274.0
33 TraesCS2A01G156200 chr4D 96.947 131 1 1 5380 5510 46139925 46139798 3.340000e-52 217.0
34 TraesCS2A01G156200 chr6A 93.893 131 5 1 5380 5510 595732651 595732778 1.570000e-45 195.0
35 TraesCS2A01G156200 chr6A 91.045 67 6 0 3057 3123 538046604 538046538 2.110000e-14 91.6
36 TraesCS2A01G156200 chr5B 92.366 131 7 1 5380 5510 236414536 236414663 3.390000e-42 183.0
37 TraesCS2A01G156200 chr5B 90.076 131 10 1 5380 5510 236737069 236737196 3.410000e-37 167.0
38 TraesCS2A01G156200 chr5B 91.379 58 5 0 3066 3123 3849930 3849873 4.580000e-11 80.5
39 TraesCS2A01G156200 chr6D 83.871 186 28 2 2943 3126 463865774 463865959 5.670000e-40 176.0
40 TraesCS2A01G156200 chr4A 88.550 131 10 2 5380 5510 657667908 657667783 2.660000e-33 154.0
41 TraesCS2A01G156200 chr1B 81.452 124 21 2 2972 3094 9984792 9984914 3.510000e-17 100.0
42 TraesCS2A01G156200 chr6B 92.537 67 5 0 3057 3123 585531206 585531140 4.540000e-16 97.1
43 TraesCS2A01G156200 chr6B 94.231 52 3 0 3074 3125 574463729 574463678 4.580000e-11 80.5
44 TraesCS2A01G156200 chrUn 86.154 65 8 1 3033 3096 323923522 323923458 9.900000e-08 69.4
45 TraesCS2A01G156200 chr7A 86.154 65 8 1 3033 3096 67678253 67678189 9.900000e-08 69.4


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 TraesCS2A01G156200 chr2A 103100774 103106283 5509 True 10176.000 10176 100.00000 1 5510 1 chr2A.!!$R1 5509
1 TraesCS2A01G156200 chr2B 156592954 156599316 6362 True 2535.000 6215 89.82300 13 5510 3 chr2B.!!$R1 5497
2 TraesCS2A01G156200 chr2D 106637178 106637914 736 True 747.000 747 85.23500 16 746 1 chr2D.!!$R1 730
3 TraesCS2A01G156200 chr2D 106627880 106632684 4804 True 674.475 1432 90.34275 755 5510 8 chr2D.!!$R3 4755
4 TraesCS2A01G156200 chr1A 369998883 369999433 550 True 398.000 398 79.92800 179 723 1 chr1A.!!$R1 544
5 TraesCS2A01G156200 chr3D 529837915 529838461 546 False 377.000 377 79.34800 179 723 1 chr3D.!!$F1 544
6 TraesCS2A01G156200 chr5D 285841012 285841559 547 False 296.000 296 76.93700 179 719 1 chr5D.!!$F2 540
7 TraesCS2A01G156200 chr4D 63078020 63078551 531 True 274.000 274 76.35000 198 723 1 chr4D.!!$R2 525


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
479 489 0.034198 TCGGTCGGCATTTGTCTTCA 59.966 50.000 0.0 0.0 0.00 3.02 F
668 702 0.677414 GAGAGAGGGACGAAGACGGT 60.677 60.000 0.0 0.0 44.46 4.83 F
1202 2077 1.004610 CTATGTCATTCCTTGCGTGCG 60.005 52.381 0.0 0.0 0.00 5.34 F
1671 2554 0.601558 TCGTGGTGCTTCTCCAGTAC 59.398 55.000 0.0 0.0 37.39 2.73 F
2181 3081 1.211949 ACCTCTCCCTCTCTCTTCTCG 59.788 57.143 0.0 0.0 0.00 4.04 F
4053 5133 1.449601 CCGTGGTATGCCCTCACAC 60.450 63.158 0.0 0.0 0.00 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1550 2425 0.035630 AAGCATCTGTCCAGGAGTGC 60.036 55.000 7.63 7.63 34.41 4.40 R
1620 2503 2.044492 TCCAGGAGTTCCACCATCTAGT 59.956 50.000 0.28 0.00 38.89 2.57 R
3087 4082 1.620819 CAGGATATGCCTCTTAGCGGT 59.379 52.381 0.00 0.00 46.97 5.68 R
3615 4610 4.617808 GTCAGTGACGCTAAGATGAGTA 57.382 45.455 7.68 0.00 0.00 2.59 R
4156 5236 2.542618 CGTCTGAGGTTGGATCGATGAG 60.543 54.545 0.54 0.00 0.00 2.90 R
5167 6523 0.044092 TGGGATAAGAGGGGCTGTGA 59.956 55.000 0.00 0.00 0.00 3.58 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
59 60 3.270027 CTTGCCATGTCGACAATCCTTA 58.730 45.455 24.13 5.94 0.00 2.69
73 74 7.067737 TCGACAATCCTTATTTGGGAAAATACC 59.932 37.037 0.00 0.00 36.37 2.73
169 170 7.633361 TTTCACACGTAATCTCAGTCTAAAC 57.367 36.000 0.00 0.00 0.00 2.01
191 192 4.220602 ACTTTTCACAGTTTCTTGTGCCTT 59.779 37.500 1.43 0.00 46.24 4.35
294 302 3.203161 GGAGAACTCCGTTTTTCATGC 57.797 47.619 5.06 0.00 40.36 4.06
336 344 2.001076 TTGTGTCCTGCTCAGAGAGA 57.999 50.000 0.00 0.00 0.00 3.10
381 389 8.843308 TGAAGATGAAATAAAATTCTCCCCAT 57.157 30.769 0.00 0.00 0.00 4.00
418 427 3.119245 GGTGGTGTTTCTAGCATAGTCGA 60.119 47.826 0.00 0.00 40.38 4.20
423 432 4.021229 TGTTTCTAGCATAGTCGAAGGGA 58.979 43.478 0.00 0.00 40.38 4.20
479 489 0.034198 TCGGTCGGCATTTGTCTTCA 59.966 50.000 0.00 0.00 0.00 3.02
517 538 6.199908 GGATCTTGTCTTCATTCGTCTATGTG 59.800 42.308 0.00 0.00 0.00 3.21
527 548 3.282831 TCGTCTATGTGTGTGTGTCTG 57.717 47.619 0.00 0.00 0.00 3.51
535 556 1.068588 GTGTGTGTGTCTGTAGGCTGA 59.931 52.381 0.00 0.00 0.00 4.26
548 569 5.045651 TCTGTAGGCTGAATCCTTTTGATCA 60.046 40.000 0.00 0.00 37.66 2.92
571 592 1.358725 CTTTTCTTCATCGGCGGCGA 61.359 55.000 36.40 36.40 0.00 5.54
591 612 1.727511 TTGCTGTTCTGGTGTGCTGC 61.728 55.000 0.00 0.00 0.00 5.25
599 620 2.466846 TCTGGTGTGCTGCTCCTATAA 58.533 47.619 0.00 0.00 0.00 0.98
607 628 3.045634 TGCTGCTCCTATAAGGCCTTAA 58.954 45.455 28.50 16.27 34.61 1.85
611 632 3.135895 TGCTCCTATAAGGCCTTAACACC 59.864 47.826 28.50 14.81 34.61 4.16
619 640 3.525800 AGGCCTTAACACCATGACTTT 57.474 42.857 0.00 0.00 0.00 2.66
620 641 3.844640 AGGCCTTAACACCATGACTTTT 58.155 40.909 0.00 0.00 0.00 2.27
624 645 4.069304 CCTTAACACCATGACTTTTCGGA 58.931 43.478 0.00 0.00 0.00 4.55
644 678 4.750098 CGGATGTCTATTACAATTCGGCTT 59.250 41.667 0.00 0.00 42.70 4.35
652 686 7.224753 GTCTATTACAATTCGGCTTCAATGAGA 59.775 37.037 0.00 0.00 0.00 3.27
658 692 0.826715 CGGCTTCAATGAGAGAGGGA 59.173 55.000 0.00 0.00 0.00 4.20
668 702 0.677414 GAGAGAGGGACGAAGACGGT 60.677 60.000 0.00 0.00 44.46 4.83
711 746 4.688879 CCAATGCTTGTAGTCGTTGTTAGA 59.311 41.667 0.00 0.00 0.00 2.10
724 763 4.400251 TCGTTGTTAGATGGTCTACGGATT 59.600 41.667 0.00 0.00 33.08 3.01
740 779 5.183014 ACGGATTTTTCTGGTGTTCTTTC 57.817 39.130 0.00 0.00 0.00 2.62
747 786 7.473027 TTTTTCTGGTGTTCTTTCTACTACG 57.527 36.000 0.00 0.00 0.00 3.51
1188 2063 3.005684 CCACTCCTGCATCTCTCTATGTC 59.994 52.174 0.00 0.00 0.00 3.06
1194 2069 4.283978 CCTGCATCTCTCTATGTCATTCCT 59.716 45.833 0.00 0.00 0.00 3.36
1197 2072 4.451774 GCATCTCTCTATGTCATTCCTTGC 59.548 45.833 0.00 0.00 0.00 4.01
1202 2077 1.004610 CTATGTCATTCCTTGCGTGCG 60.005 52.381 0.00 0.00 0.00 5.34
1203 2078 2.202349 GTCATTCCTTGCGTGCGC 60.202 61.111 9.85 9.85 42.35 6.09
1242 2117 1.129437 GCTTCGTGCTCAACAATCTCC 59.871 52.381 0.00 0.00 38.95 3.71
1296 2171 1.141645 GTGGTGTTCGACGTTATGCA 58.858 50.000 0.00 0.00 0.00 3.96
1300 2175 2.029244 GGTGTTCGACGTTATGCATGAG 59.971 50.000 10.16 2.80 0.00 2.90
1341 2216 2.939103 GCAACGCTGATATCCAGTTCTT 59.061 45.455 0.00 0.00 44.71 2.52
1386 2261 2.183478 TGTACTGTGGAATGCCTGTG 57.817 50.000 0.00 0.00 34.31 3.66
1457 2332 2.880268 TCTTGACAGACATGTTGCTTGG 59.120 45.455 0.00 0.00 40.68 3.61
1519 2394 6.017026 GGCTAGTGATTTATTCAGGCTAAACC 60.017 42.308 0.00 0.00 34.17 3.27
1530 2405 1.839424 GGCTAAACCTGTCATGGCTT 58.161 50.000 0.00 0.00 34.51 4.35
1532 2407 2.162681 GCTAAACCTGTCATGGCTTGT 58.837 47.619 0.00 0.00 0.00 3.16
1533 2408 2.162408 GCTAAACCTGTCATGGCTTGTC 59.838 50.000 0.00 0.00 0.00 3.18
1535 2410 1.237285 AACCTGTCATGGCTTGTCGC 61.237 55.000 0.00 0.00 38.13 5.19
1551 2426 4.043200 GCCTGGCGTTCCTTGTGC 62.043 66.667 1.35 0.00 0.00 4.57
1552 2427 2.594303 CCTGGCGTTCCTTGTGCA 60.594 61.111 0.00 0.00 0.00 4.57
1553 2428 2.639286 CTGGCGTTCCTTGTGCAC 59.361 61.111 10.75 10.75 0.00 4.57
1554 2429 1.893808 CTGGCGTTCCTTGTGCACT 60.894 57.895 19.41 0.00 0.00 4.40
1558 2441 1.845809 GCGTTCCTTGTGCACTCCTG 61.846 60.000 19.41 4.20 0.00 3.86
1620 2503 1.405105 GCCACTTGCACTTTCAGTTGA 59.595 47.619 0.00 0.00 40.77 3.18
1621 2504 2.796032 GCCACTTGCACTTTCAGTTGAC 60.796 50.000 0.00 0.00 40.77 3.18
1628 2511 4.318332 TGCACTTTCAGTTGACTAGATGG 58.682 43.478 0.00 0.00 0.00 3.51
1634 2517 4.537135 TCAGTTGACTAGATGGTGGAAC 57.463 45.455 0.00 0.00 0.00 3.62
1660 2543 2.253603 GATTTCATGCTTTCGTGGTGC 58.746 47.619 0.00 0.00 0.00 5.01
1666 2549 0.884704 TGCTTTCGTGGTGCTTCTCC 60.885 55.000 0.00 0.00 0.00 3.71
1671 2554 0.601558 TCGTGGTGCTTCTCCAGTAC 59.398 55.000 0.00 0.00 37.39 2.73
1737 2636 5.534654 GGAGAATCTGTACTCTGCTATCTGT 59.465 44.000 0.00 0.00 34.11 3.41
1903 2802 4.926238 TGCTTTTCTGCTTTGAACGAAAAA 59.074 33.333 0.00 0.00 35.64 1.94
2086 2986 4.454728 TCAGGGCTGAATACAATTTTGC 57.545 40.909 0.00 0.00 36.53 3.68
2089 2989 2.923020 GGGCTGAATACAATTTTGCGTG 59.077 45.455 0.00 0.00 0.00 5.34
2181 3081 1.211949 ACCTCTCCCTCTCTCTTCTCG 59.788 57.143 0.00 0.00 0.00 4.04
2258 3159 6.895040 GCGTTTGTATCTTCAATTCTAAGTCG 59.105 38.462 0.00 0.00 0.00 4.18
2431 3332 5.426504 TGGTTTTGATTGCAAGTGTGAAAT 58.573 33.333 4.94 0.00 35.51 2.17
2810 3720 7.178274 TGGCTAAATCTTTCTCAATAGGCAAAA 59.822 33.333 4.64 0.00 41.21 2.44
2811 3721 8.200120 GGCTAAATCTTTCTCAATAGGCAAAAT 58.800 33.333 0.00 0.00 36.35 1.82
2812 3722 9.242477 GCTAAATCTTTCTCAATAGGCAAAATC 57.758 33.333 0.00 0.00 0.00 2.17
2958 3952 4.769488 TGGTCAGCATGGTTTTAAATAGCA 59.231 37.500 0.00 0.00 36.16 3.49
2993 3987 6.496571 CACTATAGTGTTTAGAAGAGGTCCG 58.503 44.000 22.48 0.00 40.96 4.79
3004 3998 2.687566 AGGTCCGGTGCTAAGGGG 60.688 66.667 0.00 0.00 0.00 4.79
3087 4082 4.037684 GCTATAGCGTTTAGAAGAGGTCCA 59.962 45.833 9.40 0.00 0.00 4.02
3577 4572 9.747898 TTCTACTTGGAAATGCTCCTAAATTAA 57.252 29.630 0.00 0.00 45.64 1.40
3627 4622 9.534565 TGTGTTCATATTCTTACTCATCTTAGC 57.465 33.333 0.00 0.00 0.00 3.09
4053 5133 1.449601 CCGTGGTATGCCCTCACAC 60.450 63.158 0.00 0.00 0.00 3.82
4156 5236 3.744942 GTCCTGTTTAGGGAAGAACGTTC 59.255 47.826 20.71 20.71 44.70 3.95
4269 5349 0.832135 TGACTGGGGAGTGGACTGAC 60.832 60.000 0.00 0.00 0.00 3.51
4333 5413 7.312657 TCTGAGATACACAATTTCTTGATGC 57.687 36.000 0.00 0.00 36.20 3.91
4342 5422 7.246311 ACACAATTTCTTGATGCTTCGATTAG 58.754 34.615 0.00 0.00 36.20 1.73
4347 5427 9.512435 AATTTCTTGATGCTTCGATTAGAATTG 57.488 29.630 0.00 0.00 38.34 2.32
4358 5438 5.037385 TCGATTAGAATTGCTTGACTCTCG 58.963 41.667 0.00 0.00 0.00 4.04
4366 5446 8.397575 AGAATTGCTTGACTCTCGTATATAGA 57.602 34.615 0.00 0.00 0.00 1.98
4488 5568 1.003233 GGAGCGCTTGAAAGACCCT 60.003 57.895 13.26 0.00 0.00 4.34
4536 5616 4.198530 TGAGCAGACACATGTTTTCAGAA 58.801 39.130 0.00 0.00 0.00 3.02
4537 5617 4.035558 TGAGCAGACACATGTTTTCAGAAC 59.964 41.667 0.00 0.00 0.00 3.01
4539 5619 3.066621 GCAGACACATGTTTTCAGAACCA 59.933 43.478 0.00 0.00 0.00 3.67
4574 5654 5.755861 CCTTAGCTGTAGAAATTCTGTAGGC 59.244 44.000 5.64 5.09 0.00 3.93
4577 5657 5.181748 AGCTGTAGAAATTCTGTAGGCAAG 58.818 41.667 5.64 0.00 0.00 4.01
4583 5663 0.548510 ATTCTGTAGGCAAGGGAGGC 59.451 55.000 0.00 0.00 0.00 4.70
4609 5689 2.619849 CCTGATGTTTGGAGGAGCACAT 60.620 50.000 0.00 0.00 32.41 3.21
4620 5700 2.099756 GAGGAGCACATTTTACATGGCC 59.900 50.000 0.00 0.00 0.00 5.36
4658 5738 4.879104 TTGGCAAAAGAGCAAATTGTTG 57.121 36.364 0.00 0.00 37.83 3.33
4659 5739 3.871485 TGGCAAAAGAGCAAATTGTTGT 58.129 36.364 0.00 0.00 37.06 3.32
4660 5740 4.260170 TGGCAAAAGAGCAAATTGTTGTT 58.740 34.783 0.00 0.00 37.06 2.83
4661 5741 5.423015 TGGCAAAAGAGCAAATTGTTGTTA 58.577 33.333 0.00 0.00 37.06 2.41
4662 5742 5.877012 TGGCAAAAGAGCAAATTGTTGTTAA 59.123 32.000 0.00 0.00 37.06 2.01
4663 5743 6.036953 TGGCAAAAGAGCAAATTGTTGTTAAG 59.963 34.615 0.00 0.00 37.06 1.85
4664 5744 6.421405 GCAAAAGAGCAAATTGTTGTTAAGG 58.579 36.000 0.00 0.00 37.06 2.69
4665 5745 6.421405 CAAAAGAGCAAATTGTTGTTAAGGC 58.579 36.000 0.00 0.00 37.06 4.35
4666 5746 4.935352 AGAGCAAATTGTTGTTAAGGCA 57.065 36.364 0.00 0.00 37.06 4.75
4667 5747 5.275067 AGAGCAAATTGTTGTTAAGGCAA 57.725 34.783 0.00 0.00 37.06 4.52
4672 5752 5.752955 GCAAATTGTTGTTAAGGCAAGAGAA 59.247 36.000 0.00 0.00 37.06 2.87
4675 5755 7.770801 AATTGTTGTTAAGGCAAGAGAAAAC 57.229 32.000 0.00 0.00 0.00 2.43
4676 5756 4.915704 TGTTGTTAAGGCAAGAGAAAACG 58.084 39.130 0.00 0.00 0.00 3.60
4677 5757 3.619233 TGTTAAGGCAAGAGAAAACGC 57.381 42.857 0.00 0.00 0.00 4.84
4678 5758 3.211045 TGTTAAGGCAAGAGAAAACGCT 58.789 40.909 0.00 0.00 0.00 5.07
4680 5760 4.219802 GTTAAGGCAAGAGAAAACGCTTC 58.780 43.478 0.00 0.00 0.00 3.86
4681 5761 1.239347 AGGCAAGAGAAAACGCTTCC 58.761 50.000 0.00 0.00 0.00 3.46
4687 5767 4.065789 CAAGAGAAAACGCTTCCTAGGTT 58.934 43.478 9.08 0.00 0.00 3.50
4689 5769 5.479124 AGAGAAAACGCTTCCTAGGTTTA 57.521 39.130 9.08 0.00 33.80 2.01
4691 5771 4.964593 AGAAAACGCTTCCTAGGTTTACA 58.035 39.130 9.08 0.00 33.80 2.41
4692 5772 5.557866 AGAAAACGCTTCCTAGGTTTACAT 58.442 37.500 9.08 0.00 33.80 2.29
4700 5780 3.884895 TCCTAGGTTTACATGCCATGTG 58.115 45.455 20.36 1.45 44.60 3.21
4701 5781 2.358898 CCTAGGTTTACATGCCATGTGC 59.641 50.000 20.36 9.91 44.60 4.57
4707 5787 3.625649 TTACATGCCATGTGCTGTAGA 57.374 42.857 20.36 0.00 44.60 2.59
4708 5788 2.034104 ACATGCCATGTGCTGTAGAG 57.966 50.000 10.06 0.00 43.01 2.43
4709 5789 1.280133 ACATGCCATGTGCTGTAGAGT 59.720 47.619 10.06 0.00 43.01 3.24
4710 5790 2.501316 ACATGCCATGTGCTGTAGAGTA 59.499 45.455 10.06 0.00 43.01 2.59
4711 5791 2.672961 TGCCATGTGCTGTAGAGTAC 57.327 50.000 0.86 0.86 42.00 2.73
4716 5796 4.038042 GCCATGTGCTGTAGAGTACTATGA 59.962 45.833 15.99 0.00 35.90 2.15
4750 5831 6.204882 CCTGAGACTTTTCGGAACTTTGTATT 59.795 38.462 0.00 0.00 0.00 1.89
4755 6006 8.727910 AGACTTTTCGGAACTTTGTATTATTCC 58.272 33.333 0.00 0.00 37.79 3.01
4789 6040 4.502105 TGATGTCAAAGCTATTGCCCTA 57.498 40.909 0.00 0.00 40.80 3.53
4815 6066 4.891037 GCTGGGAGCCTGGGATGC 62.891 72.222 0.00 0.00 34.48 3.91
4816 6067 3.095163 CTGGGAGCCTGGGATGCT 61.095 66.667 0.00 0.00 43.03 3.79
4817 6068 1.767672 CTGGGAGCCTGGGATGCTA 60.768 63.158 0.00 0.00 39.69 3.49
4818 6069 1.073474 TGGGAGCCTGGGATGCTAT 60.073 57.895 0.00 0.00 39.69 2.97
4819 6070 0.193321 TGGGAGCCTGGGATGCTATA 59.807 55.000 0.00 0.00 39.69 1.31
4820 6071 1.362224 GGGAGCCTGGGATGCTATAA 58.638 55.000 0.00 0.00 39.69 0.98
4821 6072 1.705186 GGGAGCCTGGGATGCTATAAA 59.295 52.381 0.00 0.00 39.69 1.40
4822 6073 2.310052 GGGAGCCTGGGATGCTATAAAT 59.690 50.000 0.00 0.00 39.69 1.40
4823 6074 3.245407 GGGAGCCTGGGATGCTATAAATT 60.245 47.826 0.00 0.00 39.69 1.82
4824 6075 4.411013 GGAGCCTGGGATGCTATAAATTT 58.589 43.478 0.00 0.00 39.69 1.82
4825 6076 4.835056 GGAGCCTGGGATGCTATAAATTTT 59.165 41.667 0.00 0.00 39.69 1.82
4826 6077 5.305386 GGAGCCTGGGATGCTATAAATTTTT 59.695 40.000 0.00 0.00 39.69 1.94
4827 6078 6.165700 AGCCTGGGATGCTATAAATTTTTG 57.834 37.500 0.00 0.00 37.28 2.44
4828 6079 5.070847 AGCCTGGGATGCTATAAATTTTTGG 59.929 40.000 0.00 0.00 37.28 3.28
4829 6080 5.742838 GCCTGGGATGCTATAAATTTTTGGG 60.743 44.000 0.00 0.00 0.00 4.12
4830 6081 5.289083 TGGGATGCTATAAATTTTTGGGC 57.711 39.130 0.00 0.00 0.00 5.36
4831 6082 4.968080 TGGGATGCTATAAATTTTTGGGCT 59.032 37.500 0.00 0.00 0.00 5.19
4832 6083 5.163322 TGGGATGCTATAAATTTTTGGGCTG 60.163 40.000 0.00 0.00 0.00 4.85
4833 6084 5.299949 GGATGCTATAAATTTTTGGGCTGG 58.700 41.667 0.00 0.00 0.00 4.85
4834 6085 4.751767 TGCTATAAATTTTTGGGCTGGG 57.248 40.909 0.00 0.00 0.00 4.45
4835 6086 4.357325 TGCTATAAATTTTTGGGCTGGGA 58.643 39.130 0.00 0.00 0.00 4.37
4836 6087 4.405358 TGCTATAAATTTTTGGGCTGGGAG 59.595 41.667 0.00 0.00 0.00 4.30
4837 6088 3.912496 ATAAATTTTTGGGCTGGGAGC 57.088 42.857 0.00 0.00 41.46 4.70
4859 6110 5.898972 AGCCTGGGATGCTATAAAATTTTGA 59.101 36.000 13.76 0.78 37.28 2.69
4864 6115 6.183360 TGGGATGCTATAAAATTTTGAGCTGG 60.183 38.462 26.75 10.41 33.89 4.85
4865 6116 6.218746 GGATGCTATAAAATTTTGAGCTGGG 58.781 40.000 26.75 9.66 33.89 4.45
4866 6117 6.040842 GGATGCTATAAAATTTTGAGCTGGGA 59.959 38.462 26.75 15.23 33.89 4.37
4867 6118 6.455360 TGCTATAAAATTTTGAGCTGGGAG 57.545 37.500 26.75 10.95 33.89 4.30
4868 6119 5.163519 TGCTATAAAATTTTGAGCTGGGAGC 60.164 40.000 26.75 17.28 42.84 4.70
4869 6120 4.743057 ATAAAATTTTGAGCTGGGAGCC 57.257 40.909 13.76 0.00 43.77 4.70
4872 6126 0.324091 ATTTTGAGCTGGGAGCCTGG 60.324 55.000 0.00 0.00 43.77 4.45
4873 6127 2.430704 TTTTGAGCTGGGAGCCTGGG 62.431 60.000 0.00 0.00 43.77 4.45
4874 6128 3.870607 TTGAGCTGGGAGCCTGGGA 62.871 63.158 0.00 0.00 43.77 4.37
4875 6129 2.771762 GAGCTGGGAGCCTGGGAT 60.772 66.667 0.00 0.00 43.77 3.85
4876 6130 3.095163 AGCTGGGAGCCTGGGATG 61.095 66.667 0.00 0.00 43.77 3.51
4877 6131 3.415087 GCTGGGAGCCTGGGATGT 61.415 66.667 0.00 0.00 34.48 3.06
4887 6141 1.871080 CCTGGGATGTATCTCGTTGC 58.129 55.000 0.00 0.00 0.00 4.17
4924 6179 4.201724 CGAGCAGCTTGTATTTACCACTTC 60.202 45.833 0.00 0.00 0.00 3.01
4925 6180 4.651778 AGCAGCTTGTATTTACCACTTCA 58.348 39.130 0.00 0.00 0.00 3.02
4926 6181 4.455877 AGCAGCTTGTATTTACCACTTCAC 59.544 41.667 0.00 0.00 0.00 3.18
4959 6314 4.800914 GCAGTTTCAGCAAGAGTTCCTCTA 60.801 45.833 0.00 0.00 40.28 2.43
4960 6315 5.300752 CAGTTTCAGCAAGAGTTCCTCTAA 58.699 41.667 0.00 0.00 40.28 2.10
4961 6316 5.760253 CAGTTTCAGCAAGAGTTCCTCTAAA 59.240 40.000 0.00 0.00 40.28 1.85
4962 6317 6.260936 CAGTTTCAGCAAGAGTTCCTCTAAAA 59.739 38.462 0.00 0.00 40.28 1.52
4963 6318 6.484977 AGTTTCAGCAAGAGTTCCTCTAAAAG 59.515 38.462 0.00 0.00 40.28 2.27
4964 6319 5.808366 TCAGCAAGAGTTCCTCTAAAAGA 57.192 39.130 0.00 0.00 40.28 2.52
4965 6320 6.174720 TCAGCAAGAGTTCCTCTAAAAGAA 57.825 37.500 0.00 0.00 40.28 2.52
4966 6321 6.591935 TCAGCAAGAGTTCCTCTAAAAGAAA 58.408 36.000 0.00 0.00 40.28 2.52
4967 6322 6.483640 TCAGCAAGAGTTCCTCTAAAAGAAAC 59.516 38.462 0.00 0.00 40.28 2.78
4968 6323 6.260936 CAGCAAGAGTTCCTCTAAAAGAAACA 59.739 38.462 0.00 0.00 40.28 2.83
4969 6324 7.001073 AGCAAGAGTTCCTCTAAAAGAAACAT 58.999 34.615 0.00 0.00 40.28 2.71
4970 6325 7.503902 AGCAAGAGTTCCTCTAAAAGAAACATT 59.496 33.333 0.00 0.00 40.28 2.71
4971 6326 8.138074 GCAAGAGTTCCTCTAAAAGAAACATTT 58.862 33.333 0.00 0.00 40.28 2.32
5016 6371 9.706846 GGAAAAGAAACATTTTCAACAAGAATG 57.293 29.630 12.46 0.00 46.41 2.67
5039 6394 2.164827 TGGTGCTAAATGATGCTTGCTG 59.835 45.455 0.00 0.00 0.00 4.41
5043 6398 2.424601 GCTAAATGATGCTTGCTGGTGA 59.575 45.455 0.00 0.00 0.00 4.02
5056 6411 4.906065 TGCTGGTGAATTATCATGAAGC 57.094 40.909 0.00 0.96 38.01 3.86
5064 6419 5.750067 GTGAATTATCATGAAGCCGCAAAAT 59.250 36.000 0.00 0.00 38.01 1.82
5065 6420 6.917477 GTGAATTATCATGAAGCCGCAAAATA 59.083 34.615 0.00 0.00 38.01 1.40
5066 6421 7.113965 GTGAATTATCATGAAGCCGCAAAATAG 59.886 37.037 0.00 0.00 38.01 1.73
5069 6424 4.621068 TCATGAAGCCGCAAAATAGAAG 57.379 40.909 0.00 0.00 0.00 2.85
5106 6462 4.967442 TGCATTATCCCATCCAATTCCAAA 59.033 37.500 0.00 0.00 0.00 3.28
5108 6464 6.101442 TGCATTATCCCATCCAATTCCAAAAT 59.899 34.615 0.00 0.00 0.00 1.82
5110 6466 8.323567 GCATTATCCCATCCAATTCCAAAATAT 58.676 33.333 0.00 0.00 0.00 1.28
5123 6479 9.480053 CAATTCCAAAATATTAATACAGCCAGG 57.520 33.333 0.00 0.00 0.00 4.45
5137 6493 1.355720 AGCCAGGTTCCAGCTAAACAT 59.644 47.619 11.90 3.53 34.38 2.71
5172 6529 1.598962 CACTGCCAGTGGGTCACAG 60.599 63.158 17.22 11.88 42.35 3.66
5195 6552 1.771255 CCTCTTATCCCAACCCCAGAG 59.229 57.143 0.00 0.00 0.00 3.35
5291 6649 3.920841 ACTATAAAACCCCCTCCACAGTT 59.079 43.478 0.00 0.00 0.00 3.16
5320 6678 0.767060 ACTCACCCCTTTCCCTTCGT 60.767 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.983378 AGTTCGGCAAGCCCTAGGAT 60.983 55.000 11.48 0.00 0.00 3.24
1 2 1.612442 AGTTCGGCAAGCCCTAGGA 60.612 57.895 11.48 0.00 0.00 2.94
2 3 1.450312 CAGTTCGGCAAGCCCTAGG 60.450 63.158 0.06 0.06 0.00 3.02
3 4 0.036388 TTCAGTTCGGCAAGCCCTAG 60.036 55.000 5.34 0.00 0.00 3.02
4 5 0.321298 GTTCAGTTCGGCAAGCCCTA 60.321 55.000 5.34 0.00 0.00 3.53
5 6 1.600916 GTTCAGTTCGGCAAGCCCT 60.601 57.895 5.34 0.00 0.00 5.19
6 7 1.452145 TTGTTCAGTTCGGCAAGCCC 61.452 55.000 5.34 0.00 0.00 5.19
7 8 0.598065 ATTGTTCAGTTCGGCAAGCC 59.402 50.000 0.00 0.00 0.00 4.35
8 9 1.401539 GGATTGTTCAGTTCGGCAAGC 60.402 52.381 0.00 0.00 0.00 4.01
9 10 2.095567 CAGGATTGTTCAGTTCGGCAAG 60.096 50.000 0.00 0.00 0.00 4.01
10 11 1.879380 CAGGATTGTTCAGTTCGGCAA 59.121 47.619 0.00 0.00 0.00 4.52
11 12 1.522668 CAGGATTGTTCAGTTCGGCA 58.477 50.000 0.00 0.00 0.00 5.69
59 60 6.011481 TCACGGTTAAGGTATTTTCCCAAAT 58.989 36.000 0.00 0.00 36.52 2.32
136 137 7.827701 TGAGATTACGTGTGAAAAGATAGACT 58.172 34.615 0.00 0.00 0.00 3.24
137 138 7.755822 ACTGAGATTACGTGTGAAAAGATAGAC 59.244 37.037 0.00 0.00 0.00 2.59
138 139 7.827701 ACTGAGATTACGTGTGAAAAGATAGA 58.172 34.615 0.00 0.00 0.00 1.98
139 140 7.971168 AGACTGAGATTACGTGTGAAAAGATAG 59.029 37.037 0.00 0.00 0.00 2.08
140 141 7.827701 AGACTGAGATTACGTGTGAAAAGATA 58.172 34.615 0.00 0.00 0.00 1.98
141 142 6.692486 AGACTGAGATTACGTGTGAAAAGAT 58.308 36.000 0.00 0.00 0.00 2.40
143 144 7.869016 TTAGACTGAGATTACGTGTGAAAAG 57.131 36.000 0.00 0.00 0.00 2.27
149 150 7.924412 TGAAAAGTTTAGACTGAGATTACGTGT 59.076 33.333 0.00 0.00 35.91 4.49
151 152 7.924412 TGTGAAAAGTTTAGACTGAGATTACGT 59.076 33.333 0.00 0.00 35.91 3.57
152 153 8.294341 TGTGAAAAGTTTAGACTGAGATTACG 57.706 34.615 0.00 0.00 35.91 3.18
201 202 1.975407 CGAGGTAGACCGGTGGTGT 60.975 63.158 14.63 0.00 42.08 4.16
302 310 6.033966 CAGGACACAAACTCTTAACAAAACC 58.966 40.000 0.00 0.00 0.00 3.27
312 320 2.036992 CTCTGAGCAGGACACAAACTCT 59.963 50.000 0.00 0.00 0.00 3.24
314 322 2.036992 CTCTCTGAGCAGGACACAAACT 59.963 50.000 0.00 0.00 0.00 2.66
418 427 4.505742 GGAGACAAATCTTCACACTCCCTT 60.506 45.833 0.00 0.00 37.17 3.95
517 538 2.526304 TTCAGCCTACAGACACACAC 57.474 50.000 0.00 0.00 0.00 3.82
527 548 5.447818 CGTTGATCAAAAGGATTCAGCCTAC 60.448 44.000 10.35 0.00 37.26 3.18
535 556 6.089249 AGAAAAGCGTTGATCAAAAGGATT 57.911 33.333 10.35 4.97 36.00 3.01
548 569 0.165944 CGCCGATGAAGAAAAGCGTT 59.834 50.000 0.00 0.00 38.81 4.84
571 592 0.956633 CAGCACACCAGAACAGCAAT 59.043 50.000 0.00 0.00 0.00 3.56
591 612 5.071788 TCATGGTGTTAAGGCCTTATAGGAG 59.928 44.000 25.70 12.50 37.67 3.69
599 620 3.525800 AAAGTCATGGTGTTAAGGCCT 57.474 42.857 0.00 0.00 0.00 5.19
607 628 3.074412 GACATCCGAAAAGTCATGGTGT 58.926 45.455 0.00 0.00 32.68 4.16
611 632 7.770801 TGTAATAGACATCCGAAAAGTCATG 57.229 36.000 0.00 0.00 34.80 3.07
619 640 4.748102 GCCGAATTGTAATAGACATCCGAA 59.252 41.667 0.00 0.00 38.07 4.30
620 641 4.038763 AGCCGAATTGTAATAGACATCCGA 59.961 41.667 0.00 0.00 38.07 4.55
624 645 7.498900 TCATTGAAGCCGAATTGTAATAGACAT 59.501 33.333 0.00 0.00 38.07 3.06
644 678 2.755655 GTCTTCGTCCCTCTCTCATTGA 59.244 50.000 0.00 0.00 0.00 2.57
652 686 1.074423 TCACCGTCTTCGTCCCTCT 59.926 57.895 0.00 0.00 35.01 3.69
658 692 2.941964 AAACGCGTCACCGTCTTCGT 62.942 55.000 14.44 0.00 41.16 3.85
668 702 2.629210 CGAGCCAAAAACGCGTCA 59.371 55.556 14.44 0.00 0.00 4.35
711 746 4.261801 CACCAGAAAAATCCGTAGACCAT 58.738 43.478 0.00 0.00 0.00 3.55
724 763 6.576185 ACGTAGTAGAAAGAACACCAGAAAA 58.424 36.000 0.00 0.00 41.94 2.29
844 1694 2.738480 CGGTTCGACCCAGTGGAA 59.262 61.111 11.95 0.00 33.75 3.53
847 1709 2.261671 CTCCGGTTCGACCCAGTG 59.738 66.667 0.00 0.00 33.75 3.66
1014 1889 4.735132 TACGTGTCCGCAGCTGCC 62.735 66.667 32.07 19.02 37.70 4.85
1197 2072 0.596600 ATTATACGGAGGTGCGCACG 60.597 55.000 32.35 23.78 0.00 5.34
1202 2077 2.408050 CAGAGCATTATACGGAGGTGC 58.592 52.381 0.00 0.00 36.11 5.01
1203 2078 2.036475 AGCAGAGCATTATACGGAGGTG 59.964 50.000 0.00 0.00 0.00 4.00
1209 2084 2.097202 GCACGAAGCAGAGCATTATACG 60.097 50.000 0.00 0.00 44.79 3.06
1296 2171 1.078637 ACATGCGCTCACTGCTCAT 60.079 52.632 9.73 0.00 46.71 2.90
1300 2175 1.088340 ATCAGACATGCGCTCACTGC 61.088 55.000 9.73 0.00 38.57 4.40
1341 2216 1.770294 AAAAGACCGCAGAACCCAAA 58.230 45.000 0.00 0.00 0.00 3.28
1386 2261 1.129064 ACAACAAAACGACGTGGTCAC 59.871 47.619 2.90 0.00 32.09 3.67
1468 2343 3.365265 CACAAGGAACGCCAGGCC 61.365 66.667 5.63 0.00 36.29 5.19
1535 2410 2.594303 TGCACAAGGAACGCCAGG 60.594 61.111 0.00 0.00 36.29 4.45
1536 2411 1.845809 GAGTGCACAAGGAACGCCAG 61.846 60.000 21.04 0.00 36.29 4.85
1537 2412 1.891919 GAGTGCACAAGGAACGCCA 60.892 57.895 21.04 0.00 36.29 5.69
1538 2413 2.617274 GGAGTGCACAAGGAACGCC 61.617 63.158 21.04 0.00 0.00 5.68
1540 2415 1.230635 CCAGGAGTGCACAAGGAACG 61.231 60.000 21.04 0.10 0.00 3.95
1541 2416 0.108585 TCCAGGAGTGCACAAGGAAC 59.891 55.000 21.04 2.02 0.00 3.62
1543 2418 1.053835 TGTCCAGGAGTGCACAAGGA 61.054 55.000 21.04 16.50 0.00 3.36
1544 2419 0.604780 CTGTCCAGGAGTGCACAAGG 60.605 60.000 21.04 14.42 0.00 3.61
1545 2420 0.394192 TCTGTCCAGGAGTGCACAAG 59.606 55.000 21.04 5.25 0.00 3.16
1547 2422 0.322648 CATCTGTCCAGGAGTGCACA 59.677 55.000 21.04 0.00 0.00 4.57
1548 2423 1.023513 GCATCTGTCCAGGAGTGCAC 61.024 60.000 9.40 9.40 34.39 4.57
1550 2425 0.035630 AAGCATCTGTCCAGGAGTGC 60.036 55.000 7.63 7.63 34.41 4.40
1551 2426 2.486472 AAAGCATCTGTCCAGGAGTG 57.514 50.000 0.00 0.00 0.00 3.51
1552 2427 4.851639 AATAAAGCATCTGTCCAGGAGT 57.148 40.909 0.00 0.00 0.00 3.85
1553 2428 7.814264 AATTAATAAAGCATCTGTCCAGGAG 57.186 36.000 0.00 0.00 0.00 3.69
1554 2429 7.833682 TCAAATTAATAAAGCATCTGTCCAGGA 59.166 33.333 0.00 0.00 0.00 3.86
1620 2503 2.044492 TCCAGGAGTTCCACCATCTAGT 59.956 50.000 0.28 0.00 38.89 2.57
1621 2504 2.752030 TCCAGGAGTTCCACCATCTAG 58.248 52.381 0.28 0.00 38.89 2.43
1628 2511 2.424956 GCATGAAATCCAGGAGTTCCAC 59.575 50.000 23.82 11.43 36.05 4.02
1634 2517 3.012518 ACGAAAGCATGAAATCCAGGAG 58.987 45.455 0.00 0.00 0.00 3.69
1660 2543 3.594134 CTTTGGCTGAGTACTGGAGAAG 58.406 50.000 0.00 0.00 0.00 2.85
1666 2549 2.568623 AACCCTTTGGCTGAGTACTG 57.431 50.000 0.00 0.00 33.59 2.74
1671 2554 6.772716 ACATAACATATAACCCTTTGGCTGAG 59.227 38.462 0.00 0.00 33.59 3.35
1903 2802 2.563620 TGCAAGTTGAATCCATGCATGT 59.436 40.909 24.58 6.98 41.67 3.21
2181 3081 7.158099 AGCAATATTTTCTGGTCAAGGTTAC 57.842 36.000 0.00 0.00 0.00 2.50
2620 3522 4.676924 GCATTTTCGAGTCCAAACAAAGAG 59.323 41.667 0.00 0.00 0.00 2.85
2745 3654 4.039151 AGTGATAACTGATGAGAGCACG 57.961 45.455 0.00 0.00 0.00 5.34
2970 3964 5.593502 CCGGACCTCTTCTAAACACTATAGT 59.406 44.000 0.00 0.00 0.00 2.12
3004 3998 3.563808 TGTTCATGTGTTTAGACCAGTGC 59.436 43.478 0.00 0.00 0.00 4.40
3087 4082 1.620819 CAGGATATGCCTCTTAGCGGT 59.379 52.381 0.00 0.00 46.97 5.68
3538 4533 6.624352 TCCAAGTAGAAAGATGCAATATGC 57.376 37.500 0.00 0.00 45.29 3.14
3577 4572 8.370182 ACAATTTCTGAATAAGCACTGGAAAAT 58.630 29.630 0.00 0.00 0.00 1.82
3615 4610 4.617808 GTCAGTGACGCTAAGATGAGTA 57.382 45.455 7.68 0.00 0.00 2.59
4053 5133 5.417811 ACATGTGTCATAAAGCAGAGAGAG 58.582 41.667 0.00 0.00 0.00 3.20
4107 5187 5.106948 GCAGATCGAAGTTGAAACTGATCAA 60.107 40.000 18.41 0.00 39.26 2.57
4156 5236 2.542618 CGTCTGAGGTTGGATCGATGAG 60.543 54.545 0.54 0.00 0.00 2.90
4333 5413 6.291532 CGAGAGTCAAGCAATTCTAATCGAAG 60.292 42.308 0.00 0.00 34.56 3.79
4536 5616 4.471386 ACAGCTAAGGATATCTGTTGTGGT 59.529 41.667 2.05 0.00 35.50 4.16
4537 5617 5.028549 ACAGCTAAGGATATCTGTTGTGG 57.971 43.478 2.05 0.00 35.50 4.17
4539 5619 7.661536 TTCTACAGCTAAGGATATCTGTTGT 57.338 36.000 2.05 7.68 38.87 3.32
4563 5643 1.064389 GCCTCCCTTGCCTACAGAATT 60.064 52.381 0.00 0.00 0.00 2.17
4564 5644 0.548510 GCCTCCCTTGCCTACAGAAT 59.451 55.000 0.00 0.00 0.00 2.40
4567 5647 2.592308 GGCCTCCCTTGCCTACAG 59.408 66.667 0.00 0.00 45.70 2.74
4583 5663 0.682209 CCTCCAAACATCAGGCCTGG 60.682 60.000 32.23 19.57 0.00 4.45
4588 5668 1.271543 TGTGCTCCTCCAAACATCAGG 60.272 52.381 0.00 0.00 0.00 3.86
4609 5689 2.208132 ATCACCACGGCCATGTAAAA 57.792 45.000 2.24 0.00 0.00 1.52
4620 5700 2.794350 GCCAAAAGAAACAATCACCACG 59.206 45.455 0.00 0.00 0.00 4.94
4650 5730 7.010091 CGTTTTCTCTTGCCTTAACAACAATTT 59.990 33.333 0.00 0.00 0.00 1.82
4658 5738 3.898517 AGCGTTTTCTCTTGCCTTAAC 57.101 42.857 0.00 0.00 0.00 2.01
4659 5739 3.252458 GGAAGCGTTTTCTCTTGCCTTAA 59.748 43.478 0.00 0.00 28.95 1.85
4660 5740 2.812011 GGAAGCGTTTTCTCTTGCCTTA 59.188 45.455 0.00 0.00 28.95 2.69
4661 5741 1.609072 GGAAGCGTTTTCTCTTGCCTT 59.391 47.619 0.00 0.00 28.95 4.35
4662 5742 1.202818 AGGAAGCGTTTTCTCTTGCCT 60.203 47.619 0.00 0.00 34.33 4.75
4663 5743 1.239347 AGGAAGCGTTTTCTCTTGCC 58.761 50.000 0.00 0.00 34.33 4.52
4664 5744 2.416893 CCTAGGAAGCGTTTTCTCTTGC 59.583 50.000 1.05 0.00 34.08 4.01
4665 5745 3.665190 ACCTAGGAAGCGTTTTCTCTTG 58.335 45.455 17.98 0.00 0.00 3.02
4666 5746 4.353383 AACCTAGGAAGCGTTTTCTCTT 57.647 40.909 17.98 0.00 0.00 2.85
4667 5747 4.353383 AAACCTAGGAAGCGTTTTCTCT 57.647 40.909 17.98 0.00 0.00 3.10
4672 5752 3.439129 GCATGTAAACCTAGGAAGCGTTT 59.561 43.478 17.98 7.68 33.48 3.60
4675 5755 1.940613 GGCATGTAAACCTAGGAAGCG 59.059 52.381 17.98 0.00 0.00 4.68
4676 5756 2.999331 TGGCATGTAAACCTAGGAAGC 58.001 47.619 17.98 7.89 0.00 3.86
4677 5757 4.336433 CACATGGCATGTAAACCTAGGAAG 59.664 45.833 30.96 11.71 42.70 3.46
4678 5758 4.269183 CACATGGCATGTAAACCTAGGAA 58.731 43.478 30.96 0.00 42.70 3.36
4680 5760 2.358898 GCACATGGCATGTAAACCTAGG 59.641 50.000 30.96 17.56 42.70 3.02
4681 5761 3.698029 GCACATGGCATGTAAACCTAG 57.302 47.619 30.96 18.25 42.70 3.02
4700 5780 6.315091 TCCGAATTCATAGTACTCTACAGC 57.685 41.667 0.00 0.00 0.00 4.40
4701 5781 7.013464 AGGTTCCGAATTCATAGTACTCTACAG 59.987 40.741 0.00 0.00 0.00 2.74
4707 5787 5.892119 TCTCAGGTTCCGAATTCATAGTACT 59.108 40.000 6.22 0.00 0.00 2.73
4708 5788 5.978322 GTCTCAGGTTCCGAATTCATAGTAC 59.022 44.000 6.22 0.00 0.00 2.73
4709 5789 5.892119 AGTCTCAGGTTCCGAATTCATAGTA 59.108 40.000 6.22 0.00 0.00 1.82
4710 5790 4.712337 AGTCTCAGGTTCCGAATTCATAGT 59.288 41.667 6.22 0.00 0.00 2.12
4711 5791 5.269505 AGTCTCAGGTTCCGAATTCATAG 57.730 43.478 6.22 0.00 0.00 2.23
4716 5796 3.746492 CGAAAAGTCTCAGGTTCCGAATT 59.254 43.478 0.00 0.00 0.00 2.17
4750 5831 8.993404 TGACATCATAAACAATCCATGGAATA 57.007 30.769 20.67 7.69 0.00 1.75
4755 6006 7.262772 AGCTTTGACATCATAAACAATCCATG 58.737 34.615 0.00 0.00 0.00 3.66
4802 6053 3.728385 ATTTATAGCATCCCAGGCTCC 57.272 47.619 0.00 0.00 42.62 4.70
4803 6054 6.218746 CAAAAATTTATAGCATCCCAGGCTC 58.781 40.000 0.00 0.00 42.62 4.70
4813 6064 4.357325 TCCCAGCCCAAAAATTTATAGCA 58.643 39.130 0.00 0.00 0.00 3.49
4814 6065 4.740634 GCTCCCAGCCCAAAAATTTATAGC 60.741 45.833 0.00 0.00 34.48 2.97
4815 6066 4.948847 GCTCCCAGCCCAAAAATTTATAG 58.051 43.478 0.00 0.00 34.48 1.31
4817 6068 3.912496 GCTCCCAGCCCAAAAATTTAT 57.088 42.857 0.00 0.00 34.48 1.40
4829 6080 4.891037 GCATCCCAGGCTCCCAGC 62.891 72.222 0.00 0.00 41.46 4.85
4830 6081 1.132554 ATAGCATCCCAGGCTCCCAG 61.133 60.000 0.00 0.00 42.62 4.45
4831 6082 0.193321 TATAGCATCCCAGGCTCCCA 59.807 55.000 0.00 0.00 42.62 4.37
4832 6083 1.362224 TTATAGCATCCCAGGCTCCC 58.638 55.000 0.00 0.00 42.62 4.30
4833 6084 3.508845 TTTTATAGCATCCCAGGCTCC 57.491 47.619 0.00 0.00 42.62 4.70
4834 6085 6.040842 TCAAAATTTTATAGCATCCCAGGCTC 59.959 38.462 2.44 0.00 42.62 4.70
4835 6086 5.898972 TCAAAATTTTATAGCATCCCAGGCT 59.101 36.000 2.44 0.00 45.18 4.58
4836 6087 6.160576 TCAAAATTTTATAGCATCCCAGGC 57.839 37.500 2.44 0.00 0.00 4.85
4837 6088 6.041296 AGCTCAAAATTTTATAGCATCCCAGG 59.959 38.462 26.70 5.38 33.30 4.45
4859 6110 2.551856 TACATCCCAGGCTCCCAGCT 62.552 60.000 0.00 0.00 41.99 4.24
4864 6115 0.605589 CGAGATACATCCCAGGCTCC 59.394 60.000 0.00 0.00 0.00 4.70
4865 6116 1.333177 ACGAGATACATCCCAGGCTC 58.667 55.000 0.00 0.00 0.00 4.70
4866 6117 1.414181 CAACGAGATACATCCCAGGCT 59.586 52.381 0.00 0.00 0.00 4.58
4867 6118 1.871080 CAACGAGATACATCCCAGGC 58.129 55.000 0.00 0.00 0.00 4.85
4868 6119 1.414181 AGCAACGAGATACATCCCAGG 59.586 52.381 0.00 0.00 0.00 4.45
4869 6120 2.159043 ACAGCAACGAGATACATCCCAG 60.159 50.000 0.00 0.00 0.00 4.45
4872 6126 2.535984 CGAACAGCAACGAGATACATCC 59.464 50.000 0.00 0.00 0.00 3.51
4873 6127 2.535984 CCGAACAGCAACGAGATACATC 59.464 50.000 0.00 0.00 0.00 3.06
4874 6128 2.540515 CCGAACAGCAACGAGATACAT 58.459 47.619 0.00 0.00 0.00 2.29
4875 6129 1.990799 CCGAACAGCAACGAGATACA 58.009 50.000 0.00 0.00 0.00 2.29
4876 6130 0.645868 GCCGAACAGCAACGAGATAC 59.354 55.000 0.00 0.00 0.00 2.24
4877 6131 0.530744 AGCCGAACAGCAACGAGATA 59.469 50.000 0.00 0.00 34.23 1.98
4887 6141 1.805945 GCTCGTACCAGCCGAACAG 60.806 63.158 0.27 0.00 33.34 3.16
4913 6168 4.724279 ACTGGAAGGTGAAGTGGTAAAT 57.276 40.909 0.00 0.00 39.30 1.40
4925 6180 2.301346 CTGAAACTGCAACTGGAAGGT 58.699 47.619 0.00 0.00 39.30 3.50
4926 6181 1.000938 GCTGAAACTGCAACTGGAAGG 60.001 52.381 0.00 0.00 39.30 3.46
4987 6342 9.500785 TCTTGTTGAAAATGTTTCTTTTCCTTT 57.499 25.926 6.78 0.00 42.06 3.11
4988 6343 9.500785 TTCTTGTTGAAAATGTTTCTTTTCCTT 57.499 25.926 6.78 0.00 42.06 3.36
4989 6344 9.671279 ATTCTTGTTGAAAATGTTTCTTTTCCT 57.329 25.926 6.78 0.00 42.06 3.36
4990 6345 9.706846 CATTCTTGTTGAAAATGTTTCTTTTCC 57.293 29.630 6.78 0.00 42.06 3.13
5016 6371 2.925563 GCAAGCATCATTTAGCACCAAC 59.074 45.455 0.00 0.00 0.00 3.77
5018 6373 2.164827 CAGCAAGCATCATTTAGCACCA 59.835 45.455 0.00 0.00 0.00 4.17
5027 6382 4.891168 TGATAATTCACCAGCAAGCATCAT 59.109 37.500 0.00 0.00 0.00 2.45
5028 6383 4.271661 TGATAATTCACCAGCAAGCATCA 58.728 39.130 0.00 0.00 0.00 3.07
5039 6394 2.618241 TGCGGCTTCATGATAATTCACC 59.382 45.455 0.00 0.00 33.85 4.02
5043 6398 7.275888 TCTATTTTGCGGCTTCATGATAATT 57.724 32.000 0.00 0.00 0.00 1.40
5056 6411 6.481313 TCTCATCAAGATCTTCTATTTTGCGG 59.519 38.462 4.57 0.00 0.00 5.69
5064 6419 6.728089 ATGCACTCTCATCAAGATCTTCTA 57.272 37.500 4.57 0.00 32.19 2.10
5065 6420 5.617528 ATGCACTCTCATCAAGATCTTCT 57.382 39.130 4.57 0.00 32.19 2.85
5066 6421 7.118101 GGATAATGCACTCTCATCAAGATCTTC 59.882 40.741 4.57 0.00 32.19 2.87
5069 6424 5.642919 GGGATAATGCACTCTCATCAAGATC 59.357 44.000 0.00 0.00 32.19 2.75
5106 6462 5.770162 GCTGGAACCTGGCTGTATTAATATT 59.230 40.000 0.00 0.00 0.00 1.28
5108 6464 4.412199 AGCTGGAACCTGGCTGTATTAATA 59.588 41.667 9.90 0.00 34.82 0.98
5110 6466 2.576191 AGCTGGAACCTGGCTGTATTAA 59.424 45.455 9.90 0.00 34.82 1.40
5114 6470 1.651737 TTAGCTGGAACCTGGCTGTA 58.348 50.000 16.74 6.89 37.50 2.74
5120 6476 4.559153 CCAAAATGTTTAGCTGGAACCTG 58.441 43.478 0.00 0.00 0.00 4.00
5123 6479 3.989817 CAGCCAAAATGTTTAGCTGGAAC 59.010 43.478 16.62 1.82 40.85 3.62
5137 6493 0.823356 GTGTGAGAGGCCAGCCAAAA 60.823 55.000 12.03 0.00 38.92 2.44
5167 6523 0.044092 TGGGATAAGAGGGGCTGTGA 59.956 55.000 0.00 0.00 0.00 3.58
5172 6529 1.537172 GGGTTGGGATAAGAGGGGC 59.463 63.158 0.00 0.00 0.00 5.80
5180 6537 5.486332 AGATATTTCTCTGGGGTTGGGATA 58.514 41.667 0.00 0.00 0.00 2.59
5195 6552 7.922382 TGGATATTTCTCTGGGGAGATATTTC 58.078 38.462 4.80 6.41 46.51 2.17
5291 6649 1.841556 GGGGTGAGTGTGGGAGTGA 60.842 63.158 0.00 0.00 0.00 3.41
5320 6678 4.344865 GCCGCTGGGGTTTGGAGA 62.345 66.667 12.70 0.00 38.44 3.71



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

AutoCloner maintained by Alex Coulton.