Multiple sequence alignment - TraesCS3B01G345600

Loading Multiple Alignment...

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 TraesCS3B01G345600 chr3B 100.000 2506 0 0 1 2506 555245989 555243484 0.000000e+00 4628.0
1 TraesCS3B01G345600 chr3B 90.247 1825 124 27 716 2506 555156373 555154569 0.000000e+00 2335.0
2 TraesCS3B01G345600 chr3B 100.000 265 0 0 2828 3092 555243162 555242898 9.960000e-135 490.0
3 TraesCS3B01G345600 chr3B 94.444 90 3 1 2833 2920 555271028 555270939 1.500000e-28 137.0
4 TraesCS3B01G345600 chr3B 100.000 41 0 0 680 720 555156428 555156388 3.310000e-10 76.8
5 TraesCS3B01G345600 chr3D 90.505 1843 110 20 598 2408 425152650 425150841 0.000000e+00 2374.0
6 TraesCS3B01G345600 chr3A 93.546 1224 62 6 901 2118 562914258 562915470 0.000000e+00 1807.0
7 TraesCS3B01G345600 chr3A 90.056 1076 71 9 1359 2408 563394895 563395960 0.000000e+00 1362.0
8 TraesCS3B01G345600 chr3A 93.317 404 23 3 953 1353 563389029 563389431 7.380000e-166 593.0
9 TraesCS3B01G345600 chr3A 88.580 324 14 10 598 916 563388733 563389038 3.770000e-99 372.0
10 TraesCS3B01G345600 chr3A 86.420 324 23 6 598 916 562914001 562914308 4.940000e-88 335.0
11 TraesCS3B01G345600 chr3A 93.548 93 4 1 2830 2920 562911229 562911321 1.500000e-28 137.0
12 TraesCS3B01G345600 chr3A 97.436 39 1 0 2122 2160 562915497 562915535 1.990000e-07 67.6
13 TraesCS3B01G345600 chr6B 96.500 600 19 2 1 598 239618605 239619204 0.000000e+00 990.0
14 TraesCS3B01G345600 chr6B 90.173 173 16 1 2919 3091 459272009 459272180 1.120000e-54 224.0
15 TraesCS3B01G345600 chr2B 93.322 599 36 4 1 598 132076462 132077057 0.000000e+00 881.0
16 TraesCS3B01G345600 chr2B 93.012 601 38 4 1 600 800695722 800695125 0.000000e+00 874.0
17 TraesCS3B01G345600 chr2B 92.475 598 41 4 1 597 744398815 744399409 0.000000e+00 852.0
18 TraesCS3B01G345600 chr2B 92.333 600 42 4 1 600 797511026 797511621 0.000000e+00 850.0
19 TraesCS3B01G345600 chr2B 86.628 172 20 3 2919 3088 767669073 767669243 1.460000e-43 187.0
20 TraesCS3B01G345600 chr2B 84.746 177 23 4 2918 3092 526376747 526376573 1.140000e-39 174.0
21 TraesCS3B01G345600 chr5B 93.144 598 37 4 1 597 218942363 218942957 0.000000e+00 874.0
22 TraesCS3B01G345600 chr5B 92.977 598 38 4 1 597 172618848 172619442 0.000000e+00 869.0
23 TraesCS3B01G345600 chr5B 90.744 605 51 5 1 605 570085109 570084510 0.000000e+00 802.0
24 TraesCS3B01G345600 chr5B 85.795 176 23 2 2918 3092 528225810 528225984 5.270000e-43 185.0
25 TraesCS3B01G345600 chr7B 91.201 591 47 5 1 591 379751153 379751738 0.000000e+00 798.0
26 TraesCS3B01G345600 chr7B 78.388 1092 218 14 1041 2117 690904495 690905583 0.000000e+00 693.0
27 TraesCS3B01G345600 chr7B 80.634 568 101 8 1535 2096 692377201 692376637 6.130000e-117 431.0
28 TraesCS3B01G345600 chr7A 76.652 1105 224 23 1041 2117 698729490 698730588 5.750000e-162 580.0
29 TraesCS3B01G345600 chr7A 79.178 706 133 4 1419 2111 699066863 699067567 7.760000e-131 477.0
30 TraesCS3B01G345600 chr7D 79.200 500 99 5 1592 2089 607109873 607110369 2.950000e-90 342.0
31 TraesCS3B01G345600 chr7D 93.143 175 12 0 2918 3092 29300460 29300634 1.100000e-64 257.0
32 TraesCS3B01G345600 chr1D 93.143 175 12 0 2918 3092 453584875 453585049 1.100000e-64 257.0
33 TraesCS3B01G345600 chr1D 92.814 167 10 1 2926 3092 337995413 337995249 1.110000e-59 241.0
34 TraesCS3B01G345600 chr1B 89.205 176 17 2 2918 3092 592215242 592215416 5.190000e-53 219.0
35 TraesCS3B01G345600 chrUn 87.356 174 20 2 2919 3092 436997953 436997782 6.760000e-47 198.0


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 TraesCS3B01G345600 chr3B 555242898 555245989 3091 True 2559.00 4628 100.0000 1 3092 2 chr3B.!!$R3 3091
1 TraesCS3B01G345600 chr3B 555154569 555156428 1859 True 1205.90 2335 95.1235 680 2506 2 chr3B.!!$R2 1826
2 TraesCS3B01G345600 chr3D 425150841 425152650 1809 True 2374.00 2374 90.5050 598 2408 1 chr3D.!!$R1 1810
3 TraesCS3B01G345600 chr3A 563394895 563395960 1065 False 1362.00 1362 90.0560 1359 2408 1 chr3A.!!$F1 1049
4 TraesCS3B01G345600 chr3A 562911229 562915535 4306 False 586.65 1807 92.7375 598 2920 4 chr3A.!!$F2 2322
5 TraesCS3B01G345600 chr3A 563388733 563389431 698 False 482.50 593 90.9485 598 1353 2 chr3A.!!$F3 755
6 TraesCS3B01G345600 chr6B 239618605 239619204 599 False 990.00 990 96.5000 1 598 1 chr6B.!!$F1 597
7 TraesCS3B01G345600 chr2B 132076462 132077057 595 False 881.00 881 93.3220 1 598 1 chr2B.!!$F1 597
8 TraesCS3B01G345600 chr2B 800695125 800695722 597 True 874.00 874 93.0120 1 600 1 chr2B.!!$R2 599
9 TraesCS3B01G345600 chr2B 744398815 744399409 594 False 852.00 852 92.4750 1 597 1 chr2B.!!$F2 596
10 TraesCS3B01G345600 chr2B 797511026 797511621 595 False 850.00 850 92.3330 1 600 1 chr2B.!!$F4 599
11 TraesCS3B01G345600 chr5B 218942363 218942957 594 False 874.00 874 93.1440 1 597 1 chr5B.!!$F2 596
12 TraesCS3B01G345600 chr5B 172618848 172619442 594 False 869.00 869 92.9770 1 597 1 chr5B.!!$F1 596
13 TraesCS3B01G345600 chr5B 570084510 570085109 599 True 802.00 802 90.7440 1 605 1 chr5B.!!$R1 604
14 TraesCS3B01G345600 chr7B 379751153 379751738 585 False 798.00 798 91.2010 1 591 1 chr7B.!!$F1 590
15 TraesCS3B01G345600 chr7B 690904495 690905583 1088 False 693.00 693 78.3880 1041 2117 1 chr7B.!!$F2 1076
16 TraesCS3B01G345600 chr7B 692376637 692377201 564 True 431.00 431 80.6340 1535 2096 1 chr7B.!!$R1 561
17 TraesCS3B01G345600 chr7A 698729490 698730588 1098 False 580.00 580 76.6520 1041 2117 1 chr7A.!!$F1 1076
18 TraesCS3B01G345600 chr7A 699066863 699067567 704 False 477.00 477 79.1780 1419 2111 1 chr7A.!!$F2 692

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
593 599 0.034337 ACGTGTGGCAGTTATTCGGT 59.966 50.0 0.00 0.00 0.00 4.69 F
1354 3634 0.887387 GCCGCTGGTGTTTAACTCCA 60.887 55.0 16.56 16.56 39.22 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 3688 0.672342 AGAACGTACGACCACAGCTT 59.328 50.0 24.41 2.26 0.00 3.74 R
3067 5417 0.035056 AATCCGCTAGTGGCTTGCTT 60.035 50.0 18.01 3.20 39.13 3.91 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
126 127 3.705072 GTGTTCTACCCCTACAGCATAGT 59.295 47.826 0.00 0.00 0.00 2.12
190 193 2.043227 AGGTTCAGATCGGGGAGATTC 58.957 52.381 0.00 0.00 40.26 2.52
593 599 0.034337 ACGTGTGGCAGTTATTCGGT 59.966 50.000 0.00 0.00 0.00 4.69
626 2802 1.878088 GATGCCACTCCGTATACTCGA 59.122 52.381 0.56 0.00 0.00 4.04
736 2936 7.806487 GGTTTAAATCGGAAAAGGTAGAACAAG 59.194 37.037 0.00 0.00 0.00 3.16
781 2981 1.627879 AAAAGCCACGCGCAATAATG 58.372 45.000 5.73 0.00 41.38 1.90
789 2993 3.181515 CCACGCGCAATAATGAGTACAAA 60.182 43.478 5.73 0.00 0.00 2.83
794 2998 4.438744 GCGCAATAATGAGTACAAAAGCCT 60.439 41.667 0.30 0.00 0.00 4.58
838 3046 2.346803 CCCACACGAATCGTCAAATCT 58.653 47.619 4.88 0.00 38.32 2.40
854 3062 6.140737 CGTCAAATCTTAACAGCTCAAACAAC 59.859 38.462 0.00 0.00 0.00 3.32
867 3075 6.574462 CAGCTCAAACAACACAAAACAAAAAG 59.426 34.615 0.00 0.00 0.00 2.27
873 3081 5.053145 ACAACACAAAACAAAAAGCTCACA 58.947 33.333 0.00 0.00 0.00 3.58
916 3183 4.547367 CCACCTCCCGAATCGCCC 62.547 72.222 0.00 0.00 0.00 6.13
919 3186 4.547367 CCTCCCGAATCGCCCCAC 62.547 72.222 0.00 0.00 0.00 4.61
965 3232 3.606662 CGGTCCGGATCGCCTCAT 61.607 66.667 26.39 0.00 0.00 2.90
966 3233 2.340443 GGTCCGGATCGCCTCATC 59.660 66.667 7.81 0.00 0.00 2.92
967 3234 2.340443 GTCCGGATCGCCTCATCC 59.660 66.667 7.81 0.00 39.35 3.51
968 3235 2.198703 TCCGGATCGCCTCATCCT 59.801 61.111 0.00 0.00 40.45 3.24
969 3236 2.203082 TCCGGATCGCCTCATCCTG 61.203 63.158 0.00 0.00 40.45 3.86
1189 3460 1.001020 TACTTCTACCCCGACGGCA 60.001 57.895 8.86 0.00 33.26 5.69
1354 3634 0.887387 GCCGCTGGTGTTTAACTCCA 60.887 55.000 16.56 16.56 39.22 3.86
1360 3643 1.142474 GGTGTTTAACTCCACCGACG 58.858 55.000 10.87 0.00 41.55 5.12
1401 3687 3.019564 CACCCATTTCATGAGGAAGACC 58.980 50.000 5.76 0.00 36.72 3.85
1402 3688 2.649312 ACCCATTTCATGAGGAAGACCA 59.351 45.455 5.76 0.00 36.72 4.02
1486 3782 0.246635 GAAGGACGCACAAGAGGCTA 59.753 55.000 0.00 0.00 0.00 3.93
1499 3795 6.238320 GCACAAGAGGCTAATGTCAAGATTAG 60.238 42.308 1.93 3.24 38.47 1.73
1666 3975 1.968493 TCAAGGTGAAGTTCTACGGCT 59.032 47.619 4.17 0.00 0.00 5.52
1761 4070 7.153217 TCACTTCATCTACACTGATTCGTTA 57.847 36.000 0.00 0.00 0.00 3.18
1882 4194 2.224079 TGCGAGATCAAACTTTGTGAGC 59.776 45.455 0.00 3.32 0.00 4.26
2003 4315 4.860802 ATAGAATGGTTGGTGTGATGGA 57.139 40.909 0.00 0.00 0.00 3.41
2072 4384 5.933617 TGCTGATATATTGGAGAAAGCAGT 58.066 37.500 0.00 0.00 34.68 4.40
2118 4430 4.799428 GCTGACCGTAGATTAACTTGAGAC 59.201 45.833 0.00 0.00 0.00 3.36
2119 4431 5.320549 TGACCGTAGATTAACTTGAGACC 57.679 43.478 0.00 0.00 0.00 3.85
2188 4523 8.565416 AGATCTTTTGTAAAAGGGTAAGTTTCG 58.435 33.333 14.99 0.00 44.22 3.46
2193 4528 6.205101 TGTAAAAGGGTAAGTTTCGCAAAA 57.795 33.333 0.00 0.00 0.00 2.44
2198 4533 5.366829 AGGGTAAGTTTCGCAAAATGTAC 57.633 39.130 0.00 0.00 0.00 2.90
2219 4556 3.132289 ACGTCTTCGATGTCATAATGGGT 59.868 43.478 0.00 0.00 40.62 4.51
2233 4570 7.682459 TGTCATAATGGGTCACCCTATATATGT 59.318 37.037 16.04 0.00 45.70 2.29
2235 4572 9.434275 TCATAATGGGTCACCCTATATATGTAG 57.566 37.037 16.04 0.00 45.70 2.74
2263 4600 5.687828 GCTAGATAAGTAGCGTCGTTATGT 58.312 41.667 0.00 0.00 36.34 2.29
2276 4618 5.388111 CGTCGTTATGTTCTGTTGACTAGA 58.612 41.667 0.00 0.00 0.00 2.43
2318 4660 5.706369 TCGAATTTTCCCTTTATTCGGTCAA 59.294 36.000 14.16 0.00 46.34 3.18
2351 4693 7.064371 TCTCAAAGTAGTGAGTAACTAGCTACG 59.936 40.741 2.38 0.00 44.56 3.51
2386 4728 5.095691 ACTGTGAAATGTGATGAAACGTC 57.904 39.130 0.00 0.00 0.00 4.34
2398 4740 7.572759 TGTGATGAAACGTCAGAAATAGAAAC 58.427 34.615 0.00 0.00 37.14 2.78
2438 4780 7.218963 GCAAAATAACTGATCGGTTCTGAATTC 59.781 37.037 23.08 0.00 0.00 2.17
2447 4789 9.265901 CTGATCGGTTCTGAATTCTTATATTGT 57.734 33.333 7.05 0.00 0.00 2.71
2448 4790 9.261180 TGATCGGTTCTGAATTCTTATATTGTC 57.739 33.333 7.05 0.00 0.00 3.18
2467 4817 7.857734 ATTGTCGATTAATACACCATGTTCA 57.142 32.000 0.00 0.00 0.00 3.18
2478 4828 2.290367 CACCATGTTCATCGTGTGTGTT 59.710 45.455 3.14 0.00 33.62 3.32
2479 4829 2.948979 ACCATGTTCATCGTGTGTGTTT 59.051 40.909 0.00 0.00 0.00 2.83
2482 4832 4.261155 CCATGTTCATCGTGTGTGTTTCTT 60.261 41.667 0.00 0.00 0.00 2.52
2851 5201 7.962995 TTCTCTTATCTCACCAGTATTCTGT 57.037 36.000 0.00 0.00 39.82 3.41
2852 5202 7.962995 TCTCTTATCTCACCAGTATTCTGTT 57.037 36.000 0.00 0.00 39.82 3.16
2853 5203 9.475620 TTCTCTTATCTCACCAGTATTCTGTTA 57.524 33.333 0.00 0.00 39.82 2.41
2854 5204 9.647918 TCTCTTATCTCACCAGTATTCTGTTAT 57.352 33.333 0.00 0.00 39.82 1.89
2857 5207 9.265901 CTTATCTCACCAGTATTCTGTTATTGG 57.734 37.037 0.00 0.00 39.82 3.16
2858 5208 5.428253 TCTCACCAGTATTCTGTTATTGGC 58.572 41.667 0.00 0.00 39.82 4.52
2859 5209 5.045942 TCTCACCAGTATTCTGTTATTGGCA 60.046 40.000 0.00 0.00 39.82 4.92
2860 5210 5.754782 TCACCAGTATTCTGTTATTGGCAT 58.245 37.500 0.00 0.00 39.82 4.40
2861 5211 6.186957 TCACCAGTATTCTGTTATTGGCATT 58.813 36.000 0.00 0.00 39.82 3.56
2862 5212 6.663093 TCACCAGTATTCTGTTATTGGCATTT 59.337 34.615 0.00 0.00 39.82 2.32
2863 5213 6.974622 CACCAGTATTCTGTTATTGGCATTTC 59.025 38.462 0.00 0.00 39.82 2.17
2864 5214 6.663093 ACCAGTATTCTGTTATTGGCATTTCA 59.337 34.615 0.00 0.00 39.82 2.69
2865 5215 7.178274 ACCAGTATTCTGTTATTGGCATTTCAA 59.822 33.333 0.00 0.00 39.82 2.69
2866 5216 7.489113 CCAGTATTCTGTTATTGGCATTTCAAC 59.511 37.037 0.00 0.00 39.82 3.18
2867 5217 8.028354 CAGTATTCTGTTATTGGCATTTCAACA 58.972 33.333 0.00 0.00 36.97 3.33
2868 5218 8.752187 AGTATTCTGTTATTGGCATTTCAACAT 58.248 29.630 0.00 0.00 0.00 2.71
2869 5219 9.369904 GTATTCTGTTATTGGCATTTCAACATT 57.630 29.630 0.00 0.00 0.00 2.71
2870 5220 7.655236 TTCTGTTATTGGCATTTCAACATTG 57.345 32.000 0.00 0.00 0.00 2.82
2871 5221 5.638657 TCTGTTATTGGCATTTCAACATTGC 59.361 36.000 0.00 0.00 35.64 3.56
2872 5222 5.303165 TGTTATTGGCATTTCAACATTGCA 58.697 33.333 0.00 0.00 38.12 4.08
2873 5223 5.761726 TGTTATTGGCATTTCAACATTGCAA 59.238 32.000 0.00 0.00 38.12 4.08
2874 5224 4.752661 ATTGGCATTTCAACATTGCAAC 57.247 36.364 0.00 0.00 38.12 4.17
2875 5225 3.189618 TGGCATTTCAACATTGCAACA 57.810 38.095 0.00 0.00 38.12 3.33
2876 5226 3.132160 TGGCATTTCAACATTGCAACAG 58.868 40.909 0.00 0.00 38.12 3.16
2877 5227 3.181468 TGGCATTTCAACATTGCAACAGA 60.181 39.130 0.00 0.00 38.12 3.41
2878 5228 3.998341 GGCATTTCAACATTGCAACAGAT 59.002 39.130 0.00 0.00 38.12 2.90
2879 5229 4.453136 GGCATTTCAACATTGCAACAGATT 59.547 37.500 0.00 0.00 38.12 2.40
2880 5230 5.390145 GGCATTTCAACATTGCAACAGATTC 60.390 40.000 0.00 0.00 38.12 2.52
2881 5231 5.390145 GCATTTCAACATTGCAACAGATTCC 60.390 40.000 0.00 0.00 36.40 3.01
2882 5232 5.534207 TTTCAACATTGCAACAGATTCCT 57.466 34.783 0.00 0.00 0.00 3.36
2883 5233 6.647334 TTTCAACATTGCAACAGATTCCTA 57.353 33.333 0.00 0.00 0.00 2.94
2884 5234 6.839124 TTCAACATTGCAACAGATTCCTAT 57.161 33.333 0.00 0.00 0.00 2.57
2885 5235 6.198650 TCAACATTGCAACAGATTCCTATG 57.801 37.500 0.00 0.00 0.00 2.23
2886 5236 5.125900 TCAACATTGCAACAGATTCCTATGG 59.874 40.000 0.00 0.00 0.00 2.74
2887 5237 4.858850 ACATTGCAACAGATTCCTATGGA 58.141 39.130 0.00 0.00 0.00 3.41
2888 5238 5.452255 ACATTGCAACAGATTCCTATGGAT 58.548 37.500 0.00 0.00 0.00 3.41
2889 5239 6.604171 ACATTGCAACAGATTCCTATGGATA 58.396 36.000 0.00 0.00 0.00 2.59
2890 5240 6.488006 ACATTGCAACAGATTCCTATGGATAC 59.512 38.462 0.00 0.00 0.00 2.24
2891 5241 5.894298 TGCAACAGATTCCTATGGATACT 57.106 39.130 0.00 0.00 37.61 2.12
2892 5242 6.252599 TGCAACAGATTCCTATGGATACTT 57.747 37.500 0.00 0.00 37.61 2.24
2893 5243 6.057533 TGCAACAGATTCCTATGGATACTTG 58.942 40.000 0.00 0.00 37.61 3.16
2894 5244 6.126796 TGCAACAGATTCCTATGGATACTTGA 60.127 38.462 0.00 0.00 37.61 3.02
2895 5245 6.203723 GCAACAGATTCCTATGGATACTTGAC 59.796 42.308 0.00 0.00 37.61 3.18
2896 5246 7.504403 CAACAGATTCCTATGGATACTTGACT 58.496 38.462 0.00 0.00 37.61 3.41
2897 5247 7.296628 ACAGATTCCTATGGATACTTGACTC 57.703 40.000 0.00 0.00 37.61 3.36
2898 5248 6.841229 ACAGATTCCTATGGATACTTGACTCA 59.159 38.462 0.00 0.00 37.61 3.41
2899 5249 7.512058 ACAGATTCCTATGGATACTTGACTCAT 59.488 37.037 0.00 0.00 37.61 2.90
2900 5250 9.029368 CAGATTCCTATGGATACTTGACTCATA 57.971 37.037 0.00 0.00 37.61 2.15
2901 5251 9.781425 AGATTCCTATGGATACTTGACTCATAT 57.219 33.333 0.00 0.00 37.61 1.78
2902 5252 9.814899 GATTCCTATGGATACTTGACTCATATG 57.185 37.037 0.00 0.00 37.61 1.78
2903 5253 7.175347 TCCTATGGATACTTGACTCATATGC 57.825 40.000 0.00 0.00 37.61 3.14
2904 5254 6.956435 TCCTATGGATACTTGACTCATATGCT 59.044 38.462 0.00 0.00 37.61 3.79
2905 5255 7.123397 TCCTATGGATACTTGACTCATATGCTC 59.877 40.741 0.00 0.00 37.61 4.26
2906 5256 6.931790 ATGGATACTTGACTCATATGCTCT 57.068 37.500 0.00 0.00 37.61 4.09
2907 5257 6.338214 TGGATACTTGACTCATATGCTCTC 57.662 41.667 0.00 0.00 37.61 3.20
2908 5258 6.073981 TGGATACTTGACTCATATGCTCTCT 58.926 40.000 0.00 0.00 37.61 3.10
2909 5259 7.234355 TGGATACTTGACTCATATGCTCTCTA 58.766 38.462 0.00 0.00 37.61 2.43
2910 5260 7.725844 TGGATACTTGACTCATATGCTCTCTAA 59.274 37.037 0.00 0.00 37.61 2.10
2911 5261 8.580720 GGATACTTGACTCATATGCTCTCTAAA 58.419 37.037 0.00 0.00 0.00 1.85
2912 5262 9.973450 GATACTTGACTCATATGCTCTCTAAAA 57.027 33.333 0.00 0.00 0.00 1.52
2915 5265 9.107177 ACTTGACTCATATGCTCTCTAAAATTG 57.893 33.333 0.00 0.00 0.00 2.32
2916 5266 8.442632 TTGACTCATATGCTCTCTAAAATTGG 57.557 34.615 0.00 0.00 0.00 3.16
2917 5267 6.484643 TGACTCATATGCTCTCTAAAATTGGC 59.515 38.462 0.00 0.00 0.00 4.52
2918 5268 6.599445 ACTCATATGCTCTCTAAAATTGGCT 58.401 36.000 0.00 0.00 0.00 4.75
2919 5269 7.059156 ACTCATATGCTCTCTAAAATTGGCTT 58.941 34.615 0.00 0.00 0.00 4.35
2920 5270 7.559170 ACTCATATGCTCTCTAAAATTGGCTTT 59.441 33.333 0.00 0.00 0.00 3.51
2921 5271 8.297470 TCATATGCTCTCTAAAATTGGCTTTT 57.703 30.769 0.00 0.00 40.21 2.27
2922 5272 8.752187 TCATATGCTCTCTAAAATTGGCTTTTT 58.248 29.630 0.00 4.58 38.09 1.94
2938 5288 1.380524 TTTTTGGAACGAAGACGCCA 58.619 45.000 0.00 0.00 43.96 5.69
2939 5289 0.941542 TTTTGGAACGAAGACGCCAG 59.058 50.000 0.00 0.00 43.96 4.85
2940 5290 0.105224 TTTGGAACGAAGACGCCAGA 59.895 50.000 0.00 0.00 43.96 3.86
2941 5291 0.320374 TTGGAACGAAGACGCCAGAT 59.680 50.000 0.00 0.00 43.96 2.90
2942 5292 0.389817 TGGAACGAAGACGCCAGATG 60.390 55.000 0.00 0.00 43.96 2.90
2943 5293 1.696832 GGAACGAAGACGCCAGATGC 61.697 60.000 0.00 0.00 43.96 3.91
2953 5303 2.436646 CCAGATGCGTCCGGCTTT 60.437 61.111 1.23 0.00 44.05 3.51
2954 5304 1.153449 CCAGATGCGTCCGGCTTTA 60.153 57.895 1.23 0.00 44.05 1.85
2955 5305 0.742990 CCAGATGCGTCCGGCTTTAA 60.743 55.000 1.23 0.00 44.05 1.52
2956 5306 0.373716 CAGATGCGTCCGGCTTTAAC 59.626 55.000 1.23 0.00 44.05 2.01
2957 5307 0.249398 AGATGCGTCCGGCTTTAACT 59.751 50.000 1.23 0.00 44.05 2.24
2958 5308 1.084289 GATGCGTCCGGCTTTAACTT 58.916 50.000 0.00 0.00 44.05 2.66
2959 5309 2.093869 AGATGCGTCCGGCTTTAACTTA 60.094 45.455 1.23 0.00 44.05 2.24
2960 5310 2.166821 TGCGTCCGGCTTTAACTTAA 57.833 45.000 0.00 0.00 44.05 1.85
2961 5311 2.702261 TGCGTCCGGCTTTAACTTAAT 58.298 42.857 0.00 0.00 44.05 1.40
2962 5312 3.859443 TGCGTCCGGCTTTAACTTAATA 58.141 40.909 0.00 0.00 44.05 0.98
2963 5313 4.252073 TGCGTCCGGCTTTAACTTAATAA 58.748 39.130 0.00 0.00 44.05 1.40
2964 5314 4.694509 TGCGTCCGGCTTTAACTTAATAAA 59.305 37.500 0.00 0.00 44.05 1.40
2965 5315 5.163834 TGCGTCCGGCTTTAACTTAATAAAG 60.164 40.000 0.00 4.78 42.93 1.85
2976 5326 8.541899 TTTAACTTAATAAAGCCCCCAATAGG 57.458 34.615 0.00 0.00 36.05 2.57
2983 5333 3.236391 CCCCCAATAGGCAGCGTA 58.764 61.111 0.00 0.00 0.00 4.42
2984 5334 1.529796 CCCCCAATAGGCAGCGTAA 59.470 57.895 0.00 0.00 0.00 3.18
2985 5335 0.818040 CCCCCAATAGGCAGCGTAAC 60.818 60.000 0.00 0.00 0.00 2.50
2986 5336 0.107410 CCCCAATAGGCAGCGTAACA 60.107 55.000 0.00 0.00 0.00 2.41
2987 5337 1.014352 CCCAATAGGCAGCGTAACAC 58.986 55.000 0.00 0.00 0.00 3.32
2988 5338 0.650512 CCAATAGGCAGCGTAACACG 59.349 55.000 0.00 0.00 45.88 4.49
2989 5339 1.635844 CAATAGGCAGCGTAACACGA 58.364 50.000 2.35 0.00 46.05 4.35
2990 5340 1.323534 CAATAGGCAGCGTAACACGAC 59.676 52.381 2.35 0.00 46.05 4.34
2991 5341 0.528924 ATAGGCAGCGTAACACGACA 59.471 50.000 2.35 0.00 46.05 4.35
2992 5342 0.387622 TAGGCAGCGTAACACGACAC 60.388 55.000 2.35 0.00 46.05 3.67
2993 5343 1.952133 GGCAGCGTAACACGACACA 60.952 57.895 2.35 0.00 46.05 3.72
2994 5344 1.492319 GGCAGCGTAACACGACACAA 61.492 55.000 2.35 0.00 46.05 3.33
2995 5345 0.302288 GCAGCGTAACACGACACAAA 59.698 50.000 2.35 0.00 46.05 2.83
2996 5346 1.656429 GCAGCGTAACACGACACAAAG 60.656 52.381 2.35 0.00 46.05 2.77
2997 5347 1.591158 CAGCGTAACACGACACAAAGT 59.409 47.619 2.35 0.00 46.05 2.66
2998 5348 1.856597 AGCGTAACACGACACAAAGTC 59.143 47.619 2.35 0.00 46.05 3.01
2999 5349 1.856597 GCGTAACACGACACAAAGTCT 59.143 47.619 2.35 0.00 46.05 3.24
3000 5350 2.283351 GCGTAACACGACACAAAGTCTT 59.717 45.455 2.35 0.00 46.05 3.01
3001 5351 3.486841 GCGTAACACGACACAAAGTCTTA 59.513 43.478 2.35 0.00 46.05 2.10
3002 5352 4.374707 GCGTAACACGACACAAAGTCTTAG 60.375 45.833 2.35 0.00 46.05 2.18
3003 5353 4.736793 CGTAACACGACACAAAGTCTTAGT 59.263 41.667 0.00 0.00 46.05 2.24
3004 5354 5.909054 CGTAACACGACACAAAGTCTTAGTA 59.091 40.000 0.00 0.00 46.05 1.82
3005 5355 6.129613 CGTAACACGACACAAAGTCTTAGTAC 60.130 42.308 0.00 0.00 46.05 2.73
3006 5356 5.252969 ACACGACACAAAGTCTTAGTACA 57.747 39.130 0.00 0.00 45.32 2.90
3007 5357 5.279384 ACACGACACAAAGTCTTAGTACAG 58.721 41.667 0.00 0.00 45.32 2.74
3008 5358 4.148348 CACGACACAAAGTCTTAGTACAGC 59.852 45.833 0.00 0.00 45.32 4.40
3009 5359 4.202080 ACGACACAAAGTCTTAGTACAGCA 60.202 41.667 0.00 0.00 45.32 4.41
3010 5360 4.148348 CGACACAAAGTCTTAGTACAGCAC 59.852 45.833 0.00 0.00 45.32 4.40
3011 5361 4.377897 ACACAAAGTCTTAGTACAGCACC 58.622 43.478 0.00 0.00 0.00 5.01
3012 5362 4.141801 ACACAAAGTCTTAGTACAGCACCA 60.142 41.667 0.00 0.00 0.00 4.17
3013 5363 4.814234 CACAAAGTCTTAGTACAGCACCAA 59.186 41.667 0.00 0.00 0.00 3.67
3014 5364 5.295787 CACAAAGTCTTAGTACAGCACCAAA 59.704 40.000 0.00 0.00 0.00 3.28
3015 5365 5.883673 ACAAAGTCTTAGTACAGCACCAAAA 59.116 36.000 0.00 0.00 0.00 2.44
3016 5366 6.038271 ACAAAGTCTTAGTACAGCACCAAAAG 59.962 38.462 0.00 0.00 0.00 2.27
3017 5367 4.065789 AGTCTTAGTACAGCACCAAAAGC 58.934 43.478 0.00 0.00 0.00 3.51
3018 5368 3.188667 GTCTTAGTACAGCACCAAAAGCC 59.811 47.826 0.00 0.00 0.00 4.35
3019 5369 2.940994 TAGTACAGCACCAAAAGCCA 57.059 45.000 0.00 0.00 0.00 4.75
3020 5370 2.292828 AGTACAGCACCAAAAGCCAT 57.707 45.000 0.00 0.00 0.00 4.40
3021 5371 2.597455 AGTACAGCACCAAAAGCCATT 58.403 42.857 0.00 0.00 0.00 3.16
3022 5372 2.558359 AGTACAGCACCAAAAGCCATTC 59.442 45.455 0.00 0.00 0.00 2.67
3023 5373 0.681175 ACAGCACCAAAAGCCATTCC 59.319 50.000 0.00 0.00 0.00 3.01
3024 5374 0.388907 CAGCACCAAAAGCCATTCCG 60.389 55.000 0.00 0.00 0.00 4.30
3025 5375 1.079888 GCACCAAAAGCCATTCCGG 60.080 57.895 0.00 0.00 38.11 5.14
3034 5384 4.794648 CCATTCCGGCCCTCGCAA 62.795 66.667 0.00 0.00 37.59 4.85
3035 5385 3.204827 CATTCCGGCCCTCGCAAG 61.205 66.667 0.00 0.00 37.59 4.01
3036 5386 4.489771 ATTCCGGCCCTCGCAAGG 62.490 66.667 0.00 0.00 42.95 3.61
3040 5390 4.161295 CGGCCCTCGCAAGGATGA 62.161 66.667 0.00 0.00 46.67 2.92
3041 5391 2.272146 GGCCCTCGCAAGGATGAA 59.728 61.111 0.00 0.00 46.67 2.57
3042 5392 1.378514 GGCCCTCGCAAGGATGAAA 60.379 57.895 0.00 0.00 46.67 2.69
3043 5393 0.965363 GGCCCTCGCAAGGATGAAAA 60.965 55.000 0.00 0.00 46.67 2.29
3044 5394 0.171231 GCCCTCGCAAGGATGAAAAC 59.829 55.000 0.00 0.00 46.67 2.43
3045 5395 0.811281 CCCTCGCAAGGATGAAAACC 59.189 55.000 0.00 0.00 46.67 3.27
3046 5396 1.533625 CCTCGCAAGGATGAAAACCA 58.466 50.000 0.00 0.00 46.67 3.67
3047 5397 1.885887 CCTCGCAAGGATGAAAACCAA 59.114 47.619 0.00 0.00 46.67 3.67
3048 5398 2.493278 CCTCGCAAGGATGAAAACCAAT 59.507 45.455 0.00 0.00 46.67 3.16
3049 5399 3.504863 CTCGCAAGGATGAAAACCAATG 58.495 45.455 0.00 0.00 38.47 2.82
3050 5400 3.153130 TCGCAAGGATGAAAACCAATGA 58.847 40.909 0.00 0.00 38.47 2.57
3051 5401 3.571828 TCGCAAGGATGAAAACCAATGAA 59.428 39.130 0.00 0.00 38.47 2.57
3052 5402 3.922240 CGCAAGGATGAAAACCAATGAAG 59.078 43.478 0.00 0.00 0.00 3.02
3053 5403 4.559300 CGCAAGGATGAAAACCAATGAAGT 60.559 41.667 0.00 0.00 0.00 3.01
3054 5404 5.299949 GCAAGGATGAAAACCAATGAAGTT 58.700 37.500 0.00 0.00 0.00 2.66
3055 5405 5.406477 GCAAGGATGAAAACCAATGAAGTTC 59.594 40.000 0.00 0.00 0.00 3.01
3056 5406 6.514947 CAAGGATGAAAACCAATGAAGTTCA 58.485 36.000 8.27 8.27 33.08 3.18
3057 5407 6.336842 AGGATGAAAACCAATGAAGTTCAG 57.663 37.500 11.91 0.34 32.13 3.02
3058 5408 5.244626 AGGATGAAAACCAATGAAGTTCAGG 59.755 40.000 11.91 10.37 32.13 3.86
3059 5409 4.320608 TGAAAACCAATGAAGTTCAGGC 57.679 40.909 11.91 0.00 0.00 4.85
3060 5410 3.243367 TGAAAACCAATGAAGTTCAGGCG 60.243 43.478 11.91 3.30 0.00 5.52
3061 5411 2.270352 AACCAATGAAGTTCAGGCGA 57.730 45.000 11.91 0.00 0.00 5.54
3062 5412 2.270352 ACCAATGAAGTTCAGGCGAA 57.730 45.000 11.91 0.00 0.00 4.70
3063 5413 2.582052 ACCAATGAAGTTCAGGCGAAA 58.418 42.857 11.91 0.00 31.43 3.46
3064 5414 2.554032 ACCAATGAAGTTCAGGCGAAAG 59.446 45.455 11.91 0.00 31.43 2.62
3065 5415 2.554032 CCAATGAAGTTCAGGCGAAAGT 59.446 45.455 11.91 0.00 31.43 2.66
3066 5416 3.004734 CCAATGAAGTTCAGGCGAAAGTT 59.995 43.478 11.91 0.00 31.43 2.66
3067 5417 4.215399 CCAATGAAGTTCAGGCGAAAGTTA 59.785 41.667 11.91 0.00 31.43 2.24
3068 5418 5.278266 CCAATGAAGTTCAGGCGAAAGTTAA 60.278 40.000 11.91 0.00 31.43 2.01
3069 5419 5.613358 ATGAAGTTCAGGCGAAAGTTAAG 57.387 39.130 11.91 0.00 31.43 1.85
3070 5420 3.250040 TGAAGTTCAGGCGAAAGTTAAGC 59.750 43.478 0.08 0.00 31.43 3.09
3071 5421 2.846193 AGTTCAGGCGAAAGTTAAGCA 58.154 42.857 5.10 0.00 31.43 3.91
3072 5422 3.211045 AGTTCAGGCGAAAGTTAAGCAA 58.789 40.909 5.10 0.00 31.43 3.91
3073 5423 3.251004 AGTTCAGGCGAAAGTTAAGCAAG 59.749 43.478 5.10 0.00 31.43 4.01
3074 5424 1.535462 TCAGGCGAAAGTTAAGCAAGC 59.465 47.619 5.10 0.00 0.00 4.01
3075 5425 0.881796 AGGCGAAAGTTAAGCAAGCC 59.118 50.000 5.10 0.00 43.07 4.35
3076 5426 0.596082 GGCGAAAGTTAAGCAAGCCA 59.404 50.000 0.00 0.00 42.37 4.75
3077 5427 1.666023 GGCGAAAGTTAAGCAAGCCAC 60.666 52.381 0.00 0.00 42.37 5.01
3078 5428 1.266989 GCGAAAGTTAAGCAAGCCACT 59.733 47.619 0.00 0.00 0.00 4.00
3079 5429 2.482721 GCGAAAGTTAAGCAAGCCACTA 59.517 45.455 0.00 0.00 0.00 2.74
3080 5430 3.424962 GCGAAAGTTAAGCAAGCCACTAG 60.425 47.826 0.00 0.00 0.00 2.57
3081 5431 3.424962 CGAAAGTTAAGCAAGCCACTAGC 60.425 47.826 0.00 0.00 44.25 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 127 0.250234 CTCCCGATCTTGTGCTGGAA 59.750 55.000 0.00 0.00 0.00 3.53
190 193 3.623060 CGATCATGTAAAACCCAGGTGAG 59.377 47.826 0.00 0.00 0.00 3.51
593 599 4.016444 GAGTGGCATCATAAACAAAGGGA 58.984 43.478 0.00 0.00 0.00 4.20
626 2802 2.848691 TCCGTAATTGGGAAACAACGT 58.151 42.857 0.00 0.00 42.94 3.99
781 2981 5.306394 ACTACTTGGAAGGCTTTTGTACTC 58.694 41.667 0.00 0.00 0.00 2.59
789 2993 4.072839 GCTTTGTACTACTTGGAAGGCTT 58.927 43.478 0.00 0.00 0.00 4.35
794 2998 4.755123 GCTTCTGCTTTGTACTACTTGGAA 59.245 41.667 0.00 0.00 36.03 3.53
838 3046 6.216569 TGTTTTGTGTTGTTTGAGCTGTTAA 58.783 32.000 0.00 0.00 0.00 2.01
854 3062 5.953205 CGATTTGTGAGCTTTTTGTTTTGTG 59.047 36.000 0.00 0.00 0.00 3.33
867 3075 1.153958 GGCAAGGCGATTTGTGAGC 60.154 57.895 0.00 0.00 0.00 4.26
897 3127 3.782443 GCGATTCGGGAGGTGGGT 61.782 66.667 8.34 0.00 0.00 4.51
948 3215 3.559657 GATGAGGCGATCCGGACCG 62.560 68.421 15.90 15.90 37.47 4.79
949 3216 2.340443 GATGAGGCGATCCGGACC 59.660 66.667 6.12 3.19 37.47 4.46
950 3217 2.203771 AGGATGAGGCGATCCGGAC 61.204 63.158 6.12 0.00 45.93 4.79
951 3218 2.198703 AGGATGAGGCGATCCGGA 59.801 61.111 6.61 6.61 45.93 5.14
952 3219 2.341543 CAGGATGAGGCGATCCGG 59.658 66.667 11.52 0.00 45.93 5.14
953 3220 2.032860 AACCAGGATGAGGCGATCCG 62.033 60.000 11.52 7.72 45.93 4.18
954 3221 0.250081 GAACCAGGATGAGGCGATCC 60.250 60.000 9.83 9.83 42.21 3.36
955 3222 0.755686 AGAACCAGGATGAGGCGATC 59.244 55.000 0.00 0.00 39.69 3.69
956 3223 0.755686 GAGAACCAGGATGAGGCGAT 59.244 55.000 0.00 0.00 39.69 4.58
957 3224 1.330655 GGAGAACCAGGATGAGGCGA 61.331 60.000 0.00 0.00 39.69 5.54
958 3225 1.144936 GGAGAACCAGGATGAGGCG 59.855 63.158 0.00 0.00 39.69 5.52
959 3226 0.915364 AAGGAGAACCAGGATGAGGC 59.085 55.000 0.00 0.00 39.69 4.70
960 3227 2.092699 GGAAAGGAGAACCAGGATGAGG 60.093 54.545 0.00 0.00 39.69 3.86
961 3228 2.092699 GGGAAAGGAGAACCAGGATGAG 60.093 54.545 0.00 0.00 39.69 2.90
962 3229 1.916181 GGGAAAGGAGAACCAGGATGA 59.084 52.381 0.00 0.00 39.69 2.92
963 3230 1.407437 CGGGAAAGGAGAACCAGGATG 60.407 57.143 0.00 0.00 38.94 3.51
964 3231 0.912486 CGGGAAAGGAGAACCAGGAT 59.088 55.000 0.00 0.00 38.94 3.24
965 3232 1.838073 GCGGGAAAGGAGAACCAGGA 61.838 60.000 0.00 0.00 38.94 3.86
966 3233 1.377333 GCGGGAAAGGAGAACCAGG 60.377 63.158 0.00 0.00 38.94 4.45
967 3234 0.674895 CAGCGGGAAAGGAGAACCAG 60.675 60.000 0.00 0.00 38.94 4.00
968 3235 1.374947 CAGCGGGAAAGGAGAACCA 59.625 57.895 0.00 0.00 38.94 3.67
969 3236 2.041115 GCAGCGGGAAAGGAGAACC 61.041 63.158 0.00 0.00 0.00 3.62
1015 3282 3.186047 CGACATCGTCCGTTGGGC 61.186 66.667 3.18 0.00 34.11 5.36
1016 3283 2.508439 CCGACATCGTCCGTTGGG 60.508 66.667 0.00 0.00 34.67 4.12
1019 3286 4.047059 ACGCCGACATCGTCCGTT 62.047 61.111 10.24 0.00 40.56 4.44
1189 3460 0.252881 TCCTTGCTGTCCTCCCTGAT 60.253 55.000 0.00 0.00 0.00 2.90
1354 3634 4.796231 GCAGCGGTCATCGTCGGT 62.796 66.667 0.00 0.00 41.72 4.69
1356 3636 3.250323 CAGCAGCGGTCATCGTCG 61.250 66.667 0.00 0.00 41.72 5.12
1401 3687 0.782384 GAACGTACGACCACAGCTTG 59.218 55.000 24.41 0.00 0.00 4.01
1402 3688 0.672342 AGAACGTACGACCACAGCTT 59.328 50.000 24.41 2.26 0.00 3.74
1486 3782 4.400567 GGCCTCAAAGCTAATCTTGACATT 59.599 41.667 0.00 0.00 34.67 2.71
1666 3975 1.810794 GCTACTCTCGTCCCTCATCGA 60.811 57.143 0.00 0.00 34.88 3.59
1761 4070 5.308237 GTCATCTAGGTAATCCAATGGAGGT 59.692 44.000 8.40 0.44 34.05 3.85
1882 4194 3.262420 CAACAGTCCCGGTATGAAGAAG 58.738 50.000 0.00 0.00 0.00 2.85
2042 4354 8.750515 TTTCTCCAATATATCAGCAATGACAA 57.249 30.769 0.00 0.00 0.00 3.18
2072 4384 7.222805 CAGCATACTAAATTCTGCGAGTCTTAA 59.777 37.037 0.00 0.00 39.57 1.85
2118 4430 5.243981 CAGACTAATCCCAGATTGCTATGG 58.756 45.833 0.08 0.00 36.27 2.74
2119 4431 4.694509 GCAGACTAATCCCAGATTGCTATG 59.305 45.833 0.08 0.00 0.00 2.23
2188 4523 4.143200 TGACATCGAAGACGTACATTTTGC 60.143 41.667 0.00 0.00 42.51 3.68
2193 4528 5.920840 CCATTATGACATCGAAGACGTACAT 59.079 40.000 0.00 0.00 42.51 2.29
2198 4533 3.717707 ACCCATTATGACATCGAAGACG 58.282 45.455 0.00 0.00 42.51 4.18
2219 4556 8.724310 TCTAGCATAGCTACATATATAGGGTGA 58.276 37.037 0.00 0.00 40.44 4.02
2233 4570 5.291371 CGACGCTACTTATCTAGCATAGCTA 59.709 44.000 0.00 0.00 39.40 3.32
2235 4572 4.142859 ACGACGCTACTTATCTAGCATAGC 60.143 45.833 0.00 0.00 39.40 2.97
2256 4593 5.633601 TGCTTCTAGTCAACAGAACATAACG 59.366 40.000 0.00 0.00 0.00 3.18
2260 4597 4.960938 TGTGCTTCTAGTCAACAGAACAT 58.039 39.130 0.00 0.00 0.00 2.71
2263 4600 7.171508 CAGTAAATGTGCTTCTAGTCAACAGAA 59.828 37.037 0.00 0.00 0.00 3.02
2276 4618 8.419076 AAATTCGAAAAACAGTAAATGTGCTT 57.581 26.923 0.00 0.00 43.00 3.91
2311 4653 4.651778 ACTTTGAGAAATGGATTGACCGA 58.348 39.130 0.00 0.00 42.61 4.69
2318 4660 8.598041 AGTTACTCACTACTTTGAGAAATGGAT 58.402 33.333 7.12 0.00 45.19 3.41
2447 4789 6.200097 CACGATGAACATGGTGTATTAATCGA 59.800 38.462 15.87 0.00 40.95 3.59
2448 4790 6.354858 CACGATGAACATGGTGTATTAATCG 58.645 40.000 17.40 9.92 40.95 3.34
2467 4817 5.992829 TGGTATTGTAAGAAACACACACGAT 59.007 36.000 0.00 0.00 38.00 3.73
2827 5177 9.475620 TAACAGAATACTGGTGAGATAAGAGAA 57.524 33.333 0.00 0.00 44.46 2.87
2828 5178 9.647918 ATAACAGAATACTGGTGAGATAAGAGA 57.352 33.333 0.00 0.00 44.46 3.10
2831 5181 9.265901 CCAATAACAGAATACTGGTGAGATAAG 57.734 37.037 0.00 0.00 44.46 1.73
2832 5182 7.715249 GCCAATAACAGAATACTGGTGAGATAA 59.285 37.037 0.00 0.00 44.46 1.75
2833 5183 7.147567 TGCCAATAACAGAATACTGGTGAGATA 60.148 37.037 0.00 0.00 44.46 1.98
2834 5184 6.058183 GCCAATAACAGAATACTGGTGAGAT 58.942 40.000 0.00 0.00 44.46 2.75
2835 5185 5.045942 TGCCAATAACAGAATACTGGTGAGA 60.046 40.000 0.00 0.00 44.46 3.27
2836 5186 5.185454 TGCCAATAACAGAATACTGGTGAG 58.815 41.667 0.00 0.00 44.46 3.51
2837 5187 5.172687 TGCCAATAACAGAATACTGGTGA 57.827 39.130 0.00 0.00 44.46 4.02
2838 5188 6.455360 AATGCCAATAACAGAATACTGGTG 57.545 37.500 0.00 0.00 44.46 4.17
2842 5192 8.121305 TGTTGAAATGCCAATAACAGAATACT 57.879 30.769 0.00 0.00 0.00 2.12
2843 5193 8.931385 ATGTTGAAATGCCAATAACAGAATAC 57.069 30.769 0.00 0.00 35.08 1.89
2844 5194 9.368674 CAATGTTGAAATGCCAATAACAGAATA 57.631 29.630 0.00 0.00 35.08 1.75
2845 5195 7.148373 GCAATGTTGAAATGCCAATAACAGAAT 60.148 33.333 0.00 0.00 35.08 2.40
2846 5196 6.147492 GCAATGTTGAAATGCCAATAACAGAA 59.853 34.615 0.00 0.00 35.08 3.02
2847 5197 5.638657 GCAATGTTGAAATGCCAATAACAGA 59.361 36.000 0.00 0.00 35.08 3.41
2848 5198 5.408909 TGCAATGTTGAAATGCCAATAACAG 59.591 36.000 0.00 0.00 39.31 3.16
2849 5199 5.303165 TGCAATGTTGAAATGCCAATAACA 58.697 33.333 0.00 0.00 39.31 2.41
2850 5200 5.859521 TGCAATGTTGAAATGCCAATAAC 57.140 34.783 0.00 0.00 39.31 1.89
2851 5201 5.761726 TGTTGCAATGTTGAAATGCCAATAA 59.238 32.000 0.59 0.00 39.31 1.40
2852 5202 5.303165 TGTTGCAATGTTGAAATGCCAATA 58.697 33.333 0.59 0.00 39.31 1.90
2853 5203 4.135306 TGTTGCAATGTTGAAATGCCAAT 58.865 34.783 0.59 0.00 39.31 3.16
2854 5204 3.538591 TGTTGCAATGTTGAAATGCCAA 58.461 36.364 0.59 0.00 39.31 4.52
2855 5205 3.132160 CTGTTGCAATGTTGAAATGCCA 58.868 40.909 0.59 0.00 39.31 4.92
2856 5206 3.391965 TCTGTTGCAATGTTGAAATGCC 58.608 40.909 0.59 0.00 39.31 4.40
2857 5207 5.390145 GGAATCTGTTGCAATGTTGAAATGC 60.390 40.000 0.59 0.00 40.45 3.56
2858 5208 5.929992 AGGAATCTGTTGCAATGTTGAAATG 59.070 36.000 0.59 0.00 0.00 2.32
2859 5209 6.105397 AGGAATCTGTTGCAATGTTGAAAT 57.895 33.333 0.59 0.00 0.00 2.17
2860 5210 5.534207 AGGAATCTGTTGCAATGTTGAAA 57.466 34.783 0.59 0.00 0.00 2.69
2861 5211 6.350361 CCATAGGAATCTGTTGCAATGTTGAA 60.350 38.462 0.59 0.00 0.00 2.69
2862 5212 5.125900 CCATAGGAATCTGTTGCAATGTTGA 59.874 40.000 0.59 0.00 0.00 3.18
2863 5213 5.125900 TCCATAGGAATCTGTTGCAATGTTG 59.874 40.000 0.59 0.00 0.00 3.33
2864 5214 5.263599 TCCATAGGAATCTGTTGCAATGTT 58.736 37.500 0.59 0.00 0.00 2.71
2865 5215 4.858850 TCCATAGGAATCTGTTGCAATGT 58.141 39.130 0.59 0.00 0.00 2.71
2866 5216 6.713903 AGTATCCATAGGAATCTGTTGCAATG 59.286 38.462 0.59 0.00 34.34 2.82
2867 5217 6.845908 AGTATCCATAGGAATCTGTTGCAAT 58.154 36.000 0.59 0.00 34.34 3.56
2868 5218 6.252599 AGTATCCATAGGAATCTGTTGCAA 57.747 37.500 0.00 0.00 34.34 4.08
2869 5219 5.894298 AGTATCCATAGGAATCTGTTGCA 57.106 39.130 0.00 0.00 34.34 4.08
2870 5220 6.203723 GTCAAGTATCCATAGGAATCTGTTGC 59.796 42.308 0.00 0.00 34.34 4.17
2871 5221 7.504403 AGTCAAGTATCCATAGGAATCTGTTG 58.496 38.462 0.00 0.00 34.34 3.33
2872 5222 7.345653 TGAGTCAAGTATCCATAGGAATCTGTT 59.654 37.037 0.00 0.00 34.34 3.16
2873 5223 6.841229 TGAGTCAAGTATCCATAGGAATCTGT 59.159 38.462 0.00 0.00 34.34 3.41
2874 5224 7.295322 TGAGTCAAGTATCCATAGGAATCTG 57.705 40.000 0.00 0.00 34.34 2.90
2875 5225 9.781425 ATATGAGTCAAGTATCCATAGGAATCT 57.219 33.333 0.00 0.00 34.34 2.40
2876 5226 9.814899 CATATGAGTCAAGTATCCATAGGAATC 57.185 37.037 0.00 0.00 34.34 2.52
2877 5227 8.263640 GCATATGAGTCAAGTATCCATAGGAAT 58.736 37.037 6.97 0.00 34.34 3.01
2878 5228 7.455953 AGCATATGAGTCAAGTATCCATAGGAA 59.544 37.037 6.97 0.00 34.34 3.36
2879 5229 6.956435 AGCATATGAGTCAAGTATCCATAGGA 59.044 38.462 6.97 0.00 35.55 2.94
2880 5230 7.123997 AGAGCATATGAGTCAAGTATCCATAGG 59.876 40.741 6.97 0.00 0.00 2.57
2881 5231 8.065473 AGAGCATATGAGTCAAGTATCCATAG 57.935 38.462 6.97 0.00 0.00 2.23
2882 5232 7.892771 AGAGAGCATATGAGTCAAGTATCCATA 59.107 37.037 6.97 0.00 0.00 2.74
2883 5233 6.725369 AGAGAGCATATGAGTCAAGTATCCAT 59.275 38.462 6.97 0.00 0.00 3.41
2884 5234 6.073981 AGAGAGCATATGAGTCAAGTATCCA 58.926 40.000 6.97 0.00 0.00 3.41
2885 5235 6.588719 AGAGAGCATATGAGTCAAGTATCC 57.411 41.667 6.97 0.00 0.00 2.59
2886 5236 9.973450 TTTTAGAGAGCATATGAGTCAAGTATC 57.027 33.333 6.97 0.00 0.00 2.24
2889 5239 9.107177 CAATTTTAGAGAGCATATGAGTCAAGT 57.893 33.333 6.97 0.00 0.00 3.16
2890 5240 8.557864 CCAATTTTAGAGAGCATATGAGTCAAG 58.442 37.037 6.97 0.00 0.00 3.02
2891 5241 7.012704 GCCAATTTTAGAGAGCATATGAGTCAA 59.987 37.037 6.97 0.00 0.00 3.18
2892 5242 6.484643 GCCAATTTTAGAGAGCATATGAGTCA 59.515 38.462 6.97 0.00 0.00 3.41
2893 5243 6.709846 AGCCAATTTTAGAGAGCATATGAGTC 59.290 38.462 6.97 2.00 0.00 3.36
2894 5244 6.599445 AGCCAATTTTAGAGAGCATATGAGT 58.401 36.000 6.97 0.00 0.00 3.41
2895 5245 7.507733 AAGCCAATTTTAGAGAGCATATGAG 57.492 36.000 6.97 0.00 0.00 2.90
2896 5246 7.886629 AAAGCCAATTTTAGAGAGCATATGA 57.113 32.000 6.97 0.00 0.00 2.15
2897 5247 8.937634 AAAAAGCCAATTTTAGAGAGCATATG 57.062 30.769 0.00 0.00 40.27 1.78
2919 5269 1.332375 CTGGCGTCTTCGTTCCAAAAA 59.668 47.619 0.00 0.00 39.49 1.94
2920 5270 0.941542 CTGGCGTCTTCGTTCCAAAA 59.058 50.000 0.00 0.00 39.49 2.44
2921 5271 0.105224 TCTGGCGTCTTCGTTCCAAA 59.895 50.000 0.00 0.00 39.49 3.28
2922 5272 0.320374 ATCTGGCGTCTTCGTTCCAA 59.680 50.000 0.00 0.00 39.49 3.53
2923 5273 0.389817 CATCTGGCGTCTTCGTTCCA 60.390 55.000 0.00 0.00 39.49 3.53
2924 5274 1.696832 GCATCTGGCGTCTTCGTTCC 61.697 60.000 0.00 0.00 39.49 3.62
2925 5275 1.710339 GCATCTGGCGTCTTCGTTC 59.290 57.895 0.00 0.00 39.49 3.95
2926 5276 3.876300 GCATCTGGCGTCTTCGTT 58.124 55.556 0.00 0.00 39.49 3.85
2937 5287 0.373716 GTTAAAGCCGGACGCATCTG 59.626 55.000 5.05 0.00 41.38 2.90
2938 5288 0.249398 AGTTAAAGCCGGACGCATCT 59.751 50.000 5.05 0.00 41.38 2.90
2939 5289 1.084289 AAGTTAAAGCCGGACGCATC 58.916 50.000 5.05 0.00 41.38 3.91
2940 5290 2.389962 TAAGTTAAAGCCGGACGCAT 57.610 45.000 5.05 0.00 41.38 4.73
2941 5291 2.166821 TTAAGTTAAAGCCGGACGCA 57.833 45.000 5.05 0.00 41.38 5.24
2942 5292 4.863152 TTATTAAGTTAAAGCCGGACGC 57.137 40.909 5.05 0.00 37.98 5.19
2950 5300 8.638873 CCTATTGGGGGCTTTATTAAGTTAAAG 58.361 37.037 0.00 4.78 40.56 1.85
2951 5301 7.070198 GCCTATTGGGGGCTTTATTAAGTTAAA 59.930 37.037 0.00 0.00 45.57 1.52
2952 5302 6.551975 GCCTATTGGGGGCTTTATTAAGTTAA 59.448 38.462 0.00 0.00 45.57 2.01
2953 5303 6.072649 GCCTATTGGGGGCTTTATTAAGTTA 58.927 40.000 0.00 0.00 45.57 2.24
2954 5304 4.899457 GCCTATTGGGGGCTTTATTAAGTT 59.101 41.667 0.00 0.00 45.57 2.66
2955 5305 4.480115 GCCTATTGGGGGCTTTATTAAGT 58.520 43.478 0.00 0.00 45.57 2.24
2966 5316 0.818040 GTTACGCTGCCTATTGGGGG 60.818 60.000 0.00 0.00 35.12 5.40
2967 5317 0.107410 TGTTACGCTGCCTATTGGGG 60.107 55.000 0.00 0.00 35.12 4.96
2968 5318 1.014352 GTGTTACGCTGCCTATTGGG 58.986 55.000 0.00 0.00 38.36 4.12
2969 5319 0.650512 CGTGTTACGCTGCCTATTGG 59.349 55.000 0.00 0.00 33.65 3.16
2970 5320 1.323534 GTCGTGTTACGCTGCCTATTG 59.676 52.381 0.00 0.00 42.21 1.90
2971 5321 1.067425 TGTCGTGTTACGCTGCCTATT 60.067 47.619 0.00 0.00 42.21 1.73
2972 5322 0.528924 TGTCGTGTTACGCTGCCTAT 59.471 50.000 0.00 0.00 42.21 2.57
2973 5323 0.387622 GTGTCGTGTTACGCTGCCTA 60.388 55.000 0.00 0.00 42.21 3.93
2974 5324 1.663702 GTGTCGTGTTACGCTGCCT 60.664 57.895 0.00 0.00 42.21 4.75
2975 5325 1.492319 TTGTGTCGTGTTACGCTGCC 61.492 55.000 0.00 0.00 42.21 4.85
2976 5326 0.302288 TTTGTGTCGTGTTACGCTGC 59.698 50.000 0.00 0.00 42.21 5.25
2977 5327 1.591158 ACTTTGTGTCGTGTTACGCTG 59.409 47.619 0.00 0.00 42.21 5.18
2978 5328 1.856597 GACTTTGTGTCGTGTTACGCT 59.143 47.619 0.00 0.00 42.21 5.07
2979 5329 2.274718 GACTTTGTGTCGTGTTACGC 57.725 50.000 0.00 0.00 42.21 4.42
2988 5338 4.448060 GGTGCTGTACTAAGACTTTGTGTC 59.552 45.833 11.86 6.29 45.67 3.67
2989 5339 4.141801 TGGTGCTGTACTAAGACTTTGTGT 60.142 41.667 11.86 3.61 0.00 3.72
2990 5340 4.377021 TGGTGCTGTACTAAGACTTTGTG 58.623 43.478 11.86 0.00 0.00 3.33
2991 5341 4.682778 TGGTGCTGTACTAAGACTTTGT 57.317 40.909 7.44 7.44 0.00 2.83
2992 5342 6.371809 TTTTGGTGCTGTACTAAGACTTTG 57.628 37.500 0.00 0.00 31.00 2.77
2993 5343 5.008712 GCTTTTGGTGCTGTACTAAGACTTT 59.991 40.000 0.00 0.00 31.00 2.66
2994 5344 4.515567 GCTTTTGGTGCTGTACTAAGACTT 59.484 41.667 0.00 0.00 31.00 3.01
2995 5345 4.065789 GCTTTTGGTGCTGTACTAAGACT 58.934 43.478 0.00 0.00 31.00 3.24
2996 5346 3.188667 GGCTTTTGGTGCTGTACTAAGAC 59.811 47.826 0.00 0.00 31.00 3.01
2997 5347 3.181449 TGGCTTTTGGTGCTGTACTAAGA 60.181 43.478 0.00 0.00 31.00 2.10
2998 5348 3.146066 TGGCTTTTGGTGCTGTACTAAG 58.854 45.455 0.00 0.00 31.00 2.18
2999 5349 3.216187 TGGCTTTTGGTGCTGTACTAA 57.784 42.857 0.00 0.00 0.00 2.24
3000 5350 2.940994 TGGCTTTTGGTGCTGTACTA 57.059 45.000 0.00 0.00 0.00 1.82
3001 5351 2.292828 ATGGCTTTTGGTGCTGTACT 57.707 45.000 0.00 0.00 0.00 2.73
3002 5352 2.352715 GGAATGGCTTTTGGTGCTGTAC 60.353 50.000 0.00 0.00 0.00 2.90
3003 5353 1.892474 GGAATGGCTTTTGGTGCTGTA 59.108 47.619 0.00 0.00 0.00 2.74
3004 5354 0.681175 GGAATGGCTTTTGGTGCTGT 59.319 50.000 0.00 0.00 0.00 4.40
3005 5355 0.388907 CGGAATGGCTTTTGGTGCTG 60.389 55.000 0.00 0.00 0.00 4.41
3006 5356 1.535204 CCGGAATGGCTTTTGGTGCT 61.535 55.000 0.00 0.00 0.00 4.40
3007 5357 1.079888 CCGGAATGGCTTTTGGTGC 60.080 57.895 0.00 0.00 0.00 5.01
3017 5367 4.794648 TTGCGAGGGCCGGAATGG 62.795 66.667 5.05 0.00 43.60 3.16
3023 5373 3.680620 TTCATCCTTGCGAGGGCCG 62.681 63.158 20.46 8.83 43.72 6.13
3024 5374 0.965363 TTTTCATCCTTGCGAGGGCC 60.965 55.000 20.46 0.00 43.72 5.80
3025 5375 0.171231 GTTTTCATCCTTGCGAGGGC 59.829 55.000 20.46 0.00 43.72 5.19
3026 5376 0.811281 GGTTTTCATCCTTGCGAGGG 59.189 55.000 20.46 4.99 43.72 4.30
3027 5377 1.533625 TGGTTTTCATCCTTGCGAGG 58.466 50.000 14.59 14.59 45.02 4.63
3028 5378 3.191162 TCATTGGTTTTCATCCTTGCGAG 59.809 43.478 0.00 0.00 0.00 5.03
3029 5379 3.153130 TCATTGGTTTTCATCCTTGCGA 58.847 40.909 0.00 0.00 0.00 5.10
3030 5380 3.574284 TCATTGGTTTTCATCCTTGCG 57.426 42.857 0.00 0.00 0.00 4.85
3031 5381 4.886579 ACTTCATTGGTTTTCATCCTTGC 58.113 39.130 0.00 0.00 0.00 4.01
3032 5382 6.514947 TGAACTTCATTGGTTTTCATCCTTG 58.485 36.000 0.00 0.00 0.00 3.61
3033 5383 6.239402 CCTGAACTTCATTGGTTTTCATCCTT 60.239 38.462 0.00 0.00 0.00 3.36
3034 5384 5.244626 CCTGAACTTCATTGGTTTTCATCCT 59.755 40.000 0.00 0.00 0.00 3.24
3035 5385 5.473039 CCTGAACTTCATTGGTTTTCATCC 58.527 41.667 0.00 0.00 0.00 3.51
3036 5386 4.925646 GCCTGAACTTCATTGGTTTTCATC 59.074 41.667 0.00 0.00 0.00 2.92
3037 5387 4.559300 CGCCTGAACTTCATTGGTTTTCAT 60.559 41.667 0.00 0.00 0.00 2.57
3038 5388 3.243367 CGCCTGAACTTCATTGGTTTTCA 60.243 43.478 0.00 0.00 0.00 2.69
3039 5389 3.004315 TCGCCTGAACTTCATTGGTTTTC 59.996 43.478 0.00 0.00 0.00 2.29
3040 5390 2.955660 TCGCCTGAACTTCATTGGTTTT 59.044 40.909 0.00 0.00 0.00 2.43
3041 5391 2.582052 TCGCCTGAACTTCATTGGTTT 58.418 42.857 0.00 0.00 0.00 3.27
3042 5392 2.270352 TCGCCTGAACTTCATTGGTT 57.730 45.000 0.00 0.00 0.00 3.67
3043 5393 2.270352 TTCGCCTGAACTTCATTGGT 57.730 45.000 0.00 0.00 0.00 3.67
3044 5394 2.554032 ACTTTCGCCTGAACTTCATTGG 59.446 45.455 0.00 0.00 32.71 3.16
3045 5395 3.904136 ACTTTCGCCTGAACTTCATTG 57.096 42.857 0.00 0.00 32.71 2.82
3046 5396 5.562890 GCTTAACTTTCGCCTGAACTTCATT 60.563 40.000 0.00 0.00 32.71 2.57
3047 5397 4.083271 GCTTAACTTTCGCCTGAACTTCAT 60.083 41.667 0.00 0.00 32.71 2.57
3048 5398 3.250040 GCTTAACTTTCGCCTGAACTTCA 59.750 43.478 0.00 0.00 32.71 3.02
3049 5399 3.250040 TGCTTAACTTTCGCCTGAACTTC 59.750 43.478 0.00 0.00 32.71 3.01
3050 5400 3.211045 TGCTTAACTTTCGCCTGAACTT 58.789 40.909 0.00 0.00 32.71 2.66
3051 5401 2.846193 TGCTTAACTTTCGCCTGAACT 58.154 42.857 0.00 0.00 32.71 3.01
3052 5402 3.555518 CTTGCTTAACTTTCGCCTGAAC 58.444 45.455 0.00 0.00 32.71 3.18
3053 5403 2.031157 GCTTGCTTAACTTTCGCCTGAA 60.031 45.455 0.00 0.00 0.00 3.02
3054 5404 1.535462 GCTTGCTTAACTTTCGCCTGA 59.465 47.619 0.00 0.00 0.00 3.86
3055 5405 1.401539 GGCTTGCTTAACTTTCGCCTG 60.402 52.381 0.00 0.00 33.47 4.85
3056 5406 0.881796 GGCTTGCTTAACTTTCGCCT 59.118 50.000 0.00 0.00 33.47 5.52
3057 5407 0.596082 TGGCTTGCTTAACTTTCGCC 59.404 50.000 0.00 0.00 36.64 5.54
3058 5408 1.266989 AGTGGCTTGCTTAACTTTCGC 59.733 47.619 0.00 0.00 0.00 4.70
3059 5409 3.424962 GCTAGTGGCTTGCTTAACTTTCG 60.425 47.826 0.00 0.00 38.06 3.46
3060 5410 3.424962 CGCTAGTGGCTTGCTTAACTTTC 60.425 47.826 0.00 0.00 39.13 2.62
3061 5411 2.484264 CGCTAGTGGCTTGCTTAACTTT 59.516 45.455 0.00 0.00 39.13 2.66
3062 5412 2.076863 CGCTAGTGGCTTGCTTAACTT 58.923 47.619 0.00 0.00 39.13 2.66
3063 5413 1.676014 CCGCTAGTGGCTTGCTTAACT 60.676 52.381 9.93 0.00 39.13 2.24
3064 5414 0.727398 CCGCTAGTGGCTTGCTTAAC 59.273 55.000 9.93 0.00 39.13 2.01
3065 5415 0.611200 TCCGCTAGTGGCTTGCTTAA 59.389 50.000 18.01 0.00 39.13 1.85
3066 5416 0.830648 ATCCGCTAGTGGCTTGCTTA 59.169 50.000 18.01 0.00 39.13 3.09
3067 5417 0.035056 AATCCGCTAGTGGCTTGCTT 60.035 50.000 18.01 3.20 39.13 3.91
3068 5418 0.830648 TAATCCGCTAGTGGCTTGCT 59.169 50.000 19.32 4.62 39.13 3.91
3069 5419 0.938008 GTAATCCGCTAGTGGCTTGC 59.062 55.000 19.32 14.98 39.13 4.01
3070 5420 2.309528 TGTAATCCGCTAGTGGCTTG 57.690 50.000 19.32 0.00 39.13 4.01
3071 5421 2.906354 CTTGTAATCCGCTAGTGGCTT 58.094 47.619 18.01 16.53 39.13 4.35
3072 5422 2.604046 CTTGTAATCCGCTAGTGGCT 57.396 50.000 18.01 4.94 39.13 4.75


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

AutoCloner maintained by Alex Coulton.