Multiple sequence alignment - TraesCS2D01G019100

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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 TraesCS2D01G019100 chr2D 100.000 3197 0 0 1 3197 8984110 8980914 0.000000e+00 5904.0
1 TraesCS2D01G019100 chr2D 84.005 819 88 22 914 1723 8716074 8716858 0.000000e+00 747.0
2 TraesCS2D01G019100 chr2D 84.878 410 61 1 1 410 38227446 38227038 2.290000e-111 412.0
3 TraesCS2D01G019100 chr2D 84.559 408 54 7 1759 2163 8716966 8717367 2.310000e-106 396.0
4 TraesCS2D01G019100 chr2D 76.562 704 97 37 1121 1799 8920363 8921023 1.110000e-84 324.0
5 TraesCS2D01G019100 chr2B 94.408 1538 46 8 832 2346 11984396 11985916 0.000000e+00 2327.0
6 TraesCS2D01G019100 chr2B 84.091 1364 150 35 909 2238 12027074 12025744 0.000000e+00 1254.0
7 TraesCS2D01G019100 chr2B 83.832 1070 143 16 1116 2165 12077537 12076478 0.000000e+00 990.0
8 TraesCS2D01G019100 chr2B 91.892 444 35 1 2 444 11967285 11967728 1.260000e-173 619.0
9 TraesCS2D01G019100 chr2B 75.694 1296 185 73 1121 2346 70882007 70880772 2.180000e-146 529.0
10 TraesCS2D01G019100 chr2B 84.009 444 71 0 1 444 236716360 236715917 8.200000e-116 427.0
11 TraesCS2D01G019100 chr2B 89.137 313 24 3 441 750 11984071 11984376 6.470000e-102 381.0
12 TraesCS2D01G019100 chr2B 82.522 452 33 19 2572 2992 11987824 11988260 3.920000e-94 355.0
13 TraesCS2D01G019100 chr2B 87.701 187 21 2 493 677 85072219 85072405 1.930000e-52 217.0
14 TraesCS2D01G019100 chr3D 94.938 1205 53 5 974 2172 564006027 564004825 0.000000e+00 1881.0
15 TraesCS2D01G019100 chr3D 91.304 506 31 11 441 938 564006528 564006028 0.000000e+00 678.0
16 TraesCS2D01G019100 chr3D 93.034 445 29 2 1 444 564012409 564011966 0.000000e+00 649.0
17 TraesCS2D01G019100 chr2A 94.524 694 24 8 1660 2346 8045934 8046620 0.000000e+00 1059.0
18 TraesCS2D01G019100 chr2A 84.569 836 87 23 911 1726 8371029 8370216 0.000000e+00 791.0
19 TraesCS2D01G019100 chr2A 94.808 443 22 1 2 444 8043033 8043474 0.000000e+00 689.0
20 TraesCS2D01G019100 chr2A 92.568 444 31 2 2 444 8385501 8385059 1.250000e-178 636.0
21 TraesCS2D01G019100 chr2A 92.135 445 29 4 1 444 8040397 8040836 9.740000e-175 623.0
22 TraesCS2D01G019100 chr2A 75.740 1352 189 76 1111 2384 8182492 8181202 4.660000e-153 551.0
23 TraesCS2D01G019100 chr2A 88.889 459 30 9 447 903 8044836 8045275 2.170000e-151 545.0
24 TraesCS2D01G019100 chr2A 90.250 400 32 3 441 833 8371480 8371081 1.700000e-142 516.0
25 TraesCS2D01G019100 chr2A 93.215 339 16 5 441 776 8042327 8042661 2.870000e-135 492.0
26 TraesCS2D01G019100 chr2A 74.787 1293 225 52 935 2163 7806755 7808010 3.710000e-134 488.0
27 TraesCS2D01G019100 chr2A 95.669 254 11 0 1060 1313 8045366 8045619 2.970000e-110 409.0
28 TraesCS2D01G019100 chr2A 84.314 408 55 7 1759 2163 8370153 8369752 1.080000e-104 390.0
29 TraesCS2D01G019100 chr2A 85.979 378 30 11 2563 2918 8048490 8048866 1.800000e-102 383.0
30 TraesCS2D01G019100 chr2A 97.573 206 4 1 1334 1538 8045610 8045815 5.070000e-93 351.0
31 TraesCS2D01G019100 chr2A 86.275 204 14 1 3008 3197 8139827 8140030 3.230000e-50 209.0
32 TraesCS2D01G019100 chr2A 87.162 148 3 1 1485 1632 8045805 8045936 1.540000e-33 154.0
33 TraesCS2D01G019100 chr2A 100.000 36 0 0 903 938 8045296 8045331 2.060000e-07 67.6
34 TraesCS2D01G019100 chr7A 88.444 450 31 6 1944 2384 466703178 466702741 1.020000e-144 523.0
35 TraesCS2D01G019100 chr7A 75.514 1168 171 61 1247 2346 466508137 466509257 1.740000e-127 466.0
36 TraesCS2D01G019100 chr7A 94.737 76 3 1 2430 2505 466702558 466702484 2.010000e-22 117.0
37 TraesCS2D01G019100 chr6B 84.753 446 58 8 1 444 259876026 259876463 3.790000e-119 438.0
38 TraesCS2D01G019100 chr6B 93.617 47 3 0 676 722 645816495 645816541 1.590000e-08 71.3
39 TraesCS2D01G019100 chr4B 84.915 411 60 2 1 410 420523697 420523288 6.380000e-112 414.0
40 TraesCS2D01G019100 chr4B 75.362 138 31 2 1958 2092 515039920 515039783 2.660000e-06 63.9
41 TraesCS2D01G019100 chr1A 88.021 192 21 2 485 675 571578899 571579089 3.210000e-55 226.0
42 TraesCS2D01G019100 chr1B 87.000 200 24 2 480 679 642605714 642605911 1.150000e-54 224.0
43 TraesCS2D01G019100 chr5D 88.298 188 15 4 493 676 246301832 246302016 5.370000e-53 219.0
44 TraesCS2D01G019100 chr4A 93.333 45 3 0 2048 2092 46409384 46409428 2.060000e-07 67.6
45 TraesCS2D01G019100 chr6A 93.182 44 3 0 676 719 573862084 573862127 7.400000e-07 65.8


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 TraesCS2D01G019100 chr2D 8980914 8984110 3196 True 5904.000000 5904 100.000000 1 3197 1 chr2D.!!$R1 3196
1 TraesCS2D01G019100 chr2D 8716074 8717367 1293 False 571.500000 747 84.282000 914 2163 2 chr2D.!!$F2 1249
2 TraesCS2D01G019100 chr2D 8920363 8921023 660 False 324.000000 324 76.562000 1121 1799 1 chr2D.!!$F1 678
3 TraesCS2D01G019100 chr2B 12025744 12027074 1330 True 1254.000000 1254 84.091000 909 2238 1 chr2B.!!$R1 1329
4 TraesCS2D01G019100 chr2B 11984071 11988260 4189 False 1021.000000 2327 88.689000 441 2992 3 chr2B.!!$F3 2551
5 TraesCS2D01G019100 chr2B 12076478 12077537 1059 True 990.000000 990 83.832000 1116 2165 1 chr2B.!!$R2 1049
6 TraesCS2D01G019100 chr2B 70880772 70882007 1235 True 529.000000 529 75.694000 1121 2346 1 chr2B.!!$R3 1225
7 TraesCS2D01G019100 chr3D 564004825 564006528 1703 True 1279.500000 1881 93.121000 441 2172 2 chr3D.!!$R2 1731
8 TraesCS2D01G019100 chr2A 8369752 8371480 1728 True 565.666667 791 86.377667 441 2163 3 chr2A.!!$R3 1722
9 TraesCS2D01G019100 chr2A 8181202 8182492 1290 True 551.000000 551 75.740000 1111 2384 1 chr2A.!!$R1 1273
10 TraesCS2D01G019100 chr2A 7806755 7808010 1255 False 488.000000 488 74.787000 935 2163 1 chr2A.!!$F1 1228
11 TraesCS2D01G019100 chr2A 8040397 8048866 8469 False 477.260000 1059 92.995400 1 2918 10 chr2A.!!$F3 2917
12 TraesCS2D01G019100 chr7A 466508137 466509257 1120 False 466.000000 466 75.514000 1247 2346 1 chr7A.!!$F1 1099
13 TraesCS2D01G019100 chr7A 466702484 466703178 694 True 320.000000 523 91.590500 1944 2505 2 chr7A.!!$R1 561

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
941 4958 0.108585 ATCGATCCCCAAATCCACCG 59.891 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 6760 0.035152 AGCAAGCCGGATGACATGAA 60.035 50.0 5.05 0.0 0.0 2.57 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
37 38 3.117888 TGAAGGAGACATATTCTTGGGGC 60.118 47.826 0.00 0.00 33.22 5.80
70 71 3.969287 ATGGTATCCATCATCGTCTGG 57.031 47.619 0.00 0.00 40.74 3.86
71 72 2.677914 TGGTATCCATCATCGTCTGGT 58.322 47.619 0.00 0.00 34.03 4.00
72 73 2.628178 TGGTATCCATCATCGTCTGGTC 59.372 50.000 0.00 0.00 34.03 4.02
73 74 2.628178 GGTATCCATCATCGTCTGGTCA 59.372 50.000 0.00 0.00 34.03 4.02
74 75 3.305676 GGTATCCATCATCGTCTGGTCAG 60.306 52.174 0.00 0.00 34.03 3.51
112 113 0.994247 ACAGGGATGCCAGAACATGA 59.006 50.000 5.86 0.00 0.00 3.07
135 136 7.056635 TGAGGATGAGAAAAGAGAACAAAACT 58.943 34.615 0.00 0.00 0.00 2.66
142 143 5.572896 AGAAAAGAGAACAAAACTTGCAACG 59.427 36.000 0.00 0.00 0.00 4.10
145 146 2.783832 GAGAACAAAACTTGCAACGAGC 59.216 45.455 0.00 0.00 45.96 5.03
178 179 4.908736 AGTGAACAAGTTGTTGATTCACG 58.091 39.130 25.46 0.00 46.19 4.35
210 211 6.403636 CCGATAAATCTCACCTCAGGTTTTTG 60.404 42.308 0.00 0.00 31.02 2.44
221 222 7.335924 TCACCTCAGGTTTTTGTAACATATAGC 59.664 37.037 0.00 0.00 31.02 2.97
234 235 8.105097 TGTAACATATAGCAAAGCAACAAGAA 57.895 30.769 0.00 0.00 0.00 2.52
235 236 8.020819 TGTAACATATAGCAAAGCAACAAGAAC 58.979 33.333 0.00 0.00 0.00 3.01
237 238 6.980593 ACATATAGCAAAGCAACAAGAACAA 58.019 32.000 0.00 0.00 0.00 2.83
238 239 6.863126 ACATATAGCAAAGCAACAAGAACAAC 59.137 34.615 0.00 0.00 0.00 3.32
239 240 3.591196 AGCAAAGCAACAAGAACAACA 57.409 38.095 0.00 0.00 0.00 3.33
240 241 3.253230 AGCAAAGCAACAAGAACAACAC 58.747 40.909 0.00 0.00 0.00 3.32
241 242 2.992543 GCAAAGCAACAAGAACAACACA 59.007 40.909 0.00 0.00 0.00 3.72
242 243 3.181531 GCAAAGCAACAAGAACAACACAC 60.182 43.478 0.00 0.00 0.00 3.82
243 244 3.932545 AAGCAACAAGAACAACACACA 57.067 38.095 0.00 0.00 0.00 3.72
262 263 6.046593 CACACAGTAACTAAAGGTTCACTCA 58.953 40.000 0.00 0.00 39.17 3.41
302 304 5.454966 GGTATTGGGGTCAATAAGGATGTT 58.545 41.667 1.04 0.00 44.55 2.71
306 308 4.862371 TGGGGTCAATAAGGATGTTTACC 58.138 43.478 0.00 0.00 0.00 2.85
321 323 3.866910 TGTTTACCGTTCCGCTATTGATC 59.133 43.478 0.00 0.00 0.00 2.92
328 330 4.214119 CCGTTCCGCTATTGATCATTGATT 59.786 41.667 0.00 0.00 0.00 2.57
330 332 5.050159 CGTTCCGCTATTGATCATTGATTGA 60.050 40.000 0.00 0.00 39.12 2.57
331 333 6.511605 CGTTCCGCTATTGATCATTGATTGAA 60.512 38.462 0.00 0.00 38.03 2.69
360 362 7.556844 AGTTTCGGTCATGTCTATATTTCACT 58.443 34.615 0.00 0.00 0.00 3.41
428 430 3.191888 AGGAGGTTAGGAGCTTGAGAA 57.808 47.619 0.00 0.00 32.79 2.87
436 438 5.180304 GGTTAGGAGCTTGAGAAAAAGTCAG 59.820 44.000 0.00 0.00 0.00 3.51
438 440 4.133078 AGGAGCTTGAGAAAAAGTCAGTG 58.867 43.478 0.00 0.00 0.00 3.66
544 2041 9.449719 AGATTTAACCAAGTATTAGTCAAGTGG 57.550 33.333 0.00 0.00 0.00 4.00
677 2180 6.429078 TCGACTTAGACTTAGCAAGACTGTTA 59.571 38.462 9.70 0.00 35.27 2.41
762 2265 0.672401 ACAAATACGGCAGACCCACG 60.672 55.000 0.00 0.00 0.00 4.94
789 4781 1.881591 TTGGACCGGAACCTTTAACG 58.118 50.000 9.46 0.00 0.00 3.18
801 4793 3.216800 ACCTTTAACGGTTTCCAACTCC 58.783 45.455 0.00 0.00 31.94 3.85
802 4794 3.215975 CCTTTAACGGTTTCCAACTCCA 58.784 45.455 0.00 0.00 0.00 3.86
887 4879 5.517770 AGTGCGAACCGTATATTTTACAGAC 59.482 40.000 0.00 0.00 0.00 3.51
938 4955 1.133823 CACCATCGATCCCCAAATCCA 60.134 52.381 0.00 0.00 0.00 3.41
939 4956 1.133792 ACCATCGATCCCCAAATCCAC 60.134 52.381 0.00 0.00 0.00 4.02
940 4957 1.609208 CATCGATCCCCAAATCCACC 58.391 55.000 0.00 0.00 0.00 4.61
941 4958 0.108585 ATCGATCCCCAAATCCACCG 59.891 55.000 0.00 0.00 0.00 4.94
942 4959 1.525995 CGATCCCCAAATCCACCGG 60.526 63.158 0.00 0.00 0.00 5.28
960 5025 0.257905 GGTCCACCCAACCCTAATCC 59.742 60.000 0.00 0.00 0.00 3.01
964 5029 1.493446 CCACCCAACCCTAATCCCTAC 59.507 57.143 0.00 0.00 0.00 3.18
970 5035 2.299297 CAACCCTAATCCCTACCTAGCG 59.701 54.545 0.00 0.00 0.00 4.26
976 5041 2.500392 ATCCCTACCTAGCGAGCTAG 57.500 55.000 21.64 21.64 44.07 3.42
977 5042 0.250814 TCCCTACCTAGCGAGCTAGC 60.251 60.000 22.81 11.29 43.35 3.42
1128 5199 2.032550 CCGCAAAGCCATAAGTGATCAG 59.967 50.000 0.00 0.00 0.00 2.90
1131 5202 4.199310 GCAAAGCCATAAGTGATCAGGTA 58.801 43.478 0.00 0.00 0.00 3.08
1206 5277 4.067944 ACTCTCCTTCCTCCACATACTT 57.932 45.455 0.00 0.00 0.00 2.24
1326 5397 2.838225 TACCGCCCTGGCTCTAGC 60.838 66.667 6.60 0.00 43.94 3.42
1542 5680 1.270305 TGGAAGTCGTCTGCCAAAGAG 60.270 52.381 6.95 0.00 45.77 2.85
1632 5839 1.077858 GGGCTCTCTCCTTTGCTGG 60.078 63.158 0.00 0.00 0.00 4.85
1633 5840 1.077858 GGCTCTCTCCTTTGCTGGG 60.078 63.158 0.00 0.00 0.00 4.45
1634 5841 1.682257 GCTCTCTCCTTTGCTGGGT 59.318 57.895 0.00 0.00 0.00 4.51
1635 5842 0.676151 GCTCTCTCCTTTGCTGGGTG 60.676 60.000 0.00 0.00 0.00 4.61
1636 5843 0.035630 CTCTCTCCTTTGCTGGGTGG 60.036 60.000 0.00 0.00 0.00 4.61
1637 5844 0.473694 TCTCTCCTTTGCTGGGTGGA 60.474 55.000 0.00 0.00 0.00 4.02
1638 5845 0.622665 CTCTCCTTTGCTGGGTGGAT 59.377 55.000 0.00 0.00 0.00 3.41
1639 5846 0.620556 TCTCCTTTGCTGGGTGGATC 59.379 55.000 0.00 0.00 0.00 3.36
1640 5847 0.622665 CTCCTTTGCTGGGTGGATCT 59.377 55.000 0.00 0.00 0.00 2.75
1641 5848 1.005215 CTCCTTTGCTGGGTGGATCTT 59.995 52.381 0.00 0.00 0.00 2.40
1642 5849 1.004745 TCCTTTGCTGGGTGGATCTTC 59.995 52.381 0.00 0.00 0.00 2.87
1643 5850 1.005215 CCTTTGCTGGGTGGATCTTCT 59.995 52.381 0.00 0.00 0.00 2.85
1644 5851 2.363683 CTTTGCTGGGTGGATCTTCTC 58.636 52.381 0.00 0.00 0.00 2.87
1645 5852 1.361204 TTGCTGGGTGGATCTTCTCA 58.639 50.000 0.00 0.00 0.00 3.27
1646 5853 0.907486 TGCTGGGTGGATCTTCTCAG 59.093 55.000 11.36 11.36 0.00 3.35
1647 5854 1.198713 GCTGGGTGGATCTTCTCAGA 58.801 55.000 17.26 0.00 0.00 3.27
1648 5855 1.138661 GCTGGGTGGATCTTCTCAGAG 59.861 57.143 17.26 0.00 30.36 3.35
1649 5856 1.761784 CTGGGTGGATCTTCTCAGAGG 59.238 57.143 10.53 0.00 30.36 3.69
1650 5857 0.467804 GGGTGGATCTTCTCAGAGGC 59.532 60.000 0.00 0.00 30.36 4.70
1651 5858 1.198713 GGTGGATCTTCTCAGAGGCA 58.801 55.000 0.00 0.00 30.36 4.75
1652 5859 1.767681 GGTGGATCTTCTCAGAGGCAT 59.232 52.381 0.00 0.00 30.36 4.40
1653 5860 2.485124 GGTGGATCTTCTCAGAGGCATG 60.485 54.545 0.00 0.00 30.36 4.06
1654 5861 2.170187 GTGGATCTTCTCAGAGGCATGT 59.830 50.000 0.00 0.00 30.36 3.21
1655 5862 2.842496 TGGATCTTCTCAGAGGCATGTT 59.158 45.455 0.00 0.00 30.36 2.71
1656 5863 3.204526 GGATCTTCTCAGAGGCATGTTG 58.795 50.000 0.00 0.00 30.36 3.33
1657 5864 2.105006 TCTTCTCAGAGGCATGTTGC 57.895 50.000 0.00 0.00 44.08 4.17
1658 5865 1.627329 TCTTCTCAGAGGCATGTTGCT 59.373 47.619 0.00 0.00 44.28 3.91
1659 5866 2.008329 CTTCTCAGAGGCATGTTGCTC 58.992 52.381 0.00 0.00 44.28 4.26
1660 5867 1.273759 TCTCAGAGGCATGTTGCTCT 58.726 50.000 0.00 0.00 44.28 4.09
1661 5868 1.066358 TCTCAGAGGCATGTTGCTCTG 60.066 52.381 16.21 16.21 44.28 3.35
1939 6260 1.743252 GTGAGCTACCAGCCTGCAC 60.743 63.158 0.00 0.00 43.77 4.57
2093 6423 1.654954 ATGGAGAACGACGAGGTCCG 61.655 60.000 0.00 0.00 45.44 4.79
2234 6574 5.648178 TGCATACTGCTGTCATTTCATTT 57.352 34.783 0.00 0.00 45.31 2.32
2235 6575 6.756299 TGCATACTGCTGTCATTTCATTTA 57.244 33.333 0.00 0.00 45.31 1.40
2236 6576 7.337480 TGCATACTGCTGTCATTTCATTTAT 57.663 32.000 0.00 0.00 45.31 1.40
2237 6577 8.449251 TGCATACTGCTGTCATTTCATTTATA 57.551 30.769 0.00 0.00 45.31 0.98
2238 6578 8.901793 TGCATACTGCTGTCATTTCATTTATAA 58.098 29.630 0.00 0.00 45.31 0.98
2239 6579 9.903682 GCATACTGCTGTCATTTCATTTATAAT 57.096 29.630 0.00 0.00 40.96 1.28
2397 6772 5.936686 AGATATTTGCTTCATGTCATCCG 57.063 39.130 0.00 0.00 0.00 4.18
2398 6773 4.758674 AGATATTTGCTTCATGTCATCCGG 59.241 41.667 0.00 0.00 0.00 5.14
2402 6777 0.379669 GCTTCATGTCATCCGGCTTG 59.620 55.000 0.00 0.00 0.00 4.01
2404 6779 0.035152 TTCATGTCATCCGGCTTGCT 60.035 50.000 0.00 0.00 0.00 3.91
2406 6781 1.209261 TCATGTCATCCGGCTTGCTTA 59.791 47.619 0.00 0.00 0.00 3.09
2408 6783 1.953559 TGTCATCCGGCTTGCTTATC 58.046 50.000 0.00 0.00 0.00 1.75
2410 6785 0.880278 TCATCCGGCTTGCTTATCGC 60.880 55.000 0.00 0.00 39.77 4.58
2428 7623 2.176273 CAGGCATGCTACAGCGTCC 61.176 63.158 18.92 0.00 45.83 4.79
2492 8614 4.159506 GGTACAGAGAGCTCTCATCAGTTT 59.840 45.833 38.20 18.34 45.21 2.66
2546 8668 9.737427 AGTGTCTTATTTATACTCGAATGACTG 57.263 33.333 0.00 0.00 0.00 3.51
2553 8675 6.724893 TTATACTCGAATGACTGAATGGGA 57.275 37.500 0.00 0.00 0.00 4.37
2613 8973 7.453752 ACAATGAGGAGGAAGTACTTGTTACTA 59.546 37.037 14.14 0.00 40.44 1.82
2656 9021 1.676635 CGGTCCGTACAGGTCTCCA 60.677 63.158 2.08 0.00 41.99 3.86
2663 9036 1.544246 CGTACAGGTCTCCATGTGTGA 59.456 52.381 0.00 0.00 0.00 3.58
2666 9039 0.612229 CAGGTCTCCATGTGTGAGCT 59.388 55.000 10.30 10.30 43.90 4.09
2669 9042 1.354040 GTCTCCATGTGTGAGCTTCG 58.646 55.000 0.00 0.00 0.00 3.79
2683 9056 3.306595 CTTCGGCTGCTCCTCTGCA 62.307 63.158 0.00 0.00 40.89 4.41
2701 9074 2.587753 CGGTAATCCATGGCGCGT 60.588 61.111 6.96 0.00 0.00 6.01
2702 9079 2.881266 CGGTAATCCATGGCGCGTG 61.881 63.158 6.96 2.37 0.00 5.34
2734 9124 3.185203 TGCTGCTTCCCAAGGGGT 61.185 61.111 5.08 0.00 44.74 4.95
2788 9184 2.588877 GGGATGTCGACGGCCATG 60.589 66.667 22.89 0.00 0.00 3.66
2856 9256 1.924320 GACCGACGACTCTGACAGGG 61.924 65.000 0.00 0.00 0.00 4.45
2867 9267 1.133167 TCTGACAGGGTGAGGAAGACA 60.133 52.381 1.81 0.00 0.00 3.41
2932 9346 3.378512 TCTGATGGTCTTACAGGCTCAT 58.621 45.455 0.00 0.00 33.19 2.90
2936 9350 1.204704 TGGTCTTACAGGCTCATGACG 59.795 52.381 0.00 0.00 0.00 4.35
2942 9356 0.613292 ACAGGCTCATGACGTCCTCT 60.613 55.000 14.12 0.00 0.00 3.69
2943 9357 0.534412 CAGGCTCATGACGTCCTCTT 59.466 55.000 14.12 0.00 0.00 2.85
2944 9358 0.820871 AGGCTCATGACGTCCTCTTC 59.179 55.000 14.12 0.00 0.00 2.87
2945 9359 0.820871 GGCTCATGACGTCCTCTTCT 59.179 55.000 14.12 0.00 0.00 2.85
2946 9360 2.025155 GGCTCATGACGTCCTCTTCTA 58.975 52.381 14.12 0.00 0.00 2.10
2947 9361 2.223618 GGCTCATGACGTCCTCTTCTAC 60.224 54.545 14.12 0.00 0.00 2.59
2948 9362 2.539953 GCTCATGACGTCCTCTTCTACG 60.540 54.545 14.12 0.00 44.47 3.51
2949 9363 2.014857 TCATGACGTCCTCTTCTACGG 58.985 52.381 14.12 0.00 43.25 4.02
2953 9367 2.083002 GACGTCCTCTTCTACGGTTCT 58.917 52.381 3.51 0.00 43.25 3.01
2988 9402 2.904697 CTGATCTCATACAGCTGGCA 57.095 50.000 19.93 5.62 0.00 4.92
2992 9406 3.390311 TGATCTCATACAGCTGGCAGATT 59.610 43.478 20.86 5.68 0.00 2.40
2993 9407 3.920231 TCTCATACAGCTGGCAGATTT 57.080 42.857 20.86 7.87 0.00 2.17
2994 9408 4.226427 TCTCATACAGCTGGCAGATTTT 57.774 40.909 20.86 3.49 0.00 1.82
2995 9409 4.592942 TCTCATACAGCTGGCAGATTTTT 58.407 39.130 20.86 0.00 0.00 1.94
2996 9410 4.637534 TCTCATACAGCTGGCAGATTTTTC 59.362 41.667 20.86 0.00 0.00 2.29
2997 9411 4.334552 TCATACAGCTGGCAGATTTTTCA 58.665 39.130 20.86 0.00 0.00 2.69
2998 9412 4.397103 TCATACAGCTGGCAGATTTTTCAG 59.603 41.667 20.86 0.62 0.00 3.02
3000 9414 3.430779 GCTGGCAGATTTTTCAGCC 57.569 52.632 20.86 2.74 44.70 4.85
3006 9420 4.725790 GGCAGATTTTTCAGCCAAGTAT 57.274 40.909 4.71 0.00 46.26 2.12
3007 9421 5.077134 GGCAGATTTTTCAGCCAAGTATT 57.923 39.130 4.71 0.00 46.26 1.89
3008 9422 5.482006 GGCAGATTTTTCAGCCAAGTATTT 58.518 37.500 4.71 0.00 46.26 1.40
3009 9423 6.630071 GGCAGATTTTTCAGCCAAGTATTTA 58.370 36.000 4.71 0.00 46.26 1.40
3010 9424 7.267857 GGCAGATTTTTCAGCCAAGTATTTAT 58.732 34.615 4.71 0.00 46.26 1.40
3011 9425 8.413229 GGCAGATTTTTCAGCCAAGTATTTATA 58.587 33.333 4.71 0.00 46.26 0.98
3012 9426 9.455847 GCAGATTTTTCAGCCAAGTATTTATAG 57.544 33.333 0.00 0.00 0.00 1.31
3022 9436 9.817809 CAGCCAAGTATTTATAGAACTAAGACA 57.182 33.333 0.00 0.00 0.00 3.41
3055 9469 9.591792 CAATTAGAGAAATCTTTCCAATTTCCC 57.408 33.333 5.26 0.00 41.82 3.97
3056 9470 9.552695 AATTAGAGAAATCTTTCCAATTTCCCT 57.447 29.630 5.26 2.41 41.82 4.20
3058 9472 9.686683 TTAGAGAAATCTTTCCAATTTCCCTAG 57.313 33.333 5.26 0.00 41.82 3.02
3059 9473 6.605194 AGAGAAATCTTTCCAATTTCCCTAGC 59.395 38.462 5.26 0.00 41.82 3.42
3060 9474 5.658634 AGAAATCTTTCCAATTTCCCTAGCC 59.341 40.000 5.26 0.00 41.82 3.93
3061 9475 4.888626 ATCTTTCCAATTTCCCTAGCCT 57.111 40.909 0.00 0.00 0.00 4.58
3062 9476 5.994416 ATCTTTCCAATTTCCCTAGCCTA 57.006 39.130 0.00 0.00 0.00 3.93
3063 9477 5.112129 TCTTTCCAATTTCCCTAGCCTAC 57.888 43.478 0.00 0.00 0.00 3.18
3064 9478 4.538490 TCTTTCCAATTTCCCTAGCCTACA 59.462 41.667 0.00 0.00 0.00 2.74
3065 9479 3.926058 TCCAATTTCCCTAGCCTACAC 57.074 47.619 0.00 0.00 0.00 2.90
3066 9480 3.460825 TCCAATTTCCCTAGCCTACACT 58.539 45.455 0.00 0.00 0.00 3.55
3067 9481 3.454812 TCCAATTTCCCTAGCCTACACTC 59.545 47.826 0.00 0.00 0.00 3.51
3068 9482 3.199946 CCAATTTCCCTAGCCTACACTCA 59.800 47.826 0.00 0.00 0.00 3.41
3069 9483 4.324254 CCAATTTCCCTAGCCTACACTCAA 60.324 45.833 0.00 0.00 0.00 3.02
3070 9484 3.975168 TTTCCCTAGCCTACACTCAAC 57.025 47.619 0.00 0.00 0.00 3.18
3071 9485 1.471119 TCCCTAGCCTACACTCAACG 58.529 55.000 0.00 0.00 0.00 4.10
3072 9486 1.183549 CCCTAGCCTACACTCAACGT 58.816 55.000 0.00 0.00 0.00 3.99
3073 9487 1.549170 CCCTAGCCTACACTCAACGTT 59.451 52.381 0.00 0.00 0.00 3.99
3074 9488 2.756760 CCCTAGCCTACACTCAACGTTA 59.243 50.000 0.00 0.00 0.00 3.18
3075 9489 3.181489 CCCTAGCCTACACTCAACGTTAG 60.181 52.174 0.00 1.81 0.00 2.34
3076 9490 3.693085 CCTAGCCTACACTCAACGTTAGA 59.307 47.826 0.00 0.09 0.00 2.10
3077 9491 3.851976 AGCCTACACTCAACGTTAGAG 57.148 47.619 19.55 19.55 39.04 2.43
3078 9492 3.155501 AGCCTACACTCAACGTTAGAGT 58.844 45.455 20.52 20.52 46.72 3.24
3079 9493 3.190953 AGCCTACACTCAACGTTAGAGTC 59.809 47.826 22.30 14.60 44.11 3.36
3080 9494 3.672781 GCCTACACTCAACGTTAGAGTCC 60.673 52.174 22.30 10.64 44.11 3.85
3081 9495 3.119566 CCTACACTCAACGTTAGAGTCCC 60.120 52.174 22.30 0.00 44.11 4.46
3082 9496 2.595238 ACACTCAACGTTAGAGTCCCT 58.405 47.619 22.30 10.92 44.11 4.20
3083 9497 2.963782 ACACTCAACGTTAGAGTCCCTT 59.036 45.455 22.30 10.44 44.11 3.95
3084 9498 3.243771 ACACTCAACGTTAGAGTCCCTTG 60.244 47.826 22.30 16.08 44.11 3.61
3085 9499 2.963782 ACTCAACGTTAGAGTCCCTTGT 59.036 45.455 20.52 4.89 42.40 3.16
3086 9500 4.022589 CACTCAACGTTAGAGTCCCTTGTA 60.023 45.833 22.30 0.00 44.11 2.41
3087 9501 4.217983 ACTCAACGTTAGAGTCCCTTGTAG 59.782 45.833 20.52 0.00 42.40 2.74
3088 9502 4.147321 TCAACGTTAGAGTCCCTTGTAGT 58.853 43.478 0.00 0.00 0.00 2.73
3089 9503 4.586001 TCAACGTTAGAGTCCCTTGTAGTT 59.414 41.667 0.00 0.00 0.00 2.24
3090 9504 5.769662 TCAACGTTAGAGTCCCTTGTAGTTA 59.230 40.000 0.00 0.00 0.00 2.24
3091 9505 6.265196 TCAACGTTAGAGTCCCTTGTAGTTAA 59.735 38.462 0.00 0.00 0.00 2.01
3092 9506 6.655078 ACGTTAGAGTCCCTTGTAGTTAAA 57.345 37.500 0.00 0.00 0.00 1.52
3093 9507 7.237209 ACGTTAGAGTCCCTTGTAGTTAAAT 57.763 36.000 0.00 0.00 0.00 1.40
3094 9508 7.674120 ACGTTAGAGTCCCTTGTAGTTAAATT 58.326 34.615 0.00 0.00 0.00 1.82
3095 9509 7.601508 ACGTTAGAGTCCCTTGTAGTTAAATTG 59.398 37.037 0.00 0.00 0.00 2.32
3096 9510 7.816031 CGTTAGAGTCCCTTGTAGTTAAATTGA 59.184 37.037 0.00 0.00 0.00 2.57
3097 9511 9.668497 GTTAGAGTCCCTTGTAGTTAAATTGAT 57.332 33.333 0.00 0.00 0.00 2.57
3099 9513 8.567285 AGAGTCCCTTGTAGTTAAATTGATTG 57.433 34.615 0.00 0.00 0.00 2.67
3100 9514 7.121315 AGAGTCCCTTGTAGTTAAATTGATTGC 59.879 37.037 0.00 0.00 0.00 3.56
3101 9515 6.719370 AGTCCCTTGTAGTTAAATTGATTGCA 59.281 34.615 0.00 0.00 0.00 4.08
3102 9516 7.232534 AGTCCCTTGTAGTTAAATTGATTGCAA 59.767 33.333 0.00 0.00 38.60 4.08
3103 9517 7.870445 GTCCCTTGTAGTTAAATTGATTGCAAA 59.130 33.333 1.71 0.00 37.59 3.68
3104 9518 8.424918 TCCCTTGTAGTTAAATTGATTGCAAAA 58.575 29.630 1.71 0.00 37.59 2.44
3105 9519 9.218440 CCCTTGTAGTTAAATTGATTGCAAAAT 57.782 29.630 1.71 0.00 37.59 1.82
3107 9521 9.941991 CTTGTAGTTAAATTGATTGCAAAATCG 57.058 29.630 1.71 0.00 37.59 3.34
3108 9522 9.684448 TTGTAGTTAAATTGATTGCAAAATCGA 57.316 25.926 1.71 0.00 37.59 3.59
3109 9523 9.853555 TGTAGTTAAATTGATTGCAAAATCGAT 57.146 25.926 1.71 0.00 37.59 3.59
3111 9525 8.984891 AGTTAAATTGATTGCAAAATCGATCA 57.015 26.923 1.71 0.00 37.59 2.92
3112 9526 9.421806 AGTTAAATTGATTGCAAAATCGATCAA 57.578 25.926 12.01 12.01 45.65 2.57
3131 9545 9.764363 TCGATCAATATAATAAAACTGAGCAGT 57.236 29.630 0.00 0.00 44.94 4.40
3151 9565 7.365840 GCAGTAGCTGTAAAATCAAGTTACT 57.634 36.000 0.00 0.00 37.91 2.24
3152 9566 7.807680 GCAGTAGCTGTAAAATCAAGTTACTT 58.192 34.615 0.00 0.00 37.91 2.24
3153 9567 8.290325 GCAGTAGCTGTAAAATCAAGTTACTTT 58.710 33.333 0.00 0.00 37.91 2.66
3183 9597 7.912383 TCGAGAAAAAGTCGAGTTATTTTTGT 58.088 30.769 5.80 6.55 41.41 2.83
3184 9598 8.392612 TCGAGAAAAAGTCGAGTTATTTTTGTT 58.607 29.630 5.80 0.00 41.41 2.83
3185 9599 8.461398 CGAGAAAAAGTCGAGTTATTTTTGTTG 58.539 33.333 5.80 6.81 39.92 3.33
3186 9600 9.285770 GAGAAAAAGTCGAGTTATTTTTGTTGT 57.714 29.630 5.80 0.00 36.53 3.32
3196 9610 9.777843 CGAGTTATTTTTGTTGTAAAATCAAGC 57.222 29.630 0.00 0.00 38.36 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 5.996513 CCCAAGAATATGTCTCCTTCATCAG 59.003 44.000 0.00 0.00 34.56 2.90
12 13 5.163163 CCCCAAGAATATGTCTCCTTCATCA 60.163 44.000 0.00 0.00 34.56 3.07
15 16 3.117888 GCCCCAAGAATATGTCTCCTTCA 60.118 47.826 0.00 0.00 34.56 3.02
18 19 1.777272 GGCCCCAAGAATATGTCTCCT 59.223 52.381 0.00 0.00 34.56 3.69
37 38 3.053693 TGGATACCATCAAACCAAGAGGG 60.054 47.826 0.00 0.00 42.39 4.30
66 67 1.775385 TCACACTGTGTCTGACCAGA 58.225 50.000 23.87 0.44 34.79 3.86
67 68 2.827800 ATCACACTGTGTCTGACCAG 57.172 50.000 11.12 18.59 34.79 4.00
68 69 3.118445 TCAAATCACACTGTGTCTGACCA 60.118 43.478 11.12 2.33 34.79 4.02
69 70 3.466836 TCAAATCACACTGTGTCTGACC 58.533 45.455 11.12 0.00 34.79 4.02
70 71 4.751600 TGATCAAATCACACTGTGTCTGAC 59.248 41.667 11.12 0.00 33.59 3.51
71 72 4.959723 TGATCAAATCACACTGTGTCTGA 58.040 39.130 11.12 11.42 33.59 3.27
112 113 7.682981 GCAAGTTTTGTTCTCTTTTCTCATCCT 60.683 37.037 0.00 0.00 0.00 3.24
142 143 5.409826 ACTTGTTCACTATGCTAGTTTGCTC 59.590 40.000 0.00 0.00 36.76 4.26
145 146 6.959361 ACAACTTGTTCACTATGCTAGTTTG 58.041 36.000 0.00 0.00 36.76 2.93
178 179 2.427506 GTGAGATTTATCGGCATCCCC 58.572 52.381 0.00 0.00 0.00 4.81
210 211 8.020819 TGTTCTTGTTGCTTTGCTATATGTTAC 58.979 33.333 0.00 0.00 0.00 2.50
221 222 3.986572 TGTGTGTTGTTCTTGTTGCTTTG 59.013 39.130 0.00 0.00 0.00 2.77
234 235 6.093082 GTGAACCTTTAGTTACTGTGTGTTGT 59.907 38.462 0.00 0.00 39.40 3.32
235 236 6.315393 AGTGAACCTTTAGTTACTGTGTGTTG 59.685 38.462 0.00 0.00 39.40 3.33
237 238 5.985911 AGTGAACCTTTAGTTACTGTGTGT 58.014 37.500 0.00 0.00 39.40 3.72
238 239 6.046593 TGAGTGAACCTTTAGTTACTGTGTG 58.953 40.000 0.00 0.00 39.40 3.82
239 240 6.229936 TGAGTGAACCTTTAGTTACTGTGT 57.770 37.500 0.00 0.00 39.40 3.72
240 241 7.548196 TTTGAGTGAACCTTTAGTTACTGTG 57.452 36.000 0.00 0.00 39.40 3.66
243 244 9.668497 GGATATTTGAGTGAACCTTTAGTTACT 57.332 33.333 0.00 0.00 39.40 2.24
262 263 6.497954 CCCAATACCCACATGAATGGATATTT 59.502 38.462 0.00 0.00 43.02 1.40
268 269 2.318908 CCCCAATACCCACATGAATGG 58.681 52.381 0.00 0.00 39.71 3.16
284 285 4.626771 CGGTAAACATCCTTATTGACCCCA 60.627 45.833 0.00 0.00 0.00 4.96
285 286 3.881089 CGGTAAACATCCTTATTGACCCC 59.119 47.826 0.00 0.00 0.00 4.95
306 308 5.050159 TCAATCAATGATCAATAGCGGAACG 60.050 40.000 0.00 0.00 45.11 3.95
321 323 6.437928 TGACCGAAACTCTTTTCAATCAATG 58.562 36.000 0.00 0.00 41.22 2.82
328 330 4.703897 AGACATGACCGAAACTCTTTTCA 58.296 39.130 0.00 0.00 41.22 2.69
330 332 9.449719 AAATATAGACATGACCGAAACTCTTTT 57.550 29.630 0.00 0.00 0.00 2.27
331 333 9.099454 GAAATATAGACATGACCGAAACTCTTT 57.901 33.333 0.00 0.00 0.00 2.52
360 362 1.864565 CGTGTGACACTGTGGATTCA 58.135 50.000 14.42 4.14 31.34 2.57
489 1985 0.984995 GAGACCTAGCCACACCCTTT 59.015 55.000 0.00 0.00 0.00 3.11
575 2073 5.922544 AGATTCGTGCAGGATTTTCTTTTTG 59.077 36.000 10.35 0.00 0.00 2.44
587 2085 4.183865 TCTTACATTGAGATTCGTGCAGG 58.816 43.478 0.00 0.00 0.00 4.85
588 2086 5.752472 AGATCTTACATTGAGATTCGTGCAG 59.248 40.000 0.00 0.00 34.13 4.41
677 2180 9.333724 GGAATAGGCAAAATCATGATTTCAAAT 57.666 29.630 29.08 19.10 39.88 2.32
732 2235 1.399089 CCGTATTTGTTTCGCCCGATT 59.601 47.619 0.00 0.00 0.00 3.34
755 2258 2.287970 GGTCCAAATTTTGTCGTGGGTC 60.288 50.000 8.26 0.00 0.00 4.46
762 2265 2.626266 AGGTTCCGGTCCAAATTTTGTC 59.374 45.455 17.60 1.63 0.00 3.18
801 4793 2.552315 ACGGCAAACCAAGTTGTAGATG 59.448 45.455 1.45 0.00 34.57 2.90
802 4794 2.858745 ACGGCAAACCAAGTTGTAGAT 58.141 42.857 1.45 0.00 34.57 1.98
887 4879 1.069049 CTGGGTCCTGCAAAAACTTGG 59.931 52.381 0.00 0.00 0.00 3.61
938 4955 2.987431 TTAGGGTTGGGTGGACCGGT 62.987 60.000 6.92 6.92 44.64 5.28
939 4956 1.568118 ATTAGGGTTGGGTGGACCGG 61.568 60.000 0.00 0.00 44.64 5.28
940 4957 0.107361 GATTAGGGTTGGGTGGACCG 60.107 60.000 0.00 0.00 44.64 4.79
941 4958 0.257905 GGATTAGGGTTGGGTGGACC 59.742 60.000 0.00 0.00 40.81 4.46
942 4959 0.257905 GGGATTAGGGTTGGGTGGAC 59.742 60.000 0.00 0.00 0.00 4.02
1326 5397 3.083997 AGGTAGCCTCCCCGCAAG 61.084 66.667 0.00 0.00 0.00 4.01
1542 5680 2.358737 CCGGACAGCAAGACCCAC 60.359 66.667 0.00 0.00 0.00 4.61
1632 5839 1.198713 TGCCTCTGAGAAGATCCACC 58.801 55.000 6.17 0.00 0.00 4.61
1633 5840 2.170187 ACATGCCTCTGAGAAGATCCAC 59.830 50.000 6.17 0.00 0.00 4.02
1634 5841 2.475155 ACATGCCTCTGAGAAGATCCA 58.525 47.619 6.17 0.00 0.00 3.41
1635 5842 3.204526 CAACATGCCTCTGAGAAGATCC 58.795 50.000 6.17 0.00 0.00 3.36
1636 5843 2.613133 GCAACATGCCTCTGAGAAGATC 59.387 50.000 6.17 0.00 37.42 2.75
1637 5844 2.239150 AGCAACATGCCTCTGAGAAGAT 59.761 45.455 6.17 0.00 46.52 2.40
1638 5845 1.627329 AGCAACATGCCTCTGAGAAGA 59.373 47.619 6.17 0.00 46.52 2.87
1639 5846 2.008329 GAGCAACATGCCTCTGAGAAG 58.992 52.381 6.17 0.00 46.52 2.85
1640 5847 1.627329 AGAGCAACATGCCTCTGAGAA 59.373 47.619 6.17 0.00 46.52 2.87
1641 5848 1.066358 CAGAGCAACATGCCTCTGAGA 60.066 52.381 23.75 0.00 46.52 3.27
1642 5849 1.338864 ACAGAGCAACATGCCTCTGAG 60.339 52.381 29.95 15.16 46.52 3.35
1643 5850 0.689055 ACAGAGCAACATGCCTCTGA 59.311 50.000 29.95 0.00 46.52 3.27
1644 5851 0.803117 CACAGAGCAACATGCCTCTG 59.197 55.000 25.21 25.21 46.52 3.35
1645 5852 0.689055 TCACAGAGCAACATGCCTCT 59.311 50.000 5.57 5.57 46.52 3.69
1646 5853 1.669779 GATCACAGAGCAACATGCCTC 59.330 52.381 0.00 0.00 46.52 4.70
1647 5854 1.281287 AGATCACAGAGCAACATGCCT 59.719 47.619 0.00 0.00 46.52 4.75
1648 5855 1.669779 GAGATCACAGAGCAACATGCC 59.330 52.381 0.00 0.00 46.52 4.40
1649 5856 2.353323 TGAGATCACAGAGCAACATGC 58.647 47.619 0.00 0.00 45.46 4.06
1650 5857 3.126514 GGTTGAGATCACAGAGCAACATG 59.873 47.826 0.00 0.00 40.28 3.21
1651 5858 3.244665 TGGTTGAGATCACAGAGCAACAT 60.245 43.478 0.00 0.00 40.28 2.71
1652 5859 2.104622 TGGTTGAGATCACAGAGCAACA 59.895 45.455 0.00 0.00 40.28 3.33
1653 5860 2.771089 TGGTTGAGATCACAGAGCAAC 58.229 47.619 0.00 0.00 38.40 4.17
1654 5861 3.071457 TCTTGGTTGAGATCACAGAGCAA 59.929 43.478 14.14 14.14 0.00 3.91
1655 5862 2.634453 TCTTGGTTGAGATCACAGAGCA 59.366 45.455 0.00 0.00 0.00 4.26
1656 5863 2.999355 GTCTTGGTTGAGATCACAGAGC 59.001 50.000 0.00 0.00 0.00 4.09
1657 5864 4.244066 CAGTCTTGGTTGAGATCACAGAG 58.756 47.826 0.00 0.00 0.00 3.35
1658 5865 3.555795 GCAGTCTTGGTTGAGATCACAGA 60.556 47.826 0.00 0.00 0.00 3.41
1659 5866 2.740981 GCAGTCTTGGTTGAGATCACAG 59.259 50.000 0.00 0.00 0.00 3.66
1660 5867 2.104622 TGCAGTCTTGGTTGAGATCACA 59.895 45.455 0.00 0.00 0.00 3.58
1661 5868 2.771089 TGCAGTCTTGGTTGAGATCAC 58.229 47.619 0.00 0.00 0.00 3.06
1827 6127 4.747108 CAGACGATGAGTTCCAATCCATAC 59.253 45.833 0.00 0.00 0.00 2.39
1939 6260 0.514691 GGAGCAAGCTGTCTCAAACG 59.485 55.000 14.95 0.00 0.00 3.60
2093 6423 1.139947 GTAGGCTGTGGAGAGACGC 59.860 63.158 0.00 0.00 0.00 5.19
2384 6759 0.379669 GCAAGCCGGATGACATGAAG 59.620 55.000 5.05 0.00 0.00 3.02
2385 6760 0.035152 AGCAAGCCGGATGACATGAA 60.035 50.000 5.05 0.00 0.00 2.57
2386 6761 0.035152 AAGCAAGCCGGATGACATGA 60.035 50.000 5.05 0.00 0.00 3.07
2388 6763 2.498167 GATAAGCAAGCCGGATGACAT 58.502 47.619 5.05 0.00 0.00 3.06
2390 6765 0.861837 CGATAAGCAAGCCGGATGAC 59.138 55.000 5.05 0.00 0.00 3.06
2391 6766 3.289128 CGATAAGCAAGCCGGATGA 57.711 52.632 5.05 0.00 0.00 2.92
2410 6785 2.176273 GGACGCTGTAGCATGCCTG 61.176 63.158 15.66 5.26 42.21 4.85
2412 6787 3.264897 CGGACGCTGTAGCATGCC 61.265 66.667 15.66 0.00 42.21 4.40
2413 6788 3.264897 CCGGACGCTGTAGCATGC 61.265 66.667 10.51 10.51 42.21 4.06
2414 6789 3.264897 GCCGGACGCTGTAGCATG 61.265 66.667 5.05 0.00 42.21 4.06
2415 6790 4.873129 CGCCGGACGCTGTAGCAT 62.873 66.667 5.05 0.00 42.21 3.79
2418 6793 2.655364 CATCGCCGGACGCTGTAG 60.655 66.667 5.05 0.00 43.23 2.74
2421 6796 0.318360 TAATACATCGCCGGACGCTG 60.318 55.000 5.05 13.09 43.41 5.18
2422 6797 0.386476 TTAATACATCGCCGGACGCT 59.614 50.000 5.05 0.00 43.23 5.07
2423 6798 1.210870 TTTAATACATCGCCGGACGC 58.789 50.000 5.05 0.00 43.23 5.19
2424 6799 3.929417 TTTTTAATACATCGCCGGACG 57.071 42.857 5.05 9.12 45.62 4.79
2446 7641 5.396436 CCCTTCACGATAAAGAATAGGGTGT 60.396 44.000 0.00 0.00 29.27 4.16
2449 8570 5.291905 ACCCTTCACGATAAAGAATAGGG 57.708 43.478 0.00 0.00 36.07 3.53
2462 8583 1.133407 GAGCTCTCTGTACCCTTCACG 59.867 57.143 6.43 0.00 0.00 4.35
2560 8682 1.209127 CGATTGGAAACACGTGGGC 59.791 57.895 21.57 8.24 42.67 5.36
2562 8684 1.154488 CGCGATTGGAAACACGTGG 60.154 57.895 21.57 1.66 42.67 4.94
2564 8686 0.876777 TGACGCGATTGGAAACACGT 60.877 50.000 15.93 0.00 41.30 4.49
2565 8687 0.442310 ATGACGCGATTGGAAACACG 59.558 50.000 15.93 0.00 42.67 4.49
2569 8691 2.147150 TGTTGATGACGCGATTGGAAA 58.853 42.857 15.93 0.00 0.00 3.13
2570 8692 1.802069 TGTTGATGACGCGATTGGAA 58.198 45.000 15.93 0.00 0.00 3.53
2633 8998 1.304713 ACCTGTACGGACCGACCAT 60.305 57.895 23.38 0.00 38.90 3.55
2636 9001 1.652167 GGAGACCTGTACGGACCGAC 61.652 65.000 23.38 14.64 36.31 4.79
2645 9010 1.550524 GCTCACACATGGAGACCTGTA 59.449 52.381 0.00 0.00 34.24 2.74
2666 9039 3.313524 TGCAGAGGAGCAGCCGAA 61.314 61.111 0.00 0.00 43.43 4.30
2672 9045 0.175760 GATTACCGTGCAGAGGAGCA 59.824 55.000 14.49 0.00 43.35 4.26
2683 9056 2.587753 CGCGCCATGGATTACCGT 60.588 61.111 18.40 0.00 39.42 4.83
2701 9074 2.203280 CACCAAGCACCGTTCCCA 60.203 61.111 0.00 0.00 0.00 4.37
2702 9079 3.670377 GCACCAAGCACCGTTCCC 61.670 66.667 0.00 0.00 44.79 3.97
2713 9090 1.531365 CCTTGGGAAGCAGCACCAA 60.531 57.895 13.59 13.59 41.66 3.67
2714 9091 2.115910 CCTTGGGAAGCAGCACCA 59.884 61.111 10.20 5.36 0.00 4.17
2856 9256 2.425668 GCCTCTACTCTGTCTTCCTCAC 59.574 54.545 0.00 0.00 0.00 3.51
2867 9267 2.359967 GCCCAACCGCCTCTACTCT 61.360 63.158 0.00 0.00 0.00 3.24
2932 9346 1.808945 GAACCGTAGAAGAGGACGTCA 59.191 52.381 18.91 0.00 37.36 4.35
2936 9350 3.128415 GTGGTAGAACCGTAGAAGAGGAC 59.872 52.174 0.00 0.00 42.58 3.85
2942 9356 3.759581 AGACAGTGGTAGAACCGTAGAA 58.240 45.455 0.00 0.00 42.58 2.10
2943 9357 3.430042 AGACAGTGGTAGAACCGTAGA 57.570 47.619 0.00 0.00 42.58 2.59
2944 9358 3.504906 TGAAGACAGTGGTAGAACCGTAG 59.495 47.826 0.00 0.00 42.58 3.51
2945 9359 3.254166 GTGAAGACAGTGGTAGAACCGTA 59.746 47.826 0.00 0.00 42.58 4.02
2946 9360 2.035576 GTGAAGACAGTGGTAGAACCGT 59.964 50.000 0.00 0.00 42.58 4.83
2947 9361 2.673833 GTGAAGACAGTGGTAGAACCG 58.326 52.381 0.00 0.00 42.58 4.44
2948 9362 2.673833 CGTGAAGACAGTGGTAGAACC 58.326 52.381 0.00 0.00 39.22 3.62
2949 9363 2.059541 GCGTGAAGACAGTGGTAGAAC 58.940 52.381 0.00 0.00 0.00 3.01
2953 9367 1.324383 TCAGCGTGAAGACAGTGGTA 58.676 50.000 0.00 0.00 0.00 3.25
2996 9410 9.817809 TGTCTTAGTTCTATAAATACTTGGCTG 57.182 33.333 0.00 0.00 0.00 4.85
3029 9443 9.591792 GGGAAATTGGAAAGATTTCTCTAATTG 57.408 33.333 5.37 0.00 39.68 2.32
3030 9444 9.552695 AGGGAAATTGGAAAGATTTCTCTAATT 57.447 29.630 9.55 7.30 46.95 1.40
3033 9447 7.775561 GCTAGGGAAATTGGAAAGATTTCTCTA 59.224 37.037 14.85 14.85 46.95 2.43
3035 9449 6.183360 GGCTAGGGAAATTGGAAAGATTTCTC 60.183 42.308 5.37 5.66 41.93 2.87
3036 9450 5.658634 GGCTAGGGAAATTGGAAAGATTTCT 59.341 40.000 5.37 0.00 41.19 2.52
3037 9451 5.658634 AGGCTAGGGAAATTGGAAAGATTTC 59.341 40.000 0.00 0.00 40.88 2.17
3038 9452 5.593786 AGGCTAGGGAAATTGGAAAGATTT 58.406 37.500 0.00 0.00 0.00 2.17
3039 9453 5.212472 AGGCTAGGGAAATTGGAAAGATT 57.788 39.130 0.00 0.00 0.00 2.40
3040 9454 4.888626 AGGCTAGGGAAATTGGAAAGAT 57.111 40.909 0.00 0.00 0.00 2.40
3041 9455 4.538490 TGTAGGCTAGGGAAATTGGAAAGA 59.462 41.667 0.00 0.00 0.00 2.52
3042 9456 4.640647 GTGTAGGCTAGGGAAATTGGAAAG 59.359 45.833 0.00 0.00 0.00 2.62
3043 9457 4.291249 AGTGTAGGCTAGGGAAATTGGAAA 59.709 41.667 0.00 0.00 0.00 3.13
3044 9458 3.850173 AGTGTAGGCTAGGGAAATTGGAA 59.150 43.478 0.00 0.00 0.00 3.53
3045 9459 3.454812 GAGTGTAGGCTAGGGAAATTGGA 59.545 47.826 0.00 0.00 0.00 3.53
3046 9460 3.199946 TGAGTGTAGGCTAGGGAAATTGG 59.800 47.826 0.00 0.00 0.00 3.16
3047 9461 4.487714 TGAGTGTAGGCTAGGGAAATTG 57.512 45.455 0.00 0.00 0.00 2.32
3048 9462 4.623171 CGTTGAGTGTAGGCTAGGGAAATT 60.623 45.833 0.00 0.00 0.00 1.82
3049 9463 3.118738 CGTTGAGTGTAGGCTAGGGAAAT 60.119 47.826 0.00 0.00 0.00 2.17
3050 9464 2.232941 CGTTGAGTGTAGGCTAGGGAAA 59.767 50.000 0.00 0.00 0.00 3.13
3051 9465 1.822990 CGTTGAGTGTAGGCTAGGGAA 59.177 52.381 0.00 0.00 0.00 3.97
3052 9466 1.272313 ACGTTGAGTGTAGGCTAGGGA 60.272 52.381 0.00 0.00 0.00 4.20
3053 9467 1.183549 ACGTTGAGTGTAGGCTAGGG 58.816 55.000 0.00 0.00 0.00 3.53
3054 9468 3.693085 TCTAACGTTGAGTGTAGGCTAGG 59.307 47.826 11.99 0.00 0.00 3.02
3055 9469 4.395542 ACTCTAACGTTGAGTGTAGGCTAG 59.604 45.833 23.52 6.34 42.46 3.42
3056 9470 4.330250 ACTCTAACGTTGAGTGTAGGCTA 58.670 43.478 23.52 0.00 42.46 3.93
3057 9471 3.155501 ACTCTAACGTTGAGTGTAGGCT 58.844 45.455 23.52 0.00 42.46 4.58
3058 9472 3.500014 GACTCTAACGTTGAGTGTAGGC 58.500 50.000 26.94 14.75 43.88 3.93
3059 9473 3.119566 GGGACTCTAACGTTGAGTGTAGG 60.120 52.174 26.94 8.49 43.88 3.18
3060 9474 3.757493 AGGGACTCTAACGTTGAGTGTAG 59.243 47.826 26.94 11.44 43.88 2.74
3061 9475 3.759581 AGGGACTCTAACGTTGAGTGTA 58.240 45.455 26.94 2.61 43.88 2.90
3062 9476 2.595238 AGGGACTCTAACGTTGAGTGT 58.405 47.619 26.94 18.67 43.88 3.55
3063 9477 3.243771 ACAAGGGACTCTAACGTTGAGTG 60.244 47.826 26.94 18.32 43.88 3.51
3064 9478 2.963782 ACAAGGGACTCTAACGTTGAGT 59.036 45.455 24.04 24.04 46.17 3.41
3065 9479 3.662247 ACAAGGGACTCTAACGTTGAG 57.338 47.619 11.99 16.88 38.49 3.02
3066 9480 4.147321 ACTACAAGGGACTCTAACGTTGA 58.853 43.478 11.99 5.69 38.49 3.18
3067 9481 4.516365 ACTACAAGGGACTCTAACGTTG 57.484 45.455 11.99 0.97 38.49 4.10
3068 9482 6.655078 TTAACTACAAGGGACTCTAACGTT 57.345 37.500 5.88 5.88 38.49 3.99
3069 9483 6.655078 TTTAACTACAAGGGACTCTAACGT 57.345 37.500 0.00 0.00 38.49 3.99
3070 9484 7.816031 TCAATTTAACTACAAGGGACTCTAACG 59.184 37.037 0.00 0.00 38.49 3.18
3071 9485 9.668497 ATCAATTTAACTACAAGGGACTCTAAC 57.332 33.333 0.00 0.00 38.49 2.34
3073 9487 9.667107 CAATCAATTTAACTACAAGGGACTCTA 57.333 33.333 0.00 0.00 38.49 2.43
3074 9488 7.121315 GCAATCAATTTAACTACAAGGGACTCT 59.879 37.037 0.00 0.00 38.49 3.24
3075 9489 7.094377 TGCAATCAATTTAACTACAAGGGACTC 60.094 37.037 0.00 0.00 38.49 3.36
3077 9491 6.919721 TGCAATCAATTTAACTACAAGGGAC 58.080 36.000 0.00 0.00 0.00 4.46
3078 9492 7.531857 TTGCAATCAATTTAACTACAAGGGA 57.468 32.000 0.00 0.00 0.00 4.20
3079 9493 8.600449 TTTTGCAATCAATTTAACTACAAGGG 57.400 30.769 0.00 0.00 31.33 3.95
3081 9495 9.941991 CGATTTTGCAATCAATTTAACTACAAG 57.058 29.630 0.00 0.00 39.14 3.16
3082 9496 9.684448 TCGATTTTGCAATCAATTTAACTACAA 57.316 25.926 0.00 0.00 39.14 2.41
3083 9497 9.853555 ATCGATTTTGCAATCAATTTAACTACA 57.146 25.926 0.00 0.00 39.14 2.74
3086 9500 8.984891 TGATCGATTTTGCAATCAATTTAACT 57.015 26.923 0.00 0.00 39.14 2.24
3105 9519 9.764363 ACTGCTCAGTTTTATTATATTGATCGA 57.236 29.630 0.00 0.00 38.83 3.59
3127 9541 7.365840 AGTAACTTGATTTTACAGCTACTGC 57.634 36.000 0.00 0.00 34.37 4.40
3149 9563 8.983307 ACTCGACTTTTTCTCGATATTAAAGT 57.017 30.769 12.15 12.15 39.36 2.66
3157 9571 8.557029 ACAAAAATAACTCGACTTTTTCTCGAT 58.443 29.630 0.00 0.00 39.36 3.59
3158 9572 7.912383 ACAAAAATAACTCGACTTTTTCTCGA 58.088 30.769 0.00 0.00 37.82 4.04
3159 9573 8.461398 CAACAAAAATAACTCGACTTTTTCTCG 58.539 33.333 0.00 0.00 31.56 4.04
3160 9574 9.285770 ACAACAAAAATAACTCGACTTTTTCTC 57.714 29.630 0.00 0.00 31.56 2.87
3170 9584 9.777843 GCTTGATTTTACAACAAAAATAACTCG 57.222 29.630 0.00 0.00 38.77 4.18


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

AutoCloner maintained by Alex Coulton.