Multiple sequence alignment - TraesCS2A01G166100

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 TraesCS2A01G166100 chr2A 100.000 3718 0 0 1 3718 118475866 118479583 0.000000e+00 6866.0
1 TraesCS2A01G166100 chr2A 84.080 1740 252 18 1428 3154 84607180 84608907 0.000000e+00 1655.0
2 TraesCS2A01G166100 chr2A 79.811 530 96 6 3182 3711 84608965 84609483 3.510000e-100 375.0
3 TraesCS2A01G166100 chr2A 81.623 419 75 2 3247 3664 85803874 85803457 2.750000e-91 346.0
4 TraesCS2A01G166100 chr2A 81.579 418 75 2 3248 3664 86050757 86050341 9.890000e-91 344.0
5 TraesCS2A01G166100 chr2A 78.393 361 64 9 963 1313 84606788 84607144 4.830000e-54 222.0
6 TraesCS2A01G166100 chr2A 93.069 101 7 0 1325 1425 118477154 118477254 8.320000e-32 148.0
7 TraesCS2A01G166100 chr2A 93.069 101 7 0 1289 1389 118477190 118477290 8.320000e-32 148.0
8 TraesCS2A01G166100 chr2D 95.390 2321 96 6 1397 3715 117185767 117188078 0.000000e+00 3683.0
9 TraesCS2A01G166100 chr2D 83.878 1805 253 29 1365 3154 83839941 83841722 0.000000e+00 1687.0
10 TraesCS2A01G166100 chr2D 83.689 1735 264 16 1428 3153 85685729 85684005 0.000000e+00 1618.0
11 TraesCS2A01G166100 chr2D 83.782 1634 247 8 1536 3154 84927178 84925548 0.000000e+00 1533.0
12 TraesCS2A01G166100 chr2D 82.011 1701 277 20 1428 3114 84934120 84932435 0.000000e+00 1419.0
13 TraesCS2A01G166100 chr2D 92.551 537 31 3 779 1314 117185264 117185792 0.000000e+00 761.0
14 TraesCS2A01G166100 chr2D 80.377 530 94 5 3182 3711 83841780 83842299 9.680000e-106 394.0
15 TraesCS2A01G166100 chr2D 87.124 233 22 4 295 524 117184914 117185141 1.320000e-64 257.0
16 TraesCS2A01G166100 chr2D 81.570 293 46 8 973 1261 84769524 84769236 6.210000e-58 235.0
17 TraesCS2A01G166100 chr2D 78.478 381 65 12 963 1331 83839605 83839980 2.230000e-57 233.0
18 TraesCS2A01G166100 chr2D 81.046 306 42 14 973 1267 85394764 85394464 2.890000e-56 230.0
19 TraesCS2A01G166100 chr2D 79.245 318 49 12 964 1268 84927672 84927359 4.870000e-49 206.0
20 TraesCS2A01G166100 chr2D 79.757 247 34 11 1056 1289 85686103 85685860 8.260000e-37 165.0
21 TraesCS2A01G166100 chr2D 92.929 99 4 2 577 672 117185157 117185255 1.390000e-29 141.0
22 TraesCS2A01G166100 chr2B 94.606 2373 113 4 1361 3718 167494394 167496766 0.000000e+00 3659.0
23 TraesCS2A01G166100 chr2B 84.310 1740 249 17 1428 3154 135707997 135709725 0.000000e+00 1679.0
24 TraesCS2A01G166100 chr2B 81.573 1742 292 20 1428 3155 137618304 137616578 0.000000e+00 1411.0
25 TraesCS2A01G166100 chr2B 81.443 1746 287 26 1428 3155 136633878 136632152 0.000000e+00 1395.0
26 TraesCS2A01G166100 chr2B 91.738 581 34 6 779 1353 167493886 167494458 0.000000e+00 795.0
27 TraesCS2A01G166100 chr2B 81.649 485 85 3 3182 3664 135709783 135710265 2.080000e-107 399.0
28 TraesCS2A01G166100 chr2B 85.302 381 34 13 297 674 167493520 167493881 1.260000e-99 374.0
29 TraesCS2A01G166100 chr2B 80.000 485 93 4 3182 3664 137800804 137800322 4.570000e-94 355.0
30 TraesCS2A01G166100 chr2B 80.000 295 39 17 973 1254 136957001 136956714 2.260000e-47 200.0
31 TraesCS2A01G166100 chr2B 92.857 112 6 2 1 112 167493007 167493116 1.070000e-35 161.0
32 TraesCS2A01G166100 chr2B 90.435 115 4 5 163 276 167493232 167493340 1.080000e-30 145.0
33 TraesCS2A01G166100 chr2B 96.923 65 2 0 1325 1389 167494394 167494458 3.930000e-20 110.0
34 TraesCS2A01G166100 chr2B 100.000 29 0 0 1397 1425 167494394 167494422 2.000000e-03 54.7
35 TraesCS2A01G166100 chr3B 87.696 382 34 8 297 674 166526703 166527075 2.050000e-117 433.0
36 TraesCS2A01G166100 chr4A 81.862 419 74 2 3247 3664 349799400 349798983 5.910000e-93 351.0


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 TraesCS2A01G166100 chr2A 118475866 118479583 3717 False 2387.333333 6866 95.379333 1 3718 3 chr2A.!!$F2 3717
1 TraesCS2A01G166100 chr2A 84606788 84609483 2695 False 750.666667 1655 80.761333 963 3711 3 chr2A.!!$F1 2748
2 TraesCS2A01G166100 chr2D 84932435 84934120 1685 True 1419.000000 1419 82.011000 1428 3114 1 chr2D.!!$R2 1686
3 TraesCS2A01G166100 chr2D 117184914 117188078 3164 False 1210.500000 3683 91.998500 295 3715 4 chr2D.!!$F2 3420
4 TraesCS2A01G166100 chr2D 85684005 85686103 2098 True 891.500000 1618 81.723000 1056 3153 2 chr2D.!!$R5 2097
5 TraesCS2A01G166100 chr2D 84925548 84927672 2124 True 869.500000 1533 81.513500 964 3154 2 chr2D.!!$R4 2190
6 TraesCS2A01G166100 chr2D 83839605 83842299 2694 False 771.333333 1687 80.911000 963 3711 3 chr2D.!!$F1 2748
7 TraesCS2A01G166100 chr2B 137616578 137618304 1726 True 1411.000000 1411 81.573000 1428 3155 1 chr2B.!!$R3 1727
8 TraesCS2A01G166100 chr2B 136632152 136633878 1726 True 1395.000000 1395 81.443000 1428 3155 1 chr2B.!!$R1 1727
9 TraesCS2A01G166100 chr2B 135707997 135710265 2268 False 1039.000000 1679 82.979500 1428 3664 2 chr2B.!!$F1 2236
10 TraesCS2A01G166100 chr2B 167493007 167496766 3759 False 756.957143 3659 93.123000 1 3718 7 chr2B.!!$F2 3717


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
288 387 0.036952 CACGAAGCCTCTCCACACAT 60.037 55.0 0.00 0.00 0.00 3.21 F
289 388 0.036952 ACGAAGCCTCTCCACACATG 60.037 55.0 0.00 0.00 0.00 3.21 F
1685 2038 0.040067 GGTTCCTCAAACAGCGCAAG 60.040 55.0 11.47 3.78 39.81 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 2275 0.179020 TCTGTCCCAGGCAACACAAG 60.179 55.0 0.0 0.0 41.41 3.16 R
2019 2386 1.668419 GGAGTAACATGCTCGCCATT 58.332 50.0 0.0 0.0 34.00 3.16 R
3495 3913 0.655733 AAGTTGGTGTTTCACGCTCG 59.344 50.0 0.0 0.0 34.83 5.03 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
86 87 0.527817 CCCGTAACGAGGCATCAGTC 60.528 60.000 0.00 0.00 0.00 3.51
87 88 0.527817 CCGTAACGAGGCATCAGTCC 60.528 60.000 0.00 0.00 0.00 3.85
88 89 0.456221 CGTAACGAGGCATCAGTCCT 59.544 55.000 0.00 0.00 36.46 3.85
89 90 1.135083 CGTAACGAGGCATCAGTCCTT 60.135 52.381 0.00 0.00 33.24 3.36
112 113 3.553105 GTCGTCTTCACGGTGTTTTAACT 59.447 43.478 8.17 0.00 46.70 2.24
113 114 3.798337 TCGTCTTCACGGTGTTTTAACTC 59.202 43.478 8.17 0.00 46.70 3.01
114 115 3.060070 CGTCTTCACGGTGTTTTAACTCC 60.060 47.826 8.17 4.10 42.73 3.85
121 122 2.747436 GGTGTTTTAACTCCGTCGACT 58.253 47.619 14.70 0.00 33.46 4.18
122 123 3.126073 GGTGTTTTAACTCCGTCGACTT 58.874 45.455 14.70 3.40 33.46 3.01
123 124 3.183172 GGTGTTTTAACTCCGTCGACTTC 59.817 47.826 14.70 0.00 33.46 3.01
124 125 4.047142 GTGTTTTAACTCCGTCGACTTCT 58.953 43.478 14.70 0.00 0.00 2.85
125 126 4.147826 GTGTTTTAACTCCGTCGACTTCTC 59.852 45.833 14.70 0.00 0.00 2.87
126 127 4.037208 TGTTTTAACTCCGTCGACTTCTCT 59.963 41.667 14.70 0.00 0.00 3.10
127 128 4.416505 TTTAACTCCGTCGACTTCTCTC 57.583 45.455 14.70 0.00 0.00 3.20
128 129 1.166989 AACTCCGTCGACTTCTCTCC 58.833 55.000 14.70 0.00 0.00 3.71
129 130 0.677414 ACTCCGTCGACTTCTCTCCC 60.677 60.000 14.70 0.00 0.00 4.30
130 131 1.707239 CTCCGTCGACTTCTCTCCCG 61.707 65.000 14.70 0.00 0.00 5.14
131 132 2.100603 CGTCGACTTCTCTCCCGC 59.899 66.667 14.70 0.00 0.00 6.13
132 133 2.490685 GTCGACTTCTCTCCCGCC 59.509 66.667 8.70 0.00 0.00 6.13
133 134 3.132139 TCGACTTCTCTCCCGCCG 61.132 66.667 0.00 0.00 0.00 6.46
134 135 3.132139 CGACTTCTCTCCCGCCGA 61.132 66.667 0.00 0.00 0.00 5.54
135 136 2.802106 GACTTCTCTCCCGCCGAG 59.198 66.667 0.00 0.00 40.30 4.63
136 137 1.749638 GACTTCTCTCCCGCCGAGA 60.750 63.158 0.00 1.11 45.75 4.04
141 142 2.675371 TCTCCCGCCGAGAGAGAA 59.325 61.111 0.00 0.00 42.97 2.87
142 143 1.001269 TCTCCCGCCGAGAGAGAAA 60.001 57.895 0.00 0.00 42.97 2.52
143 144 0.611062 TCTCCCGCCGAGAGAGAAAA 60.611 55.000 0.00 0.00 42.97 2.29
144 145 0.461961 CTCCCGCCGAGAGAGAAAAT 59.538 55.000 0.00 0.00 41.63 1.82
145 146 1.681793 CTCCCGCCGAGAGAGAAAATA 59.318 52.381 0.00 0.00 41.63 1.40
146 147 1.407979 TCCCGCCGAGAGAGAAAATAC 59.592 52.381 0.00 0.00 0.00 1.89
161 162 8.697507 AGAGAAAATACTGTCCATTTCAGTTT 57.302 30.769 3.98 0.00 42.50 2.66
162 163 9.136323 AGAGAAAATACTGTCCATTTCAGTTTT 57.864 29.630 3.98 0.76 42.50 2.43
165 166 9.129209 GAAAATACTGTCCATTTCAGTTTTAGC 57.871 33.333 3.98 0.00 42.50 3.09
166 167 6.759497 ATACTGTCCATTTCAGTTTTAGCC 57.241 37.500 3.98 0.00 42.50 3.93
168 169 3.745799 TGTCCATTTCAGTTTTAGCCGA 58.254 40.909 0.00 0.00 0.00 5.54
170 171 4.764823 TGTCCATTTCAGTTTTAGCCGAAT 59.235 37.500 0.00 0.00 0.00 3.34
171 172 5.095490 GTCCATTTCAGTTTTAGCCGAATG 58.905 41.667 0.00 0.00 0.00 2.67
248 347 5.263185 CAACGGATGTCAATTTTCGGATAC 58.737 41.667 0.00 0.00 0.00 2.24
249 348 4.766375 ACGGATGTCAATTTTCGGATACT 58.234 39.130 0.00 0.00 0.00 2.12
250 349 4.570772 ACGGATGTCAATTTTCGGATACTG 59.429 41.667 0.00 0.00 0.00 2.74
259 358 6.255670 TCAATTTTCGGATACTGACTGAATCG 59.744 38.462 0.00 0.00 33.52 3.34
272 371 1.781429 CTGAATCGTTATCGGCTCACG 59.219 52.381 0.00 0.00 46.11 4.35
283 382 2.973899 GCTCACGAAGCCTCTCCA 59.026 61.111 0.00 0.00 45.92 3.86
284 383 1.446966 GCTCACGAAGCCTCTCCAC 60.447 63.158 0.00 0.00 45.92 4.02
285 384 1.967535 CTCACGAAGCCTCTCCACA 59.032 57.895 0.00 0.00 0.00 4.17
286 385 0.389166 CTCACGAAGCCTCTCCACAC 60.389 60.000 0.00 0.00 0.00 3.82
288 387 0.036952 CACGAAGCCTCTCCACACAT 60.037 55.000 0.00 0.00 0.00 3.21
289 388 0.036952 ACGAAGCCTCTCCACACATG 60.037 55.000 0.00 0.00 0.00 3.21
310 567 6.599638 ACATGGGCAACTCTTCTTATTACTTC 59.400 38.462 0.00 0.00 0.00 3.01
332 589 3.352648 CTGCCTAGCTAGTATCCTCCTC 58.647 54.545 19.31 0.00 0.00 3.71
340 597 7.990886 CCTAGCTAGTATCCTCCTCTACTTATG 59.009 44.444 19.31 0.00 30.98 1.90
375 632 9.602568 TTTAAGTTTCCTAAATGGGTTCAAAAC 57.397 29.630 0.00 0.00 36.20 2.43
403 660 6.993786 AATAAGAGCTCTAAAGTGCTTTCC 57.006 37.500 18.59 0.00 43.90 3.13
409 666 4.276926 AGCTCTAAAGTGCTTTCCAAAGTG 59.723 41.667 0.00 0.00 41.50 3.16
410 667 4.557496 GCTCTAAAGTGCTTTCCAAAGTGG 60.557 45.833 0.00 0.00 38.28 4.00
411 668 4.787551 TCTAAAGTGCTTTCCAAAGTGGA 58.212 39.130 0.00 0.00 46.61 4.02
427 684 2.093235 AGTGGAGTAGCATCTTTGGAGC 60.093 50.000 0.00 0.00 0.00 4.70
479 737 9.801873 CGAATGTGATCCTATGGTAAAAATTTT 57.198 29.630 0.00 0.00 0.00 1.82
499 758 5.467902 TTTGCAAGCACTCAAAACATTTC 57.532 34.783 0.00 0.00 30.19 2.17
503 762 5.010922 TGCAAGCACTCAAAACATTTCCTAT 59.989 36.000 0.00 0.00 0.00 2.57
507 766 7.759489 AGCACTCAAAACATTTCCTATTGTA 57.241 32.000 0.00 0.00 0.00 2.41
512 771 6.559810 TCAAAACATTTCCTATTGTATGCCG 58.440 36.000 0.00 0.00 0.00 5.69
513 772 6.151985 TCAAAACATTTCCTATTGTATGCCGT 59.848 34.615 0.00 0.00 0.00 5.68
515 774 7.817418 AAACATTTCCTATTGTATGCCGTAT 57.183 32.000 0.00 0.00 0.00 3.06
606 865 1.144057 CCCGAGCTACATGTCCCAC 59.856 63.158 0.00 0.00 0.00 4.61
628 887 6.161381 CACTGCTAATTTTCTTGAGGCAATT 58.839 36.000 0.00 0.00 0.00 2.32
629 888 6.647895 CACTGCTAATTTTCTTGAGGCAATTT 59.352 34.615 0.00 0.00 0.00 1.82
635 894 9.868389 CTAATTTTCTTGAGGCAATTTGTTTTC 57.132 29.630 0.00 0.00 0.00 2.29
692 956 5.437289 TTTTAGACAACTGTGGCAATCTG 57.563 39.130 0.00 0.00 33.83 2.90
693 957 1.242076 AGACAACTGTGGCAATCTGC 58.758 50.000 0.00 0.00 44.08 4.26
694 958 1.202855 AGACAACTGTGGCAATCTGCT 60.203 47.619 0.00 0.00 44.28 4.24
695 959 0.956633 ACAACTGTGGCAATCTGCTG 59.043 50.000 0.00 0.00 44.28 4.41
696 960 0.388134 CAACTGTGGCAATCTGCTGC 60.388 55.000 0.00 0.00 44.28 5.25
697 961 0.538977 AACTGTGGCAATCTGCTGCT 60.539 50.000 0.00 0.00 44.28 4.24
698 962 0.959372 ACTGTGGCAATCTGCTGCTC 60.959 55.000 0.00 0.00 44.28 4.26
699 963 0.677098 CTGTGGCAATCTGCTGCTCT 60.677 55.000 0.00 0.00 44.28 4.09
700 964 0.251033 TGTGGCAATCTGCTGCTCTT 60.251 50.000 0.00 0.00 44.28 2.85
701 965 0.886563 GTGGCAATCTGCTGCTCTTT 59.113 50.000 0.00 0.00 44.28 2.52
702 966 1.271656 GTGGCAATCTGCTGCTCTTTT 59.728 47.619 0.00 0.00 44.28 2.27
703 967 1.965643 TGGCAATCTGCTGCTCTTTTT 59.034 42.857 0.00 0.00 44.28 1.94
747 1011 6.847956 TTTTTGAGACAATGGCAAAATCAG 57.152 33.333 10.16 0.00 40.09 2.90
748 1012 3.581024 TGAGACAATGGCAAAATCAGC 57.419 42.857 0.00 0.00 0.00 4.26
749 1013 3.159472 TGAGACAATGGCAAAATCAGCT 58.841 40.909 0.00 0.00 0.00 4.24
750 1014 3.575256 TGAGACAATGGCAAAATCAGCTT 59.425 39.130 0.00 0.00 0.00 3.74
751 1015 4.039488 TGAGACAATGGCAAAATCAGCTTT 59.961 37.500 0.00 0.00 0.00 3.51
752 1016 4.964593 AGACAATGGCAAAATCAGCTTTT 58.035 34.783 0.00 0.00 37.54 2.27
753 1017 5.370679 AGACAATGGCAAAATCAGCTTTTT 58.629 33.333 0.00 0.00 34.80 1.94
776 1040 4.470334 TTAGGGAAATGGCAAAATCAGC 57.530 40.909 0.00 0.00 0.00 4.26
777 1041 2.543635 AGGGAAATGGCAAAATCAGCT 58.456 42.857 0.00 0.00 0.00 4.24
794 1058 1.202940 AGCTGTTCCTTTGTCCCCTTC 60.203 52.381 0.00 0.00 0.00 3.46
833 1097 2.613474 GCAAATGGAAATGCAGCCTCAA 60.613 45.455 0.00 0.00 42.12 3.02
834 1098 3.666274 CAAATGGAAATGCAGCCTCAAA 58.334 40.909 0.00 0.00 0.00 2.69
856 1120 1.086634 GCAGGCTGGCTAAAGACGAG 61.087 60.000 17.64 0.00 0.00 4.18
873 1137 0.767375 GAGCCATCCAGAGCCCATAA 59.233 55.000 0.00 0.00 0.00 1.90
895 1159 1.153529 CGCTAACGGCCCACATACA 60.154 57.895 0.00 0.00 37.74 2.29
896 1160 1.151777 CGCTAACGGCCCACATACAG 61.152 60.000 0.00 0.00 37.74 2.74
897 1161 0.177141 GCTAACGGCCCACATACAGA 59.823 55.000 0.00 0.00 34.27 3.41
1271 1566 0.611200 TTCACTGTACCCATCACCCG 59.389 55.000 0.00 0.00 0.00 5.28
1304 1620 4.935885 CAATCTTGCTTGGTAGTCTCAC 57.064 45.455 0.00 0.00 0.00 3.51
1305 1621 4.573900 CAATCTTGCTTGGTAGTCTCACT 58.426 43.478 0.00 0.00 0.00 3.41
1306 1622 3.944055 TCTTGCTTGGTAGTCTCACTC 57.056 47.619 0.00 0.00 0.00 3.51
1307 1623 2.229062 TCTTGCTTGGTAGTCTCACTCG 59.771 50.000 0.00 0.00 0.00 4.18
1308 1624 1.617322 TGCTTGGTAGTCTCACTCGT 58.383 50.000 0.00 0.00 0.00 4.18
1309 1625 1.540267 TGCTTGGTAGTCTCACTCGTC 59.460 52.381 0.00 0.00 0.00 4.20
1310 1626 1.813786 GCTTGGTAGTCTCACTCGTCT 59.186 52.381 0.00 0.00 0.00 4.18
1311 1627 2.414824 GCTTGGTAGTCTCACTCGTCTG 60.415 54.545 0.00 0.00 0.00 3.51
1312 1628 2.853235 TGGTAGTCTCACTCGTCTGA 57.147 50.000 0.00 0.00 0.00 3.27
1313 1629 3.136009 TGGTAGTCTCACTCGTCTGAA 57.864 47.619 0.00 0.00 0.00 3.02
1314 1630 3.687125 TGGTAGTCTCACTCGTCTGAAT 58.313 45.455 0.00 0.00 0.00 2.57
1315 1631 4.840271 TGGTAGTCTCACTCGTCTGAATA 58.160 43.478 0.00 0.00 0.00 1.75
1316 1632 5.437946 TGGTAGTCTCACTCGTCTGAATAT 58.562 41.667 0.00 0.00 0.00 1.28
1317 1633 5.886474 TGGTAGTCTCACTCGTCTGAATATT 59.114 40.000 0.00 0.00 0.00 1.28
1318 1634 6.183360 TGGTAGTCTCACTCGTCTGAATATTG 60.183 42.308 0.00 0.00 0.00 1.90
1319 1635 5.906113 AGTCTCACTCGTCTGAATATTGT 57.094 39.130 0.00 0.00 0.00 2.71
1320 1636 5.645624 AGTCTCACTCGTCTGAATATTGTG 58.354 41.667 0.00 0.00 0.00 3.33
1321 1637 4.800993 GTCTCACTCGTCTGAATATTGTGG 59.199 45.833 0.00 0.00 0.00 4.17
1322 1638 3.521560 TCACTCGTCTGAATATTGTGGC 58.478 45.455 0.00 0.00 0.00 5.01
1323 1639 3.056179 TCACTCGTCTGAATATTGTGGCA 60.056 43.478 0.00 0.00 0.00 4.92
1324 1640 3.873361 CACTCGTCTGAATATTGTGGCAT 59.127 43.478 0.00 0.00 0.00 4.40
1325 1641 4.333649 CACTCGTCTGAATATTGTGGCATT 59.666 41.667 0.00 0.00 0.00 3.56
1326 1642 4.333649 ACTCGTCTGAATATTGTGGCATTG 59.666 41.667 0.00 0.00 0.00 2.82
1327 1643 3.065233 TCGTCTGAATATTGTGGCATTGC 59.935 43.478 0.00 0.00 0.00 3.56
1328 1644 3.065786 CGTCTGAATATTGTGGCATTGCT 59.934 43.478 8.82 0.00 0.00 3.91
1329 1645 4.439153 CGTCTGAATATTGTGGCATTGCTT 60.439 41.667 8.82 0.00 0.00 3.91
1330 1646 4.802039 GTCTGAATATTGTGGCATTGCTTG 59.198 41.667 8.82 0.00 0.00 4.01
1331 1647 4.116961 CTGAATATTGTGGCATTGCTTGG 58.883 43.478 8.82 0.00 0.00 3.61
1332 1648 3.514706 TGAATATTGTGGCATTGCTTGGT 59.485 39.130 8.82 0.00 0.00 3.67
1333 1649 4.708909 TGAATATTGTGGCATTGCTTGGTA 59.291 37.500 8.82 0.00 0.00 3.25
1334 1650 4.654091 ATATTGTGGCATTGCTTGGTAC 57.346 40.909 8.82 1.82 0.00 3.34
1375 1713 1.350684 TGGCATTGCTTGGTAGTCTGA 59.649 47.619 8.82 0.00 0.00 3.27
1378 1716 3.065925 GGCATTGCTTGGTAGTCTGATTC 59.934 47.826 8.82 0.00 0.00 2.52
1379 1717 3.242543 GCATTGCTTGGTAGTCTGATTCG 60.243 47.826 0.16 0.00 0.00 3.34
1380 1718 3.678056 TTGCTTGGTAGTCTGATTCGT 57.322 42.857 0.00 0.00 0.00 3.85
1382 1720 2.826128 TGCTTGGTAGTCTGATTCGTCT 59.174 45.455 0.00 0.00 0.00 4.18
1384 1722 3.119459 GCTTGGTAGTCTGATTCGTCTGA 60.119 47.826 0.00 0.00 0.00 3.27
1385 1723 4.618460 GCTTGGTAGTCTGATTCGTCTGAA 60.618 45.833 0.00 0.00 38.76 3.02
1387 1725 4.998788 TGGTAGTCTGATTCGTCTGAATG 58.001 43.478 0.00 0.00 44.79 2.67
1388 1726 4.462834 TGGTAGTCTGATTCGTCTGAATGT 59.537 41.667 0.00 0.00 44.79 2.71
1389 1727 5.038033 GGTAGTCTGATTCGTCTGAATGTC 58.962 45.833 0.00 0.00 44.79 3.06
1390 1728 4.790765 AGTCTGATTCGTCTGAATGTCA 57.209 40.909 0.00 0.00 44.79 3.58
1391 1729 5.336150 AGTCTGATTCGTCTGAATGTCAT 57.664 39.130 0.00 0.00 44.79 3.06
1392 1730 5.107824 AGTCTGATTCGTCTGAATGTCATG 58.892 41.667 0.00 0.00 44.79 3.07
1393 1731 4.269603 GTCTGATTCGTCTGAATGTCATGG 59.730 45.833 0.00 0.00 44.79 3.66
1394 1732 2.938451 TGATTCGTCTGAATGTCATGGC 59.062 45.455 0.00 0.00 44.79 4.40
1395 1733 2.470983 TTCGTCTGAATGTCATGGCA 57.529 45.000 0.60 0.60 0.00 4.92
1408 1746 2.098117 GTCATGGCATTGCTTGGTAGTC 59.902 50.000 8.82 0.00 0.00 2.59
1478 1831 0.763035 ACTACGGGTGCAGAAAAGGT 59.237 50.000 0.00 0.00 0.00 3.50
1685 2038 0.040067 GGTTCCTCAAACAGCGCAAG 60.040 55.000 11.47 3.78 39.81 4.01
1787 2146 2.206576 ACTGGAGATCCTTTGCCAAC 57.793 50.000 0.00 0.00 36.82 3.77
1789 2148 2.089980 CTGGAGATCCTTTGCCAACAG 58.910 52.381 0.00 0.00 36.82 3.16
1870 2237 3.392882 TCAGGCACTATGACATATTGCG 58.607 45.455 23.64 15.05 40.92 4.85
1902 2269 3.003480 GGTGATGGTTACTCTCAACAGC 58.997 50.000 0.00 0.00 0.00 4.40
1908 2275 0.670546 TTACTCTCAACAGCTGCCGC 60.671 55.000 15.27 0.00 0.00 6.53
1958 2325 0.804989 GGTGTGAATTCAGCTTCCGG 59.195 55.000 8.80 0.00 33.69 5.14
2019 2386 3.557054 GGCAGTTTATCTCACTGGTCACA 60.557 47.826 2.43 0.00 41.81 3.58
2030 2397 1.002257 TGGTCACAATGGCGAGCAT 60.002 52.632 3.28 0.00 34.88 3.79
2253 2625 1.398390 GACAATGCTTACAGGCCTTCG 59.602 52.381 0.00 0.00 0.00 3.79
2286 2658 0.240678 TGTGCTGTGCATTAAAGGCG 59.759 50.000 0.00 0.00 41.91 5.52
2324 2696 0.478072 ATCAAGGGGTGCTGTTGACA 59.522 50.000 0.00 0.00 33.16 3.58
2368 2740 5.759059 TGATTTCTCCATTCCAGTAGCATT 58.241 37.500 0.00 0.00 0.00 3.56
2421 2793 3.686016 TGGCTGTGGTTTCTTAGGAATC 58.314 45.455 0.00 0.00 0.00 2.52
2630 3007 7.701924 GTGATGATGTTCAAGAAACTTTGTCAA 59.298 33.333 0.00 0.00 38.76 3.18
2647 3024 3.493129 TGTCAACAGAAGCGACAACATAC 59.507 43.478 0.00 0.00 36.75 2.39
2697 3074 6.640907 CGACGAGTTGACATCCAAATATATGA 59.359 38.462 0.00 0.00 36.36 2.15
2787 3175 0.252375 AGCAAAACCCATCCAGCCAT 60.252 50.000 0.00 0.00 0.00 4.40
2788 3176 1.006998 AGCAAAACCCATCCAGCCATA 59.993 47.619 0.00 0.00 0.00 2.74
2828 3216 0.471617 AAGGAAGGAGATCATGCCGG 59.528 55.000 0.00 0.00 0.00 6.13
2838 3226 1.028330 ATCATGCCGGTGACAGCAAG 61.028 55.000 1.90 0.04 43.36 4.01
3042 3430 1.195115 TCCTGCGCTTGGAAGAGTAT 58.805 50.000 17.84 0.00 0.00 2.12
3174 3592 2.512056 TCAAGTTCTTGGGGGTGAAGAA 59.488 45.455 11.82 0.00 37.15 2.52
3199 3617 3.991773 TCTGAAATTTACGGTGAAGTCGG 59.008 43.478 0.00 0.00 0.00 4.79
3219 3637 1.741770 GCAGAGGCAGGTTACCGTG 60.742 63.158 0.00 0.00 40.72 4.94
3307 3725 0.387622 CTGTTCATGCAACAAGCCGG 60.388 55.000 0.00 0.00 44.71 6.13
3465 3883 5.747565 TCACGCAACTACAGAAAGAATTTG 58.252 37.500 0.00 0.00 39.27 2.32
3495 3913 8.178964 CGCTACTACAGAGATATTAGACCATTC 58.821 40.741 0.00 0.00 0.00 2.67
3498 3916 8.330466 ACTACAGAGATATTAGACCATTCGAG 57.670 38.462 0.00 0.00 0.00 4.04
3590 4008 1.719117 CACAAACTGCCGTTGTCGT 59.281 52.632 0.00 0.00 32.65 4.34
3680 4098 5.353678 CAGAAGAATCAAGAACCTAGCCAAG 59.646 44.000 0.00 0.00 0.00 3.61
3687 4105 4.137543 CAAGAACCTAGCCAAGTTTGAGT 58.862 43.478 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.666190 TTCCTCGCTGCACTGTGC 60.666 61.111 25.15 25.15 45.29 4.57
49 50 2.675056 GCTTCCTCGCTGCACTGTG 61.675 63.158 2.76 2.76 0.00 3.66
80 81 3.305398 GTGAAGACGACAAGGACTGAT 57.695 47.619 0.00 0.00 0.00 2.90
112 113 1.744368 CGGGAGAGAAGTCGACGGA 60.744 63.158 10.46 0.00 0.00 4.69
113 114 2.792599 CGGGAGAGAAGTCGACGG 59.207 66.667 10.46 0.00 0.00 4.79
114 115 2.100603 GCGGGAGAGAAGTCGACG 59.899 66.667 10.46 0.00 0.00 5.12
115 116 2.490685 GGCGGGAGAGAAGTCGAC 59.509 66.667 7.70 7.70 0.00 4.20
116 117 3.132139 CGGCGGGAGAGAAGTCGA 61.132 66.667 0.00 0.00 0.00 4.20
117 118 3.114647 CTCGGCGGGAGAGAAGTCG 62.115 68.421 0.00 0.00 46.23 4.18
118 119 1.749638 TCTCGGCGGGAGAGAAGTC 60.750 63.158 4.77 0.00 46.80 3.01
119 120 2.355502 TCTCGGCGGGAGAGAAGT 59.644 61.111 4.77 0.00 46.80 3.01
125 126 0.461961 ATTTTCTCTCTCGGCGGGAG 59.538 55.000 30.32 30.32 44.58 4.30
126 127 1.407979 GTATTTTCTCTCTCGGCGGGA 59.592 52.381 10.05 10.05 0.00 5.14
127 128 1.409427 AGTATTTTCTCTCTCGGCGGG 59.591 52.381 7.21 2.41 0.00 6.13
128 129 2.159226 ACAGTATTTTCTCTCTCGGCGG 60.159 50.000 7.21 0.00 0.00 6.13
129 130 3.109619 GACAGTATTTTCTCTCTCGGCG 58.890 50.000 0.00 0.00 0.00 6.46
130 131 3.119101 TGGACAGTATTTTCTCTCTCGGC 60.119 47.826 0.00 0.00 0.00 5.54
131 132 4.720649 TGGACAGTATTTTCTCTCTCGG 57.279 45.455 0.00 0.00 0.00 4.63
132 133 6.813649 TGAAATGGACAGTATTTTCTCTCTCG 59.186 38.462 0.00 0.00 0.00 4.04
133 134 7.821846 ACTGAAATGGACAGTATTTTCTCTCTC 59.178 37.037 0.00 0.00 45.10 3.20
134 135 7.684529 ACTGAAATGGACAGTATTTTCTCTCT 58.315 34.615 0.00 0.00 45.10 3.10
135 136 7.913674 ACTGAAATGGACAGTATTTTCTCTC 57.086 36.000 0.00 0.00 45.10 3.20
136 137 8.697507 AAACTGAAATGGACAGTATTTTCTCT 57.302 30.769 0.00 0.00 46.01 3.10
139 140 9.129209 GCTAAAACTGAAATGGACAGTATTTTC 57.871 33.333 0.00 0.00 46.01 2.29
140 141 8.088365 GGCTAAAACTGAAATGGACAGTATTTT 58.912 33.333 0.00 0.00 46.01 1.82
141 142 7.574967 CGGCTAAAACTGAAATGGACAGTATTT 60.575 37.037 0.00 0.00 46.01 1.40
142 143 6.128007 CGGCTAAAACTGAAATGGACAGTATT 60.128 38.462 0.00 0.00 46.01 1.89
143 144 5.354234 CGGCTAAAACTGAAATGGACAGTAT 59.646 40.000 0.00 0.00 46.01 2.12
144 145 4.693566 CGGCTAAAACTGAAATGGACAGTA 59.306 41.667 0.00 0.00 46.01 2.74
146 147 3.751175 TCGGCTAAAACTGAAATGGACAG 59.249 43.478 0.00 0.00 40.68 3.51
161 162 5.957842 AAAAGATCACAACATTCGGCTAA 57.042 34.783 0.00 0.00 0.00 3.09
162 163 7.201696 GGAATAAAAGATCACAACATTCGGCTA 60.202 37.037 0.00 0.00 0.00 3.93
163 164 6.404734 GGAATAAAAGATCACAACATTCGGCT 60.405 38.462 0.00 0.00 0.00 5.52
164 165 5.743872 GGAATAAAAGATCACAACATTCGGC 59.256 40.000 0.00 0.00 0.00 5.54
165 166 5.965334 CGGAATAAAAGATCACAACATTCGG 59.035 40.000 0.00 0.00 0.00 4.30
166 167 6.771076 TCGGAATAAAAGATCACAACATTCG 58.229 36.000 0.00 0.00 0.00 3.34
168 169 7.390440 TGTCTCGGAATAAAAGATCACAACATT 59.610 33.333 0.00 0.00 0.00 2.71
170 171 6.227522 TGTCTCGGAATAAAAGATCACAACA 58.772 36.000 0.00 0.00 0.00 3.33
171 172 6.183360 CCTGTCTCGGAATAAAAGATCACAAC 60.183 42.308 0.00 0.00 0.00 3.32
213 312 2.928396 CCGTTGGGAGGGTCCAGT 60.928 66.667 0.00 0.00 38.64 4.00
214 313 2.606519 TCCGTTGGGAGGGTCCAG 60.607 66.667 0.00 0.00 38.64 3.86
248 347 3.046390 GAGCCGATAACGATTCAGTCAG 58.954 50.000 0.00 0.00 42.66 3.51
249 348 2.425668 TGAGCCGATAACGATTCAGTCA 59.574 45.455 0.00 0.00 42.66 3.41
250 349 2.789893 GTGAGCCGATAACGATTCAGTC 59.210 50.000 0.00 0.00 42.66 3.51
281 380 0.883833 GAAGAGTTGCCCATGTGTGG 59.116 55.000 0.00 0.00 45.61 4.17
282 381 1.901591 AGAAGAGTTGCCCATGTGTG 58.098 50.000 0.00 0.00 0.00 3.82
283 382 2.664402 AAGAAGAGTTGCCCATGTGT 57.336 45.000 0.00 0.00 0.00 3.72
284 383 5.882557 AGTAATAAGAAGAGTTGCCCATGTG 59.117 40.000 0.00 0.00 0.00 3.21
285 384 6.067217 AGTAATAAGAAGAGTTGCCCATGT 57.933 37.500 0.00 0.00 0.00 3.21
286 385 6.038714 GGAAGTAATAAGAAGAGTTGCCCATG 59.961 42.308 0.00 0.00 0.00 3.66
288 387 5.250774 AGGAAGTAATAAGAAGAGTTGCCCA 59.749 40.000 0.00 0.00 0.00 5.36
289 388 5.586643 CAGGAAGTAATAAGAAGAGTTGCCC 59.413 44.000 0.00 0.00 0.00 5.36
290 389 5.065346 GCAGGAAGTAATAAGAAGAGTTGCC 59.935 44.000 0.00 0.00 0.00 4.52
291 390 5.065346 GGCAGGAAGTAATAAGAAGAGTTGC 59.935 44.000 0.00 0.00 0.00 4.17
292 391 6.410540 AGGCAGGAAGTAATAAGAAGAGTTG 58.589 40.000 0.00 0.00 0.00 3.16
293 392 6.628644 AGGCAGGAAGTAATAAGAAGAGTT 57.371 37.500 0.00 0.00 0.00 3.01
295 394 6.041523 AGCTAGGCAGGAAGTAATAAGAAGAG 59.958 42.308 0.00 0.00 0.00 2.85
297 396 6.168270 AGCTAGGCAGGAAGTAATAAGAAG 57.832 41.667 0.00 0.00 0.00 2.85
340 597 9.692749 CCATTTAGGAAACTTAAAAGAAAGACC 57.307 33.333 0.00 0.00 43.67 3.85
403 660 4.326826 TCCAAAGATGCTACTCCACTTTG 58.673 43.478 0.00 0.00 43.61 2.77
409 666 2.698855 TGCTCCAAAGATGCTACTCC 57.301 50.000 0.00 0.00 0.00 3.85
410 667 5.363939 ACTATTGCTCCAAAGATGCTACTC 58.636 41.667 0.00 0.00 0.00 2.59
411 668 5.365021 ACTATTGCTCCAAAGATGCTACT 57.635 39.130 0.00 0.00 0.00 2.57
412 669 6.442513 AAACTATTGCTCCAAAGATGCTAC 57.557 37.500 0.00 0.00 0.00 3.58
413 670 7.466746 AAAAACTATTGCTCCAAAGATGCTA 57.533 32.000 0.00 0.00 0.00 3.49
439 697 1.019278 CATTCGTGGAAGTCGTGGGG 61.019 60.000 0.00 0.00 0.00 4.96
451 709 6.918892 TTTTACCATAGGATCACATTCGTG 57.081 37.500 0.00 0.00 45.08 4.35
469 727 7.748241 TGTTTTGAGTGCTTGCAAAATTTTTAC 59.252 29.630 0.00 0.00 43.37 2.01
471 729 6.675987 TGTTTTGAGTGCTTGCAAAATTTTT 58.324 28.000 0.00 0.00 43.37 1.94
479 737 3.132646 AGGAAATGTTTTGAGTGCTTGCA 59.867 39.130 0.00 0.00 0.00 4.08
480 738 3.721035 AGGAAATGTTTTGAGTGCTTGC 58.279 40.909 0.00 0.00 0.00 4.01
606 865 6.647895 ACAAATTGCCTCAAGAAAATTAGCAG 59.352 34.615 0.00 0.00 0.00 4.24
674 938 1.202855 AGCAGATTGCCACAGTTGTCT 60.203 47.619 0.00 0.00 46.52 3.41
675 939 1.068748 CAGCAGATTGCCACAGTTGTC 60.069 52.381 0.00 0.00 46.52 3.18
676 940 0.956633 CAGCAGATTGCCACAGTTGT 59.043 50.000 0.00 0.00 46.52 3.32
677 941 0.388134 GCAGCAGATTGCCACAGTTG 60.388 55.000 0.00 0.00 46.52 3.16
678 942 0.538977 AGCAGCAGATTGCCACAGTT 60.539 50.000 0.00 0.00 46.52 3.16
679 943 0.959372 GAGCAGCAGATTGCCACAGT 60.959 55.000 0.00 0.00 46.52 3.55
680 944 0.677098 AGAGCAGCAGATTGCCACAG 60.677 55.000 0.00 0.00 46.52 3.66
681 945 0.251033 AAGAGCAGCAGATTGCCACA 60.251 50.000 0.00 0.00 46.52 4.17
682 946 0.886563 AAAGAGCAGCAGATTGCCAC 59.113 50.000 0.00 0.00 46.52 5.01
683 947 1.624336 AAAAGAGCAGCAGATTGCCA 58.376 45.000 0.00 0.00 46.52 4.92
684 948 2.738013 AAAAAGAGCAGCAGATTGCC 57.262 45.000 0.00 0.00 46.52 4.52
724 988 5.236911 GCTGATTTTGCCATTGTCTCAAAAA 59.763 36.000 10.56 0.00 41.26 1.94
725 989 4.751098 GCTGATTTTGCCATTGTCTCAAAA 59.249 37.500 9.54 9.54 41.86 2.44
726 990 4.039488 AGCTGATTTTGCCATTGTCTCAAA 59.961 37.500 0.00 0.00 0.00 2.69
727 991 3.575256 AGCTGATTTTGCCATTGTCTCAA 59.425 39.130 0.00 0.00 0.00 3.02
728 992 3.159472 AGCTGATTTTGCCATTGTCTCA 58.841 40.909 0.00 0.00 0.00 3.27
729 993 3.863142 AGCTGATTTTGCCATTGTCTC 57.137 42.857 0.00 0.00 0.00 3.36
730 994 4.612264 AAAGCTGATTTTGCCATTGTCT 57.388 36.364 0.00 0.00 0.00 3.41
731 995 5.678132 AAAAAGCTGATTTTGCCATTGTC 57.322 34.783 4.20 0.00 40.27 3.18
752 1016 5.704978 GCTGATTTTGCCATTTCCCTAAAAA 59.295 36.000 0.00 0.00 0.00 1.94
753 1017 5.012975 AGCTGATTTTGCCATTTCCCTAAAA 59.987 36.000 0.00 0.00 0.00 1.52
754 1018 4.531732 AGCTGATTTTGCCATTTCCCTAAA 59.468 37.500 0.00 0.00 0.00 1.85
755 1019 4.081531 CAGCTGATTTTGCCATTTCCCTAA 60.082 41.667 8.42 0.00 0.00 2.69
756 1020 3.448301 CAGCTGATTTTGCCATTTCCCTA 59.552 43.478 8.42 0.00 0.00 3.53
757 1021 2.235402 CAGCTGATTTTGCCATTTCCCT 59.765 45.455 8.42 0.00 0.00 4.20
758 1022 2.027837 ACAGCTGATTTTGCCATTTCCC 60.028 45.455 23.35 0.00 0.00 3.97
759 1023 3.323751 ACAGCTGATTTTGCCATTTCC 57.676 42.857 23.35 0.00 0.00 3.13
760 1024 3.681417 GGAACAGCTGATTTTGCCATTTC 59.319 43.478 23.35 9.21 0.00 2.17
761 1025 3.325716 AGGAACAGCTGATTTTGCCATTT 59.674 39.130 23.35 0.00 0.00 2.32
762 1026 2.901839 AGGAACAGCTGATTTTGCCATT 59.098 40.909 23.35 0.00 0.00 3.16
763 1027 2.532843 AGGAACAGCTGATTTTGCCAT 58.467 42.857 23.35 0.00 0.00 4.40
764 1028 1.999648 AGGAACAGCTGATTTTGCCA 58.000 45.000 23.35 0.00 0.00 4.92
765 1029 3.062042 CAAAGGAACAGCTGATTTTGCC 58.938 45.455 23.35 5.73 0.00 4.52
766 1030 3.721035 ACAAAGGAACAGCTGATTTTGC 58.279 40.909 23.35 9.96 0.00 3.68
767 1031 4.301628 GGACAAAGGAACAGCTGATTTTG 58.698 43.478 23.35 22.84 0.00 2.44
768 1032 3.321968 GGGACAAAGGAACAGCTGATTTT 59.678 43.478 23.35 11.59 0.00 1.82
769 1033 2.893489 GGGACAAAGGAACAGCTGATTT 59.107 45.455 23.35 12.31 0.00 2.17
770 1034 2.519013 GGGACAAAGGAACAGCTGATT 58.481 47.619 23.35 11.07 0.00 2.57
771 1035 1.272147 GGGGACAAAGGAACAGCTGAT 60.272 52.381 23.35 9.01 0.00 2.90
772 1036 0.110486 GGGGACAAAGGAACAGCTGA 59.890 55.000 23.35 0.00 0.00 4.26
773 1037 0.111253 AGGGGACAAAGGAACAGCTG 59.889 55.000 13.48 13.48 0.00 4.24
774 1038 0.853530 AAGGGGACAAAGGAACAGCT 59.146 50.000 0.00 0.00 0.00 4.24
775 1039 1.248486 GAAGGGGACAAAGGAACAGC 58.752 55.000 0.00 0.00 0.00 4.40
776 1040 1.071699 TCGAAGGGGACAAAGGAACAG 59.928 52.381 0.00 0.00 0.00 3.16
777 1041 1.133363 TCGAAGGGGACAAAGGAACA 58.867 50.000 0.00 0.00 0.00 3.18
833 1097 0.401738 TCTTTAGCCAGCCTGCTGTT 59.598 50.000 17.23 8.23 42.77 3.16
834 1098 0.322008 GTCTTTAGCCAGCCTGCTGT 60.322 55.000 17.23 3.18 42.77 4.40
856 1120 0.538287 GGTTATGGGCTCTGGATGGC 60.538 60.000 0.00 0.00 0.00 4.40
891 1155 7.290014 AGTTTTCCCTCCATTTTGTTTCTGTAT 59.710 33.333 0.00 0.00 0.00 2.29
892 1156 6.609616 AGTTTTCCCTCCATTTTGTTTCTGTA 59.390 34.615 0.00 0.00 0.00 2.74
893 1157 5.425217 AGTTTTCCCTCCATTTTGTTTCTGT 59.575 36.000 0.00 0.00 0.00 3.41
895 1159 6.156083 TGAAGTTTTCCCTCCATTTTGTTTCT 59.844 34.615 0.00 0.00 0.00 2.52
896 1160 6.345298 TGAAGTTTTCCCTCCATTTTGTTTC 58.655 36.000 0.00 0.00 0.00 2.78
897 1161 6.156083 TCTGAAGTTTTCCCTCCATTTTGTTT 59.844 34.615 0.00 0.00 0.00 2.83
1299 1615 4.678044 GCCACAATATTCAGACGAGTGAGA 60.678 45.833 0.00 0.00 0.00 3.27
1300 1616 3.553511 GCCACAATATTCAGACGAGTGAG 59.446 47.826 0.00 0.00 0.00 3.51
1301 1617 3.056179 TGCCACAATATTCAGACGAGTGA 60.056 43.478 0.00 0.00 0.00 3.41
1302 1618 3.261580 TGCCACAATATTCAGACGAGTG 58.738 45.455 0.00 0.00 0.00 3.51
1303 1619 3.610040 TGCCACAATATTCAGACGAGT 57.390 42.857 0.00 0.00 0.00 4.18
1304 1620 4.787563 GCAATGCCACAATATTCAGACGAG 60.788 45.833 0.00 0.00 0.00 4.18
1305 1621 3.065233 GCAATGCCACAATATTCAGACGA 59.935 43.478 0.00 0.00 0.00 4.20
1306 1622 3.065786 AGCAATGCCACAATATTCAGACG 59.934 43.478 0.00 0.00 0.00 4.18
1307 1623 4.644103 AGCAATGCCACAATATTCAGAC 57.356 40.909 0.00 0.00 0.00 3.51
1308 1624 4.142116 CCAAGCAATGCCACAATATTCAGA 60.142 41.667 0.00 0.00 0.00 3.27
1309 1625 4.116961 CCAAGCAATGCCACAATATTCAG 58.883 43.478 0.00 0.00 0.00 3.02
1310 1626 3.514706 ACCAAGCAATGCCACAATATTCA 59.485 39.130 0.00 0.00 0.00 2.57
1311 1627 4.127566 ACCAAGCAATGCCACAATATTC 57.872 40.909 0.00 0.00 0.00 1.75
1312 1628 4.711355 AGTACCAAGCAATGCCACAATATT 59.289 37.500 0.00 0.00 0.00 1.28
1313 1629 4.280819 AGTACCAAGCAATGCCACAATAT 58.719 39.130 0.00 0.00 0.00 1.28
1314 1630 3.694072 GAGTACCAAGCAATGCCACAATA 59.306 43.478 0.00 0.00 0.00 1.90
1315 1631 2.493278 GAGTACCAAGCAATGCCACAAT 59.507 45.455 0.00 0.00 0.00 2.71
1316 1632 1.885887 GAGTACCAAGCAATGCCACAA 59.114 47.619 0.00 0.00 0.00 3.33
1317 1633 1.073763 AGAGTACCAAGCAATGCCACA 59.926 47.619 0.00 0.00 0.00 4.17
1318 1634 1.470098 CAGAGTACCAAGCAATGCCAC 59.530 52.381 0.00 0.00 0.00 5.01
1319 1635 1.350684 TCAGAGTACCAAGCAATGCCA 59.649 47.619 0.00 0.00 0.00 4.92
1320 1636 2.113860 TCAGAGTACCAAGCAATGCC 57.886 50.000 0.00 0.00 0.00 4.40
1321 1637 3.242543 CGAATCAGAGTACCAAGCAATGC 60.243 47.826 0.00 0.00 0.00 3.56
1322 1638 3.935203 ACGAATCAGAGTACCAAGCAATG 59.065 43.478 0.00 0.00 0.00 2.82
1323 1639 4.081420 AGACGAATCAGAGTACCAAGCAAT 60.081 41.667 0.00 0.00 0.00 3.56
1324 1640 3.258372 AGACGAATCAGAGTACCAAGCAA 59.742 43.478 0.00 0.00 0.00 3.91
1325 1641 2.826128 AGACGAATCAGAGTACCAAGCA 59.174 45.455 0.00 0.00 0.00 3.91
1326 1642 3.119459 TCAGACGAATCAGAGTACCAAGC 60.119 47.826 0.00 0.00 0.00 4.01
1327 1643 4.703645 TCAGACGAATCAGAGTACCAAG 57.296 45.455 0.00 0.00 0.00 3.61
1328 1644 5.047306 ACATTCAGACGAATCAGAGTACCAA 60.047 40.000 0.00 0.00 39.96 3.67
1329 1645 4.462834 ACATTCAGACGAATCAGAGTACCA 59.537 41.667 0.00 0.00 39.96 3.25
1330 1646 5.000012 ACATTCAGACGAATCAGAGTACC 58.000 43.478 0.00 0.00 39.96 3.34
1331 1647 4.731000 CGACATTCAGACGAATCAGAGTAC 59.269 45.833 0.00 0.00 39.96 2.73
1332 1648 4.395231 ACGACATTCAGACGAATCAGAGTA 59.605 41.667 0.00 0.00 39.96 2.59
1333 1649 3.191581 ACGACATTCAGACGAATCAGAGT 59.808 43.478 0.00 0.00 39.96 3.24
1334 1650 3.545475 CACGACATTCAGACGAATCAGAG 59.455 47.826 0.00 0.00 39.96 3.35
1375 1713 2.989909 TGCCATGACATTCAGACGAAT 58.010 42.857 0.00 0.00 42.81 3.34
1378 1716 2.793585 GCAATGCCATGACATTCAGACG 60.794 50.000 4.02 0.00 38.19 4.18
1379 1717 2.426024 AGCAATGCCATGACATTCAGAC 59.574 45.455 4.02 0.00 38.19 3.51
1380 1718 2.730382 AGCAATGCCATGACATTCAGA 58.270 42.857 4.02 0.00 38.19 3.27
1382 1720 2.093921 CCAAGCAATGCCATGACATTCA 60.094 45.455 4.02 0.00 38.19 2.57
1384 1722 1.903860 ACCAAGCAATGCCATGACATT 59.096 42.857 0.00 0.80 40.90 2.71
1385 1723 1.563924 ACCAAGCAATGCCATGACAT 58.436 45.000 0.00 0.00 0.00 3.06
1387 1725 2.094675 ACTACCAAGCAATGCCATGAC 58.905 47.619 0.00 0.00 0.00 3.06
1388 1726 2.025981 AGACTACCAAGCAATGCCATGA 60.026 45.455 0.00 0.00 0.00 3.07
1389 1727 2.098607 CAGACTACCAAGCAATGCCATG 59.901 50.000 0.00 1.14 0.00 3.66
1390 1728 2.025981 TCAGACTACCAAGCAATGCCAT 60.026 45.455 0.00 0.00 0.00 4.40
1391 1729 1.350684 TCAGACTACCAAGCAATGCCA 59.649 47.619 0.00 0.00 0.00 4.92
1392 1730 2.113860 TCAGACTACCAAGCAATGCC 57.886 50.000 0.00 0.00 0.00 4.40
1393 1731 3.242543 CGAATCAGACTACCAAGCAATGC 60.243 47.826 0.00 0.00 0.00 3.56
1394 1732 3.935203 ACGAATCAGACTACCAAGCAATG 59.065 43.478 0.00 0.00 0.00 2.82
1395 1733 4.081420 AGACGAATCAGACTACCAAGCAAT 60.081 41.667 0.00 0.00 0.00 3.56
1408 1746 4.568359 CCTACCAACATTCAGACGAATCAG 59.432 45.833 0.00 0.00 39.96 2.90
1478 1831 1.599171 CCGTGCACGCTTGAAAAATCA 60.599 47.619 33.17 0.00 38.18 2.57
1685 2038 3.372954 CTCTTCGTCATACGGGTCATTC 58.627 50.000 0.00 0.00 42.81 2.67
1758 2117 3.643237 AGGATCTCCAGTATTTGTCGGA 58.357 45.455 0.00 0.00 38.89 4.55
1787 2146 9.178427 GTCACATTTCTCTTTTTCTTCAATCTG 57.822 33.333 0.00 0.00 0.00 2.90
1789 2148 8.962111 GTGTCACATTTCTCTTTTTCTTCAATC 58.038 33.333 0.00 0.00 0.00 2.67
1881 2248 3.003480 GCTGTTGAGAGTAACCATCACC 58.997 50.000 0.00 0.00 0.00 4.02
1888 2255 1.071605 CGGCAGCTGTTGAGAGTAAC 58.928 55.000 16.64 0.00 0.00 2.50
1902 2269 3.289834 AGGCAACACAAGCGGCAG 61.290 61.111 1.45 0.00 41.41 4.85
1908 2275 0.179020 TCTGTCCCAGGCAACACAAG 60.179 55.000 0.00 0.00 41.41 3.16
1958 2325 2.039348 TGCCAGGTGTTCCTTAAGGTAC 59.961 50.000 21.09 21.09 43.07 3.34
2019 2386 1.668419 GGAGTAACATGCTCGCCATT 58.332 50.000 0.00 0.00 34.00 3.16
2030 2397 3.766691 GCCTCGGCGGGAGTAACA 61.767 66.667 9.18 0.00 41.46 2.41
2368 2740 2.809174 CGCACTCGACGATGGCAA 60.809 61.111 17.50 0.00 38.10 4.52
2421 2793 2.031516 CAACCACTGCTCGCTCCAG 61.032 63.158 0.00 0.00 36.41 3.86
2630 3007 2.433868 ACGTATGTTGTCGCTTCTGT 57.566 45.000 0.00 0.00 0.00 3.41
2647 3024 4.093556 GCTCCTTCCAGAGTTTATCAAACG 59.906 45.833 0.00 0.00 45.88 3.60
2697 3074 5.376625 TCACTAGCACCAAATTCTTTCTGT 58.623 37.500 0.00 0.00 0.00 3.41
2708 3087 1.270839 GCACTTCCTCACTAGCACCAA 60.271 52.381 0.00 0.00 0.00 3.67
2774 3162 1.825105 ATCAGTATGGCTGGATGGGT 58.175 50.000 0.00 0.00 45.08 4.51
2787 3175 3.041211 CCCATCCTCCACTGAATCAGTA 58.959 50.000 16.28 0.00 43.43 2.74
2788 3176 1.842562 CCCATCCTCCACTGAATCAGT 59.157 52.381 10.56 10.56 46.51 3.41
2828 3216 4.072131 TGTTATCTTTCCCTTGCTGTCAC 58.928 43.478 0.00 0.00 0.00 3.67
2838 3226 7.929941 ATCAGAGAACTTTGTTATCTTTCCC 57.070 36.000 5.04 0.00 0.00 3.97
3042 3430 1.996191 GCGGCACTTGTGTTTTTGAAA 59.004 42.857 0.00 0.00 0.00 2.69
3174 3592 4.642429 ACTTCACCGTAAATTTCAGAGCT 58.358 39.130 0.00 0.00 0.00 4.09
3199 3617 2.272471 GGTAACCTGCCTCTGCCC 59.728 66.667 0.00 0.00 36.33 5.36
3219 3637 5.522824 GTGGGTATATTCCGACTTCAAGTTC 59.477 44.000 6.32 0.00 34.21 3.01
3465 3883 4.506886 AATATCTCTGTAGTAGCGTGGC 57.493 45.455 0.00 0.00 0.00 5.01
3495 3913 0.655733 AAGTTGGTGTTTCACGCTCG 59.344 50.000 0.00 0.00 34.83 5.03
3498 3916 0.736053 TCCAAGTTGGTGTTTCACGC 59.264 50.000 21.35 0.00 39.03 5.34
3680 4098 9.950680 TTCACAGATGATAAAAGAAACTCAAAC 57.049 29.630 0.00 0.00 33.85 2.93
3687 4105 8.690203 TGGAGTTTCACAGATGATAAAAGAAA 57.310 30.769 0.00 0.00 33.85 2.52



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

AutoCloner maintained by Alex Coulton.