Multiple sequence alignment - TraesCS2B01G163400

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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 TraesCS2B01G163400 chr2B 100.000 4687 0 0 1 4687 135706564 135711250 0.000000e+00 8656.0
1 TraesCS2B01G163400 chr2B 88.112 2473 259 24 1425 3893 137802576 137800135 0.000000e+00 2905.0
2 TraesCS2B01G163400 chr2B 85.908 2214 276 24 1561 3767 136627563 136625379 0.000000e+00 2327.0
3 TraesCS2B01G163400 chr2B 81.596 2168 328 40 1027 3162 167494074 167496202 0.000000e+00 1727.0
4 TraesCS2B01G163400 chr2B 78.571 392 68 10 1397 1784 136811556 136811177 1.300000e-60 244.0
5 TraesCS2B01G163400 chr2B 82.517 143 23 2 80 220 536623579 536623437 1.770000e-24 124.0
6 TraesCS2B01G163400 chr2D 90.861 4574 272 69 1 4514 83838550 83843037 0.000000e+00 5997.0
7 TraesCS2B01G163400 chr2D 89.041 2482 261 9 1425 3904 85685738 85683266 0.000000e+00 3066.0
8 TraesCS2B01G163400 chr2D 87.527 1868 221 7 1561 3418 84927156 84925291 0.000000e+00 2148.0
9 TraesCS2B01G163400 chr2D 78.534 573 73 31 931 1474 84769638 84769087 9.720000e-87 331.0
10 TraesCS2B01G163400 chr2D 78.407 565 81 30 931 1473 84927762 84927217 3.500000e-86 329.0
11 TraesCS2B01G163400 chr2D 81.379 435 47 17 931 1344 85394884 85394463 1.630000e-84 324.0
12 TraesCS2B01G163400 chr2D 80.674 445 62 15 935 1370 85686284 85685855 1.630000e-84 324.0
13 TraesCS2B01G163400 chr2D 92.308 91 6 1 1384 1473 85394400 85394310 1.370000e-25 128.0
14 TraesCS2B01G163400 chr2A 93.942 3384 170 17 807 4181 84606566 84609923 0.000000e+00 5081.0
15 TraesCS2B01G163400 chr2A 87.526 2373 277 14 1662 4024 85805502 85803139 0.000000e+00 2724.0
16 TraesCS2B01G163400 chr2A 87.221 2371 286 12 1662 4024 85921409 85919048 0.000000e+00 2684.0
17 TraesCS2B01G163400 chr2A 87.483 2237 264 13 1798 4024 86052253 86050023 0.000000e+00 2566.0
18 TraesCS2B01G163400 chr2A 84.514 2286 315 24 1561 3839 85603678 85601425 0.000000e+00 2224.0
19 TraesCS2B01G163400 chr2A 88.444 225 24 2 1435 1658 86054984 86054761 2.150000e-68 270.0
20 TraesCS2B01G163400 chr2A 91.304 138 8 4 4554 4687 337724439 337724576 8.010000e-43 185.0
21 TraesCS2B01G163400 chr2A 90.580 138 9 4 4554 4687 337864245 337864382 3.730000e-41 180.0
22 TraesCS2B01G163400 chr2A 76.765 340 61 10 1023 1360 118476828 118477151 1.730000e-39 174.0
23 TraesCS2B01G163400 chr2A 86.577 149 14 2 1 144 84606408 84606555 4.850000e-35 159.0
24 TraesCS2B01G163400 chr4A 87.526 2373 277 14 1662 4024 349801028 349798665 0.000000e+00 2724.0
25 TraesCS2B01G163400 chr7A 78.681 1637 295 33 1122 2741 571323494 571321895 0.000000e+00 1040.0
26 TraesCS2B01G163400 chr7A 82.710 214 21 11 1134 1344 571279947 571279747 4.820000e-40 176.0
27 TraesCS2B01G163400 chr7A 93.407 91 5 1 1384 1473 571279684 571279594 2.940000e-27 134.0
28 TraesCS2B01G163400 chr7B 91.791 134 8 3 4557 4687 32019078 32018945 2.880000e-42 183.0
29 TraesCS2B01G163400 chr7B 96.429 112 3 1 4557 4667 517098126 517098015 2.880000e-42 183.0
30 TraesCS2B01G163400 chr6D 95.614 114 3 2 4555 4667 292079065 292078953 1.040000e-41 182.0
31 TraesCS2B01G163400 chr6D 85.333 75 10 1 84 158 346257033 346257106 5.030000e-10 76.8
32 TraesCS2B01G163400 chr1D 94.167 120 6 1 4555 4673 472516440 472516321 1.040000e-41 182.0
33 TraesCS2B01G163400 chr1D 89.873 79 5 3 80 156 413606938 413607015 1.070000e-16 99.0
34 TraesCS2B01G163400 chr1D 90.769 65 6 0 100 164 308579750 308579686 2.320000e-13 87.9
35 TraesCS2B01G163400 chr3D 94.737 114 6 0 4554 4667 12551299 12551186 1.340000e-40 178.0
36 TraesCS2B01G163400 chr3D 88.489 139 8 4 4554 4687 403482852 403482987 1.350000e-35 161.0
37 TraesCS2B01G163400 chr3A 92.683 123 7 2 4553 4673 17466092 17466214 4.820000e-40 176.0
38 TraesCS2B01G163400 chr5D 82.759 116 17 1 82 197 221861129 221861017 2.980000e-17 100.0
39 TraesCS2B01G163400 chr5A 87.356 87 11 0 80 166 365962117 365962203 2.980000e-17 100.0
40 TraesCS2B01G163400 chr6B 86.364 88 11 1 80 167 277804384 277804298 1.390000e-15 95.3


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G163400 chr2B 135706564 135711250 4686 False 8656.0 8656 100.0000 1 4687 1 chr2B.!!$F1 4686
1 TraesCS2B01G163400 chr2B 137800135 137802576 2441 True 2905.0 2905 88.1120 1425 3893 1 chr2B.!!$R3 2468
2 TraesCS2B01G163400 chr2B 136625379 136627563 2184 True 2327.0 2327 85.9080 1561 3767 1 chr2B.!!$R1 2206
3 TraesCS2B01G163400 chr2B 167494074 167496202 2128 False 1727.0 1727 81.5960 1027 3162 1 chr2B.!!$F2 2135
4 TraesCS2B01G163400 chr2D 83838550 83843037 4487 False 5997.0 5997 90.8610 1 4514 1 chr2D.!!$F1 4513
5 TraesCS2B01G163400 chr2D 85683266 85686284 3018 True 1695.0 3066 84.8575 935 3904 2 chr2D.!!$R4 2969
6 TraesCS2B01G163400 chr2D 84925291 84927762 2471 True 1238.5 2148 82.9670 931 3418 2 chr2D.!!$R2 2487
7 TraesCS2B01G163400 chr2D 84769087 84769638 551 True 331.0 331 78.5340 931 1474 1 chr2D.!!$R1 543
8 TraesCS2B01G163400 chr2D 85394310 85394884 574 True 226.0 324 86.8435 931 1473 2 chr2D.!!$R3 542
9 TraesCS2B01G163400 chr2A 85803139 85805502 2363 True 2724.0 2724 87.5260 1662 4024 1 chr2A.!!$R2 2362
10 TraesCS2B01G163400 chr2A 85919048 85921409 2361 True 2684.0 2684 87.2210 1662 4024 1 chr2A.!!$R3 2362
11 TraesCS2B01G163400 chr2A 84606408 84609923 3515 False 2620.0 5081 90.2595 1 4181 2 chr2A.!!$F4 4180
12 TraesCS2B01G163400 chr2A 85601425 85603678 2253 True 2224.0 2224 84.5140 1561 3839 1 chr2A.!!$R1 2278
13 TraesCS2B01G163400 chr2A 86050023 86054984 4961 True 1418.0 2566 87.9635 1435 4024 2 chr2A.!!$R4 2589
14 TraesCS2B01G163400 chr4A 349798665 349801028 2363 True 2724.0 2724 87.5260 1662 4024 1 chr4A.!!$R1 2362
15 TraesCS2B01G163400 chr7A 571321895 571323494 1599 True 1040.0 1040 78.6810 1122 2741 1 chr7A.!!$R1 1619

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
382 418 0.031111 CTAGGGGAGGGGTGATGACA 60.031 60.000 0.00 0.0 0.00 3.58 F
1215 1306 0.031449 CACCGCCCGTTTTGTTCAAT 59.969 50.000 0.00 0.0 0.00 2.57 F
1477 1696 2.496070 TGCCTGTGTACTATGGACTCAC 59.504 50.000 0.00 0.0 0.00 3.51 F
2185 4814 1.271325 TGTTGACATCAAGGATGCGGT 60.271 47.619 6.15 0.0 43.15 5.68 F
3410 6053 0.034089 AGATTGGGGTTAGCACTGCC 60.034 55.000 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1682 1903 0.954452 CAGTGAGGTCCCTTTTGTGC 59.046 55.0 0.00 0.0 0.00 4.57 R
2183 4812 0.958822 CTTTACACCCTGCAACCACC 59.041 55.0 0.00 0.0 0.00 4.61 R
3060 5695 1.090728 TTGTTTGCTGCGACACTTGA 58.909 45.0 7.98 0.0 0.00 3.02 R
3601 6250 0.882927 GGCAGTTTGTACGCAGTCCA 60.883 55.0 0.00 0.0 43.93 4.02 R
4609 7267 0.041576 GAAAATATCGCCGGTTCGCC 60.042 55.0 1.90 0.0 0.00 5.54 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
36 37 0.104671 TGAGATTGCATGATCGGCGA 59.895 50.000 13.87 13.87 0.00 5.54
39 40 0.657312 GATTGCATGATCGGCGACAA 59.343 50.000 13.76 12.34 0.00 3.18
63 64 1.342819 GAGCGATGAGGCTTAGATGGT 59.657 52.381 0.00 0.00 44.93 3.55
136 142 4.157105 GTGACCGGGCATGTAAAAACTATT 59.843 41.667 16.47 0.00 0.00 1.73
161 169 6.486657 TCATACTTGTCTCTTTTTGGTTCTGG 59.513 38.462 0.00 0.00 0.00 3.86
185 193 1.134367 GGTACTGTGTGATCTAGCGCA 59.866 52.381 11.47 0.00 0.00 6.09
232 240 3.328382 TTCGAATTGACTGTACCTGGG 57.672 47.619 0.00 0.00 0.00 4.45
234 242 1.751437 GAATTGACTGTACCTGGGCC 58.249 55.000 0.00 0.00 0.00 5.80
246 282 0.605589 CCTGGGCCGACTCTCATATC 59.394 60.000 0.00 0.00 0.00 1.63
251 287 1.604185 GGCCGACTCTCATATCAGTGC 60.604 57.143 0.00 0.00 0.00 4.40
252 288 1.604185 GCCGACTCTCATATCAGTGCC 60.604 57.143 0.00 0.00 0.00 5.01
264 300 0.251209 TCAGTGCCTGTAGACGGTCT 60.251 55.000 15.95 15.95 32.61 3.85
336 372 2.489938 TGCCCTAATCTCGTTTGCTT 57.510 45.000 0.00 0.00 0.00 3.91
347 383 5.464030 TCTCGTTTGCTTAGAGTTTAGGT 57.536 39.130 0.00 0.00 33.96 3.08
382 418 0.031111 CTAGGGGAGGGGTGATGACA 60.031 60.000 0.00 0.00 0.00 3.58
397 433 4.818005 GTGATGACAATGGCATCTATGTGA 59.182 41.667 27.23 5.57 42.00 3.58
410 446 1.683385 CTATGTGATGTCCTGGCGAGA 59.317 52.381 0.00 0.00 0.00 4.04
429 465 2.162681 GACCCTCTTTGGAATGGTGTG 58.837 52.381 0.00 0.00 38.35 3.82
444 480 2.292016 TGGTGTGCGTGAGGTTTTTATG 59.708 45.455 0.00 0.00 0.00 1.90
468 504 1.086696 CCACTCAGCCGGTTGTTATG 58.913 55.000 18.51 13.82 0.00 1.90
504 540 9.577110 TGATTTTTCATAATCAACTGAGCAATC 57.423 29.630 0.00 0.00 40.55 2.67
513 549 2.746362 CAACTGAGCAATCTGAGTTCCC 59.254 50.000 0.00 0.00 41.87 3.97
514 550 1.280421 ACTGAGCAATCTGAGTTCCCC 59.720 52.381 0.00 0.00 32.75 4.81
521 557 3.829026 GCAATCTGAGTTCCCCTTTCTTT 59.171 43.478 0.00 0.00 0.00 2.52
523 559 5.565637 GCAATCTGAGTTCCCCTTTCTTTTC 60.566 44.000 0.00 0.00 0.00 2.29
537 573 6.707161 CCCTTTCTTTTCAATGAATGCAGAAA 59.293 34.615 17.30 17.30 0.00 2.52
539 575 8.780249 CCTTTCTTTTCAATGAATGCAGAAATT 58.220 29.630 18.02 0.00 29.98 1.82
540 576 9.807386 CTTTCTTTTCAATGAATGCAGAAATTC 57.193 29.630 18.02 0.00 37.13 2.17
541 577 9.550406 TTTCTTTTCAATGAATGCAGAAATTCT 57.450 25.926 15.62 0.00 37.44 2.40
542 578 8.528917 TCTTTTCAATGAATGCAGAAATTCTG 57.471 30.769 18.02 18.02 46.90 3.02
555 591 6.864360 CAGAAATTCTGCCATTTTGGAAAA 57.136 33.333 10.30 0.00 39.92 2.29
598 634 7.844493 AATATCACAATTGTATGGAAGGCAT 57.156 32.000 11.53 0.00 0.00 4.40
599 635 4.987408 TCACAATTGTATGGAAGGCATG 57.013 40.909 11.53 0.00 0.00 4.06
600 636 3.130869 TCACAATTGTATGGAAGGCATGC 59.869 43.478 11.53 9.90 0.00 4.06
601 637 3.098377 ACAATTGTATGGAAGGCATGCA 58.902 40.909 21.36 0.00 0.00 3.96
602 638 3.131577 ACAATTGTATGGAAGGCATGCAG 59.868 43.478 21.36 0.00 30.55 4.41
646 683 3.498481 GCTTCAGGGGTAATATGGCATGA 60.498 47.826 10.98 0.00 0.00 3.07
649 686 6.461577 TTCAGGGGTAATATGGCATGATAA 57.538 37.500 10.98 0.00 0.00 1.75
650 687 6.656965 TCAGGGGTAATATGGCATGATAAT 57.343 37.500 10.98 0.00 0.00 1.28
651 688 6.425735 TCAGGGGTAATATGGCATGATAATG 58.574 40.000 10.98 0.00 0.00 1.90
665 702 6.213677 GCATGATAATGATGAATGTTGCACT 58.786 36.000 0.00 0.00 0.00 4.40
700 737 9.995003 AGTGTATTCATTGCTGGATTTTAAAAA 57.005 25.926 4.44 0.00 0.00 1.94
772 809 0.250727 TTTCTTTCGGGGGTCTGCTG 60.251 55.000 0.00 0.00 0.00 4.41
780 817 1.472480 CGGGGGTCTGCTGTTTTATTG 59.528 52.381 0.00 0.00 0.00 1.90
785 822 3.691609 GGGTCTGCTGTTTTATTGAGAGG 59.308 47.826 0.00 0.00 0.00 3.69
786 823 4.327680 GGTCTGCTGTTTTATTGAGAGGT 58.672 43.478 0.00 0.00 0.00 3.85
788 825 5.106515 GGTCTGCTGTTTTATTGAGAGGTTC 60.107 44.000 0.00 0.00 0.00 3.62
790 827 5.934625 TCTGCTGTTTTATTGAGAGGTTCTC 59.065 40.000 0.00 0.00 43.65 2.87
796 835 8.980481 TGTTTTATTGAGAGGTTCTCTTTTCT 57.020 30.769 7.52 0.00 43.73 2.52
819 858 7.335627 TCTGGAGAGCGGATTTCTTTTATTTA 58.664 34.615 0.00 0.00 0.00 1.40
847 892 2.555547 GGTGACAGCCCAACAGCAC 61.556 63.158 0.00 0.00 34.23 4.40
860 905 3.514645 CAACAGCACATGGGAATTTAGC 58.485 45.455 0.00 0.00 0.00 3.09
871 916 3.269381 TGGGAATTTAGCCTCATCCACTT 59.731 43.478 0.00 0.00 31.63 3.16
872 917 3.633986 GGGAATTTAGCCTCATCCACTTG 59.366 47.826 0.00 0.00 31.63 3.16
884 929 1.739562 CCACTTGACGCAGAGCCTC 60.740 63.158 0.00 0.00 0.00 4.70
886 931 2.210013 ACTTGACGCAGAGCCTCCA 61.210 57.895 0.00 0.00 0.00 3.86
887 932 1.447489 CTTGACGCAGAGCCTCCAG 60.447 63.158 0.00 0.00 0.00 3.86
888 933 3.596066 TTGACGCAGAGCCTCCAGC 62.596 63.158 0.00 0.00 44.25 4.85
889 934 4.828925 GACGCAGAGCCTCCAGCC 62.829 72.222 1.67 0.00 45.47 4.85
893 938 3.007920 CAGAGCCTCCAGCCCAGT 61.008 66.667 0.00 0.00 45.47 4.00
898 943 3.406200 CCTCCAGCCCAGTCCAGG 61.406 72.222 0.00 0.00 0.00 4.45
905 950 1.002502 GCCCAGTCCAGGTACAACC 60.003 63.158 0.00 0.00 38.99 3.77
912 957 1.740296 CCAGGTACAACCGCGGAAG 60.740 63.158 35.90 25.21 44.90 3.46
913 958 1.005394 CAGGTACAACCGCGGAAGT 60.005 57.895 35.90 29.38 44.90 3.01
924 969 4.367023 CGGAAGTGGAACCGCGGA 62.367 66.667 35.90 6.02 42.55 5.54
925 970 2.741211 GGAAGTGGAACCGCGGAC 60.741 66.667 35.90 24.12 37.80 4.79
926 971 2.741211 GAAGTGGAACCGCGGACC 60.741 66.667 35.90 31.45 37.80 4.46
927 972 3.236003 GAAGTGGAACCGCGGACCT 62.236 63.158 35.90 17.93 37.80 3.85
928 973 3.530910 AAGTGGAACCGCGGACCTG 62.531 63.158 35.90 4.58 37.80 4.00
977 1030 1.067495 AGCGAGGGAAAACTCTCTTCG 60.067 52.381 0.00 0.00 35.33 3.79
1008 1079 2.680913 GCGCGCACAGATGGAAACT 61.681 57.895 29.10 0.00 0.00 2.66
1101 1178 4.451150 GATGTCGCTGCGGACCCA 62.451 66.667 23.03 13.73 36.07 4.51
1154 1231 2.042843 CCTGGTACGCTCTCCCCT 60.043 66.667 0.00 0.00 0.00 4.79
1215 1306 0.031449 CACCGCCCGTTTTGTTCAAT 59.969 50.000 0.00 0.00 0.00 2.57
1225 1316 3.480668 CGTTTTGTTCAATTCCGTGTGTC 59.519 43.478 0.00 0.00 0.00 3.67
1475 1694 3.639094 AGATGCCTGTGTACTATGGACTC 59.361 47.826 0.00 0.00 0.00 3.36
1477 1696 2.496070 TGCCTGTGTACTATGGACTCAC 59.504 50.000 0.00 0.00 0.00 3.51
1532 1751 3.936564 AGTTGAAGATTGCTCAGACCTC 58.063 45.455 0.00 0.00 0.00 3.85
1682 1903 7.870509 TGATATCAAGGGATTCTTCAAACAG 57.129 36.000 1.98 0.00 34.89 3.16
1931 4552 3.834447 GACGGTTGTTTTGCCCGGC 62.834 63.158 1.04 1.04 45.85 6.13
2018 4642 5.525012 TGAGGAAATTGCAGATTATCTCACG 59.475 40.000 14.81 0.00 0.00 4.35
2183 4812 3.557577 TTTGTTGACATCAAGGATGCG 57.442 42.857 6.15 0.00 43.15 4.73
2185 4814 1.271325 TGTTGACATCAAGGATGCGGT 60.271 47.619 6.15 0.00 43.15 5.68
2388 5017 2.532186 GCATGTGCTGTTGTCGAGA 58.468 52.632 0.00 0.00 38.21 4.04
2579 5213 4.796038 CATGGAAGACCTTGCTGAAAAT 57.204 40.909 3.10 0.00 35.20 1.82
2787 5422 3.273080 CTTGAGGTGCAAAGCCCGC 62.273 63.158 0.00 0.00 35.74 6.13
3038 5673 1.296715 GGAGGTGACATTCCTGCGT 59.703 57.895 2.56 0.00 34.07 5.24
3060 5695 6.238293 GCGTTTGGTAGAGTACTTCAAAAACT 60.238 38.462 0.00 0.00 33.55 2.66
3212 5848 8.721133 AAAAGAATTATCTTGGTAAGGTGGTT 57.279 30.769 0.00 0.00 45.19 3.67
3410 6053 0.034089 AGATTGGGGTTAGCACTGCC 60.034 55.000 0.00 0.00 0.00 4.85
3446 6089 1.710816 ACTACAGCCTGCCCTATCTC 58.289 55.000 0.00 0.00 0.00 2.75
3546 6195 6.968263 TCATACCATTTGAAGGTGAAACAA 57.032 33.333 0.00 0.00 40.26 2.83
3601 6250 1.541233 CCTTCCTGTTTGTCTGTCGCT 60.541 52.381 0.00 0.00 0.00 4.93
3642 6291 1.285578 GATCGAGGAAGAGCAACAGC 58.714 55.000 0.00 0.00 0.00 4.40
3681 6330 2.490509 TCAGTTGCAGGCAATGATGAAG 59.509 45.455 10.21 0.00 38.28 3.02
3770 6420 5.734855 TCTTCATATTTTGGACGCTTAGC 57.265 39.130 0.00 0.00 0.00 3.09
3800 6451 3.129109 GCCGTTGTAGTTAAGCTATCCC 58.871 50.000 0.00 0.00 31.50 3.85
3831 6482 7.171630 ACTCTGAACCTCTGTTATTATTCGT 57.828 36.000 0.00 0.00 33.97 3.85
3899 6550 4.432980 ACTAGTAGGTTGCAGTTTGGTT 57.567 40.909 1.45 0.00 0.00 3.67
3924 6575 3.870419 TGAATTTCTTGCTTGGTTTGTGC 59.130 39.130 0.00 0.00 0.00 4.57
3950 6601 6.791887 TCTTGAAACTCTTGTATGCTCAAG 57.208 37.500 9.42 9.42 44.08 3.02
3953 6604 5.368145 TGAAACTCTTGTATGCTCAAGTGT 58.632 37.500 13.97 13.97 46.73 3.55
3954 6605 5.466728 TGAAACTCTTGTATGCTCAAGTGTC 59.533 40.000 17.39 11.00 45.22 3.67
3965 6616 2.350522 CTCAAGTGTCAAATCCTCCGG 58.649 52.381 0.00 0.00 0.00 5.14
4132 6783 4.878397 GCACTGCTCAGGATTACAAACTAT 59.122 41.667 1.66 0.00 0.00 2.12
4157 6808 8.890410 TGTAAGTAGTAAGATTCTGTAAGGGT 57.110 34.615 0.00 0.00 0.00 4.34
4162 6813 6.793505 AGTAAGATTCTGTAAGGGTAGTGG 57.206 41.667 0.00 0.00 0.00 4.00
4181 6832 1.606994 GGCAACCTACGTGACATGTGA 60.607 52.381 1.15 0.00 0.00 3.58
4182 6833 1.726791 GCAACCTACGTGACATGTGAG 59.273 52.381 1.15 4.19 0.00 3.51
4183 6834 2.609491 GCAACCTACGTGACATGTGAGA 60.609 50.000 1.15 0.00 0.00 3.27
4184 6835 3.849911 CAACCTACGTGACATGTGAGAT 58.150 45.455 1.15 0.00 0.00 2.75
4185 6836 3.510388 ACCTACGTGACATGTGAGATG 57.490 47.619 1.15 0.00 0.00 2.90
4186 6837 2.166459 ACCTACGTGACATGTGAGATGG 59.834 50.000 1.15 0.79 0.00 3.51
4187 6838 2.196749 CTACGTGACATGTGAGATGGC 58.803 52.381 1.15 0.00 0.00 4.40
4188 6839 0.610174 ACGTGACATGTGAGATGGCT 59.390 50.000 1.15 0.00 0.00 4.75
4189 6840 1.004595 CGTGACATGTGAGATGGCTG 58.995 55.000 1.15 0.00 0.00 4.85
4190 6841 1.404583 CGTGACATGTGAGATGGCTGA 60.405 52.381 1.15 0.00 0.00 4.26
4191 6842 2.703416 GTGACATGTGAGATGGCTGAA 58.297 47.619 1.15 0.00 0.00 3.02
4192 6843 2.676839 GTGACATGTGAGATGGCTGAAG 59.323 50.000 1.15 0.00 0.00 3.02
4193 6844 2.568509 TGACATGTGAGATGGCTGAAGA 59.431 45.455 1.15 0.00 0.00 2.87
4194 6845 3.199289 TGACATGTGAGATGGCTGAAGAT 59.801 43.478 1.15 0.00 0.00 2.40
4207 6858 4.646945 TGGCTGAAGATGGAAGTAGAGTAG 59.353 45.833 0.00 0.00 0.00 2.57
4227 6878 1.338655 GGGTGCACGTTGTTTTGGTAT 59.661 47.619 11.45 0.00 0.00 2.73
4230 6881 3.296628 GTGCACGTTGTTTTGGTATCTG 58.703 45.455 0.00 0.00 0.00 2.90
4237 6888 4.452455 CGTTGTTTTGGTATCTGAGAAGCT 59.548 41.667 0.00 0.00 0.00 3.74
4275 6927 4.511454 TCAGTTTCATGTGCTGTTACAGAC 59.489 41.667 17.40 11.52 33.44 3.51
4276 6928 4.273235 CAGTTTCATGTGCTGTTACAGACA 59.727 41.667 17.40 16.40 36.65 3.41
4323 6975 7.816640 TCATACAGATACCTTTGCTTGTTTTC 58.183 34.615 0.00 0.00 0.00 2.29
4388 7046 5.596361 TCTTTTTGTTACCATTGGCTTCAGA 59.404 36.000 1.54 0.00 0.00 3.27
4391 7049 5.389859 TTGTTACCATTGGCTTCAGAATG 57.610 39.130 1.54 0.00 37.54 2.67
4392 7050 4.406456 TGTTACCATTGGCTTCAGAATGT 58.594 39.130 1.54 0.00 37.40 2.71
4406 7064 6.672266 TTCAGAATGTTTCTCTCTGGTAGT 57.328 37.500 0.00 0.00 38.11 2.73
4408 7066 7.962995 TCAGAATGTTTCTCTCTGGTAGTAT 57.037 36.000 0.00 0.00 38.11 2.12
4409 7067 8.367660 TCAGAATGTTTCTCTCTGGTAGTATT 57.632 34.615 0.00 0.00 38.11 1.89
4414 7072 7.062749 TGTTTCTCTCTGGTAGTATTGTTGT 57.937 36.000 0.00 0.00 0.00 3.32
4421 7079 3.823873 CTGGTAGTATTGTTGTGGCCAAA 59.176 43.478 7.24 0.00 30.94 3.28
4422 7080 4.411927 TGGTAGTATTGTTGTGGCCAAAT 58.588 39.130 7.24 6.27 30.94 2.32
4424 7082 6.010850 TGGTAGTATTGTTGTGGCCAAATTA 58.989 36.000 7.24 0.00 30.94 1.40
4429 7087 4.679373 TTGTTGTGGCCAAATTATGTGT 57.321 36.364 7.24 0.00 30.94 3.72
4433 7091 5.478332 TGTTGTGGCCAAATTATGTGTATCA 59.522 36.000 7.24 0.00 30.94 2.15
4439 7097 7.927629 GTGGCCAAATTATGTGTATCATGAAAT 59.072 33.333 7.24 0.00 37.91 2.17
4440 7098 8.484575 TGGCCAAATTATGTGTATCATGAAATT 58.515 29.630 0.61 0.00 37.91 1.82
4441 7099 8.767085 GGCCAAATTATGTGTATCATGAAATTG 58.233 33.333 0.00 0.00 37.91 2.32
4442 7100 9.316730 GCCAAATTATGTGTATCATGAAATTGT 57.683 29.630 0.00 0.00 37.91 2.71
4497 7155 2.125773 ATAGATACTCCCCGCGGTAG 57.874 55.000 26.12 22.56 0.00 3.18
4498 7156 0.767375 TAGATACTCCCCGCGGTAGT 59.233 55.000 27.27 27.27 0.00 2.73
4501 7159 0.178970 ATACTCCCCGCGGTAGTCAT 60.179 55.000 27.77 18.15 0.00 3.06
4538 7196 7.833285 TCTAAATTTTGCCCTTTAGTTCTGT 57.167 32.000 0.00 0.00 36.67 3.41
4539 7197 7.882179 TCTAAATTTTGCCCTTTAGTTCTGTC 58.118 34.615 0.00 0.00 36.67 3.51
4540 7198 5.468540 AATTTTGCCCTTTAGTTCTGTCC 57.531 39.130 0.00 0.00 0.00 4.02
4541 7199 3.876309 TTTGCCCTTTAGTTCTGTCCT 57.124 42.857 0.00 0.00 0.00 3.85
4542 7200 2.859165 TGCCCTTTAGTTCTGTCCTG 57.141 50.000 0.00 0.00 0.00 3.86
4543 7201 1.351017 TGCCCTTTAGTTCTGTCCTGG 59.649 52.381 0.00 0.00 0.00 4.45
4544 7202 1.351350 GCCCTTTAGTTCTGTCCTGGT 59.649 52.381 0.00 0.00 0.00 4.00
4545 7203 2.224793 GCCCTTTAGTTCTGTCCTGGTT 60.225 50.000 0.00 0.00 0.00 3.67
4546 7204 3.412386 CCCTTTAGTTCTGTCCTGGTTG 58.588 50.000 0.00 0.00 0.00 3.77
4547 7205 2.814336 CCTTTAGTTCTGTCCTGGTTGC 59.186 50.000 0.00 0.00 0.00 4.17
4548 7206 3.476552 CTTTAGTTCTGTCCTGGTTGCA 58.523 45.455 0.00 0.00 0.00 4.08
4549 7207 2.839486 TAGTTCTGTCCTGGTTGCAG 57.161 50.000 0.00 1.69 0.00 4.41
4550 7208 0.839946 AGTTCTGTCCTGGTTGCAGT 59.160 50.000 12.55 0.00 0.00 4.40
4551 7209 0.947244 GTTCTGTCCTGGTTGCAGTG 59.053 55.000 12.55 0.00 0.00 3.66
4552 7210 0.546122 TTCTGTCCTGGTTGCAGTGT 59.454 50.000 12.55 0.00 0.00 3.55
4553 7211 0.106708 TCTGTCCTGGTTGCAGTGTC 59.893 55.000 12.55 0.00 0.00 3.67
4554 7212 0.107456 CTGTCCTGGTTGCAGTGTCT 59.893 55.000 0.00 0.00 0.00 3.41
4555 7213 1.344438 CTGTCCTGGTTGCAGTGTCTA 59.656 52.381 0.00 0.00 0.00 2.59
4556 7214 1.765904 TGTCCTGGTTGCAGTGTCTAA 59.234 47.619 0.00 0.00 0.00 2.10
4557 7215 2.224281 TGTCCTGGTTGCAGTGTCTAAG 60.224 50.000 0.00 0.00 0.00 2.18
4558 7216 2.037251 GTCCTGGTTGCAGTGTCTAAGA 59.963 50.000 0.00 0.00 0.00 2.10
4559 7217 2.300152 TCCTGGTTGCAGTGTCTAAGAG 59.700 50.000 0.00 0.00 0.00 2.85
4560 7218 2.072298 CTGGTTGCAGTGTCTAAGAGC 58.928 52.381 0.00 0.00 0.00 4.09
4561 7219 1.416030 TGGTTGCAGTGTCTAAGAGCA 59.584 47.619 0.00 0.00 0.00 4.26
4562 7220 2.038952 TGGTTGCAGTGTCTAAGAGCAT 59.961 45.455 0.00 0.00 34.87 3.79
4563 7221 2.675348 GGTTGCAGTGTCTAAGAGCATC 59.325 50.000 0.00 0.00 34.87 3.91
4575 7233 2.675519 GAGCATCTCCAGCTGTTCG 58.324 57.895 13.81 0.00 43.58 3.95
4576 7234 1.427592 GAGCATCTCCAGCTGTTCGC 61.428 60.000 13.81 7.78 43.58 4.70
4577 7235 2.467826 GCATCTCCAGCTGTTCGCC 61.468 63.158 13.81 0.00 40.39 5.54
4578 7236 1.817099 CATCTCCAGCTGTTCGCCC 60.817 63.158 13.81 0.00 40.39 6.13
4579 7237 3.036429 ATCTCCAGCTGTTCGCCCC 62.036 63.158 13.81 0.00 40.39 5.80
4580 7238 4.785453 CTCCAGCTGTTCGCCCCC 62.785 72.222 13.81 0.00 40.39 5.40
4626 7284 3.727146 GGCGAACCGGCGATATTT 58.273 55.556 9.30 0.00 43.33 1.40
4627 7285 2.019337 GGCGAACCGGCGATATTTT 58.981 52.632 9.30 0.00 43.33 1.82
4628 7286 0.041576 GGCGAACCGGCGATATTTTC 60.042 55.000 9.30 1.82 43.33 2.29
4637 7295 1.938861 CGATATTTTCGGCGTGGGG 59.061 57.895 6.85 0.00 44.28 4.96
4638 7296 1.503818 CGATATTTTCGGCGTGGGGG 61.504 60.000 6.85 0.00 44.28 5.40
4639 7297 1.792118 GATATTTTCGGCGTGGGGGC 61.792 60.000 6.85 0.00 37.98 5.80
4648 7306 4.096003 CGTGGGGGCGATCAGGTT 62.096 66.667 0.00 0.00 0.00 3.50
4649 7307 2.124695 GTGGGGGCGATCAGGTTC 60.125 66.667 0.00 0.00 0.00 3.62
4650 7308 3.407967 TGGGGGCGATCAGGTTCC 61.408 66.667 0.00 0.00 0.00 3.62
4651 7309 4.191015 GGGGGCGATCAGGTTCCC 62.191 72.222 0.00 0.00 38.03 3.97
4652 7310 3.407967 GGGGCGATCAGGTTCCCA 61.408 66.667 0.00 0.00 40.53 4.37
4653 7311 2.190578 GGGCGATCAGGTTCCCAG 59.809 66.667 0.00 0.00 38.62 4.45
4654 7312 2.514824 GGCGATCAGGTTCCCAGC 60.515 66.667 0.00 0.00 0.00 4.85
4655 7313 2.514824 GCGATCAGGTTCCCAGCC 60.515 66.667 0.00 0.00 0.00 4.85
4656 7314 2.202932 CGATCAGGTTCCCAGCCG 60.203 66.667 0.00 0.00 0.00 5.52
4657 7315 2.514824 GATCAGGTTCCCAGCCGC 60.515 66.667 0.00 0.00 0.00 6.53
4658 7316 4.115199 ATCAGGTTCCCAGCCGCC 62.115 66.667 0.00 0.00 0.00 6.13
4676 7334 4.678743 GCCCCCAGACGCCCTTTT 62.679 66.667 0.00 0.00 0.00 2.27
4677 7335 2.676471 CCCCCAGACGCCCTTTTG 60.676 66.667 0.00 0.00 0.00 2.44
4678 7336 2.115266 CCCCAGACGCCCTTTTGT 59.885 61.111 0.00 0.00 0.00 2.83
4679 7337 1.377229 CCCCAGACGCCCTTTTGTA 59.623 57.895 0.00 0.00 0.00 2.41
4680 7338 0.250989 CCCCAGACGCCCTTTTGTAA 60.251 55.000 0.00 0.00 0.00 2.41
4681 7339 1.611519 CCCAGACGCCCTTTTGTAAA 58.388 50.000 0.00 0.00 0.00 2.01
4682 7340 2.167662 CCCAGACGCCCTTTTGTAAAT 58.832 47.619 0.00 0.00 0.00 1.40
4683 7341 3.349022 CCCAGACGCCCTTTTGTAAATA 58.651 45.455 0.00 0.00 0.00 1.40
4684 7342 3.951680 CCCAGACGCCCTTTTGTAAATAT 59.048 43.478 0.00 0.00 0.00 1.28
4685 7343 4.401202 CCCAGACGCCCTTTTGTAAATATT 59.599 41.667 0.00 0.00 0.00 1.28
4686 7344 5.105513 CCCAGACGCCCTTTTGTAAATATTT 60.106 40.000 5.89 5.89 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.469782 TGCAATCTCAACCTTCTTCTTTTT 57.530 33.333 0.00 0.00 0.00 1.94
36 37 0.322975 AGCCTCATCGCTCACTTTGT 59.677 50.000 0.00 0.00 32.06 2.83
39 40 2.103373 TCTAAGCCTCATCGCTCACTT 58.897 47.619 0.00 0.00 38.44 3.16
96 102 4.935205 CGGTCACAAAAGAATATCAGTCCA 59.065 41.667 0.00 0.00 0.00 4.02
136 142 6.486657 CCAGAACCAAAAAGAGACAAGTATGA 59.513 38.462 0.00 0.00 0.00 2.15
161 169 2.223525 GCTAGATCACACAGTACCCGAC 60.224 54.545 0.00 0.00 0.00 4.79
185 193 4.679373 AATCTTCCTGATCACATAGCGT 57.321 40.909 0.00 0.00 33.57 5.07
201 209 9.612620 GTACAGTCAATTCGAAATTCAAATCTT 57.387 29.630 0.00 0.00 0.00 2.40
203 211 8.237267 AGGTACAGTCAATTCGAAATTCAAATC 58.763 33.333 0.00 0.00 0.00 2.17
232 240 1.604185 GGCACTGATATGAGAGTCGGC 60.604 57.143 0.00 0.00 0.00 5.54
251 287 2.190756 GGTGGAGACCGTCTACAGG 58.809 63.158 14.12 0.00 38.17 4.00
264 300 1.755395 CCGTCTATGGACCGGTGGA 60.755 63.158 14.63 0.00 39.15 4.02
276 312 3.296854 AGCTGGACAATGTATCCGTCTA 58.703 45.455 0.00 0.00 39.30 2.59
336 372 6.239887 GGCATCATTCCCATACCTAAACTCTA 60.240 42.308 0.00 0.00 0.00 2.43
347 383 3.184628 CCCTAGAGGCATCATTCCCATA 58.815 50.000 0.00 0.00 0.00 2.74
373 409 4.023450 CACATAGATGCCATTGTCATCACC 60.023 45.833 10.07 0.00 41.98 4.02
397 433 2.039624 AGGGTCTCGCCAGGACAT 59.960 61.111 0.00 0.00 39.65 3.06
402 438 1.078848 CCAAAGAGGGTCTCGCCAG 60.079 63.158 0.00 0.00 39.65 4.85
410 446 1.823250 GCACACCATTCCAAAGAGGGT 60.823 52.381 0.00 0.00 38.24 4.34
429 465 2.315901 GCACACATAAAAACCTCACGC 58.684 47.619 0.00 0.00 0.00 5.34
468 504 6.811170 TGATTATGAAAAATCAGGCGAAAACC 59.189 34.615 0.00 0.00 40.17 3.27
504 540 5.536161 TCATTGAAAAGAAAGGGGAACTCAG 59.464 40.000 0.00 0.00 0.00 3.35
513 549 7.718272 TTTCTGCATTCATTGAAAAGAAAGG 57.282 32.000 20.27 5.23 31.30 3.11
514 550 9.807386 GAATTTCTGCATTCATTGAAAAGAAAG 57.193 29.630 24.24 14.15 35.34 2.62
573 609 7.658525 TGCCTTCCATACAATTGTGATATTT 57.341 32.000 21.42 0.00 0.00 1.40
580 616 3.098377 TGCATGCCTTCCATACAATTGT 58.902 40.909 16.68 16.68 31.47 2.71
598 634 3.096852 TGGAGGTAACATCCCTGCA 57.903 52.632 0.00 0.00 46.68 4.41
599 635 2.507407 TTTGGAGGTAACATCCCTGC 57.493 50.000 0.00 0.00 40.57 4.85
600 636 5.373812 ACTATTTGGAGGTAACATCCCTG 57.626 43.478 0.00 0.00 35.86 4.45
601 637 5.755849 CAACTATTTGGAGGTAACATCCCT 58.244 41.667 0.00 0.00 35.86 4.20
602 638 4.338400 GCAACTATTTGGAGGTAACATCCC 59.662 45.833 0.00 0.00 35.86 3.85
696 733 9.942850 CATTTGGGAGGTATGAAAACTATTTTT 57.057 29.630 0.00 0.00 37.65 1.94
697 734 9.320295 TCATTTGGGAGGTATGAAAACTATTTT 57.680 29.630 0.00 0.00 35.12 1.82
700 737 9.492730 AAATCATTTGGGAGGTATGAAAACTAT 57.507 29.630 0.00 0.00 32.54 2.12
701 738 8.893563 AAATCATTTGGGAGGTATGAAAACTA 57.106 30.769 0.00 0.00 32.54 2.24
702 739 7.797121 AAATCATTTGGGAGGTATGAAAACT 57.203 32.000 0.00 0.00 32.54 2.66
703 740 8.093927 TCAAAATCATTTGGGAGGTATGAAAAC 58.906 33.333 1.86 0.00 44.88 2.43
746 783 1.215924 ACCCCCGAAAGAAACAGGAAA 59.784 47.619 0.00 0.00 0.00 3.13
749 786 0.400594 AGACCCCCGAAAGAAACAGG 59.599 55.000 0.00 0.00 0.00 4.00
750 787 1.523758 CAGACCCCCGAAAGAAACAG 58.476 55.000 0.00 0.00 0.00 3.16
752 789 0.250770 AGCAGACCCCCGAAAGAAAC 60.251 55.000 0.00 0.00 0.00 2.78
753 790 0.250727 CAGCAGACCCCCGAAAGAAA 60.251 55.000 0.00 0.00 0.00 2.52
755 792 1.415672 AACAGCAGACCCCCGAAAGA 61.416 55.000 0.00 0.00 0.00 2.52
756 793 0.537371 AAACAGCAGACCCCCGAAAG 60.537 55.000 0.00 0.00 0.00 2.62
761 798 2.755103 CTCAATAAAACAGCAGACCCCC 59.245 50.000 0.00 0.00 0.00 5.40
772 809 8.293157 CCAGAAAAGAGAACCTCTCAATAAAAC 58.707 37.037 6.45 0.00 45.73 2.43
780 817 4.620567 GCTCTCCAGAAAAGAGAACCTCTC 60.621 50.000 4.38 0.00 40.28 3.20
785 822 2.028930 TCCGCTCTCCAGAAAAGAGAAC 60.029 50.000 4.38 0.00 42.39 3.01
786 823 2.248248 TCCGCTCTCCAGAAAAGAGAA 58.752 47.619 4.38 0.00 42.39 2.87
788 825 2.977772 ATCCGCTCTCCAGAAAAGAG 57.022 50.000 0.00 0.00 42.62 2.85
790 827 3.604582 AGAAATCCGCTCTCCAGAAAAG 58.395 45.455 0.00 0.00 0.00 2.27
796 835 7.228706 GGATAAATAAAAGAAATCCGCTCTCCA 59.771 37.037 0.00 0.00 0.00 3.86
830 869 1.174712 ATGTGCTGTTGGGCTGTCAC 61.175 55.000 0.00 0.00 0.00 3.67
834 879 2.642254 CCCATGTGCTGTTGGGCTG 61.642 63.158 5.63 0.00 45.83 4.85
844 889 2.378038 TGAGGCTAAATTCCCATGTGC 58.622 47.619 0.00 0.00 0.00 4.57
847 892 3.571401 GTGGATGAGGCTAAATTCCCATG 59.429 47.826 0.00 0.00 0.00 3.66
852 897 4.034510 CGTCAAGTGGATGAGGCTAAATTC 59.965 45.833 0.00 0.00 34.22 2.17
856 901 2.672961 CGTCAAGTGGATGAGGCTAA 57.327 50.000 0.00 0.00 34.22 3.09
860 905 0.247460 TCTGCGTCAAGTGGATGAGG 59.753 55.000 0.00 0.00 38.05 3.86
871 916 4.074526 GCTGGAGGCTCTGCGTCA 62.075 66.667 15.23 2.23 44.00 4.35
872 917 4.828925 GGCTGGAGGCTCTGCGTC 62.829 72.222 15.23 0.76 41.88 5.19
884 929 1.488705 TTGTACCTGGACTGGGCTGG 61.489 60.000 0.00 0.00 0.00 4.85
886 931 1.489560 GGTTGTACCTGGACTGGGCT 61.490 60.000 0.00 0.00 34.73 5.19
887 932 1.002502 GGTTGTACCTGGACTGGGC 60.003 63.158 0.00 0.00 34.73 5.36
888 933 1.295423 CGGTTGTACCTGGACTGGG 59.705 63.158 0.00 0.00 35.66 4.45
889 934 1.375523 GCGGTTGTACCTGGACTGG 60.376 63.158 0.00 0.00 35.66 4.00
893 938 2.162338 CTTCCGCGGTTGTACCTGGA 62.162 60.000 27.15 0.00 38.27 3.86
898 943 0.600782 TTCCACTTCCGCGGTTGTAC 60.601 55.000 27.15 0.00 0.00 2.90
920 965 1.745489 ATTTTCTCGCCAGGTCCGC 60.745 57.895 0.00 0.00 0.00 5.54
921 966 1.369091 CCATTTTCTCGCCAGGTCCG 61.369 60.000 0.00 0.00 0.00 4.79
922 967 0.035439 TCCATTTTCTCGCCAGGTCC 60.035 55.000 0.00 0.00 0.00 4.46
923 968 1.373570 CTCCATTTTCTCGCCAGGTC 58.626 55.000 0.00 0.00 0.00 3.85
924 969 0.035056 CCTCCATTTTCTCGCCAGGT 60.035 55.000 0.00 0.00 0.00 4.00
925 970 0.749454 CCCTCCATTTTCTCGCCAGG 60.749 60.000 0.00 0.00 0.00 4.45
926 971 0.253044 TCCCTCCATTTTCTCGCCAG 59.747 55.000 0.00 0.00 0.00 4.85
927 972 0.695924 TTCCCTCCATTTTCTCGCCA 59.304 50.000 0.00 0.00 0.00 5.69
928 973 1.834188 TTTCCCTCCATTTTCTCGCC 58.166 50.000 0.00 0.00 0.00 5.54
1215 1306 2.029739 TGCGAGATTAAGACACACGGAA 60.030 45.455 0.00 0.00 0.00 4.30
1225 1316 3.707793 GTCAGTACCCTGCGAGATTAAG 58.292 50.000 0.00 0.00 38.66 1.85
1356 1458 3.600388 ACCTACTGTAGATTGCAGTTGC 58.400 45.455 16.22 0.00 43.87 4.17
1357 1459 5.470098 ACAAACCTACTGTAGATTGCAGTTG 59.530 40.000 22.26 9.77 43.87 3.16
1359 1461 6.014499 ACTACAAACCTACTGTAGATTGCAGT 60.014 38.462 21.11 21.11 46.12 4.40
1362 1464 7.519002 CAAACTACAAACCTACTGTAGATTGC 58.481 38.462 22.26 0.00 45.23 3.56
1365 1467 9.654663 GAATCAAACTACAAACCTACTGTAGAT 57.345 33.333 16.22 0.00 46.12 1.98
1366 1468 7.811236 CGAATCAAACTACAAACCTACTGTAGA 59.189 37.037 16.22 0.00 46.12 2.59
1368 1470 7.436118 ACGAATCAAACTACAAACCTACTGTA 58.564 34.615 0.00 0.00 0.00 2.74
1369 1471 6.285990 ACGAATCAAACTACAAACCTACTGT 58.714 36.000 0.00 0.00 0.00 3.55
1370 1472 6.645415 AGACGAATCAAACTACAAACCTACTG 59.355 38.462 0.00 0.00 0.00 2.74
1371 1473 6.645415 CAGACGAATCAAACTACAAACCTACT 59.355 38.462 0.00 0.00 0.00 2.57
1372 1474 6.643770 TCAGACGAATCAAACTACAAACCTAC 59.356 38.462 0.00 0.00 0.00 3.18
1475 1694 3.546815 CCACGCTGAGAAACTCTTTTGTG 60.547 47.826 0.00 0.00 0.00 3.33
1477 1696 2.872245 TCCACGCTGAGAAACTCTTTTG 59.128 45.455 0.00 0.00 0.00 2.44
1532 1751 4.388773 TGCGCACACTTATTCTCTACAAAG 59.611 41.667 5.66 0.00 0.00 2.77
1544 1763 0.998669 CGATGACATGCGCACACTTA 59.001 50.000 14.90 0.00 0.00 2.24
1547 1766 2.400798 CCGATGACATGCGCACAC 59.599 61.111 14.90 7.90 0.00 3.82
1682 1903 0.954452 CAGTGAGGTCCCTTTTGTGC 59.046 55.000 0.00 0.00 0.00 4.57
1922 4543 2.725008 CTTTTCGTGCCGGGCAAA 59.275 55.556 25.70 13.08 41.47 3.68
1931 4552 1.566018 GACCCGTCAGGCTTTTCGTG 61.566 60.000 0.00 0.00 40.58 4.35
2183 4812 0.958822 CTTTACACCCTGCAACCACC 59.041 55.000 0.00 0.00 0.00 4.61
2185 4814 2.969821 ATCTTTACACCCTGCAACCA 57.030 45.000 0.00 0.00 0.00 3.67
2242 4871 2.460330 CAGAAGGCCTGTAAGCACG 58.540 57.895 5.69 0.00 38.10 5.34
2388 5017 2.800250 CCAGCTTTCCTTGGTCTCATT 58.200 47.619 0.00 0.00 0.00 2.57
2579 5213 4.876125 TGTCGCCAAAATATGCAAAGAAA 58.124 34.783 0.00 0.00 0.00 2.52
2660 5294 3.868077 CGTCTAGCTCCTTCCAGATTTTG 59.132 47.826 0.00 0.00 0.00 2.44
2661 5295 3.769844 TCGTCTAGCTCCTTCCAGATTTT 59.230 43.478 0.00 0.00 0.00 1.82
2787 5422 3.855379 CCAACTGAATCATGTTGATTGCG 59.145 43.478 19.63 1.77 46.20 4.85
3038 5673 8.795842 TTGAGTTTTTGAAGTACTCTACCAAA 57.204 30.769 0.00 2.51 39.18 3.28
3060 5695 1.090728 TTGTTTGCTGCGACACTTGA 58.909 45.000 7.98 0.00 0.00 3.02
3209 5845 6.801862 CCTTGACTGTAAATTTTCGATCAACC 59.198 38.462 0.00 0.00 0.00 3.77
3212 5848 6.234920 TCCCTTGACTGTAAATTTTCGATCA 58.765 36.000 0.00 0.00 0.00 2.92
3446 6089 1.550130 TTTGCCTCCAGGTCCTACCG 61.550 60.000 0.00 0.00 44.90 4.02
3546 6195 3.593442 TTTGTCTGGGATCCAAGTTGT 57.407 42.857 16.19 0.00 30.80 3.32
3601 6250 0.882927 GGCAGTTTGTACGCAGTCCA 60.883 55.000 0.00 0.00 43.93 4.02
3642 6291 2.864946 CTGATCCATCTTCAGTTCTGCG 59.135 50.000 0.00 0.00 36.64 5.18
3681 6330 3.580731 GTTCTTCTGAGTGTGTCTAGGC 58.419 50.000 0.00 0.00 0.00 3.93
3730 6379 5.118990 TGAAGAACTTGAGAGTTTGACAGG 58.881 41.667 0.00 0.00 45.88 4.00
3772 6422 8.770753 ATAGCTTAACTACAACGGCTAACGCA 62.771 42.308 0.00 0.00 39.07 5.24
3773 6423 6.465492 ATAGCTTAACTACAACGGCTAACGC 61.465 44.000 0.00 0.00 39.07 4.84
3774 6424 5.039333 ATAGCTTAACTACAACGGCTAACG 58.961 41.667 0.00 0.00 40.55 3.18
3775 6425 5.461407 GGATAGCTTAACTACAACGGCTAAC 59.539 44.000 0.00 0.00 36.19 2.34
3800 6451 2.149578 CAGAGGTTCAGAGTTTGCCTG 58.850 52.381 0.00 0.00 0.00 4.85
3879 6530 5.049405 CAGAAACCAAACTGCAACCTACTAG 60.049 44.000 0.00 0.00 0.00 2.57
3899 6550 5.811613 CACAAACCAAGCAAGAAATTCAGAA 59.188 36.000 0.00 0.00 0.00 3.02
3924 6575 7.194607 TGAGCATACAAGAGTTTCAAGAAAG 57.805 36.000 0.00 0.00 0.00 2.62
3965 6616 2.291741 CAGCAAAGAAGTGGTGTCTTCC 59.708 50.000 3.32 0.00 43.17 3.46
4024 6675 6.449635 AGTCTATCAAGTGCTTCTACTGAG 57.550 41.667 0.00 0.00 0.00 3.35
4132 6783 8.890410 ACCCTTACAGAATCTTACTACTTACA 57.110 34.615 0.00 0.00 0.00 2.41
4157 6808 1.330234 TGTCACGTAGGTTGCCACTA 58.670 50.000 0.00 0.00 0.00 2.74
4162 6813 1.726791 CTCACATGTCACGTAGGTTGC 59.273 52.381 0.00 0.00 0.00 4.17
4181 6832 4.293494 TCTACTTCCATCTTCAGCCATCT 58.707 43.478 0.00 0.00 0.00 2.90
4182 6833 4.100808 ACTCTACTTCCATCTTCAGCCATC 59.899 45.833 0.00 0.00 0.00 3.51
4183 6834 4.036518 ACTCTACTTCCATCTTCAGCCAT 58.963 43.478 0.00 0.00 0.00 4.40
4184 6835 3.445008 ACTCTACTTCCATCTTCAGCCA 58.555 45.455 0.00 0.00 0.00 4.75
4185 6836 4.038642 CCTACTCTACTTCCATCTTCAGCC 59.961 50.000 0.00 0.00 0.00 4.85
4186 6837 4.038642 CCCTACTCTACTTCCATCTTCAGC 59.961 50.000 0.00 0.00 0.00 4.26
4187 6838 5.068460 CACCCTACTCTACTTCCATCTTCAG 59.932 48.000 0.00 0.00 0.00 3.02
4188 6839 4.956700 CACCCTACTCTACTTCCATCTTCA 59.043 45.833 0.00 0.00 0.00 3.02
4189 6840 4.202172 GCACCCTACTCTACTTCCATCTTC 60.202 50.000 0.00 0.00 0.00 2.87
4190 6841 3.707102 GCACCCTACTCTACTTCCATCTT 59.293 47.826 0.00 0.00 0.00 2.40
4191 6842 3.301274 GCACCCTACTCTACTTCCATCT 58.699 50.000 0.00 0.00 0.00 2.90
4192 6843 3.031736 TGCACCCTACTCTACTTCCATC 58.968 50.000 0.00 0.00 0.00 3.51
4193 6844 2.766828 GTGCACCCTACTCTACTTCCAT 59.233 50.000 5.22 0.00 0.00 3.41
4194 6845 2.176889 GTGCACCCTACTCTACTTCCA 58.823 52.381 5.22 0.00 0.00 3.53
4207 6858 0.739561 TACCAAAACAACGTGCACCC 59.260 50.000 12.15 0.00 0.00 4.61
4227 6878 1.270518 GGTCTTGCACAGCTTCTCAGA 60.271 52.381 0.00 0.00 0.00 3.27
4230 6881 1.155042 CTGGTCTTGCACAGCTTCTC 58.845 55.000 0.00 0.00 0.00 2.87
4237 6888 2.418368 ACTGAAACTGGTCTTGCACA 57.582 45.000 0.00 0.00 0.00 4.57
4289 6941 8.243426 GCAAAGGTATCTGTATGATGTCAAAAA 58.757 33.333 0.00 0.00 36.65 1.94
4290 6942 7.611467 AGCAAAGGTATCTGTATGATGTCAAAA 59.389 33.333 0.00 0.00 36.65 2.44
4291 6943 7.112122 AGCAAAGGTATCTGTATGATGTCAAA 58.888 34.615 0.00 0.00 36.65 2.69
4292 6944 6.653020 AGCAAAGGTATCTGTATGATGTCAA 58.347 36.000 0.00 0.00 36.65 3.18
4293 6945 6.239217 AGCAAAGGTATCTGTATGATGTCA 57.761 37.500 0.00 0.00 36.65 3.58
4294 6946 6.540189 ACAAGCAAAGGTATCTGTATGATGTC 59.460 38.462 0.00 0.00 36.65 3.06
4295 6947 6.418101 ACAAGCAAAGGTATCTGTATGATGT 58.582 36.000 0.00 0.00 36.65 3.06
4296 6948 6.932356 ACAAGCAAAGGTATCTGTATGATG 57.068 37.500 0.00 0.00 36.65 3.07
4297 6949 7.944729 AAACAAGCAAAGGTATCTGTATGAT 57.055 32.000 0.00 0.00 39.11 2.45
4298 6950 7.446931 TGAAAACAAGCAAAGGTATCTGTATGA 59.553 33.333 0.00 0.00 0.00 2.15
4299 6951 7.592938 TGAAAACAAGCAAAGGTATCTGTATG 58.407 34.615 0.00 0.00 0.00 2.39
4300 6952 7.094205 CCTGAAAACAAGCAAAGGTATCTGTAT 60.094 37.037 0.00 0.00 0.00 2.29
4301 6953 6.206634 CCTGAAAACAAGCAAAGGTATCTGTA 59.793 38.462 0.00 0.00 0.00 2.74
4302 6954 5.010012 CCTGAAAACAAGCAAAGGTATCTGT 59.990 40.000 0.00 0.00 0.00 3.41
4303 6955 5.010012 ACCTGAAAACAAGCAAAGGTATCTG 59.990 40.000 0.00 0.00 36.28 2.90
4304 6956 5.010012 CACCTGAAAACAAGCAAAGGTATCT 59.990 40.000 0.00 0.00 35.87 1.98
4305 6957 5.222631 CACCTGAAAACAAGCAAAGGTATC 58.777 41.667 0.00 0.00 35.87 2.24
4306 6958 4.501400 GCACCTGAAAACAAGCAAAGGTAT 60.501 41.667 0.00 0.00 35.87 2.73
4307 6959 3.181480 GCACCTGAAAACAAGCAAAGGTA 60.181 43.478 0.00 0.00 35.87 3.08
4308 6960 2.418609 GCACCTGAAAACAAGCAAAGGT 60.419 45.455 0.00 0.00 38.57 3.50
4309 6961 2.204237 GCACCTGAAAACAAGCAAAGG 58.796 47.619 0.00 0.00 0.00 3.11
4310 6962 2.861935 CTGCACCTGAAAACAAGCAAAG 59.138 45.455 0.00 0.00 0.00 2.77
4311 6963 2.495270 TCTGCACCTGAAAACAAGCAAA 59.505 40.909 0.00 0.00 0.00 3.68
4312 6964 2.098614 TCTGCACCTGAAAACAAGCAA 58.901 42.857 0.00 0.00 0.00 3.91
4323 6975 0.530650 AACGTCTGTGTCTGCACCTG 60.531 55.000 0.00 0.00 44.65 4.00
4336 6988 3.146847 GGATTTTGAACCCTGAACGTCT 58.853 45.455 0.00 0.00 0.00 4.18
4338 6990 3.223674 AGGATTTTGAACCCTGAACGT 57.776 42.857 0.00 0.00 0.00 3.99
4388 7046 8.157476 ACAACAATACTACCAGAGAGAAACATT 58.843 33.333 0.00 0.00 0.00 2.71
4391 7049 6.369065 CCACAACAATACTACCAGAGAGAAAC 59.631 42.308 0.00 0.00 0.00 2.78
4392 7050 6.464222 CCACAACAATACTACCAGAGAGAAA 58.536 40.000 0.00 0.00 0.00 2.52
4406 7064 6.352016 ACACATAATTTGGCCACAACAATA 57.648 33.333 3.88 0.00 36.06 1.90
4408 7066 4.679373 ACACATAATTTGGCCACAACAA 57.321 36.364 3.88 0.00 36.06 2.83
4409 7067 5.478332 TGATACACATAATTTGGCCACAACA 59.522 36.000 3.88 0.00 36.06 3.33
4414 7072 7.415592 TTTCATGATACACATAATTTGGCCA 57.584 32.000 0.00 0.00 37.46 5.36
4466 7124 9.880157 GCGGGGAGTATCTATAAATTTGTTATA 57.120 33.333 0.00 0.00 33.73 0.98
4477 7135 2.573462 ACTACCGCGGGGAGTATCTATA 59.427 50.000 31.76 7.38 36.97 1.31
4514 7172 7.039993 GGACAGAACTAAAGGGCAAAATTTAGA 60.040 37.037 10.71 0.00 40.06 2.10
4515 7173 7.039714 AGGACAGAACTAAAGGGCAAAATTTAG 60.040 37.037 0.00 3.75 42.24 1.85
4516 7174 6.780522 AGGACAGAACTAAAGGGCAAAATTTA 59.219 34.615 0.00 0.00 0.00 1.40
4517 7175 5.602561 AGGACAGAACTAAAGGGCAAAATTT 59.397 36.000 0.00 0.00 0.00 1.82
4518 7176 5.011023 CAGGACAGAACTAAAGGGCAAAATT 59.989 40.000 0.00 0.00 0.00 1.82
4519 7177 4.524328 CAGGACAGAACTAAAGGGCAAAAT 59.476 41.667 0.00 0.00 0.00 1.82
4520 7178 3.888930 CAGGACAGAACTAAAGGGCAAAA 59.111 43.478 0.00 0.00 0.00 2.44
4521 7179 3.486383 CAGGACAGAACTAAAGGGCAAA 58.514 45.455 0.00 0.00 0.00 3.68
4522 7180 2.224769 CCAGGACAGAACTAAAGGGCAA 60.225 50.000 0.00 0.00 0.00 4.52
4523 7181 1.351017 CCAGGACAGAACTAAAGGGCA 59.649 52.381 0.00 0.00 0.00 5.36
4524 7182 1.351350 ACCAGGACAGAACTAAAGGGC 59.649 52.381 0.00 0.00 0.00 5.19
4525 7183 3.412386 CAACCAGGACAGAACTAAAGGG 58.588 50.000 0.00 0.00 0.00 3.95
4526 7184 2.814336 GCAACCAGGACAGAACTAAAGG 59.186 50.000 0.00 0.00 0.00 3.11
4527 7185 3.476552 TGCAACCAGGACAGAACTAAAG 58.523 45.455 0.00 0.00 0.00 1.85
4528 7186 3.118038 ACTGCAACCAGGACAGAACTAAA 60.118 43.478 13.64 0.00 43.53 1.85
4529 7187 2.438021 ACTGCAACCAGGACAGAACTAA 59.562 45.455 13.64 0.00 43.53 2.24
4530 7188 2.047061 ACTGCAACCAGGACAGAACTA 58.953 47.619 13.64 0.00 43.53 2.24
4531 7189 0.839946 ACTGCAACCAGGACAGAACT 59.160 50.000 13.64 0.00 43.53 3.01
4532 7190 0.947244 CACTGCAACCAGGACAGAAC 59.053 55.000 13.64 0.00 43.53 3.01
4533 7191 0.546122 ACACTGCAACCAGGACAGAA 59.454 50.000 13.64 0.00 43.53 3.02
4534 7192 0.106708 GACACTGCAACCAGGACAGA 59.893 55.000 13.64 0.00 43.53 3.41
4535 7193 0.107456 AGACACTGCAACCAGGACAG 59.893 55.000 0.00 0.00 43.53 3.51
4536 7194 1.419381 TAGACACTGCAACCAGGACA 58.581 50.000 0.00 0.00 43.53 4.02
4537 7195 2.037251 TCTTAGACACTGCAACCAGGAC 59.963 50.000 0.00 0.00 43.53 3.85
4538 7196 2.300152 CTCTTAGACACTGCAACCAGGA 59.700 50.000 0.00 0.00 43.53 3.86
4539 7197 2.693069 CTCTTAGACACTGCAACCAGG 58.307 52.381 0.00 0.00 43.53 4.45
4540 7198 2.072298 GCTCTTAGACACTGCAACCAG 58.928 52.381 0.00 0.00 44.80 4.00
4541 7199 1.416030 TGCTCTTAGACACTGCAACCA 59.584 47.619 0.00 0.00 0.00 3.67
4542 7200 2.169832 TGCTCTTAGACACTGCAACC 57.830 50.000 0.00 0.00 0.00 3.77
4543 7201 3.594134 AGATGCTCTTAGACACTGCAAC 58.406 45.455 0.00 0.00 37.20 4.17
4544 7202 3.368843 GGAGATGCTCTTAGACACTGCAA 60.369 47.826 0.00 0.00 37.20 4.08
4545 7203 2.167281 GGAGATGCTCTTAGACACTGCA 59.833 50.000 0.00 0.00 38.05 4.41
4546 7204 2.167281 TGGAGATGCTCTTAGACACTGC 59.833 50.000 0.00 0.00 0.00 4.40
4547 7205 3.737663 GCTGGAGATGCTCTTAGACACTG 60.738 52.174 0.00 0.00 0.00 3.66
4548 7206 2.430332 GCTGGAGATGCTCTTAGACACT 59.570 50.000 0.00 0.00 0.00 3.55
4549 7207 2.430332 AGCTGGAGATGCTCTTAGACAC 59.570 50.000 0.00 0.00 35.67 3.67
4550 7208 2.429971 CAGCTGGAGATGCTCTTAGACA 59.570 50.000 5.57 0.00 38.92 3.41
4551 7209 2.430332 ACAGCTGGAGATGCTCTTAGAC 59.570 50.000 19.93 0.00 38.92 2.59
4552 7210 2.744760 ACAGCTGGAGATGCTCTTAGA 58.255 47.619 19.93 0.00 38.92 2.10
4553 7211 3.456280 GAACAGCTGGAGATGCTCTTAG 58.544 50.000 19.93 0.00 38.92 2.18
4554 7212 2.159184 CGAACAGCTGGAGATGCTCTTA 60.159 50.000 19.93 0.00 38.92 2.10
4555 7213 1.405256 CGAACAGCTGGAGATGCTCTT 60.405 52.381 19.93 0.00 38.92 2.85
4556 7214 0.175302 CGAACAGCTGGAGATGCTCT 59.825 55.000 19.93 0.00 38.92 4.09
4557 7215 1.427592 GCGAACAGCTGGAGATGCTC 61.428 60.000 19.93 1.91 44.04 4.26
4558 7216 1.449246 GCGAACAGCTGGAGATGCT 60.449 57.895 19.93 0.00 44.04 3.79
4559 7217 3.096791 GCGAACAGCTGGAGATGC 58.903 61.111 19.93 10.58 44.04 3.91
4607 7265 3.819877 AATATCGCCGGTTCGCCCC 62.820 63.158 1.90 0.00 0.00 5.80
4608 7266 1.441732 AAAATATCGCCGGTTCGCCC 61.442 55.000 1.90 0.00 0.00 6.13
4609 7267 0.041576 GAAAATATCGCCGGTTCGCC 60.042 55.000 1.90 0.00 0.00 5.54
4610 7268 0.382636 CGAAAATATCGCCGGTTCGC 60.383 55.000 1.90 0.00 45.89 4.70
4611 7269 3.702792 CGAAAATATCGCCGGTTCG 57.297 52.632 1.90 4.88 45.89 3.95
4620 7278 1.792118 GCCCCCACGCCGAAAATATC 61.792 60.000 0.00 0.00 0.00 1.63
4621 7279 1.826487 GCCCCCACGCCGAAAATAT 60.826 57.895 0.00 0.00 0.00 1.28
4622 7280 2.438795 GCCCCCACGCCGAAAATA 60.439 61.111 0.00 0.00 0.00 1.40
4631 7289 4.096003 AACCTGATCGCCCCCACG 62.096 66.667 0.00 0.00 0.00 4.94
4632 7290 2.124695 GAACCTGATCGCCCCCAC 60.125 66.667 0.00 0.00 0.00 4.61
4633 7291 3.407967 GGAACCTGATCGCCCCCA 61.408 66.667 0.00 0.00 0.00 4.96
4659 7317 4.678743 AAAAGGGCGTCTGGGGGC 62.679 66.667 0.00 0.00 0.00 5.80
4660 7318 2.132089 TACAAAAGGGCGTCTGGGGG 62.132 60.000 0.00 0.00 0.00 5.40
4661 7319 0.250989 TTACAAAAGGGCGTCTGGGG 60.251 55.000 0.00 0.00 0.00 4.96
4662 7320 1.611519 TTTACAAAAGGGCGTCTGGG 58.388 50.000 0.00 0.00 0.00 4.45
4663 7321 5.576447 AATATTTACAAAAGGGCGTCTGG 57.424 39.130 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.