Multiple sequence alignment - TraesCS2B01G009900

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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 TraesCS2B01G009900 chr2B 100.000 3245 0 0 1 3245 5602155 5605399 0.000000e+00 5993.0
1 TraesCS2B01G009900 chr2B 85.556 180 16 4 10 188 5597220 5597390 2.570000e-41 180.0
2 TraesCS2B01G009900 chr2A 83.113 1510 147 55 507 2009 4323433 4322025 0.000000e+00 1277.0
3 TraesCS2B01G009900 chr2A 87.891 479 48 8 9 480 4323906 4323431 3.660000e-154 555.0
4 TraesCS2B01G009900 chr2A 90.576 191 13 2 2489 2678 4321751 4321565 6.950000e-62 248.0
5 TraesCS2B01G009900 chr2A 90.517 116 9 1 3130 3245 4320830 4320717 5.610000e-33 152.0
6 TraesCS2B01G009900 chr2A 80.874 183 13 11 2880 3040 4321109 4320927 1.220000e-24 124.0
7 TraesCS2B01G009900 chr2D 85.740 1101 76 27 1193 2242 5877284 5876214 0.000000e+00 1088.0
8 TraesCS2B01G009900 chr2D 84.695 771 84 21 393 1148 5878050 5877299 0.000000e+00 739.0
9 TraesCS2B01G009900 chr2D 84.114 491 69 5 669 1158 5886043 5885561 1.760000e-127 466.0
10 TraesCS2B01G009900 chr2D 87.968 374 35 8 16 382 5881991 5881621 1.790000e-117 433.0
11 TraesCS2B01G009900 chr2D 91.739 230 11 3 2268 2497 5876065 5875844 2.430000e-81 313.0
12 TraesCS2B01G009900 chr2D 83.803 142 14 8 2096 2233 5883484 5883348 3.400000e-25 126.0
13 TraesCS2B01G009900 chr2D 89.744 78 8 0 346 423 5890914 5890837 2.060000e-17 100.0
14 TraesCS2B01G009900 chr2D 93.548 62 4 0 2900 2961 5875642 5875581 3.450000e-15 93.5
15 TraesCS2B01G009900 chr2D 88.889 72 4 1 2607 2678 5875844 5875777 5.770000e-13 86.1
16 TraesCS2B01G009900 chr2D 94.872 39 1 1 915 953 355308614 355308651 3.500000e-05 60.2
17 TraesCS2B01G009900 chr6B 91.463 410 22 6 2269 2678 645340056 645339660 4.730000e-153 551.0
18 TraesCS2B01G009900 chr6B 95.732 164 7 0 2095 2258 645340282 645340119 6.900000e-67 265.0
19 TraesCS2B01G009900 chr6B 95.714 70 3 0 2663 2732 645339640 645339571 2.650000e-21 113.0
20 TraesCS2B01G009900 chr7A 87.500 160 18 2 187 344 398270164 398270323 1.990000e-42 183.0
21 TraesCS2B01G009900 chr7A 88.158 152 16 2 187 337 719336177 719336327 2.570000e-41 180.0
22 TraesCS2B01G009900 chr7A 86.420 162 20 2 187 347 719012439 719012599 3.330000e-40 176.0
23 TraesCS2B01G009900 chr7A 100.000 33 0 0 2210 2242 22915249 22915217 9.720000e-06 62.1
24 TraesCS2B01G009900 chr7A 100.000 28 0 0 1666 1693 22897997 22897970 6.000000e-03 52.8
25 TraesCS2B01G009900 chr5B 85.890 163 22 1 187 348 316708985 316709147 4.300000e-39 172.0
26 TraesCS2B01G009900 chr3D 85.890 163 22 1 186 347 449740281 449740443 4.300000e-39 172.0
27 TraesCS2B01G009900 chrUn 86.842 152 19 1 186 336 47689588 47689739 5.570000e-38 169.0
28 TraesCS2B01G009900 chr7D 85.185 162 23 1 187 347 199348845 199349006 7.200000e-37 165.0
29 TraesCS2B01G009900 chr7D 88.000 50 6 0 1666 1715 22269876 22269827 3.500000e-05 60.2
30 TraesCS2B01G009900 chr7D 100.000 28 0 0 1666 1693 22522630 22522603 6.000000e-03 52.8


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 TraesCS2B01G009900 chr2B 5602155 5605399 3244 False 5993.000000 5993 100.0000 1 3245 1 chr2B.!!$F2 3244
1 TraesCS2B01G009900 chr2A 4320717 4323906 3189 True 471.200000 1277 86.5942 9 3245 5 chr2A.!!$R1 3236
2 TraesCS2B01G009900 chr2D 5875581 5886043 10462 True 418.075000 1088 87.5620 16 2961 8 chr2D.!!$R2 2945
3 TraesCS2B01G009900 chr6B 645339571 645340282 711 True 309.666667 551 94.3030 2095 2732 3 chr6B.!!$R1 637

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
797 8415 0.098200 CGCTGATGGTTGCATGTCAG 59.902 55.0 11.55 11.55 40.71 3.51 F
1457 9105 0.316841 GAGAAGCTAGGCCGGATCTG 59.683 60.0 5.05 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2064 9778 0.254462 TCGCTATGGCACCAAATCCA 59.746 50.0 0.74 0.0 38.6 3.41 R
3119 11281 0.036875 AAGGAAAACAGCGAGAGGGG 59.963 55.0 0.00 0.0 0.0 4.79 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 4074 6.098124 TCCAGAAATTGATGGCGGAATATTTT 59.902 34.615 4.61 0.00 36.47 1.82
199 4241 3.643237 TCGATCCATACTCCCTCTGTTT 58.357 45.455 0.00 0.00 0.00 2.83
356 4400 8.934023 AAGAACAAAGGGAGTATTATTTGTCA 57.066 30.769 2.95 0.00 43.17 3.58
459 8063 5.275067 ACTCTCATTGCTCCTCAAGATAC 57.725 43.478 0.00 0.00 38.22 2.24
469 8073 8.668510 TTGCTCCTCAAGATACTATCAAATTC 57.331 34.615 0.00 0.00 0.00 2.17
556 8162 5.842907 TGCTAGATACGTATGTTTCTGCAT 58.157 37.500 13.97 0.00 37.07 3.96
559 8165 5.409643 AGATACGTATGTTTCTGCATTGC 57.590 39.130 13.97 0.46 35.43 3.56
578 8184 6.633683 CATTGCGATATTGAAATCAGTTTGC 58.366 36.000 0.00 0.00 0.00 3.68
586 8192 9.585099 GATATTGAAATCAGTTTGCCAATACAA 57.415 29.630 0.00 0.00 31.94 2.41
587 8193 9.941325 ATATTGAAATCAGTTTGCCAATACAAA 57.059 25.926 0.00 0.00 37.20 2.83
653 8271 3.599285 GAATCGGCCGTGTCACCCA 62.599 63.158 27.15 2.48 0.00 4.51
667 8285 3.437795 CCCAAGCTTGCCTGCTCG 61.438 66.667 21.43 5.31 43.24 5.03
675 8293 2.994387 CTTGCCTGCTCGTCCACACA 62.994 60.000 0.00 0.00 0.00 3.72
713 8331 9.227777 GGAATTTCTTTTAAGTAAGACCTAGCA 57.772 33.333 0.00 0.00 34.04 3.49
718 8336 9.569122 TTCTTTTAAGTAAGACCTAGCAAACAT 57.431 29.630 0.00 0.00 34.04 2.71
729 8347 2.745884 CAAACATCGCCGCCTCCA 60.746 61.111 0.00 0.00 0.00 3.86
751 8369 2.573915 GCCCTATCCTCCCTTCCTAATG 59.426 54.545 0.00 0.00 0.00 1.90
791 8409 2.672651 CCACCGCTGATGGTTGCA 60.673 61.111 0.00 0.00 41.38 4.08
795 8413 1.308069 ACCGCTGATGGTTGCATGTC 61.308 55.000 0.00 0.00 39.99 3.06
797 8415 0.098200 CGCTGATGGTTGCATGTCAG 59.902 55.000 11.55 11.55 40.71 3.51
802 8420 1.601419 ATGGTTGCATGTCAGCTGGC 61.601 55.000 12.53 12.53 34.99 4.85
813 8431 0.469705 TCAGCTGGCATTTGTTGGGT 60.470 50.000 15.13 0.00 0.00 4.51
816 8434 1.490069 AGCTGGCATTTGTTGGGTTTT 59.510 42.857 0.00 0.00 0.00 2.43
817 8435 2.092484 AGCTGGCATTTGTTGGGTTTTT 60.092 40.909 0.00 0.00 0.00 1.94
822 8440 4.133820 GGCATTTGTTGGGTTTTTAAGCT 58.866 39.130 0.00 0.00 0.00 3.74
826 8444 6.565811 GCATTTGTTGGGTTTTTAAGCTTAGC 60.566 38.462 6.24 0.00 0.00 3.09
842 8460 3.057315 GCTTAGCAGCTTGGAACAATCAA 60.057 43.478 0.00 0.00 43.51 2.57
855 8473 5.420421 TGGAACAATCAACAAGTTTTCCTCA 59.580 36.000 12.16 0.00 31.92 3.86
865 8483 8.744652 TCAACAAGTTTTCCTCATGTAAGAAAA 58.255 29.630 12.86 12.86 37.20 2.29
866 8484 9.364989 CAACAAGTTTTCCTCATGTAAGAAAAA 57.635 29.630 16.31 0.00 40.20 1.94
890 8508 4.508551 AAGGTATCAGTTCATGGATGCA 57.491 40.909 0.00 0.00 0.00 3.96
980 8598 4.471904 TTCTAGTCCTGCATTCATTCGT 57.528 40.909 0.00 0.00 0.00 3.85
990 8608 3.252944 TGCATTCATTCGTGAACACATGT 59.747 39.130 0.00 0.00 0.00 3.21
995 8613 7.096271 GCATTCATTCGTGAACACATGTTTTTA 60.096 33.333 0.00 0.00 38.56 1.52
1048 8666 8.818141 ATAGTACGGATGAATTTATCACAGTG 57.182 34.615 11.86 0.00 41.93 3.66
1051 8669 4.883585 ACGGATGAATTTATCACAGTGCAT 59.116 37.500 11.86 0.00 41.93 3.96
1052 8670 5.209977 CGGATGAATTTATCACAGTGCATG 58.790 41.667 11.86 0.00 41.93 4.06
1061 8679 9.539825 AATTTATCACAGTGCATGTTTTAAACA 57.460 25.926 13.12 13.12 46.94 2.83
1064 8682 7.642071 ATCACAGTGCATGTTTTAAACAATC 57.358 32.000 14.70 9.63 45.86 2.67
1190 8823 6.691754 TTTTTGAGAATCTGCTGTGTAACA 57.308 33.333 0.00 0.00 40.28 2.41
1191 8824 6.691754 TTTTGAGAATCTGCTGTGTAACAA 57.308 33.333 0.00 0.00 41.77 2.83
1212 8845 3.760580 TTTGGTTGCAAATTCGGGATT 57.239 38.095 0.00 0.00 0.00 3.01
1220 8853 1.067213 CAAATTCGGGATTGGGCGTTT 60.067 47.619 0.00 0.00 0.00 3.60
1233 8866 3.213402 CGTTTGTGGGCCGTGGTT 61.213 61.111 0.00 0.00 0.00 3.67
1262 8895 1.410153 CAGCCAGCCAAGAAACAAAGT 59.590 47.619 0.00 0.00 0.00 2.66
1276 8909 6.064060 AGAAACAAAGTTGATGGATGAGTCA 58.936 36.000 0.00 0.00 0.00 3.41
1285 8918 2.905415 TGGATGAGTCAGCCCATTTT 57.095 45.000 24.26 0.00 39.46 1.82
1286 8919 2.449464 TGGATGAGTCAGCCCATTTTG 58.551 47.619 24.26 0.00 39.46 2.44
1424 9072 5.514914 CGAGAGAGAGAGGAAATTTCTTTCG 59.485 44.000 17.42 10.29 41.45 3.46
1457 9105 0.316841 GAGAAGCTAGGCCGGATCTG 59.683 60.000 5.05 0.00 0.00 2.90
1459 9107 0.972883 GAAGCTAGGCCGGATCTGAT 59.027 55.000 5.05 0.00 0.00 2.90
1505 9153 4.430765 CAGGTTCTACGGCGGCGT 62.431 66.667 38.68 38.68 0.00 5.68
1790 9462 3.519930 GGAGGAGTCCGGCGAGTC 61.520 72.222 9.30 7.05 37.68 3.36
1791 9463 3.878519 GAGGAGTCCGGCGAGTCG 61.879 72.222 9.30 8.54 39.09 4.18
1800 9472 4.176851 GGCGAGTCGGACGAGGAC 62.177 72.222 15.52 0.00 34.62 3.85
1801 9473 3.126225 GCGAGTCGGACGAGGACT 61.126 66.667 15.52 7.33 46.91 3.85
1804 9476 2.045143 AGTCGGACGAGGACTCCC 60.045 66.667 1.89 0.00 40.63 4.30
1805 9477 3.139469 GTCGGACGAGGACTCCCC 61.139 72.222 0.00 0.00 0.00 4.81
1806 9478 4.790962 TCGGACGAGGACTCCCCG 62.791 72.222 16.74 16.74 40.97 5.73
1808 9480 4.437587 GGACGAGGACTCCCCGGA 62.438 72.222 0.73 0.00 40.87 5.14
1809 9481 3.139469 GACGAGGACTCCCCGGAC 61.139 72.222 0.73 0.00 40.87 4.79
1810 9482 3.641925 GACGAGGACTCCCCGGACT 62.642 68.421 0.73 0.00 40.87 3.85
1811 9483 2.829458 CGAGGACTCCCCGGACTC 60.829 72.222 0.73 0.00 40.87 3.36
1812 9484 2.442458 GAGGACTCCCCGGACTCC 60.442 72.222 0.73 0.13 40.87 3.85
1986 9700 1.518302 GACGAGGAAGAGGAAGGCC 59.482 63.158 0.00 0.00 0.00 5.19
2056 9770 4.439289 GCTAATGGTCCACTTCTTTGATGC 60.439 45.833 0.00 0.00 0.00 3.91
2057 9771 1.522668 TGGTCCACTTCTTTGATGCG 58.477 50.000 0.00 0.00 0.00 4.73
2058 9772 1.202758 TGGTCCACTTCTTTGATGCGT 60.203 47.619 0.00 0.00 0.00 5.24
2061 9775 3.125316 GGTCCACTTCTTTGATGCGTTAG 59.875 47.826 0.00 0.00 0.00 2.34
2062 9776 3.994392 GTCCACTTCTTTGATGCGTTAGA 59.006 43.478 0.00 0.00 0.00 2.10
2063 9777 4.631813 GTCCACTTCTTTGATGCGTTAGAT 59.368 41.667 0.00 0.00 0.00 1.98
2064 9778 5.122396 GTCCACTTCTTTGATGCGTTAGATT 59.878 40.000 0.00 0.00 0.00 2.40
2067 9781 5.122239 CACTTCTTTGATGCGTTAGATTGGA 59.878 40.000 0.00 0.00 0.00 3.53
2068 9782 5.882557 ACTTCTTTGATGCGTTAGATTGGAT 59.117 36.000 0.00 0.00 0.00 3.41
2070 9784 6.757897 TCTTTGATGCGTTAGATTGGATTT 57.242 33.333 0.00 0.00 0.00 2.17
2071 9785 6.554419 TCTTTGATGCGTTAGATTGGATTTG 58.446 36.000 0.00 0.00 0.00 2.32
2072 9786 4.898829 TGATGCGTTAGATTGGATTTGG 57.101 40.909 0.00 0.00 0.00 3.28
2073 9787 4.269183 TGATGCGTTAGATTGGATTTGGT 58.731 39.130 0.00 0.00 0.00 3.67
2074 9788 4.096231 TGATGCGTTAGATTGGATTTGGTG 59.904 41.667 0.00 0.00 0.00 4.17
2075 9789 2.163412 TGCGTTAGATTGGATTTGGTGC 59.837 45.455 0.00 0.00 0.00 5.01
2084 9798 0.663153 GGATTTGGTGCCATAGCGAC 59.337 55.000 0.00 0.00 44.31 5.19
2087 9801 0.676466 TTTGGTGCCATAGCGACTGG 60.676 55.000 0.00 0.00 44.31 4.00
2114 9832 3.420214 CTTGGTGATGCCGCATGCC 62.420 63.158 11.49 12.97 41.21 4.40
2125 9843 2.376538 CGCATGCCGTGTGTTCGTA 61.377 57.895 13.15 0.00 33.61 3.43
2178 9896 7.237263 AGTGCTCCTATATCTGAATCAAATCCT 59.763 37.037 0.00 0.00 0.00 3.24
2272 10116 3.805422 TGAACATCGTCTTGTGTAACCAC 59.195 43.478 0.00 0.00 42.19 4.16
2322 10166 9.661187 CAATCTGAATTCAAATGCTACATCTAC 57.339 33.333 9.88 0.00 0.00 2.59
2330 10174 8.710835 TTCAAATGCTACATCTACGAACATTA 57.289 30.769 0.00 0.00 0.00 1.90
2341 10185 9.778741 ACATCTACGAACATTACCAATATGAAT 57.221 29.630 0.00 0.00 0.00 2.57
2351 10195 8.850156 ACATTACCAATATGAATTGCTACTTCC 58.150 33.333 0.00 0.00 41.06 3.46
2374 10218 6.884295 TCCTAGTAACACCATTTTTGATCAGG 59.116 38.462 0.00 0.00 0.00 3.86
2422 10266 2.238521 TCCCCAATCTGTTCTTGTTGC 58.761 47.619 0.00 0.00 0.00 4.17
2435 10279 3.602483 TCTTGTTGCTACCGGGATTTAC 58.398 45.455 6.32 0.00 0.00 2.01
2439 10283 0.176219 TGCTACCGGGATTTACGTGG 59.824 55.000 6.32 0.00 0.00 4.94
2440 10284 0.531311 GCTACCGGGATTTACGTGGG 60.531 60.000 6.32 0.00 0.00 4.61
2441 10285 0.531311 CTACCGGGATTTACGTGGGC 60.531 60.000 6.32 0.00 0.00 5.36
2442 10286 0.977108 TACCGGGATTTACGTGGGCT 60.977 55.000 6.32 0.00 0.00 5.19
2656 10501 8.344831 CAATCTGTTCTTGTTCATGTTGAGTAA 58.655 33.333 0.00 0.00 0.00 2.24
2657 10502 7.482654 TCTGTTCTTGTTCATGTTGAGTAAG 57.517 36.000 0.00 0.00 0.00 2.34
2659 10504 8.201464 TCTGTTCTTGTTCATGTTGAGTAAGTA 58.799 33.333 0.00 0.00 0.00 2.24
2660 10505 8.138365 TGTTCTTGTTCATGTTGAGTAAGTAC 57.862 34.615 0.00 0.00 30.24 2.73
2661 10506 7.766738 TGTTCTTGTTCATGTTGAGTAAGTACA 59.233 33.333 0.00 0.00 33.60 2.90
2705 10651 6.308766 GGCAAATAAGTGTATTGCTGAAAGTG 59.691 38.462 9.28 0.00 35.30 3.16
2722 10668 1.145819 TGCCTTTGCCAAACCAAGC 59.854 52.632 0.00 0.00 36.33 4.01
2738 10684 3.940209 CAAGCTGACCTTGGCAAATAA 57.060 42.857 0.00 0.00 45.78 1.40
2739 10685 3.841643 CAAGCTGACCTTGGCAAATAAG 58.158 45.455 0.00 0.00 45.78 1.73
2740 10686 1.821136 AGCTGACCTTGGCAAATAAGC 59.179 47.619 11.09 11.09 0.00 3.09
2757 10703 2.327228 GCCGTTGCTTGGTACTGTT 58.673 52.632 0.00 0.00 33.53 3.16
2761 10707 2.552315 CCGTTGCTTGGTACTGTTTCAT 59.448 45.455 0.00 0.00 0.00 2.57
2762 10708 3.554524 CGTTGCTTGGTACTGTTTCATG 58.445 45.455 0.00 0.00 0.00 3.07
2763 10709 3.003275 CGTTGCTTGGTACTGTTTCATGT 59.997 43.478 0.00 0.00 0.00 3.21
2764 10710 4.212425 CGTTGCTTGGTACTGTTTCATGTA 59.788 41.667 0.00 0.00 0.00 2.29
2765 10711 5.449304 GTTGCTTGGTACTGTTTCATGTAC 58.551 41.667 0.00 0.00 38.52 2.90
2766 10712 4.968259 TGCTTGGTACTGTTTCATGTACT 58.032 39.130 0.00 0.00 39.04 2.73
2767 10713 6.104146 TGCTTGGTACTGTTTCATGTACTA 57.896 37.500 0.00 0.00 39.04 1.82
2768 10714 6.707290 TGCTTGGTACTGTTTCATGTACTAT 58.293 36.000 0.00 0.00 39.04 2.12
2769 10715 6.593770 TGCTTGGTACTGTTTCATGTACTATG 59.406 38.462 0.00 0.00 39.04 2.23
2770 10716 6.594159 GCTTGGTACTGTTTCATGTACTATGT 59.406 38.462 0.00 0.00 39.04 2.29
2772 10718 8.911918 TTGGTACTGTTTCATGTACTATGTTT 57.088 30.769 0.00 0.00 39.04 2.83
2773 10719 8.911918 TGGTACTGTTTCATGTACTATGTTTT 57.088 30.769 0.00 0.00 39.04 2.43
2774 10720 9.344772 TGGTACTGTTTCATGTACTATGTTTTT 57.655 29.630 0.00 0.00 39.04 1.94
2820 10766 8.786937 ATTTAATAATGATCGTTGTGTGCATC 57.213 30.769 10.54 0.00 0.00 3.91
2821 10767 7.552458 TTAATAATGATCGTTGTGTGCATCT 57.448 32.000 10.54 0.00 0.00 2.90
2822 10768 6.441093 AATAATGATCGTTGTGTGCATCTT 57.559 33.333 10.54 0.00 0.00 2.40
2823 10769 4.771590 AATGATCGTTGTGTGCATCTTT 57.228 36.364 0.00 0.00 0.00 2.52
2824 10770 4.771590 ATGATCGTTGTGTGCATCTTTT 57.228 36.364 0.00 0.00 0.00 2.27
2825 10771 3.887741 TGATCGTTGTGTGCATCTTTTG 58.112 40.909 0.00 0.00 0.00 2.44
2826 10772 3.563390 TGATCGTTGTGTGCATCTTTTGA 59.437 39.130 0.00 0.00 0.00 2.69
2827 10773 4.216042 TGATCGTTGTGTGCATCTTTTGAT 59.784 37.500 0.00 0.00 40.34 2.57
2841 10787 4.728772 TCTTTTGATGTATGGGCCTATGG 58.271 43.478 12.67 0.00 0.00 2.74
2842 10788 4.167892 TCTTTTGATGTATGGGCCTATGGT 59.832 41.667 12.67 0.00 0.00 3.55
2843 10789 4.534647 TTTGATGTATGGGCCTATGGTT 57.465 40.909 12.67 0.00 0.00 3.67
2844 10790 4.534647 TTGATGTATGGGCCTATGGTTT 57.465 40.909 12.67 0.00 0.00 3.27
2845 10791 4.534647 TGATGTATGGGCCTATGGTTTT 57.465 40.909 12.67 0.00 0.00 2.43
2847 10793 4.079500 TGATGTATGGGCCTATGGTTTTCA 60.080 41.667 12.67 5.07 0.00 2.69
2848 10794 4.323569 TGTATGGGCCTATGGTTTTCAA 57.676 40.909 12.67 0.00 0.00 2.69
2849 10795 4.277476 TGTATGGGCCTATGGTTTTCAAG 58.723 43.478 12.67 0.00 0.00 3.02
2850 10796 1.555967 TGGGCCTATGGTTTTCAAGC 58.444 50.000 4.53 0.00 0.00 4.01
2851 10797 1.077005 TGGGCCTATGGTTTTCAAGCT 59.923 47.619 4.53 0.00 0.00 3.74
2852 10798 1.751351 GGGCCTATGGTTTTCAAGCTC 59.249 52.381 0.84 0.00 0.00 4.09
2853 10799 1.751351 GGCCTATGGTTTTCAAGCTCC 59.249 52.381 0.00 0.00 0.00 4.70
2854 10800 2.621668 GGCCTATGGTTTTCAAGCTCCT 60.622 50.000 0.00 0.00 0.00 3.69
2857 10803 4.021104 GCCTATGGTTTTCAAGCTCCTTTT 60.021 41.667 0.00 0.00 0.00 2.27
2863 10949 6.234177 TGGTTTTCAAGCTCCTTTTCAAAAA 58.766 32.000 0.00 0.00 0.00 1.94
2891 10986 7.797121 ATCTGGATAAAAATCTGTTTTGGGT 57.203 32.000 0.00 0.00 37.59 4.51
2961 11058 0.322546 GTTGGCACCCCCTTCAGTAG 60.323 60.000 0.00 0.00 0.00 2.57
2962 11059 0.474854 TTGGCACCCCCTTCAGTAGA 60.475 55.000 0.00 0.00 0.00 2.59
2963 11060 0.474854 TGGCACCCCCTTCAGTAGAA 60.475 55.000 0.00 0.00 0.00 2.10
2964 11061 0.035343 GGCACCCCCTTCAGTAGAAC 60.035 60.000 0.00 0.00 0.00 3.01
2965 11062 0.690762 GCACCCCCTTCAGTAGAACA 59.309 55.000 0.00 0.00 0.00 3.18
2966 11063 1.282157 GCACCCCCTTCAGTAGAACAT 59.718 52.381 0.00 0.00 0.00 2.71
2968 11065 2.840651 CACCCCCTTCAGTAGAACATCT 59.159 50.000 0.00 0.00 0.00 2.90
2969 11066 3.108376 ACCCCCTTCAGTAGAACATCTC 58.892 50.000 0.00 0.00 0.00 2.75
2970 11067 2.436173 CCCCCTTCAGTAGAACATCTCC 59.564 54.545 0.00 0.00 0.00 3.71
2972 11069 3.133721 CCCCTTCAGTAGAACATCTCCTG 59.866 52.174 0.00 0.00 32.45 3.86
2974 11071 4.956700 CCCTTCAGTAGAACATCTCCTGTA 59.043 45.833 0.75 0.00 36.98 2.74
2986 11103 8.912988 AGAACATCTCCTGTAGAAGATAAGAAG 58.087 37.037 0.00 0.00 36.98 2.85
3022 11139 3.575687 AGAAATGAAGAGCCCACTTTTGG 59.424 43.478 0.00 0.00 43.50 3.28
3040 11157 7.715249 CACTTTTGGCAGGTAGCTAAGATTATA 59.285 37.037 8.09 0.00 44.89 0.98
3042 11159 6.740944 TTGGCAGGTAGCTAAGATTATACA 57.259 37.500 0.00 0.00 44.79 2.29
3044 11161 6.075315 TGGCAGGTAGCTAAGATTATACAGA 58.925 40.000 0.00 0.00 44.79 3.41
3045 11162 6.726299 TGGCAGGTAGCTAAGATTATACAGAT 59.274 38.462 0.00 0.00 44.79 2.90
3046 11163 7.038659 GGCAGGTAGCTAAGATTATACAGATG 58.961 42.308 0.00 0.00 44.79 2.90
3047 11164 6.533367 GCAGGTAGCTAAGATTATACAGATGC 59.467 42.308 0.00 0.00 41.15 3.91
3048 11165 7.606349 CAGGTAGCTAAGATTATACAGATGCA 58.394 38.462 0.00 0.00 0.00 3.96
3049 11166 7.758980 CAGGTAGCTAAGATTATACAGATGCAG 59.241 40.741 0.00 0.00 0.00 4.41
3068 11230 7.558807 AGATGCAGTTTCTTCAATCATGGATAA 59.441 33.333 0.00 0.00 0.00 1.75
3095 11257 9.734984 AACATACTTTGTAATTTGTAGGTAGCT 57.265 29.630 0.00 0.00 37.68 3.32
3096 11258 9.379791 ACATACTTTGTAATTTGTAGGTAGCTC 57.620 33.333 0.00 0.00 36.57 4.09
3097 11259 8.827677 CATACTTTGTAATTTGTAGGTAGCTCC 58.172 37.037 0.00 0.00 0.00 4.70
3098 11260 6.178324 ACTTTGTAATTTGTAGGTAGCTCCC 58.822 40.000 0.00 0.00 36.75 4.30
3099 11261 5.765576 TTGTAATTTGTAGGTAGCTCCCA 57.234 39.130 0.00 0.00 36.75 4.37
3100 11262 5.968676 TGTAATTTGTAGGTAGCTCCCAT 57.031 39.130 0.00 0.00 36.75 4.00
3101 11263 6.321821 TGTAATTTGTAGGTAGCTCCCATT 57.678 37.500 0.00 0.00 36.75 3.16
3102 11264 6.727394 TGTAATTTGTAGGTAGCTCCCATTT 58.273 36.000 0.00 0.00 36.75 2.32
3103 11265 6.826741 TGTAATTTGTAGGTAGCTCCCATTTC 59.173 38.462 0.00 0.00 36.75 2.17
3104 11266 5.717119 ATTTGTAGGTAGCTCCCATTTCT 57.283 39.130 0.00 0.00 36.75 2.52
3105 11267 4.755266 TTGTAGGTAGCTCCCATTTCTC 57.245 45.455 0.00 0.00 36.75 2.87
3106 11268 2.693591 TGTAGGTAGCTCCCATTTCTCG 59.306 50.000 0.00 0.00 36.75 4.04
3107 11269 2.160721 AGGTAGCTCCCATTTCTCGA 57.839 50.000 0.00 0.00 36.75 4.04
3108 11270 2.683768 AGGTAGCTCCCATTTCTCGAT 58.316 47.619 0.00 0.00 36.75 3.59
3109 11271 2.630580 AGGTAGCTCCCATTTCTCGATC 59.369 50.000 0.00 0.00 36.75 3.69
3110 11272 2.289133 GGTAGCTCCCATTTCTCGATCC 60.289 54.545 0.00 0.00 0.00 3.36
3111 11273 1.799933 AGCTCCCATTTCTCGATCCT 58.200 50.000 0.00 0.00 0.00 3.24
3112 11274 2.122768 AGCTCCCATTTCTCGATCCTT 58.877 47.619 0.00 0.00 0.00 3.36
3113 11275 2.158842 AGCTCCCATTTCTCGATCCTTG 60.159 50.000 0.00 0.00 0.00 3.61
3114 11276 2.420687 GCTCCCATTTCTCGATCCTTGT 60.421 50.000 0.00 0.00 0.00 3.16
3115 11277 3.181465 GCTCCCATTTCTCGATCCTTGTA 60.181 47.826 0.00 0.00 0.00 2.41
3116 11278 4.503991 GCTCCCATTTCTCGATCCTTGTAT 60.504 45.833 0.00 0.00 0.00 2.29
3117 11279 5.279506 GCTCCCATTTCTCGATCCTTGTATA 60.280 44.000 0.00 0.00 0.00 1.47
3118 11280 6.575254 GCTCCCATTTCTCGATCCTTGTATAT 60.575 42.308 0.00 0.00 0.00 0.86
3119 11281 6.936279 TCCCATTTCTCGATCCTTGTATATC 58.064 40.000 0.00 0.00 0.00 1.63
3120 11282 6.070767 TCCCATTTCTCGATCCTTGTATATCC 60.071 42.308 0.00 0.00 0.00 2.59
3121 11283 6.109359 CCATTTCTCGATCCTTGTATATCCC 58.891 44.000 0.00 0.00 0.00 3.85
3122 11284 5.740290 TTTCTCGATCCTTGTATATCCCC 57.260 43.478 0.00 0.00 0.00 4.81
3123 11285 4.676799 TCTCGATCCTTGTATATCCCCT 57.323 45.455 0.00 0.00 0.00 4.79
3126 11288 4.601084 TCGATCCTTGTATATCCCCTCTC 58.399 47.826 0.00 0.00 0.00 3.20
3128 11290 2.526432 TCCTTGTATATCCCCTCTCGC 58.474 52.381 0.00 0.00 0.00 5.03
3238 11400 2.653726 TGGCACTTCAATTCAGTGTGT 58.346 42.857 13.49 0.00 43.21 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.576118 TCCGCCATCAATTTCTGGAAAAA 59.424 39.130 7.15 0.00 34.24 1.94
8 9 3.161067 TCCGCCATCAATTTCTGGAAAA 58.839 40.909 7.15 0.00 34.24 2.29
9 10 2.801483 TCCGCCATCAATTTCTGGAAA 58.199 42.857 7.15 0.00 34.24 3.13
10 11 2.505650 TCCGCCATCAATTTCTGGAA 57.494 45.000 7.15 0.00 34.24 3.53
11 12 2.505650 TTCCGCCATCAATTTCTGGA 57.494 45.000 7.15 0.00 34.24 3.86
12 13 5.458041 AATATTCCGCCATCAATTTCTGG 57.542 39.130 0.00 0.00 35.53 3.86
13 14 6.979817 TGAAAATATTCCGCCATCAATTTCTG 59.020 34.615 0.00 0.00 34.49 3.02
14 15 7.111247 TGAAAATATTCCGCCATCAATTTCT 57.889 32.000 0.00 0.00 34.49 2.52
103 4141 9.687717 GTTTCCATGATTTGTAAAATTAATGCG 57.312 29.630 0.00 0.00 0.00 4.73
124 4166 8.986477 AAGTAGTTGCAATAAATGATGTTTCC 57.014 30.769 0.59 0.00 0.00 3.13
152 4194 8.877864 AGGGAGTACAATTAATGATGTTTTCA 57.122 30.769 0.00 0.00 39.12 2.69
213 4255 9.322773 TGCAGTCTATATTGAAATCTCTGAAAG 57.677 33.333 6.10 0.00 0.00 2.62
214 4256 9.842775 ATGCAGTCTATATTGAAATCTCTGAAA 57.157 29.630 0.00 0.00 0.00 2.69
265 4307 9.846248 ACAAAGCAAAATAATGAATCTACACTC 57.154 29.630 0.00 0.00 0.00 3.51
332 4376 9.533831 AATGACAAATAATACTCCCTTTGTTCT 57.466 29.630 0.00 0.00 40.76 3.01
365 4409 7.224753 CGCCACTGATTTAGTATGAAGTTGTAT 59.775 37.037 0.00 0.00 37.60 2.29
387 4431 3.767131 TCTCCGATCCATATTAATCGCCA 59.233 43.478 9.86 0.92 42.57 5.69
388 4432 4.098044 TCTCTCCGATCCATATTAATCGCC 59.902 45.833 9.86 0.00 42.57 5.54
389 4433 5.163602 ACTCTCTCCGATCCATATTAATCGC 60.164 44.000 9.86 0.00 42.57 4.58
448 8052 8.206867 CACCTGAATTTGATAGTATCTTGAGGA 58.793 37.037 17.44 0.00 0.00 3.71
459 8063 5.375417 TGCAACACACCTGAATTTGATAG 57.625 39.130 0.00 0.00 0.00 2.08
469 8073 4.639824 GCACATGCAACACACCTG 57.360 55.556 0.00 0.00 41.59 4.00
489 8094 9.683069 AATGCGACAAAGATAATTTCCATAATC 57.317 29.630 0.00 0.00 0.00 1.75
531 8137 6.103330 TGCAGAAACATACGTATCTAGCAAA 58.897 36.000 4.74 0.00 0.00 3.68
532 8138 5.656480 TGCAGAAACATACGTATCTAGCAA 58.344 37.500 4.74 0.00 0.00 3.91
533 8139 5.257082 TGCAGAAACATACGTATCTAGCA 57.743 39.130 4.74 10.14 0.00 3.49
552 8158 5.503662 ACTGATTTCAATATCGCAATGCA 57.496 34.783 5.91 0.00 0.00 3.96
556 8162 5.101628 GGCAAACTGATTTCAATATCGCAA 58.898 37.500 0.00 0.00 0.00 4.85
559 8165 7.914871 TGTATTGGCAAACTGATTTCAATATCG 59.085 33.333 3.01 0.00 32.20 2.92
615 8221 9.037737 CCGATTCGGTTCTCATAAAAAGTATAA 57.962 33.333 17.08 0.00 42.73 0.98
634 8252 3.186047 GGTGACACGGCCGATTCG 61.186 66.667 35.90 19.05 0.00 3.34
635 8253 2.818274 GGGTGACACGGCCGATTC 60.818 66.667 35.90 26.17 0.00 2.52
644 8262 1.529244 AGGCAAGCTTGGGTGACAC 60.529 57.895 27.10 8.86 0.00 3.67
653 8271 2.359230 GGACGAGCAGGCAAGCTT 60.359 61.111 5.93 0.00 46.75 3.74
667 8285 3.830755 TCCTAGGTAAGTCTTGTGTGGAC 59.169 47.826 9.08 0.00 0.00 4.02
713 8331 2.436646 CTGGAGGCGGCGATGTTT 60.437 61.111 12.98 0.00 0.00 2.83
729 8347 1.558865 TAGGAAGGGAGGATAGGGCT 58.441 55.000 0.00 0.00 0.00 5.19
791 8409 1.274167 CCAACAAATGCCAGCTGACAT 59.726 47.619 17.39 13.50 0.00 3.06
795 8413 0.393820 AACCCAACAAATGCCAGCTG 59.606 50.000 6.78 6.78 0.00 4.24
797 8415 1.965935 AAAACCCAACAAATGCCAGC 58.034 45.000 0.00 0.00 0.00 4.85
802 8420 6.481644 TGCTAAGCTTAAAAACCCAACAAATG 59.518 34.615 7.74 0.00 0.00 2.32
822 8440 3.888323 TGTTGATTGTTCCAAGCTGCTAA 59.112 39.130 0.90 0.00 0.00 3.09
826 8444 4.311816 ACTTGTTGATTGTTCCAAGCTG 57.688 40.909 0.00 0.00 38.24 4.24
829 8447 6.340522 AGGAAAACTTGTTGATTGTTCCAAG 58.659 36.000 13.20 0.00 40.05 3.61
833 8451 6.980397 ACATGAGGAAAACTTGTTGATTGTTC 59.020 34.615 0.00 0.00 0.00 3.18
839 8457 7.873719 TTCTTACATGAGGAAAACTTGTTGA 57.126 32.000 0.00 0.00 0.00 3.18
865 8483 7.062322 TGCATCCATGAACTGATACCTTAATT 58.938 34.615 0.00 0.00 0.00 1.40
866 8484 6.604171 TGCATCCATGAACTGATACCTTAAT 58.396 36.000 0.00 0.00 0.00 1.40
867 8485 6.000246 TGCATCCATGAACTGATACCTTAA 58.000 37.500 0.00 0.00 0.00 1.85
878 8496 5.456497 CACGATACATTTTGCATCCATGAAC 59.544 40.000 0.00 0.00 0.00 3.18
887 8505 5.826586 ACAAGAAACACGATACATTTTGCA 58.173 33.333 0.00 0.00 0.00 4.08
890 8508 9.790389 TTTGTAACAAGAAACACGATACATTTT 57.210 25.926 0.00 0.00 0.00 1.82
953 8571 4.579869 TGAATGCAGGACTAGAAAGGTTC 58.420 43.478 0.00 0.00 0.00 3.62
1028 8646 4.260985 TGCACTGTGATAAATTCATCCGT 58.739 39.130 12.86 0.00 36.54 4.69
1030 8648 6.140303 ACATGCACTGTGATAAATTCATCC 57.860 37.500 12.86 0.00 36.48 3.51
1031 8649 8.470040 AAAACATGCACTGTGATAAATTCATC 57.530 30.769 12.86 0.00 38.39 2.92
1046 8664 9.848172 CTTTGTTAGATTGTTTAAAACATGCAC 57.152 29.630 0.00 0.00 41.79 4.57
1048 8666 9.040939 ACCTTTGTTAGATTGTTTAAAACATGC 57.959 29.630 0.00 0.00 41.79 4.06
1061 8679 5.440610 CTCTGCCCATACCTTTGTTAGATT 58.559 41.667 0.00 0.00 0.00 2.40
1064 8682 2.945668 GCTCTGCCCATACCTTTGTTAG 59.054 50.000 0.00 0.00 0.00 2.34
1078 8696 6.677781 TTAAACATATGTTGTAGCTCTGCC 57.322 37.500 21.46 0.00 37.68 4.85
1167 8800 6.691754 TGTTACACAGCAGATTCTCAAAAA 57.308 33.333 0.00 0.00 0.00 1.94
1168 8801 6.691754 TTGTTACACAGCAGATTCTCAAAA 57.308 33.333 0.00 0.00 0.00 2.44
1169 8802 6.882610 ATTGTTACACAGCAGATTCTCAAA 57.117 33.333 0.00 0.00 0.00 2.69
1170 8803 6.882610 AATTGTTACACAGCAGATTCTCAA 57.117 33.333 0.00 0.00 0.00 3.02
1171 8804 6.294120 CCAAATTGTTACACAGCAGATTCTCA 60.294 38.462 0.00 0.00 0.00 3.27
1172 8805 6.088824 CCAAATTGTTACACAGCAGATTCTC 58.911 40.000 0.00 0.00 0.00 2.87
1173 8806 5.536161 ACCAAATTGTTACACAGCAGATTCT 59.464 36.000 0.00 0.00 0.00 2.40
1174 8807 5.772521 ACCAAATTGTTACACAGCAGATTC 58.227 37.500 0.00 0.00 0.00 2.52
1175 8808 5.789643 ACCAAATTGTTACACAGCAGATT 57.210 34.783 0.00 0.00 0.00 2.40
1176 8809 5.531634 CAACCAAATTGTTACACAGCAGAT 58.468 37.500 0.00 0.00 33.20 2.90
1177 8810 4.736168 GCAACCAAATTGTTACACAGCAGA 60.736 41.667 0.00 0.00 40.77 4.26
1178 8811 3.490526 GCAACCAAATTGTTACACAGCAG 59.509 43.478 0.00 0.00 40.77 4.24
1179 8812 3.118992 TGCAACCAAATTGTTACACAGCA 60.119 39.130 0.00 0.00 40.77 4.41
1180 8813 3.452474 TGCAACCAAATTGTTACACAGC 58.548 40.909 0.00 0.00 40.77 4.40
1181 8814 6.601741 ATTTGCAACCAAATTGTTACACAG 57.398 33.333 0.00 0.00 46.66 3.66
1220 8853 1.826054 CTGAAAACCACGGCCCACA 60.826 57.895 0.00 0.00 0.00 4.17
1248 8881 4.320608 TCCATCAACTTTGTTTCTTGGC 57.679 40.909 0.00 0.00 0.00 4.52
1250 8883 6.742109 ACTCATCCATCAACTTTGTTTCTTG 58.258 36.000 0.00 0.00 0.00 3.02
1251 8884 6.547141 TGACTCATCCATCAACTTTGTTTCTT 59.453 34.615 0.00 0.00 0.00 2.52
1253 8886 6.317789 TGACTCATCCATCAACTTTGTTTC 57.682 37.500 0.00 0.00 0.00 2.78
1254 8887 5.278660 GCTGACTCATCCATCAACTTTGTTT 60.279 40.000 0.00 0.00 0.00 2.83
1262 8895 1.288188 TGGGCTGACTCATCCATCAA 58.712 50.000 1.40 0.00 0.00 2.57
1276 8909 1.301637 GCGCCAAACAAAATGGGCT 60.302 52.632 0.00 0.00 44.23 5.19
1338 8975 1.594564 GGCGGGAGAGTTTATCGGC 60.595 63.158 0.00 0.00 39.02 5.54
1424 9072 2.627699 AGCTTCTCGATCTCTTGATCCC 59.372 50.000 0.00 0.00 44.61 3.85
1606 9254 2.829458 GAGACGGAGGCGCCTACT 60.829 66.667 35.21 26.49 0.00 2.57
1608 9256 4.435970 TGGAGACGGAGGCGCCTA 62.436 66.667 32.97 8.37 0.00 3.93
1691 9339 0.961358 CTCCTCGTCCTTGTCCTCGT 60.961 60.000 0.00 0.00 0.00 4.18
1693 9341 0.323542 TCCTCCTCGTCCTTGTCCTC 60.324 60.000 0.00 0.00 0.00 3.71
1694 9342 0.323908 CTCCTCCTCGTCCTTGTCCT 60.324 60.000 0.00 0.00 0.00 3.85
1787 9459 2.045143 GGGAGTCCTCGTCCGACT 60.045 66.667 9.58 2.24 43.28 4.18
1788 9460 3.139469 GGGGAGTCCTCGTCCGAC 61.139 72.222 9.58 0.00 34.56 4.79
1789 9461 4.790962 CGGGGAGTCCTCGTCCGA 62.791 72.222 23.96 0.00 44.17 4.55
1791 9463 4.437587 TCCGGGGAGTCCTCGTCC 62.438 72.222 29.17 11.26 0.00 4.79
1792 9464 3.139469 GTCCGGGGAGTCCTCGTC 61.139 72.222 29.17 17.91 0.00 4.20
1793 9465 3.641925 GAGTCCGGGGAGTCCTCGT 62.642 68.421 29.17 11.98 38.33 4.18
1794 9466 2.829458 GAGTCCGGGGAGTCCTCG 60.829 72.222 25.27 25.27 38.33 4.63
1813 9485 3.827898 CACCTCCTCCGACTCGCC 61.828 72.222 0.00 0.00 0.00 5.54
1814 9486 3.827898 CCACCTCCTCCGACTCGC 61.828 72.222 0.00 0.00 0.00 5.03
1815 9487 3.827898 GCCACCTCCTCCGACTCG 61.828 72.222 0.00 0.00 0.00 4.18
1859 9573 1.448717 GCGACAGCCTTCTTCCTCC 60.449 63.158 0.00 0.00 37.42 4.30
1957 9671 3.518998 CCTCGTCGATGGCGTCCT 61.519 66.667 4.48 0.00 38.98 3.85
1966 9680 1.313812 GCCTTCCTCTTCCTCGTCGA 61.314 60.000 0.00 0.00 0.00 4.20
2027 9741 1.097547 AGTGGACCATTAGCGCATGC 61.098 55.000 11.47 7.91 43.24 4.06
2028 9742 1.331756 GAAGTGGACCATTAGCGCATG 59.668 52.381 11.47 5.29 0.00 4.06
2030 9744 0.613260 AGAAGTGGACCATTAGCGCA 59.387 50.000 11.47 0.00 0.00 6.09
2036 9750 2.489329 CGCATCAAAGAAGTGGACCATT 59.511 45.455 0.00 0.00 0.00 3.16
2056 9770 2.752354 TGGCACCAAATCCAATCTAACG 59.248 45.455 0.00 0.00 0.00 3.18
2057 9771 5.507985 GCTATGGCACCAAATCCAATCTAAC 60.508 44.000 0.00 0.00 35.75 2.34
2058 9772 4.584325 GCTATGGCACCAAATCCAATCTAA 59.416 41.667 0.00 0.00 35.75 2.10
2061 9775 2.287788 CGCTATGGCACCAAATCCAATC 60.288 50.000 0.74 0.00 38.60 2.67
2062 9776 1.682854 CGCTATGGCACCAAATCCAAT 59.317 47.619 0.74 0.00 38.60 3.16
2063 9777 1.102154 CGCTATGGCACCAAATCCAA 58.898 50.000 0.74 0.00 38.60 3.53
2064 9778 0.254462 TCGCTATGGCACCAAATCCA 59.746 50.000 0.74 0.00 38.60 3.41
2067 9781 1.382522 CAGTCGCTATGGCACCAAAT 58.617 50.000 0.74 0.00 38.60 2.32
2068 9782 0.676466 CCAGTCGCTATGGCACCAAA 60.676 55.000 0.74 0.00 38.60 3.28
2070 9784 2.584064 CCAGTCGCTATGGCACCA 59.416 61.111 0.74 0.00 38.60 4.17
2071 9785 2.203070 CCCAGTCGCTATGGCACC 60.203 66.667 0.74 0.00 36.43 5.01
2072 9786 2.203070 CCCCAGTCGCTATGGCAC 60.203 66.667 0.74 0.00 36.43 5.01
2073 9787 4.175337 GCCCCAGTCGCTATGGCA 62.175 66.667 0.74 0.00 41.76 4.92
2075 9789 3.849951 ACGCCCCAGTCGCTATGG 61.850 66.667 0.00 0.00 37.58 2.74
2084 9798 1.746615 CACCAAGATCACGCCCCAG 60.747 63.158 0.00 0.00 0.00 4.45
2087 9801 1.718757 GCATCACCAAGATCACGCCC 61.719 60.000 0.00 0.00 33.72 6.13
2114 9832 2.159841 CCAGCATTTCTACGAACACACG 60.160 50.000 0.00 0.00 39.31 4.49
2125 9843 1.625818 AGACCTCGTTCCAGCATTTCT 59.374 47.619 0.00 0.00 0.00 2.52
2272 10116 7.443477 TGGGAATACATTTGCAATTCATATGG 58.557 34.615 11.65 0.00 38.11 2.74
2341 10185 6.368779 AATGGTGTTACTAGGAAGTAGCAA 57.631 37.500 7.60 0.00 46.79 3.91
2351 10195 7.530010 CACCTGATCAAAAATGGTGTTACTAG 58.470 38.462 18.47 0.00 42.11 2.57
2374 10218 2.229543 TGAATTCAGATGGCAGCAACAC 59.770 45.455 5.19 0.00 0.00 3.32
2422 10266 0.531311 GCCCACGTAAATCCCGGTAG 60.531 60.000 0.00 0.00 0.00 3.18
2623 10468 5.200483 TGAACAAGAACAGATTGGGAACTT 58.800 37.500 0.00 0.00 31.76 2.66
2705 10651 0.881600 CAGCTTGGTTTGGCAAAGGC 60.882 55.000 13.94 14.51 40.13 4.35
2739 10685 0.666374 AAACAGTACCAAGCAACGGC 59.334 50.000 0.00 0.00 41.61 5.68
2740 10686 1.944024 TGAAACAGTACCAAGCAACGG 59.056 47.619 0.00 0.00 0.00 4.44
2741 10687 3.003275 ACATGAAACAGTACCAAGCAACG 59.997 43.478 0.00 0.00 0.00 4.10
2742 10688 4.568152 ACATGAAACAGTACCAAGCAAC 57.432 40.909 0.00 0.00 0.00 4.17
2744 10690 4.968259 AGTACATGAAACAGTACCAAGCA 58.032 39.130 0.00 0.00 41.07 3.91
2745 10691 6.594159 ACATAGTACATGAAACAGTACCAAGC 59.406 38.462 0.00 0.00 41.07 4.01
2746 10692 8.547967 AACATAGTACATGAAACAGTACCAAG 57.452 34.615 0.00 0.00 41.07 3.61
2747 10693 8.911918 AAACATAGTACATGAAACAGTACCAA 57.088 30.769 0.00 0.00 41.07 3.67
2794 10740 9.236691 GATGCACACAACGATCATTATTAAATT 57.763 29.630 0.00 0.00 0.00 1.82
2795 10741 8.623903 AGATGCACACAACGATCATTATTAAAT 58.376 29.630 0.00 0.00 0.00 1.40
2796 10742 7.984391 AGATGCACACAACGATCATTATTAAA 58.016 30.769 0.00 0.00 0.00 1.52
2797 10743 7.552458 AGATGCACACAACGATCATTATTAA 57.448 32.000 0.00 0.00 0.00 1.40
2799 10745 6.441093 AAGATGCACACAACGATCATTATT 57.559 33.333 0.00 0.00 0.00 1.40
2800 10746 6.441093 AAAGATGCACACAACGATCATTAT 57.559 33.333 0.00 0.00 0.00 1.28
2802 10748 4.771590 AAAGATGCACACAACGATCATT 57.228 36.364 0.00 0.00 0.00 2.57
2804 10750 3.563390 TCAAAAGATGCACACAACGATCA 59.437 39.130 0.00 0.00 0.00 2.92
2805 10751 4.145876 TCAAAAGATGCACACAACGATC 57.854 40.909 0.00 0.00 0.00 3.69
2806 10752 4.022935 ACATCAAAAGATGCACACAACGAT 60.023 37.500 5.44 0.00 36.08 3.73
2807 10753 3.314913 ACATCAAAAGATGCACACAACGA 59.685 39.130 5.44 0.00 36.08 3.85
2808 10754 3.631144 ACATCAAAAGATGCACACAACG 58.369 40.909 5.44 0.00 36.08 4.10
2809 10755 5.574055 CCATACATCAAAAGATGCACACAAC 59.426 40.000 5.44 0.00 36.08 3.32
2811 10757 4.158209 CCCATACATCAAAAGATGCACACA 59.842 41.667 5.44 0.00 36.08 3.72
2814 10760 3.491447 GGCCCATACATCAAAAGATGCAC 60.491 47.826 5.44 0.00 36.08 4.57
2815 10761 2.694628 GGCCCATACATCAAAAGATGCA 59.305 45.455 5.44 0.00 36.08 3.96
2816 10762 2.961062 AGGCCCATACATCAAAAGATGC 59.039 45.455 0.00 0.00 36.08 3.91
2817 10763 5.184479 CCATAGGCCCATACATCAAAAGATG 59.816 44.000 0.00 4.06 38.46 2.90
2818 10764 5.162947 ACCATAGGCCCATACATCAAAAGAT 60.163 40.000 0.00 0.00 0.00 2.40
2820 10766 4.473444 ACCATAGGCCCATACATCAAAAG 58.527 43.478 0.00 0.00 0.00 2.27
2821 10767 4.534647 ACCATAGGCCCATACATCAAAA 57.465 40.909 0.00 0.00 0.00 2.44
2822 10768 4.534647 AACCATAGGCCCATACATCAAA 57.465 40.909 0.00 0.00 0.00 2.69
2823 10769 4.534647 AAACCATAGGCCCATACATCAA 57.465 40.909 0.00 0.00 0.00 2.57
2824 10770 4.079500 TGAAAACCATAGGCCCATACATCA 60.080 41.667 0.00 0.00 0.00 3.07
2825 10771 4.469657 TGAAAACCATAGGCCCATACATC 58.530 43.478 0.00 0.00 0.00 3.06
2826 10772 4.534647 TGAAAACCATAGGCCCATACAT 57.465 40.909 0.00 0.00 0.00 2.29
2827 10773 4.277476 CTTGAAAACCATAGGCCCATACA 58.723 43.478 0.00 0.00 0.00 2.29
2828 10774 3.068165 GCTTGAAAACCATAGGCCCATAC 59.932 47.826 0.00 0.00 0.00 2.39
2830 10776 2.110578 GCTTGAAAACCATAGGCCCAT 58.889 47.619 0.00 0.00 0.00 4.00
2832 10778 1.751351 GAGCTTGAAAACCATAGGCCC 59.249 52.381 0.00 0.00 0.00 5.80
2833 10779 1.751351 GGAGCTTGAAAACCATAGGCC 59.249 52.381 0.00 0.00 0.00 5.19
2834 10780 2.728007 AGGAGCTTGAAAACCATAGGC 58.272 47.619 0.00 0.00 0.00 3.93
2835 10781 5.243730 TGAAAAGGAGCTTGAAAACCATAGG 59.756 40.000 0.00 0.00 0.00 2.57
2837 10783 6.723298 TTGAAAAGGAGCTTGAAAACCATA 57.277 33.333 0.00 0.00 0.00 2.74
2838 10784 5.612725 TTGAAAAGGAGCTTGAAAACCAT 57.387 34.783 0.00 0.00 0.00 3.55
2839 10785 5.413309 TTTGAAAAGGAGCTTGAAAACCA 57.587 34.783 0.00 0.00 0.00 3.67
2840 10786 6.735678 TTTTTGAAAAGGAGCTTGAAAACC 57.264 33.333 0.00 0.00 0.00 3.27
2866 10952 8.206126 ACCCAAAACAGATTTTTATCCAGATT 57.794 30.769 0.00 0.00 35.79 2.40
2868 10954 7.010160 AGACCCAAAACAGATTTTTATCCAGA 58.990 34.615 0.00 0.00 35.79 3.86
2875 10961 4.081198 TGTGCAGACCCAAAACAGATTTTT 60.081 37.500 0.00 0.00 35.79 1.94
2879 10965 2.363306 TGTGCAGACCCAAAACAGAT 57.637 45.000 0.00 0.00 0.00 2.90
2882 10968 3.176552 CAAATGTGCAGACCCAAAACA 57.823 42.857 0.00 0.00 0.00 2.83
2924 11019 3.304257 CCAACTGCATCTGTTTGACACTC 60.304 47.826 0.00 0.00 0.00 3.51
2961 11058 8.691797 ACTTCTTATCTTCTACAGGAGATGTTC 58.308 37.037 9.89 0.00 39.96 3.18
2962 11059 8.474025 CACTTCTTATCTTCTACAGGAGATGTT 58.526 37.037 9.89 0.00 39.96 2.71
2963 11060 7.069331 CCACTTCTTATCTTCTACAGGAGATGT 59.931 40.741 9.89 0.00 46.45 3.06
2964 11061 7.432869 CCACTTCTTATCTTCTACAGGAGATG 58.567 42.308 9.89 0.00 32.88 2.90
2965 11062 6.041523 GCCACTTCTTATCTTCTACAGGAGAT 59.958 42.308 5.38 5.38 32.88 2.75
2966 11063 5.361285 GCCACTTCTTATCTTCTACAGGAGA 59.639 44.000 0.00 0.00 0.00 3.71
2968 11065 5.023452 TGCCACTTCTTATCTTCTACAGGA 58.977 41.667 0.00 0.00 0.00 3.86
2969 11066 5.127845 TCTGCCACTTCTTATCTTCTACAGG 59.872 44.000 0.00 0.00 0.00 4.00
2970 11067 6.214191 TCTGCCACTTCTTATCTTCTACAG 57.786 41.667 0.00 0.00 0.00 2.74
2972 11069 9.771534 AATATTCTGCCACTTCTTATCTTCTAC 57.228 33.333 0.00 0.00 0.00 2.59
2974 11071 8.489489 TGAATATTCTGCCACTTCTTATCTTCT 58.511 33.333 16.24 0.00 0.00 2.85
2986 11103 7.325660 TCTTCATTTCTGAATATTCTGCCAC 57.674 36.000 16.24 0.00 40.52 5.01
3022 11139 6.533367 GCATCTGTATAATCTTAGCTACCTGC 59.467 42.308 0.00 0.00 43.29 4.85
3028 11145 8.428063 AGAAACTGCATCTGTATAATCTTAGCT 58.572 33.333 0.00 0.00 0.00 3.32
3040 11157 5.105877 CCATGATTGAAGAAACTGCATCTGT 60.106 40.000 0.00 0.00 0.00 3.41
3042 11159 5.258841 TCCATGATTGAAGAAACTGCATCT 58.741 37.500 0.00 0.00 0.00 2.90
3044 11161 7.649533 TTATCCATGATTGAAGAAACTGCAT 57.350 32.000 0.00 0.00 0.00 3.96
3045 11162 7.465353 TTTATCCATGATTGAAGAAACTGCA 57.535 32.000 0.00 0.00 0.00 4.41
3046 11163 7.814107 TGTTTTATCCATGATTGAAGAAACTGC 59.186 33.333 0.00 0.00 0.00 4.40
3047 11164 9.865321 ATGTTTTATCCATGATTGAAGAAACTG 57.135 29.630 0.00 0.00 0.00 3.16
3086 11248 2.957006 TCGAGAAATGGGAGCTACCTAC 59.043 50.000 18.18 4.88 38.98 3.18
3087 11249 3.308035 TCGAGAAATGGGAGCTACCTA 57.692 47.619 18.18 2.63 38.98 3.08
3088 11250 2.160721 TCGAGAAATGGGAGCTACCT 57.839 50.000 18.18 0.00 38.98 3.08
3089 11251 2.289133 GGATCGAGAAATGGGAGCTACC 60.289 54.545 8.55 8.55 38.08 3.18
3090 11252 2.630580 AGGATCGAGAAATGGGAGCTAC 59.369 50.000 0.00 0.00 0.00 3.58
3091 11253 2.964209 AGGATCGAGAAATGGGAGCTA 58.036 47.619 0.00 0.00 0.00 3.32
3092 11254 1.799933 AGGATCGAGAAATGGGAGCT 58.200 50.000 0.00 0.00 0.00 4.09
3093 11255 2.216898 CAAGGATCGAGAAATGGGAGC 58.783 52.381 0.00 0.00 0.00 4.70
3094 11256 3.550437 ACAAGGATCGAGAAATGGGAG 57.450 47.619 0.00 0.00 0.00 4.30
3095 11257 6.070767 GGATATACAAGGATCGAGAAATGGGA 60.071 42.308 0.00 0.00 0.00 4.37
3096 11258 6.109359 GGATATACAAGGATCGAGAAATGGG 58.891 44.000 0.00 0.00 0.00 4.00
3097 11259 6.109359 GGGATATACAAGGATCGAGAAATGG 58.891 44.000 0.00 0.00 0.00 3.16
3098 11260 6.070538 AGGGGATATACAAGGATCGAGAAATG 60.071 42.308 0.00 0.00 0.00 2.32
3099 11261 6.026186 AGGGGATATACAAGGATCGAGAAAT 58.974 40.000 0.00 0.00 0.00 2.17
3100 11262 5.403512 AGGGGATATACAAGGATCGAGAAA 58.596 41.667 0.00 0.00 0.00 2.52
3101 11263 5.011982 AGGGGATATACAAGGATCGAGAA 57.988 43.478 0.00 0.00 0.00 2.87
3102 11264 4.292571 AGAGGGGATATACAAGGATCGAGA 59.707 45.833 0.00 0.00 0.00 4.04
3103 11265 4.605183 AGAGGGGATATACAAGGATCGAG 58.395 47.826 0.00 0.00 0.00 4.04
3104 11266 4.601084 GAGAGGGGATATACAAGGATCGA 58.399 47.826 0.00 0.00 0.00 3.59
3105 11267 3.378742 CGAGAGGGGATATACAAGGATCG 59.621 52.174 0.00 0.00 0.00 3.69
3106 11268 3.131400 GCGAGAGGGGATATACAAGGATC 59.869 52.174 0.00 0.00 0.00 3.36
3107 11269 3.100671 GCGAGAGGGGATATACAAGGAT 58.899 50.000 0.00 0.00 0.00 3.24
3108 11270 2.110188 AGCGAGAGGGGATATACAAGGA 59.890 50.000 0.00 0.00 0.00 3.36
3109 11271 2.232452 CAGCGAGAGGGGATATACAAGG 59.768 54.545 0.00 0.00 0.00 3.61
3110 11272 2.894126 ACAGCGAGAGGGGATATACAAG 59.106 50.000 0.00 0.00 0.00 3.16
3111 11273 2.958818 ACAGCGAGAGGGGATATACAA 58.041 47.619 0.00 0.00 0.00 2.41
3112 11274 2.677542 ACAGCGAGAGGGGATATACA 57.322 50.000 0.00 0.00 0.00 2.29
3113 11275 4.308265 GAAAACAGCGAGAGGGGATATAC 58.692 47.826 0.00 0.00 0.00 1.47
3114 11276 3.323979 GGAAAACAGCGAGAGGGGATATA 59.676 47.826 0.00 0.00 0.00 0.86
3115 11277 2.104963 GGAAAACAGCGAGAGGGGATAT 59.895 50.000 0.00 0.00 0.00 1.63
3116 11278 1.485066 GGAAAACAGCGAGAGGGGATA 59.515 52.381 0.00 0.00 0.00 2.59
3117 11279 0.253327 GGAAAACAGCGAGAGGGGAT 59.747 55.000 0.00 0.00 0.00 3.85
3118 11280 0.836400 AGGAAAACAGCGAGAGGGGA 60.836 55.000 0.00 0.00 0.00 4.81
3119 11281 0.036875 AAGGAAAACAGCGAGAGGGG 59.963 55.000 0.00 0.00 0.00 4.79
3120 11282 1.897560 AAAGGAAAACAGCGAGAGGG 58.102 50.000 0.00 0.00 0.00 4.30
3121 11283 3.990318 AAAAAGGAAAACAGCGAGAGG 57.010 42.857 0.00 0.00 0.00 3.69
3178 11340 3.735591 TCACCAGAAAACGGTAGGAAAG 58.264 45.455 0.00 0.00 34.02 2.62
3208 11370 2.418368 TGAAGTGCCAACTCAACTGT 57.582 45.000 0.00 0.00 34.77 3.55


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

AutoCloner maintained by Alex Coulton.