Multiple sequence alignment - TraesCS3A01G210500

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 TraesCS3A01G210500 chr3A 100.000 3153 0 0 1 3153 376784426 376781274 0.000000e+00 5823.0
1 TraesCS3A01G210500 chr3D 95.132 719 28 5 1 716 287299573 287298859 0.000000e+00 1127.0
2 TraesCS3A01G210500 chr3D 91.568 842 31 15 2340 3151 287293086 287292255 0.000000e+00 1125.0
3 TraesCS3A01G210500 chr3D 87.735 799 38 26 799 1591 287294425 287293681 0.000000e+00 878.0
4 TraesCS3A01G210500 chr3D 83.897 621 25 36 1628 2221 287293674 287293102 1.000000e-144 523.0
5 TraesCS3A01G210500 chr3D 100.000 37 0 0 2268 2304 278514998 278515034 5.640000e-08 69.4
6 TraesCS3A01G210500 chr3D 89.474 57 2 2 2247 2299 380048723 380048779 5.640000e-08 69.4
7 TraesCS3A01G210500 chr3B 97.078 616 15 3 1 614 380514046 380513432 0.000000e+00 1035.0
8 TraesCS3A01G210500 chr3B 94.165 617 21 6 2361 2966 380507997 380507385 0.000000e+00 926.0
9 TraesCS3A01G210500 chr3B 82.603 730 45 28 1005 1730 380509027 380508376 1.270000e-158 569.0
10 TraesCS3A01G210500 chr3B 90.190 316 13 3 677 992 380510345 380510048 2.280000e-106 396.0
11 TraesCS3A01G210500 chr3B 81.844 347 27 18 1777 2114 380508377 380508058 3.120000e-65 259.0
12 TraesCS3A01G210500 chr3B 91.813 171 7 3 2990 3153 380507319 380507149 6.800000e-57 231.0
13 TraesCS3A01G210500 chr3B 93.103 58 2 2 614 671 380513348 380513293 2.020000e-12 84.2
14 TraesCS3A01G210500 chr1D 100.000 37 0 0 2268 2304 206041034 206041070 5.640000e-08 69.4
15 TraesCS3A01G210500 chr2A 100.000 36 0 0 2268 2303 703998900 703998935 2.030000e-07 67.6
16 TraesCS3A01G210500 chrUn 85.938 64 3 4 2247 2304 156526224 156526287 2.630000e-06 63.9
17 TraesCS3A01G210500 chr7A 86.667 60 2 4 2247 2300 567475424 567475365 9.440000e-06 62.1
18 TraesCS3A01G210500 chr5B 86.667 60 2 4 2247 2300 356213738 356213797 9.440000e-06 62.1
19 TraesCS3A01G210500 chr1B 85.714 63 3 4 2247 2303 342124882 342124820 9.440000e-06 62.1
20 TraesCS3A01G210500 chr4A 84.615 65 4 5 2247 2305 498135563 498135499 3.400000e-05 60.2


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 TraesCS3A01G210500 chr3A 376781274 376784426 3152 True 5823.000000 5823 100.000000 1 3153 1 chr3A.!!$R1 3152
1 TraesCS3A01G210500 chr3D 287298859 287299573 714 True 1127.000000 1127 95.132000 1 716 1 chr3D.!!$R1 715
2 TraesCS3A01G210500 chr3D 287292255 287294425 2170 True 842.000000 1125 87.733333 799 3151 3 chr3D.!!$R2 2352
3 TraesCS3A01G210500 chr3B 380507149 380514046 6897 True 500.028571 1035 90.113714 1 3153 7 chr3B.!!$R1 3152

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
887 3915 0.192064 GGAGGAGATGGAGATCCCCA 59.808 60.0 0.00 0.00 41.05 4.96 F
1620 5675 0.179089 CCAGTGAGAATGAGGCCTCG 60.179 60.0 27.43 9.74 32.30 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 5801 0.320421 TACTCGCTGCAGTTTGGTCC 60.320 55.0 16.64 0.0 0.00 4.46 R
2804 6922 0.759436 AGAACAGGGTCCACGACAGT 60.759 55.0 0.00 0.0 33.68 3.55 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
25 26 7.097834 ACTTAGTAAAGTCACATTCTAGCACC 58.902 38.462 0.00 0.00 42.42 5.01
88 89 5.467735 CGAGAGCACATTGATATTTGGATCA 59.532 40.000 0.00 0.00 33.96 2.92
148 149 2.512692 TCAACAACTATGGCATGGCT 57.487 45.000 21.08 8.52 0.00 4.75
176 177 0.745486 TGTCCAGCATGAATGGCGAG 60.745 55.000 11.54 0.00 39.69 5.03
353 356 1.617947 GCCCCAGGTCATCTCTTCGT 61.618 60.000 0.00 0.00 0.00 3.85
430 433 0.895530 TGTTAGCCTTGACCTCCTCG 59.104 55.000 0.00 0.00 0.00 4.63
544 547 5.589855 ACAGACAGTGTGTTCAATTCATTCA 59.410 36.000 0.00 0.00 38.28 2.57
663 899 6.249260 CGTGTTGTGGTATTACTAGTAACGAC 59.751 42.308 17.45 16.73 0.00 4.34
664 900 7.308435 GTGTTGTGGTATTACTAGTAACGACT 58.692 38.462 17.45 4.71 39.92 4.18
665 901 7.809806 GTGTTGTGGTATTACTAGTAACGACTT 59.190 37.037 17.45 4.34 37.10 3.01
666 902 9.008965 TGTTGTGGTATTACTAGTAACGACTTA 57.991 33.333 17.45 3.37 37.10 2.24
692 3719 4.584743 AGAAGCTAAAGAACAAAACCTGGG 59.415 41.667 0.00 0.00 0.00 4.45
694 3721 4.542697 AGCTAAAGAACAAAACCTGGGAA 58.457 39.130 0.00 0.00 0.00 3.97
697 3724 5.753438 GCTAAAGAACAAAACCTGGGAAAAG 59.247 40.000 0.00 0.00 0.00 2.27
709 3737 4.010349 CCTGGGAAAAGAGTTGTCATACC 58.990 47.826 0.00 0.00 0.00 2.73
741 3769 5.651530 ACTGTTTATGTGAGGTATGAGACG 58.348 41.667 0.00 0.00 0.00 4.18
789 3817 4.095782 TGAGTTCTTTTGTTTCTTCGGTGG 59.904 41.667 0.00 0.00 0.00 4.61
809 3837 1.367659 GACGGAGCTAGTACAGACGT 58.632 55.000 0.00 0.00 34.68 4.34
821 3849 4.430765 AGACGTTACCCTGGCGCG 62.431 66.667 0.00 0.00 0.00 6.86
887 3915 0.192064 GGAGGAGATGGAGATCCCCA 59.808 60.000 0.00 0.00 41.05 4.96
898 3926 1.237458 GATCCCCAGGCTAGACCCT 59.763 63.158 0.00 0.00 40.58 4.34
923 3951 4.764823 ACGATAAATTTTCCTTGTGCCAGA 59.235 37.500 0.00 0.00 0.00 3.86
1013 5050 8.260099 ACATACATGATGCTATATATGAGGCT 57.740 34.615 0.00 0.00 39.39 4.58
1063 5101 2.075489 CCGATCGATCAGTACGCGC 61.075 63.158 24.40 0.00 0.00 6.86
1077 5115 1.006805 CGCGCCTGAAGCTAGCTAT 60.007 57.895 19.70 8.44 40.39 2.97
1078 5116 1.006314 CGCGCCTGAAGCTAGCTATC 61.006 60.000 19.70 17.19 40.39 2.08
1079 5117 0.316841 GCGCCTGAAGCTAGCTATCT 59.683 55.000 19.70 1.41 40.39 1.98
1080 5118 1.542030 GCGCCTGAAGCTAGCTATCTA 59.458 52.381 19.70 3.86 40.39 1.98
1126 5164 4.816786 GGAAACCAAGTTAAACGTAGCA 57.183 40.909 0.00 0.00 0.00 3.49
1127 5165 4.530388 GGAAACCAAGTTAAACGTAGCAC 58.470 43.478 0.00 0.00 0.00 4.40
1163 5201 1.078918 CAGGCCAGAATCGTCAGCA 60.079 57.895 5.01 0.00 0.00 4.41
1165 5203 2.467826 GGCCAGAATCGTCAGCAGC 61.468 63.158 0.00 0.00 0.00 5.25
1166 5204 2.806856 GCCAGAATCGTCAGCAGCG 61.807 63.158 0.00 0.00 0.00 5.18
1167 5205 1.153765 CCAGAATCGTCAGCAGCGA 60.154 57.895 0.00 0.19 42.75 4.93
1168 5206 0.737367 CCAGAATCGTCAGCAGCGAA 60.737 55.000 1.75 0.00 41.84 4.70
1169 5207 1.070821 CAGAATCGTCAGCAGCGAAA 58.929 50.000 1.75 0.00 41.84 3.46
1170 5208 1.060266 CAGAATCGTCAGCAGCGAAAG 59.940 52.381 1.75 0.00 41.84 2.62
1298 5340 3.285484 GCTGAGATGGATGAAATGGTGT 58.715 45.455 0.00 0.00 0.00 4.16
1316 5371 2.793288 GTTCCCCTGAACCCGAATTA 57.207 50.000 0.00 0.00 44.20 1.40
1317 5372 3.076079 GTTCCCCTGAACCCGAATTAA 57.924 47.619 0.00 0.00 44.20 1.40
1318 5373 2.751259 GTTCCCCTGAACCCGAATTAAC 59.249 50.000 0.00 0.00 44.20 2.01
1319 5374 1.282738 TCCCCTGAACCCGAATTAACC 59.717 52.381 0.00 0.00 0.00 2.85
1320 5375 1.283905 CCCCTGAACCCGAATTAACCT 59.716 52.381 0.00 0.00 0.00 3.50
1321 5376 2.291346 CCCCTGAACCCGAATTAACCTT 60.291 50.000 0.00 0.00 0.00 3.50
1322 5377 3.427573 CCCTGAACCCGAATTAACCTTT 58.572 45.455 0.00 0.00 0.00 3.11
1323 5378 3.192633 CCCTGAACCCGAATTAACCTTTG 59.807 47.826 0.00 0.00 0.00 2.77
1324 5379 3.366985 CCTGAACCCGAATTAACCTTTGC 60.367 47.826 0.00 0.00 0.00 3.68
1325 5380 3.223435 TGAACCCGAATTAACCTTTGCA 58.777 40.909 0.00 0.00 0.00 4.08
1326 5381 3.254657 TGAACCCGAATTAACCTTTGCAG 59.745 43.478 0.00 0.00 0.00 4.41
1327 5382 1.544246 ACCCGAATTAACCTTTGCAGC 59.456 47.619 0.00 0.00 0.00 5.25
1328 5383 1.818674 CCCGAATTAACCTTTGCAGCT 59.181 47.619 0.00 0.00 0.00 4.24
1329 5384 2.415893 CCCGAATTAACCTTTGCAGCTG 60.416 50.000 10.11 10.11 0.00 4.24
1330 5385 2.228822 CCGAATTAACCTTTGCAGCTGT 59.771 45.455 16.64 0.00 0.00 4.40
1331 5386 3.438781 CCGAATTAACCTTTGCAGCTGTA 59.561 43.478 16.64 8.31 0.00 2.74
1332 5387 4.403453 CGAATTAACCTTTGCAGCTGTAC 58.597 43.478 16.64 0.00 0.00 2.90
1333 5388 4.154195 CGAATTAACCTTTGCAGCTGTACT 59.846 41.667 16.64 0.00 0.00 2.73
1350 5405 5.413833 GCTGTACTGTACTGTACCTACTGAA 59.586 44.000 29.33 14.92 41.34 3.02
1353 5408 7.823665 TGTACTGTACTGTACCTACTGAATTG 58.176 38.462 29.33 0.00 41.34 2.32
1354 5409 6.912951 ACTGTACTGTACCTACTGAATTGT 57.087 37.500 14.91 0.00 0.00 2.71
1355 5410 8.950210 GTACTGTACTGTACCTACTGAATTGTA 58.050 37.037 24.87 0.00 37.43 2.41
1356 5411 7.824672 ACTGTACTGTACCTACTGAATTGTAC 58.175 38.462 14.91 0.00 35.32 2.90
1359 5414 7.606073 TGTACTGTACCTACTGAATTGTACGTA 59.394 37.037 14.91 0.00 37.08 3.57
1376 5431 8.934507 TTGTACGTATGACATTATGTTGATGA 57.065 30.769 0.00 0.00 0.00 2.92
1377 5432 9.541143 TTGTACGTATGACATTATGTTGATGAT 57.459 29.630 0.00 0.00 0.00 2.45
1448 5503 2.187946 GACCATCCTCGGCCACAG 59.812 66.667 2.24 0.00 0.00 3.66
1494 5549 3.357079 CGGCTGCACAGGGTGTTC 61.357 66.667 0.50 0.00 35.75 3.18
1502 5557 2.433446 CAGGGTGTTCCAGCTGCT 59.567 61.111 8.66 0.00 38.24 4.24
1611 5666 3.411517 CCCCCGCCCAGTGAGAAT 61.412 66.667 0.00 0.00 0.00 2.40
1612 5667 2.124570 CCCCGCCCAGTGAGAATG 60.125 66.667 0.00 0.00 0.00 2.67
1613 5668 2.669133 CCCCGCCCAGTGAGAATGA 61.669 63.158 0.00 0.00 0.00 2.57
1614 5669 1.153289 CCCGCCCAGTGAGAATGAG 60.153 63.158 0.00 0.00 0.00 2.90
1615 5670 1.153289 CCGCCCAGTGAGAATGAGG 60.153 63.158 0.00 0.00 0.00 3.86
1616 5671 1.817099 CGCCCAGTGAGAATGAGGC 60.817 63.158 0.00 0.00 37.03 4.70
1617 5672 1.452833 GCCCAGTGAGAATGAGGCC 60.453 63.158 0.00 0.00 34.23 5.19
1618 5673 1.919600 GCCCAGTGAGAATGAGGCCT 61.920 60.000 3.86 3.86 34.23 5.19
1619 5674 0.179936 CCCAGTGAGAATGAGGCCTC 59.820 60.000 26.78 26.78 0.00 4.70
1620 5675 0.179089 CCAGTGAGAATGAGGCCTCG 60.179 60.000 27.43 9.74 32.30 4.63
1621 5676 0.179089 CAGTGAGAATGAGGCCTCGG 60.179 60.000 27.43 4.76 32.30 4.63
1625 5680 2.586357 GAATGAGGCCTCGGACGC 60.586 66.667 27.43 11.25 0.00 5.19
1626 5681 3.077556 AATGAGGCCTCGGACGCT 61.078 61.111 27.43 5.32 0.00 5.07
1648 5709 2.404789 GCGACGAACCGACGGATA 59.595 61.111 23.38 0.00 43.80 2.59
1664 5725 5.462398 CGACGGATAAGAAATCCAAGGTTAG 59.538 44.000 4.98 0.00 38.08 2.34
1667 5728 5.445964 GGATAAGAAATCCAAGGTTAGCCA 58.554 41.667 0.00 0.00 38.09 4.75
1723 5787 1.832167 TTGCAGGGGAGGCACAAAC 60.832 57.895 0.00 0.00 41.75 2.93
1734 5798 2.617274 GCACAAACAGGAGACGGCC 61.617 63.158 0.00 0.00 0.00 6.13
1735 5799 1.227823 CACAAACAGGAGACGGCCA 60.228 57.895 2.24 0.00 0.00 5.36
1736 5800 0.817634 CACAAACAGGAGACGGCCAA 60.818 55.000 2.24 0.00 0.00 4.52
1737 5801 0.535102 ACAAACAGGAGACGGCCAAG 60.535 55.000 2.24 0.00 0.00 3.61
1738 5802 1.073199 AAACAGGAGACGGCCAAGG 59.927 57.895 2.24 0.00 0.00 3.61
1739 5803 1.415672 AAACAGGAGACGGCCAAGGA 61.416 55.000 2.24 0.00 0.00 3.36
1740 5804 2.113243 AACAGGAGACGGCCAAGGAC 62.113 60.000 2.24 0.00 0.00 3.85
1741 5805 3.003763 AGGAGACGGCCAAGGACC 61.004 66.667 2.24 0.00 0.00 4.46
1742 5806 3.319198 GGAGACGGCCAAGGACCA 61.319 66.667 2.24 0.00 0.00 4.02
1743 5807 2.747686 GAGACGGCCAAGGACCAA 59.252 61.111 2.24 0.00 0.00 3.67
1744 5808 1.072505 GAGACGGCCAAGGACCAAA 59.927 57.895 2.24 0.00 0.00 3.28
1745 5809 1.228154 AGACGGCCAAGGACCAAAC 60.228 57.895 2.24 0.00 0.00 2.93
1746 5810 1.228154 GACGGCCAAGGACCAAACT 60.228 57.895 2.24 0.00 0.00 2.66
1747 5811 1.515521 GACGGCCAAGGACCAAACTG 61.516 60.000 2.24 0.00 0.00 3.16
1748 5812 2.919494 CGGCCAAGGACCAAACTGC 61.919 63.158 2.24 0.00 0.00 4.40
1749 5813 1.832167 GGCCAAGGACCAAACTGCA 60.832 57.895 0.00 0.00 0.00 4.41
1750 5814 1.662044 GCCAAGGACCAAACTGCAG 59.338 57.895 13.48 13.48 0.00 4.41
1751 5815 1.662044 CCAAGGACCAAACTGCAGC 59.338 57.895 15.27 0.00 0.00 5.25
1752 5816 1.283793 CAAGGACCAAACTGCAGCG 59.716 57.895 15.27 2.10 0.00 5.18
1753 5817 1.148273 AAGGACCAAACTGCAGCGA 59.852 52.632 15.27 0.00 0.00 4.93
1754 5818 0.886490 AAGGACCAAACTGCAGCGAG 60.886 55.000 15.27 3.01 0.00 5.03
1755 5819 1.598130 GGACCAAACTGCAGCGAGT 60.598 57.895 15.27 6.28 0.00 4.18
1756 5820 0.320421 GGACCAAACTGCAGCGAGTA 60.320 55.000 15.27 0.00 0.00 2.59
1757 5821 1.071605 GACCAAACTGCAGCGAGTAG 58.928 55.000 15.27 0.21 35.87 2.57
1775 5839 4.060667 CAAGGAACCCCCGGCCAT 62.061 66.667 2.24 0.00 40.87 4.40
1838 5911 3.184628 AGGTGGTGAAAGGAGATGATGA 58.815 45.455 0.00 0.00 0.00 2.92
2036 6124 4.651503 CCATAGGCTCTTCTCCAGAAACTA 59.348 45.833 0.00 0.00 33.07 2.24
2037 6125 5.221422 CCATAGGCTCTTCTCCAGAAACTAG 60.221 48.000 0.00 0.00 33.07 2.57
2039 6127 4.023291 AGGCTCTTCTCCAGAAACTAGAG 58.977 47.826 0.00 0.00 33.07 2.43
2047 6144 4.400884 TCTCCAGAAACTAGAGATCACTGC 59.599 45.833 2.56 0.00 31.80 4.40
2116 6216 3.223953 CGATACAAGCGGATGTACTACG 58.776 50.000 0.00 0.00 38.53 3.51
2117 6217 3.059393 CGATACAAGCGGATGTACTACGA 60.059 47.826 8.25 0.00 38.53 3.43
2118 6218 2.556534 ACAAGCGGATGTACTACGAC 57.443 50.000 8.25 1.45 0.00 4.34
2119 6219 1.133790 ACAAGCGGATGTACTACGACC 59.866 52.381 8.25 0.00 0.00 4.79
2120 6220 0.379669 AAGCGGATGTACTACGACCG 59.620 55.000 15.22 15.22 40.44 4.79
2132 6232 2.857575 TACGACCGTAGCTGCCGAGA 62.858 60.000 8.96 0.00 0.00 4.04
2133 6233 2.835705 CGACCGTAGCTGCCGAGAT 61.836 63.158 8.96 0.00 0.00 2.75
2134 6234 1.504647 CGACCGTAGCTGCCGAGATA 61.505 60.000 8.96 0.00 0.00 1.98
2135 6235 0.666913 GACCGTAGCTGCCGAGATAA 59.333 55.000 8.96 0.00 0.00 1.75
2136 6236 1.066605 GACCGTAGCTGCCGAGATAAA 59.933 52.381 8.96 0.00 0.00 1.40
2137 6237 1.687123 ACCGTAGCTGCCGAGATAAAT 59.313 47.619 8.96 0.00 0.00 1.40
2168 6268 5.347907 ACGTGAGGAATAAATTCTCGTCAAC 59.652 40.000 2.91 4.59 37.00 3.18
2199 6301 9.815936 TTAATGATACTATCACGTACGTACATG 57.184 33.333 22.34 20.13 43.01 3.21
2206 6308 7.751732 ACTATCACGTACGTACATGACTAAAA 58.248 34.615 25.00 3.92 30.73 1.52
2249 6354 8.451908 AATAAAATGGTACTATCACTTGCTCC 57.548 34.615 0.00 0.00 0.00 4.70
2250 6355 4.423625 AATGGTACTATCACTTGCTCCC 57.576 45.455 0.00 0.00 0.00 4.30
2251 6356 1.754803 TGGTACTATCACTTGCTCCCG 59.245 52.381 0.00 0.00 0.00 5.14
2252 6357 1.538419 GGTACTATCACTTGCTCCCGC 60.538 57.143 0.00 0.00 0.00 6.13
2253 6358 1.409427 GTACTATCACTTGCTCCCGCT 59.591 52.381 0.00 0.00 36.97 5.52
2254 6359 0.176680 ACTATCACTTGCTCCCGCTG 59.823 55.000 0.00 0.00 36.97 5.18
2255 6360 0.176680 CTATCACTTGCTCCCGCTGT 59.823 55.000 0.00 0.00 36.97 4.40
2256 6361 1.409064 CTATCACTTGCTCCCGCTGTA 59.591 52.381 0.00 0.00 36.97 2.74
2257 6362 0.613260 ATCACTTGCTCCCGCTGTAA 59.387 50.000 0.00 0.00 36.97 2.41
2258 6363 0.394938 TCACTTGCTCCCGCTGTAAA 59.605 50.000 0.00 0.00 36.97 2.01
2259 6364 0.798776 CACTTGCTCCCGCTGTAAAG 59.201 55.000 0.00 0.00 36.97 1.85
2266 6371 2.159379 GCTCCCGCTGTAAAGAAATTGG 60.159 50.000 0.00 0.00 0.00 3.16
2276 6381 6.567891 GCTGTAAAGAAATTGGTAAACGCTCT 60.568 38.462 0.00 0.00 0.00 4.09
2290 6395 8.810427 TGGTAAACGCTCTTATATTTCTTTACG 58.190 33.333 0.00 0.00 0.00 3.18
2291 6396 9.023967 GGTAAACGCTCTTATATTTCTTTACGA 57.976 33.333 0.00 0.00 0.00 3.43
2294 6399 7.695869 ACGCTCTTATATTTCTTTACGAAGG 57.304 36.000 0.00 0.00 33.56 3.46
2295 6400 6.700520 ACGCTCTTATATTTCTTTACGAAGGG 59.299 38.462 0.00 0.00 33.56 3.95
2296 6401 6.921857 CGCTCTTATATTTCTTTACGAAGGGA 59.078 38.462 0.00 0.00 33.56 4.20
2297 6402 7.115095 CGCTCTTATATTTCTTTACGAAGGGAG 59.885 40.741 0.00 0.00 33.56 4.30
2298 6403 7.927092 GCTCTTATATTTCTTTACGAAGGGAGT 59.073 37.037 0.00 0.00 33.56 3.85
2303 6408 8.888579 ATATTTCTTTACGAAGGGAGTACATG 57.111 34.615 0.00 0.00 33.56 3.21
2304 6409 4.119442 TCTTTACGAAGGGAGTACATGC 57.881 45.455 0.00 0.00 33.56 4.06
2305 6410 2.572191 TTACGAAGGGAGTACATGCG 57.428 50.000 0.00 0.00 0.00 4.73
2306 6411 1.466856 TACGAAGGGAGTACATGCGT 58.533 50.000 0.00 0.00 0.00 5.24
2307 6412 1.466856 ACGAAGGGAGTACATGCGTA 58.533 50.000 0.00 0.00 0.00 4.42
2308 6413 1.820519 ACGAAGGGAGTACATGCGTAA 59.179 47.619 0.00 0.00 0.00 3.18
2309 6414 2.231964 ACGAAGGGAGTACATGCGTAAA 59.768 45.455 0.00 0.00 0.00 2.01
2310 6415 3.255725 CGAAGGGAGTACATGCGTAAAA 58.744 45.455 0.00 0.00 0.00 1.52
2311 6416 3.869246 CGAAGGGAGTACATGCGTAAAAT 59.131 43.478 0.00 0.00 0.00 1.82
2312 6417 5.045215 CGAAGGGAGTACATGCGTAAAATA 58.955 41.667 0.00 0.00 0.00 1.40
2313 6418 5.694910 CGAAGGGAGTACATGCGTAAAATAT 59.305 40.000 0.00 0.00 0.00 1.28
2314 6419 6.864685 CGAAGGGAGTACATGCGTAAAATATA 59.135 38.462 0.00 0.00 0.00 0.86
2315 6420 7.148853 CGAAGGGAGTACATGCGTAAAATATAC 60.149 40.741 0.00 0.00 0.00 1.47
2316 6421 7.299246 AGGGAGTACATGCGTAAAATATACT 57.701 36.000 0.00 0.00 0.00 2.12
2317 6422 7.376615 AGGGAGTACATGCGTAAAATATACTC 58.623 38.462 0.00 0.00 37.43 2.59
2318 6423 6.307318 GGGAGTACATGCGTAAAATATACTCG 59.693 42.308 0.00 0.00 38.51 4.18
2319 6424 6.183359 GGAGTACATGCGTAAAATATACTCGC 60.183 42.308 0.00 0.00 45.70 5.03
2324 6429 3.732943 GCGTAAAATATACTCGCATGGC 58.267 45.455 0.00 0.00 45.01 4.40
2325 6430 3.424433 GCGTAAAATATACTCGCATGGCC 60.424 47.826 0.00 0.00 45.01 5.36
2326 6431 3.743911 CGTAAAATATACTCGCATGGCCA 59.256 43.478 8.56 8.56 0.00 5.36
2327 6432 4.391830 CGTAAAATATACTCGCATGGCCAT 59.608 41.667 14.09 14.09 0.00 4.40
2328 6433 5.445939 CGTAAAATATACTCGCATGGCCATC 60.446 44.000 17.61 10.14 0.00 3.51
2329 6434 3.988976 AATATACTCGCATGGCCATCT 57.011 42.857 17.61 0.00 0.00 2.90
2330 6435 3.988976 ATATACTCGCATGGCCATCTT 57.011 42.857 17.61 0.00 0.00 2.40
2331 6436 5.420725 AATATACTCGCATGGCCATCTTA 57.579 39.130 17.61 2.47 0.00 2.10
2332 6437 3.988976 ATACTCGCATGGCCATCTTAT 57.011 42.857 17.61 5.33 0.00 1.73
2333 6438 2.645838 ACTCGCATGGCCATCTTATT 57.354 45.000 17.61 0.00 0.00 1.40
2334 6439 2.936202 ACTCGCATGGCCATCTTATTT 58.064 42.857 17.61 0.00 0.00 1.40
2335 6440 3.290710 ACTCGCATGGCCATCTTATTTT 58.709 40.909 17.61 0.00 0.00 1.82
2338 6443 3.698539 TCGCATGGCCATCTTATTTTTCA 59.301 39.130 17.61 0.00 0.00 2.69
2342 6447 6.515531 CGCATGGCCATCTTATTTTTCATAGT 60.516 38.462 17.61 0.00 0.00 2.12
2359 6464 7.649533 TTCATAGTCCTGCATTTTCATGATT 57.350 32.000 0.00 0.00 31.07 2.57
2365 6470 8.937634 AGTCCTGCATTTTCATGATTTATTTC 57.062 30.769 0.00 0.00 31.07 2.17
2412 6517 4.878397 CAGGAGGCTTAGGAAAATACACAG 59.122 45.833 0.00 0.00 0.00 3.66
2449 6554 3.513515 GCCCAACAATTTCCATGTCCTTA 59.486 43.478 0.00 0.00 0.00 2.69
2485 6590 8.246180 ACAAGTTCCATTTGATAATGCAGTAAG 58.754 33.333 0.00 0.00 39.87 2.34
2578 6693 3.502979 TGCCACCCACTACGAAAATAAAC 59.497 43.478 0.00 0.00 0.00 2.01
2579 6694 3.502979 GCCACCCACTACGAAAATAAACA 59.497 43.478 0.00 0.00 0.00 2.83
2580 6695 4.157105 GCCACCCACTACGAAAATAAACAT 59.843 41.667 0.00 0.00 0.00 2.71
2744 6860 3.852205 GCAATCGATTGTGCCATCATCAG 60.852 47.826 32.52 9.04 39.88 2.90
2778 6894 6.735678 TTGTACAACCATATGCACAGTAAG 57.264 37.500 3.59 0.00 28.81 2.34
2948 7072 1.110442 AGAGAACATCAGAGCTCCCG 58.890 55.000 10.93 1.67 0.00 5.14
2953 7077 1.227497 CATCAGAGCTCCCGCCTTC 60.227 63.158 10.93 0.00 36.60 3.46
2973 7122 5.046304 CCTTCAATTCTAGAGTTGAGGTCCA 60.046 44.000 27.27 15.27 38.11 4.02
3071 7240 6.426937 GGCACTCACAAGTTTCAAATAGAGTA 59.573 38.462 0.00 0.00 33.72 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.047274 GCTCCAACAGCGGTGCTA 60.047 61.111 15.82 0.00 41.37 3.49
88 89 1.003355 CGGGTCCAATGAGTGCTGT 60.003 57.895 0.00 0.00 0.00 4.40
148 149 0.035152 CATGCTGGACAAGGGCACTA 60.035 55.000 0.00 0.00 38.83 2.74
176 177 2.000447 GATGGTAACGAGTGACTTGGC 59.000 52.381 4.63 0.00 42.51 4.52
190 191 1.380785 AACCTCGCCGGAGATGGTA 60.381 57.895 22.61 0.00 43.27 3.25
353 356 7.673180 AGGAATTCAAGATCAAAATGAAAGCA 58.327 30.769 7.93 0.00 36.72 3.91
424 427 8.615211 TGATGATCAAATCAAAATAACGAGGAG 58.385 33.333 0.00 0.00 43.50 3.69
425 428 8.504812 TGATGATCAAATCAAAATAACGAGGA 57.495 30.769 0.00 0.00 43.50 3.71
430 433 6.074676 GGCGCTGATGATCAAATCAAAATAAC 60.075 38.462 7.64 0.00 43.50 1.89
544 547 2.564062 CAACTGGAACAAGGGCATCAAT 59.436 45.455 0.00 0.00 38.70 2.57
665 901 9.010029 CCAGGTTTTGTTCTTTAGCTTCTTATA 57.990 33.333 0.00 0.00 0.00 0.98
666 902 7.039714 CCCAGGTTTTGTTCTTTAGCTTCTTAT 60.040 37.037 0.00 0.00 0.00 1.73
692 3719 4.906618 TCCCAGGTATGACAACTCTTTTC 58.093 43.478 0.00 0.00 0.00 2.29
694 3721 6.636454 TTATCCCAGGTATGACAACTCTTT 57.364 37.500 0.00 0.00 0.00 2.52
697 3724 5.817816 CAGTTTATCCCAGGTATGACAACTC 59.182 44.000 0.00 0.00 0.00 3.01
709 3737 6.180472 ACCTCACATAAACAGTTTATCCCAG 58.820 40.000 14.64 10.30 33.73 4.45
765 3793 5.392595 CCACCGAAGAAACAAAAGAACTCAA 60.393 40.000 0.00 0.00 0.00 3.02
766 3794 4.095782 CCACCGAAGAAACAAAAGAACTCA 59.904 41.667 0.00 0.00 0.00 3.41
780 3808 2.488771 TAGCTCCGTCCCACCGAAGA 62.489 60.000 0.00 0.00 0.00 2.87
789 3817 0.656785 CGTCTGTACTAGCTCCGTCC 59.343 60.000 0.00 0.00 0.00 4.79
821 3849 1.629013 GCTCATTAAACTTTGGGCGC 58.371 50.000 0.00 0.00 28.09 6.53
862 3890 3.309121 GGATCTCCATCTCCTCCTCCTAG 60.309 56.522 0.00 0.00 35.64 3.02
863 3891 2.652348 GGATCTCCATCTCCTCCTCCTA 59.348 54.545 0.00 0.00 35.64 2.94
864 3892 1.432807 GGATCTCCATCTCCTCCTCCT 59.567 57.143 0.00 0.00 35.64 3.69
887 3915 2.750141 TTATCGTGAGGGTCTAGCCT 57.250 50.000 0.00 0.00 37.43 4.58
898 3926 4.520874 TGGCACAAGGAAAATTTATCGTGA 59.479 37.500 11.42 0.00 31.92 4.35
923 3951 0.540597 GCTTTTCTTGAGGGGCTGGT 60.541 55.000 0.00 0.00 0.00 4.00
1013 5050 1.816835 CACCTAGAGTTACTGCCACGA 59.183 52.381 0.00 0.00 0.00 4.35
1063 5101 4.703093 GGTACCTAGATAGCTAGCTTCAGG 59.297 50.000 24.88 21.28 42.29 3.86
1077 5115 1.406539 GGCGATCAAACGGTACCTAGA 59.593 52.381 10.90 2.68 0.00 2.43
1078 5116 1.537562 GGGCGATCAAACGGTACCTAG 60.538 57.143 10.90 0.00 0.00 3.02
1079 5117 0.461135 GGGCGATCAAACGGTACCTA 59.539 55.000 10.90 0.00 0.00 3.08
1080 5118 1.219935 GGGCGATCAAACGGTACCT 59.780 57.895 10.90 0.00 0.00 3.08
1116 5154 0.798159 TCTCTCGCGTGCTACGTTTA 59.202 50.000 5.77 0.00 44.73 2.01
1121 5159 0.867753 CCATGTCTCTCGCGTGCTAC 60.868 60.000 5.77 5.90 0.00 3.58
1122 5160 1.433471 CCATGTCTCTCGCGTGCTA 59.567 57.895 5.77 0.00 0.00 3.49
1123 5161 2.182791 CCATGTCTCTCGCGTGCT 59.817 61.111 5.77 0.00 0.00 4.40
1124 5162 3.558411 GCCATGTCTCTCGCGTGC 61.558 66.667 5.77 0.00 0.00 5.34
1125 5163 3.250323 CGCCATGTCTCTCGCGTG 61.250 66.667 5.77 3.13 39.78 5.34
1126 5164 3.402691 CTCGCCATGTCTCTCGCGT 62.403 63.158 5.77 0.00 44.73 6.01
1127 5165 2.653448 CTCGCCATGTCTCTCGCG 60.653 66.667 0.00 0.00 45.76 5.87
1128 5166 2.959071 GCTCGCCATGTCTCTCGC 60.959 66.667 0.00 0.00 0.00 5.03
1129 5167 1.588403 CTGCTCGCCATGTCTCTCG 60.588 63.158 0.00 0.00 0.00 4.04
1130 5168 1.227205 CCTGCTCGCCATGTCTCTC 60.227 63.158 0.00 0.00 0.00 3.20
1131 5169 2.898738 CCTGCTCGCCATGTCTCT 59.101 61.111 0.00 0.00 0.00 3.10
1132 5170 2.894387 GCCTGCTCGCCATGTCTC 60.894 66.667 0.00 0.00 0.00 3.36
1150 5188 1.060266 CTTTCGCTGCTGACGATTCTG 59.940 52.381 9.94 0.00 39.65 3.02
1187 5225 1.063649 CCACTCGTACACGGGATCG 59.936 63.158 8.93 0.00 43.86 3.69
1190 5228 1.973281 GACCCACTCGTACACGGGA 60.973 63.158 8.93 0.00 43.86 5.14
1298 5340 2.291089 GGTTAATTCGGGTTCAGGGGAA 60.291 50.000 0.00 0.00 0.00 3.97
1325 5380 4.942483 CAGTAGGTACAGTACAGTACAGCT 59.058 45.833 24.58 17.22 44.76 4.24
1326 5381 4.940046 TCAGTAGGTACAGTACAGTACAGC 59.060 45.833 24.58 15.52 44.76 4.40
1327 5382 7.627298 ATTCAGTAGGTACAGTACAGTACAG 57.373 40.000 24.58 7.52 44.76 2.74
1328 5383 7.449395 ACAATTCAGTAGGTACAGTACAGTACA 59.551 37.037 24.58 7.50 44.76 2.90
1329 5384 7.824672 ACAATTCAGTAGGTACAGTACAGTAC 58.175 38.462 17.67 17.67 42.78 2.73
1330 5385 8.950210 GTACAATTCAGTAGGTACAGTACAGTA 58.050 37.037 12.89 0.00 36.87 2.74
1331 5386 6.912951 ACAATTCAGTAGGTACAGTACAGT 57.087 37.500 12.89 0.00 0.00 3.55
1332 5387 6.965500 CGTACAATTCAGTAGGTACAGTACAG 59.035 42.308 12.89 0.00 36.72 2.74
1333 5388 6.430925 ACGTACAATTCAGTAGGTACAGTACA 59.569 38.462 12.89 0.00 40.21 2.90
1334 5389 6.846350 ACGTACAATTCAGTAGGTACAGTAC 58.154 40.000 1.59 1.59 40.21 2.73
1335 5390 8.615211 CATACGTACAATTCAGTAGGTACAGTA 58.385 37.037 0.00 8.48 43.72 2.74
1336 5391 5.972107 ACGTACAATTCAGTAGGTACAGT 57.028 39.130 0.00 0.00 40.21 3.55
1337 5392 7.642978 GTCATACGTACAATTCAGTAGGTACAG 59.357 40.741 0.00 6.97 43.72 2.74
1338 5393 7.121020 TGTCATACGTACAATTCAGTAGGTACA 59.879 37.037 0.00 5.35 43.72 2.90
1350 5405 9.541143 TCATCAACATAATGTCATACGTACAAT 57.459 29.630 0.00 0.00 0.00 2.71
1353 5408 9.191995 TGATCATCAACATAATGTCATACGTAC 57.808 33.333 0.00 0.00 0.00 3.67
1354 5409 9.757227 TTGATCATCAACATAATGTCATACGTA 57.243 29.630 0.00 0.00 30.26 3.57
1355 5410 8.661352 TTGATCATCAACATAATGTCATACGT 57.339 30.769 0.00 0.00 30.26 3.57
1356 5411 8.225777 CCTTGATCATCAACATAATGTCATACG 58.774 37.037 0.00 0.00 32.21 3.06
1359 5414 7.064866 ACCCTTGATCATCAACATAATGTCAT 58.935 34.615 0.00 0.00 32.21 3.06
1375 5430 3.264450 TCCTCCTTCTTGAACCCTTGATC 59.736 47.826 0.00 0.00 0.00 2.92
1376 5431 3.009584 GTCCTCCTTCTTGAACCCTTGAT 59.990 47.826 0.00 0.00 0.00 2.57
1377 5432 2.372172 GTCCTCCTTCTTGAACCCTTGA 59.628 50.000 0.00 0.00 0.00 3.02
1428 5483 3.083349 TGGCCGAGGATGGTCAGG 61.083 66.667 0.00 0.00 39.11 3.86
1431 5486 1.899437 TTCTGTGGCCGAGGATGGTC 61.899 60.000 0.00 0.00 0.00 4.02
1433 5488 1.450312 GTTCTGTGGCCGAGGATGG 60.450 63.158 0.00 0.00 0.00 3.51
1458 5513 4.143333 ACGTTCCCATCTCCGGCG 62.143 66.667 0.00 0.00 0.00 6.46
1460 5515 2.511600 GCACGTTCCCATCTCCGG 60.512 66.667 0.00 0.00 0.00 5.14
1487 5542 0.464554 GGATAGCAGCTGGAACACCC 60.465 60.000 17.12 0.00 0.00 4.61
1494 5549 0.602106 CGGATGTGGATAGCAGCTGG 60.602 60.000 17.12 0.00 0.00 4.85
1502 5557 1.315690 GTCGAGGTCGGATGTGGATA 58.684 55.000 0.00 0.00 40.29 2.59
1594 5649 3.411517 ATTCTCACTGGGCGGGGG 61.412 66.667 0.00 0.00 0.00 5.40
1595 5650 2.124570 CATTCTCACTGGGCGGGG 60.125 66.667 0.00 0.00 0.00 5.73
1596 5651 1.153289 CTCATTCTCACTGGGCGGG 60.153 63.158 0.00 0.00 0.00 6.13
1597 5652 1.153289 CCTCATTCTCACTGGGCGG 60.153 63.158 0.00 0.00 0.00 6.13
1598 5653 1.817099 GCCTCATTCTCACTGGGCG 60.817 63.158 0.00 0.00 0.00 6.13
1599 5654 1.452833 GGCCTCATTCTCACTGGGC 60.453 63.158 0.00 0.00 38.92 5.36
1600 5655 0.179936 GAGGCCTCATTCTCACTGGG 59.820 60.000 28.43 0.00 0.00 4.45
1601 5656 0.179089 CGAGGCCTCATTCTCACTGG 60.179 60.000 31.67 8.04 0.00 4.00
1602 5657 0.179089 CCGAGGCCTCATTCTCACTG 60.179 60.000 31.67 12.17 0.00 3.66
1603 5658 0.324738 TCCGAGGCCTCATTCTCACT 60.325 55.000 31.67 0.00 0.00 3.41
1604 5659 0.179097 GTCCGAGGCCTCATTCTCAC 60.179 60.000 31.67 14.02 0.00 3.51
1605 5660 1.667154 CGTCCGAGGCCTCATTCTCA 61.667 60.000 31.67 5.91 0.00 3.27
1606 5661 1.066587 CGTCCGAGGCCTCATTCTC 59.933 63.158 31.67 15.25 0.00 2.87
1607 5662 3.082579 GCGTCCGAGGCCTCATTCT 62.083 63.158 31.67 0.00 0.00 2.40
1608 5663 2.586357 GCGTCCGAGGCCTCATTC 60.586 66.667 31.67 18.58 0.00 2.67
1609 5664 3.077556 AGCGTCCGAGGCCTCATT 61.078 61.111 31.67 7.63 0.00 2.57
1610 5665 3.842923 CAGCGTCCGAGGCCTCAT 61.843 66.667 31.67 7.60 0.00 2.90
1612 5667 4.500116 GACAGCGTCCGAGGCCTC 62.500 72.222 23.79 23.79 0.00 4.70
1636 5691 3.788937 TGGATTTCTTATCCGTCGGTTC 58.211 45.455 11.88 0.00 41.03 3.62
1641 5702 5.236695 GCTAACCTTGGATTTCTTATCCGTC 59.763 44.000 0.00 0.00 41.03 4.79
1648 5709 3.333680 TCCTGGCTAACCTTGGATTTCTT 59.666 43.478 0.00 0.00 35.38 2.52
1723 5787 2.266055 GTCCTTGGCCGTCTCCTG 59.734 66.667 0.00 0.00 0.00 3.86
1734 5798 1.165907 TCGCTGCAGTTTGGTCCTTG 61.166 55.000 16.64 0.00 0.00 3.61
1735 5799 0.886490 CTCGCTGCAGTTTGGTCCTT 60.886 55.000 16.64 0.00 0.00 3.36
1736 5800 1.302033 CTCGCTGCAGTTTGGTCCT 60.302 57.895 16.64 0.00 0.00 3.85
1737 5801 0.320421 TACTCGCTGCAGTTTGGTCC 60.320 55.000 16.64 0.00 0.00 4.46
1738 5802 1.071605 CTACTCGCTGCAGTTTGGTC 58.928 55.000 16.64 0.00 0.00 4.02
1739 5803 0.951040 GCTACTCGCTGCAGTTTGGT 60.951 55.000 16.64 11.54 35.14 3.67
1740 5804 0.950555 TGCTACTCGCTGCAGTTTGG 60.951 55.000 16.64 6.11 40.11 3.28
1741 5805 0.867746 TTGCTACTCGCTGCAGTTTG 59.132 50.000 16.64 7.93 40.46 2.93
1742 5806 1.151668 CTTGCTACTCGCTGCAGTTT 58.848 50.000 16.64 0.00 40.46 2.66
1743 5807 0.671781 CCTTGCTACTCGCTGCAGTT 60.672 55.000 16.64 0.00 40.46 3.16
1744 5808 1.079543 CCTTGCTACTCGCTGCAGT 60.080 57.895 16.64 5.27 40.46 4.40
1745 5809 0.390340 TTCCTTGCTACTCGCTGCAG 60.390 55.000 10.11 10.11 40.46 4.41
1746 5810 0.670546 GTTCCTTGCTACTCGCTGCA 60.671 55.000 0.00 0.00 40.11 4.41
1747 5811 1.362406 GGTTCCTTGCTACTCGCTGC 61.362 60.000 0.00 0.00 40.11 5.25
1748 5812 0.741221 GGGTTCCTTGCTACTCGCTG 60.741 60.000 0.00 0.00 40.11 5.18
1749 5813 1.597461 GGGTTCCTTGCTACTCGCT 59.403 57.895 0.00 0.00 40.11 4.93
1750 5814 1.449778 GGGGTTCCTTGCTACTCGC 60.450 63.158 0.00 0.00 39.77 5.03
1751 5815 1.221021 GGGGGTTCCTTGCTACTCG 59.779 63.158 0.00 0.00 0.00 4.18
1752 5816 1.221021 CGGGGGTTCCTTGCTACTC 59.779 63.158 0.00 0.00 0.00 2.59
1753 5817 2.298661 CCGGGGGTTCCTTGCTACT 61.299 63.158 0.00 0.00 0.00 2.57
1754 5818 2.271173 CCGGGGGTTCCTTGCTAC 59.729 66.667 0.00 0.00 0.00 3.58
1755 5819 3.723922 GCCGGGGGTTCCTTGCTA 61.724 66.667 2.18 0.00 0.00 3.49
1775 5839 2.093394 TGTTTCCTGTCGTCCACTTTCA 60.093 45.455 0.00 0.00 0.00 2.69
1810 5874 2.294512 CTCCTTTCACCACCTTTTCTGC 59.705 50.000 0.00 0.00 0.00 4.26
1838 5911 1.280421 GCTTCTCCTTGTGGTCCTGAT 59.720 52.381 0.00 0.00 34.23 2.90
1917 6002 1.296715 CCACTTGAACCCCTCCTCG 59.703 63.158 0.00 0.00 0.00 4.63
2047 6144 0.726827 ACGGACGCTGCATTTACATG 59.273 50.000 0.00 0.00 0.00 3.21
2116 6216 0.666913 TTATCTCGGCAGCTACGGTC 59.333 55.000 9.72 0.00 0.00 4.79
2117 6217 1.108776 TTTATCTCGGCAGCTACGGT 58.891 50.000 9.72 0.00 0.00 4.83
2118 6218 2.440539 ATTTATCTCGGCAGCTACGG 57.559 50.000 9.72 0.00 0.00 4.02
2119 6219 9.544314 GTATATATATTTATCTCGGCAGCTACG 57.456 37.037 0.00 3.77 0.00 3.51
2120 6220 9.544314 CGTATATATATTTATCTCGGCAGCTAC 57.456 37.037 0.00 0.00 0.00 3.58
2168 6268 7.795734 ACGTACGTGATAGTATCATTAAACTCG 59.204 37.037 22.14 14.02 42.04 4.18
2223 6328 8.903820 GGAGCAAGTGATAGTACCATTTTATTT 58.096 33.333 0.00 0.00 0.00 1.40
2225 6330 6.998673 GGGAGCAAGTGATAGTACCATTTTAT 59.001 38.462 0.00 0.00 0.00 1.40
2226 6331 6.354130 GGGAGCAAGTGATAGTACCATTTTA 58.646 40.000 0.00 0.00 0.00 1.52
2228 6333 4.683400 CGGGAGCAAGTGATAGTACCATTT 60.683 45.833 0.00 0.00 0.00 2.32
2230 6335 2.365617 CGGGAGCAAGTGATAGTACCAT 59.634 50.000 0.00 0.00 0.00 3.55
2231 6336 1.754803 CGGGAGCAAGTGATAGTACCA 59.245 52.381 0.00 0.00 0.00 3.25
2232 6337 2.510768 CGGGAGCAAGTGATAGTACC 57.489 55.000 0.00 0.00 0.00 3.34
2246 6351 3.081804 ACCAATTTCTTTACAGCGGGAG 58.918 45.455 0.00 0.00 0.00 4.30
2247 6352 3.149005 ACCAATTTCTTTACAGCGGGA 57.851 42.857 0.00 0.00 0.00 5.14
2248 6353 5.158494 GTTTACCAATTTCTTTACAGCGGG 58.842 41.667 0.00 0.00 0.00 6.13
2249 6354 4.849383 CGTTTACCAATTTCTTTACAGCGG 59.151 41.667 0.00 0.00 0.00 5.52
2250 6355 4.319901 GCGTTTACCAATTTCTTTACAGCG 59.680 41.667 0.00 0.00 0.00 5.18
2251 6356 5.458015 AGCGTTTACCAATTTCTTTACAGC 58.542 37.500 0.00 0.00 0.00 4.40
2252 6357 6.899114 AGAGCGTTTACCAATTTCTTTACAG 58.101 36.000 0.00 0.00 0.00 2.74
2253 6358 6.870971 AGAGCGTTTACCAATTTCTTTACA 57.129 33.333 0.00 0.00 0.00 2.41
2285 6390 2.231964 ACGCATGTACTCCCTTCGTAAA 59.768 45.455 0.00 0.00 0.00 2.01
2286 6391 1.820519 ACGCATGTACTCCCTTCGTAA 59.179 47.619 0.00 0.00 0.00 3.18
2287 6392 1.466856 ACGCATGTACTCCCTTCGTA 58.533 50.000 0.00 0.00 0.00 3.43
2288 6393 1.466856 TACGCATGTACTCCCTTCGT 58.533 50.000 0.00 0.00 0.00 3.85
2289 6394 2.572191 TTACGCATGTACTCCCTTCG 57.428 50.000 0.00 0.00 0.00 3.79
2290 6395 7.871463 AGTATATTTTACGCATGTACTCCCTTC 59.129 37.037 0.00 0.00 0.00 3.46
2291 6396 7.732996 AGTATATTTTACGCATGTACTCCCTT 58.267 34.615 0.00 0.00 0.00 3.95
2292 6397 7.299246 AGTATATTTTACGCATGTACTCCCT 57.701 36.000 0.00 0.00 0.00 4.20
2293 6398 6.307318 CGAGTATATTTTACGCATGTACTCCC 59.693 42.308 10.38 0.00 40.03 4.30
2294 6399 6.183359 GCGAGTATATTTTACGCATGTACTCC 60.183 42.308 0.00 3.34 46.75 3.85
2295 6400 6.739561 GCGAGTATATTTTACGCATGTACTC 58.260 40.000 0.00 7.45 46.75 2.59
2296 6401 6.686130 GCGAGTATATTTTACGCATGTACT 57.314 37.500 0.00 0.00 46.75 2.73
2304 6409 3.743911 TGGCCATGCGAGTATATTTTACG 59.256 43.478 0.00 0.00 0.00 3.18
2305 6410 5.643777 AGATGGCCATGCGAGTATATTTTAC 59.356 40.000 26.56 1.96 0.00 2.01
2306 6411 5.804639 AGATGGCCATGCGAGTATATTTTA 58.195 37.500 26.56 0.00 0.00 1.52
2307 6412 4.655963 AGATGGCCATGCGAGTATATTTT 58.344 39.130 26.56 0.00 0.00 1.82
2308 6413 4.292186 AGATGGCCATGCGAGTATATTT 57.708 40.909 26.56 0.00 0.00 1.40
2309 6414 3.988976 AGATGGCCATGCGAGTATATT 57.011 42.857 26.56 0.00 0.00 1.28
2310 6415 3.988976 AAGATGGCCATGCGAGTATAT 57.011 42.857 26.56 0.00 0.00 0.86
2311 6416 5.420725 AATAAGATGGCCATGCGAGTATA 57.579 39.130 26.56 5.61 0.00 1.47
2312 6417 3.988976 ATAAGATGGCCATGCGAGTAT 57.011 42.857 26.56 9.89 0.00 2.12
2313 6418 3.769739 AATAAGATGGCCATGCGAGTA 57.230 42.857 26.56 7.89 0.00 2.59
2314 6419 2.645838 AATAAGATGGCCATGCGAGT 57.354 45.000 26.56 3.45 0.00 4.18
2315 6420 3.996150 AAAATAAGATGGCCATGCGAG 57.004 42.857 26.56 0.00 0.00 5.03
2316 6421 3.698539 TGAAAAATAAGATGGCCATGCGA 59.301 39.130 26.56 7.83 0.00 5.10
2317 6422 4.044336 TGAAAAATAAGATGGCCATGCG 57.956 40.909 26.56 0.00 0.00 4.73
2318 6423 6.752168 ACTATGAAAAATAAGATGGCCATGC 58.248 36.000 26.56 14.84 0.00 4.06
2319 6424 7.232127 AGGACTATGAAAAATAAGATGGCCATG 59.768 37.037 26.56 5.61 0.00 3.66
2320 6425 7.232127 CAGGACTATGAAAAATAAGATGGCCAT 59.768 37.037 20.96 20.96 0.00 4.40
2321 6426 6.547141 CAGGACTATGAAAAATAAGATGGCCA 59.453 38.462 8.56 8.56 0.00 5.36
2322 6427 6.515696 GCAGGACTATGAAAAATAAGATGGCC 60.516 42.308 0.00 0.00 0.00 5.36
2323 6428 6.039717 TGCAGGACTATGAAAAATAAGATGGC 59.960 38.462 0.00 0.00 0.00 4.40
2324 6429 7.572523 TGCAGGACTATGAAAAATAAGATGG 57.427 36.000 0.00 0.00 0.00 3.51
2328 6433 9.859427 TGAAAATGCAGGACTATGAAAAATAAG 57.141 29.630 0.00 0.00 0.00 1.73
2330 6435 9.806203 CATGAAAATGCAGGACTATGAAAAATA 57.194 29.630 0.00 0.00 0.00 1.40
2331 6436 8.533657 TCATGAAAATGCAGGACTATGAAAAAT 58.466 29.630 0.00 0.00 0.00 1.82
2332 6437 7.894708 TCATGAAAATGCAGGACTATGAAAAA 58.105 30.769 0.00 0.00 0.00 1.94
2333 6438 7.465353 TCATGAAAATGCAGGACTATGAAAA 57.535 32.000 0.00 0.00 0.00 2.29
2334 6439 7.649533 ATCATGAAAATGCAGGACTATGAAA 57.350 32.000 0.00 0.00 30.77 2.69
2335 6440 7.649533 AATCATGAAAATGCAGGACTATGAA 57.350 32.000 0.00 0.00 30.77 2.57
2342 6447 9.947433 AAAGAAATAAATCATGAAAATGCAGGA 57.053 25.926 0.00 0.00 32.72 3.86
2371 6476 5.338871 CCTCCTGGCTTTGTACCTTACATAA 60.339 44.000 0.00 0.00 38.68 1.90
2372 6477 4.163458 CCTCCTGGCTTTGTACCTTACATA 59.837 45.833 0.00 0.00 38.68 2.29
2373 6478 3.054361 CCTCCTGGCTTTGTACCTTACAT 60.054 47.826 0.00 0.00 38.68 2.29
2374 6479 2.304761 CCTCCTGGCTTTGTACCTTACA 59.695 50.000 0.00 0.00 36.79 2.41
2375 6480 2.987232 CCTCCTGGCTTTGTACCTTAC 58.013 52.381 0.00 0.00 0.00 2.34
2399 6504 6.583806 CGTCGTTAACTACTGTGTATTTTCCT 59.416 38.462 8.45 0.00 0.00 3.36
2412 6517 2.741930 GGGCACCGTCGTTAACTAC 58.258 57.895 3.71 1.87 40.86 2.73
2449 6554 2.638480 TGGAACTTGTGCAGCTTAGT 57.362 45.000 0.00 0.00 0.00 2.24
2594 6709 1.081094 GGCGCAGTTGTACGGTAAAT 58.919 50.000 10.83 0.00 0.00 1.40
2744 6860 1.269723 GGTTGTACAAAAGGCCTGCTC 59.730 52.381 5.69 0.00 0.00 4.26
2778 6894 1.531578 GCCGATCTTTTAATCGCCCTC 59.468 52.381 0.91 0.00 45.56 4.30
2804 6922 0.759436 AGAACAGGGTCCACGACAGT 60.759 55.000 0.00 0.00 33.68 3.55
2948 7072 4.837972 ACCTCAACTCTAGAATTGAAGGC 58.162 43.478 21.84 0.00 34.52 4.35
2953 7077 7.693969 ATTTTGGACCTCAACTCTAGAATTG 57.306 36.000 7.62 7.62 34.67 2.32
2973 7122 4.085357 TGTCTCTGTGTGCCACTATTTT 57.915 40.909 0.00 0.00 35.11 1.82
3037 7204 2.038557 ACTTGTGAGTGCCCGATAGTTT 59.961 45.455 0.00 0.00 33.99 2.66
3078 7247 6.815641 GCACATGATTCTATAGATCCATCGTT 59.184 38.462 2.58 0.00 0.00 3.85
3080 7249 6.335777 TGCACATGATTCTATAGATCCATCG 58.664 40.000 2.58 7.63 0.00 3.84


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

AutoCloner maintained by Alex Coulton.