Multiple sequence alignment - TraesCS1D01G017100

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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 TraesCS1D01G017100 chr1D 100.000 3482 0 0 1 3482 7714736 7718217 0.000000e+00 6431.0
1 TraesCS1D01G017100 chr1D 83.036 1963 230 54 104 2020 7342940 7341035 0.000000e+00 1685.0
2 TraesCS1D01G017100 chr1D 83.167 1604 195 45 457 2020 7768155 7769723 0.000000e+00 1397.0
3 TraesCS1D01G017100 chr1D 80.050 802 132 18 2026 2807 7769765 7770558 1.400000e-158 569.0
4 TraesCS1D01G017100 chr1D 90.688 247 16 4 104 349 7767850 7768090 4.340000e-84 322.0
5 TraesCS1D01G017100 chr1D 80.157 383 56 11 107 481 7765192 7765562 5.730000e-68 268.0
6 TraesCS1D01G017100 chr1D 79.474 380 70 6 2283 2657 7340955 7340579 2.670000e-66 263.0
7 TraesCS1D01G017100 chr1D 85.417 240 24 4 3130 3365 7771452 7771684 4.490000e-59 239.0
8 TraesCS1D01G017100 chr1B 79.472 1666 246 57 989 2590 9935122 9936755 0.000000e+00 1094.0
9 TraesCS1D01G017100 chr1B 88.268 716 64 11 256 965 9934427 9935128 0.000000e+00 839.0
10 TraesCS1D01G017100 chr1B 78.346 762 113 34 1270 2005 9915362 9916097 2.470000e-121 446.0
11 TraesCS1D01G017100 chr1B 86.005 393 37 12 891 1274 9909953 9910336 4.180000e-109 405.0
12 TraesCS1D01G017100 chr1B 81.604 424 60 11 2386 2808 9937890 9938296 5.570000e-88 335.0
13 TraesCS1D01G017100 chr1B 93.220 59 4 0 2750 2808 9916806 9916864 1.720000e-13 87.9
14 TraesCS1D01G017100 chr1A 83.496 921 121 21 1981 2879 9222523 9223434 0.000000e+00 830.0
15 TraesCS1D01G017100 chr1A 78.967 1065 143 36 867 1876 9221799 9220761 0.000000e+00 651.0
16 TraesCS1D01G017100 chr1A 87.572 523 55 6 256 777 9202821 9203334 6.430000e-167 597.0
17 TraesCS1D01G017100 chr1A 79.602 804 133 20 2026 2807 9204590 9205384 6.570000e-152 547.0
18 TraesCS1D01G017100 chr1A 86.042 480 48 7 2891 3365 9206249 9206714 6.710000e-137 497.0
19 TraesCS1D01G017100 chr1A 82.135 431 43 18 419 836 9222278 9221869 4.300000e-89 339.0
20 TraesCS1D01G017100 chr1A 74.937 794 152 25 1911 2666 9220609 9219825 1.560000e-83 320.0
21 TraesCS1D01G017100 chr1A 78.638 426 80 7 2386 2808 9224646 9225063 4.430000e-69 272.0
22 TraesCS1D01G017100 chr1A 80.000 385 53 14 109 481 9200902 9201274 2.670000e-66 263.0
23 TraesCS1D01G017100 chr1A 77.344 384 50 17 109 481 9173523 9173880 3.550000e-45 193.0
24 TraesCS1D01G017100 chr1A 90.179 112 11 0 236 347 9222415 9222304 2.800000e-31 147.0
25 TraesCS1D01G017100 chr1A 74.163 209 49 3 2075 2279 554071454 554071247 8.010000e-12 82.4
26 TraesCS1D01G017100 chrUn 77.344 384 50 17 109 481 278887699 278887342 3.550000e-45 193.0
27 TraesCS1D01G017100 chr7D 81.429 70 11 2 2039 2107 545256027 545256095 4.860000e-04 56.5


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 TraesCS1D01G017100 chr1D 7714736 7718217 3481 False 6431.00 6431 100.000000 1 3482 1 chr1D.!!$F1 3481
1 TraesCS1D01G017100 chr1D 7340579 7342940 2361 True 974.00 1685 81.255000 104 2657 2 chr1D.!!$R1 2553
2 TraesCS1D01G017100 chr1D 7765192 7771684 6492 False 559.00 1397 83.895800 104 3365 5 chr1D.!!$F2 3261
3 TraesCS1D01G017100 chr1B 9934427 9938296 3869 False 756.00 1094 83.114667 256 2808 3 chr1B.!!$F3 2552
4 TraesCS1D01G017100 chr1B 9915362 9916864 1502 False 266.95 446 85.783000 1270 2808 2 chr1B.!!$F2 1538
5 TraesCS1D01G017100 chr1A 9222523 9225063 2540 False 551.00 830 81.067000 1981 2879 2 chr1A.!!$F3 898
6 TraesCS1D01G017100 chr1A 9200902 9206714 5812 False 476.00 597 83.304000 109 3365 4 chr1A.!!$F2 3256
7 TraesCS1D01G017100 chr1A 9219825 9222415 2590 True 364.25 651 81.554500 236 2666 4 chr1A.!!$R2 2430

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
557 4928 0.883153 TTGTCACATGCATGCCAGAC 59.117 50.0 27.38 27.38 0.00 3.51 F
1504 5998 0.026027 CTACTACGACGTGGCGAGTC 59.974 60.0 11.56 2.56 35.41 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 6411 0.033796 ACATGGGCTGGTCTCCAATG 60.034 55.0 0.00 0.0 36.54 2.82 R
3402 8999 0.031857 TCGAACAAAGTACGCCGGAA 59.968 50.0 5.05 0.0 0.00 4.30 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
55 56 7.921786 TTTTCAGTGATGTATAGTTTCCCTG 57.078 36.000 0.00 0.00 0.00 4.45
56 57 5.614324 TCAGTGATGTATAGTTTCCCTGG 57.386 43.478 0.00 0.00 0.00 4.45
57 58 5.030147 TCAGTGATGTATAGTTTCCCTGGT 58.970 41.667 0.00 0.00 0.00 4.00
58 59 6.199376 TCAGTGATGTATAGTTTCCCTGGTA 58.801 40.000 0.00 0.00 0.00 3.25
59 60 6.670464 TCAGTGATGTATAGTTTCCCTGGTAA 59.330 38.462 0.00 0.00 0.00 2.85
61 62 6.099845 AGTGATGTATAGTTTCCCTGGTAAGG 59.900 42.308 0.00 0.00 44.06 2.69
62 63 5.968167 TGATGTATAGTTTCCCTGGTAAGGT 59.032 40.000 0.00 0.00 42.74 3.50
63 64 7.070322 GTGATGTATAGTTTCCCTGGTAAGGTA 59.930 40.741 0.00 0.00 42.74 3.08
64 65 7.624478 TGATGTATAGTTTCCCTGGTAAGGTAA 59.376 37.037 0.00 0.00 42.74 2.85
65 66 7.186570 TGTATAGTTTCCCTGGTAAGGTAAC 57.813 40.000 0.00 0.00 42.74 2.50
93 94 8.738645 ATATCTATGTTGGTTCTCAAAAGGAC 57.261 34.615 0.00 0.00 37.08 3.85
94 95 5.935945 TCTATGTTGGTTCTCAAAAGGACA 58.064 37.500 0.00 0.00 37.08 4.02
95 96 6.361433 TCTATGTTGGTTCTCAAAAGGACAA 58.639 36.000 0.00 0.00 37.08 3.18
96 97 5.930837 ATGTTGGTTCTCAAAAGGACAAA 57.069 34.783 0.00 0.00 37.08 2.83
99 100 6.105333 TGTTGGTTCTCAAAAGGACAAATTG 58.895 36.000 0.00 0.00 37.08 2.32
102 103 6.940739 TGGTTCTCAAAAGGACAAATTGAAA 58.059 32.000 0.00 0.00 31.94 2.69
198 2758 2.035961 GCTATGTAGGAAGGATGCGACA 59.964 50.000 0.00 0.00 36.97 4.35
271 4602 2.033662 GCATCTAATTGTCGACGGCTTC 60.034 50.000 11.62 0.00 0.00 3.86
289 4620 3.798337 GCTTCAAACATGATTATTGGCCG 59.202 43.478 0.00 0.00 0.00 6.13
408 4779 7.749666 ACAACCATATTATATGGAACTCAGCT 58.250 34.615 31.21 9.10 41.64 4.24
429 4800 5.531659 AGCTGATCTAGAGCATCAAATTTGG 59.468 40.000 17.90 4.32 39.05 3.28
431 4802 5.443283 TGATCTAGAGCATCAAATTTGGCT 58.557 37.500 18.28 18.28 37.82 4.75
432 4803 6.594744 TGATCTAGAGCATCAAATTTGGCTA 58.405 36.000 18.26 11.37 37.82 3.93
442 4813 5.964958 TCAAATTTGGCTAGTTTCCAGAG 57.035 39.130 17.90 0.00 34.66 3.35
557 4928 0.883153 TTGTCACATGCATGCCAGAC 59.117 50.000 27.38 27.38 0.00 3.51
625 5003 5.624159 TGATGTTCTCTTGACCAAAGATGT 58.376 37.500 0.00 0.00 44.02 3.06
661 5043 3.744660 AGAGTTGAACATGTGAAGACCC 58.255 45.455 0.00 0.00 0.00 4.46
668 5050 1.302511 ATGTGAAGACCCACCGTGC 60.303 57.895 0.00 0.00 36.26 5.34
722 5108 2.343506 TGCCATCAAGCAACACCAG 58.656 52.632 0.00 0.00 40.56 4.00
736 5122 1.677576 ACACCAGTTGCAGACACAATG 59.322 47.619 0.00 0.00 0.00 2.82
737 5123 1.001048 CACCAGTTGCAGACACAATGG 60.001 52.381 0.41 0.41 35.80 3.16
745 5131 2.104451 TGCAGACACAATGGGCAATTTT 59.896 40.909 0.00 0.00 0.00 1.82
748 5134 2.971330 AGACACAATGGGCAATTTTCCA 59.029 40.909 0.00 0.00 37.46 3.53
752 5138 4.202440 ACACAATGGGCAATTTTCCAATGA 60.202 37.500 15.17 0.00 37.38 2.57
756 5142 5.703730 ATGGGCAATTTTCCAATGAGATT 57.296 34.783 1.14 0.00 36.54 2.40
768 5154 4.227982 TCCAATGAGATTGATTCTGGACCA 59.772 41.667 0.00 0.00 42.83 4.02
864 5260 4.980805 GGCGACGTGGCTGGTTGA 62.981 66.667 22.08 0.00 40.72 3.18
882 5312 6.202331 TGGTTGATTGGTCTATAAGAGGAGA 58.798 40.000 0.00 0.00 0.00 3.71
884 5314 6.325286 GGTTGATTGGTCTATAAGAGGAGAGT 59.675 42.308 0.00 0.00 0.00 3.24
892 5322 6.300703 GTCTATAAGAGGAGAGTCAAGGCTA 58.699 44.000 0.00 0.00 0.00 3.93
911 5344 4.418392 GCTATGTGCTTCTTTGTTCCATG 58.582 43.478 0.00 0.00 38.95 3.66
928 5366 8.078060 TGTTCCATGAGTAGTTCATTCATCTA 57.922 34.615 0.00 0.00 44.14 1.98
936 5374 6.520272 AGTAGTTCATTCATCTATGCCACTC 58.480 40.000 0.00 0.00 0.00 3.51
937 5375 4.375272 AGTTCATTCATCTATGCCACTCG 58.625 43.478 0.00 0.00 0.00 4.18
938 5376 3.391506 TCATTCATCTATGCCACTCGG 57.608 47.619 0.00 0.00 0.00 4.63
1018 5470 3.391506 CGATGAGCATGGAACCATCTA 57.608 47.619 3.10 0.00 34.75 1.98
1034 5486 0.813184 TCTAGGGTCGTAACTTGCGG 59.187 55.000 0.00 0.00 0.00 5.69
1083 5538 4.038522 GCTGCTTGGAGTAGTGATGATAGA 59.961 45.833 0.00 0.00 30.12 1.98
1089 5544 8.364142 GCTTGGAGTAGTGATGATAGAATTAGT 58.636 37.037 0.00 0.00 0.00 2.24
1182 5655 0.744414 CCCCAGCCACACACGATAAG 60.744 60.000 0.00 0.00 0.00 1.73
1197 5670 5.889853 ACACGATAAGGACTGTAGTTATCCA 59.110 40.000 12.55 0.00 34.73 3.41
1220 5696 1.202806 CCAGGTGTTCAAGGAAGCAGA 60.203 52.381 0.00 0.00 0.00 4.26
1245 5721 1.599542 GCGTTCCATGCTGACTATTCC 59.400 52.381 0.00 0.00 0.00 3.01
1248 5724 3.682718 CGTTCCATGCTGACTATTCCCTT 60.683 47.826 0.00 0.00 0.00 3.95
1300 5776 1.379044 CCAAGCCTGGTGGATGTCC 60.379 63.158 0.00 0.00 38.54 4.02
1301 5777 1.687612 CAAGCCTGGTGGATGTCCT 59.312 57.895 0.09 0.00 36.82 3.85
1393 5881 1.686325 GGCGGAGAGGGTGAAGCATA 61.686 60.000 0.00 0.00 0.00 3.14
1410 5898 2.624838 GCATATGGCTGCTAACCAATGT 59.375 45.455 4.56 0.00 41.49 2.71
1415 5903 3.961849 TGGCTGCTAACCAATGTATCAA 58.038 40.909 0.00 0.00 33.12 2.57
1422 5910 5.045942 TGCTAACCAATGTATCAAGGACTCA 60.046 40.000 0.00 0.00 0.00 3.41
1452 5940 3.056821 CACTCCAGGAGATGTACAACGAA 60.057 47.826 24.45 0.00 33.32 3.85
1460 5948 4.082136 GGAGATGTACAACGAAGTCTCCTT 60.082 45.833 24.42 0.00 45.00 3.36
1470 5958 2.667137 GAAGTCTCCTTCGTGTCACAG 58.333 52.381 3.42 0.00 37.92 3.66
1492 5980 4.925576 CCCGCAGCCGCTACTACG 62.926 72.222 0.00 0.00 35.30 3.51
1504 5998 0.026027 CTACTACGACGTGGCGAGTC 59.974 60.000 11.56 2.56 35.41 3.36
1507 6001 1.632948 CTACGACGTGGCGAGTCTCA 61.633 60.000 11.56 0.00 36.53 3.27
1509 6009 2.179517 GACGTGGCGAGTCTCAGG 59.820 66.667 0.00 0.00 35.84 3.86
1512 6015 2.888863 GTGGCGAGTCTCAGGGAG 59.111 66.667 0.00 0.00 0.00 4.30
1581 6087 4.205181 CAGTTCATGCGTAGTTATGACGAG 59.795 45.833 0.00 0.00 42.98 4.18
1589 6095 0.456221 AGTTATGACGAGGACAGCGG 59.544 55.000 0.00 0.00 0.00 5.52
1591 6097 2.292794 TTATGACGAGGACAGCGGCC 62.293 60.000 0.00 0.00 35.47 6.13
1606 6112 2.819595 GCCACATGGATGACGCGT 60.820 61.111 13.85 13.85 37.39 6.01
1609 6115 1.226101 CACATGGATGACGCGTTGC 60.226 57.895 15.53 3.87 0.00 4.17
1610 6116 1.375908 ACATGGATGACGCGTTGCT 60.376 52.632 15.53 0.00 0.00 3.91
1612 6118 2.167219 ATGGATGACGCGTTGCTCG 61.167 57.895 15.53 0.00 43.12 5.03
1647 6153 0.811915 ACTTCGAGCGCATCTACACT 59.188 50.000 11.47 0.00 0.00 3.55
1668 6174 5.297029 CACTGACATCATGATGCTTGAGAAT 59.703 40.000 31.17 12.58 42.39 2.40
1736 6242 2.690510 GCCCTCTCTCTGGCCCTT 60.691 66.667 0.00 0.00 41.97 3.95
1738 6244 1.306482 CCCTCTCTCTGGCCCTTGA 60.306 63.158 0.00 0.00 0.00 3.02
1747 6259 1.774254 TCTGGCCCTTGAAGAAGTTCA 59.226 47.619 0.00 0.00 41.13 3.18
1765 6277 3.748863 ATCGTTGCGATGAGAAGCT 57.251 47.368 3.08 0.00 45.24 3.74
1781 6293 1.043022 AGCTGCCTGAAAAACCAAGG 58.957 50.000 0.00 0.00 0.00 3.61
1786 6298 1.669795 GCCTGAAAAACCAAGGCGATG 60.670 52.381 0.00 0.00 35.86 3.84
1787 6299 1.885887 CCTGAAAAACCAAGGCGATGA 59.114 47.619 0.00 0.00 0.00 2.92
1788 6300 2.095059 CCTGAAAAACCAAGGCGATGAG 60.095 50.000 0.00 0.00 0.00 2.90
1792 6304 1.168714 AAACCAAGGCGATGAGAAGC 58.831 50.000 0.00 0.00 0.00 3.86
1795 6307 1.167851 CCAAGGCGATGAGAAGCAAA 58.832 50.000 0.00 0.00 34.54 3.68
1798 6310 1.293924 AGGCGATGAGAAGCAAATCG 58.706 50.000 0.00 0.00 44.59 3.34
1799 6311 1.134699 AGGCGATGAGAAGCAAATCGA 60.135 47.619 8.35 0.00 44.57 3.59
1800 6312 1.260033 GGCGATGAGAAGCAAATCGAG 59.740 52.381 8.35 0.00 44.57 4.04
1801 6313 2.196749 GCGATGAGAAGCAAATCGAGA 58.803 47.619 8.35 0.00 44.57 4.04
1802 6314 2.604914 GCGATGAGAAGCAAATCGAGAA 59.395 45.455 8.35 0.00 44.57 2.87
1803 6315 3.302350 GCGATGAGAAGCAAATCGAGAAG 60.302 47.826 8.35 0.00 44.57 2.85
1813 6325 3.511699 CAAATCGAGAAGGACGACATCA 58.488 45.455 0.00 0.00 42.37 3.07
1876 6388 2.100197 TCTGGTTCTACATCGTGGGAG 58.900 52.381 0.00 0.00 0.00 4.30
1878 6390 2.496070 CTGGTTCTACATCGTGGGAGAA 59.504 50.000 0.53 0.53 0.00 2.87
1881 6393 3.683340 GGTTCTACATCGTGGGAGAAAAC 59.317 47.826 5.52 0.26 29.29 2.43
1884 6396 4.566004 TCTACATCGTGGGAGAAAACAAG 58.434 43.478 0.00 0.00 0.00 3.16
1885 6397 3.485463 ACATCGTGGGAGAAAACAAGA 57.515 42.857 0.00 0.00 0.00 3.02
1887 6399 3.815401 ACATCGTGGGAGAAAACAAGAAG 59.185 43.478 0.00 0.00 0.00 2.85
1889 6401 1.880027 CGTGGGAGAAAACAAGAAGGG 59.120 52.381 0.00 0.00 0.00 3.95
1891 6403 0.881796 GGGAGAAAACAAGAAGGGCG 59.118 55.000 0.00 0.00 0.00 6.13
1892 6404 1.544759 GGGAGAAAACAAGAAGGGCGA 60.545 52.381 0.00 0.00 0.00 5.54
1893 6405 1.807142 GGAGAAAACAAGAAGGGCGAG 59.193 52.381 0.00 0.00 0.00 5.03
1894 6406 2.550208 GGAGAAAACAAGAAGGGCGAGA 60.550 50.000 0.00 0.00 0.00 4.04
1896 6408 3.077359 AGAAAACAAGAAGGGCGAGATG 58.923 45.455 0.00 0.00 0.00 2.90
1909 6538 0.533755 CGAGATGCCCATTGGAGACC 60.534 60.000 3.62 0.00 0.00 3.85
1929 6558 4.914983 ACCAGCCCATGTCATTATCTATG 58.085 43.478 0.00 0.00 35.45 2.23
1945 6574 2.663630 TATGAGCGTCGCCGAGCTTC 62.664 60.000 14.86 4.16 44.69 3.86
1946 6575 4.484258 GAGCGTCGCCGAGCTTCT 62.484 66.667 14.86 0.00 44.69 2.85
1971 6600 1.135315 GTTGGTATCACGCTCGTACCA 60.135 52.381 10.45 10.45 44.44 3.25
1977 6606 0.386352 TCACGCTCGTACCAAAGACG 60.386 55.000 0.00 0.00 41.69 4.18
2010 6639 1.609783 GCTAGTGGACATGGGCCTT 59.390 57.895 4.53 0.00 0.00 4.35
2015 6644 0.890683 GTGGACATGGGCCTTGAAAG 59.109 55.000 24.70 0.00 0.00 2.62
2119 6784 1.482593 CCTTCGAGTTATGCAGGACCT 59.517 52.381 0.00 0.00 0.00 3.85
2144 6830 7.645402 TCAGATTTCGATGAAATTGATGATGG 58.355 34.615 6.26 0.00 41.56 3.51
2163 6849 2.039480 TGGAAATTCTGCTGTCTGCTCT 59.961 45.455 3.20 0.00 43.37 4.09
2194 6880 0.671472 CTTCGTCATGCTGCTGGACA 60.671 55.000 19.04 8.00 0.00 4.02
2229 6915 1.066573 CATGACCTGCGAGAAAGAGGT 60.067 52.381 0.00 0.00 43.06 3.85
2258 6944 1.896694 GAGGAGGACTCACCAGCAG 59.103 63.158 1.32 0.00 45.85 4.24
2259 6945 0.902516 GAGGAGGACTCACCAGCAGT 60.903 60.000 1.32 0.00 45.85 4.40
2270 6956 2.644212 CCAGCAGTGAGACGCTCCT 61.644 63.158 0.00 0.09 35.96 3.69
2271 6957 1.153862 CAGCAGTGAGACGCTCCTC 60.154 63.158 0.00 0.00 35.96 3.71
2279 6965 2.165437 GTGAGACGCTCCTCTTCTTCAT 59.835 50.000 4.73 0.00 34.38 2.57
2312 6998 2.119484 AACATGCGGGTCGGAAGGAA 62.119 55.000 0.00 0.00 0.00 3.36
2335 7021 7.715686 GGAACTACCTCAAGATAATGGTAAAGG 59.284 40.741 0.00 0.00 35.02 3.11
2367 7053 4.392047 TCAAGCAGAAGATGACATGTTGT 58.608 39.130 1.97 0.00 0.00 3.32
2405 7091 7.411486 TCTCCATTAAGAAGAACAGGACTAG 57.589 40.000 0.00 0.00 0.00 2.57
2413 7099 5.010933 AGAAGAACAGGACTAGAATCGTGA 58.989 41.667 9.33 0.00 37.79 4.35
2421 7107 3.181489 GGACTAGAATCGTGACGGTGATT 60.181 47.826 4.70 0.00 37.52 2.57
2424 7110 3.313012 AGAATCGTGACGGTGATTTCA 57.687 42.857 4.70 0.00 35.06 2.69
2426 7112 1.359848 ATCGTGACGGTGATTTCAGC 58.640 50.000 4.70 0.00 40.68 4.26
2462 7148 2.167861 GCATCTTGTCGTCGCTCCC 61.168 63.158 0.00 0.00 0.00 4.30
2514 7204 6.516693 CGGACATGATTCTAGTACCATTAGCA 60.517 42.308 0.00 0.00 0.00 3.49
2604 7310 9.885934 TCAATTGAAATTCTTTGCATTTGAATG 57.114 25.926 5.45 0.00 39.40 2.67
2607 7313 8.665643 TTGAAATTCTTTGCATTTGAATGACT 57.334 26.923 7.86 0.70 38.70 3.41
2739 7455 8.311836 CCACTTGGTACATAGTAGTATAATGGG 58.688 40.741 0.00 0.00 39.30 4.00
2748 7464 9.007901 ACATAGTAGTATAATGGGACGAGTTAC 57.992 37.037 0.00 0.00 0.00 2.50
2754 7473 3.543680 AATGGGACGAGTTACAGGATG 57.456 47.619 0.00 0.00 46.00 3.51
2800 7519 3.435275 TCTTGTAGTGAGTGAGAGGCAT 58.565 45.455 0.00 0.00 0.00 4.40
2808 7768 4.141041 AGTGAGTGAGAGGCATCTACCTAT 60.141 45.833 0.00 0.00 41.32 2.57
2814 7774 7.647827 AGTGAGAGGCATCTACCTATATGTAT 58.352 38.462 0.00 0.00 41.32 2.29
2859 7819 5.221185 GGTCGTACCTCTACATTATCAAGCA 60.221 44.000 0.00 0.00 34.73 3.91
2860 7820 5.686397 GTCGTACCTCTACATTATCAAGCAC 59.314 44.000 0.00 0.00 0.00 4.40
2861 7821 5.593095 TCGTACCTCTACATTATCAAGCACT 59.407 40.000 0.00 0.00 0.00 4.40
2863 7823 4.446371 ACCTCTACATTATCAAGCACTGC 58.554 43.478 0.00 0.00 0.00 4.40
2865 7825 4.272018 CCTCTACATTATCAAGCACTGCAC 59.728 45.833 3.30 0.00 0.00 4.57
2866 7826 5.089970 TCTACATTATCAAGCACTGCACT 57.910 39.130 3.30 0.00 0.00 4.40
2867 7827 6.220726 TCTACATTATCAAGCACTGCACTA 57.779 37.500 3.30 0.00 0.00 2.74
2868 7828 6.639563 TCTACATTATCAAGCACTGCACTAA 58.360 36.000 3.30 0.00 0.00 2.24
2870 7830 6.573664 ACATTATCAAGCACTGCACTAAAA 57.426 33.333 3.30 0.00 0.00 1.52
2871 7831 7.161773 ACATTATCAAGCACTGCACTAAAAT 57.838 32.000 3.30 0.00 0.00 1.82
2872 7832 7.253422 ACATTATCAAGCACTGCACTAAAATC 58.747 34.615 3.30 0.00 0.00 2.17
2874 7834 5.909621 ATCAAGCACTGCACTAAAATCAT 57.090 34.783 3.30 0.00 0.00 2.45
2875 7835 8.504812 TTATCAAGCACTGCACTAAAATCATA 57.495 30.769 3.30 0.00 0.00 2.15
2876 7836 6.426980 TCAAGCACTGCACTAAAATCATAG 57.573 37.500 3.30 0.00 0.00 2.23
2877 7837 4.889832 AGCACTGCACTAAAATCATAGC 57.110 40.909 3.30 0.00 0.00 2.97
2879 7839 3.309682 GCACTGCACTAAAATCATAGCGA 59.690 43.478 0.00 0.00 0.00 4.93
2880 7840 4.783450 GCACTGCACTAAAATCATAGCGAC 60.783 45.833 0.00 0.00 0.00 5.19
2881 7841 3.551890 ACTGCACTAAAATCATAGCGACG 59.448 43.478 0.00 0.00 0.00 5.12
2887 8389 3.520290 AAAATCATAGCGACGGTCTCA 57.480 42.857 1.23 0.00 0.00 3.27
2889 8391 3.735237 AATCATAGCGACGGTCTCAAT 57.265 42.857 1.23 0.00 0.00 2.57
2904 8406 5.045872 GGTCTCAATTAAAATCATGGCAGC 58.954 41.667 0.00 0.00 0.00 5.25
2943 8525 8.737175 TGAGGATGTACTATTTACGCCTATTAG 58.263 37.037 0.00 0.00 0.00 1.73
3004 8586 8.791327 TTTGTATCTGAATCATAACAAGCTGA 57.209 30.769 0.00 0.00 0.00 4.26
3039 8621 6.460103 AGCATCCTTTTATGACCTGGATAT 57.540 37.500 0.00 0.00 35.95 1.63
3040 8622 6.856757 AGCATCCTTTTATGACCTGGATATT 58.143 36.000 0.00 0.00 35.95 1.28
3104 8686 6.260936 ACAACTTTGAACTGATGGAAGTACAG 59.739 38.462 0.00 0.00 37.62 2.74
3117 8703 5.977635 TGGAAGTACAGTGACATATCAAGG 58.022 41.667 0.00 0.00 36.31 3.61
3118 8704 5.719563 TGGAAGTACAGTGACATATCAAGGA 59.280 40.000 0.00 0.00 36.31 3.36
3119 8705 6.212589 TGGAAGTACAGTGACATATCAAGGAA 59.787 38.462 0.00 0.00 36.31 3.36
3120 8706 6.758886 GGAAGTACAGTGACATATCAAGGAAG 59.241 42.308 0.00 0.00 36.31 3.46
3121 8707 6.227298 AGTACAGTGACATATCAAGGAAGG 57.773 41.667 0.00 0.00 36.31 3.46
3122 8708 5.958380 AGTACAGTGACATATCAAGGAAGGA 59.042 40.000 0.00 0.00 36.31 3.36
3123 8709 5.350504 ACAGTGACATATCAAGGAAGGAG 57.649 43.478 0.00 0.00 36.31 3.69
3126 8712 6.013379 ACAGTGACATATCAAGGAAGGAGAAA 60.013 38.462 0.00 0.00 36.31 2.52
3211 8803 8.754080 AGGATCCACTGCTATATATAGTTCAAC 58.246 37.037 15.82 4.88 32.96 3.18
3214 8806 9.712305 ATCCACTGCTATATATAGTTCAACAAC 57.288 33.333 18.81 3.03 32.96 3.32
3246 8839 4.537135 TGAAGACTGTCCCTGTAATCAC 57.463 45.455 3.76 0.00 0.00 3.06
3308 8905 3.213206 TCTTGTCAAGGCAACATCTGT 57.787 42.857 12.66 0.00 41.41 3.41
3309 8906 3.554934 TCTTGTCAAGGCAACATCTGTT 58.445 40.909 12.66 0.00 39.12 3.16
3310 8907 4.713553 TCTTGTCAAGGCAACATCTGTTA 58.286 39.130 12.66 0.00 36.32 2.41
3311 8908 5.129634 TCTTGTCAAGGCAACATCTGTTAA 58.870 37.500 12.66 0.00 36.32 2.01
3355 8952 4.574599 ATGTTGCTGGTTCTCAAAAGAC 57.425 40.909 0.00 0.00 0.00 3.01
3365 8962 5.163457 TGGTTCTCAAAAGACCAATTTGGAC 60.163 40.000 22.19 15.62 40.96 4.02
3366 8963 5.069119 GGTTCTCAAAAGACCAATTTGGACT 59.931 40.000 22.19 17.68 44.11 3.85
3367 8964 6.209361 GTTCTCAAAAGACCAATTTGGACTC 58.791 40.000 22.19 9.92 41.50 3.36
3368 8965 5.445069 TCTCAAAAGACCAATTTGGACTCA 58.555 37.500 22.19 5.74 41.50 3.41
3370 8967 7.230747 TCTCAAAAGACCAATTTGGACTCATA 58.769 34.615 22.19 7.10 41.50 2.15
3371 8968 7.890127 TCTCAAAAGACCAATTTGGACTCATAT 59.110 33.333 22.19 3.42 41.50 1.78
3372 8969 9.177608 CTCAAAAGACCAATTTGGACTCATATA 57.822 33.333 22.19 6.20 41.50 0.86
3373 8970 9.699410 TCAAAAGACCAATTTGGACTCATATAT 57.301 29.630 22.19 2.36 41.50 0.86
3374 8971 9.740239 CAAAAGACCAATTTGGACTCATATATG 57.260 33.333 22.19 6.36 41.50 1.78
3375 8972 9.479549 AAAAGACCAATTTGGACTCATATATGT 57.520 29.630 22.19 0.95 41.50 2.29
3377 8974 8.455903 AGACCAATTTGGACTCATATATGTTG 57.544 34.615 22.19 9.21 38.06 3.33
3378 8975 7.503566 AGACCAATTTGGACTCATATATGTTGG 59.496 37.037 22.19 18.73 38.06 3.77
3379 8976 6.040842 ACCAATTTGGACTCATATATGTTGGC 59.959 38.462 22.19 13.42 40.96 4.52
3380 8977 6.040729 CCAATTTGGACTCATATATGTTGGCA 59.959 38.462 10.03 0.00 40.96 4.92
3381 8978 6.639632 ATTTGGACTCATATATGTTGGCAC 57.360 37.500 12.42 4.83 0.00 5.01
3382 8979 4.769345 TGGACTCATATATGTTGGCACA 57.231 40.909 12.42 6.91 37.31 4.57
3385 8982 4.752101 GGACTCATATATGTTGGCACAGAC 59.248 45.833 12.42 1.79 42.39 3.51
3386 8983 4.708177 ACTCATATATGTTGGCACAGACC 58.292 43.478 12.42 0.00 42.39 3.85
3387 8984 4.067896 CTCATATATGTTGGCACAGACCC 58.932 47.826 12.42 0.00 42.39 4.46
3388 8985 2.613026 TATATGTTGGCACAGACCCG 57.387 50.000 0.00 0.00 42.39 5.28
3389 8986 0.618458 ATATGTTGGCACAGACCCGT 59.382 50.000 0.00 0.00 42.39 5.28
3392 8989 1.070105 GTTGGCACAGACCCGTACA 59.930 57.895 0.00 0.00 42.39 2.90
3393 8990 1.070105 TTGGCACAGACCCGTACAC 59.930 57.895 0.00 0.00 42.39 2.90
3394 8991 2.047560 GGCACAGACCCGTACACC 60.048 66.667 0.00 0.00 0.00 4.16
3395 8992 2.431942 GCACAGACCCGTACACCG 60.432 66.667 0.00 0.00 0.00 4.94
3397 8994 1.211969 CACAGACCCGTACACCGAG 59.788 63.158 0.00 0.00 39.56 4.63
3398 8995 1.228367 ACAGACCCGTACACCGAGT 60.228 57.895 0.00 0.00 39.56 4.18
3399 8996 0.036732 ACAGACCCGTACACCGAGTA 59.963 55.000 0.00 0.00 39.56 2.59
3408 9005 0.527565 TACACCGAGTACTTTCCGGC 59.472 55.000 18.57 0.00 46.54 6.13
3410 9007 2.270986 ACCGAGTACTTTCCGGCGT 61.271 57.895 18.57 0.94 46.54 5.68
3414 9011 1.135575 CGAGTACTTTCCGGCGTACTT 60.136 52.381 23.00 12.70 44.51 2.24
3415 9012 2.669391 CGAGTACTTTCCGGCGTACTTT 60.669 50.000 23.00 9.77 44.51 2.66
3416 9013 2.665052 GAGTACTTTCCGGCGTACTTTG 59.335 50.000 23.00 0.00 44.51 2.77
3418 9015 1.957668 ACTTTCCGGCGTACTTTGTT 58.042 45.000 6.01 0.00 0.00 2.83
3419 9016 1.869132 ACTTTCCGGCGTACTTTGTTC 59.131 47.619 6.01 0.00 0.00 3.18
3421 9018 0.031857 TTCCGGCGTACTTTGTTCGA 59.968 50.000 6.01 0.00 0.00 3.71
3422 9019 0.664166 TCCGGCGTACTTTGTTCGAC 60.664 55.000 6.01 0.00 31.18 4.20
3424 9021 2.509845 GGCGTACTTTGTTCGACGT 58.490 52.632 0.00 0.00 37.61 4.34
3425 9022 0.160182 GGCGTACTTTGTTCGACGTG 59.840 55.000 0.00 0.00 37.61 4.49
3427 9024 1.717645 GCGTACTTTGTTCGACGTGAT 59.282 47.619 0.00 0.00 37.61 3.06
3428 9025 2.154389 GCGTACTTTGTTCGACGTGATT 59.846 45.455 0.00 0.00 37.61 2.57
3429 9026 3.717177 GCGTACTTTGTTCGACGTGATTC 60.717 47.826 0.00 0.00 37.61 2.52
3430 9027 3.181546 CGTACTTTGTTCGACGTGATTCC 60.182 47.826 0.00 0.00 0.00 3.01
3431 9028 1.790623 ACTTTGTTCGACGTGATTCCG 59.209 47.619 0.00 0.00 0.00 4.30
3432 9029 1.126113 CTTTGTTCGACGTGATTCCGG 59.874 52.381 0.00 0.00 0.00 5.14
3433 9030 1.286354 TTGTTCGACGTGATTCCGGC 61.286 55.000 0.00 0.00 0.00 6.13
3441 9038 4.776322 TGATTCCGGCGGCCTGTG 62.776 66.667 23.83 5.58 0.00 3.66
3454 9051 2.357517 CTGTGCTTTCGGCCGTCT 60.358 61.111 27.15 0.00 40.92 4.18
3455 9052 1.080093 CTGTGCTTTCGGCCGTCTA 60.080 57.895 27.15 9.28 40.92 2.59
3456 9053 1.352156 CTGTGCTTTCGGCCGTCTAC 61.352 60.000 27.15 17.64 40.92 2.59
3458 9055 2.263540 GCTTTCGGCCGTCTACCA 59.736 61.111 27.15 0.06 34.27 3.25
3460 9057 1.888018 CTTTCGGCCGTCTACCAGA 59.112 57.895 27.15 0.00 0.00 3.86
3461 9058 0.458025 CTTTCGGCCGTCTACCAGAC 60.458 60.000 27.15 0.00 41.71 3.51
3462 9059 0.896940 TTTCGGCCGTCTACCAGACT 60.897 55.000 27.15 0.00 42.92 3.24
3463 9060 0.035152 TTCGGCCGTCTACCAGACTA 60.035 55.000 27.15 0.00 42.92 2.59
3464 9061 0.745845 TCGGCCGTCTACCAGACTAC 60.746 60.000 27.15 0.00 42.92 2.73
3465 9062 1.722636 CGGCCGTCTACCAGACTACC 61.723 65.000 19.50 4.98 42.92 3.18
3466 9063 0.682209 GGCCGTCTACCAGACTACCA 60.682 60.000 4.91 0.00 42.92 3.25
3468 9065 1.830279 CCGTCTACCAGACTACCACA 58.170 55.000 4.91 0.00 42.92 4.17
3469 9066 1.471684 CCGTCTACCAGACTACCACAC 59.528 57.143 4.91 0.00 42.92 3.82
3470 9067 1.129998 CGTCTACCAGACTACCACACG 59.870 57.143 4.91 0.00 42.92 4.49
3472 9069 3.338249 GTCTACCAGACTACCACACGTA 58.662 50.000 0.00 0.00 41.88 3.57
3473 9070 3.126000 GTCTACCAGACTACCACACGTAC 59.874 52.174 0.00 0.00 41.88 3.67
3474 9071 0.877071 ACCAGACTACCACACGTACG 59.123 55.000 15.01 15.01 0.00 3.67
3475 9072 0.877071 CCAGACTACCACACGTACGT 59.123 55.000 16.72 16.72 0.00 3.57
3477 9074 2.159653 CCAGACTACCACACGTACGTAC 60.160 54.545 22.34 15.90 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.622713 AGGTAGTATACTACTGCTGATACGAT 58.377 38.462 32.01 9.70 46.06 3.73
3 4 7.002250 AGGTAGTATACTACTGCTGATACGA 57.998 40.000 32.01 1.57 46.06 3.43
4 5 8.945481 ATAGGTAGTATACTACTGCTGATACG 57.055 38.462 32.01 0.00 46.06 3.06
30 31 7.393234 CCAGGGAAACTATACATCACTGAAAAA 59.607 37.037 5.86 0.00 45.40 1.94
32 33 6.012858 ACCAGGGAAACTATACATCACTGAAA 60.013 38.462 5.86 0.00 45.40 2.69
34 35 5.030147 ACCAGGGAAACTATACATCACTGA 58.970 41.667 5.86 0.00 45.40 3.41
35 36 5.359194 ACCAGGGAAACTATACATCACTG 57.641 43.478 0.00 0.00 42.86 3.66
36 37 6.099845 CCTTACCAGGGAAACTATACATCACT 59.900 42.308 0.00 0.00 36.36 3.41
37 38 6.126854 ACCTTACCAGGGAAACTATACATCAC 60.127 42.308 0.00 0.00 46.01 3.06
39 40 6.496144 ACCTTACCAGGGAAACTATACATC 57.504 41.667 0.00 0.00 46.01 3.06
40 41 7.626487 AGTTACCTTACCAGGGAAACTATACAT 59.374 37.037 8.69 0.00 45.60 2.29
41 42 6.961721 AGTTACCTTACCAGGGAAACTATACA 59.038 38.462 8.69 0.00 45.60 2.29
42 43 7.429374 AGTTACCTTACCAGGGAAACTATAC 57.571 40.000 8.69 0.00 45.60 1.47
44 45 6.964876 AAGTTACCTTACCAGGGAAACTAT 57.035 37.500 10.16 2.15 45.60 2.12
46 47 6.964876 ATAAGTTACCTTACCAGGGAAACT 57.035 37.500 5.77 5.77 45.60 2.66
48 49 8.865244 AGATATAAGTTACCTTACCAGGGAAA 57.135 34.615 0.00 0.00 45.60 3.13
51 52 9.322769 ACATAGATATAAGTTACCTTACCAGGG 57.677 37.037 0.00 0.00 46.01 4.45
67 68 9.832445 GTCCTTTTGAGAACCAACATAGATATA 57.168 33.333 0.00 0.00 33.85 0.86
69 70 7.685481 TGTCCTTTTGAGAACCAACATAGATA 58.315 34.615 0.00 0.00 33.85 1.98
70 71 6.542821 TGTCCTTTTGAGAACCAACATAGAT 58.457 36.000 0.00 0.00 33.85 1.98
71 72 5.935945 TGTCCTTTTGAGAACCAACATAGA 58.064 37.500 0.00 0.00 33.85 1.98
75 76 5.930837 ATTTGTCCTTTTGAGAACCAACA 57.069 34.783 0.00 0.00 33.85 3.33
76 77 6.337356 TCAATTTGTCCTTTTGAGAACCAAC 58.663 36.000 0.00 0.00 33.85 3.77
78 79 6.537453 TTCAATTTGTCCTTTTGAGAACCA 57.463 33.333 0.00 0.00 31.54 3.67
79 80 7.841915 TTTTCAATTTGTCCTTTTGAGAACC 57.158 32.000 0.00 0.00 31.54 3.62
87 88 9.492973 CCAACATAGATTTTCAATTTGTCCTTT 57.507 29.630 0.00 0.00 0.00 3.11
89 90 8.193953 ACCAACATAGATTTTCAATTTGTCCT 57.806 30.769 0.00 0.00 0.00 3.85
91 92 9.696917 AGAACCAACATAGATTTTCAATTTGTC 57.303 29.630 0.00 0.00 0.00 3.18
92 93 9.696917 GAGAACCAACATAGATTTTCAATTTGT 57.303 29.630 0.00 0.00 0.00 2.83
93 94 9.695526 TGAGAACCAACATAGATTTTCAATTTG 57.304 29.630 0.00 0.00 0.00 2.32
99 100 8.576442 TCCTTTTGAGAACCAACATAGATTTTC 58.424 33.333 0.00 0.00 33.85 2.29
102 103 7.004086 TGTCCTTTTGAGAACCAACATAGATT 58.996 34.615 0.00 0.00 33.85 2.40
107 108 6.484364 AATTGTCCTTTTGAGAACCAACAT 57.516 33.333 0.00 0.00 33.85 2.71
163 2719 6.920817 TCCTACATAGCCAGATATTTACACG 58.079 40.000 0.00 0.00 0.00 4.49
198 2758 0.038744 CTGGTGGAATGAGTTGGGCT 59.961 55.000 0.00 0.00 0.00 5.19
247 2807 1.556564 CGTCGACAATTAGATGCCGT 58.443 50.000 17.16 0.00 0.00 5.68
271 4602 3.441496 AGCGGCCAATAATCATGTTTG 57.559 42.857 2.24 0.00 0.00 2.93
404 4775 6.431278 CAAATTTGATGCTCTAGATCAGCTG 58.569 40.000 13.08 7.63 37.79 4.24
408 4779 5.443283 AGCCAAATTTGATGCTCTAGATCA 58.557 37.500 19.86 0.00 0.00 2.92
429 4800 2.030185 TGTGACGTCTCTGGAAACTAGC 60.030 50.000 17.92 0.00 0.00 3.42
431 4802 2.295349 GGTGTGACGTCTCTGGAAACTA 59.705 50.000 17.92 0.00 0.00 2.24
432 4803 1.068741 GGTGTGACGTCTCTGGAAACT 59.931 52.381 17.92 0.00 0.00 2.66
442 4813 1.952635 GTCCGGTTGGTGTGACGTC 60.953 63.158 9.11 9.11 36.30 4.34
513 4884 5.509501 CCAGCTGTATCCAAATTGTGTTTGT 60.510 40.000 13.81 0.00 0.00 2.83
515 4886 4.588528 ACCAGCTGTATCCAAATTGTGTTT 59.411 37.500 13.81 0.00 0.00 2.83
596 4974 3.057245 TGGTCAAGAGAACATCAGAGACG 60.057 47.826 0.00 0.00 36.30 4.18
668 5050 1.536766 TGTACCTCTGTCGTACGTTGG 59.463 52.381 16.05 12.91 39.16 3.77
676 5058 3.313012 TTGGTCAATGTACCTCTGTCG 57.687 47.619 0.00 0.00 40.44 4.35
722 5108 0.388659 TTGCCCATTGTGTCTGCAAC 59.611 50.000 0.00 0.00 37.04 4.17
732 5118 4.834534 TCTCATTGGAAAATTGCCCATTG 58.165 39.130 11.86 11.86 35.97 2.82
736 5122 5.088680 TCAATCTCATTGGAAAATTGCCC 57.911 39.130 0.00 0.00 40.61 5.36
737 5123 7.011109 CAGAATCAATCTCATTGGAAAATTGCC 59.989 37.037 0.00 0.00 40.61 4.52
745 5131 4.227982 TGGTCCAGAATCAATCTCATTGGA 59.772 41.667 0.00 0.00 40.61 3.53
748 5134 5.198965 CCTTGGTCCAGAATCAATCTCATT 58.801 41.667 0.00 0.00 35.73 2.57
752 5138 2.357569 GGCCTTGGTCCAGAATCAATCT 60.358 50.000 0.00 0.00 39.68 2.40
756 5142 1.198094 TCGGCCTTGGTCCAGAATCA 61.198 55.000 0.00 0.00 0.00 2.57
864 5260 6.553100 CCTTGACTCTCCTCTTATAGACCAAT 59.447 42.308 0.00 0.00 0.00 3.16
911 5344 6.520272 AGTGGCATAGATGAATGAACTACTC 58.480 40.000 0.00 0.00 0.00 2.59
936 5374 1.735571 ACCTAAATACAAACGCAGCCG 59.264 47.619 0.00 0.00 41.14 5.52
937 5375 3.311596 CCTACCTAAATACAAACGCAGCC 59.688 47.826 0.00 0.00 0.00 4.85
938 5376 3.937079 ACCTACCTAAATACAAACGCAGC 59.063 43.478 0.00 0.00 0.00 5.25
942 5383 7.710896 ACTAGCTACCTACCTAAATACAAACG 58.289 38.462 0.00 0.00 0.00 3.60
1018 5470 2.047560 GCCGCAAGTTACGACCCT 60.048 61.111 0.00 0.00 0.00 4.34
1036 5488 1.378514 CTTCCATGGACCAACCCGG 60.379 63.158 15.91 0.00 42.50 5.73
1083 5538 7.008021 AGGCAATGATGTTTGGAAACTAATT 57.992 32.000 4.02 0.00 39.59 1.40
1089 5544 3.195396 GGCTAGGCAATGATGTTTGGAAA 59.805 43.478 12.16 0.00 0.00 3.13
1101 5556 3.368843 CGCTATCACTATGGCTAGGCAAT 60.369 47.826 24.12 13.88 37.44 3.56
1162 5629 2.813226 TTATCGTGTGTGGCTGGGGC 62.813 60.000 0.00 0.00 37.82 5.80
1182 5655 4.409247 ACCTGGATTGGATAACTACAGTCC 59.591 45.833 0.00 0.00 42.06 3.85
1197 5670 2.158475 TGCTTCCTTGAACACCTGGATT 60.158 45.455 0.00 0.00 0.00 3.01
1245 5721 5.152623 TCTTCTGTTCCATACTGTCAAGG 57.847 43.478 0.00 0.00 0.00 3.61
1248 5724 6.210584 TGTGTATCTTCTGTTCCATACTGTCA 59.789 38.462 0.00 0.00 0.00 3.58
1354 5830 1.153369 CCATCACGCCGGAATGACT 60.153 57.895 5.05 0.00 0.00 3.41
1393 5881 4.169059 TGATACATTGGTTAGCAGCCAT 57.831 40.909 0.00 0.00 35.71 4.40
1401 5889 5.629133 GCCTGAGTCCTTGATACATTGGTTA 60.629 44.000 0.00 0.00 0.00 2.85
1410 5898 0.687757 AGCGGCCTGAGTCCTTGATA 60.688 55.000 0.00 0.00 0.00 2.15
1415 5903 3.386237 GTGAGCGGCCTGAGTCCT 61.386 66.667 0.00 0.00 0.00 3.85
1422 5910 4.704103 TCCTGGAGTGAGCGGCCT 62.704 66.667 0.00 0.00 0.00 5.19
1484 5972 1.297451 CTCGCCACGTCGTAGTAGC 60.297 63.158 0.00 0.00 0.00 3.58
1492 5980 2.179517 CCTGAGACTCGCCACGTC 59.820 66.667 0.00 0.00 0.00 4.34
1504 5998 2.417719 CAAAAAGTCGTCCTCCCTGAG 58.582 52.381 0.00 0.00 0.00 3.35
1507 6001 0.250770 GGCAAAAAGTCGTCCTCCCT 60.251 55.000 0.00 0.00 0.00 4.20
1509 6009 1.866925 CGGCAAAAAGTCGTCCTCC 59.133 57.895 0.00 0.00 41.32 4.30
1581 6087 3.704231 ATCCATGTGGCCGCTGTCC 62.704 63.158 18.96 0.00 34.44 4.02
1589 6095 2.398554 AACGCGTCATCCATGTGGC 61.399 57.895 14.44 0.00 34.44 5.01
1591 6097 1.226101 GCAACGCGTCATCCATGTG 60.226 57.895 14.44 5.42 0.00 3.21
1606 6112 1.567504 GCGTAGAAATAGCCGAGCAA 58.432 50.000 0.00 0.00 0.00 3.91
1647 6153 5.433526 TGATTCTCAAGCATCATGATGTCA 58.566 37.500 31.09 22.10 40.80 3.58
1668 6174 1.207488 CCACCACCCAAGGGATCTGA 61.207 60.000 13.15 0.00 38.96 3.27
1725 6231 1.734655 ACTTCTTCAAGGGCCAGAGA 58.265 50.000 6.18 0.00 33.37 3.10
1727 6233 1.774254 TGAACTTCTTCAAGGGCCAGA 59.226 47.619 6.18 0.00 33.20 3.86
1736 6242 2.749776 TCGCAACGATGAACTTCTTCA 58.250 42.857 0.00 0.00 40.77 3.02
1765 6277 0.753479 TCGCCTTGGTTTTTCAGGCA 60.753 50.000 9.96 0.00 45.22 4.75
1781 6293 2.196749 TCTCGATTTGCTTCTCATCGC 58.803 47.619 0.00 0.00 39.73 4.58
1786 6298 2.600867 CGTCCTTCTCGATTTGCTTCTC 59.399 50.000 0.00 0.00 0.00 2.87
1787 6299 2.231478 TCGTCCTTCTCGATTTGCTTCT 59.769 45.455 0.00 0.00 32.30 2.85
1788 6300 2.345942 GTCGTCCTTCTCGATTTGCTTC 59.654 50.000 0.00 0.00 39.45 3.86
1792 6304 3.511699 TGATGTCGTCCTTCTCGATTTG 58.488 45.455 0.00 0.00 39.45 2.32
1795 6307 2.031595 CGATGATGTCGTCCTTCTCGAT 60.032 50.000 0.00 0.00 45.19 3.59
1813 6325 3.511934 GGTTCATAGCCAGGATCTACGAT 59.488 47.826 0.00 0.00 0.00 3.73
1876 6388 2.414691 GCATCTCGCCCTTCTTGTTTTC 60.415 50.000 0.00 0.00 32.94 2.29
1878 6390 1.168714 GCATCTCGCCCTTCTTGTTT 58.831 50.000 0.00 0.00 32.94 2.83
1889 6401 1.146930 TCTCCAATGGGCATCTCGC 59.853 57.895 0.00 0.00 41.28 5.03
1891 6403 0.548031 TGGTCTCCAATGGGCATCTC 59.452 55.000 0.00 0.00 0.00 2.75
1892 6404 0.549950 CTGGTCTCCAATGGGCATCT 59.450 55.000 0.00 0.00 30.80 2.90
1893 6405 1.105759 GCTGGTCTCCAATGGGCATC 61.106 60.000 0.00 0.00 30.80 3.91
1894 6406 1.076485 GCTGGTCTCCAATGGGCAT 60.076 57.895 0.00 0.00 30.80 4.40
1896 6408 2.440980 GGCTGGTCTCCAATGGGC 60.441 66.667 0.00 0.00 30.80 5.36
1899 6411 0.033796 ACATGGGCTGGTCTCCAATG 60.034 55.000 0.00 0.00 36.54 2.82
1900 6412 0.257039 GACATGGGCTGGTCTCCAAT 59.743 55.000 0.00 0.00 36.54 3.16
1901 6413 1.133181 TGACATGGGCTGGTCTCCAA 61.133 55.000 0.00 0.00 36.54 3.53
1902 6414 0.915872 ATGACATGGGCTGGTCTCCA 60.916 55.000 0.00 0.00 37.46 3.86
1909 6538 4.634883 GCTCATAGATAATGACATGGGCTG 59.365 45.833 0.00 0.00 40.88 4.85
1945 6574 0.179171 AGCGTGATACCAACGTCGAG 60.179 55.000 0.00 0.00 0.00 4.04
1946 6575 0.179181 GAGCGTGATACCAACGTCGA 60.179 55.000 0.00 0.00 0.00 4.20
1953 6582 1.175654 TTGGTACGAGCGTGATACCA 58.824 50.000 11.00 11.00 45.22 3.25
1971 6600 2.222027 CCTGCTTCTGTTTCCGTCTTT 58.778 47.619 0.00 0.00 0.00 2.52
1977 6606 1.003696 ACTAGCCCTGCTTCTGTTTCC 59.996 52.381 0.00 0.00 40.44 3.13
2010 6639 4.515191 CCGAAGAAGTGATGTTTCCTTTCA 59.485 41.667 0.00 0.00 0.00 2.69
2015 6644 1.128692 CGCCGAAGAAGTGATGTTTCC 59.871 52.381 0.00 0.00 0.00 3.13
2021 6650 1.546476 AGAGAACGCCGAAGAAGTGAT 59.454 47.619 0.00 0.00 0.00 3.06
2024 6653 0.244178 GGAGAGAACGCCGAAGAAGT 59.756 55.000 0.00 0.00 0.00 3.01
2119 6784 7.499895 TCCATCATCAATTTCATCGAAATCTGA 59.500 33.333 2.62 8.74 40.77 3.27
2163 6849 3.616560 GCATGACGAAGAGTTGGAGGTAA 60.617 47.826 0.00 0.00 0.00 2.85
2258 6944 1.542030 TGAAGAAGAGGAGCGTCTCAC 59.458 52.381 11.00 5.65 34.07 3.51
2259 6945 1.911057 TGAAGAAGAGGAGCGTCTCA 58.089 50.000 11.00 0.00 34.07 3.27
2312 6998 7.417570 CGACCTTTACCATTATCTTGAGGTAGT 60.418 40.741 0.00 0.00 37.85 2.73
2332 7018 1.001406 CTGCTTGAAGTCCTCGACCTT 59.999 52.381 0.00 0.00 32.18 3.50
2335 7021 2.333014 CTTCTGCTTGAAGTCCTCGAC 58.667 52.381 10.50 0.00 45.26 4.20
2359 7045 4.156313 GCCACAGCTTGACACAACATGT 62.156 50.000 0.00 0.00 39.47 3.21
2384 7070 7.436673 CGATTCTAGTCCTGTTCTTCTTAATGG 59.563 40.741 0.00 0.00 0.00 3.16
2405 7091 2.222819 GCTGAAATCACCGTCACGATTC 60.223 50.000 0.00 0.00 30.64 2.52
2413 7099 1.176527 CCAATGGCTGAAATCACCGT 58.823 50.000 0.00 0.00 0.00 4.83
2421 7107 4.188462 CGATAACTACACCAATGGCTGAA 58.812 43.478 0.00 0.00 0.00 3.02
2424 7110 2.745152 GCCGATAACTACACCAATGGCT 60.745 50.000 0.00 0.00 37.03 4.75
2426 7112 2.912771 TGCCGATAACTACACCAATGG 58.087 47.619 0.00 0.00 0.00 3.16
2514 7204 5.165961 AGGTGTACAAGTAGAACATGCAT 57.834 39.130 0.00 0.00 0.00 3.96
2595 7297 5.050644 TGCAGCTTGTAGTCATTCAAATG 57.949 39.130 0.00 0.00 37.75 2.32
2598 7300 4.325972 TGATGCAGCTTGTAGTCATTCAA 58.674 39.130 2.53 0.00 0.00 2.69
2604 7310 2.821307 GCTTGATGCAGCTTGTAGTC 57.179 50.000 2.53 0.00 42.31 2.59
2693 7401 4.709886 GTGGTTGTTTAATTAGGGCCTGAT 59.290 41.667 18.53 11.45 0.00 2.90
2694 7402 4.083565 GTGGTTGTTTAATTAGGGCCTGA 58.916 43.478 18.53 8.90 0.00 3.86
2737 7453 4.667519 ATTACATCCTGTAACTCGTCCC 57.332 45.455 2.06 0.00 44.54 4.46
2738 7454 6.157211 CCATATTACATCCTGTAACTCGTCC 58.843 44.000 2.06 0.00 44.54 4.79
2739 7455 6.746120 ACCATATTACATCCTGTAACTCGTC 58.254 40.000 2.06 0.00 44.54 4.20
2748 7464 9.739276 ATATAACACCAACCATATTACATCCTG 57.261 33.333 0.00 0.00 0.00 3.86
2785 7504 2.024464 AGGTAGATGCCTCTCACTCACT 60.024 50.000 0.00 0.00 32.39 3.41
2800 7519 7.584396 TGACCTCCTCATACATATAGGTAGA 57.416 40.000 3.38 1.10 37.47 2.59
2808 7768 3.832490 CCCGAATGACCTCCTCATACATA 59.168 47.826 0.00 0.00 38.82 2.29
2814 7774 1.306141 AGCCCGAATGACCTCCTCA 60.306 57.895 0.00 0.00 0.00 3.86
2857 7817 3.309682 TCGCTATGATTTTAGTGCAGTGC 59.690 43.478 8.58 8.58 31.24 4.40
2859 7819 3.551890 CGTCGCTATGATTTTAGTGCAGT 59.448 43.478 0.00 0.00 31.24 4.40
2860 7820 3.060272 CCGTCGCTATGATTTTAGTGCAG 60.060 47.826 0.00 0.00 31.24 4.41
2861 7821 2.863740 CCGTCGCTATGATTTTAGTGCA 59.136 45.455 0.00 0.00 31.24 4.57
2863 7823 4.360563 AGACCGTCGCTATGATTTTAGTG 58.639 43.478 0.00 0.00 0.00 2.74
2865 7825 4.607955 TGAGACCGTCGCTATGATTTTAG 58.392 43.478 3.83 0.00 0.00 1.85
2866 7826 4.642445 TGAGACCGTCGCTATGATTTTA 57.358 40.909 3.83 0.00 0.00 1.52
2867 7827 3.520290 TGAGACCGTCGCTATGATTTT 57.480 42.857 3.83 0.00 0.00 1.82
2868 7828 3.520290 TTGAGACCGTCGCTATGATTT 57.480 42.857 3.83 0.00 0.00 2.17
2870 7830 3.735237 AATTGAGACCGTCGCTATGAT 57.265 42.857 3.83 0.00 0.00 2.45
2871 7831 4.642445 TTAATTGAGACCGTCGCTATGA 57.358 40.909 3.83 0.00 0.00 2.15
2872 7832 5.712217 TTTTAATTGAGACCGTCGCTATG 57.288 39.130 3.83 0.00 0.00 2.23
2874 7834 5.412640 TGATTTTAATTGAGACCGTCGCTA 58.587 37.500 3.83 0.00 0.00 4.26
2875 7835 4.250464 TGATTTTAATTGAGACCGTCGCT 58.750 39.130 3.83 0.00 0.00 4.93
2876 7836 4.593597 TGATTTTAATTGAGACCGTCGC 57.406 40.909 0.00 0.00 0.00 5.19
2877 7837 5.501715 CCATGATTTTAATTGAGACCGTCG 58.498 41.667 0.00 0.00 0.00 5.12
2879 7839 4.704540 TGCCATGATTTTAATTGAGACCGT 59.295 37.500 0.00 0.00 0.00 4.83
2880 7840 5.247507 TGCCATGATTTTAATTGAGACCG 57.752 39.130 0.00 0.00 0.00 4.79
2881 7841 5.045872 GCTGCCATGATTTTAATTGAGACC 58.954 41.667 0.00 0.00 0.00 3.85
2887 8389 7.290061 TCTAGGTAGCTGCCATGATTTTAATT 58.710 34.615 23.78 0.00 0.00 1.40
2889 8391 6.247229 TCTAGGTAGCTGCCATGATTTTAA 57.753 37.500 23.78 0.00 0.00 1.52
2994 8576 6.072008 TGCTAATTGCTTGATTCAGCTTGTTA 60.072 34.615 8.77 5.62 43.37 2.41
3004 8586 8.698210 TCATAAAAGGATGCTAATTGCTTGATT 58.302 29.630 0.00 0.00 43.37 2.57
3024 8606 9.565090 CAGATCTTCAAATATCCAGGTCATAAA 57.435 33.333 0.00 0.00 0.00 1.40
3104 8686 7.627300 GCTTTTTCTCCTTCCTTGATATGTCAC 60.627 40.741 0.00 0.00 33.11 3.67
3117 8703 4.948847 ACATTGTTGGCTTTTTCTCCTTC 58.051 39.130 0.00 0.00 0.00 3.46
3118 8704 6.478512 TTACATTGTTGGCTTTTTCTCCTT 57.521 33.333 0.00 0.00 0.00 3.36
3119 8705 6.478512 TTTACATTGTTGGCTTTTTCTCCT 57.521 33.333 0.00 0.00 0.00 3.69
3120 8706 8.708742 GTTATTTACATTGTTGGCTTTTTCTCC 58.291 33.333 0.00 0.00 0.00 3.71
3121 8707 9.476202 AGTTATTTACATTGTTGGCTTTTTCTC 57.524 29.630 0.00 0.00 0.00 2.87
3122 8708 9.830975 AAGTTATTTACATTGTTGGCTTTTTCT 57.169 25.926 0.00 0.00 0.00 2.52
3151 8739 6.543465 TCCAGTAATCTTGATAGGTGCATTTG 59.457 38.462 0.00 0.00 0.00 2.32
3211 8803 6.473455 GGACAGTCTTCATTTGTTCAAAGTTG 59.527 38.462 0.00 0.00 0.00 3.16
3214 8806 5.300286 AGGGACAGTCTTCATTTGTTCAAAG 59.700 40.000 0.00 0.00 0.00 2.77
3246 8839 6.690194 AACTTAGGTGGTATACTACTGACG 57.310 41.667 17.66 7.43 0.00 4.35
3294 8891 6.071952 ACCACTAATTAACAGATGTTGCCTTG 60.072 38.462 8.46 0.00 38.90 3.61
3355 8952 6.040729 TGCCAACATATATGAGTCCAAATTGG 59.959 38.462 19.63 18.11 39.43 3.16
3365 8962 4.067896 GGGTCTGTGCCAACATATATGAG 58.932 47.826 19.63 10.68 35.22 2.90
3366 8963 3.494223 CGGGTCTGTGCCAACATATATGA 60.494 47.826 19.63 0.00 35.22 2.15
3367 8964 2.807967 CGGGTCTGTGCCAACATATATG 59.192 50.000 11.29 11.29 35.22 1.78
3368 8965 2.438021 ACGGGTCTGTGCCAACATATAT 59.562 45.455 0.00 0.00 35.22 0.86
3370 8967 0.618458 ACGGGTCTGTGCCAACATAT 59.382 50.000 0.00 0.00 35.22 1.78
3371 8968 1.066716 GTACGGGTCTGTGCCAACATA 60.067 52.381 0.00 0.00 35.22 2.29
3372 8969 0.321298 GTACGGGTCTGTGCCAACAT 60.321 55.000 0.00 0.00 35.22 2.71
3373 8970 1.070105 GTACGGGTCTGTGCCAACA 59.930 57.895 0.00 0.00 34.34 3.33
3374 8971 1.070105 TGTACGGGTCTGTGCCAAC 59.930 57.895 0.00 0.00 0.00 3.77
3375 8972 1.070105 GTGTACGGGTCTGTGCCAA 59.930 57.895 0.00 0.00 0.00 4.52
3377 8974 2.047560 GGTGTACGGGTCTGTGCC 60.048 66.667 0.00 0.00 0.00 5.01
3378 8975 2.431942 CGGTGTACGGGTCTGTGC 60.432 66.667 0.00 0.00 39.42 4.57
3379 8976 1.211969 CTCGGTGTACGGGTCTGTG 59.788 63.158 0.00 0.00 44.45 3.66
3380 8977 3.677527 CTCGGTGTACGGGTCTGT 58.322 61.111 0.00 0.00 44.45 3.41
3389 8986 0.527565 GCCGGAAAGTACTCGGTGTA 59.472 55.000 19.28 0.00 44.97 2.90
3392 8989 0.960364 TACGCCGGAAAGTACTCGGT 60.960 55.000 19.28 6.60 44.97 4.69
3393 8990 0.524180 GTACGCCGGAAAGTACTCGG 60.524 60.000 20.73 15.30 45.84 4.63
3394 8991 2.935651 GTACGCCGGAAAGTACTCG 58.064 57.895 20.73 9.48 39.86 4.18
3397 8994 2.407090 ACAAAGTACGCCGGAAAGTAC 58.593 47.619 20.55 20.55 42.42 2.73
3398 8995 2.818130 ACAAAGTACGCCGGAAAGTA 57.182 45.000 5.05 2.74 0.00 2.24
3399 8996 1.869132 GAACAAAGTACGCCGGAAAGT 59.131 47.619 5.05 3.92 0.00 2.66
3400 8997 1.136446 CGAACAAAGTACGCCGGAAAG 60.136 52.381 5.05 0.00 0.00 2.62
3402 8999 0.031857 TCGAACAAAGTACGCCGGAA 59.968 50.000 5.05 0.00 0.00 4.30
3404 9001 1.777199 GTCGAACAAAGTACGCCGG 59.223 57.895 0.00 0.00 0.00 6.13
3405 9002 1.270777 ACGTCGAACAAAGTACGCCG 61.271 55.000 0.00 0.00 38.87 6.46
3407 9004 1.122849 TCACGTCGAACAAAGTACGC 58.877 50.000 0.00 0.00 38.87 4.42
3408 9005 3.181546 GGAATCACGTCGAACAAAGTACG 60.182 47.826 0.00 0.00 40.99 3.67
3410 9007 2.981805 CGGAATCACGTCGAACAAAGTA 59.018 45.455 0.00 0.00 0.00 2.24
3414 9011 1.286354 GCCGGAATCACGTCGAACAA 61.286 55.000 5.05 0.00 0.00 2.83
3415 9012 1.735198 GCCGGAATCACGTCGAACA 60.735 57.895 5.05 0.00 0.00 3.18
3416 9013 2.785105 CGCCGGAATCACGTCGAAC 61.785 63.158 5.05 0.00 0.00 3.95
3418 9015 4.485834 CCGCCGGAATCACGTCGA 62.486 66.667 5.05 0.00 0.00 4.20
3424 9021 4.776322 CACAGGCCGCCGGAATCA 62.776 66.667 17.16 0.00 0.00 2.57
3436 9033 2.501223 TAGACGGCCGAAAGCACAGG 62.501 60.000 35.90 0.00 46.50 4.00
3437 9034 1.080093 TAGACGGCCGAAAGCACAG 60.080 57.895 35.90 0.00 46.50 3.66
3439 9036 2.098831 GGTAGACGGCCGAAAGCAC 61.099 63.158 35.90 20.18 46.50 4.40
3441 9038 1.810030 CTGGTAGACGGCCGAAAGC 60.810 63.158 35.90 24.37 42.60 3.51
3442 9039 0.458025 GTCTGGTAGACGGCCGAAAG 60.458 60.000 35.90 18.20 35.28 2.62
3443 9040 1.588082 GTCTGGTAGACGGCCGAAA 59.412 57.895 35.90 13.90 35.28 3.46
3452 9049 2.574006 ACGTGTGGTAGTCTGGTAGA 57.426 50.000 0.00 0.00 0.00 2.59
3454 9051 2.076100 CGTACGTGTGGTAGTCTGGTA 58.924 52.381 7.22 0.00 0.00 3.25
3455 9052 0.877071 CGTACGTGTGGTAGTCTGGT 59.123 55.000 7.22 0.00 0.00 4.00
3456 9053 0.877071 ACGTACGTGTGGTAGTCTGG 59.123 55.000 22.14 0.00 0.00 3.86
3458 9055 1.726791 CGTACGTACGTGTGGTAGTCT 59.273 52.381 33.95 1.85 44.13 3.24


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

AutoCloner maintained by Alex Coulton.