Multiple sequence alignment - TraesCS1D01G163400

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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 TraesCS1D01G163400 chr1D 100.000 9595 0 0 1 9595 233916234 233906640 0.000000e+00 17719.0
1 TraesCS1D01G163400 chr1B 93.739 5910 265 46 1 5869 368565620 368559775 0.000000e+00 8767.0
2 TraesCS1D01G163400 chr1B 92.739 1873 96 19 5944 7808 368559782 368557942 0.000000e+00 2669.0
3 TraesCS1D01G163400 chr1B 89.750 1122 51 27 8002 9063 368557951 368556834 0.000000e+00 1376.0
4 TraesCS1D01G163400 chr1B 91.396 523 30 2 9088 9595 368556589 368556067 0.000000e+00 702.0
5 TraesCS1D01G163400 chr1B 100.000 30 0 0 9061 9090 368556731 368556702 1.000000e-03 56.5
6 TraesCS1D01G163400 chr1A 92.787 4686 255 35 1 4670 313729735 313734353 0.000000e+00 6704.0
7 TraesCS1D01G163400 chr1A 95.824 2251 51 7 6483 8729 313736212 313738423 0.000000e+00 3596.0
8 TraesCS1D01G163400 chr1A 96.333 1200 35 7 4670 5869 313734390 313735580 0.000000e+00 1964.0
9 TraesCS1D01G163400 chr1A 98.883 537 3 2 5944 6480 313735573 313736106 0.000000e+00 955.0
10 TraesCS1D01G163400 chr1A 91.818 550 30 2 9061 9595 313738695 313739244 0.000000e+00 752.0
11 TraesCS1D01G163400 chr1A 88.889 207 9 4 8858 9063 313738421 313738614 9.630000e-60 243.0
12 TraesCS1D01G163400 chr5B 91.917 866 57 6 1258 2123 645504686 645503834 0.000000e+00 1199.0
13 TraesCS1D01G163400 chr5B 91.339 866 62 6 1258 2123 655891075 655890223 0.000000e+00 1171.0
14 TraesCS1D01G163400 chr5B 84.564 149 20 3 7855 8002 491090028 491090174 2.790000e-30 145.0
15 TraesCS1D01G163400 chr5B 95.385 65 0 1 5873 5937 466771979 466772040 6.130000e-17 100.0
16 TraesCS1D01G163400 chr7B 91.600 500 35 4 1258 1757 673940872 673940380 0.000000e+00 684.0
17 TraesCS1D01G163400 chr7B 91.736 363 24 2 1761 2123 673925876 673925520 5.170000e-137 499.0
18 TraesCS1D01G163400 chr7B 85.714 147 19 2 7860 8005 558903168 558903313 4.640000e-33 154.0
19 TraesCS1D01G163400 chr3A 79.241 843 159 10 6178 7012 93901025 93900191 3.010000e-159 573.0
20 TraesCS1D01G163400 chr3A 100.000 45 0 0 5871 5915 526764864 526764820 6.170000e-12 84.2
21 TraesCS1D01G163400 chr3A 88.889 63 3 4 5856 5915 740537642 740537703 3.720000e-09 75.0
22 TraesCS1D01G163400 chr3B 78.985 847 152 18 6179 7012 126007123 126006290 1.090000e-153 555.0
23 TraesCS1D01G163400 chrUn 93.913 115 7 0 1258 1372 37029079 37029193 3.560000e-39 174.0
24 TraesCS1D01G163400 chrUn 97.674 43 1 0 5873 5915 308182888 308182846 3.720000e-09 75.0
25 TraesCS1D01G163400 chr5A 85.616 146 13 7 7860 8000 569797008 569796866 7.760000e-31 147.0
26 TraesCS1D01G163400 chr5A 97.959 49 1 0 5867 5915 355158695 355158647 1.720000e-12 86.1
27 TraesCS1D01G163400 chr2D 81.119 143 19 1 7860 8002 101967805 101967671 3.660000e-19 108.0
28 TraesCS1D01G163400 chr3D 97.959 49 1 0 5867 5915 28128585 28128537 1.720000e-12 86.1
29 TraesCS1D01G163400 chr3D 100.000 31 0 0 6999 7029 79180363 79180333 3.740000e-04 58.4
30 TraesCS1D01G163400 chr2A 92.982 57 1 3 5859 5915 568280910 568280963 7.990000e-11 80.5
31 TraesCS1D01G163400 chr4A 92.727 55 3 1 5861 5915 31621263 31621210 2.870000e-10 78.7
32 TraesCS1D01G163400 chr2B 91.379 58 3 2 5860 5915 656947856 656947913 2.870000e-10 78.7


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 TraesCS1D01G163400 chr1D 233906640 233916234 9594 True 17719.0 17719 100.0000 1 9595 1 chr1D.!!$R1 9594
1 TraesCS1D01G163400 chr1B 368556067 368565620 9553 True 2714.1 8767 93.5248 1 9595 5 chr1B.!!$R1 9594
2 TraesCS1D01G163400 chr1A 313729735 313739244 9509 False 2369.0 6704 94.0890 1 9595 6 chr1A.!!$F1 9594
3 TraesCS1D01G163400 chr5B 645503834 645504686 852 True 1199.0 1199 91.9170 1258 2123 1 chr5B.!!$R1 865
4 TraesCS1D01G163400 chr5B 655890223 655891075 852 True 1171.0 1171 91.3390 1258 2123 1 chr5B.!!$R2 865
5 TraesCS1D01G163400 chr3A 93900191 93901025 834 True 573.0 573 79.2410 6178 7012 1 chr3A.!!$R1 834
6 TraesCS1D01G163400 chr3B 126006290 126007123 833 True 555.0 555 78.9850 6179 7012 1 chr3B.!!$R1 833

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
847 857 0.107459 AGCTCCCGAATCAAAGCTCC 60.107 55.000 0.00 0.00 41.05 4.70 F
1472 1498 0.318441 TCTGTGACAGGCGAAAGAGG 59.682 55.000 13.33 0.00 31.51 3.69 F
2244 2270 0.178068 TTCTGTTCGCCCCTATCAGC 59.822 55.000 0.00 0.00 0.00 4.26 F
3144 3173 2.049156 CTCGCTTGACTGGTCGCA 60.049 61.111 0.00 0.00 0.00 5.10 F
4157 4187 1.332640 CGAGCTGCTGTTATTGATGCG 60.333 52.381 7.01 0.00 0.00 4.73 F
5395 5462 0.035439 CTGTACTTGGTTGGCCGGAT 60.035 55.000 5.05 0.00 37.67 4.18 F
5924 5992 0.036590 TGCCTTGTGAGCTACATGCA 59.963 50.000 12.58 12.58 45.94 3.96 F
5925 5993 0.449388 GCCTTGTGAGCTACATGCAC 59.551 55.000 0.00 0.00 45.94 4.57 F
5928 5996 0.673333 TTGTGAGCTACATGCACCGG 60.673 55.000 0.00 0.00 45.94 5.28 F
7134 7311 0.246635 GAAGCTACTCTCACCCGCAA 59.753 55.000 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 2209 0.035056 ACTACCTCAATGGCCACTGC 60.035 55.000 8.16 0.00 40.22 4.40 R
3102 3131 0.713883 AAGCGTACGCAATTGTCTCG 59.286 50.000 38.58 4.87 44.88 4.04 R
3242 3271 1.134753 ACAGCTTCTGATCTCTGCTCG 59.865 52.381 0.29 0.00 35.18 5.03 R
4928 4995 2.221906 GAGCTGCCTTTGCCATGGTG 62.222 60.000 14.67 1.49 36.33 4.17 R
5905 5973 0.036590 TGCATGTAGCTCACAAGGCA 59.963 50.000 15.33 15.33 44.47 4.75 R
7116 7293 0.685097 TTTGCGGGTGAGAGTAGCTT 59.315 50.000 0.00 0.00 0.00 3.74 R
7117 7294 0.685097 TTTTGCGGGTGAGAGTAGCT 59.315 50.000 0.00 0.00 0.00 3.32 R
7118 7295 1.519408 TTTTTGCGGGTGAGAGTAGC 58.481 50.000 0.00 0.00 0.00 3.58 R
7812 8001 4.412199 CCCAGTAATTTGATCCTAGGTCCA 59.588 45.833 9.08 5.21 0.00 4.02 R
8787 9021 0.029300 CCTTCACAACGCAACTGTGG 59.971 55.000 9.26 0.00 43.60 4.17 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
33 34 1.299089 GACACACAAAAGCACCCGC 60.299 57.895 0.00 0.00 38.99 6.13
41 42 1.250840 AAAAGCACCCGCCCAGATTC 61.251 55.000 0.00 0.00 39.83 2.52
50 51 1.051812 CGCCCAGATTCATAGGACCT 58.948 55.000 0.00 0.00 0.00 3.85
61 62 2.024941 TCATAGGACCTGAGACAGAGCA 60.025 50.000 3.53 0.00 32.44 4.26
104 105 2.100916 ACACTAATAGCGGCGAGAACAT 59.899 45.455 12.98 0.00 0.00 2.71
115 116 3.046390 GGCGAGAACATCTGTATCGAAG 58.954 50.000 17.17 0.00 38.72 3.79
122 123 6.307776 AGAACATCTGTATCGAAGGGAGATA 58.692 40.000 0.00 0.00 0.00 1.98
127 128 7.122948 ACATCTGTATCGAAGGGAGATATAACC 59.877 40.741 0.00 0.00 33.72 2.85
157 158 2.601067 CTGCCACCATTGCCACCA 60.601 61.111 0.00 0.00 0.00 4.17
163 164 0.964860 CACCATTGCCACCATCGGAA 60.965 55.000 0.00 0.00 0.00 4.30
166 167 0.964860 CATTGCCACCATCGGAACCA 60.965 55.000 0.00 0.00 0.00 3.67
190 191 3.259123 AGCCATGAACAATCAAAACCCTC 59.741 43.478 0.00 0.00 39.49 4.30
191 192 3.006752 GCCATGAACAATCAAAACCCTCA 59.993 43.478 0.00 0.00 39.49 3.86
192 193 4.559153 CCATGAACAATCAAAACCCTCAC 58.441 43.478 0.00 0.00 39.49 3.51
196 197 4.467795 TGAACAATCAAAACCCTCACCAAA 59.532 37.500 0.00 0.00 30.99 3.28
231 232 1.702491 GGACACACGCGGAATAAGGC 61.702 60.000 12.47 0.00 0.00 4.35
235 236 0.107897 ACACGCGGAATAAGGCATCA 60.108 50.000 12.47 0.00 0.00 3.07
281 282 4.148825 GGCAGTCGGCGGAGATGT 62.149 66.667 7.21 0.00 46.16 3.06
288 289 2.990479 GGCGGAGATGTGGGAACT 59.010 61.111 0.00 0.00 0.00 3.01
319 320 2.325583 TGTGTCGAGGTTGCTTTCTT 57.674 45.000 0.00 0.00 0.00 2.52
346 347 4.026744 CTCTCTCTACATTGGTTCCTGGA 58.973 47.826 0.00 0.00 0.00 3.86
362 363 0.621571 TGGAGGCTAGGGCTGATTGT 60.622 55.000 0.00 0.00 38.98 2.71
432 433 0.853530 GCCCCTTCCACCATAAGGAT 59.146 55.000 3.44 0.00 45.41 3.24
544 545 2.422597 TCATCGTCATCCACCAAACAC 58.577 47.619 0.00 0.00 0.00 3.32
563 564 3.935203 ACACAGATTTCATTCGCCAGTAG 59.065 43.478 0.00 0.00 0.00 2.57
567 568 2.004583 TTTCATTCGCCAGTAGGTCG 57.995 50.000 0.00 0.00 37.19 4.79
576 577 2.093783 CGCCAGTAGGTCGTTTCAATTC 59.906 50.000 0.00 0.00 37.19 2.17
619 626 6.073819 CCTTTTACCATTTACTGCTTTGCAAC 60.074 38.462 0.00 0.00 38.41 4.17
621 628 3.716601 ACCATTTACTGCTTTGCAACAC 58.283 40.909 0.00 0.00 38.41 3.32
623 630 2.483583 TTTACTGCTTTGCAACACGG 57.516 45.000 0.00 1.39 38.41 4.94
662 671 5.704217 CTTGACTATCAAGTTTCTACGCC 57.296 43.478 9.90 0.00 46.50 5.68
738 747 4.035091 TGTGGCATAATCGAAATTTCTCCG 59.965 41.667 15.92 4.14 0.00 4.63
743 752 5.235616 GCATAATCGAAATTTCTCCGTACCA 59.764 40.000 15.92 0.00 0.00 3.25
756 765 1.713830 GTACCACCGCATCTTTCGC 59.286 57.895 0.00 0.00 0.00 4.70
757 766 1.448893 TACCACCGCATCTTTCGCC 60.449 57.895 0.00 0.00 0.00 5.54
758 767 2.862674 TACCACCGCATCTTTCGCCC 62.863 60.000 0.00 0.00 0.00 6.13
759 768 3.508840 CACCGCATCTTTCGCCCC 61.509 66.667 0.00 0.00 0.00 5.80
760 769 4.796495 ACCGCATCTTTCGCCCCC 62.796 66.667 0.00 0.00 0.00 5.40
777 786 2.696759 CCCCCAAGTTTAAGCCGCG 61.697 63.158 0.00 0.00 0.00 6.46
837 847 3.625745 GAGGTTCAAAGCTCCCGAA 57.374 52.632 10.18 0.00 45.32 4.30
838 848 2.115343 GAGGTTCAAAGCTCCCGAAT 57.885 50.000 10.18 0.00 45.32 3.34
839 849 2.010497 GAGGTTCAAAGCTCCCGAATC 58.990 52.381 10.18 0.00 45.32 2.52
840 850 1.351017 AGGTTCAAAGCTCCCGAATCA 59.649 47.619 5.95 0.00 29.15 2.57
841 851 2.159382 GGTTCAAAGCTCCCGAATCAA 58.841 47.619 0.00 0.00 0.00 2.57
842 852 2.556622 GGTTCAAAGCTCCCGAATCAAA 59.443 45.455 0.00 0.00 0.00 2.69
843 853 3.366374 GGTTCAAAGCTCCCGAATCAAAG 60.366 47.826 0.00 0.00 0.00 2.77
844 854 1.812571 TCAAAGCTCCCGAATCAAAGC 59.187 47.619 0.00 0.00 34.95 3.51
845 855 1.815003 CAAAGCTCCCGAATCAAAGCT 59.185 47.619 0.00 0.00 46.66 3.74
846 856 1.743996 AAGCTCCCGAATCAAAGCTC 58.256 50.000 2.24 0.00 44.03 4.09
847 857 0.107459 AGCTCCCGAATCAAAGCTCC 60.107 55.000 0.00 0.00 41.05 4.70
848 858 0.392998 GCTCCCGAATCAAAGCTCCA 60.393 55.000 0.00 0.00 0.00 3.86
849 859 1.950484 GCTCCCGAATCAAAGCTCCAA 60.950 52.381 0.00 0.00 0.00 3.53
850 860 2.436417 CTCCCGAATCAAAGCTCCAAA 58.564 47.619 0.00 0.00 0.00 3.28
851 861 2.421424 CTCCCGAATCAAAGCTCCAAAG 59.579 50.000 0.00 0.00 0.00 2.77
888 898 0.745468 ATCCCGCCTCTACTTCGAAC 59.255 55.000 0.00 0.00 0.00 3.95
895 905 2.202703 CTACTTCGAACCCGCCCG 60.203 66.667 0.00 0.00 35.37 6.13
932 945 2.076863 GTGGTTCTTAATCGCAGCAGT 58.923 47.619 0.00 0.00 0.00 4.40
1132 1146 2.226330 GGAATTTTGGTTTTGGGGTGC 58.774 47.619 0.00 0.00 0.00 5.01
1177 1191 5.159925 GTGAGGTGTCATCATCTATGATCG 58.840 45.833 2.41 0.53 46.21 3.69
1210 1224 1.604278 GGCGGTGATTTCTAGGAATGC 59.396 52.381 0.00 0.00 0.00 3.56
1216 1230 2.147150 GATTTCTAGGAATGCGGCTCC 58.853 52.381 0.00 0.09 0.00 4.70
1268 1282 4.280677 TGAAATACCTTCTGTTTGGCTTGG 59.719 41.667 0.00 0.00 34.86 3.61
1296 1317 0.713883 ACTGATTCGTTTACTGCGCG 59.286 50.000 0.00 0.00 0.00 6.86
1343 1364 4.792068 TGGAAAGGAAGCTGAAGAAAGAA 58.208 39.130 0.00 0.00 0.00 2.52
1408 1429 6.323210 TGGAGTAGGAGAATACACTAGTCA 57.677 41.667 0.00 0.00 38.37 3.41
1411 1432 7.122353 TGGAGTAGGAGAATACACTAGTCAAAC 59.878 40.741 0.00 0.00 38.37 2.93
1418 1439 7.117956 GGAGAATACACTAGTCAAACTGTTTCC 59.882 40.741 2.13 0.00 0.00 3.13
1472 1498 0.318441 TCTGTGACAGGCGAAAGAGG 59.682 55.000 13.33 0.00 31.51 3.69
1504 1530 1.696063 AGCTCAAGGCAAAGCAGAAA 58.304 45.000 8.22 0.00 44.79 2.52
1560 1586 3.221771 CCAACTCATGTCTTGGTTTGGA 58.778 45.455 13.17 0.00 38.76 3.53
1561 1587 3.004734 CCAACTCATGTCTTGGTTTGGAC 59.995 47.826 13.17 0.00 38.76 4.02
1562 1588 3.864789 ACTCATGTCTTGGTTTGGACT 57.135 42.857 0.00 0.00 34.01 3.85
1563 1589 4.170468 ACTCATGTCTTGGTTTGGACTT 57.830 40.909 0.00 0.00 34.01 3.01
1564 1590 4.536765 ACTCATGTCTTGGTTTGGACTTT 58.463 39.130 0.00 0.00 34.01 2.66
1565 1591 4.339247 ACTCATGTCTTGGTTTGGACTTTG 59.661 41.667 0.00 0.00 34.01 2.77
1566 1592 3.636300 TCATGTCTTGGTTTGGACTTTGG 59.364 43.478 0.00 0.00 34.01 3.28
1697 1723 5.658198 TCCTGAGGATTTCATTGATCCAT 57.342 39.130 0.00 0.00 44.50 3.41
1724 1750 2.498167 CCACTGGACAGAAGAAACTGG 58.502 52.381 6.29 0.00 41.59 4.00
1757 1783 2.978018 GCCAAACAGTACAGCCCGC 61.978 63.158 0.00 0.00 0.00 6.13
1929 1955 4.395854 CACAGTATTTTGTAGCAGATGCCA 59.604 41.667 0.14 0.00 43.38 4.92
1981 2007 1.044790 CCCTCCATGACCCAAATGGC 61.045 60.000 0.00 0.00 43.70 4.40
2064 2090 5.688823 TGATTTCACACTGTAAATCTTGCG 58.311 37.500 12.97 0.00 40.92 4.85
2067 2093 5.585500 TTCACACTGTAAATCTTGCGTAC 57.415 39.130 0.00 0.00 0.00 3.67
2076 2102 8.726988 ACTGTAAATCTTGCGTACAACATAATT 58.273 29.630 0.00 0.00 0.00 1.40
2183 2209 3.491964 CCTTCACATAGGCCATGCAATTG 60.492 47.826 5.01 0.00 38.29 2.32
2244 2270 0.178068 TTCTGTTCGCCCCTATCAGC 59.822 55.000 0.00 0.00 0.00 4.26
2409 2435 4.696877 TGCTTCATGTTGTCTGATAAGTGG 59.303 41.667 0.00 0.00 0.00 4.00
2450 2476 4.503398 ACATATATACTGGGTCCAAGGCT 58.497 43.478 0.00 0.00 0.00 4.58
2480 2508 9.413048 GTATCTATCTTCTGCACAAGTTATACC 57.587 37.037 1.44 0.00 0.00 2.73
2484 2512 9.167311 CTATCTTCTGCACAAGTTATACCTTTT 57.833 33.333 1.44 0.00 0.00 2.27
2622 2650 9.118236 GTAGCAAGTGTTTCATCTAACAAAATC 57.882 33.333 0.00 0.00 39.54 2.17
2626 2654 8.682016 CAAGTGTTTCATCTAACAAAATCGTTC 58.318 33.333 0.00 0.00 39.54 3.95
2645 2673 2.307768 TCACCTCCATATCAGGTCGTC 58.692 52.381 0.39 0.00 42.85 4.20
2744 2772 3.055819 GCACTCTGATTTCTGACCCACTA 60.056 47.826 0.00 0.00 0.00 2.74
3144 3173 2.049156 CTCGCTTGACTGGTCGCA 60.049 61.111 0.00 0.00 0.00 5.10
3186 3215 5.337571 CCGATTCCTCCATTGCTATAGCTAA 60.338 44.000 24.61 16.87 42.66 3.09
3188 3217 6.350528 CGATTCCTCCATTGCTATAGCTAAGA 60.351 42.308 24.61 16.45 42.66 2.10
3192 3221 7.573710 TCCTCCATTGCTATAGCTAAGAAAAA 58.426 34.615 24.61 9.77 42.66 1.94
3199 3228 9.793252 ATTGCTATAGCTAAGAAAAACAACATG 57.207 29.630 24.61 0.00 42.66 3.21
3242 3271 9.744468 ATAGTTTTTCAGTGTTTTACAATGGAC 57.256 29.630 7.32 2.97 43.60 4.02
3385 3414 8.397906 GCTTATGTGTTTGCTCATCTTATGTTA 58.602 33.333 0.00 0.00 32.01 2.41
3589 3619 8.443937 GCAGGGTTGTATCTTATATTTCGATTC 58.556 37.037 0.00 0.00 0.00 2.52
3729 3759 3.859411 TTGGGTGAAATTATCGTTGCC 57.141 42.857 0.00 0.00 0.00 4.52
3738 3768 5.123186 TGAAATTATCGTTGCCACAACTAGG 59.877 40.000 8.66 0.00 0.00 3.02
3846 3876 3.672808 TCCGTTTAATGGCCGAAAACTA 58.327 40.909 19.25 9.22 32.25 2.24
3945 3975 2.629617 AGCTGGTTTGGAACTTTGGATG 59.370 45.455 0.00 0.00 0.00 3.51
4031 4061 4.820716 GCTCATGATAGCAAGGACTTCAAT 59.179 41.667 0.00 0.00 42.30 2.57
4157 4187 1.332640 CGAGCTGCTGTTATTGATGCG 60.333 52.381 7.01 0.00 0.00 4.73
4271 4301 5.404466 TGCTTATCCTCAATGTTTTTGGG 57.596 39.130 0.00 0.00 0.00 4.12
4276 4306 7.525360 GCTTATCCTCAATGTTTTTGGGAAAGA 60.525 37.037 0.00 0.00 0.00 2.52
4385 4415 4.543590 AGAGTCGTCTTGGATGTGATTT 57.456 40.909 0.00 0.00 0.00 2.17
4394 4424 6.744537 CGTCTTGGATGTGATTTGATTTCTTC 59.255 38.462 0.00 0.00 0.00 2.87
4533 4563 4.621068 ATGGAAGCATTACGTTGACATG 57.379 40.909 0.00 0.00 0.00 3.21
4573 4603 5.513495 TGTTATTCCGTATTTTGATTTGCGC 59.487 36.000 0.00 0.00 0.00 6.09
4665 4695 8.314021 TCTGGCATTGTCGTAATATATGAGAAT 58.686 33.333 0.00 0.00 37.95 2.40
4686 4753 8.763984 AGAATTCTTGAAGATGGCTGATTAAT 57.236 30.769 0.88 0.00 0.00 1.40
4687 4754 9.857656 AGAATTCTTGAAGATGGCTGATTAATA 57.142 29.630 0.88 0.00 0.00 0.98
4700 4767 8.810652 TGGCTGATTAATAAGTTGTTTGTTTC 57.189 30.769 1.65 0.00 0.00 2.78
4726 4793 7.873719 TTCAAAGTTTGATCTTGTTACCTGA 57.126 32.000 18.69 0.00 39.84 3.86
4853 4920 6.489361 ACAGAGGCATGGAAAATAATGAGATC 59.511 38.462 0.00 0.00 0.00 2.75
4928 4995 5.410132 GCCCCAATGGTTTGTTAATTGTAAC 59.590 40.000 0.00 0.00 37.30 2.50
4950 5017 0.172803 CATGGCAAAGGCAGCTCTTC 59.827 55.000 0.00 0.00 42.43 2.87
5033 5100 6.823689 ACAGGTACATCCTATTTGCTTTACTG 59.176 38.462 0.00 0.00 46.24 2.74
5035 5102 7.336931 CAGGTACATCCTATTTGCTTTACTGTT 59.663 37.037 0.00 0.00 46.24 3.16
5037 5104 7.120726 GGTACATCCTATTTGCTTTACTGTTGT 59.879 37.037 0.00 0.00 0.00 3.32
5038 5105 7.524717 ACATCCTATTTGCTTTACTGTTGTT 57.475 32.000 0.00 0.00 0.00 2.83
5039 5106 7.593825 ACATCCTATTTGCTTTACTGTTGTTC 58.406 34.615 0.00 0.00 0.00 3.18
5042 5109 6.770785 TCCTATTTGCTTTACTGTTGTTCTGT 59.229 34.615 0.00 0.00 0.00 3.41
5043 5110 6.857964 CCTATTTGCTTTACTGTTGTTCTGTG 59.142 38.462 0.00 0.00 0.00 3.66
5044 5111 4.630894 TTGCTTTACTGTTGTTCTGTGG 57.369 40.909 0.00 0.00 0.00 4.17
5045 5112 3.879998 TGCTTTACTGTTGTTCTGTGGA 58.120 40.909 0.00 0.00 0.00 4.02
5047 5114 4.515191 TGCTTTACTGTTGTTCTGTGGATC 59.485 41.667 0.00 0.00 0.00 3.36
5049 5116 5.239525 GCTTTACTGTTGTTCTGTGGATCTT 59.760 40.000 0.00 0.00 0.00 2.40
5050 5117 6.238759 GCTTTACTGTTGTTCTGTGGATCTTT 60.239 38.462 0.00 0.00 0.00 2.52
5051 5118 6.861065 TTACTGTTGTTCTGTGGATCTTTC 57.139 37.500 0.00 0.00 0.00 2.62
5052 5119 4.137543 ACTGTTGTTCTGTGGATCTTTCC 58.862 43.478 0.00 0.00 42.94 3.13
5079 5146 3.247442 TGGATCAGTTTACGCTAACACG 58.753 45.455 0.00 0.00 39.50 4.49
5395 5462 0.035439 CTGTACTTGGTTGGCCGGAT 60.035 55.000 5.05 0.00 37.67 4.18
5540 5607 9.104965 CATTTCGAAAGGTAATATGTAGGTTGA 57.895 33.333 16.80 0.00 0.00 3.18
5638 5705 1.801178 GTGCTTTGCTCCTGTACTGTC 59.199 52.381 0.00 0.00 0.00 3.51
5651 5718 4.001652 CTGTACTGTCGAACCACTCTCTA 58.998 47.826 0.00 0.00 0.00 2.43
5684 5751 3.249799 TGCTTACGTTCAACTTGGTGATG 59.750 43.478 0.00 0.00 0.00 3.07
5706 5773 3.783943 GTGTGACTGCTACAACAAAAACG 59.216 43.478 0.00 0.00 0.00 3.60
5869 5937 6.824305 ATATTTTGCTGCACCTATATGTCC 57.176 37.500 0.00 0.00 0.00 4.02
5870 5938 2.238942 TTGCTGCACCTATATGTCCG 57.761 50.000 0.00 0.00 0.00 4.79
5871 5939 0.392706 TGCTGCACCTATATGTCCGG 59.607 55.000 0.00 0.00 0.00 5.14
5872 5940 0.320771 GCTGCACCTATATGTCCGGG 60.321 60.000 0.00 0.00 0.00 5.73
5873 5941 0.321671 CTGCACCTATATGTCCGGGG 59.678 60.000 0.00 0.00 0.00 5.73
5874 5942 0.105401 TGCACCTATATGTCCGGGGA 60.105 55.000 0.00 0.00 0.00 4.81
5875 5943 1.053424 GCACCTATATGTCCGGGGAA 58.947 55.000 0.00 0.00 0.00 3.97
5876 5944 1.002087 GCACCTATATGTCCGGGGAAG 59.998 57.143 0.00 0.00 0.00 3.46
5877 5945 1.623811 CACCTATATGTCCGGGGAAGG 59.376 57.143 0.00 3.10 0.00 3.46
5878 5946 1.276622 CCTATATGTCCGGGGAAGGG 58.723 60.000 0.00 0.00 0.00 3.95
5879 5947 1.276622 CTATATGTCCGGGGAAGGGG 58.723 60.000 0.00 0.00 0.00 4.79
5880 5948 0.868894 TATATGTCCGGGGAAGGGGA 59.131 55.000 0.00 0.00 0.00 4.81
5881 5949 0.473886 ATATGTCCGGGGAAGGGGAG 60.474 60.000 0.00 0.00 31.73 4.30
5886 5954 4.115199 CGGGGAAGGGGAGCCTTG 62.115 72.222 0.00 0.00 0.00 3.61
5887 5955 3.744155 GGGGAAGGGGAGCCTTGG 61.744 72.222 0.00 0.00 0.00 3.61
5888 5956 4.448976 GGGAAGGGGAGCCTTGGC 62.449 72.222 2.97 2.97 0.00 4.52
5889 5957 4.803908 GGAAGGGGAGCCTTGGCG 62.804 72.222 5.95 0.00 0.00 5.69
5897 5965 3.605749 GAGCCTTGGCGCAGTGGTA 62.606 63.158 10.83 0.00 0.00 3.25
5898 5966 2.671619 GCCTTGGCGCAGTGGTAA 60.672 61.111 10.83 0.00 0.00 2.85
5899 5967 2.265182 GCCTTGGCGCAGTGGTAAA 61.265 57.895 10.83 0.00 0.00 2.01
5900 5968 1.875963 CCTTGGCGCAGTGGTAAAG 59.124 57.895 10.83 0.71 0.00 1.85
5901 5969 1.210155 CTTGGCGCAGTGGTAAAGC 59.790 57.895 10.83 0.00 0.00 3.51
5902 5970 1.228124 TTGGCGCAGTGGTAAAGCT 60.228 52.632 10.83 0.00 0.00 3.74
5903 5971 1.514678 TTGGCGCAGTGGTAAAGCTG 61.515 55.000 10.83 0.00 35.93 4.24
5908 5976 1.878775 CAGTGGTAAAGCTGCTGCC 59.121 57.895 12.44 7.07 40.80 4.85
5909 5977 0.607489 CAGTGGTAAAGCTGCTGCCT 60.607 55.000 12.44 2.45 40.80 4.75
5910 5978 0.111253 AGTGGTAAAGCTGCTGCCTT 59.889 50.000 12.44 8.34 40.80 4.35
5911 5979 0.242017 GTGGTAAAGCTGCTGCCTTG 59.758 55.000 12.44 0.00 40.80 3.61
5912 5980 0.178992 TGGTAAAGCTGCTGCCTTGT 60.179 50.000 12.44 0.00 40.80 3.16
5913 5981 0.242017 GGTAAAGCTGCTGCCTTGTG 59.758 55.000 12.44 0.00 40.80 3.33
5914 5982 1.238439 GTAAAGCTGCTGCCTTGTGA 58.762 50.000 12.44 0.00 40.80 3.58
5915 5983 1.198637 GTAAAGCTGCTGCCTTGTGAG 59.801 52.381 12.44 0.00 40.80 3.51
5916 5984 1.803366 AAAGCTGCTGCCTTGTGAGC 61.803 55.000 12.44 0.00 40.80 4.26
5917 5985 2.672307 GCTGCTGCCTTGTGAGCT 60.672 61.111 3.85 0.00 36.11 4.09
5918 5986 1.376424 GCTGCTGCCTTGTGAGCTA 60.376 57.895 3.85 0.00 36.11 3.32
5919 5987 1.642952 GCTGCTGCCTTGTGAGCTAC 61.643 60.000 3.85 0.00 36.11 3.58
5920 5988 0.321034 CTGCTGCCTTGTGAGCTACA 60.321 55.000 0.00 0.00 36.11 2.74
5921 5989 0.325933 TGCTGCCTTGTGAGCTACAT 59.674 50.000 0.00 0.00 39.48 2.29
5922 5990 0.731417 GCTGCCTTGTGAGCTACATG 59.269 55.000 0.00 0.00 39.48 3.21
5923 5991 0.731417 CTGCCTTGTGAGCTACATGC 59.269 55.000 0.00 0.00 39.48 4.06
5924 5992 0.036590 TGCCTTGTGAGCTACATGCA 59.963 50.000 12.58 12.58 45.94 3.96
5925 5993 0.449388 GCCTTGTGAGCTACATGCAC 59.551 55.000 0.00 0.00 45.94 4.57
5926 5994 1.089920 CCTTGTGAGCTACATGCACC 58.910 55.000 0.00 0.00 45.94 5.01
5927 5995 0.723414 CTTGTGAGCTACATGCACCG 59.277 55.000 0.00 0.00 45.94 4.94
5928 5996 0.673333 TTGTGAGCTACATGCACCGG 60.673 55.000 0.00 0.00 45.94 5.28
5929 5997 1.815421 GTGAGCTACATGCACCGGG 60.815 63.158 6.32 0.00 45.94 5.73
5930 5998 2.897350 GAGCTACATGCACCGGGC 60.897 66.667 6.32 7.25 45.94 6.13
5931 5999 3.391665 GAGCTACATGCACCGGGCT 62.392 63.158 6.32 0.81 45.94 5.19
5932 6000 3.204827 GCTACATGCACCGGGCTG 61.205 66.667 6.32 9.21 45.15 4.85
5933 6001 3.204827 CTACATGCACCGGGCTGC 61.205 66.667 6.32 8.50 45.15 5.25
5934 6002 4.794648 TACATGCACCGGGCTGCC 62.795 66.667 11.05 11.05 45.15 4.85
5940 6008 2.917227 CACCGGGCTGCCCTTTTT 60.917 61.111 33.39 13.23 42.67 1.94
6081 6149 2.054799 ACACCAGTTCTTTAGGGAGCA 58.945 47.619 0.00 0.00 0.00 4.26
7092 7269 3.837213 TTTCGAGAACGGTACTGTAGG 57.163 47.619 8.00 0.00 40.21 3.18
7116 7293 2.472695 ACTGCGCAGGATTAACAAGA 57.527 45.000 38.27 0.00 0.00 3.02
7117 7294 2.778299 ACTGCGCAGGATTAACAAGAA 58.222 42.857 38.27 0.00 0.00 2.52
7118 7295 2.744202 ACTGCGCAGGATTAACAAGAAG 59.256 45.455 38.27 12.02 0.00 2.85
7119 7296 1.468520 TGCGCAGGATTAACAAGAAGC 59.531 47.619 5.66 0.00 0.00 3.86
7120 7297 1.740025 GCGCAGGATTAACAAGAAGCT 59.260 47.619 0.30 0.00 0.00 3.74
7121 7298 2.936498 GCGCAGGATTAACAAGAAGCTA 59.064 45.455 0.30 0.00 0.00 3.32
7122 7299 3.242446 GCGCAGGATTAACAAGAAGCTAC 60.242 47.826 0.30 0.00 0.00 3.58
7123 7300 4.184629 CGCAGGATTAACAAGAAGCTACT 58.815 43.478 0.00 0.00 0.00 2.57
7124 7301 4.268884 CGCAGGATTAACAAGAAGCTACTC 59.731 45.833 0.00 0.00 0.00 2.59
7125 7302 5.423886 GCAGGATTAACAAGAAGCTACTCT 58.576 41.667 0.00 0.00 0.00 3.24
7126 7303 5.522097 GCAGGATTAACAAGAAGCTACTCTC 59.478 44.000 0.00 0.00 0.00 3.20
7127 7304 6.634805 CAGGATTAACAAGAAGCTACTCTCA 58.365 40.000 0.00 0.00 0.00 3.27
7128 7305 6.533367 CAGGATTAACAAGAAGCTACTCTCAC 59.467 42.308 0.00 0.00 0.00 3.51
7129 7306 5.813157 GGATTAACAAGAAGCTACTCTCACC 59.187 44.000 0.00 0.00 0.00 4.02
7130 7307 3.686916 AACAAGAAGCTACTCTCACCC 57.313 47.619 0.00 0.00 0.00 4.61
7131 7308 1.546476 ACAAGAAGCTACTCTCACCCG 59.454 52.381 0.00 0.00 0.00 5.28
7132 7309 0.533032 AAGAAGCTACTCTCACCCGC 59.467 55.000 0.00 0.00 0.00 6.13
7133 7310 0.612174 AGAAGCTACTCTCACCCGCA 60.612 55.000 0.00 0.00 0.00 5.69
7134 7311 0.246635 GAAGCTACTCTCACCCGCAA 59.753 55.000 0.00 0.00 0.00 4.85
7135 7312 0.685097 AAGCTACTCTCACCCGCAAA 59.315 50.000 0.00 0.00 0.00 3.68
7136 7313 0.685097 AGCTACTCTCACCCGCAAAA 59.315 50.000 0.00 0.00 0.00 2.44
7137 7314 1.071699 AGCTACTCTCACCCGCAAAAA 59.928 47.619 0.00 0.00 0.00 1.94
7275 7456 7.390823 TGTTATCACTACTTGTGCCTGATAAA 58.609 34.615 0.00 0.00 45.81 1.40
7333 7514 8.868522 AAGTTGAGAATGAAATGGAGATTGTA 57.131 30.769 0.00 0.00 0.00 2.41
7415 7596 7.078228 GTGTGTTTCTGTTCACCAAATAGATC 58.922 38.462 0.00 0.00 35.34 2.75
7527 7715 8.824159 TGCTCTTTTCTAGCTGATAACATATC 57.176 34.615 0.00 0.00 40.73 1.63
7596 7784 2.283145 AGAGATTGCAGCCACTGTTT 57.717 45.000 0.00 0.00 33.43 2.83
7674 7862 5.579511 TGACAGATCATGCAATATCTATGCG 59.420 40.000 12.39 5.05 46.76 4.73
7702 7891 5.113383 TCTGTCTTTTCTTGCACTTTCGTA 58.887 37.500 0.00 0.00 0.00 3.43
7901 8090 6.126796 TGCCTGGACATCATAGTAAATTCAGA 60.127 38.462 0.00 0.00 0.00 3.27
7966 8155 4.893829 TTTTTGTTTTATAGGGGGTGCC 57.106 40.909 0.00 0.00 0.00 5.01
7967 8156 3.544698 TTTGTTTTATAGGGGGTGCCA 57.455 42.857 0.00 0.00 0.00 4.92
7968 8157 3.767309 TTGTTTTATAGGGGGTGCCAT 57.233 42.857 0.00 0.00 0.00 4.40
7969 8158 3.025322 TGTTTTATAGGGGGTGCCATG 57.975 47.619 0.00 0.00 0.00 3.66
7970 8159 2.316108 GTTTTATAGGGGGTGCCATGG 58.684 52.381 7.63 7.63 0.00 3.66
7971 8160 0.187361 TTTATAGGGGGTGCCATGGC 59.813 55.000 30.54 30.54 42.35 4.40
7988 8177 2.605295 CACCCACGTCACCCCCTA 60.605 66.667 0.00 0.00 0.00 3.53
7989 8178 2.284405 ACCCACGTCACCCCCTAG 60.284 66.667 0.00 0.00 0.00 3.02
8113 8332 3.725740 GCCTGCAATTCGAAATTGATACG 59.274 43.478 18.43 0.00 0.00 3.06
8183 8406 2.158842 CCTGACAGAGGATGATCCAACC 60.159 54.545 14.90 2.40 46.33 3.77
8382 8610 7.755582 ATTGGTCTTTTCTTTTTGAACTTCG 57.244 32.000 0.00 0.00 33.88 3.79
8398 8626 8.928844 TTGAACTTCGATTCGTTTTCTTTATC 57.071 30.769 5.89 0.00 0.00 1.75
8399 8627 8.306680 TGAACTTCGATTCGTTTTCTTTATCT 57.693 30.769 5.89 0.00 0.00 1.98
8401 8629 9.595357 GAACTTCGATTCGTTTTCTTTATCTTT 57.405 29.630 5.89 0.00 0.00 2.52
8402 8630 8.934973 ACTTCGATTCGTTTTCTTTATCTTTG 57.065 30.769 5.89 0.00 0.00 2.77
8419 8651 3.259876 TCTTTGGTAGTAACATGCTCCGT 59.740 43.478 0.00 0.00 0.00 4.69
8447 8679 3.568443 TCACCAATGCAGGCAATATGAT 58.432 40.909 0.00 0.00 0.00 2.45
8451 8683 4.084287 CCAATGCAGGCAATATGATACCT 58.916 43.478 0.00 0.00 0.00 3.08
8665 8897 3.234353 TGCATCTAGATGGACGATCCTT 58.766 45.455 29.43 0.00 39.16 3.36
8774 9008 5.278660 CGTGACATGTCTAGATGGATCATCA 60.279 44.000 25.55 0.00 42.72 3.07
8782 9016 6.495872 TGTCTAGATGGATCATCATCATCACA 59.504 38.462 12.67 9.03 44.30 3.58
8783 9017 7.036829 GTCTAGATGGATCATCATCATCACAG 58.963 42.308 12.67 8.52 44.30 3.66
8784 9018 5.827326 AGATGGATCATCATCATCACAGT 57.173 39.130 12.67 0.00 44.30 3.55
8785 9019 6.189036 AGATGGATCATCATCATCACAGTT 57.811 37.500 12.67 0.00 44.30 3.16
8786 9020 5.998363 AGATGGATCATCATCATCACAGTTG 59.002 40.000 12.67 0.00 44.30 3.16
8787 9021 3.881089 TGGATCATCATCATCACAGTTGC 59.119 43.478 0.00 0.00 0.00 4.17
8889 9140 1.185315 CATGGGTGTGCTTTTAGGGG 58.815 55.000 0.00 0.00 0.00 4.79
8919 9170 9.485591 CATCTTATGCATTTTCAAAATTTCAGC 57.514 29.630 3.54 0.00 0.00 4.26
9022 9275 7.383029 TGAGAGAATTTGTGCTTTGCAAAATAG 59.617 33.333 13.84 2.55 41.47 1.73
9216 9688 4.133820 TGTAACACAATGGGTCAAGTCAG 58.866 43.478 0.00 0.00 0.00 3.51
9318 9804 2.939103 GCGAAGAGGTGCAAATATCTGT 59.061 45.455 0.00 0.00 0.00 3.41
9341 9828 1.137872 GGATCGTCTGCTCCTGTGATT 59.862 52.381 0.00 0.00 0.00 2.57
9349 9836 1.421268 TGCTCCTGTGATTGTCAAGGT 59.579 47.619 0.00 0.00 31.26 3.50
9355 9842 0.798776 GTGATTGTCAAGGTGCTCCG 59.201 55.000 0.00 0.00 39.05 4.63
9397 9884 5.416952 AGTTCTTTTCAGGGCATCAACATAG 59.583 40.000 0.00 0.00 0.00 2.23
9411 9898 6.205658 GCATCAACATAGGGTAAAATCCTCTC 59.794 42.308 0.00 0.00 35.92 3.20
9433 9920 6.767902 TCTCAACATCAGGTCCATAATAAAGC 59.232 38.462 0.00 0.00 0.00 3.51
9436 9923 5.300752 ACATCAGGTCCATAATAAAGCGAG 58.699 41.667 0.00 0.00 0.00 5.03
9456 9943 1.109323 AATATCGCCTTTGCCTGGGC 61.109 55.000 4.43 4.43 44.43 5.36
9577 10064 5.531659 CAGCTTCTTGAGGATCTGCATTATT 59.468 40.000 0.00 0.00 34.92 1.40
9579 10066 7.228108 CAGCTTCTTGAGGATCTGCATTATTAA 59.772 37.037 0.00 0.00 34.92 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.408702 GGTGCTTTTGTGTGTCATGGT 59.591 47.619 0.00 0.00 0.00 3.55
33 34 3.323403 GTCTCAGGTCCTATGAATCTGGG 59.677 52.174 0.00 0.00 0.00 4.45
41 42 2.382882 TGCTCTGTCTCAGGTCCTATG 58.617 52.381 0.00 0.00 31.51 2.23
61 62 2.246067 TGGATCTAGGAGGCAGAGTCTT 59.754 50.000 0.00 0.00 0.00 3.01
104 105 6.549242 TGGTTATATCTCCCTTCGATACAGA 58.451 40.000 0.00 0.00 0.00 3.41
115 116 6.756542 GCAAATGTGTTTTGGTTATATCTCCC 59.243 38.462 0.79 0.00 44.10 4.30
127 128 1.598601 GGTGGCAGCAAATGTGTTTTG 59.401 47.619 12.58 0.00 46.22 2.44
157 158 0.911769 TTCATGGCTCTGGTTCCGAT 59.088 50.000 0.00 0.00 0.00 4.18
163 164 2.885135 TGATTGTTCATGGCTCTGGT 57.115 45.000 0.00 0.00 0.00 4.00
166 167 3.259123 GGGTTTTGATTGTTCATGGCTCT 59.741 43.478 0.00 0.00 0.00 4.09
196 197 2.041216 GTGTCCAGGAGTATGGGGTTTT 59.959 50.000 0.00 0.00 41.01 2.43
209 210 0.390603 TTATTCCGCGTGTGTCCAGG 60.391 55.000 4.92 0.00 0.00 4.45
231 232 0.394565 GAGGGAGGGGAATCGTGATG 59.605 60.000 0.00 0.00 0.00 3.07
235 236 2.040779 GGGAGGGAGGGGAATCGT 60.041 66.667 0.00 0.00 0.00 3.73
281 282 3.566322 CACAAACGTTATTGGAGTTCCCA 59.434 43.478 0.00 0.00 44.93 4.37
288 289 3.061322 CCTCGACACAAACGTTATTGGA 58.939 45.455 0.00 0.00 34.56 3.53
298 299 2.639065 AGAAAGCAACCTCGACACAAA 58.361 42.857 0.00 0.00 0.00 2.83
299 300 2.325583 AGAAAGCAACCTCGACACAA 57.674 45.000 0.00 0.00 0.00 3.33
300 301 2.325583 AAGAAAGCAACCTCGACACA 57.674 45.000 0.00 0.00 0.00 3.72
319 320 4.712337 GGAACCAATGTAGAGAGAGGAGAA 59.288 45.833 0.00 0.00 0.00 2.87
346 347 2.907458 AAAACAATCAGCCCTAGCCT 57.093 45.000 0.00 0.00 41.25 4.58
384 385 6.477669 TCTGTCGTAATCGAGGTACATATC 57.522 41.667 9.11 0.00 46.96 1.63
385 386 6.872628 TTCTGTCGTAATCGAGGTACATAT 57.127 37.500 9.11 0.00 46.96 1.78
394 395 2.223735 GGCCAGATTCTGTCGTAATCGA 60.224 50.000 12.54 0.00 44.12 3.59
529 530 4.278170 TGAAATCTGTGTTTGGTGGATGAC 59.722 41.667 0.00 0.00 0.00 3.06
531 532 4.852134 TGAAATCTGTGTTTGGTGGATG 57.148 40.909 0.00 0.00 0.00 3.51
532 533 5.335897 CGAATGAAATCTGTGTTTGGTGGAT 60.336 40.000 0.00 0.00 0.00 3.41
544 545 3.535561 ACCTACTGGCGAATGAAATCTG 58.464 45.455 0.00 0.00 36.63 2.90
563 564 1.905637 AGGTGGGAATTGAAACGACC 58.094 50.000 0.00 0.00 0.00 4.79
567 568 5.670485 AGAAAACAAGGTGGGAATTGAAAC 58.330 37.500 0.00 0.00 0.00 2.78
576 577 0.313987 GGCGAAGAAAACAAGGTGGG 59.686 55.000 0.00 0.00 0.00 4.61
619 626 0.880441 TTCATGTGCATTGACCCGTG 59.120 50.000 2.10 0.00 0.00 4.94
621 628 1.541147 AGTTTCATGTGCATTGACCCG 59.459 47.619 2.10 0.00 0.00 5.28
623 630 3.983344 GTCAAGTTTCATGTGCATTGACC 59.017 43.478 17.80 3.43 40.22 4.02
660 669 1.536073 GGAAGCCAAGTTCTTGGGGC 61.536 60.000 26.37 16.51 46.77 5.80
661 670 0.178964 TGGAAGCCAAGTTCTTGGGG 60.179 55.000 26.37 8.65 42.31 4.96
662 671 1.703411 TTGGAAGCCAAGTTCTTGGG 58.297 50.000 26.37 12.83 38.75 4.12
738 747 1.702491 GGCGAAAGATGCGGTGGTAC 61.702 60.000 0.00 0.00 0.00 3.34
743 752 4.796495 GGGGGCGAAAGATGCGGT 62.796 66.667 0.00 0.00 0.00 5.68
759 768 2.696759 CGCGGCTTAAACTTGGGGG 61.697 63.158 0.00 0.00 0.00 5.40
760 769 1.238625 TTCGCGGCTTAAACTTGGGG 61.239 55.000 6.13 0.00 0.00 4.96
761 770 0.109919 GTTCGCGGCTTAAACTTGGG 60.110 55.000 6.13 0.00 0.00 4.12
777 786 2.385091 TTTTAGCGCGCGGAGGTTC 61.385 57.895 33.06 13.74 0.00 3.62
844 854 2.747855 GGGCGGAGTGCTTTGGAG 60.748 66.667 0.00 0.00 45.43 3.86
845 855 4.344865 GGGGCGGAGTGCTTTGGA 62.345 66.667 0.00 0.00 45.43 3.53
853 863 4.779733 ATCAGACGGGGGCGGAGT 62.780 66.667 0.00 0.00 0.00 3.85
854 864 3.917760 GATCAGACGGGGGCGGAG 61.918 72.222 0.00 0.00 0.00 4.63
895 905 2.161609 ACCACTGCGATTTTTCCGATTC 59.838 45.455 0.00 0.00 0.00 2.52
901 911 5.508224 CGATTAAGAACCACTGCGATTTTTC 59.492 40.000 0.00 0.00 0.00 2.29
1132 1146 2.395619 ACCCCCAAATCCGTACTAGAG 58.604 52.381 0.00 0.00 0.00 2.43
1177 1191 4.419921 CCGCCACCTAACCCCACC 62.420 72.222 0.00 0.00 0.00 4.61
1210 1224 1.668419 CCAGGTGAAAATAGGAGCCG 58.332 55.000 0.00 0.00 0.00 5.52
1216 1230 2.497273 CCCAAAGGCCAGGTGAAAATAG 59.503 50.000 5.01 0.00 0.00 1.73
1268 1282 6.355638 CAGTAAACGAATCAGTTCAGACAAC 58.644 40.000 0.00 0.00 33.86 3.32
1296 1317 3.260483 CTCATCGAGCGGCTGCAC 61.260 66.667 21.93 13.30 46.23 4.57
1307 1328 4.517285 TCCTTTCCAAATCCTTCTCATCG 58.483 43.478 0.00 0.00 0.00 3.84
1343 1364 4.999950 CAGATTAGAACAAGCACCTTCTGT 59.000 41.667 0.00 0.00 0.00 3.41
1408 1429 5.099042 ACTACTCACACAGGAAACAGTTT 57.901 39.130 0.00 0.00 0.00 2.66
1411 1432 6.018180 GGTAAAACTACTCACACAGGAAACAG 60.018 42.308 0.00 0.00 0.00 3.16
1472 1498 2.168313 CCTTGAGCTTCTTCTCCTCCTC 59.832 54.545 0.00 0.00 32.22 3.71
1504 1530 0.032615 CCTGTAGTCTGGCCTCCTCT 60.033 60.000 3.32 0.00 0.00 3.69
1548 1574 2.623416 CCTCCAAAGTCCAAACCAAGAC 59.377 50.000 0.00 0.00 0.00 3.01
1560 1586 2.695585 ACAGAACCTCTCCTCCAAAGT 58.304 47.619 0.00 0.00 0.00 2.66
1561 1587 3.778954 AACAGAACCTCTCCTCCAAAG 57.221 47.619 0.00 0.00 0.00 2.77
1562 1588 3.458118 TCAAACAGAACCTCTCCTCCAAA 59.542 43.478 0.00 0.00 0.00 3.28
1563 1589 3.045634 TCAAACAGAACCTCTCCTCCAA 58.954 45.455 0.00 0.00 0.00 3.53
1564 1590 2.368875 GTCAAACAGAACCTCTCCTCCA 59.631 50.000 0.00 0.00 0.00 3.86
1565 1591 2.635427 AGTCAAACAGAACCTCTCCTCC 59.365 50.000 0.00 0.00 0.00 4.30
1566 1592 3.322254 TCAGTCAAACAGAACCTCTCCTC 59.678 47.826 0.00 0.00 0.00 3.71
1697 1723 4.603094 TCTTCTGTCCAGTGGGAGTATA 57.397 45.455 9.92 0.00 46.12 1.47
1724 1750 2.802247 GTTTGGCCATTTGAGAAGCAAC 59.198 45.455 6.09 0.00 35.91 4.17
1757 1783 2.004583 TACGATTTCTCAACAGCGGG 57.995 50.000 0.00 0.00 0.00 6.13
1929 1955 0.751643 AACGGTGGCTTTGAGCTTGT 60.752 50.000 0.00 0.00 41.99 3.16
2183 2209 0.035056 ACTACCTCAATGGCCACTGC 60.035 55.000 8.16 0.00 40.22 4.40
2191 2217 9.823647 AGTACAGATAAAATCACTACCTCAATG 57.176 33.333 0.00 0.00 0.00 2.82
2244 2270 4.589216 AAGAACATGAACACCACCAATG 57.411 40.909 0.00 0.00 0.00 2.82
2257 2283 7.637132 GTCAATGCAAAGAAACAAAAGAACATG 59.363 33.333 0.00 0.00 0.00 3.21
2409 2435 7.969536 ATATGTTCTATGCACTGGAATGTAC 57.030 36.000 0.00 0.00 0.00 2.90
2450 2476 5.658634 ACTTGTGCAGAAGATAGATACTGGA 59.341 40.000 28.57 0.00 0.00 3.86
2479 2507 2.482864 GCCATGAACAACCACAAAAGG 58.517 47.619 0.00 0.00 0.00 3.11
2480 2508 2.102925 AGGCCATGAACAACCACAAAAG 59.897 45.455 5.01 0.00 0.00 2.27
2484 2512 1.423541 ACTAGGCCATGAACAACCACA 59.576 47.619 5.01 0.00 0.00 4.17
2487 2515 7.094762 GCTAATAATACTAGGCCATGAACAACC 60.095 40.741 5.01 0.00 0.00 3.77
2622 2650 2.543861 CGACCTGATATGGAGGTGAACG 60.544 54.545 7.62 2.78 44.28 3.95
2626 2654 1.001268 CGACGACCTGATATGGAGGTG 60.001 57.143 7.62 4.03 44.28 4.00
2645 2673 2.416547 ACGCATGATCTTCTTTTCCACG 59.583 45.455 0.00 0.00 0.00 4.94
2823 2851 8.201554 TGAGCAAAATACATAACAGATGACTC 57.798 34.615 0.00 0.00 0.00 3.36
3102 3131 0.713883 AAGCGTACGCAATTGTCTCG 59.286 50.000 38.58 4.87 44.88 4.04
3144 3173 2.624838 TCGGACAAGGACTTTACTTCGT 59.375 45.455 0.00 0.00 0.00 3.85
3188 3217 9.825972 CGATATTTAGACAGACATGTTGTTTTT 57.174 29.630 0.00 0.68 40.68 1.94
3192 3221 6.106003 TGCGATATTTAGACAGACATGTTGT 58.894 36.000 0.00 6.59 40.68 3.32
3199 3228 9.851043 GAAAAACTATGCGATATTTAGACAGAC 57.149 33.333 0.00 0.00 0.00 3.51
3212 3241 7.017498 TGTAAAACACTGAAAAACTATGCGA 57.983 32.000 0.00 0.00 0.00 5.10
3213 3242 7.672351 TTGTAAAACACTGAAAAACTATGCG 57.328 32.000 0.00 0.00 0.00 4.73
3242 3271 1.134753 ACAGCTTCTGATCTCTGCTCG 59.865 52.381 0.29 0.00 35.18 5.03
3729 3759 6.638873 CGAGCATAGTTTCTATCCTAGTTGTG 59.361 42.308 0.00 0.00 0.00 3.33
3738 3768 6.094061 GGTATCACCGAGCATAGTTTCTATC 58.906 44.000 0.00 0.00 0.00 2.08
3846 3876 3.627577 AGTCATCGGCGCAAATTATTTCT 59.372 39.130 10.83 0.00 0.00 2.52
3945 3975 5.098211 GCACTGATTTCTGAATGTAAAGGC 58.902 41.667 0.00 0.00 0.00 4.35
4031 4061 2.890311 CAGGTTATGCTGTTTCCCAACA 59.110 45.455 0.00 0.00 40.82 3.33
4213 4243 6.000219 ACAACTACATGAATGAAGCAGAACT 59.000 36.000 0.00 0.00 0.00 3.01
4214 4244 6.246420 ACAACTACATGAATGAAGCAGAAC 57.754 37.500 0.00 0.00 0.00 3.01
4394 4424 9.781834 TTACACTCCATAAATTAGCAAAATTCG 57.218 29.630 0.00 0.00 0.00 3.34
4551 4581 5.513495 GTGCGCAAATCAAAATACGGAATAA 59.487 36.000 14.00 0.00 0.00 1.40
4665 4695 9.466497 AACTTATTAATCAGCCATCTTCAAGAA 57.534 29.630 0.00 0.00 0.00 2.52
4687 4754 9.050601 TCAAACTTTGAATGAAACAAACAACTT 57.949 25.926 1.47 0.00 36.59 2.66
4688 4755 8.600449 TCAAACTTTGAATGAAACAAACAACT 57.400 26.923 1.47 0.00 36.59 3.16
4700 4767 8.352201 TCAGGTAACAAGATCAAACTTTGAATG 58.648 33.333 8.28 10.01 41.14 2.67
4721 4788 7.415206 GCGACAAACAAGGATAAATAATCAGGT 60.415 37.037 0.00 0.00 36.20 4.00
4739 4806 4.779987 ACGGAAAAAGATAAGCGACAAAC 58.220 39.130 0.00 0.00 0.00 2.93
4790 4857 9.979578 AGTTATTGACAAGTGCAAATTGATTAA 57.020 25.926 17.34 10.19 46.37 1.40
4815 4882 3.300388 TGCCTCTGTATAGACCCTTCAG 58.700 50.000 0.00 0.00 0.00 3.02
4853 4920 5.176958 AGTTCTTGAACAACGACCTAATTCG 59.823 40.000 14.80 0.00 44.87 3.34
4928 4995 2.221906 GAGCTGCCTTTGCCATGGTG 62.222 60.000 14.67 1.49 36.33 4.17
4950 5017 5.578005 ATCTCTTTGGATTTCACAGCATG 57.422 39.130 0.00 0.00 46.00 4.06
5043 5110 7.888250 AACTGATCCATAAAAGGAAAGATCC 57.112 36.000 0.00 0.00 46.98 3.36
5045 5112 8.893727 CGTAAACTGATCCATAAAAGGAAAGAT 58.106 33.333 0.00 0.00 41.92 2.40
5047 5114 6.967199 GCGTAAACTGATCCATAAAAGGAAAG 59.033 38.462 0.00 0.00 41.92 2.62
5049 5116 6.177610 AGCGTAAACTGATCCATAAAAGGAA 58.822 36.000 0.00 0.00 41.92 3.36
5050 5117 5.741011 AGCGTAAACTGATCCATAAAAGGA 58.259 37.500 0.00 0.00 43.01 3.36
5051 5118 7.065324 TGTTAGCGTAAACTGATCCATAAAAGG 59.935 37.037 0.00 0.00 0.00 3.11
5052 5119 7.903431 GTGTTAGCGTAAACTGATCCATAAAAG 59.097 37.037 0.00 0.00 0.00 2.27
5079 5146 6.761714 ACAGTAGTGGATGGATTATTCGTTTC 59.238 38.462 1.92 0.00 0.00 2.78
5638 5705 1.464734 TCTGCCTAGAGAGTGGTTCG 58.535 55.000 0.00 0.00 0.00 3.95
5672 5739 2.287188 GCAGTCACACATCACCAAGTTG 60.287 50.000 0.00 0.00 0.00 3.16
5684 5751 3.783943 CGTTTTTGTTGTAGCAGTCACAC 59.216 43.478 0.00 0.00 0.00 3.82
5706 5773 7.229506 CAGAACCCCCAAGAGTGATAATAATTC 59.770 40.741 0.00 0.00 0.00 2.17
5879 5947 3.605749 TACCACTGCGCCAAGGCTC 62.606 63.158 4.18 1.20 39.32 4.70
5880 5948 2.690653 TTTACCACTGCGCCAAGGCT 62.691 55.000 4.18 0.00 39.32 4.58
5881 5949 2.200170 CTTTACCACTGCGCCAAGGC 62.200 60.000 4.18 0.00 37.85 4.35
5882 5950 1.875963 CTTTACCACTGCGCCAAGG 59.124 57.895 4.18 6.21 0.00 3.61
5883 5951 1.210155 GCTTTACCACTGCGCCAAG 59.790 57.895 4.18 0.00 0.00 3.61
5884 5952 1.228124 AGCTTTACCACTGCGCCAA 60.228 52.632 4.18 0.00 0.00 4.52
5885 5953 1.965930 CAGCTTTACCACTGCGCCA 60.966 57.895 4.18 0.00 0.00 5.69
5886 5954 2.870372 CAGCTTTACCACTGCGCC 59.130 61.111 4.18 0.00 0.00 6.53
5890 5958 0.607489 AGGCAGCAGCTTTACCACTG 60.607 55.000 0.00 0.00 41.70 3.66
5891 5959 0.111253 AAGGCAGCAGCTTTACCACT 59.889 50.000 0.00 0.00 38.40 4.00
5892 5960 0.242017 CAAGGCAGCAGCTTTACCAC 59.758 55.000 0.00 0.00 38.07 4.16
5893 5961 0.178992 ACAAGGCAGCAGCTTTACCA 60.179 50.000 0.00 0.00 38.07 3.25
5894 5962 0.242017 CACAAGGCAGCAGCTTTACC 59.758 55.000 0.00 0.00 38.07 2.85
5895 5963 1.198637 CTCACAAGGCAGCAGCTTTAC 59.801 52.381 0.00 0.00 38.07 2.01
5896 5964 1.527034 CTCACAAGGCAGCAGCTTTA 58.473 50.000 0.00 0.00 38.07 1.85
5897 5965 1.803366 GCTCACAAGGCAGCAGCTTT 61.803 55.000 0.00 0.00 41.17 3.51
5898 5966 2.266627 GCTCACAAGGCAGCAGCTT 61.267 57.895 0.00 0.00 41.70 3.74
5899 5967 1.834856 TAGCTCACAAGGCAGCAGCT 61.835 55.000 7.72 7.72 43.00 4.24
5900 5968 1.376424 TAGCTCACAAGGCAGCAGC 60.376 57.895 0.00 0.00 38.18 5.25
5901 5969 0.321034 TGTAGCTCACAAGGCAGCAG 60.321 55.000 0.00 0.00 38.18 4.24
5902 5970 0.325933 ATGTAGCTCACAAGGCAGCA 59.674 50.000 0.00 0.00 41.55 4.41
5903 5971 0.731417 CATGTAGCTCACAAGGCAGC 59.269 55.000 0.00 0.00 41.55 5.25
5904 5972 0.731417 GCATGTAGCTCACAAGGCAG 59.269 55.000 0.00 0.00 41.55 4.85
5905 5973 0.036590 TGCATGTAGCTCACAAGGCA 59.963 50.000 15.33 15.33 44.47 4.75
5906 5974 0.449388 GTGCATGTAGCTCACAAGGC 59.551 55.000 0.00 3.26 45.94 4.35
5907 5975 1.089920 GGTGCATGTAGCTCACAAGG 58.910 55.000 5.68 0.00 45.94 3.61
5908 5976 0.723414 CGGTGCATGTAGCTCACAAG 59.277 55.000 11.25 0.00 45.94 3.16
5909 5977 0.673333 CCGGTGCATGTAGCTCACAA 60.673 55.000 11.25 0.00 45.94 3.33
5910 5978 1.079197 CCGGTGCATGTAGCTCACA 60.079 57.895 11.25 0.00 45.94 3.58
5911 5979 1.815421 CCCGGTGCATGTAGCTCAC 60.815 63.158 11.25 1.84 45.94 3.51
5912 5980 2.584064 CCCGGTGCATGTAGCTCA 59.416 61.111 11.25 0.00 45.94 4.26
5913 5981 2.897350 GCCCGGTGCATGTAGCTC 60.897 66.667 11.25 0.00 45.94 4.09
5914 5982 3.402681 AGCCCGGTGCATGTAGCT 61.403 61.111 15.92 4.82 45.94 3.32
5915 5983 3.204827 CAGCCCGGTGCATGTAGC 61.205 66.667 15.92 2.56 44.83 3.58
5916 5984 3.204827 GCAGCCCGGTGCATGTAG 61.205 66.667 13.70 0.91 43.41 2.74
5917 5985 4.794648 GGCAGCCCGGTGCATGTA 62.795 66.667 19.47 0.00 45.93 2.29
5945 6013 9.750125 CTGCTTGTAAGTAGATAATGTGACATA 57.250 33.333 0.00 0.00 40.66 2.29
5946 6014 8.260818 ACTGCTTGTAAGTAGATAATGTGACAT 58.739 33.333 15.17 0.00 40.66 3.06
7116 7293 0.685097 TTTGCGGGTGAGAGTAGCTT 59.315 50.000 0.00 0.00 0.00 3.74
7117 7294 0.685097 TTTTGCGGGTGAGAGTAGCT 59.315 50.000 0.00 0.00 0.00 3.32
7118 7295 1.519408 TTTTTGCGGGTGAGAGTAGC 58.481 50.000 0.00 0.00 0.00 3.58
7216 7397 7.499321 TGTGGGGTATATAATTGCTTAAACG 57.501 36.000 0.00 0.00 0.00 3.60
7333 7514 5.362143 TCTCAGCTTACTCACAGCATCTAAT 59.638 40.000 0.00 0.00 39.99 1.73
7415 7596 5.630680 GCCATACTGTGTGAAACTCAAAATG 59.369 40.000 6.08 0.00 40.14 2.32
7527 7715 5.529060 GGCTCCTGTTGAGGTGAAAATATAG 59.471 44.000 0.00 0.00 41.73 1.31
7674 7862 7.112148 CGAAAGTGCAAGAAAAGACAGAAATAC 59.888 37.037 0.00 0.00 0.00 1.89
7749 7938 7.745717 AGTATATGGTTACTTGTGGCACATAT 58.254 34.615 22.73 15.07 44.52 1.78
7812 8001 4.412199 CCCAGTAATTTGATCCTAGGTCCA 59.588 45.833 9.08 5.21 0.00 4.02
7965 8154 3.055719 GTGACGTGGGTGCCATGG 61.056 66.667 7.63 7.63 44.23 3.66
7966 8155 3.055719 GGTGACGTGGGTGCCATG 61.056 66.667 0.00 0.00 45.34 3.66
7967 8156 4.344865 GGGTGACGTGGGTGCCAT 62.345 66.667 0.00 0.00 35.28 4.40
7971 8160 2.605295 TAGGGGGTGACGTGGGTG 60.605 66.667 0.00 0.00 0.00 4.61
7972 8161 2.284405 CTAGGGGGTGACGTGGGT 60.284 66.667 0.00 0.00 0.00 4.51
7973 8162 2.038329 TCTAGGGGGTGACGTGGG 59.962 66.667 0.00 0.00 0.00 4.61
8183 8406 3.061848 GTGGCACAATCGGGTGGG 61.062 66.667 13.86 0.00 44.16 4.61
8398 8626 3.596214 ACGGAGCATGTTACTACCAAAG 58.404 45.455 0.00 0.00 0.00 2.77
8399 8627 3.688694 ACGGAGCATGTTACTACCAAA 57.311 42.857 0.00 0.00 0.00 3.28
8401 8629 3.688694 AAACGGAGCATGTTACTACCA 57.311 42.857 0.00 0.00 0.00 3.25
8402 8630 3.373130 GGAAAACGGAGCATGTTACTACC 59.627 47.826 0.00 0.00 0.00 3.18
8419 8651 1.275856 GCCTGCATTGGTGATGGAAAA 59.724 47.619 0.00 0.00 35.52 2.29
8447 8679 4.515191 GCACTCATTTTCTGTGACAAGGTA 59.485 41.667 0.00 0.00 33.95 3.08
8451 8683 4.579753 TGATGCACTCATTTTCTGTGACAA 59.420 37.500 0.00 0.00 33.95 3.18
8665 8897 0.762842 AGTGACTGTACAGGGTGCCA 60.763 55.000 26.12 12.61 0.00 4.92
8774 9008 2.555325 CAACTGTGGCAACTGTGATGAT 59.445 45.455 4.30 0.00 38.37 2.45
8782 9016 1.312371 ACAACGCAACTGTGGCAACT 61.312 50.000 8.09 0.00 37.61 3.16
8783 9017 1.138671 ACAACGCAACTGTGGCAAC 59.861 52.632 8.09 0.00 0.00 4.17
8784 9018 1.138459 CACAACGCAACTGTGGCAA 59.862 52.632 8.09 0.00 40.44 4.52
8785 9019 1.308783 TTCACAACGCAACTGTGGCA 61.309 50.000 8.09 0.00 43.60 4.92
8786 9020 0.592247 CTTCACAACGCAACTGTGGC 60.592 55.000 0.00 0.00 43.60 5.01
8787 9021 0.029300 CCTTCACAACGCAACTGTGG 59.971 55.000 9.26 0.00 43.60 4.17
8889 9140 7.781548 ATTTTGAAAATGCATAAGATGAGGC 57.218 32.000 0.00 0.00 0.00 4.70
9022 9275 3.944422 TGCGTGAAGAGAAAACAGTTC 57.056 42.857 0.00 0.00 0.00 3.01
9216 9688 0.322008 ACAAAGCTAGGACAGGCAGC 60.322 55.000 0.00 0.00 35.49 5.25
9310 9796 3.894427 AGCAGACGATCCTCACAGATATT 59.106 43.478 0.00 0.00 0.00 1.28
9313 9799 1.680735 GAGCAGACGATCCTCACAGAT 59.319 52.381 0.00 0.00 0.00 2.90
9341 9828 0.684535 TTCATCGGAGCACCTTGACA 59.315 50.000 0.00 0.00 0.00 3.58
9349 9836 1.612146 TGGAGGGTTCATCGGAGCA 60.612 57.895 0.00 0.00 0.00 4.26
9355 9842 3.983044 ACTGTTAGTGGAGGGTTCATC 57.017 47.619 0.00 0.00 0.00 2.92
9397 9884 4.884164 CCTGATGTTGAGAGGATTTTACCC 59.116 45.833 0.00 0.00 0.00 3.69
9411 9898 5.527214 TCGCTTTATTATGGACCTGATGTTG 59.473 40.000 0.00 0.00 0.00 3.33
9436 9923 0.954452 CCCAGGCAAAGGCGATATTC 59.046 55.000 0.00 0.00 42.47 1.75
9447 9934 1.748879 GCTACATTCGCCCAGGCAA 60.749 57.895 9.78 2.90 42.06 4.52
9456 9943 1.081892 AAGTGCAGCAGCTACATTCG 58.918 50.000 1.76 0.00 42.74 3.34
9519 10006 1.679680 ACATAGCCATTGCACATGAGC 59.320 47.619 8.32 8.32 41.13 4.26
9526 10013 1.549620 CCCAAACACATAGCCATTGCA 59.450 47.619 0.00 0.00 41.13 4.08
9561 10048 7.879070 GCATCTTTTAATAATGCAGATCCTCA 58.121 34.615 10.62 0.00 44.07 3.86


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

AutoCloner maintained by Alex Coulton.