Multiple sequence alignment - TraesCS7A01G273800

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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 TraesCS7A01G273800 chr7A 100.000 2831 0 0 1 2831 287471700 287474530 0.000000e+00 5228
1 TraesCS7A01G273800 chr7A 82.101 1447 142 63 390 1776 287482226 287483615 0.000000e+00 1129
2 TraesCS7A01G273800 chr7A 84.755 879 117 14 906 1776 287484841 287485710 0.000000e+00 865
3 TraesCS7A01G273800 chr7A 86.744 777 93 8 1003 1776 287526371 287527140 0.000000e+00 856
4 TraesCS7A01G273800 chr7A 95.513 312 13 1 1773 2083 148252111 148252422 5.450000e-137 497
5 TraesCS7A01G273800 chr7A 90.094 212 18 3 2080 2290 287483611 287483820 3.590000e-69 272
6 TraesCS7A01G273800 chr7A 82.474 194 28 6 2080 2270 287495030 287495220 6.270000e-37 165
7 TraesCS7A01G273800 chr7A 79.121 182 23 8 2089 2269 287529066 287529233 8.290000e-21 111
8 TraesCS7A01G273800 chr7B 90.171 1750 111 31 56 1776 244393111 244394828 0.000000e+00 2222
9 TraesCS7A01G273800 chr7B 86.194 775 100 5 1003 1776 244406932 244407700 0.000000e+00 832
10 TraesCS7A01G273800 chr7B 86.804 341 34 9 2080 2414 244394824 244395159 1.240000e-98 370
11 TraesCS7A01G273800 chr7B 80.749 187 29 7 2080 2265 244396995 244397175 3.800000e-29 139
12 TraesCS7A01G273800 chr7D 90.933 1125 73 14 669 1776 264026466 264027578 0.000000e+00 1485
13 TraesCS7A01G273800 chr7D 85.358 881 109 14 906 1776 264054315 264055185 0.000000e+00 894
14 TraesCS7A01G273800 chr7D 84.510 878 120 10 906 1776 264028817 264029685 0.000000e+00 854
15 TraesCS7A01G273800 chr7D 86.247 778 95 10 1003 1776 264034768 264035537 0.000000e+00 833
16 TraesCS7A01G273800 chr7D 95.833 312 13 0 1772 2083 539381770 539382081 3.250000e-139 505
17 TraesCS7A01G273800 chr7D 95.779 308 12 1 1775 2081 265508076 265507769 1.960000e-136 496
18 TraesCS7A01G273800 chr7D 90.187 214 18 3 2080 2292 264027574 264027785 2.780000e-70 276
19 TraesCS7A01G273800 chr7D 89.781 137 13 1 83 219 264025750 264025885 1.040000e-39 174
20 TraesCS7A01G273800 chr7D 82.902 193 28 5 2080 2270 264037431 264037620 4.850000e-38 169
21 TraesCS7A01G273800 chr7D 83.333 138 19 4 2080 2217 264029681 264029814 1.060000e-24 124
22 TraesCS7A01G273800 chr7D 89.011 91 6 4 2089 2179 264057170 264057256 2.980000e-20 110
23 TraesCS7A01G273800 chr5A 93.541 418 27 0 2414 2831 484441614 484442031 8.610000e-175 623
24 TraesCS7A01G273800 chr5A 93.525 417 26 1 2415 2831 484439315 484439730 1.110000e-173 619
25 TraesCS7A01G273800 chr6D 92.124 419 31 2 2414 2831 11351907 11351490 8.740000e-165 590
26 TraesCS7A01G273800 chr5D 91.726 423 33 2 2410 2831 302889505 302889084 1.130000e-163 586
27 TraesCS7A01G273800 chr5D 91.647 419 33 2 2414 2831 382355252 382354835 1.890000e-161 579
28 TraesCS7A01G273800 chr5D 95.765 307 13 0 1775 2081 351152811 351153117 1.960000e-136 496
29 TraesCS7A01G273800 chr4D 91.667 420 33 2 2413 2831 27571237 27571655 5.260000e-162 580
30 TraesCS7A01G273800 chr1D 91.667 420 33 2 2413 2831 314437234 314436816 5.260000e-162 580
31 TraesCS7A01G273800 chr1D 91.101 427 35 3 2407 2831 357322553 357322128 2.450000e-160 575
32 TraesCS7A01G273800 chr1D 95.765 307 13 0 1775 2081 103031927 103032233 1.960000e-136 496
33 TraesCS7A01G273800 chr3D 91.587 416 33 2 2414 2828 335676227 335676641 8.800000e-160 573
34 TraesCS7A01G273800 chr6A 95.498 311 14 0 1775 2085 588602429 588602119 5.450000e-137 497
35 TraesCS7A01G273800 chr6A 94.340 318 18 0 1771 2088 600260912 600261229 3.280000e-134 488
36 TraesCS7A01G273800 chr5B 94.154 325 17 2 1765 2089 288645868 288646190 7.050000e-136 494
37 TraesCS7A01G273800 chr2D 94.620 316 15 1 1772 2085 213696992 213697307 3.280000e-134 488


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 TraesCS7A01G273800 chr7A 287471700 287474530 2830 False 5228.000000 5228 100.0000 1 2831 1 chr7A.!!$F2 2830
1 TraesCS7A01G273800 chr7A 287482226 287485710 3484 False 755.333333 1129 85.6500 390 2290 3 chr7A.!!$F4 1900
2 TraesCS7A01G273800 chr7A 287526371 287529233 2862 False 483.500000 856 82.9325 1003 2269 2 chr7A.!!$F5 1266
3 TraesCS7A01G273800 chr7B 244393111 244397175 4064 False 910.333333 2222 85.9080 56 2414 3 chr7B.!!$F2 2358
4 TraesCS7A01G273800 chr7B 244406932 244407700 768 False 832.000000 832 86.1940 1003 1776 1 chr7B.!!$F1 773
5 TraesCS7A01G273800 chr7D 264025750 264029814 4064 False 582.600000 1485 87.7488 83 2292 5 chr7D.!!$F2 2209
6 TraesCS7A01G273800 chr7D 264054315 264057256 2941 False 502.000000 894 87.1845 906 2179 2 chr7D.!!$F4 1273
7 TraesCS7A01G273800 chr7D 264034768 264037620 2852 False 501.000000 833 84.5745 1003 2270 2 chr7D.!!$F3 1267
8 TraesCS7A01G273800 chr5A 484439315 484442031 2716 False 621.000000 623 93.5330 2414 2831 2 chr5A.!!$F1 417

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
457 621 0.039437 ACGTCACGCCACAAGACTAG 60.039 55.0 0.00 0.00 0.0 2.57 F
707 928 0.321919 AACATGCATGCCTCGACACT 60.322 50.0 26.53 0.28 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1424 1695 0.469494 TGCCTTGACTTGAGCAGACA 59.531 50.0 0.0 0.00 0.00 3.41 R
2414 4668 0.605589 GCCCCTATGCCGGTCATAAC 60.606 60.0 16.1 6.26 37.22 1.89 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
23 24 6.999705 ATACATACATAGTTTACCCCGGAA 57.000 37.500 0.73 0.00 0.00 4.30
24 25 5.899631 ACATACATAGTTTACCCCGGAAT 57.100 39.130 0.73 0.00 0.00 3.01
25 26 5.861727 ACATACATAGTTTACCCCGGAATC 58.138 41.667 0.73 0.00 0.00 2.52
26 27 3.464111 ACATAGTTTACCCCGGAATCG 57.536 47.619 0.73 0.00 0.00 3.34
27 28 2.140717 CATAGTTTACCCCGGAATCGC 58.859 52.381 0.73 0.00 34.56 4.58
28 29 0.102844 TAGTTTACCCCGGAATCGCG 59.897 55.000 0.73 0.00 34.56 5.87
29 30 1.448365 GTTTACCCCGGAATCGCGT 60.448 57.895 0.73 0.00 34.56 6.01
30 31 1.153588 TTTACCCCGGAATCGCGTC 60.154 57.895 0.73 0.00 34.56 5.19
31 32 2.887463 TTTACCCCGGAATCGCGTCG 62.887 60.000 0.73 6.47 34.56 5.12
44 45 4.312383 CGTCGGCGCATACACATA 57.688 55.556 10.83 0.00 0.00 2.29
45 46 1.844003 CGTCGGCGCATACACATAC 59.156 57.895 10.83 0.00 0.00 2.39
46 47 0.868177 CGTCGGCGCATACACATACA 60.868 55.000 10.83 0.00 0.00 2.29
47 48 1.497991 GTCGGCGCATACACATACAT 58.502 50.000 10.83 0.00 0.00 2.29
48 49 1.192312 GTCGGCGCATACACATACATG 59.808 52.381 10.83 0.00 0.00 3.21
49 50 0.110688 CGGCGCATACACATACATGC 60.111 55.000 10.83 0.00 43.30 4.06
50 51 0.943673 GGCGCATACACATACATGCA 59.056 50.000 10.83 0.00 46.32 3.96
51 52 1.536766 GGCGCATACACATACATGCAT 59.463 47.619 10.83 0.00 46.32 3.96
52 53 2.577450 GCGCATACACATACATGCATG 58.423 47.619 25.09 25.09 46.32 4.06
53 54 2.031769 GCGCATACACATACATGCATGT 60.032 45.455 33.20 33.20 46.32 3.21
54 55 3.186205 GCGCATACACATACATGCATGTA 59.814 43.478 35.03 35.03 46.32 2.29
219 220 2.297701 GTTTGCTGTCTTGTCCTTCCA 58.702 47.619 0.00 0.00 0.00 3.53
220 221 1.967319 TTGCTGTCTTGTCCTTCCAC 58.033 50.000 0.00 0.00 0.00 4.02
221 222 0.108585 TGCTGTCTTGTCCTTCCACC 59.891 55.000 0.00 0.00 0.00 4.61
222 223 0.398318 GCTGTCTTGTCCTTCCACCT 59.602 55.000 0.00 0.00 0.00 4.00
226 227 1.278413 GTCTTGTCCTTCCACCTACCC 59.722 57.143 0.00 0.00 0.00 3.69
232 233 0.328258 CCTTCCACCTACCCAACCTG 59.672 60.000 0.00 0.00 0.00 4.00
233 234 1.064825 CTTCCACCTACCCAACCTGT 58.935 55.000 0.00 0.00 0.00 4.00
234 235 1.003233 CTTCCACCTACCCAACCTGTC 59.997 57.143 0.00 0.00 0.00 3.51
269 293 1.568504 TCCAACTAGGGCACTGGTAG 58.431 55.000 4.99 0.06 37.45 3.18
274 298 4.275810 CAACTAGGGCACTGGTAGTACTA 58.724 47.826 4.99 0.00 37.45 1.82
275 299 3.895998 ACTAGGGCACTGGTAGTACTAC 58.104 50.000 22.53 22.53 36.57 2.73
276 300 3.526841 ACTAGGGCACTGGTAGTACTACT 59.473 47.826 27.71 9.82 36.57 2.57
277 301 3.015675 AGGGCACTGGTAGTACTACTC 57.984 52.381 27.71 19.42 36.36 2.59
279 303 3.784763 AGGGCACTGGTAGTACTACTCTA 59.215 47.826 27.71 15.79 36.36 2.43
280 304 3.882288 GGGCACTGGTAGTACTACTCTAC 59.118 52.174 27.71 14.58 37.58 2.59
282 306 5.192176 GGCACTGGTAGTACTACTCTACTT 58.808 45.833 27.71 8.20 38.16 2.24
283 307 6.352516 GGCACTGGTAGTACTACTCTACTTA 58.647 44.000 27.71 8.94 38.16 2.24
369 528 1.202065 GCTGCACATACACATGGTTCG 60.202 52.381 0.00 0.00 36.39 3.95
386 550 3.619038 GGTTCGCTCATCTTGGAAGTTAG 59.381 47.826 0.00 0.00 0.00 2.34
387 551 4.246458 GTTCGCTCATCTTGGAAGTTAGT 58.754 43.478 0.00 0.00 0.00 2.24
388 552 5.408356 GTTCGCTCATCTTGGAAGTTAGTA 58.592 41.667 0.00 0.00 0.00 1.82
455 619 1.299926 GACGTCACGCCACAAGACT 60.300 57.895 11.55 0.00 0.00 3.24
456 620 0.039798 GACGTCACGCCACAAGACTA 60.040 55.000 11.55 0.00 0.00 2.59
457 621 0.039437 ACGTCACGCCACAAGACTAG 60.039 55.000 0.00 0.00 0.00 2.57
505 669 0.657840 CGAATCCCTTTCATCCGCAC 59.342 55.000 0.00 0.00 33.66 5.34
515 679 1.441738 TCATCCGCACACACATTCAG 58.558 50.000 0.00 0.00 0.00 3.02
522 686 2.139917 GCACACACATTCAGGACGTAA 58.860 47.619 0.00 0.00 0.00 3.18
525 689 3.993736 CACACACATTCAGGACGTAATCA 59.006 43.478 0.00 0.00 0.00 2.57
550 726 6.206634 ACGGACATTCATACAATTCTGTGTTT 59.793 34.615 0.00 0.00 36.96 2.83
552 728 7.594758 CGGACATTCATACAATTCTGTGTTTTT 59.405 33.333 0.00 0.00 36.96 1.94
553 729 9.906660 GGACATTCATACAATTCTGTGTTTTTA 57.093 29.630 0.00 0.00 36.96 1.52
629 815 2.169832 ACTCATCTGAACCCAACACG 57.830 50.000 0.00 0.00 0.00 4.49
637 823 0.586802 GAACCCAACACGCTCTTGAC 59.413 55.000 0.00 0.00 0.00 3.18
641 827 1.608590 CCCAACACGCTCTTGACAAAT 59.391 47.619 0.00 0.00 0.00 2.32
648 863 5.931532 ACACGCTCTTGACAAATTGAATAG 58.068 37.500 0.00 0.00 0.00 1.73
652 867 7.059945 CACGCTCTTGACAAATTGAATAGAAAC 59.940 37.037 0.00 0.00 0.00 2.78
657 872 9.076781 TCTTGACAAATTGAATAGAAACATGGA 57.923 29.630 0.00 0.00 0.00 3.41
695 916 0.897401 TCGGATTGCCCAAACATGCA 60.897 50.000 0.00 0.00 34.14 3.96
697 918 1.658994 GGATTGCCCAAACATGCATG 58.341 50.000 25.09 25.09 34.14 4.06
698 919 1.011333 GATTGCCCAAACATGCATGC 58.989 50.000 26.53 11.82 0.00 4.06
699 920 0.393267 ATTGCCCAAACATGCATGCC 60.393 50.000 26.53 8.56 0.00 4.40
707 928 0.321919 AACATGCATGCCTCGACACT 60.322 50.000 26.53 0.28 0.00 3.55
708 929 0.536724 ACATGCATGCCTCGACACTA 59.463 50.000 26.53 0.00 0.00 2.74
709 930 1.215244 CATGCATGCCTCGACACTAG 58.785 55.000 14.93 0.00 0.00 2.57
749 970 2.810852 CCTGTGCTCTTCTGTTTCTTCC 59.189 50.000 0.00 0.00 0.00 3.46
908 1160 2.157738 AAGCAACAGCTTGTCTGGATC 58.842 47.619 1.39 0.00 46.30 3.36
926 1178 2.479566 TCAGATTCTTGCTGTCCACC 57.520 50.000 0.00 0.00 34.98 4.61
974 1227 6.322931 TCAGCCTCTCCCATATAAATACAGA 58.677 40.000 0.00 0.00 0.00 3.41
1023 1292 5.370880 ACAGCCTACCATTCTCTTCCATTAT 59.629 40.000 0.00 0.00 0.00 1.28
1037 1306 8.988060 TCTCTTCCATTATTACCATACACAAGA 58.012 33.333 0.00 0.00 0.00 3.02
1038 1307 9.613428 CTCTTCCATTATTACCATACACAAGAA 57.387 33.333 0.00 0.00 0.00 2.52
1131 1401 1.132262 CGCTCCAACAACACACAAGTT 59.868 47.619 0.00 0.00 0.00 2.66
1239 1509 2.123342 GACATCTACAGCTGCATCGAC 58.877 52.381 15.27 0.00 0.00 4.20
1327 1597 4.361971 AGCTCGGACGGTCCCTCA 62.362 66.667 21.06 4.89 31.13 3.86
1424 1695 1.444836 CTCAAGAGAGGAGACGACGT 58.555 55.000 0.00 0.00 38.26 4.34
1467 1738 0.034670 CCAGGCTAGCCAAGAAAGCT 60.035 55.000 34.70 9.43 44.49 3.74
1518 1789 4.688021 AGACTGCTTCCGATAAGAATGAC 58.312 43.478 2.10 0.00 0.00 3.06
1530 1801 1.280457 AGAATGACTCCAGGGTGGTC 58.720 55.000 0.00 7.06 39.03 4.02
1572 1843 4.019501 AGAGAGATCACCATTTCACTGCTT 60.020 41.667 0.00 0.00 0.00 3.91
1581 1852 3.495193 CATTTCACTGCTTGAATCCACG 58.505 45.455 2.65 0.00 43.99 4.94
1600 1871 1.341531 CGTCCTCAGTCTTGTCCAAGT 59.658 52.381 6.90 0.00 39.38 3.16
1680 1951 0.523072 GCGAAGAGGAGCAATTGCAA 59.477 50.000 30.89 0.00 45.16 4.08
1683 1954 0.524862 AAGAGGAGCAATTGCAAGCG 59.475 50.000 30.89 0.00 45.16 4.68
1776 3953 4.442375 TTCTCTTCTCAACGCTCTTAGG 57.558 45.455 0.00 0.00 0.00 2.69
1777 3954 2.164624 TCTCTTCTCAACGCTCTTAGGC 59.835 50.000 0.00 0.00 0.00 3.93
1778 3955 1.204941 TCTTCTCAACGCTCTTAGGCC 59.795 52.381 0.00 0.00 0.00 5.19
1779 3956 1.205893 CTTCTCAACGCTCTTAGGCCT 59.794 52.381 11.78 11.78 0.00 5.19
1780 3957 1.267121 TCTCAACGCTCTTAGGCCTT 58.733 50.000 12.58 0.00 0.00 4.35
1781 3958 1.623811 TCTCAACGCTCTTAGGCCTTT 59.376 47.619 12.58 0.00 0.00 3.11
1782 3959 2.038557 TCTCAACGCTCTTAGGCCTTTT 59.961 45.455 12.58 0.00 0.00 2.27
1783 3960 2.814336 CTCAACGCTCTTAGGCCTTTTT 59.186 45.455 12.58 0.00 0.00 1.94
1806 3983 8.713708 TTTTGGTTCATAGGGTAGAAAAATCA 57.286 30.769 0.00 0.00 0.00 2.57
1807 3984 8.893563 TTTGGTTCATAGGGTAGAAAAATCAT 57.106 30.769 0.00 0.00 0.00 2.45
1808 3985 9.983024 TTTGGTTCATAGGGTAGAAAAATCATA 57.017 29.630 0.00 0.00 0.00 2.15
1809 3986 9.627123 TTGGTTCATAGGGTAGAAAAATCATAG 57.373 33.333 0.00 0.00 0.00 2.23
1810 3987 8.217799 TGGTTCATAGGGTAGAAAAATCATAGG 58.782 37.037 0.00 0.00 0.00 2.57
1811 3988 8.437575 GGTTCATAGGGTAGAAAAATCATAGGA 58.562 37.037 0.00 0.00 0.00 2.94
1812 3989 9.847224 GTTCATAGGGTAGAAAAATCATAGGAA 57.153 33.333 0.00 0.00 0.00 3.36
1834 4011 9.844257 AGGAATAGAAAAGTCATAGGAAATGAG 57.156 33.333 0.00 0.00 0.00 2.90
1835 4012 9.838339 GGAATAGAAAAGTCATAGGAAATGAGA 57.162 33.333 0.00 0.00 0.00 3.27
1839 4016 8.729805 AGAAAAGTCATAGGAAATGAGATGAC 57.270 34.615 5.86 5.86 45.57 3.06
1840 4017 8.324306 AGAAAAGTCATAGGAAATGAGATGACA 58.676 33.333 14.37 0.00 46.94 3.58
1841 4018 9.118300 GAAAAGTCATAGGAAATGAGATGACAT 57.882 33.333 14.37 1.96 46.94 3.06
1842 4019 8.447924 AAAGTCATAGGAAATGAGATGACATG 57.552 34.615 14.37 0.00 46.94 3.21
1843 4020 7.134362 AGTCATAGGAAATGAGATGACATGT 57.866 36.000 14.37 0.00 46.94 3.21
1844 4021 8.255111 AGTCATAGGAAATGAGATGACATGTA 57.745 34.615 14.37 0.00 46.94 2.29
1845 4022 8.878211 AGTCATAGGAAATGAGATGACATGTAT 58.122 33.333 14.37 0.00 46.94 2.29
1846 4023 9.149225 GTCATAGGAAATGAGATGACATGTATC 57.851 37.037 0.00 2.87 44.91 2.24
1847 4024 9.097946 TCATAGGAAATGAGATGACATGTATCT 57.902 33.333 14.05 14.05 37.59 1.98
1848 4025 9.368674 CATAGGAAATGAGATGACATGTATCTC 57.631 37.037 24.04 24.04 46.82 2.75
1882 4059 7.444703 AAGTAGGAATAGAAAAGGAGATGCT 57.555 36.000 0.00 0.00 0.00 3.79
1883 4060 7.061566 AGTAGGAATAGAAAAGGAGATGCTC 57.938 40.000 0.00 0.00 0.00 4.26
1884 4061 6.843861 AGTAGGAATAGAAAAGGAGATGCTCT 59.156 38.462 0.00 0.00 0.00 4.09
1885 4062 6.573712 AGGAATAGAAAAGGAGATGCTCTT 57.426 37.500 0.00 0.00 0.00 2.85
1886 4063 6.967897 AGGAATAGAAAAGGAGATGCTCTTT 58.032 36.000 0.00 0.00 31.12 2.52
1887 4064 6.827762 AGGAATAGAAAAGGAGATGCTCTTTG 59.172 38.462 0.00 0.00 30.33 2.77
1888 4065 6.825721 GGAATAGAAAAGGAGATGCTCTTTGA 59.174 38.462 0.00 0.00 30.33 2.69
1889 4066 7.501892 GGAATAGAAAAGGAGATGCTCTTTGAT 59.498 37.037 0.00 0.00 30.33 2.57
1890 4067 8.820153 AATAGAAAAGGAGATGCTCTTTGATT 57.180 30.769 0.00 0.00 30.33 2.57
1891 4068 6.756299 AGAAAAGGAGATGCTCTTTGATTC 57.244 37.500 0.00 0.00 30.33 2.52
1892 4069 6.243900 AGAAAAGGAGATGCTCTTTGATTCA 58.756 36.000 0.00 0.00 30.33 2.57
1893 4070 5.893897 AAAGGAGATGCTCTTTGATTCAC 57.106 39.130 0.00 0.00 30.33 3.18
1894 4071 4.564782 AGGAGATGCTCTTTGATTCACA 57.435 40.909 0.00 0.00 0.00 3.58
1895 4072 5.113446 AGGAGATGCTCTTTGATTCACAT 57.887 39.130 0.00 0.00 0.00 3.21
1896 4073 5.124645 AGGAGATGCTCTTTGATTCACATC 58.875 41.667 6.23 6.23 35.31 3.06
1897 4074 4.880120 GGAGATGCTCTTTGATTCACATCA 59.120 41.667 13.54 0.00 37.67 3.07
1898 4075 5.531659 GGAGATGCTCTTTGATTCACATCAT 59.468 40.000 13.54 2.83 39.28 2.45
1899 4076 6.709397 GGAGATGCTCTTTGATTCACATCATA 59.291 38.462 13.54 0.00 39.28 2.15
1900 4077 7.095144 GGAGATGCTCTTTGATTCACATCATAG 60.095 40.741 13.54 1.94 39.28 2.23
1901 4078 6.711194 AGATGCTCTTTGATTCACATCATAGG 59.289 38.462 13.54 0.00 39.28 2.57
1902 4079 5.993055 TGCTCTTTGATTCACATCATAGGA 58.007 37.500 3.71 0.00 39.28 2.94
1903 4080 6.598503 TGCTCTTTGATTCACATCATAGGAT 58.401 36.000 3.71 0.00 39.28 3.24
1904 4081 7.058525 TGCTCTTTGATTCACATCATAGGATT 58.941 34.615 0.00 0.00 39.28 3.01
1905 4082 7.558807 TGCTCTTTGATTCACATCATAGGATTT 59.441 33.333 0.00 0.00 39.28 2.17
1906 4083 8.411683 GCTCTTTGATTCACATCATAGGATTTT 58.588 33.333 0.00 0.00 39.28 1.82
1928 4105 6.757897 TTTTCCATTGAGTGTAGGCTAATG 57.242 37.500 0.00 0.00 0.00 1.90
1929 4106 5.435686 TTCCATTGAGTGTAGGCTAATGT 57.564 39.130 0.00 0.00 0.00 2.71
1930 4107 5.435686 TCCATTGAGTGTAGGCTAATGTT 57.564 39.130 0.00 0.00 0.00 2.71
1931 4108 5.815581 TCCATTGAGTGTAGGCTAATGTTT 58.184 37.500 0.00 0.00 0.00 2.83
1932 4109 6.953101 TCCATTGAGTGTAGGCTAATGTTTA 58.047 36.000 0.00 0.00 0.00 2.01
1933 4110 7.573710 TCCATTGAGTGTAGGCTAATGTTTAT 58.426 34.615 0.00 0.00 0.00 1.40
1934 4111 8.052748 TCCATTGAGTGTAGGCTAATGTTTATT 58.947 33.333 0.00 0.00 0.00 1.40
1935 4112 8.686334 CCATTGAGTGTAGGCTAATGTTTATTT 58.314 33.333 0.00 0.00 0.00 1.40
1938 4115 8.276252 TGAGTGTAGGCTAATGTTTATTTTCC 57.724 34.615 0.00 0.00 0.00 3.13
1939 4116 8.107095 TGAGTGTAGGCTAATGTTTATTTTCCT 58.893 33.333 0.00 0.00 33.86 3.36
1940 4117 9.609346 GAGTGTAGGCTAATGTTTATTTTCCTA 57.391 33.333 0.00 0.00 32.55 2.94
1953 4130 8.748412 TGTTTATTTTCCTATGAAATGTGGAGG 58.252 33.333 0.00 0.00 40.08 4.30
1954 4131 8.966868 GTTTATTTTCCTATGAAATGTGGAGGA 58.033 33.333 0.00 0.00 40.08 3.71
1955 4132 9.713684 TTTATTTTCCTATGAAATGTGGAGGAT 57.286 29.630 0.00 0.00 40.08 3.24
1957 4134 8.930846 ATTTTCCTATGAAATGTGGAGGATAG 57.069 34.615 0.00 0.00 40.08 2.08
1958 4135 6.439636 TTCCTATGAAATGTGGAGGATAGG 57.560 41.667 0.00 0.00 36.22 2.57
1959 4136 5.726560 TCCTATGAAATGTGGAGGATAGGA 58.273 41.667 0.00 0.00 39.29 2.94
1960 4137 6.150332 TCCTATGAAATGTGGAGGATAGGAA 58.850 40.000 0.00 0.00 38.86 3.36
1961 4138 6.270927 TCCTATGAAATGTGGAGGATAGGAAG 59.729 42.308 0.00 0.00 38.86 3.46
1962 4139 6.270927 CCTATGAAATGTGGAGGATAGGAAGA 59.729 42.308 0.00 0.00 36.16 2.87
1963 4140 6.581388 ATGAAATGTGGAGGATAGGAAGAA 57.419 37.500 0.00 0.00 0.00 2.52
1964 4141 6.581388 TGAAATGTGGAGGATAGGAAGAAT 57.419 37.500 0.00 0.00 0.00 2.40
1965 4142 6.973642 TGAAATGTGGAGGATAGGAAGAATT 58.026 36.000 0.00 0.00 0.00 2.17
1966 4143 7.056635 TGAAATGTGGAGGATAGGAAGAATTC 58.943 38.462 0.00 0.00 46.67 2.17
1986 4163 3.318313 TCCTCCACAGGAATAGGATTCC 58.682 50.000 9.79 9.79 46.84 3.01
1987 4164 3.048600 CCTCCACAGGAATAGGATTCCA 58.951 50.000 18.17 0.00 43.65 3.53
1988 4165 3.654806 CCTCCACAGGAATAGGATTCCAT 59.345 47.826 18.17 5.37 43.65 3.41
1989 4166 4.105377 CCTCCACAGGAATAGGATTCCATT 59.895 45.833 18.17 3.02 43.65 3.16
1990 4167 5.310409 TCCACAGGAATAGGATTCCATTC 57.690 43.478 18.17 11.30 41.00 2.67
2003 4180 7.651027 AGGATTCCATTCCTACAAATCAAAG 57.349 36.000 5.29 0.00 44.50 2.77
2004 4181 6.608808 AGGATTCCATTCCTACAAATCAAAGG 59.391 38.462 5.29 0.00 44.50 3.11
2005 4182 6.183360 GGATTCCATTCCTACAAATCAAAGGG 60.183 42.308 0.00 0.00 32.68 3.95
2006 4183 4.023291 TCCATTCCTACAAATCAAAGGGC 58.977 43.478 0.00 0.00 0.00 5.19
2007 4184 4.026052 CCATTCCTACAAATCAAAGGGCT 58.974 43.478 0.00 0.00 0.00 5.19
2008 4185 4.098501 CCATTCCTACAAATCAAAGGGCTC 59.901 45.833 0.00 0.00 0.00 4.70
2009 4186 4.657814 TTCCTACAAATCAAAGGGCTCT 57.342 40.909 0.00 0.00 0.00 4.09
2010 4187 5.772393 TTCCTACAAATCAAAGGGCTCTA 57.228 39.130 0.00 0.00 0.00 2.43
2011 4188 5.772393 TCCTACAAATCAAAGGGCTCTAA 57.228 39.130 0.00 0.00 0.00 2.10
2012 4189 6.134535 TCCTACAAATCAAAGGGCTCTAAA 57.865 37.500 0.00 0.00 0.00 1.85
2013 4190 6.180472 TCCTACAAATCAAAGGGCTCTAAAG 58.820 40.000 0.00 0.00 0.00 1.85
2014 4191 5.358160 CCTACAAATCAAAGGGCTCTAAAGG 59.642 44.000 0.00 0.00 0.00 3.11
2015 4192 4.998051 ACAAATCAAAGGGCTCTAAAGGA 58.002 39.130 0.00 0.00 0.00 3.36
2016 4193 5.393866 ACAAATCAAAGGGCTCTAAAGGAA 58.606 37.500 0.00 0.00 0.00 3.36
2017 4194 6.019108 ACAAATCAAAGGGCTCTAAAGGAAT 58.981 36.000 0.00 0.00 0.00 3.01
2018 4195 6.498303 ACAAATCAAAGGGCTCTAAAGGAATT 59.502 34.615 0.00 0.00 0.00 2.17
2019 4196 7.016563 ACAAATCAAAGGGCTCTAAAGGAATTT 59.983 33.333 0.00 0.00 0.00 1.82
2020 4197 7.559335 AATCAAAGGGCTCTAAAGGAATTTT 57.441 32.000 0.00 0.00 0.00 1.82
2021 4198 6.994421 TCAAAGGGCTCTAAAGGAATTTTT 57.006 33.333 0.00 0.00 0.00 1.94
2063 4240 9.838339 TCCTATGAAATTTCTACAAGATTCCTC 57.162 33.333 18.64 0.00 0.00 3.71
2064 4241 9.844257 CCTATGAAATTTCTACAAGATTCCTCT 57.156 33.333 18.64 0.00 0.00 3.69
2070 4247 9.807921 AAATTTCTACAAGATTCCTCTAAACCA 57.192 29.630 0.00 0.00 0.00 3.67
2071 4248 9.807921 AATTTCTACAAGATTCCTCTAAACCAA 57.192 29.630 0.00 0.00 0.00 3.67
2072 4249 9.807921 ATTTCTACAAGATTCCTCTAAACCAAA 57.192 29.630 0.00 0.00 0.00 3.28
2073 4250 8.848474 TTCTACAAGATTCCTCTAAACCAAAG 57.152 34.615 0.00 0.00 0.00 2.77
2074 4251 7.394816 TCTACAAGATTCCTCTAAACCAAAGG 58.605 38.462 0.00 0.00 0.00 3.11
2075 4252 6.200878 ACAAGATTCCTCTAAACCAAAGGA 57.799 37.500 0.00 0.00 37.42 3.36
2076 4253 6.241645 ACAAGATTCCTCTAAACCAAAGGAG 58.758 40.000 0.00 0.00 40.21 3.69
2077 4254 5.443230 AGATTCCTCTAAACCAAAGGAGG 57.557 43.478 0.00 0.00 44.69 4.30
2078 4255 3.434940 TTCCTCTAAACCAAAGGAGGC 57.565 47.619 0.00 0.00 43.46 4.70
2079 4256 1.633945 TCCTCTAAACCAAAGGAGGCC 59.366 52.381 0.00 0.00 43.46 5.19
2080 4257 1.636003 CCTCTAAACCAAAGGAGGCCT 59.364 52.381 3.86 3.86 38.82 5.19
2082 4259 3.265995 CCTCTAAACCAAAGGAGGCCTTA 59.734 47.826 6.77 0.00 43.92 2.69
2083 4260 4.518249 CTCTAAACCAAAGGAGGCCTTAG 58.482 47.826 6.77 0.67 43.92 2.18
2229 4409 9.103861 ACTTAACTGAAAAGAGAAGAGAAACAG 57.896 33.333 0.00 0.00 0.00 3.16
2322 4534 6.935208 ACTAACTGACTTGGTTTCTCATAACC 59.065 38.462 0.00 0.00 46.31 2.85
2334 4546 6.348295 GGTTTCTCATAACCGGAAGAAAAGAC 60.348 42.308 9.46 4.62 38.33 3.01
2358 4584 7.129425 ACCTCTCTCCTCAAACATACTATCTT 58.871 38.462 0.00 0.00 0.00 2.40
2381 4635 8.289618 TCTTATTTACAAGCAAGTAAGCAACAG 58.710 33.333 2.03 0.00 35.57 3.16
2408 4662 9.752228 AAAAATAACATAGAATTTGGGGCATTT 57.248 25.926 0.00 0.00 0.00 2.32
2414 4668 4.276058 AGAATTTGGGGCATTTCTGTTG 57.724 40.909 0.00 0.00 0.00 3.33
2416 4670 4.102996 AGAATTTGGGGCATTTCTGTTGTT 59.897 37.500 0.00 0.00 0.00 2.83
2417 4671 5.306678 AGAATTTGGGGCATTTCTGTTGTTA 59.693 36.000 0.00 0.00 0.00 2.41
2418 4672 5.760484 ATTTGGGGCATTTCTGTTGTTAT 57.240 34.783 0.00 0.00 0.00 1.89
2477 4927 5.711976 CCCAAGTATCTTAATTAGGGGCATG 59.288 44.000 0.00 0.00 0.00 4.06
2478 4928 6.467194 CCCAAGTATCTTAATTAGGGGCATGA 60.467 42.308 0.00 0.00 0.00 3.07
2719 5344 3.339093 CGCCCTTCCCCCTCCTTT 61.339 66.667 0.00 0.00 0.00 3.11
2764 8449 4.461781 CCGAGAAGAACCCTAGTTTCTACA 59.538 45.833 4.67 0.00 35.94 2.74
2774 8459 7.991084 ACCCTAGTTTCTACAAATTTGGTAC 57.009 36.000 21.74 11.39 0.00 3.34
2778 8463 7.449086 CCTAGTTTCTACAAATTTGGTACCCAA 59.551 37.037 21.74 4.90 42.29 4.12
2805 8490 3.004419 TCGGGTTCTATCATGTCGTCATC 59.996 47.826 0.00 0.00 31.15 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.999705 TTCCGGGGTAAACTATGTATGTAT 57.000 37.500 0.00 0.00 0.00 2.29
2 3 5.510179 CGATTCCGGGGTAAACTATGTATGT 60.510 44.000 0.00 0.00 0.00 2.29
3 4 4.927425 CGATTCCGGGGTAAACTATGTATG 59.073 45.833 0.00 0.00 0.00 2.39
5 6 3.243839 GCGATTCCGGGGTAAACTATGTA 60.244 47.826 0.00 0.00 36.06 2.29
6 7 2.484241 GCGATTCCGGGGTAAACTATGT 60.484 50.000 0.00 0.00 36.06 2.29
7 8 2.140717 GCGATTCCGGGGTAAACTATG 58.859 52.381 0.00 0.00 36.06 2.23
8 9 1.269936 CGCGATTCCGGGGTAAACTAT 60.270 52.381 0.00 0.00 43.81 2.12
9 10 0.102844 CGCGATTCCGGGGTAAACTA 59.897 55.000 0.00 0.00 43.81 2.24
10 11 1.153509 CGCGATTCCGGGGTAAACT 60.154 57.895 0.00 0.00 43.81 2.66
11 12 3.402185 CGCGATTCCGGGGTAAAC 58.598 61.111 0.00 0.00 43.81 2.01
27 28 0.868177 TGTATGTGTATGCGCCGACG 60.868 55.000 4.18 0.00 44.07 5.12
28 29 1.192312 CATGTATGTGTATGCGCCGAC 59.808 52.381 4.18 2.86 0.00 4.79
29 30 1.496934 CATGTATGTGTATGCGCCGA 58.503 50.000 4.18 0.00 0.00 5.54
30 31 0.110688 GCATGTATGTGTATGCGCCG 60.111 55.000 4.18 0.00 40.09 6.46
31 32 3.753774 GCATGTATGTGTATGCGCC 57.246 52.632 4.18 0.00 40.09 6.53
35 36 6.875195 TGATCCTACATGCATGTATGTGTATG 59.125 38.462 33.66 21.75 44.54 2.39
36 37 7.008021 TGATCCTACATGCATGTATGTGTAT 57.992 36.000 33.66 21.70 41.92 2.29
37 38 6.418057 TGATCCTACATGCATGTATGTGTA 57.582 37.500 33.66 19.93 41.92 2.90
38 39 5.294734 TGATCCTACATGCATGTATGTGT 57.705 39.130 33.66 23.69 41.92 3.72
39 40 6.171213 AGATGATCCTACATGCATGTATGTG 58.829 40.000 33.66 24.99 41.92 3.21
40 41 6.370186 AGATGATCCTACATGCATGTATGT 57.630 37.500 33.66 28.66 41.92 2.29
41 42 5.519206 CGAGATGATCCTACATGCATGTATG 59.481 44.000 33.66 30.11 41.92 2.39
42 43 5.394993 CCGAGATGATCCTACATGCATGTAT 60.395 44.000 33.66 23.34 41.92 2.29
43 44 4.082026 CCGAGATGATCCTACATGCATGTA 60.082 45.833 31.98 31.98 41.97 2.29
44 45 3.306571 CCGAGATGATCCTACATGCATGT 60.307 47.826 33.20 33.20 44.48 3.21
45 46 3.056322 TCCGAGATGATCCTACATGCATG 60.056 47.826 25.09 25.09 0.00 4.06
46 47 3.168292 TCCGAGATGATCCTACATGCAT 58.832 45.455 0.00 0.00 0.00 3.96
47 48 2.597455 TCCGAGATGATCCTACATGCA 58.403 47.619 0.00 0.00 0.00 3.96
48 49 3.883830 ATCCGAGATGATCCTACATGC 57.116 47.619 0.00 0.00 0.00 4.06
49 50 5.657826 AGAATCCGAGATGATCCTACATG 57.342 43.478 0.00 0.00 0.00 3.21
50 51 7.233553 TGTTTAGAATCCGAGATGATCCTACAT 59.766 37.037 0.00 0.00 0.00 2.29
51 52 6.549736 TGTTTAGAATCCGAGATGATCCTACA 59.450 38.462 0.00 0.00 0.00 2.74
52 53 6.982852 TGTTTAGAATCCGAGATGATCCTAC 58.017 40.000 0.00 0.00 0.00 3.18
53 54 7.597288 TTGTTTAGAATCCGAGATGATCCTA 57.403 36.000 0.00 0.00 0.00 2.94
54 55 6.485830 TTGTTTAGAATCCGAGATGATCCT 57.514 37.500 0.00 0.00 0.00 3.24
107 108 2.791503 CGTCGTATATATCAGGCCAGCG 60.792 54.545 5.01 0.00 0.00 5.18
219 220 1.697982 GACAAGACAGGTTGGGTAGGT 59.302 52.381 0.00 0.00 0.00 3.08
220 221 1.978580 AGACAAGACAGGTTGGGTAGG 59.021 52.381 0.00 0.00 0.00 3.18
221 222 2.900546 AGAGACAAGACAGGTTGGGTAG 59.099 50.000 0.00 0.00 0.00 3.18
222 223 2.897969 GAGAGACAAGACAGGTTGGGTA 59.102 50.000 0.00 0.00 0.00 3.69
226 227 3.056891 GGAGAGAGAGACAAGACAGGTTG 60.057 52.174 0.00 0.00 0.00 3.77
232 233 3.360867 TGGATGGAGAGAGAGACAAGAC 58.639 50.000 0.00 0.00 0.00 3.01
233 234 3.746792 TGGATGGAGAGAGAGACAAGA 57.253 47.619 0.00 0.00 0.00 3.02
234 235 3.768757 AGTTGGATGGAGAGAGAGACAAG 59.231 47.826 0.00 0.00 0.00 3.16
308 332 3.064324 GCAATCAGCCCGTGCCTT 61.064 61.111 0.00 0.00 38.69 4.35
359 518 1.399440 CCAAGATGAGCGAACCATGTG 59.601 52.381 0.00 0.00 0.00 3.21
369 528 6.341316 TGATGTACTAACTTCCAAGATGAGC 58.659 40.000 0.00 0.00 0.00 4.26
386 550 3.146066 TGCAAGTCCCAGTTTGATGTAC 58.854 45.455 0.00 0.00 0.00 2.90
387 551 3.411446 CTGCAAGTCCCAGTTTGATGTA 58.589 45.455 0.00 0.00 0.00 2.29
388 552 2.233271 CTGCAAGTCCCAGTTTGATGT 58.767 47.619 0.00 0.00 0.00 3.06
455 619 5.598417 TGCTGCTGGATGAAAGATACTACTA 59.402 40.000 0.00 0.00 0.00 1.82
456 620 4.406972 TGCTGCTGGATGAAAGATACTACT 59.593 41.667 0.00 0.00 0.00 2.57
457 621 4.697514 TGCTGCTGGATGAAAGATACTAC 58.302 43.478 0.00 0.00 0.00 2.73
501 665 1.221466 ACGTCCTGAATGTGTGTGCG 61.221 55.000 0.00 0.00 0.00 5.34
505 669 3.060761 CGTGATTACGTCCTGAATGTGTG 59.939 47.826 1.18 0.00 44.99 3.82
522 686 6.037500 CACAGAATTGTATGAATGTCCGTGAT 59.962 38.462 0.00 0.00 35.25 3.06
525 689 5.245531 ACACAGAATTGTATGAATGTCCGT 58.754 37.500 0.00 0.00 35.25 4.69
550 726 4.267690 CGCTAGCTGTGACAAATCGATAAA 59.732 41.667 13.93 0.00 0.00 1.40
552 728 3.066203 TCGCTAGCTGTGACAAATCGATA 59.934 43.478 13.93 0.00 0.00 2.92
553 729 2.159240 TCGCTAGCTGTGACAAATCGAT 60.159 45.455 13.93 0.00 0.00 3.59
629 815 8.857216 CATGTTTCTATTCAATTTGTCAAGAGC 58.143 33.333 0.00 0.00 0.00 4.09
637 823 8.139989 GGATCCTCCATGTTTCTATTCAATTTG 58.860 37.037 3.84 0.00 36.28 2.32
641 827 6.359804 CAGGATCCTCCATGTTTCTATTCAA 58.640 40.000 12.69 0.00 39.61 2.69
648 863 1.213926 AGGCAGGATCCTCCATGTTTC 59.786 52.381 23.98 0.59 39.61 2.78
652 867 1.228184 GCAGGCAGGATCCTCCATG 60.228 63.158 23.98 19.77 39.61 3.66
657 872 3.806667 GCAGGCAGGCAGGATCCT 61.807 66.667 9.02 9.02 36.78 3.24
695 916 3.562343 TCTCTACTAGTGTCGAGGCAT 57.438 47.619 5.39 0.00 36.85 4.40
697 918 4.904253 ATTTCTCTACTAGTGTCGAGGC 57.096 45.455 5.39 0.00 36.85 4.70
698 919 6.127703 TGGAAATTTCTCTACTAGTGTCGAGG 60.128 42.308 17.42 0.00 36.85 4.63
699 920 6.748198 GTGGAAATTTCTCTACTAGTGTCGAG 59.252 42.308 17.42 8.76 37.35 4.04
707 928 4.222145 AGGTGCGTGGAAATTTCTCTACTA 59.778 41.667 17.42 4.91 0.00 1.82
708 929 3.008049 AGGTGCGTGGAAATTTCTCTACT 59.992 43.478 17.42 5.13 0.00 2.57
709 930 3.125316 CAGGTGCGTGGAAATTTCTCTAC 59.875 47.826 17.42 12.67 0.00 2.59
736 957 6.159988 AGAGTATGAACGGAAGAAACAGAAG 58.840 40.000 0.00 0.00 0.00 2.85
749 970 4.142160 TGGGTTCAGATGAGAGTATGAACG 60.142 45.833 9.93 0.00 46.14 3.95
778 999 3.056536 AGAGTAAGATGCACGCTCAAGAA 60.057 43.478 0.00 0.00 0.00 2.52
908 1160 1.081892 CGGTGGACAGCAAGAATCTG 58.918 55.000 2.25 0.00 37.56 2.90
926 1178 3.730061 GCAATTGGTTGATGAAGAGAGCG 60.730 47.826 7.72 0.00 37.53 5.03
1038 1307 3.632145 ACTGAAGCTTCGGTGATGTTTTT 59.368 39.130 34.67 11.26 44.70 1.94
1050 1319 3.190118 CCATTGTTGAGGACTGAAGCTTC 59.810 47.826 19.89 19.89 0.00 3.86
1053 1323 1.200948 GCCATTGTTGAGGACTGAAGC 59.799 52.381 0.00 0.00 0.00 3.86
1239 1509 2.670229 GCTTGGTGTGCACATCATCTTG 60.670 50.000 32.16 21.74 36.77 3.02
1424 1695 0.469494 TGCCTTGACTTGAGCAGACA 59.531 50.000 0.00 0.00 0.00 3.41
1467 1738 5.278169 GCTGATCTTCTTGAACTGCTTTTGA 60.278 40.000 0.00 0.00 38.63 2.69
1509 1780 2.838202 GACCACCCTGGAGTCATTCTTA 59.162 50.000 0.00 0.00 40.96 2.10
1518 1789 0.911769 TTAGCATGACCACCCTGGAG 59.088 55.000 0.00 0.00 40.96 3.86
1548 1819 4.019501 AGCAGTGAAATGGTGATCTCTCTT 60.020 41.667 0.00 0.00 0.00 2.85
1572 1843 1.924731 AGACTGAGGACGTGGATTCA 58.075 50.000 0.00 0.00 0.00 2.57
1581 1852 4.602340 TTACTTGGACAAGACTGAGGAC 57.398 45.455 18.15 0.00 40.79 3.85
1600 1871 4.016444 GACCACTTGGGCATCTCAATTTA 58.984 43.478 0.00 0.00 44.76 1.40
1654 1925 2.651361 CTCCTCTTCGCACACGGT 59.349 61.111 0.00 0.00 40.63 4.83
1683 1954 2.659897 CCGATACTGCGCTCCAGC 60.660 66.667 9.73 0.00 45.78 4.85
1780 3957 9.148879 TGATTTTTCTACCCTATGAACCAAAAA 57.851 29.630 0.00 0.00 0.00 1.94
1781 3958 8.713708 TGATTTTTCTACCCTATGAACCAAAA 57.286 30.769 0.00 0.00 0.00 2.44
1782 3959 8.893563 ATGATTTTTCTACCCTATGAACCAAA 57.106 30.769 0.00 0.00 0.00 3.28
1783 3960 9.627123 CTATGATTTTTCTACCCTATGAACCAA 57.373 33.333 0.00 0.00 0.00 3.67
1784 3961 8.217799 CCTATGATTTTTCTACCCTATGAACCA 58.782 37.037 0.00 0.00 0.00 3.67
1785 3962 8.437575 TCCTATGATTTTTCTACCCTATGAACC 58.562 37.037 0.00 0.00 0.00 3.62
1786 3963 9.847224 TTCCTATGATTTTTCTACCCTATGAAC 57.153 33.333 0.00 0.00 0.00 3.18
1808 3985 9.844257 CTCATTTCCTATGACTTTTCTATTCCT 57.156 33.333 0.00 0.00 0.00 3.36
1809 3986 9.838339 TCTCATTTCCTATGACTTTTCTATTCC 57.162 33.333 0.00 0.00 0.00 3.01
1813 3990 9.823647 GTCATCTCATTTCCTATGACTTTTCTA 57.176 33.333 0.00 0.00 43.07 2.10
1814 3991 8.324306 TGTCATCTCATTTCCTATGACTTTTCT 58.676 33.333 13.59 0.00 45.40 2.52
1815 3992 8.498054 TGTCATCTCATTTCCTATGACTTTTC 57.502 34.615 13.59 0.00 45.40 2.29
1816 3993 8.900781 CATGTCATCTCATTTCCTATGACTTTT 58.099 33.333 13.59 0.00 45.40 2.27
1817 3994 8.051535 ACATGTCATCTCATTTCCTATGACTTT 58.948 33.333 13.59 1.75 45.40 2.66
1818 3995 7.571919 ACATGTCATCTCATTTCCTATGACTT 58.428 34.615 13.59 6.42 45.40 3.01
1819 3996 7.134362 ACATGTCATCTCATTTCCTATGACT 57.866 36.000 13.59 0.19 45.40 3.41
1820 3997 9.149225 GATACATGTCATCTCATTTCCTATGAC 57.851 37.037 0.00 7.23 45.40 3.06
1821 3998 9.097946 AGATACATGTCATCTCATTTCCTATGA 57.902 33.333 0.00 0.00 0.00 2.15
1822 3999 9.368674 GAGATACATGTCATCTCATTTCCTATG 57.631 37.037 24.95 0.00 45.17 2.23
1856 4033 9.165057 AGCATCTCCTTTTCTATTCCTACTTAT 57.835 33.333 0.00 0.00 0.00 1.73
1857 4034 8.554490 AGCATCTCCTTTTCTATTCCTACTTA 57.446 34.615 0.00 0.00 0.00 2.24
1858 4035 7.444703 AGCATCTCCTTTTCTATTCCTACTT 57.555 36.000 0.00 0.00 0.00 2.24
1859 4036 7.061566 GAGCATCTCCTTTTCTATTCCTACT 57.938 40.000 0.00 0.00 0.00 2.57
1872 4049 8.071977 ATGATGTGAATCAAAGAGCATCTCCTT 61.072 37.037 10.68 0.00 37.05 3.36
1873 4050 6.635185 ATGATGTGAATCAAAGAGCATCTCCT 60.635 38.462 10.68 0.00 37.05 3.69
1874 4051 5.531659 ATGATGTGAATCAAAGAGCATCTCC 59.468 40.000 10.68 0.00 37.05 3.71
1875 4052 6.621316 ATGATGTGAATCAAAGAGCATCTC 57.379 37.500 10.68 0.00 37.05 2.75
1876 4053 6.711194 CCTATGATGTGAATCAAAGAGCATCT 59.289 38.462 10.68 2.28 38.87 2.90
1877 4054 6.709397 TCCTATGATGTGAATCAAAGAGCATC 59.291 38.462 4.45 4.45 33.83 3.91
1878 4055 6.598503 TCCTATGATGTGAATCAAAGAGCAT 58.401 36.000 0.00 0.00 33.83 3.79
1879 4056 5.993055 TCCTATGATGTGAATCAAAGAGCA 58.007 37.500 0.00 0.00 33.83 4.26
1880 4057 7.507733 AATCCTATGATGTGAATCAAAGAGC 57.492 36.000 0.00 0.00 33.83 4.09
1904 4081 6.719370 ACATTAGCCTACACTCAATGGAAAAA 59.281 34.615 0.00 0.00 32.20 1.94
1905 4082 6.245408 ACATTAGCCTACACTCAATGGAAAA 58.755 36.000 0.00 0.00 32.20 2.29
1906 4083 5.815581 ACATTAGCCTACACTCAATGGAAA 58.184 37.500 0.00 0.00 32.20 3.13
1907 4084 5.435686 ACATTAGCCTACACTCAATGGAA 57.564 39.130 0.00 0.00 32.20 3.53
1908 4085 5.435686 AACATTAGCCTACACTCAATGGA 57.564 39.130 0.00 0.00 32.20 3.41
1909 4086 7.807977 ATAAACATTAGCCTACACTCAATGG 57.192 36.000 0.00 0.00 32.20 3.16
1912 4089 8.736244 GGAAAATAAACATTAGCCTACACTCAA 58.264 33.333 0.00 0.00 0.00 3.02
1913 4090 8.107095 AGGAAAATAAACATTAGCCTACACTCA 58.893 33.333 0.00 0.00 0.00 3.41
1914 4091 8.507524 AGGAAAATAAACATTAGCCTACACTC 57.492 34.615 0.00 0.00 0.00 3.51
1927 4104 8.748412 CCTCCACATTTCATAGGAAAATAAACA 58.252 33.333 6.65 0.00 45.52 2.83
1928 4105 8.966868 TCCTCCACATTTCATAGGAAAATAAAC 58.033 33.333 6.65 0.00 45.52 2.01
1929 4106 9.713684 ATCCTCCACATTTCATAGGAAAATAAA 57.286 29.630 6.65 0.00 45.52 1.40
1932 4109 7.946776 CCTATCCTCCACATTTCATAGGAAAAT 59.053 37.037 6.65 0.00 45.52 1.82
1933 4110 7.128728 TCCTATCCTCCACATTTCATAGGAAAA 59.871 37.037 6.65 0.00 45.52 2.29
1934 4111 6.619437 TCCTATCCTCCACATTTCATAGGAAA 59.381 38.462 4.85 4.85 46.36 3.13
1935 4112 6.150332 TCCTATCCTCCACATTTCATAGGAA 58.850 40.000 3.47 0.00 39.17 3.36
1936 4113 5.726560 TCCTATCCTCCACATTTCATAGGA 58.273 41.667 2.01 2.01 39.61 2.94
1937 4114 6.270927 TCTTCCTATCCTCCACATTTCATAGG 59.729 42.308 0.00 0.00 35.93 2.57
1938 4115 7.308450 TCTTCCTATCCTCCACATTTCATAG 57.692 40.000 0.00 0.00 0.00 2.23
1939 4116 7.690454 TTCTTCCTATCCTCCACATTTCATA 57.310 36.000 0.00 0.00 0.00 2.15
1940 4117 6.581388 TTCTTCCTATCCTCCACATTTCAT 57.419 37.500 0.00 0.00 0.00 2.57
1941 4118 6.581388 ATTCTTCCTATCCTCCACATTTCA 57.419 37.500 0.00 0.00 0.00 2.69
1942 4119 6.488344 GGAATTCTTCCTATCCTCCACATTTC 59.512 42.308 5.23 0.00 46.57 2.17
1943 4120 6.368805 GGAATTCTTCCTATCCTCCACATTT 58.631 40.000 5.23 0.00 46.57 2.32
1944 4121 5.946486 GGAATTCTTCCTATCCTCCACATT 58.054 41.667 5.23 0.00 46.57 2.71
1945 4122 5.574970 GGAATTCTTCCTATCCTCCACAT 57.425 43.478 5.23 0.00 46.57 3.21
1966 4143 3.048600 TGGAATCCTATTCCTGTGGAGG 58.951 50.000 17.27 0.00 41.39 4.30
1967 4144 4.989875 ATGGAATCCTATTCCTGTGGAG 57.010 45.455 17.27 0.00 39.31 3.86
1968 4145 4.104738 GGAATGGAATCCTATTCCTGTGGA 59.895 45.833 23.95 0.29 45.66 4.02
1969 4146 4.401925 GGAATGGAATCCTATTCCTGTGG 58.598 47.826 23.95 0.00 45.66 4.17
1980 4157 6.183360 CCCTTTGATTTGTAGGAATGGAATCC 60.183 42.308 0.00 0.00 39.96 3.01
1981 4158 6.683861 GCCCTTTGATTTGTAGGAATGGAATC 60.684 42.308 0.00 0.00 0.00 2.52
1982 4159 5.129320 GCCCTTTGATTTGTAGGAATGGAAT 59.871 40.000 0.00 0.00 0.00 3.01
1983 4160 4.466015 GCCCTTTGATTTGTAGGAATGGAA 59.534 41.667 0.00 0.00 0.00 3.53
1984 4161 4.023291 GCCCTTTGATTTGTAGGAATGGA 58.977 43.478 0.00 0.00 0.00 3.41
1985 4162 4.026052 AGCCCTTTGATTTGTAGGAATGG 58.974 43.478 0.00 0.00 0.00 3.16
1986 4163 4.952335 AGAGCCCTTTGATTTGTAGGAATG 59.048 41.667 0.00 0.00 0.00 2.67
1987 4164 5.198602 AGAGCCCTTTGATTTGTAGGAAT 57.801 39.130 0.00 0.00 0.00 3.01
1988 4165 4.657814 AGAGCCCTTTGATTTGTAGGAA 57.342 40.909 0.00 0.00 0.00 3.36
1989 4166 5.772393 TTAGAGCCCTTTGATTTGTAGGA 57.228 39.130 0.00 0.00 0.00 2.94
1990 4167 5.358160 CCTTTAGAGCCCTTTGATTTGTAGG 59.642 44.000 0.00 0.00 0.00 3.18
1991 4168 6.180472 TCCTTTAGAGCCCTTTGATTTGTAG 58.820 40.000 0.00 0.00 0.00 2.74
1992 4169 6.134535 TCCTTTAGAGCCCTTTGATTTGTA 57.865 37.500 0.00 0.00 0.00 2.41
1993 4170 4.998051 TCCTTTAGAGCCCTTTGATTTGT 58.002 39.130 0.00 0.00 0.00 2.83
1994 4171 5.982890 TTCCTTTAGAGCCCTTTGATTTG 57.017 39.130 0.00 0.00 0.00 2.32
1995 4172 7.559335 AAATTCCTTTAGAGCCCTTTGATTT 57.441 32.000 0.00 0.00 0.00 2.17
1996 4173 7.559335 AAAATTCCTTTAGAGCCCTTTGATT 57.441 32.000 0.00 0.00 0.00 2.57
1997 4174 7.559335 AAAAATTCCTTTAGAGCCCTTTGAT 57.441 32.000 0.00 0.00 0.00 2.57
1998 4175 6.994421 AAAAATTCCTTTAGAGCCCTTTGA 57.006 33.333 0.00 0.00 0.00 2.69
2037 4214 9.838339 GAGGAATCTTGTAGAAATTTCATAGGA 57.162 33.333 19.99 11.18 0.00 2.94
2038 4215 9.844257 AGAGGAATCTTGTAGAAATTTCATAGG 57.156 33.333 19.99 6.56 0.00 2.57
2044 4221 9.807921 TGGTTTAGAGGAATCTTGTAGAAATTT 57.192 29.630 0.00 0.00 0.00 1.82
2045 4222 9.807921 TTGGTTTAGAGGAATCTTGTAGAAATT 57.192 29.630 0.00 0.00 0.00 1.82
2046 4223 9.807921 TTTGGTTTAGAGGAATCTTGTAGAAAT 57.192 29.630 0.00 0.00 0.00 2.17
2047 4224 9.284968 CTTTGGTTTAGAGGAATCTTGTAGAAA 57.715 33.333 0.00 0.00 0.00 2.52
2048 4225 7.883311 CCTTTGGTTTAGAGGAATCTTGTAGAA 59.117 37.037 0.00 0.00 32.11 2.10
2049 4226 7.236847 TCCTTTGGTTTAGAGGAATCTTGTAGA 59.763 37.037 0.00 0.00 36.67 2.59
2050 4227 7.394816 TCCTTTGGTTTAGAGGAATCTTGTAG 58.605 38.462 0.00 0.00 36.67 2.74
2051 4228 7.324388 TCCTTTGGTTTAGAGGAATCTTGTA 57.676 36.000 0.00 0.00 36.67 2.41
2052 4229 6.200878 TCCTTTGGTTTAGAGGAATCTTGT 57.799 37.500 0.00 0.00 36.67 3.16
2053 4230 6.749923 CTCCTTTGGTTTAGAGGAATCTTG 57.250 41.667 0.00 0.00 39.00 3.02
2060 4237 2.041755 AAGGCCTCCTTTGGTTTAGAGG 59.958 50.000 5.23 0.43 41.69 3.69
2061 4238 3.441500 AAGGCCTCCTTTGGTTTAGAG 57.558 47.619 5.23 0.00 41.69 2.43
2062 4239 3.914435 ACTAAGGCCTCCTTTGGTTTAGA 59.086 43.478 5.23 0.00 41.69 2.10
2063 4240 4.302559 ACTAAGGCCTCCTTTGGTTTAG 57.697 45.455 5.23 2.88 41.69 1.85
2064 4241 4.734843 AACTAAGGCCTCCTTTGGTTTA 57.265 40.909 5.23 0.00 41.69 2.01
2065 4242 3.612795 AACTAAGGCCTCCTTTGGTTT 57.387 42.857 5.23 0.00 41.69 3.27
2066 4243 3.230976 CAAACTAAGGCCTCCTTTGGTT 58.769 45.455 5.23 1.01 44.45 3.67
2067 4244 2.177016 ACAAACTAAGGCCTCCTTTGGT 59.823 45.455 23.60 12.30 41.69 3.67
2068 4245 2.876581 ACAAACTAAGGCCTCCTTTGG 58.123 47.619 23.60 11.80 41.69 3.28
2069 4246 4.906618 TCTACAAACTAAGGCCTCCTTTG 58.093 43.478 20.46 20.46 41.69 2.77
2070 4247 5.780958 ATCTACAAACTAAGGCCTCCTTT 57.219 39.130 5.23 0.46 41.69 3.11
2071 4248 5.130643 GGTATCTACAAACTAAGGCCTCCTT 59.869 44.000 5.23 3.40 46.63 3.36
2072 4249 4.654724 GGTATCTACAAACTAAGGCCTCCT 59.345 45.833 5.23 0.00 33.87 3.69
2073 4250 4.654724 AGGTATCTACAAACTAAGGCCTCC 59.345 45.833 5.23 0.00 0.00 4.30
2074 4251 5.873146 AGGTATCTACAAACTAAGGCCTC 57.127 43.478 5.23 0.00 0.00 4.70
2075 4252 5.724854 TCAAGGTATCTACAAACTAAGGCCT 59.275 40.000 0.00 0.00 0.00 5.19
2076 4253 5.985911 TCAAGGTATCTACAAACTAAGGCC 58.014 41.667 0.00 0.00 0.00 5.19
2077 4254 5.524281 GCTCAAGGTATCTACAAACTAAGGC 59.476 44.000 0.00 0.00 0.00 4.35
2078 4255 6.879400 AGCTCAAGGTATCTACAAACTAAGG 58.121 40.000 0.00 0.00 0.00 2.69
2079 4256 7.777095 AGAGCTCAAGGTATCTACAAACTAAG 58.223 38.462 17.77 0.00 0.00 2.18
2080 4257 7.719871 AGAGCTCAAGGTATCTACAAACTAA 57.280 36.000 17.77 0.00 0.00 2.24
2081 4258 8.053963 ACTAGAGCTCAAGGTATCTACAAACTA 58.946 37.037 17.77 0.00 0.00 2.24
2082 4259 6.893005 ACTAGAGCTCAAGGTATCTACAAACT 59.107 38.462 17.77 0.00 0.00 2.66
2083 4260 7.102847 ACTAGAGCTCAAGGTATCTACAAAC 57.897 40.000 17.77 0.00 0.00 2.93
2141 4318 7.114388 CCAAAATTGCTATCATGATGATTGACG 59.886 37.037 18.72 5.49 38.26 4.35
2193 4373 9.449719 TCTCTTTTCAGTTAAGTGAACTTTCTT 57.550 29.630 22.49 0.00 46.79 2.52
2210 4390 6.404734 GCCAAACTGTTTCTCTTCTCTTTTCA 60.405 38.462 2.13 0.00 0.00 2.69
2296 4503 7.444487 GGTTATGAGAAACCAAGTCAGTTAGTT 59.556 37.037 0.94 0.00 46.85 2.24
2322 4534 2.829120 AGGAGAGAGGTCTTTTCTTCCG 59.171 50.000 0.00 0.00 30.97 4.30
2334 4546 7.595819 AAGATAGTATGTTTGAGGAGAGAGG 57.404 40.000 0.00 0.00 0.00 3.69
2358 4584 7.737972 TCTGTTGCTTACTTGCTTGTAAATA 57.262 32.000 4.29 0.00 32.80 1.40
2381 4635 8.962884 ATGCCCCAAATTCTATGTTATTTTTC 57.037 30.769 0.00 0.00 0.00 2.29
2408 4662 2.779755 ATGCCGGTCATAACAACAGA 57.220 45.000 1.90 0.00 32.59 3.41
2414 4668 0.605589 GCCCCTATGCCGGTCATAAC 60.606 60.000 16.10 6.26 37.22 1.89
2416 4670 0.766674 AAGCCCCTATGCCGGTCATA 60.767 55.000 15.01 15.01 36.63 2.15
2417 4671 0.766674 TAAGCCCCTATGCCGGTCAT 60.767 55.000 14.43 14.43 39.17 3.06
2418 4672 1.383386 TAAGCCCCTATGCCGGTCA 60.383 57.895 1.90 1.38 0.00 4.02
2440 4890 2.442236 ACTTGGGCCATAATCCACTG 57.558 50.000 7.26 0.00 32.00 3.66
2477 4927 8.997621 TGCTAATACGATAAGATAATTGGGTC 57.002 34.615 0.00 0.00 0.00 4.46
2478 4928 9.601217 GATGCTAATACGATAAGATAATTGGGT 57.399 33.333 0.00 0.00 0.00 4.51
2609 5234 1.129917 GGCTAGGGTTTAGGTCTCCC 58.870 60.000 0.00 0.00 41.36 4.30
2739 5364 4.670765 AGAAACTAGGGTTCTTCTCGGTA 58.329 43.478 5.37 0.00 34.14 4.02
2744 5369 9.067986 CAAATTTGTAGAAACTAGGGTTCTTCT 57.932 33.333 14.13 7.19 34.14 2.85
2774 8459 4.150897 TGATAGAACCCGATTCTTTGGG 57.849 45.455 7.14 0.00 46.05 4.12
2778 8463 4.099573 ACGACATGATAGAACCCGATTCTT 59.900 41.667 0.00 0.00 46.05 2.52
2782 8467 2.956333 TGACGACATGATAGAACCCGAT 59.044 45.455 0.00 0.00 0.00 4.18
2791 8476 3.196685 TGGGTGTTGATGACGACATGATA 59.803 43.478 4.80 0.00 41.66 2.15


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

AutoCloner maintained by Alex Coulton.