Multiple sequence alignment - TraesCS2B01G074100

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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 TraesCS2B01G074100 chr2B 100.000 5348 0 0 1 5348 40065910 40071257 0.000000e+00 9877.0
1 TraesCS2B01G074100 chr2B 81.420 1437 154 58 3049 4441 40277614 40278981 0.000000e+00 1070.0
2 TraesCS2B01G074100 chr2B 91.383 499 41 2 2085 2582 40276608 40277105 0.000000e+00 682.0
3 TraesCS2B01G074100 chr2B 88.740 373 30 8 2638 3004 40277251 40277617 3.800000e-121 446.0
4 TraesCS2B01G074100 chr2B 83.221 447 54 14 1423 1854 40275709 40276149 1.810000e-104 390.0
5 TraesCS2B01G074100 chr2B 86.761 355 35 10 108 451 40274752 40275105 8.400000e-103 385.0
6 TraesCS2B01G074100 chr2B 88.333 240 23 4 1856 2094 40276211 40276446 3.150000e-72 283.0
7 TraesCS2B01G074100 chr2B 83.495 103 12 5 4447 4545 40279014 40279115 2.050000e-14 91.6
8 TraesCS2B01G074100 chr2B 100.000 34 0 0 4608 4641 40070484 40070517 4.470000e-06 63.9
9 TraesCS2B01G074100 chr2B 100.000 34 0 0 4575 4608 40070517 40070550 4.470000e-06 63.9
10 TraesCS2B01G074100 chr2D 93.702 2080 83 16 2581 4645 24703806 24701760 0.000000e+00 3072.0
11 TraesCS2B01G074100 chr2D 94.247 1408 56 12 1182 2582 24705245 24703856 0.000000e+00 2128.0
12 TraesCS2B01G074100 chr2D 83.345 1429 141 43 3052 4441 24560299 24558929 0.000000e+00 1230.0
13 TraesCS2B01G074100 chr2D 93.548 465 28 2 733 1195 24705663 24705199 0.000000e+00 691.0
14 TraesCS2B01G074100 chr2D 90.982 499 43 2 2085 2582 24561301 24560804 0.000000e+00 671.0
15 TraesCS2B01G074100 chr2D 84.865 555 64 8 1311 1854 24562305 24561760 4.710000e-150 542.0
16 TraesCS2B01G074100 chr2D 85.466 461 41 13 3 460 24563438 24563001 1.760000e-124 457.0
17 TraesCS2B01G074100 chr2D 88.172 372 27 8 2638 3004 24560658 24560299 1.380000e-115 427.0
18 TraesCS2B01G074100 chr2D 86.857 350 34 6 137 482 24706589 24706248 1.090000e-101 381.0
19 TraesCS2B01G074100 chr2D 82.247 445 58 12 701 1140 24562841 24562413 1.090000e-96 364.0
20 TraesCS2B01G074100 chr2D 88.750 240 22 4 1856 2094 24561698 24561463 6.780000e-74 289.0
21 TraesCS2B01G074100 chr2D 93.182 44 3 0 4575 4618 24701797 24701754 1.240000e-06 65.8
22 TraesCS2B01G074100 chr2A 93.896 1409 78 3 1182 2582 27328468 27329876 0.000000e+00 2119.0
23 TraesCS2B01G074100 chr2A 94.345 1061 45 9 2581 3636 27329926 27330976 0.000000e+00 1613.0
24 TraesCS2B01G074100 chr2A 90.977 1075 70 15 137 1195 27327451 27328514 0.000000e+00 1423.0
25 TraesCS2B01G074100 chr2A 88.889 1089 67 19 3888 4934 27331082 27332158 0.000000e+00 1291.0
26 TraesCS2B01G074100 chr2A 86.733 799 79 17 3049 3833 27342249 27343034 0.000000e+00 863.0
27 TraesCS2B01G074100 chr2A 90.581 499 45 2 2085 2582 27341250 27341747 0.000000e+00 660.0
28 TraesCS2B01G074100 chr2A 83.633 556 70 14 1311 1854 27340245 27340791 2.220000e-138 503.0
29 TraesCS2B01G074100 chr2A 82.852 554 62 11 3908 4437 27343059 27343603 2.920000e-127 466.0
30 TraesCS2B01G074100 chr2A 87.366 372 30 9 2638 3004 27341893 27342252 1.390000e-110 411.0
31 TraesCS2B01G074100 chr2A 85.464 399 44 10 4963 5348 27332646 27333043 2.320000e-108 403.0
32 TraesCS2B01G074100 chr2A 81.607 473 55 18 4773 5221 27347449 27347913 3.940000e-96 363.0
33 TraesCS2B01G074100 chr2A 79.750 400 62 13 744 1137 27339748 27340134 6.830000e-69 272.0
34 TraesCS2B01G074100 chr2A 84.091 264 35 5 97 358 27338857 27339115 1.150000e-61 248.0
35 TraesCS2B01G074100 chr2A 82.528 269 23 13 209 462 27339116 27339375 1.170000e-51 215.0
36 TraesCS2B01G074100 chr2A 92.727 110 7 1 3680 3788 27330983 27331092 1.990000e-34 158.0
37 TraesCS2B01G074100 chr2A 86.916 107 8 6 4447 4548 27343644 27343749 1.220000e-21 115.0
38 TraesCS2B01G074100 chr2A 90.000 50 4 1 12 60 27327353 27327402 4.470000e-06 63.9
39 TraesCS2B01G074100 chr5B 84.762 105 10 5 4450 4548 49007353 49007249 3.410000e-17 100.0


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 TraesCS2B01G074100 chr2B 40065910 40071257 5347 False 3334.933333 9877 100.000000 1 5348 3 chr2B.!!$F1 5347
1 TraesCS2B01G074100 chr2B 40274752 40279115 4363 False 478.228571 1070 86.193286 108 4545 7 chr2B.!!$F2 4437
2 TraesCS2B01G074100 chr2D 24701754 24706589 4835 True 1267.560000 3072 92.307200 137 4645 5 chr2D.!!$R2 4508
3 TraesCS2B01G074100 chr2D 24558929 24563438 4509 True 568.571429 1230 86.261000 3 4441 7 chr2D.!!$R1 4438
4 TraesCS2B01G074100 chr2A 27327353 27333043 5690 False 1010.128571 2119 90.899714 12 5348 7 chr2A.!!$F1 5336
5 TraesCS2B01G074100 chr2A 27338857 27347913 9056 False 411.600000 863 84.605700 97 5221 10 chr2A.!!$F2 5124

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
134 143 0.475906 CCAATCCTCCTCATCCACCC 59.524 60.000 0.00 0.00 0.00 4.61 F
196 205 0.535797 GTAGGGTTCCAGTTCCGAGG 59.464 60.000 0.00 0.00 0.00 4.63 F
248 280 1.279271 CCGTCTTTCAGTCCATCCCTT 59.721 52.381 0.00 0.00 0.00 3.95 F
1331 1951 0.457851 AGGATCGAAGAGCTCCGTTG 59.542 55.000 10.93 2.82 45.45 4.10 F
2449 3309 0.681733 TGACTCTGAGCTCACCAACC 59.318 55.000 13.74 1.98 0.00 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1294 1914 0.662619 CTTGCGAGGCACACTGAAAA 59.337 50.0 0.00 0.00 38.71 2.29 R
1305 1925 0.873743 GCTCTTCGATCCTTGCGAGG 60.874 60.0 14.59 14.59 45.02 4.63 R
1387 2007 1.122019 ACCCCCACACTGAGACTGAC 61.122 60.0 0.00 0.00 0.00 3.51 R
2473 3333 1.896220 TGTTGGCAAGTAAGAGGCAG 58.104 50.0 0.00 0.00 41.52 4.85 R
4387 5429 0.598680 GCCATCCATCTCTCGTTCGG 60.599 60.0 0.00 0.00 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
47 48 3.179339 TCCCCTTTCCCGCCAACA 61.179 61.111 0.00 0.00 0.00 3.33
50 51 1.191489 CCCCTTTCCCGCCAACAAAT 61.191 55.000 0.00 0.00 0.00 2.32
75 82 3.373565 CTGGCGGCAACTTTCCCC 61.374 66.667 14.48 0.00 0.00 4.81
91 98 4.263572 CCCGCCCGGCAATATCCA 62.264 66.667 10.77 0.00 0.00 3.41
92 99 2.669569 CCGCCCGGCAATATCCAG 60.670 66.667 10.77 0.00 0.00 3.86
93 100 2.425592 CGCCCGGCAATATCCAGA 59.574 61.111 10.77 0.00 0.00 3.86
94 101 1.669115 CGCCCGGCAATATCCAGAG 60.669 63.158 10.77 0.00 0.00 3.35
95 102 1.451936 GCCCGGCAATATCCAGAGT 59.548 57.895 3.91 0.00 0.00 3.24
99 106 2.421388 CCCGGCAATATCCAGAGTCAAA 60.421 50.000 0.00 0.00 0.00 2.69
106 113 5.594926 CAATATCCAGAGTCAAATTTGCCC 58.405 41.667 13.54 6.45 0.00 5.36
110 117 1.821136 CAGAGTCAAATTTGCCCCCTC 59.179 52.381 13.54 13.90 0.00 4.30
127 134 4.161295 CCGCGCCAATCCTCCTCA 62.161 66.667 0.00 0.00 0.00 3.86
128 135 2.109799 CGCGCCAATCCTCCTCAT 59.890 61.111 0.00 0.00 0.00 2.90
131 138 1.832219 CGCCAATCCTCCTCATCCA 59.168 57.895 0.00 0.00 0.00 3.41
134 143 0.475906 CCAATCCTCCTCATCCACCC 59.524 60.000 0.00 0.00 0.00 4.61
154 163 1.338107 CCCTCCTCATACATACGGCA 58.662 55.000 0.00 0.00 0.00 5.69
164 173 6.407412 CCTCATACATACGGCAATATCCAGAT 60.407 42.308 0.00 0.00 0.00 2.90
195 204 1.477295 GAGTAGGGTTCCAGTTCCGAG 59.523 57.143 0.00 0.00 0.00 4.63
196 205 0.535797 GTAGGGTTCCAGTTCCGAGG 59.464 60.000 0.00 0.00 0.00 4.63
248 280 1.279271 CCGTCTTTCAGTCCATCCCTT 59.721 52.381 0.00 0.00 0.00 3.95
390 587 2.430465 CAGGGTCCAGATCTGTGTTTG 58.570 52.381 21.11 9.05 0.00 2.93
477 683 2.688958 ACTCTGAATCTACCGTGGCTAC 59.311 50.000 0.00 0.00 0.00 3.58
489 695 4.021916 ACCGTGGCTACTACTCTTGTAAT 58.978 43.478 0.00 0.00 0.00 1.89
494 700 7.234384 CGTGGCTACTACTCTTGTAATTTTTG 58.766 38.462 0.00 0.00 0.00 2.44
496 702 6.940298 TGGCTACTACTCTTGTAATTTTTGCT 59.060 34.615 0.00 0.00 0.00 3.91
497 703 7.094805 TGGCTACTACTCTTGTAATTTTTGCTG 60.095 37.037 0.00 0.00 0.00 4.41
498 704 7.244192 GCTACTACTCTTGTAATTTTTGCTGG 58.756 38.462 0.00 0.00 0.00 4.85
499 705 6.013842 ACTACTCTTGTAATTTTTGCTGGC 57.986 37.500 0.00 0.00 0.00 4.85
615 884 2.269241 GGGCTTCCCTCTTCACGG 59.731 66.667 0.00 0.00 41.34 4.94
637 906 2.586425 CACAGGGATGTGGTTTCTGTT 58.414 47.619 0.37 0.00 36.66 3.16
642 911 5.178797 CAGGGATGTGGTTTCTGTTAGTAG 58.821 45.833 0.00 0.00 0.00 2.57
644 913 5.046520 AGGGATGTGGTTTCTGTTAGTAGTC 60.047 44.000 0.00 0.00 0.00 2.59
656 925 3.813166 TGTTAGTAGTCAAAGGCTGCAAC 59.187 43.478 0.50 0.00 0.00 4.17
657 926 2.638480 AGTAGTCAAAGGCTGCAACA 57.362 45.000 0.50 0.00 0.00 3.33
661 930 3.375782 AGTCAAAGGCTGCAACATTTC 57.624 42.857 0.50 0.00 0.00 2.17
663 932 3.054878 GTCAAAGGCTGCAACATTTCTG 58.945 45.455 0.50 0.00 0.00 3.02
664 933 2.694628 TCAAAGGCTGCAACATTTCTGT 59.305 40.909 0.50 0.00 37.12 3.41
666 935 3.923017 AAGGCTGCAACATTTCTGTAC 57.077 42.857 0.50 0.00 33.36 2.90
667 936 2.862541 AGGCTGCAACATTTCTGTACA 58.137 42.857 0.50 0.00 33.36 2.90
669 938 4.588899 AGGCTGCAACATTTCTGTACATA 58.411 39.130 0.50 0.00 33.36 2.29
670 939 4.396166 AGGCTGCAACATTTCTGTACATAC 59.604 41.667 0.50 0.00 33.36 2.39
699 976 5.991606 TGTTCAACGTTCTCAATTCATCTCT 59.008 36.000 0.00 0.00 0.00 3.10
836 1414 5.922544 AGCTAATTGCAATGTTCTCAAACAC 59.077 36.000 13.82 0.00 45.48 3.32
955 1547 5.005012 TGCTTATACGCGACATTTACTTGAC 59.995 40.000 15.93 0.00 0.00 3.18
967 1559 7.464178 CGACATTTACTTGACTATAACACCTGC 60.464 40.741 0.00 0.00 0.00 4.85
1047 1640 6.743575 ACAAATAAGGCACTCAATCTGTAC 57.256 37.500 0.00 0.00 38.49 2.90
1056 1649 4.328440 GCACTCAATCTGTACACTGTCATC 59.672 45.833 0.00 0.00 0.00 2.92
1174 1794 6.775594 TTATGAAGAAGATTCCGAGACTGA 57.224 37.500 0.00 0.00 0.00 3.41
1175 1795 4.710423 TGAAGAAGATTCCGAGACTGAG 57.290 45.455 0.00 0.00 0.00 3.35
1176 1796 4.336280 TGAAGAAGATTCCGAGACTGAGA 58.664 43.478 0.00 0.00 0.00 3.27
1177 1797 4.952957 TGAAGAAGATTCCGAGACTGAGAT 59.047 41.667 0.00 0.00 0.00 2.75
1178 1798 6.122964 TGAAGAAGATTCCGAGACTGAGATA 58.877 40.000 0.00 0.00 0.00 1.98
1179 1799 6.603599 TGAAGAAGATTCCGAGACTGAGATAA 59.396 38.462 0.00 0.00 0.00 1.75
1180 1800 6.385649 AGAAGATTCCGAGACTGAGATAAC 57.614 41.667 0.00 0.00 0.00 1.89
1181 1801 6.126409 AGAAGATTCCGAGACTGAGATAACT 58.874 40.000 0.00 0.00 0.00 2.24
1182 1802 5.766150 AGATTCCGAGACTGAGATAACTG 57.234 43.478 0.00 0.00 0.00 3.16
1183 1803 5.441500 AGATTCCGAGACTGAGATAACTGA 58.558 41.667 0.00 0.00 0.00 3.41
1184 1804 6.068010 AGATTCCGAGACTGAGATAACTGAT 58.932 40.000 0.00 0.00 0.00 2.90
1185 1805 6.549364 AGATTCCGAGACTGAGATAACTGATT 59.451 38.462 0.00 0.00 0.00 2.57
1186 1806 5.759506 TCCGAGACTGAGATAACTGATTC 57.240 43.478 0.00 0.00 0.00 2.52
1187 1807 5.441500 TCCGAGACTGAGATAACTGATTCT 58.558 41.667 0.00 0.00 0.00 2.40
1188 1808 5.298026 TCCGAGACTGAGATAACTGATTCTG 59.702 44.000 0.00 0.00 0.00 3.02
1189 1809 5.298026 CCGAGACTGAGATAACTGATTCTGA 59.702 44.000 0.00 0.00 0.00 3.27
1190 1810 6.183360 CCGAGACTGAGATAACTGATTCTGAA 60.183 42.308 0.00 0.00 0.00 3.02
1191 1811 6.912051 CGAGACTGAGATAACTGATTCTGAAG 59.088 42.308 0.00 0.00 0.00 3.02
1192 1812 7.201688 CGAGACTGAGATAACTGATTCTGAAGA 60.202 40.741 0.00 0.00 0.00 2.87
1193 1813 8.359875 AGACTGAGATAACTGATTCTGAAGAA 57.640 34.615 0.00 0.00 38.56 2.52
1194 1814 8.469200 AGACTGAGATAACTGATTCTGAAGAAG 58.531 37.037 0.00 0.00 37.48 2.85
1195 1815 8.359875 ACTGAGATAACTGATTCTGAAGAAGA 57.640 34.615 8.59 0.00 37.48 2.87
1196 1816 8.980596 ACTGAGATAACTGATTCTGAAGAAGAT 58.019 33.333 8.59 1.11 37.48 2.40
1197 1817 9.820725 CTGAGATAACTGATTCTGAAGAAGATT 57.179 33.333 8.59 3.60 37.48 2.40
1198 1818 9.814899 TGAGATAACTGATTCTGAAGAAGATTC 57.185 33.333 8.59 0.00 37.48 2.52
1199 1819 9.260002 GAGATAACTGATTCTGAAGAAGATTCC 57.740 37.037 8.59 0.00 37.48 3.01
1200 1820 8.766476 AGATAACTGATTCTGAAGAAGATTCCA 58.234 33.333 8.59 0.00 37.48 3.53
1201 1821 9.388506 GATAACTGATTCTGAAGAAGATTCCAA 57.611 33.333 8.59 0.00 37.48 3.53
1202 1822 7.684937 AACTGATTCTGAAGAAGATTCCAAG 57.315 36.000 8.59 0.00 37.48 3.61
1203 1823 7.013823 ACTGATTCTGAAGAAGATTCCAAGA 57.986 36.000 8.59 0.00 37.48 3.02
1204 1824 6.878389 ACTGATTCTGAAGAAGATTCCAAGAC 59.122 38.462 8.59 0.00 37.48 3.01
1205 1825 7.013823 TGATTCTGAAGAAGATTCCAAGACT 57.986 36.000 0.00 0.00 37.48 3.24
1206 1826 7.102346 TGATTCTGAAGAAGATTCCAAGACTC 58.898 38.462 0.00 0.00 37.48 3.36
1247 1867 1.544825 TTGCCTCTCCTTCACCCTCG 61.545 60.000 0.00 0.00 0.00 4.63
1275 1895 7.310664 ACTTAATGTTGCTTCTGTTGATGATG 58.689 34.615 0.00 0.00 0.00 3.07
1289 1909 2.093500 TGATGATGGTTCCGGTGAAGAG 60.093 50.000 0.00 0.00 0.00 2.85
1294 1914 1.702957 TGGTTCCGGTGAAGAGGATTT 59.297 47.619 0.00 0.00 36.28 2.17
1296 1916 3.154710 GGTTCCGGTGAAGAGGATTTTT 58.845 45.455 0.00 0.00 36.28 1.94
1327 1947 0.873743 CGCAAGGATCGAAGAGCTCC 60.874 60.000 10.93 0.00 45.45 4.70
1331 1951 0.457851 AGGATCGAAGAGCTCCGTTG 59.542 55.000 10.93 2.82 45.45 4.10
1387 2007 1.839994 TGAAGGATCTGGCACTAAGGG 59.160 52.381 0.00 0.00 0.00 3.95
1483 2103 7.542130 TGCTTTGAAACAGAAGAAAGAAAAGAC 59.458 33.333 0.00 0.00 0.00 3.01
1485 2105 9.410556 CTTTGAAACAGAAGAAAGAAAAGACAA 57.589 29.630 0.00 0.00 0.00 3.18
1507 2127 3.010420 CCCCTTCTAAGGCGAAAAGAAG 58.990 50.000 3.03 11.67 45.10 2.85
1554 2177 8.546244 CACATGCTACAAAACTAGATACATCAG 58.454 37.037 0.00 0.00 0.00 2.90
1603 2226 5.238583 ACAAACTTCCCTATTCGAGTCAAG 58.761 41.667 0.00 0.00 0.00 3.02
1604 2227 4.473477 AACTTCCCTATTCGAGTCAAGG 57.527 45.455 0.00 0.00 0.00 3.61
1774 2404 5.334957 CGACTTCTGTCTTTCAGCTAGTACA 60.335 44.000 0.00 0.00 43.32 2.90
1898 2590 1.272037 TGCTGCATCAGTTTCCCATCA 60.272 47.619 0.00 0.00 33.43 3.07
2332 3192 4.202050 ACTGCCAATTTTGACACTCAAGAC 60.202 41.667 0.00 0.00 37.70 3.01
2449 3309 0.681733 TGACTCTGAGCTCACCAACC 59.318 55.000 13.74 1.98 0.00 3.77
2450 3310 0.681733 GACTCTGAGCTCACCAACCA 59.318 55.000 13.74 0.00 0.00 3.67
2473 3333 3.369756 CAGCAAATGTTTCACATGATGGC 59.630 43.478 0.00 0.00 37.97 4.40
2508 3368 2.094675 CAACATGGAGGGGTCATCAAC 58.905 52.381 0.00 0.00 0.00 3.18
2515 3375 2.372172 GGAGGGGTCATCAACGGATATT 59.628 50.000 0.00 0.00 30.87 1.28
2544 3404 7.040755 TCAGTTAAGTGGTACAATGAATGTTGG 60.041 37.037 10.39 0.00 44.16 3.77
2588 3499 6.877855 TGATCAAGAATCAAGAGAAACTGGAG 59.122 38.462 0.00 0.00 41.49 3.86
2703 3653 7.937942 AGGATCAATTGAAGATCATACTCCAAG 59.062 37.037 13.09 0.00 42.84 3.61
2733 3683 1.280421 GTCCCAGAGAAAGGTCTGCAT 59.720 52.381 0.00 0.00 42.40 3.96
2742 3692 4.512484 AGAAAGGTCTGCATAGCTCTTTC 58.488 43.478 4.11 10.86 39.78 2.62
2911 3861 6.932356 CAATCTATGCCATCTTGTAGTGTT 57.068 37.500 0.00 0.00 0.00 3.32
2912 3862 7.325660 CAATCTATGCCATCTTGTAGTGTTT 57.674 36.000 0.00 0.00 0.00 2.83
2913 3863 7.765307 CAATCTATGCCATCTTGTAGTGTTTT 58.235 34.615 0.00 0.00 0.00 2.43
2914 3864 7.944729 ATCTATGCCATCTTGTAGTGTTTTT 57.055 32.000 0.00 0.00 0.00 1.94
2915 3865 9.461312 AATCTATGCCATCTTGTAGTGTTTTTA 57.539 29.630 0.00 0.00 0.00 1.52
3037 3995 3.238108 AGTCAAGCATTACCTCAGACG 57.762 47.619 0.00 0.00 0.00 4.18
3069 4027 8.873830 CAAGCAATACCGATCTATATTAACCAG 58.126 37.037 0.00 0.00 0.00 4.00
3144 4102 6.884472 TCTTAAGTCAACAGAATCCCCATA 57.116 37.500 1.63 0.00 0.00 2.74
3304 4262 5.341462 CGAAAATTTGTCATCAGAAGCACAG 59.659 40.000 0.00 0.00 0.00 3.66
3433 4400 9.617975 AACAATAACACAAAAATTGTTGTTTGG 57.382 25.926 20.20 10.58 46.60 3.28
3434 4401 8.787852 ACAATAACACAAAAATTGTTGTTTGGT 58.212 25.926 20.20 11.08 43.23 3.67
3449 4416 7.877003 TGTTGTTTGGTAAGTTACACCATATG 58.123 34.615 14.81 0.00 45.32 1.78
3526 4496 2.452295 TTCTCTGTCAGCTGCTTCTG 57.548 50.000 9.47 6.41 35.46 3.02
3563 4533 8.854614 ACATAATATAAGGCTAAAGCTCCTTG 57.145 34.615 13.37 0.20 42.29 3.61
3786 4787 3.366052 TTTCCTCTGAATTAGGTGGGC 57.634 47.619 0.00 0.00 35.48 5.36
3835 4837 8.037382 AGATATTGCAAGATCATGAATTACCG 57.963 34.615 30.02 0.00 0.00 4.02
3836 4838 7.879677 AGATATTGCAAGATCATGAATTACCGA 59.120 33.333 30.02 0.00 0.00 4.69
3837 4839 6.889301 ATTGCAAGATCATGAATTACCGAT 57.111 33.333 4.94 0.00 0.00 4.18
3838 4840 5.678132 TGCAAGATCATGAATTACCGATG 57.322 39.130 0.00 0.00 0.00 3.84
3839 4841 5.367302 TGCAAGATCATGAATTACCGATGA 58.633 37.500 0.00 0.00 0.00 2.92
3840 4842 5.821995 TGCAAGATCATGAATTACCGATGAA 59.178 36.000 0.00 0.00 30.14 2.57
3841 4843 6.487668 TGCAAGATCATGAATTACCGATGAAT 59.512 34.615 0.00 0.00 30.14 2.57
3883 4885 1.942657 TGAAGTTCACAGCTGCTTGAC 59.057 47.619 15.27 7.79 0.00 3.18
3911 4913 1.077169 TGAGGCCCAACTCTAGTCTGA 59.923 52.381 0.00 0.00 38.32 3.27
3922 4924 8.428063 CCCAACTCTAGTCTGATCAGATATTTT 58.572 37.037 27.51 13.43 39.97 1.82
4078 5093 8.514594 TGGTATCTCTGCTTTTAAGATTGTTTG 58.485 33.333 0.00 0.00 32.25 2.93
4079 5094 8.730680 GGTATCTCTGCTTTTAAGATTGTTTGA 58.269 33.333 0.00 0.00 32.25 2.69
4083 5098 9.283768 TCTCTGCTTTTAAGATTGTTTGATACA 57.716 29.630 0.00 0.00 34.12 2.29
4084 5099 9.334693 CTCTGCTTTTAAGATTGTTTGATACAC 57.665 33.333 0.00 0.00 36.21 2.90
4160 5194 1.909986 ACACTAGAGGGAAAGAAGGCC 59.090 52.381 0.00 0.00 0.00 5.19
4195 5229 0.245539 TTGCCGAGGAAACGTAGGAG 59.754 55.000 0.00 0.00 0.00 3.69
4225 5259 0.179034 GCGGATGAAGCTGGAGGAAT 60.179 55.000 0.00 0.00 0.00 3.01
4308 5345 9.420118 AGTCATAAACATTATTTGGGCTGATTA 57.580 29.630 0.00 0.00 0.00 1.75
4314 5351 5.650266 ACATTATTTGGGCTGATTACGTCAA 59.350 36.000 0.00 0.00 36.14 3.18
4321 5358 3.429085 GGCTGATTACGTCAAGCAATTG 58.571 45.455 0.00 0.00 36.14 2.32
4368 5405 6.694447 ACAATGAAGAATCAAACAAGATGGG 58.306 36.000 0.00 0.00 39.49 4.00
4371 5408 2.460669 AGAATCAAACAAGATGGGCCC 58.539 47.619 17.59 17.59 0.00 5.80
4372 5409 2.043526 AGAATCAAACAAGATGGGCCCT 59.956 45.455 25.70 8.64 0.00 5.19
4461 5536 5.916661 TCCCTCTCACTGTATGTTTAGAC 57.083 43.478 0.00 0.00 0.00 2.59
4548 5644 7.750229 AGACAAGAATCAACTTCTGCAATTA 57.250 32.000 0.00 0.00 43.60 1.40
4549 5645 8.345724 AGACAAGAATCAACTTCTGCAATTAT 57.654 30.769 0.00 0.00 43.60 1.28
4696 9016 0.321564 TAGCTGGTGCGCAATTCACT 60.322 50.000 14.00 9.14 45.42 3.41
4699 9019 1.133025 GCTGGTGCGCAATTCACTATT 59.867 47.619 14.00 0.00 34.97 1.73
4700 9020 2.415893 GCTGGTGCGCAATTCACTATTT 60.416 45.455 14.00 0.00 34.97 1.40
4712 9032 7.501515 GCAATTCACTATTTGTTTGCTGTAAC 58.498 34.615 0.00 0.00 39.88 2.50
4717 9037 8.384607 TCACTATTTGTTTGCTGTAACACATA 57.615 30.769 0.00 0.00 37.72 2.29
4718 9038 8.841300 TCACTATTTGTTTGCTGTAACACATAA 58.159 29.630 0.00 0.00 37.72 1.90
4720 9040 9.062524 ACTATTTGTTTGCTGTAACACATAAGA 57.937 29.630 0.00 0.00 37.72 2.10
4722 9042 6.935741 TTGTTTGCTGTAACACATAAGAGT 57.064 33.333 0.00 0.00 37.72 3.24
4723 9043 6.299023 TGTTTGCTGTAACACATAAGAGTG 57.701 37.500 0.00 0.00 44.93 3.51
4731 9051 4.584327 AACACATAAGAGTGGTTTTGCC 57.416 40.909 0.00 0.00 43.72 4.52
4732 9052 3.561143 ACACATAAGAGTGGTTTTGCCA 58.439 40.909 0.00 0.00 46.95 4.92
4754 9090 6.901265 CCATTTTGGGCTGAAAGTAAAAATG 58.099 36.000 10.29 10.29 42.70 2.32
4766 9102 2.825532 AGTAAAAATGCCGGTTGCTCAT 59.174 40.909 1.90 0.00 42.00 2.90
4767 9103 2.837532 AAAAATGCCGGTTGCTCATT 57.162 40.000 1.90 0.15 42.00 2.57
4869 9467 5.012354 TCGTAGAGTTGTGGGGTCTAAATTT 59.988 40.000 0.00 0.00 0.00 1.82
4872 9470 5.454966 AGAGTTGTGGGGTCTAAATTTTGT 58.545 37.500 0.00 0.00 0.00 2.83
4877 9475 2.224917 TGGGGTCTAAATTTTGTCCGCT 60.225 45.455 23.61 0.00 0.00 5.52
4912 9511 7.651808 AGGGAAAACATGAATTATCGCTAATG 58.348 34.615 0.00 0.00 0.00 1.90
4925 9524 8.958119 ATTATCGCTAATGAACCAGAGTTAAA 57.042 30.769 0.00 0.00 35.94 1.52
4954 9616 6.919721 TCTTAACTAAATTGTTCACCCATGC 58.080 36.000 0.00 0.00 0.00 4.06
4968 9630 5.782047 TCACCCATGCAAATGTAAAAGAAG 58.218 37.500 0.00 0.00 0.00 2.85
4969 9631 4.389687 CACCCATGCAAATGTAAAAGAAGC 59.610 41.667 0.00 0.00 0.00 3.86
4983 10041 4.602340 AAAGAAGCCAGACGAACTAAGA 57.398 40.909 0.00 0.00 0.00 2.10
5044 10103 4.454161 TGAATATGTGTGACGGTTTTCCTG 59.546 41.667 0.00 0.00 37.95 3.86
5053 10112 2.416893 GACGGTTTTCCTGATTCTGAGC 59.583 50.000 0.00 0.00 37.95 4.26
5069 10130 7.448161 TGATTCTGAGCCAAGAGATTTTTGTAA 59.552 33.333 0.00 0.00 0.00 2.41
5092 10156 4.948847 AGTCCCAATCAACTTTGAAAAGC 58.051 39.130 2.69 0.00 41.13 3.51
5121 10187 8.831000 ACTTTAGTTTAGTAAAAAGTGCAACG 57.169 30.769 9.41 0.00 45.86 4.10
5126 10192 3.963383 AGTAAAAAGTGCAACGTCCAG 57.037 42.857 0.00 0.00 45.86 3.86
5129 10195 2.844122 AAAAGTGCAACGTCCAGTTC 57.156 45.000 8.99 0.00 45.86 3.01
5160 10228 8.584157 AGAAATGTGTATGGAAAATTGCAAGTA 58.416 29.630 4.94 0.00 30.51 2.24
5171 10239 9.118300 TGGAAAATTGCAAGTAACATTTTTCAT 57.882 25.926 23.29 0.51 42.98 2.57
5271 10343 5.982890 ACCAAAATCAACCTGGACATAAG 57.017 39.130 0.00 0.00 34.16 1.73
5287 10359 5.883673 GGACATAAGCAAACCCTATGTGTAA 59.116 40.000 0.00 0.00 32.24 2.41
5289 10361 5.650703 ACATAAGCAAACCCTATGTGTAACC 59.349 40.000 0.00 0.00 34.36 2.85
5290 10362 2.706890 AGCAAACCCTATGTGTAACCG 58.293 47.619 0.00 0.00 34.36 4.44
5306 10378 0.032017 ACCGCTAGAGGAGACCCAAT 60.032 55.000 20.46 0.00 34.73 3.16
5337 10409 2.094675 AGCACACACCCATATTTCAGC 58.905 47.619 0.00 0.00 0.00 4.26
5338 10410 1.202177 GCACACACCCATATTTCAGCG 60.202 52.381 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.680989 GCCGCCAGGGTTGGTATTT 60.681 57.895 0.00 0.00 46.80 1.40
50 51 3.571216 TTGCCGCCAGGGTTGGTA 61.571 61.111 0.00 0.00 46.80 3.25
75 82 2.669569 CTGGATATTGCCGGGCGG 60.670 66.667 15.40 0.00 38.57 6.13
81 88 5.045872 GCAAATTTGACTCTGGATATTGCC 58.954 41.667 22.31 0.00 35.76 4.52
82 89 5.045872 GGCAAATTTGACTCTGGATATTGC 58.954 41.667 22.31 1.35 39.76 3.56
83 90 5.452356 GGGGCAAATTTGACTCTGGATATTG 60.452 44.000 23.02 0.00 32.48 1.90
84 91 4.651045 GGGGCAAATTTGACTCTGGATATT 59.349 41.667 23.02 0.00 32.48 1.28
85 92 4.218312 GGGGCAAATTTGACTCTGGATAT 58.782 43.478 23.02 0.00 32.48 1.63
86 93 3.627237 GGGGGCAAATTTGACTCTGGATA 60.627 47.826 23.14 0.00 36.71 2.59
87 94 2.460669 GGGGCAAATTTGACTCTGGAT 58.539 47.619 23.02 0.00 32.48 3.41
88 95 1.549950 GGGGGCAAATTTGACTCTGGA 60.550 52.381 23.14 0.00 36.71 3.86
89 96 0.897621 GGGGGCAAATTTGACTCTGG 59.102 55.000 23.14 0.00 36.71 3.86
90 97 1.821136 GAGGGGGCAAATTTGACTCTG 59.179 52.381 23.14 0.00 36.71 3.35
91 98 1.272704 GGAGGGGGCAAATTTGACTCT 60.273 52.381 23.14 19.35 36.71 3.24
92 99 1.186200 GGAGGGGGCAAATTTGACTC 58.814 55.000 23.02 19.83 35.32 3.36
93 100 0.611896 CGGAGGGGGCAAATTTGACT 60.612 55.000 23.02 13.16 36.14 3.41
94 101 1.890174 CGGAGGGGGCAAATTTGAC 59.110 57.895 22.31 19.34 34.70 3.18
95 102 1.981853 GCGGAGGGGGCAAATTTGA 60.982 57.895 22.31 0.00 0.00 2.69
106 113 4.918201 GAGGATTGGCGCGGAGGG 62.918 72.222 8.83 0.00 46.11 4.30
110 117 3.466791 ATGAGGAGGATTGGCGCGG 62.467 63.158 8.83 0.00 0.00 6.46
119 126 2.372688 GGGGGTGGATGAGGAGGA 59.627 66.667 0.00 0.00 0.00 3.71
134 143 0.608640 GCCGTATGTATGAGGAGGGG 59.391 60.000 0.00 0.00 0.00 4.79
154 163 5.304101 ACTCTGCTTCTCGAATCTGGATATT 59.696 40.000 0.00 0.00 0.00 1.28
164 173 2.217510 ACCCTACTCTGCTTCTCGAA 57.782 50.000 0.00 0.00 0.00 3.71
248 280 2.650116 GGAGGCGCTGACCTTGAGA 61.650 63.158 7.64 0.00 41.32 3.27
390 587 1.196808 TCGGCTTGAGATGCGAAAAAC 59.803 47.619 0.00 0.00 0.00 2.43
477 683 6.259550 AGCCAGCAAAAATTACAAGAGTAG 57.740 37.500 0.00 0.00 0.00 2.57
496 702 1.123861 CAGGCCTAGGATGCTAGCCA 61.124 60.000 25.34 0.24 0.00 4.75
497 703 0.833834 TCAGGCCTAGGATGCTAGCC 60.834 60.000 14.75 18.06 0.00 3.93
498 704 0.320050 GTCAGGCCTAGGATGCTAGC 59.680 60.000 14.75 8.10 0.00 3.42
499 705 1.617850 CTGTCAGGCCTAGGATGCTAG 59.382 57.143 14.75 14.02 0.00 3.42
629 898 5.334182 GCAGCCTTTGACTACTAACAGAAAC 60.334 44.000 0.00 0.00 0.00 2.78
633 902 3.664107 TGCAGCCTTTGACTACTAACAG 58.336 45.455 0.00 0.00 0.00 3.16
637 906 3.762407 TGTTGCAGCCTTTGACTACTA 57.238 42.857 0.00 0.00 0.00 1.82
642 911 3.054878 CAGAAATGTTGCAGCCTTTGAC 58.945 45.455 8.44 0.00 0.00 3.18
644 913 3.102052 ACAGAAATGTTGCAGCCTTTG 57.898 42.857 8.44 0.00 0.00 2.77
666 935 4.982295 TGAGAACGTTGAACAGACAGTATG 59.018 41.667 5.00 0.00 46.00 2.39
667 936 5.196341 TGAGAACGTTGAACAGACAGTAT 57.804 39.130 5.00 0.00 0.00 2.12
669 938 3.520290 TGAGAACGTTGAACAGACAGT 57.480 42.857 5.00 0.00 0.00 3.55
670 939 5.006649 TGAATTGAGAACGTTGAACAGACAG 59.993 40.000 5.00 0.00 0.00 3.51
699 976 0.550914 AAACTGTGCTTCCAGTGGGA 59.449 50.000 9.92 0.00 44.74 4.37
836 1414 4.707030 TTATGCCTGAAGAAGCACAATG 57.293 40.909 0.00 0.00 42.84 2.82
843 1421 5.831702 AGCATCTTTTATGCCTGAAGAAG 57.168 39.130 6.36 0.00 45.59 2.85
955 1547 8.268850 AGACATACAAAAAGCAGGTGTTATAG 57.731 34.615 0.00 0.00 0.00 1.31
967 1559 4.941873 GGGTCCCTGTAGACATACAAAAAG 59.058 45.833 0.00 0.00 41.33 2.27
1047 1640 1.471287 CATTGTGGCCAGATGACAGTG 59.529 52.381 19.69 11.30 0.00 3.66
1056 1649 2.768253 TCTACAGACATTGTGGCCAG 57.232 50.000 5.11 0.00 41.10 4.85
1118 1711 1.301423 TTACACGGGTGTTCTTGCAC 58.699 50.000 10.04 0.00 41.83 4.57
1174 1794 8.766476 TGGAATCTTCTTCAGAATCAGTTATCT 58.234 33.333 0.00 0.00 33.46 1.98
1175 1795 8.954950 TGGAATCTTCTTCAGAATCAGTTATC 57.045 34.615 0.00 0.00 33.46 1.75
1176 1796 9.393512 CTTGGAATCTTCTTCAGAATCAGTTAT 57.606 33.333 0.00 0.00 33.46 1.89
1177 1797 8.597167 TCTTGGAATCTTCTTCAGAATCAGTTA 58.403 33.333 0.00 0.00 33.46 2.24
1178 1798 7.390162 GTCTTGGAATCTTCTTCAGAATCAGTT 59.610 37.037 0.00 0.00 33.46 3.16
1179 1799 6.878389 GTCTTGGAATCTTCTTCAGAATCAGT 59.122 38.462 0.00 0.00 33.46 3.41
1180 1800 7.104939 AGTCTTGGAATCTTCTTCAGAATCAG 58.895 38.462 0.00 0.00 33.46 2.90
1181 1801 7.013823 AGTCTTGGAATCTTCTTCAGAATCA 57.986 36.000 0.00 0.00 33.46 2.57
1182 1802 7.102346 TGAGTCTTGGAATCTTCTTCAGAATC 58.898 38.462 0.00 0.00 34.16 2.52
1183 1803 7.013823 TGAGTCTTGGAATCTTCTTCAGAAT 57.986 36.000 0.00 0.00 34.16 2.40
1184 1804 6.268617 TCTGAGTCTTGGAATCTTCTTCAGAA 59.731 38.462 0.00 0.00 34.16 3.02
1185 1805 5.777223 TCTGAGTCTTGGAATCTTCTTCAGA 59.223 40.000 0.00 0.00 35.33 3.27
1186 1806 6.035368 TCTGAGTCTTGGAATCTTCTTCAG 57.965 41.667 0.00 0.00 0.00 3.02
1187 1807 6.617782 ATCTGAGTCTTGGAATCTTCTTCA 57.382 37.500 0.00 0.00 0.00 3.02
1188 1808 8.257306 AGTTATCTGAGTCTTGGAATCTTCTTC 58.743 37.037 0.00 0.00 0.00 2.87
1189 1809 8.040132 CAGTTATCTGAGTCTTGGAATCTTCTT 58.960 37.037 0.00 0.00 43.76 2.52
1190 1810 7.398618 TCAGTTATCTGAGTCTTGGAATCTTCT 59.601 37.037 0.00 0.00 44.58 2.85
1191 1811 7.551585 TCAGTTATCTGAGTCTTGGAATCTTC 58.448 38.462 0.00 0.00 44.58 2.87
1192 1812 7.487822 TCAGTTATCTGAGTCTTGGAATCTT 57.512 36.000 0.00 0.00 44.58 2.40
1206 1826 7.413877 GGCAACTTCTTCAGAATCAGTTATCTG 60.414 40.741 6.75 0.00 43.51 2.90
1247 1867 6.072112 TCAACAGAAGCAACATTAAGTTCC 57.928 37.500 0.00 0.00 38.74 3.62
1275 1895 2.491675 AAATCCTCTTCACCGGAACC 57.508 50.000 9.46 0.00 32.12 3.62
1294 1914 0.662619 CTTGCGAGGCACACTGAAAA 59.337 50.000 0.00 0.00 38.71 2.29
1296 1916 1.597854 CCTTGCGAGGCACACTGAA 60.598 57.895 7.18 0.00 38.71 3.02
1297 1917 1.830587 ATCCTTGCGAGGCACACTGA 61.831 55.000 16.01 0.00 43.21 3.41
1305 1925 0.873743 GCTCTTCGATCCTTGCGAGG 60.874 60.000 14.59 14.59 45.02 4.63
1327 1947 7.807680 AGCCTTCTTATTCTTAACTTTCAACG 58.192 34.615 0.00 0.00 0.00 4.10
1331 1951 7.923414 TGGAGCCTTCTTATTCTTAACTTTC 57.077 36.000 0.00 0.00 0.00 2.62
1387 2007 1.122019 ACCCCCACACTGAGACTGAC 61.122 60.000 0.00 0.00 0.00 3.51
1507 2127 2.411904 GAGAAGATGATGCATCCGTCC 58.588 52.381 23.67 9.93 41.36 4.79
1554 2177 6.597280 ACAGGACTAATTTCATCTCTCTTTGC 59.403 38.462 0.00 0.00 0.00 3.68
1603 2226 1.734465 GTGTCACTAAGTCATGCAGCC 59.266 52.381 0.00 0.00 0.00 4.85
1604 2227 2.414481 CTGTGTCACTAAGTCATGCAGC 59.586 50.000 4.27 0.00 0.00 5.25
1724 2348 8.719648 GCTGTGAGGATTGATCTTCAATATAAG 58.280 37.037 7.29 3.33 46.20 1.73
1854 2546 1.741706 CAGATGAATGGTCACAGGTGC 59.258 52.381 0.00 0.00 36.31 5.01
1898 2590 5.163581 GCTGCTGTCCACATTCATTATCTTT 60.164 40.000 0.00 0.00 0.00 2.52
2245 3105 2.168106 TGTGGCTGCTTGTTCAACATTT 59.832 40.909 0.00 0.00 0.00 2.32
2332 3192 3.314541 ACTATATTTTCTAGCCGCCCG 57.685 47.619 0.00 0.00 0.00 6.13
2473 3333 1.896220 TGTTGGCAAGTAAGAGGCAG 58.104 50.000 0.00 0.00 41.52 4.85
2508 3368 7.207383 TGTACCACTTAACTGATCAATATCCG 58.793 38.462 0.00 0.00 0.00 4.18
2515 3375 7.882791 ACATTCATTGTACCACTTAACTGATCA 59.117 33.333 0.00 0.00 36.57 2.92
2544 3404 9.661187 CTTGATCATTAACAGATCTACAAATGC 57.339 33.333 16.41 6.22 41.85 3.56
2588 3499 6.224665 AGAGGAGCTATCTGATATTGCATC 57.775 41.667 10.40 5.11 0.00 3.91
2703 3653 4.036852 CCTTTCTCTGGGACAACAGTTTTC 59.963 45.833 0.00 0.00 38.70 2.29
2733 3683 8.450578 TCTTTGAAACTTGATTGAAAGAGCTA 57.549 30.769 0.00 0.00 30.98 3.32
2972 3929 7.616313 AGATTAATCTTTCTCTCTGAAACGGT 58.384 34.615 12.37 0.00 39.50 4.83
3012 3970 6.404403 CGTCTGAGGTAATGCTTGACTACTTA 60.404 42.308 0.00 0.00 0.00 2.24
3018 3976 2.924290 GTCGTCTGAGGTAATGCTTGAC 59.076 50.000 0.00 0.00 0.00 3.18
3037 3995 4.946784 AGATCGGTATTGCTTGTTTGTC 57.053 40.909 0.00 0.00 0.00 3.18
3069 4027 5.140747 TCTGCTCTTAAGTTTCCTGTCTC 57.859 43.478 1.63 0.00 0.00 3.36
3112 4070 7.787725 TTCTGTTGACTTAAGAACTCCTTTC 57.212 36.000 10.09 0.00 36.34 2.62
3144 4102 3.871485 GATGAACTTGTCAGCTCAGGAT 58.129 45.455 0.00 0.00 39.67 3.24
3304 4262 7.114953 GCAGTGTTAAAATTAGGAAGCAAAGAC 59.885 37.037 0.00 0.00 0.00 3.01
3316 4274 4.643463 TCACCTCGGCAGTGTTAAAATTA 58.357 39.130 0.00 0.00 36.58 1.40
3422 4389 6.777213 TGGTGTAACTTACCAAACAACAAT 57.223 33.333 0.00 0.00 44.79 2.71
3432 4399 8.188139 CCAAATCAACATATGGTGTAACTTACC 58.812 37.037 20.02 0.00 41.14 2.85
3433 4400 8.952278 TCCAAATCAACATATGGTGTAACTTAC 58.048 33.333 20.02 0.00 41.14 2.34
3434 4401 9.173021 CTCCAAATCAACATATGGTGTAACTTA 57.827 33.333 20.02 0.14 41.14 2.24
3449 4416 7.656707 ACATATTTTTGTGCTCCAAATCAAC 57.343 32.000 3.50 0.00 42.45 3.18
3469 4437 9.378551 ACGCAGAAGACAAATCTTAAATACATA 57.621 29.630 0.00 0.00 45.60 2.29
3563 4533 9.751542 ATCATAGCATCAAAGTACTAGTAACAC 57.248 33.333 3.61 0.00 0.00 3.32
3595 4571 8.951787 TGCTGTACAAGAAGAAACTAACTTTA 57.048 30.769 0.00 0.00 0.00 1.85
3706 4684 5.587844 AGAAAGCACATATTAAGCAGGAGTG 59.412 40.000 0.00 0.00 0.00 3.51
3713 4691 5.819901 AGACAGGAGAAAGCACATATTAAGC 59.180 40.000 0.00 0.00 0.00 3.09
3883 4885 1.067821 GAGTTGGGCCTCATCTACTCG 59.932 57.143 4.53 0.00 0.00 4.18
3965 4967 3.523157 TCTCCACCTTTAATGCATCCTCA 59.477 43.478 0.00 0.00 0.00 3.86
4078 5093 8.988934 TCAGAAAACACTTCAATACTGTGTATC 58.011 33.333 0.00 0.00 43.11 2.24
4079 5094 8.902540 TCAGAAAACACTTCAATACTGTGTAT 57.097 30.769 0.00 0.00 43.11 2.29
4080 5095 8.609176 GTTCAGAAAACACTTCAATACTGTGTA 58.391 33.333 0.00 0.00 43.11 2.90
4081 5096 7.336931 AGTTCAGAAAACACTTCAATACTGTGT 59.663 33.333 0.00 0.00 45.42 3.72
4082 5097 7.697691 AGTTCAGAAAACACTTCAATACTGTG 58.302 34.615 0.00 0.00 37.67 3.66
4083 5098 7.865706 AGTTCAGAAAACACTTCAATACTGT 57.134 32.000 0.00 0.00 0.00 3.55
4195 5229 1.521423 CTTCATCCGCGAACGTTATCC 59.479 52.381 8.23 0.00 37.70 2.59
4225 5259 3.407424 ACACATTAACAGAGCAGAGCA 57.593 42.857 0.00 0.00 0.00 4.26
4308 5345 4.624336 TTACAACACAATTGCTTGACGT 57.376 36.364 18.70 10.23 36.20 4.34
4314 5351 9.762933 AAATCAACTTATTACAACACAATTGCT 57.237 25.926 5.05 0.00 0.00 3.91
4321 5358 9.944663 TTGTCAGAAATCAACTTATTACAACAC 57.055 29.630 0.00 0.00 0.00 3.32
4341 5378 7.541091 CCATCTTGTTTGATTCTTCATTGTCAG 59.459 37.037 0.00 0.00 0.00 3.51
4382 5424 3.671008 TCCATCTCTCGTTCGGAAAAA 57.329 42.857 0.00 0.00 0.00 1.94
4383 5425 3.521560 CATCCATCTCTCGTTCGGAAAA 58.478 45.455 0.00 0.00 0.00 2.29
4387 5429 0.598680 GCCATCCATCTCTCGTTCGG 60.599 60.000 0.00 0.00 0.00 4.30
4461 5536 2.621055 AGCCACTTCATAGACTCTAGCG 59.379 50.000 0.00 0.00 0.00 4.26
4696 9016 9.062524 ACTCTTATGTGTTACAGCAAACAAATA 57.937 29.630 5.74 5.74 40.85 1.40
4699 9019 6.238621 CCACTCTTATGTGTTACAGCAAACAA 60.239 38.462 1.46 0.00 40.85 2.83
4700 9020 5.238432 CCACTCTTATGTGTTACAGCAAACA 59.762 40.000 0.00 0.00 37.03 2.83
4731 9051 6.372981 GCATTTTTACTTTCAGCCCAAAATG 58.627 36.000 9.71 9.71 41.43 2.32
4732 9052 5.473162 GGCATTTTTACTTTCAGCCCAAAAT 59.527 36.000 0.00 0.00 34.71 1.82
4733 9053 4.819088 GGCATTTTTACTTTCAGCCCAAAA 59.181 37.500 0.00 0.00 34.71 2.44
4734 9054 4.384940 GGCATTTTTACTTTCAGCCCAAA 58.615 39.130 0.00 0.00 34.71 3.28
4766 9102 4.263435 ACACAAGAAACAAGGTTACGGAA 58.737 39.130 0.00 0.00 0.00 4.30
4767 9103 3.876341 ACACAAGAAACAAGGTTACGGA 58.124 40.909 0.00 0.00 0.00 4.69
4812 9410 7.962964 TTGAATTCAACGAACTAGTCAGAAT 57.037 32.000 16.91 0.00 33.31 2.40
4821 9419 4.097892 AGTGCCTTTTGAATTCAACGAACT 59.902 37.500 20.35 16.25 35.28 3.01
4869 9467 1.822990 CCTCTAACCACTAGCGGACAA 59.177 52.381 3.15 0.00 34.81 3.18
4872 9470 0.627451 TCCCTCTAACCACTAGCGGA 59.373 55.000 3.15 0.00 34.81 5.54
4877 9475 6.442541 TTCATGTTTTCCCTCTAACCACTA 57.557 37.500 0.00 0.00 0.00 2.74
4940 9602 5.480642 TTACATTTGCATGGGTGAACAAT 57.519 34.783 0.00 0.00 34.27 2.71
4943 9605 5.537188 TCTTTTACATTTGCATGGGTGAAC 58.463 37.500 0.00 0.00 34.27 3.18
4954 9616 5.356882 TCGTCTGGCTTCTTTTACATTTG 57.643 39.130 0.00 0.00 0.00 2.32
5018 10077 2.004583 ACCGTCACACATATTCACCG 57.995 50.000 0.00 0.00 0.00 4.94
5032 10091 2.416893 GCTCAGAATCAGGAAAACCGTC 59.583 50.000 0.00 0.00 0.00 4.79
5044 10103 6.264841 ACAAAAATCTCTTGGCTCAGAATC 57.735 37.500 0.00 0.00 0.00 2.52
5053 10112 6.648879 TGGGACTTTACAAAAATCTCTTGG 57.351 37.500 0.00 0.00 0.00 3.61
5069 10130 5.359756 GCTTTTCAAAGTTGATTGGGACTT 58.640 37.500 1.37 0.00 38.28 3.01
5121 10187 7.278868 CCATACACATTTCTAGAAGAACTGGAC 59.721 40.741 5.12 0.00 38.66 4.02
5129 10195 9.294030 GCAATTTTCCATACACATTTCTAGAAG 57.706 33.333 5.12 0.00 0.00 2.85
5187 10255 9.631257 AAATTCAAATCAACCCAGAAAAGAAAT 57.369 25.926 0.00 0.00 0.00 2.17
5237 10309 9.108284 CAGGTTGATTTTGGTTTTCTTACAATT 57.892 29.630 0.00 0.00 0.00 2.32
5239 10311 7.044798 CCAGGTTGATTTTGGTTTTCTTACAA 58.955 34.615 0.00 0.00 0.00 2.41
5253 10325 5.279456 GGTTTGCTTATGTCCAGGTTGATTT 60.279 40.000 0.00 0.00 0.00 2.17
5255 10327 3.763897 GGTTTGCTTATGTCCAGGTTGAT 59.236 43.478 0.00 0.00 0.00 2.57
5271 10343 1.131693 GCGGTTACACATAGGGTTTGC 59.868 52.381 0.00 0.00 0.00 3.68
5287 10359 0.032017 ATTGGGTCTCCTCTAGCGGT 60.032 55.000 0.00 0.00 0.00 5.68
5289 10361 1.339610 CTCATTGGGTCTCCTCTAGCG 59.660 57.143 0.00 0.00 0.00 4.26
5290 10362 2.627699 CTCTCATTGGGTCTCCTCTAGC 59.372 54.545 0.00 0.00 0.00 3.42
5306 10378 0.250038 GTGTGTGCTTGCTCCTCTCA 60.250 55.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.