Multiple sequence alignment - TraesCS2B01G121900

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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 TraesCS2B01G121900 chr2B 100.000 4066 0 0 1 4066 89430206 89434271 0.000000e+00 7509.0
1 TraesCS2B01G121900 chr2B 83.538 650 89 9 2349 2984 89327560 89328205 3.500000e-165 592.0
2 TraesCS2B01G121900 chr2B 83.871 310 39 5 3670 3969 89329022 89329330 6.650000e-73 285.0
3 TraesCS2B01G121900 chr2D 89.696 1349 81 27 1 1340 56444872 56446171 0.000000e+00 1668.0
4 TraesCS2B01G121900 chr2D 85.489 1461 66 56 1823 3256 56298593 56299934 0.000000e+00 1389.0
5 TraesCS2B01G121900 chr2D 92.602 757 44 7 2250 3004 56446924 56447670 0.000000e+00 1077.0
6 TraesCS2B01G121900 chr2D 91.271 779 46 10 561 1339 56297552 56298308 0.000000e+00 1042.0
7 TraesCS2B01G121900 chr2D 87.195 820 67 13 3253 4065 56299975 56300763 0.000000e+00 898.0
8 TraesCS2B01G121900 chr2D 90.958 553 32 8 1 543 56297021 56297565 0.000000e+00 728.0
9 TraesCS2B01G121900 chr2D 82.195 820 115 22 3259 4063 56301721 56302524 0.000000e+00 676.0
10 TraesCS2B01G121900 chr2D 83.994 656 84 10 2349 2984 56255256 56255910 9.660000e-171 610.0
11 TraesCS2B01G121900 chr2D 88.435 441 29 8 3017 3453 56449835 56450257 2.800000e-141 512.0
12 TraesCS2B01G121900 chr2D 92.241 348 23 3 3478 3822 56450399 56450745 1.310000e-134 490.0
13 TraesCS2B01G121900 chr2D 93.173 249 15 1 3818 4066 56456703 56456949 8.310000e-97 364.0
14 TraesCS2B01G121900 chr2D 85.099 302 41 4 3670 3969 56257369 56257668 5.110000e-79 305.0
15 TraesCS2B01G121900 chr2D 90.995 211 16 2 1453 1662 56446216 56446424 8.600000e-72 281.0
16 TraesCS2B01G121900 chr2D 82.812 320 45 5 3651 3969 56323129 56323439 1.110000e-70 278.0
17 TraesCS2B01G121900 chr2D 89.231 195 11 3 2007 2199 56446727 56446913 6.790000e-58 235.0
18 TraesCS2B01G121900 chr2D 93.210 162 1 2 1823 1984 56446420 56446571 3.160000e-56 230.0
19 TraesCS2B01G121900 chr2D 74.419 516 97 21 1030 1523 56253901 56254403 5.370000e-44 189.0
20 TraesCS2B01G121900 chr2D 78.033 305 56 7 1027 1330 56320132 56320426 8.980000e-42 182.0
21 TraesCS2B01G121900 chr2D 81.319 182 19 7 3040 3220 56301465 56301632 2.550000e-27 134.0
22 TraesCS2B01G121900 chr2A 87.757 972 65 20 2314 3257 57890152 57891097 0.000000e+00 1086.0
23 TraesCS2B01G121900 chr2A 89.762 547 39 8 700 1236 57888783 57889322 0.000000e+00 684.0
24 TraesCS2B01G121900 chr2A 83.385 650 93 10 2349 2984 57865528 57866176 4.530000e-164 588.0
25 TraesCS2B01G121900 chr2A 84.058 552 51 10 1 543 57888101 57888624 7.850000e-137 497.0
26 TraesCS2B01G121900 chr2A 92.378 328 24 1 3739 4066 57891647 57891973 2.210000e-127 466.0
27 TraesCS2B01G121900 chr2A 86.640 247 19 3 3253 3493 57891136 57891374 1.120000e-65 261.0
28 TraesCS2B01G121900 chr2A 91.398 186 3 4 1823 2008 57889756 57889928 4.060000e-60 243.0
29 TraesCS2B01G121900 chr2A 93.878 147 7 1 561 705 57888611 57888757 1.900000e-53 220.0
30 TraesCS2B01G121900 chr2A 77.850 307 59 9 1027 1330 57864199 57864499 8.980000e-42 182.0
31 TraesCS2B01G121900 chr2A 91.057 123 4 4 2213 2330 57890014 57890134 4.210000e-35 159.0
32 TraesCS2B01G121900 chr3B 95.213 188 7 2 1661 1848 548082605 548082420 3.070000e-76 296.0
33 TraesCS2B01G121900 chr3B 98.795 166 2 0 1662 1827 810265402 810265567 3.070000e-76 296.0
34 TraesCS2B01G121900 chr3B 96.571 175 6 0 1659 1833 651427719 651427893 1.430000e-74 291.0
35 TraesCS2B01G121900 chr4A 97.661 171 4 0 1661 1831 619191246 619191076 1.110000e-75 294.0
36 TraesCS2B01G121900 chr4A 95.135 185 8 1 1655 1838 586860330 586860514 1.430000e-74 291.0
37 TraesCS2B01G121900 chr4A 95.082 183 7 2 1660 1840 559949215 559949033 1.850000e-73 287.0
38 TraesCS2B01G121900 chr6A 95.082 183 7 2 1654 1835 564683624 564683443 1.850000e-73 287.0
39 TraesCS2B01G121900 chr3A 96.552 174 4 1 1654 1825 217823195 217823368 1.850000e-73 287.0
40 TraesCS2B01G121900 chr5A 92.000 200 7 9 1645 1843 126624461 126624270 5.180000e-69 272.0
41 TraesCS2B01G121900 chr1B 100.000 32 0 0 509 540 635155758 635155789 4.390000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G121900 chr2B 89430206 89434271 4065 False 7509.000000 7509 100.000000 1 4066 1 chr2B.!!$F1 4065
1 TraesCS2B01G121900 chr2B 89327560 89329330 1770 False 438.500000 592 83.704500 2349 3969 2 chr2B.!!$F2 1620
2 TraesCS2B01G121900 chr2D 56297021 56302524 5503 False 811.166667 1389 86.404500 1 4065 6 chr2D.!!$F3 4064
3 TraesCS2B01G121900 chr2D 56444872 56450745 5873 False 641.857143 1668 90.915714 1 3822 7 chr2D.!!$F5 3821
4 TraesCS2B01G121900 chr2D 56253901 56257668 3767 False 368.000000 610 81.170667 1030 3969 3 chr2D.!!$F2 2939
5 TraesCS2B01G121900 chr2D 56320132 56323439 3307 False 230.000000 278 80.422500 1027 3969 2 chr2D.!!$F4 2942
6 TraesCS2B01G121900 chr2A 57888101 57891973 3872 False 452.000000 1086 89.616000 1 4066 8 chr2A.!!$F2 4065
7 TraesCS2B01G121900 chr2A 57864199 57866176 1977 False 385.000000 588 80.617500 1027 2984 2 chr2A.!!$F1 1957

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
970 1035 1.133761 TGAGCACGCCCTACTCTCTAT 60.134 52.381 0.00 0.00 0.00 1.98 F
1332 1406 0.103937 GCTCCAGGAGAAGGTGATCG 59.896 60.000 21.89 0.00 0.00 3.69 F
1375 1449 0.810648 TACCCGTGCAACTACCTACG 59.189 55.000 0.00 0.00 36.39 3.51 F
1376 1450 1.181098 ACCCGTGCAACTACCTACGT 61.181 55.000 0.00 0.00 34.96 3.57 F
1378 1452 1.406539 CCCGTGCAACTACCTACGTAT 59.593 52.381 0.00 0.00 34.96 3.06 F
1528 1725 1.593196 TAGGCGCCAATGATTAGTGC 58.407 50.000 31.54 0.46 36.30 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2492 3556 0.460987 CGCCTTGGATGAGGAGTGAC 60.461 60.000 0.00 0.00 39.25 3.67 R
2907 3995 1.000163 CCCTAACGATCCCGACATGAG 60.000 57.143 0.00 0.00 39.50 2.90 R
3025 6284 1.140161 CCCCATGCATGCAAAGTCG 59.860 57.895 26.68 10.66 0.00 4.18 R
3026 6285 1.406539 CTACCCCATGCATGCAAAGTC 59.593 52.381 26.68 0.00 0.00 3.01 R
3028 6287 1.477553 ACTACCCCATGCATGCAAAG 58.522 50.000 26.68 19.65 0.00 2.77 R
3431 7723 1.494721 TCCTGCTTGTTGAGGTTCCTT 59.505 47.619 0.00 0.00 0.00 3.36 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
65 66 1.337823 GGGAAGCACACGAAAGCTAGA 60.338 52.381 0.00 0.00 40.90 2.43
194 198 7.649306 GTGCAAAAGACCCATAGCTAAATATTG 59.351 37.037 0.00 0.00 0.00 1.90
358 363 2.914059 CGGGATTGGTAAATCTCCGTT 58.086 47.619 14.77 0.00 43.85 4.44
427 432 5.475220 TCTTAAATGGAGATCCGTGCAAAAA 59.525 36.000 0.00 0.00 39.43 1.94
489 502 7.730364 TTAAGATTTTGTCAAGTCTCAGTCC 57.270 36.000 3.80 0.00 28.98 3.85
571 584 4.374843 TTTTGAGGATATGTGTGCATGC 57.625 40.909 11.82 11.82 36.58 4.06
572 585 2.713863 TGAGGATATGTGTGCATGCA 57.286 45.000 18.46 18.46 36.58 3.96
573 586 3.217681 TGAGGATATGTGTGCATGCAT 57.782 42.857 25.64 10.48 36.58 3.96
970 1035 1.133761 TGAGCACGCCCTACTCTCTAT 60.134 52.381 0.00 0.00 0.00 1.98
1107 1172 3.558411 GCGACGCTGCAGACCATC 61.558 66.667 20.43 7.37 34.15 3.51
1201 1269 2.586079 CTATGTCGGTGCTGGGCG 60.586 66.667 0.00 0.00 0.00 6.13
1232 1300 1.300697 GCGGTGTGGAGTCGTCTTT 60.301 57.895 0.00 0.00 0.00 2.52
1245 1316 2.528127 TCTTTGGGGACAGGCCGA 60.528 61.111 0.00 0.00 44.54 5.54
1274 1345 0.547712 CCAGGTGGGAGGAGGAAGAA 60.548 60.000 0.00 0.00 40.01 2.52
1276 1347 1.003696 CAGGTGGGAGGAGGAAGAAAC 59.996 57.143 0.00 0.00 0.00 2.78
1332 1406 0.103937 GCTCCAGGAGAAGGTGATCG 59.896 60.000 21.89 0.00 0.00 3.69
1339 1413 4.563580 CCAGGAGAAGGTGATCGAAGAAAA 60.564 45.833 0.00 0.00 43.58 2.29
1343 1417 5.877564 GGAGAAGGTGATCGAAGAAAATCTT 59.122 40.000 0.00 0.00 43.58 2.40
1344 1418 6.372937 GGAGAAGGTGATCGAAGAAAATCTTT 59.627 38.462 0.00 0.00 43.58 2.52
1346 1420 8.485976 AGAAGGTGATCGAAGAAAATCTTTAG 57.514 34.615 0.00 0.00 43.58 1.85
1347 1421 8.314751 AGAAGGTGATCGAAGAAAATCTTTAGA 58.685 33.333 0.00 0.00 43.58 2.10
1350 1424 6.037281 GGTGATCGAAGAAAATCTTTAGACCC 59.963 42.308 0.00 0.00 43.58 4.46
1352 1426 7.010645 GTGATCGAAGAAAATCTTTAGACCCTC 59.989 40.741 0.00 0.00 43.58 4.30
1356 1430 8.759782 TCGAAGAAAATCTTTAGACCCTCTATT 58.240 33.333 0.00 0.00 36.73 1.73
1368 1442 1.485066 CCCTCTATTACCCGTGCAACT 59.515 52.381 0.00 0.00 31.75 3.16
1371 1445 3.492137 CCTCTATTACCCGTGCAACTACC 60.492 52.174 0.00 0.00 31.75 3.18
1372 1446 3.368248 TCTATTACCCGTGCAACTACCT 58.632 45.455 0.00 0.00 31.75 3.08
1373 1447 4.535781 TCTATTACCCGTGCAACTACCTA 58.464 43.478 0.00 0.00 31.75 3.08
1375 1449 0.810648 TACCCGTGCAACTACCTACG 59.189 55.000 0.00 0.00 36.39 3.51
1376 1450 1.181098 ACCCGTGCAACTACCTACGT 61.181 55.000 0.00 0.00 34.96 3.57
1378 1452 1.406539 CCCGTGCAACTACCTACGTAT 59.593 52.381 0.00 0.00 34.96 3.06
1379 1453 2.618241 CCCGTGCAACTACCTACGTATA 59.382 50.000 0.00 0.00 34.96 1.47
1381 1455 3.294943 CGTGCAACTACCTACGTATAGC 58.705 50.000 0.00 0.00 31.75 2.97
1382 1456 3.003068 CGTGCAACTACCTACGTATAGCT 59.997 47.826 0.00 0.00 31.75 3.32
1383 1457 4.212004 CGTGCAACTACCTACGTATAGCTA 59.788 45.833 0.00 0.00 31.75 3.32
1388 1462 6.402011 GCAACTACCTACGTATAGCTACTAGC 60.402 46.154 0.00 0.00 42.84 3.42
1389 1463 6.352016 ACTACCTACGTATAGCTACTAGCA 57.648 41.667 10.73 0.00 45.56 3.49
1391 1465 7.041107 ACTACCTACGTATAGCTACTAGCATC 58.959 42.308 10.73 0.00 45.56 3.91
1406 1480 7.810759 GCTACTAGCATCTCACTAGAAATAACC 59.189 40.741 2.96 0.00 41.89 2.85
1409 1483 6.552445 AGCATCTCACTAGAAATAACCACT 57.448 37.500 0.00 0.00 34.73 4.00
1410 1484 6.951971 AGCATCTCACTAGAAATAACCACTT 58.048 36.000 0.00 0.00 34.73 3.16
1411 1485 8.079211 AGCATCTCACTAGAAATAACCACTTA 57.921 34.615 0.00 0.00 34.73 2.24
1413 1487 9.331282 GCATCTCACTAGAAATAACCACTTATT 57.669 33.333 0.00 0.00 34.54 1.40
1415 1489 8.718102 TCTCACTAGAAATAACCACTTATTGC 57.282 34.615 0.00 0.00 33.56 3.56
1416 1490 8.318412 TCTCACTAGAAATAACCACTTATTGCA 58.682 33.333 0.00 0.00 33.56 4.08
1418 1516 8.726988 TCACTAGAAATAACCACTTATTGCAAC 58.273 33.333 0.00 0.00 33.56 4.17
1478 1674 7.885297 TCCAACTATCTCTTTTCCAAATTGTG 58.115 34.615 0.00 0.00 0.00 3.33
1493 1689 6.884096 CAAATTGTGCTATTAATTTGGCGA 57.116 33.333 12.27 0.00 44.51 5.54
1511 1708 2.418334 GCGACCTAGTGGGGAACTTTAG 60.418 54.545 0.00 0.00 40.56 1.85
1523 1720 2.427095 GGAACTTTAGGCGCCAATGATT 59.573 45.455 31.54 17.09 0.00 2.57
1528 1725 1.593196 TAGGCGCCAATGATTAGTGC 58.407 50.000 31.54 0.46 36.30 4.40
1542 1739 6.583912 TGATTAGTGCACGAAAAGTATAGC 57.416 37.500 16.50 0.00 0.00 2.97
1554 1751 6.183360 ACGAAAAGTATAGCCTGCTTCTGATA 60.183 38.462 0.00 0.00 0.00 2.15
1556 1753 7.386299 CGAAAAGTATAGCCTGCTTCTGATAAT 59.614 37.037 0.00 0.00 0.00 1.28
1591 1791 5.852229 TCGTTGTTGTTGTTGTCAAAAGTAC 59.148 36.000 0.00 0.00 35.20 2.73
1672 2035 3.274095 GTACTGTAGTACTCCCTCCGT 57.726 52.381 13.51 0.00 45.47 4.69
1673 2036 2.895242 ACTGTAGTACTCCCTCCGTT 57.105 50.000 0.00 0.00 0.00 4.44
1674 2037 2.720915 ACTGTAGTACTCCCTCCGTTC 58.279 52.381 0.00 0.00 0.00 3.95
1675 2038 2.022934 CTGTAGTACTCCCTCCGTTCC 58.977 57.143 0.00 0.00 0.00 3.62
1676 2039 1.637553 TGTAGTACTCCCTCCGTTCCT 59.362 52.381 0.00 0.00 0.00 3.36
1677 2040 2.846206 TGTAGTACTCCCTCCGTTCCTA 59.154 50.000 0.00 0.00 0.00 2.94
1678 2041 3.266772 TGTAGTACTCCCTCCGTTCCTAA 59.733 47.826 0.00 0.00 0.00 2.69
1679 2042 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
1680 2043 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
1681 2044 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
1682 2045 4.892345 AGTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
1683 2046 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
1684 2047 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
1685 2048 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
1686 2049 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
1687 2050 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
1688 2051 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
1689 2052 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
1690 2053 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
1691 2054 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
1692 2055 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
1693 2056 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
1694 2057 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
1695 2058 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
1696 2059 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
1697 2060 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
1698 2061 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
1699 2062 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
1700 2063 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
1702 2065 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
1703 2066 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
1704 2067 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
1705 2068 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
1706 2069 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
1707 2070 6.317789 TGTCTTTCTAGGCATTTCAACAAG 57.682 37.500 0.00 0.00 29.10 3.16
1708 2071 5.827797 TGTCTTTCTAGGCATTTCAACAAGT 59.172 36.000 0.00 0.00 29.10 3.16
1709 2072 6.145535 GTCTTTCTAGGCATTTCAACAAGTG 58.854 40.000 0.00 0.00 0.00 3.16
1710 2073 6.017109 GTCTTTCTAGGCATTTCAACAAGTGA 60.017 38.462 0.00 0.00 0.00 3.41
1711 2074 5.689383 TTCTAGGCATTTCAACAAGTGAC 57.311 39.130 0.00 0.00 35.39 3.67
1712 2075 4.973168 TCTAGGCATTTCAACAAGTGACT 58.027 39.130 0.00 0.00 40.60 3.41
1713 2076 6.109156 TCTAGGCATTTCAACAAGTGACTA 57.891 37.500 0.00 0.00 38.51 2.59
1714 2077 5.932303 TCTAGGCATTTCAACAAGTGACTAC 59.068 40.000 0.00 0.00 38.51 2.73
1715 2078 4.460263 AGGCATTTCAACAAGTGACTACA 58.540 39.130 0.00 0.00 35.84 2.74
1716 2079 5.072741 AGGCATTTCAACAAGTGACTACAT 58.927 37.500 0.00 0.00 35.84 2.29
1717 2080 6.237901 AGGCATTTCAACAAGTGACTACATA 58.762 36.000 0.00 0.00 35.84 2.29
1718 2081 6.149474 AGGCATTTCAACAAGTGACTACATAC 59.851 38.462 0.00 0.00 35.84 2.39
1719 2082 6.314784 GCATTTCAACAAGTGACTACATACC 58.685 40.000 0.00 0.00 35.39 2.73
1720 2083 6.534059 CATTTCAACAAGTGACTACATACCG 58.466 40.000 0.00 0.00 35.39 4.02
1721 2084 5.456548 TTCAACAAGTGACTACATACCGA 57.543 39.130 0.00 0.00 35.39 4.69
1722 2085 5.055642 TCAACAAGTGACTACATACCGAG 57.944 43.478 0.00 0.00 0.00 4.63
1723 2086 3.505464 ACAAGTGACTACATACCGAGC 57.495 47.619 0.00 0.00 0.00 5.03
1724 2087 2.823747 ACAAGTGACTACATACCGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
1725 2088 3.257375 ACAAGTGACTACATACCGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
1726 2089 4.242475 CAAGTGACTACATACCGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
1727 2090 4.530710 AGTGACTACATACCGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
1728 2091 5.086104 AGTGACTACATACCGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
1729 2092 4.870426 AGTGACTACATACCGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
1730 2093 4.868171 GTGACTACATACCGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
1731 2094 5.005779 GTGACTACATACCGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
1732 2095 5.086104 ACTACATACCGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
1733 2096 4.870426 ACTACATACCGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
1734 2097 3.937814 ACATACCGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
1735 2098 4.323417 ACATACCGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
1736 2099 4.943705 ACATACCGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
1737 2100 5.065218 ACATACCGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
1738 2101 3.679389 ACCGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
1739 2102 4.832248 ACCGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
1740 2103 4.631813 ACCGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
1741 2104 4.631377 CCGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
1742 2105 5.446473 CCGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
1816 2179 9.211485 TCTAGAAAAACAAGTATTTAGGAACGG 57.789 33.333 0.00 0.00 0.00 4.44
1817 2180 9.211485 CTAGAAAAACAAGTATTTAGGAACGGA 57.789 33.333 0.00 0.00 0.00 4.69
1818 2181 8.095937 AGAAAAACAAGTATTTAGGAACGGAG 57.904 34.615 0.00 0.00 0.00 4.63
1819 2182 6.812879 AAAACAAGTATTTAGGAACGGAGG 57.187 37.500 0.00 0.00 0.00 4.30
1820 2183 4.482952 ACAAGTATTTAGGAACGGAGGG 57.517 45.455 0.00 0.00 0.00 4.30
1821 2184 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
1822 2185 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
1823 2186 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
1824 2187 5.134725 AGTATTTAGGAACGGAGGGAGTA 57.865 43.478 0.00 0.00 0.00 2.59
1825 2188 5.139001 AGTATTTAGGAACGGAGGGAGTAG 58.861 45.833 0.00 0.00 0.00 2.57
1826 2189 3.463048 TTTAGGAACGGAGGGAGTAGT 57.537 47.619 0.00 0.00 0.00 2.73
1841 2204 9.057089 GGAGGGAGTAGTTGTTAATTAATCATG 57.943 37.037 0.31 0.00 0.00 3.07
1842 2205 9.614792 GAGGGAGTAGTTGTTAATTAATCATGT 57.385 33.333 0.31 0.00 0.00 3.21
1843 2206 9.614792 AGGGAGTAGTTGTTAATTAATCATGTC 57.385 33.333 0.31 0.00 0.00 3.06
1844 2207 9.614792 GGGAGTAGTTGTTAATTAATCATGTCT 57.385 33.333 0.31 0.00 0.00 3.41
1986 2411 5.916661 AGCCCGAGGTACTTACATATATG 57.083 43.478 11.29 11.29 41.55 1.78
2004 2429 8.796475 ACATATATGTCTTTTTCTGTTGTGCTT 58.204 29.630 12.75 0.00 35.87 3.91
2009 2434 5.182950 TGTCTTTTTCTGTTGTGCTTCAAGA 59.817 36.000 0.00 0.00 36.66 3.02
2010 2435 6.092748 GTCTTTTTCTGTTGTGCTTCAAGAA 58.907 36.000 0.00 0.00 36.66 2.52
2014 2439 4.637483 TCTGTTGTGCTTCAAGAAAAGG 57.363 40.909 0.00 0.00 36.66 3.11
2016 2441 3.360867 TGTTGTGCTTCAAGAAAAGGGA 58.639 40.909 0.00 0.00 36.66 4.20
2128 2664 5.724328 TGTCAAAGTATAGCTGAAGAGTGG 58.276 41.667 0.00 0.00 0.00 4.00
2182 2809 4.692228 ACACTTGCCAACTGGTTAATTTG 58.308 39.130 0.00 0.00 37.57 2.32
2183 2810 4.161377 ACACTTGCCAACTGGTTAATTTGT 59.839 37.500 0.00 0.00 37.57 2.83
2190 2817 6.096987 TGCCAACTGGTTAATTTGTTAGTTGA 59.903 34.615 18.75 5.45 44.59 3.18
2191 2818 6.640907 GCCAACTGGTTAATTTGTTAGTTGAG 59.359 38.462 18.75 13.03 44.59 3.02
2192 2819 6.640907 CCAACTGGTTAATTTGTTAGTTGAGC 59.359 38.462 18.75 0.00 44.59 4.26
2193 2820 7.425606 CAACTGGTTAATTTGTTAGTTGAGCT 58.574 34.615 14.84 0.00 44.59 4.09
2195 2822 7.649057 ACTGGTTAATTTGTTAGTTGAGCTTC 58.351 34.615 0.00 0.00 0.00 3.86
2197 2824 8.232913 TGGTTAATTTGTTAGTTGAGCTTCTT 57.767 30.769 0.00 0.00 0.00 2.52
2198 2825 8.691797 TGGTTAATTTGTTAGTTGAGCTTCTTT 58.308 29.630 0.00 0.00 0.00 2.52
2199 2826 9.529325 GGTTAATTTGTTAGTTGAGCTTCTTTT 57.471 29.630 0.00 0.00 0.00 2.27
2474 3538 3.225798 GGCCAGCACACCTGCAAA 61.226 61.111 0.00 0.00 46.97 3.68
2492 3556 4.078516 GACCCCTCCACGTTCCGG 62.079 72.222 0.00 0.00 0.00 5.14
2499 3563 2.048503 CCACGTTCCGGTCACTCC 60.049 66.667 0.00 0.00 0.00 3.85
2559 3623 1.742268 GCTCAAACCTCATCAGCTTCC 59.258 52.381 0.00 0.00 0.00 3.46
2560 3624 2.877300 GCTCAAACCTCATCAGCTTCCA 60.877 50.000 0.00 0.00 0.00 3.53
2662 3738 1.829849 GGTACCTTACTCCCGCTTCTT 59.170 52.381 4.06 0.00 0.00 2.52
2677 3753 2.999355 GCTTCTTCAACTACAGCTCCTG 59.001 50.000 0.00 0.00 37.52 3.86
3025 6284 3.285523 ATGCATGCAACACACGGCC 62.286 57.895 26.68 0.00 32.33 6.13
3028 6287 3.353836 ATGCAACACACGGCCGAC 61.354 61.111 35.90 11.90 0.00 4.79
3108 6376 6.237901 TGTATATTGGGCATGTGGATAGAAC 58.762 40.000 0.00 0.00 0.00 3.01
3109 6377 3.668141 ATTGGGCATGTGGATAGAACA 57.332 42.857 0.00 0.00 0.00 3.18
3110 6378 3.668141 TTGGGCATGTGGATAGAACAT 57.332 42.857 0.00 0.00 38.81 2.71
3111 6379 4.787135 TTGGGCATGTGGATAGAACATA 57.213 40.909 0.00 0.00 36.10 2.29
3112 6380 4.356405 TGGGCATGTGGATAGAACATAG 57.644 45.455 0.00 0.00 36.10 2.23
3113 6381 3.973305 TGGGCATGTGGATAGAACATAGA 59.027 43.478 0.00 0.00 36.10 1.98
3137 6430 8.850156 AGAAGGTAATATGTTTGTATTGGATGC 58.150 33.333 0.00 0.00 0.00 3.91
3140 6433 7.014230 AGGTAATATGTTTGTATTGGATGCCAC 59.986 37.037 0.00 0.00 30.78 5.01
3141 6434 7.014230 GGTAATATGTTTGTATTGGATGCCACT 59.986 37.037 0.00 0.00 30.78 4.00
3154 6451 6.935741 TGGATGCCACTTGTAAACATATAC 57.064 37.500 0.00 0.00 0.00 1.47
3155 6452 6.658849 TGGATGCCACTTGTAAACATATACT 58.341 36.000 0.00 0.00 0.00 2.12
3160 6457 9.760077 ATGCCACTTGTAAACATATACTAGTAC 57.240 33.333 4.31 0.00 38.98 2.73
3162 6459 9.460906 GCCACTTGTAAACATATACTAGTACTC 57.539 37.037 4.31 0.00 38.98 2.59
3163 6460 9.661187 CCACTTGTAAACATATACTAGTACTCG 57.339 37.037 4.31 0.00 38.98 4.18
3164 6461 9.661187 CACTTGTAAACATATACTAGTACTCGG 57.339 37.037 4.31 0.00 38.98 4.63
3165 6462 8.844244 ACTTGTAAACATATACTAGTACTCGGG 58.156 37.037 4.31 0.00 39.15 5.14
3166 6463 8.978874 TTGTAAACATATACTAGTACTCGGGA 57.021 34.615 4.31 0.00 0.00 5.14
3173 6473 3.786368 ACTAGTACTCGGGATAGGGAC 57.214 52.381 0.00 0.00 0.00 4.46
3208 6509 4.682320 GCCTGTACGACCTTGAATTATGGA 60.682 45.833 0.00 0.00 0.00 3.41
3302 7421 9.533253 CAATTGTCTCTTGTCCAAAATAAAAGT 57.467 29.630 0.00 0.00 0.00 2.66
3313 7605 9.565213 TGTCCAAAATAAAAGTTTTGCAATTTG 57.435 25.926 11.18 14.03 44.02 2.32
3339 7631 2.888414 GTTAAACCAAGTGGCAAGCCTA 59.112 45.455 12.96 0.00 39.32 3.93
3344 7636 2.290323 ACCAAGTGGCAAGCCTAGTAAG 60.290 50.000 12.96 0.00 39.32 2.34
3355 7647 5.768317 CAAGCCTAGTAAGCTATCTCAGAC 58.232 45.833 0.00 0.00 40.49 3.51
3358 7650 4.457949 GCCTAGTAAGCTATCTCAGACTCC 59.542 50.000 0.00 0.00 0.00 3.85
3359 7651 4.693566 CCTAGTAAGCTATCTCAGACTCCG 59.306 50.000 0.00 0.00 0.00 4.63
3383 7675 6.144078 AGTCAACAACTTTAATGGTGGAAC 57.856 37.500 10.80 5.87 36.15 3.62
3431 7723 6.928492 GGAAAAGCACAACAAGATTATTTCCA 59.072 34.615 8.21 0.00 41.67 3.53
3455 7748 3.416156 GAACCTCAACAAGCAGGAGAAT 58.584 45.455 0.00 0.00 33.52 2.40
3457 7750 3.416156 ACCTCAACAAGCAGGAGAATTC 58.584 45.455 0.00 0.00 33.52 2.17
3458 7751 3.073650 ACCTCAACAAGCAGGAGAATTCT 59.926 43.478 7.95 7.95 33.52 2.40
3460 7753 5.045286 ACCTCAACAAGCAGGAGAATTCTAT 60.045 40.000 8.25 0.00 33.52 1.98
3461 7754 5.526846 CCTCAACAAGCAGGAGAATTCTATC 59.473 44.000 8.25 4.09 30.32 2.08
3465 7766 5.734720 ACAAGCAGGAGAATTCTATCGAAA 58.265 37.500 8.25 0.00 31.91 3.46
3467 7768 6.314896 ACAAGCAGGAGAATTCTATCGAAAAG 59.685 38.462 8.25 0.00 31.91 2.27
3548 7961 9.502091 ACAAAGAAGTTATGCACTAGTTCAATA 57.498 29.630 15.87 0.00 32.94 1.90
3581 7995 5.010617 ACGGTTATTTCCATGTTTTGCTCTT 59.989 36.000 0.00 0.00 0.00 2.85
3582 7996 5.572896 CGGTTATTTCCATGTTTTGCTCTTC 59.427 40.000 0.00 0.00 0.00 2.87
3605 8019 2.093764 GTGGTCATTCCCTCTCTCACAG 60.094 54.545 0.00 0.00 34.77 3.66
3607 8021 2.569404 GGTCATTCCCTCTCTCACAGTT 59.431 50.000 0.00 0.00 0.00 3.16
3674 8090 3.987220 CGAAAATCGGACCAAAAGCATTT 59.013 39.130 0.00 0.00 36.49 2.32
3686 8102 7.855409 GGACCAAAAGCATTTCAAATTTACAAC 59.145 33.333 0.00 0.00 37.28 3.32
3798 8352 0.675522 ACCCGGTTTGTAGCAATCCG 60.676 55.000 18.84 18.84 40.72 4.18
3814 8368 4.497507 GCAATCCGTTATAGCCTTTCAACC 60.498 45.833 0.00 0.00 0.00 3.77
3828 8382 7.459234 AGCCTTTCAACCAAGTTACTAGTATT 58.541 34.615 2.79 0.00 0.00 1.89
3833 8387 5.941647 TCAACCAAGTTACTAGTATTTGCCC 59.058 40.000 16.53 0.00 0.00 5.36
3842 8396 9.392259 AGTTACTAGTATTTGCCCTTGTTTATC 57.608 33.333 2.79 0.00 0.00 1.75
3852 8406 3.304257 GCCCTTGTTTATCAGATGATGCG 60.304 47.826 5.58 0.00 36.05 4.73
3876 8430 5.705905 GTGTCACTAAGCTAACCCTTGAAAT 59.294 40.000 0.00 0.00 0.00 2.17
3998 8561 5.982356 TGCTTCTAGAGTTATTGTCATGCT 58.018 37.500 0.00 0.00 0.00 3.79
4024 8587 5.125578 ACTTTCCAAGTCTTTCACTCCAAAC 59.874 40.000 0.00 0.00 37.02 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.183046 GGTCTGCCTCGTCTCTGC 59.817 66.667 0.00 0.00 0.00 4.26
49 50 0.390472 GCCTCTAGCTTTCGTGTGCT 60.390 55.000 0.00 0.00 42.67 4.40
65 66 2.045926 CACGCAAAGGGCTAGCCT 60.046 61.111 32.18 16.16 41.67 4.58
140 144 2.912956 AGAAGGGCCAGTTAATGTCTGA 59.087 45.455 6.18 0.00 35.20 3.27
143 147 2.239907 AGGAGAAGGGCCAGTTAATGTC 59.760 50.000 6.18 0.00 0.00 3.06
477 490 3.068024 GGCTAGATCTGGACTGAGACTTG 59.932 52.174 10.75 0.00 0.00 3.16
489 502 3.256879 ACATACGGATGTGGCTAGATCTG 59.743 47.826 13.83 13.67 44.90 2.90
549 562 4.220163 TGCATGCACACATATCCTCAAAAA 59.780 37.500 18.46 0.00 33.67 1.94
550 563 3.762823 TGCATGCACACATATCCTCAAAA 59.237 39.130 18.46 0.00 33.67 2.44
551 564 3.354467 TGCATGCACACATATCCTCAAA 58.646 40.909 18.46 0.00 33.67 2.69
552 565 3.002038 TGCATGCACACATATCCTCAA 57.998 42.857 18.46 0.00 33.67 3.02
553 566 2.713863 TGCATGCACACATATCCTCA 57.286 45.000 18.46 0.00 33.67 3.86
554 567 2.882761 ACATGCATGCACACATATCCTC 59.117 45.455 25.37 0.00 33.67 3.71
555 568 2.940158 ACATGCATGCACACATATCCT 58.060 42.857 25.37 0.00 33.67 3.24
556 569 3.067040 TCAACATGCATGCACACATATCC 59.933 43.478 25.37 0.00 33.67 2.59
557 570 4.295857 TCAACATGCATGCACACATATC 57.704 40.909 25.37 0.00 33.67 1.63
558 571 4.929819 ATCAACATGCATGCACACATAT 57.070 36.364 25.37 11.52 33.67 1.78
559 572 4.276431 CCTATCAACATGCATGCACACATA 59.724 41.667 25.37 13.37 33.67 2.29
560 573 3.067601 CCTATCAACATGCATGCACACAT 59.932 43.478 25.37 12.94 36.79 3.21
561 574 2.424246 CCTATCAACATGCATGCACACA 59.576 45.455 25.37 5.79 0.00 3.72
562 575 2.684374 TCCTATCAACATGCATGCACAC 59.316 45.455 25.37 0.00 0.00 3.82
563 576 3.002038 TCCTATCAACATGCATGCACA 57.998 42.857 25.37 10.43 0.00 4.57
564 577 4.579454 AATCCTATCAACATGCATGCAC 57.421 40.909 25.37 0.00 0.00 4.57
565 578 6.243148 AGATAATCCTATCAACATGCATGCA 58.757 36.000 26.53 25.04 37.05 3.96
566 579 6.754702 AGATAATCCTATCAACATGCATGC 57.245 37.500 26.53 11.82 37.05 4.06
615 631 7.041440 TCCTACAATTTGTTGATGCATATACCG 60.041 37.037 7.45 0.00 0.00 4.02
635 653 8.809066 TGCTAGAACAAAAACTATACTCCTACA 58.191 33.333 0.00 0.00 0.00 2.74
970 1035 1.069204 CTTGCGAGCTATTAGAGGGCA 59.931 52.381 0.00 0.00 0.00 5.36
1146 1211 0.324738 TCATCCCCTTCACGAGCTCT 60.325 55.000 12.85 0.00 0.00 4.09
1213 1281 1.745320 AAAGACGACTCCACACCGCT 61.745 55.000 0.00 0.00 0.00 5.52
1214 1282 1.300697 AAAGACGACTCCACACCGC 60.301 57.895 0.00 0.00 0.00 5.68
1215 1283 0.944311 CCAAAGACGACTCCACACCG 60.944 60.000 0.00 0.00 0.00 4.94
1256 1327 1.003696 GTTTCTTCCTCCTCCCACCTG 59.996 57.143 0.00 0.00 0.00 4.00
1257 1328 1.363246 GTTTCTTCCTCCTCCCACCT 58.637 55.000 0.00 0.00 0.00 4.00
1258 1329 0.328592 GGTTTCTTCCTCCTCCCACC 59.671 60.000 0.00 0.00 0.00 4.61
1259 1330 0.328592 GGGTTTCTTCCTCCTCCCAC 59.671 60.000 0.00 0.00 35.43 4.61
1260 1331 1.198759 CGGGTTTCTTCCTCCTCCCA 61.199 60.000 0.00 0.00 35.08 4.37
1261 1332 1.602771 CGGGTTTCTTCCTCCTCCC 59.397 63.158 0.00 0.00 0.00 4.30
1339 1413 5.539193 CACGGGTAATAGAGGGTCTAAAGAT 59.461 44.000 0.00 0.00 31.96 2.40
1343 1417 2.961062 GCACGGGTAATAGAGGGTCTAA 59.039 50.000 0.00 0.00 31.96 2.10
1344 1418 2.091720 TGCACGGGTAATAGAGGGTCTA 60.092 50.000 0.00 0.00 32.87 2.59
1346 1420 1.117150 TGCACGGGTAATAGAGGGTC 58.883 55.000 0.00 0.00 0.00 4.46
1347 1421 1.208776 GTTGCACGGGTAATAGAGGGT 59.791 52.381 0.00 0.00 0.00 4.34
1350 1424 3.383825 AGGTAGTTGCACGGGTAATAGAG 59.616 47.826 0.00 0.00 0.00 2.43
1352 1426 3.814005 AGGTAGTTGCACGGGTAATAG 57.186 47.619 0.00 0.00 0.00 1.73
1356 1430 0.810648 CGTAGGTAGTTGCACGGGTA 59.189 55.000 0.00 0.00 0.00 3.69
1358 1432 0.810648 TACGTAGGTAGTTGCACGGG 59.189 55.000 0.00 0.00 38.67 5.28
1368 1442 7.093596 TGAGATGCTAGTAGCTATACGTAGGTA 60.094 40.741 22.34 0.00 42.97 3.08
1371 1445 6.814644 AGTGAGATGCTAGTAGCTATACGTAG 59.185 42.308 22.34 0.00 42.97 3.51
1372 1446 6.699366 AGTGAGATGCTAGTAGCTATACGTA 58.301 40.000 22.34 0.00 42.97 3.57
1373 1447 5.553123 AGTGAGATGCTAGTAGCTATACGT 58.447 41.667 22.34 0.00 42.97 3.57
1375 1449 8.780846 TTCTAGTGAGATGCTAGTAGCTATAC 57.219 38.462 22.34 13.54 42.97 1.47
1376 1450 9.967451 ATTTCTAGTGAGATGCTAGTAGCTATA 57.033 33.333 22.34 3.36 42.97 1.31
1378 1452 9.794719 TTATTTCTAGTGAGATGCTAGTAGCTA 57.205 33.333 22.34 9.84 42.97 3.32
1379 1453 8.573035 GTTATTTCTAGTGAGATGCTAGTAGCT 58.427 37.037 22.34 0.00 42.97 3.32
1381 1455 8.851145 TGGTTATTTCTAGTGAGATGCTAGTAG 58.149 37.037 0.00 0.00 37.69 2.57
1382 1456 8.630917 GTGGTTATTTCTAGTGAGATGCTAGTA 58.369 37.037 0.00 0.00 37.69 1.82
1383 1457 7.343316 AGTGGTTATTTCTAGTGAGATGCTAGT 59.657 37.037 0.00 0.00 37.69 2.57
1389 1463 9.331282 GCAATAAGTGGTTATTTCTAGTGAGAT 57.669 33.333 0.00 0.00 36.83 2.75
1391 1465 8.492673 TGCAATAAGTGGTTATTTCTAGTGAG 57.507 34.615 0.00 0.00 36.83 3.51
1426 1524 7.606073 GGAGCCCACAATAATTTGTAAAATTGT 59.394 33.333 7.96 4.39 44.24 2.71
1428 1526 7.917003 AGGAGCCCACAATAATTTGTAAAATT 58.083 30.769 3.66 3.66 44.24 1.82
1433 1531 4.017958 TGGAGGAGCCCACAATAATTTGTA 60.018 41.667 0.00 0.00 39.09 2.41
1444 1542 1.414550 GAGATAGTTGGAGGAGCCCAC 59.585 57.143 0.00 0.00 35.62 4.61
1453 1551 7.523709 GCACAATTTGGAAAAGAGATAGTTGGA 60.524 37.037 0.78 0.00 0.00 3.53
1454 1552 6.587608 GCACAATTTGGAAAAGAGATAGTTGG 59.412 38.462 0.78 0.00 0.00 3.77
1455 1553 7.373493 AGCACAATTTGGAAAAGAGATAGTTG 58.627 34.615 0.78 0.00 0.00 3.16
1478 1674 4.213482 CCACTAGGTCGCCAAATTAATAGC 59.787 45.833 0.00 0.00 0.00 2.97
1493 1689 1.914108 GCCTAAAGTTCCCCACTAGGT 59.086 52.381 0.00 0.00 34.63 3.08
1511 1708 0.248621 GTGCACTAATCATTGGCGCC 60.249 55.000 22.73 22.73 0.00 6.53
1523 1720 4.430007 CAGGCTATACTTTTCGTGCACTA 58.570 43.478 16.19 0.00 0.00 2.74
1528 1725 4.033358 CAGAAGCAGGCTATACTTTTCGTG 59.967 45.833 0.00 0.00 0.00 4.35
1542 1739 4.412796 TGGTCAGATTATCAGAAGCAGG 57.587 45.455 0.00 0.00 0.00 4.85
1554 1751 3.945285 ACAACAACGAACTTGGTCAGATT 59.055 39.130 0.00 0.00 33.66 2.40
1556 1753 2.980568 ACAACAACGAACTTGGTCAGA 58.019 42.857 0.00 0.00 33.66 3.27
1591 1791 6.630444 AGTAATCTTAATTGGCAGCATCTG 57.370 37.500 0.00 0.00 34.12 2.90
1662 2025 3.991683 AGTATTTAGGAACGGAGGGAGT 58.008 45.455 0.00 0.00 0.00 3.85
1663 2026 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
1664 2027 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
1665 2028 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
1666 2029 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
1667 2030 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
1668 2031 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
1669 2032 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
1670 2033 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
1671 2034 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
1672 2035 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
1673 2036 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
1674 2037 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
1676 2039 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
1677 2040 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
1678 2041 8.515414 GTTGAAATGCCTAGAAAGACAAGTATT 58.485 33.333 0.00 0.00 0.00 1.89
1679 2042 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
1680 2043 6.995686 TGTTGAAATGCCTAGAAAGACAAGTA 59.004 34.615 0.00 0.00 0.00 2.24
1681 2044 5.827797 TGTTGAAATGCCTAGAAAGACAAGT 59.172 36.000 0.00 0.00 0.00 3.16
1682 2045 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
1683 2046 6.321181 ACTTGTTGAAATGCCTAGAAAGACAA 59.679 34.615 0.00 0.00 0.00 3.18
1684 2047 5.827797 ACTTGTTGAAATGCCTAGAAAGACA 59.172 36.000 0.00 0.00 0.00 3.41
1685 2048 6.017109 TCACTTGTTGAAATGCCTAGAAAGAC 60.017 38.462 0.00 0.00 0.00 3.01
1686 2049 6.017109 GTCACTTGTTGAAATGCCTAGAAAGA 60.017 38.462 0.00 0.00 35.39 2.52
1687 2050 6.016777 AGTCACTTGTTGAAATGCCTAGAAAG 60.017 38.462 0.00 0.00 35.39 2.62
1688 2051 5.827797 AGTCACTTGTTGAAATGCCTAGAAA 59.172 36.000 0.00 0.00 35.39 2.52
1689 2052 5.376625 AGTCACTTGTTGAAATGCCTAGAA 58.623 37.500 0.00 0.00 35.39 2.10
1690 2053 4.973168 AGTCACTTGTTGAAATGCCTAGA 58.027 39.130 0.00 0.00 35.39 2.43
1691 2054 5.700832 TGTAGTCACTTGTTGAAATGCCTAG 59.299 40.000 0.00 0.00 35.39 3.02
1692 2055 5.616270 TGTAGTCACTTGTTGAAATGCCTA 58.384 37.500 0.00 0.00 35.39 3.93
1693 2056 4.460263 TGTAGTCACTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 35.39 4.75
1694 2057 4.829064 TGTAGTCACTTGTTGAAATGCC 57.171 40.909 0.00 0.00 35.39 4.40
1695 2058 6.314784 GGTATGTAGTCACTTGTTGAAATGC 58.685 40.000 0.00 0.00 35.39 3.56
1696 2059 6.367695 TCGGTATGTAGTCACTTGTTGAAATG 59.632 38.462 0.00 0.00 35.39 2.32
1697 2060 6.460781 TCGGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
1698 2061 5.845103 TCGGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
1699 2062 5.456548 TCGGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
1700 2063 4.617530 GCTCGGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
1701 2064 3.612860 GCTCGGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
1702 2065 3.257375 TGCTCGGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
1703 2066 2.823747 TGCTCGGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
1704 2067 3.503827 TGCTCGGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
1705 2068 4.530710 TTTGCTCGGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
1706 2069 4.530710 TTTTGCTCGGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
1707 2070 4.868171 TCATTTTGCTCGGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
1708 2071 5.079689 TCATTTTGCTCGGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
1709 2072 5.005779 CACTCATTTTGCTCGGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
1710 2073 4.870426 CACTCATTTTGCTCGGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
1711 2074 5.109210 TCACTCATTTTGCTCGGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
1712 2075 5.079689 TCACTCATTTTGCTCGGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
1713 2076 3.937814 TCACTCATTTTGCTCGGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
1714 2077 4.944962 TTCACTCATTTTGCTCGGTATG 57.055 40.909 0.00 0.00 0.00 2.39
1715 2078 5.431765 AGATTCACTCATTTTGCTCGGTAT 58.568 37.500 0.00 0.00 0.00 2.73
1716 2079 4.832248 AGATTCACTCATTTTGCTCGGTA 58.168 39.130 0.00 0.00 0.00 4.02
1717 2080 3.679389 AGATTCACTCATTTTGCTCGGT 58.321 40.909 0.00 0.00 0.00 4.69
1718 2081 4.631377 TGTAGATTCACTCATTTTGCTCGG 59.369 41.667 0.00 0.00 0.00 4.63
1719 2082 5.349817 AGTGTAGATTCACTCATTTTGCTCG 59.650 40.000 0.00 0.00 44.07 5.03
1720 2083 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
1790 2153 9.211485 CCGTTCCTAAATACTTGTTTTTCTAGA 57.789 33.333 0.00 0.00 0.00 2.43
1791 2154 9.211485 TCCGTTCCTAAATACTTGTTTTTCTAG 57.789 33.333 0.00 0.00 0.00 2.43
1792 2155 9.211485 CTCCGTTCCTAAATACTTGTTTTTCTA 57.789 33.333 0.00 0.00 0.00 2.10
1793 2156 7.174426 CCTCCGTTCCTAAATACTTGTTTTTCT 59.826 37.037 0.00 0.00 0.00 2.52
1794 2157 7.303261 CCTCCGTTCCTAAATACTTGTTTTTC 58.697 38.462 0.00 0.00 0.00 2.29
1795 2158 6.208007 CCCTCCGTTCCTAAATACTTGTTTTT 59.792 38.462 0.00 0.00 0.00 1.94
1796 2159 5.708697 CCCTCCGTTCCTAAATACTTGTTTT 59.291 40.000 0.00 0.00 0.00 2.43
1797 2160 5.013391 TCCCTCCGTTCCTAAATACTTGTTT 59.987 40.000 0.00 0.00 0.00 2.83
1798 2161 4.533311 TCCCTCCGTTCCTAAATACTTGTT 59.467 41.667 0.00 0.00 0.00 2.83
1799 2162 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
1800 2163 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
1801 2164 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
1802 2165 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
1803 2166 4.892345 ACTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
1804 2167 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
1805 2168 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
1806 2169 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
1807 2170 3.094572 CAACTACTCCCTCCGTTCCTAA 58.905 50.000 0.00 0.00 0.00 2.69
1808 2171 2.042162 ACAACTACTCCCTCCGTTCCTA 59.958 50.000 0.00 0.00 0.00 2.94
1809 2172 1.203149 ACAACTACTCCCTCCGTTCCT 60.203 52.381 0.00 0.00 0.00 3.36
1810 2173 1.264295 ACAACTACTCCCTCCGTTCC 58.736 55.000 0.00 0.00 0.00 3.62
1811 2174 4.525912 TTAACAACTACTCCCTCCGTTC 57.474 45.455 0.00 0.00 0.00 3.95
1812 2175 5.494390 AATTAACAACTACTCCCTCCGTT 57.506 39.130 0.00 0.00 0.00 4.44
1813 2176 6.610075 TTAATTAACAACTACTCCCTCCGT 57.390 37.500 0.00 0.00 0.00 4.69
1814 2177 7.270047 TGATTAATTAACAACTACTCCCTCCG 58.730 38.462 0.00 0.00 0.00 4.63
1815 2178 9.057089 CATGATTAATTAACAACTACTCCCTCC 57.943 37.037 0.00 0.00 0.00 4.30
1816 2179 9.614792 ACATGATTAATTAACAACTACTCCCTC 57.385 33.333 0.00 0.00 0.00 4.30
1817 2180 9.614792 GACATGATTAATTAACAACTACTCCCT 57.385 33.333 0.00 0.00 0.00 4.20
1818 2181 9.614792 AGACATGATTAATTAACAACTACTCCC 57.385 33.333 0.00 0.00 0.00 4.30
1841 2204 5.066375 TGCCATGCATAACAGATTAACAGAC 59.934 40.000 0.00 0.00 31.71 3.51
1842 2205 5.192176 TGCCATGCATAACAGATTAACAGA 58.808 37.500 0.00 0.00 31.71 3.41
1843 2206 5.503662 TGCCATGCATAACAGATTAACAG 57.496 39.130 0.00 0.00 31.71 3.16
1844 2207 4.338964 CCTGCCATGCATAACAGATTAACA 59.661 41.667 23.16 1.50 38.13 2.41
1845 2208 4.339247 ACCTGCCATGCATAACAGATTAAC 59.661 41.667 23.16 0.00 38.13 2.01
1846 2209 4.535781 ACCTGCCATGCATAACAGATTAA 58.464 39.130 23.16 0.00 38.13 1.40
1847 2210 4.136796 GACCTGCCATGCATAACAGATTA 58.863 43.478 23.16 0.00 38.13 1.75
1848 2211 2.954318 GACCTGCCATGCATAACAGATT 59.046 45.455 23.16 13.10 38.13 2.40
1965 2328 5.418209 AGACATATATGTAAGTACCTCGGGC 59.582 44.000 18.28 1.74 41.95 6.13
1986 2411 5.640732 TCTTGAAGCACAACAGAAAAAGAC 58.359 37.500 0.00 0.00 34.56 3.01
2022 2514 9.696572 ACTTCATAGTTCATACTACCTCAGTTA 57.303 33.333 0.00 0.00 39.59 2.24
2034 2530 7.685398 GCATGAGACCTCACTTCATAGTTCATA 60.685 40.741 0.00 0.00 43.11 2.15
2035 2531 6.580788 CATGAGACCTCACTTCATAGTTCAT 58.419 40.000 1.31 0.00 43.11 2.57
2036 2532 5.625426 GCATGAGACCTCACTTCATAGTTCA 60.625 44.000 0.00 0.00 43.11 3.18
2037 2533 4.808364 GCATGAGACCTCACTTCATAGTTC 59.192 45.833 0.00 0.00 43.11 3.01
2038 2534 4.223700 TGCATGAGACCTCACTTCATAGTT 59.776 41.667 0.00 0.00 43.11 2.24
2039 2535 3.771479 TGCATGAGACCTCACTTCATAGT 59.229 43.478 0.00 0.00 43.11 2.12
2040 2536 4.397481 TGCATGAGACCTCACTTCATAG 57.603 45.455 0.00 0.00 43.11 2.23
2128 2664 9.657121 GCTAGCTTCAACTAATGATTCAATAAC 57.343 33.333 7.70 0.00 38.03 1.89
2241 2889 7.363431 ACAACTAGCTAATCAAAAAGCTCAAC 58.637 34.615 0.00 0.00 45.92 3.18
2331 3210 3.830121 TGGATGTGCCATTGTGCATATA 58.170 40.909 8.54 0.00 42.25 0.86
2492 3556 0.460987 CGCCTTGGATGAGGAGTGAC 60.461 60.000 0.00 0.00 39.25 3.67
2559 3623 2.622629 CGCGCCATTGATCGACTG 59.377 61.111 0.00 0.00 0.00 3.51
2560 3624 2.586079 CCGCGCCATTGATCGACT 60.586 61.111 0.00 0.00 0.00 4.18
2643 3719 2.494870 TGAAGAAGCGGGAGTAAGGTAC 59.505 50.000 0.00 0.00 0.00 3.34
2662 3738 1.888436 CGGCCAGGAGCTGTAGTTGA 61.888 60.000 2.24 0.00 43.46 3.18
2907 3995 1.000163 CCCTAACGATCCCGACATGAG 60.000 57.143 0.00 0.00 39.50 2.90
3025 6284 1.140161 CCCCATGCATGCAAAGTCG 59.860 57.895 26.68 10.66 0.00 4.18
3026 6285 1.406539 CTACCCCATGCATGCAAAGTC 59.593 52.381 26.68 0.00 0.00 3.01
3028 6287 1.477553 ACTACCCCATGCATGCAAAG 58.522 50.000 26.68 19.65 0.00 2.77
3111 6379 8.850156 GCATCCAATACAAACATATTACCTTCT 58.150 33.333 0.00 0.00 0.00 2.85
3112 6380 8.082242 GGCATCCAATACAAACATATTACCTTC 58.918 37.037 0.00 0.00 0.00 3.46
3113 6381 7.563188 TGGCATCCAATACAAACATATTACCTT 59.437 33.333 0.00 0.00 0.00 3.50
3137 6430 9.661187 CGAGTACTAGTATATGTTTACAAGTGG 57.339 37.037 5.75 0.00 0.00 4.00
3140 6433 9.060347 TCCCGAGTACTAGTATATGTTTACAAG 57.940 37.037 5.75 0.00 0.00 3.16
3141 6434 8.978874 TCCCGAGTACTAGTATATGTTTACAA 57.021 34.615 5.75 0.00 0.00 2.41
3154 6451 5.045724 ACATAGTCCCTATCCCGAGTACTAG 60.046 48.000 0.00 0.00 0.00 2.57
3155 6452 4.848660 ACATAGTCCCTATCCCGAGTACTA 59.151 45.833 0.00 0.00 0.00 1.82
3160 6457 4.664392 ACTTACATAGTCCCTATCCCGAG 58.336 47.826 0.00 0.00 28.23 4.63
3162 6459 5.539048 CAAACTTACATAGTCCCTATCCCG 58.461 45.833 0.00 0.00 35.54 5.14
3163 6460 5.306394 GCAAACTTACATAGTCCCTATCCC 58.694 45.833 0.00 0.00 35.54 3.85
3164 6461 5.071923 AGGCAAACTTACATAGTCCCTATCC 59.928 44.000 0.00 0.00 35.54 2.59
3165 6462 5.992217 CAGGCAAACTTACATAGTCCCTATC 59.008 44.000 0.00 0.00 35.54 2.08
3166 6463 5.428783 ACAGGCAAACTTACATAGTCCCTAT 59.571 40.000 0.00 0.00 35.54 2.57
3173 6473 4.565564 GGTCGTACAGGCAAACTTACATAG 59.434 45.833 0.00 0.00 0.00 2.23
3233 6548 9.503427 GTGCAAGGTGATAAAACATTCTAATAC 57.497 33.333 0.00 0.00 0.00 1.89
3302 7421 9.994432 CTTGGTTTAACAATACAAATTGCAAAA 57.006 25.926 1.71 0.00 45.41 2.44
3313 7605 4.684242 GCTTGCCACTTGGTTTAACAATAC 59.316 41.667 0.00 0.00 37.57 1.89
3339 7631 4.141574 ACTCGGAGTCTGAGATAGCTTACT 60.142 45.833 31.45 6.56 36.93 2.24
3344 7636 2.566913 TGACTCGGAGTCTGAGATAGC 58.433 52.381 31.45 18.24 45.27 2.97
3355 7647 4.755123 ACCATTAAAGTTGTTGACTCGGAG 59.245 41.667 2.83 2.83 37.72 4.63
3358 7650 4.513692 TCCACCATTAAAGTTGTTGACTCG 59.486 41.667 0.00 0.00 37.72 4.18
3359 7651 6.206498 GTTCCACCATTAAAGTTGTTGACTC 58.794 40.000 0.00 0.00 37.72 3.36
3431 7723 1.494721 TCCTGCTTGTTGAGGTTCCTT 59.505 47.619 0.00 0.00 0.00 3.36
3455 7748 7.996098 AAGGTGATTTTCCTTTTCGATAGAA 57.004 32.000 0.00 0.00 44.10 2.10
3460 7753 8.231837 CGTAAATAAGGTGATTTTCCTTTTCGA 58.768 33.333 2.56 0.00 41.86 3.71
3461 7754 8.231837 TCGTAAATAAGGTGATTTTCCTTTTCG 58.768 33.333 2.56 0.00 41.86 3.46
3465 7766 7.989416 TGTCGTAAATAAGGTGATTTTCCTT 57.011 32.000 2.81 2.81 45.72 3.36
3467 7768 9.465985 TTTTTGTCGTAAATAAGGTGATTTTCC 57.534 29.630 0.00 0.00 31.51 3.13
3485 7896 5.163953 ACGAATATCACTGCTCTTTTTGTCG 60.164 40.000 0.00 0.00 0.00 4.35
3548 7961 8.519799 AACATGGAAATAACCGTCTTCATTAT 57.480 30.769 0.00 0.00 0.00 1.28
3581 7995 0.041238 AGAGAGGGAATGACCACCGA 59.959 55.000 0.00 0.00 41.20 4.69
3582 7996 0.461961 GAGAGAGGGAATGACCACCG 59.538 60.000 0.00 0.00 41.20 4.94
3643 8058 4.571919 TGGTCCGATTTTCGTTACAGAAT 58.428 39.130 0.00 0.00 38.40 2.40
3653 8068 4.987912 TGAAATGCTTTTGGTCCGATTTTC 59.012 37.500 1.76 0.00 0.00 2.29
3757 8310 2.877786 TGTACTGTCAAACCATGTGCAG 59.122 45.455 0.00 0.00 38.30 4.41
3798 8352 7.683437 AGTAACTTGGTTGAAAGGCTATAAC 57.317 36.000 0.00 0.00 0.00 1.89
3814 8368 7.448748 AACAAGGGCAAATACTAGTAACTTG 57.551 36.000 17.67 17.67 38.85 3.16
3828 8382 4.098349 GCATCATCTGATAAACAAGGGCAA 59.902 41.667 0.00 0.00 32.63 4.52
3833 8387 5.063817 TGACACGCATCATCTGATAAACAAG 59.936 40.000 0.00 0.00 32.63 3.16
3842 8396 2.283617 GCTTAGTGACACGCATCATCTG 59.716 50.000 0.00 0.00 0.00 2.90
3852 8406 4.267349 TCAAGGGTTAGCTTAGTGACAC 57.733 45.455 0.00 0.00 0.00 3.67
3876 8430 1.667236 CTTGTGTGGCAGTGTCTTGA 58.333 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.