Multiple sequence alignment - TraesCS3B01G470900

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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 TraesCS3B01G470900 chr3B 100.000 3373 0 0 1 3373 719422893 719419521 0.000000e+00 6229
1 TraesCS3B01G470900 chr3B 96.429 168 5 1 1651 1817 602591116 602591283 3.320000e-70 276
2 TraesCS3B01G470900 chr3D 95.099 1408 42 12 1 1395 543768142 543766749 0.000000e+00 2193
3 TraesCS3B01G470900 chr3D 89.836 1220 47 18 2185 3373 543766559 543765386 0.000000e+00 1495
4 TraesCS3B01G470900 chr3D 95.833 168 7 0 2013 2180 543766759 543766592 4.290000e-69 272
5 TraesCS3B01G470900 chr3A 93.030 990 40 9 676 1656 680732395 680731426 0.000000e+00 1419
6 TraesCS3B01G470900 chr3A 89.453 1005 40 22 2185 3167 680728915 680727955 0.000000e+00 1208
7 TraesCS3B01G470900 chr3A 94.603 630 26 4 1 623 680733021 680732393 0.000000e+00 968
8 TraesCS3B01G470900 chr3A 86.769 325 16 5 1814 2112 680731427 680731104 1.500000e-88 337
9 TraesCS3B01G470900 chr3A 92.308 208 9 5 3170 3373 680727531 680727327 4.260000e-74 289
10 TraesCS3B01G470900 chr3A 95.858 169 6 1 1651 1818 581269292 581269124 4.290000e-69 272
11 TraesCS3B01G470900 chr3A 94.767 172 7 2 1648 1818 478426325 478426495 2.000000e-67 267
12 TraesCS3B01G470900 chr3A 93.750 80 4 1 2101 2180 680729057 680728979 5.910000e-23 119
13 TraesCS3B01G470900 chr3A 91.892 74 3 3 636 708 680732411 680732482 2.140000e-17 100
14 TraesCS3B01G470900 chr4D 87.704 1228 79 22 2187 3373 426853036 426854232 0.000000e+00 1365
15 TraesCS3B01G470900 chr4D 89.721 1041 76 22 636 1656 426851606 426852635 0.000000e+00 1301
16 TraesCS3B01G470900 chr4D 96.364 165 5 1 1652 1815 230542714 230542550 1.540000e-68 270
17 TraesCS3B01G470900 chr4D 87.342 158 15 2 1814 1970 426852634 426852787 3.460000e-40 176
18 TraesCS3B01G470900 chr4B 89.317 1039 77 24 636 1656 522522399 522523421 0.000000e+00 1273
19 TraesCS3B01G470900 chr4B 88.215 577 41 9 2447 2998 522532916 522533490 0.000000e+00 664
20 TraesCS3B01G470900 chr4B 89.460 389 25 6 2987 3369 522533595 522533973 8.470000e-131 477
21 TraesCS3B01G470900 chr4B 89.199 287 26 3 189 474 474384385 474384103 1.490000e-93 353
22 TraesCS3B01G470900 chr4B 91.379 232 18 1 2182 2413 522532688 522532917 1.950000e-82 316
23 TraesCS3B01G470900 chr4B 96.933 163 4 1 1655 1816 63754002 63753840 4.290000e-69 272
24 TraesCS3B01G470900 chr4A 91.727 822 45 9 849 1656 38696121 38695309 0.000000e+00 1120
25 TraesCS3B01G470900 chr4A 87.602 984 71 24 1814 2753 38695310 38694334 0.000000e+00 1094
26 TraesCS3B01G470900 chr4A 91.014 345 17 4 2877 3208 38694337 38693994 1.430000e-123 453
27 TraesCS3B01G470900 chr4A 91.438 292 18 3 1 287 154317931 154317642 8.770000e-106 394
28 TraesCS3B01G470900 chr2D 94.483 435 18 2 1 430 74518592 74518159 0.000000e+00 665
29 TraesCS3B01G470900 chr2D 94.483 435 17 3 1 430 31398078 31398510 0.000000e+00 664
30 TraesCS3B01G470900 chr2D 93.563 435 21 3 1 430 9184806 9184374 2.840000e-180 641
31 TraesCS3B01G470900 chr6D 91.358 243 16 1 1 238 319288979 319289221 9.020000e-86 327
32 TraesCS3B01G470900 chr6A 89.754 244 18 3 1 238 457094202 457094444 4.230000e-79 305
33 TraesCS3B01G470900 chr6B 96.970 165 4 1 1655 1818 699977610 699977446 3.320000e-70 276
34 TraesCS3B01G470900 chr5D 94.318 176 7 3 1654 1827 296949520 296949346 2.000000e-67 267
35 TraesCS3B01G470900 chr2A 94.767 172 7 2 1648 1818 573679164 573679334 2.000000e-67 267
36 TraesCS3B01G470900 chr1D 92.350 183 10 3 1648 1827 332216308 332216489 1.200000e-64 257
37 TraesCS3B01G470900 chr2B 83.784 259 19 12 1 238 197992827 197992571 1.220000e-54 224


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 TraesCS3B01G470900 chr3B 719419521 719422893 3372 True 6229.000000 6229 100.000000 1 3373 1 chr3B.!!$R1 3372
1 TraesCS3B01G470900 chr3D 543765386 543768142 2756 True 1320.000000 2193 93.589333 1 3373 3 chr3D.!!$R1 3372
2 TraesCS3B01G470900 chr3A 680727327 680733021 5694 True 723.333333 1419 91.652167 1 3373 6 chr3A.!!$R2 3372
3 TraesCS3B01G470900 chr4D 426851606 426854232 2626 False 947.333333 1365 88.255667 636 3373 3 chr4D.!!$F1 2737
4 TraesCS3B01G470900 chr4B 522522399 522523421 1022 False 1273.000000 1273 89.317000 636 1656 1 chr4B.!!$F1 1020
5 TraesCS3B01G470900 chr4B 522532688 522533973 1285 False 485.666667 664 89.684667 2182 3369 3 chr4B.!!$F2 1187
6 TraesCS3B01G470900 chr4A 38693994 38696121 2127 True 889.000000 1120 90.114333 849 3208 3 chr4A.!!$R2 2359

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
92 94 0.038166 GCAAGGTCCCTGGATGACAA 59.962 55.0 0.00 0.00 34.36 3.18 F
1330 1366 0.322975 TGTCTGCAGAAGGGCTTCTC 59.677 55.0 20.19 2.87 46.13 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 1847 2.203584 TCTACTACTCCCTCCGTTCCT 58.796 52.381 0.0 0.0 0.0 3.36 R
2570 4787 0.602905 AGGCTTTGAAACCCGTCTCG 60.603 55.000 0.0 0.0 0.0 4.04 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
46 48 9.282247 GTTCAGTTTTATCTGTCAGCATAAATG 57.718 33.333 13.55 11.33 36.85 2.32
55 57 6.417258 TCTGTCAGCATAAATGAAAGATCCA 58.583 36.000 0.00 0.00 36.35 3.41
92 94 0.038166 GCAAGGTCCCTGGATGACAA 59.962 55.000 0.00 0.00 34.36 3.18
213 220 4.207891 TGGTTCCTTCTTCAGTATGCTC 57.792 45.455 0.00 0.00 34.76 4.26
249 256 5.756347 CCATCCATAAATTTGCAACTGATGG 59.244 40.000 18.13 18.13 40.34 3.51
276 283 7.985184 AGAACTCATTGTACACTTGTAACTTGA 59.015 33.333 0.00 0.00 31.52 3.02
343 350 9.118300 CATCCATCTATTTGCTTTTTCTAGAGT 57.882 33.333 0.00 0.00 0.00 3.24
377 384 3.387699 TCAGTCACCATTTGTCACTGAGA 59.612 43.478 0.00 0.00 38.81 3.27
456 464 5.722021 TGTGCAACTCTGACACTCTAATA 57.278 39.130 0.00 0.00 38.04 0.98
459 467 8.011844 TGTGCAACTCTGACACTCTAATATAT 57.988 34.615 0.00 0.00 38.04 0.86
691 707 9.342308 AGTCTAATTAATTGGGTGTGACATATG 57.658 33.333 11.05 0.00 0.00 1.78
700 716 7.669089 TTGGGTGTGACATATGTATCTCTAA 57.331 36.000 8.71 0.06 0.00 2.10
807 830 9.185680 ACTGTTCAAAATTTAGTACTGGTTCTT 57.814 29.630 5.39 0.00 0.00 2.52
826 850 4.689062 TCTTGTCTATTTCTGGACCCTCT 58.311 43.478 0.00 0.00 32.19 3.69
911 936 3.195396 TCAGCCAAATAATTTGCAGGGAC 59.805 43.478 0.00 0.00 39.31 4.46
944 971 2.103153 TCTTCTGTCAAGAGGGGTGT 57.897 50.000 0.00 0.00 32.79 4.16
963 990 3.657537 GTGTTCGCACATTTCCTCG 57.342 52.632 0.00 0.00 46.85 4.63
1052 1079 2.488153 GGTGCAACATCTTGACTAACCC 59.512 50.000 0.00 0.00 39.98 4.11
1235 1265 3.054361 TGTTAAGAAGGAATCTCAGGGGC 60.054 47.826 0.00 0.00 37.42 5.80
1238 1268 1.493871 AGAAGGAATCTCAGGGGCATG 59.506 52.381 0.00 0.00 30.46 4.06
1261 1291 5.120674 TGTCTTCAGTAATCAATTGCTGTCG 59.879 40.000 16.91 11.03 46.34 4.35
1330 1366 0.322975 TGTCTGCAGAAGGGCTTCTC 59.677 55.000 20.19 2.87 46.13 2.87
1356 1395 1.200020 GGTACATTGTTGGTGCTGCTC 59.800 52.381 0.00 0.00 0.00 4.26
1627 1672 7.988028 ACTTGTTTCTCTATACTGATTAAGCCC 59.012 37.037 0.00 0.00 0.00 5.19
1646 1694 9.990360 TTAAGCCCTTTTATTTTAAAGTTGGAG 57.010 29.630 0.00 0.00 34.11 3.86
1660 1708 9.511272 TTTAAAGTTGGAGAAATAACTACTCCC 57.489 33.333 0.00 0.00 46.57 4.30
1661 1709 6.954352 AAGTTGGAGAAATAACTACTCCCT 57.046 37.500 0.00 0.00 46.57 4.20
1662 1710 6.547930 AGTTGGAGAAATAACTACTCCCTC 57.452 41.667 0.00 0.00 46.57 4.30
1663 1711 5.425862 AGTTGGAGAAATAACTACTCCCTCC 59.574 44.000 0.00 0.00 46.57 4.30
1664 1712 3.958798 TGGAGAAATAACTACTCCCTCCG 59.041 47.826 0.00 0.00 46.57 4.63
1665 1713 3.959449 GGAGAAATAACTACTCCCTCCGT 59.041 47.826 0.00 0.00 42.84 4.69
1666 1714 4.405036 GGAGAAATAACTACTCCCTCCGTT 59.595 45.833 0.00 0.00 42.84 4.44
1667 1715 5.451659 GGAGAAATAACTACTCCCTCCGTTC 60.452 48.000 0.00 0.00 42.84 3.95
1668 1716 4.405036 AGAAATAACTACTCCCTCCGTTCC 59.595 45.833 0.00 0.00 0.00 3.62
1669 1717 2.905415 TAACTACTCCCTCCGTTCCA 57.095 50.000 0.00 0.00 0.00 3.53
1670 1718 2.019807 AACTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
1671 1719 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
1672 1720 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
1673 1721 3.716431 ACTACTCCCTCCGTTCCAAATA 58.284 45.455 0.00 0.00 0.00 1.40
1674 1722 4.296056 ACTACTCCCTCCGTTCCAAATAT 58.704 43.478 0.00 0.00 0.00 1.28
1675 1723 5.461327 ACTACTCCCTCCGTTCCAAATATA 58.539 41.667 0.00 0.00 0.00 0.86
1676 1724 5.901276 ACTACTCCCTCCGTTCCAAATATAA 59.099 40.000 0.00 0.00 0.00 0.98
1677 1725 5.291905 ACTCCCTCCGTTCCAAATATAAG 57.708 43.478 0.00 0.00 0.00 1.73
1678 1726 4.720273 ACTCCCTCCGTTCCAAATATAAGT 59.280 41.667 0.00 0.00 0.00 2.24
1679 1727 5.163332 ACTCCCTCCGTTCCAAATATAAGTC 60.163 44.000 0.00 0.00 0.00 3.01
1680 1728 4.966805 TCCCTCCGTTCCAAATATAAGTCT 59.033 41.667 0.00 0.00 0.00 3.24
1681 1729 5.427481 TCCCTCCGTTCCAAATATAAGTCTT 59.573 40.000 0.00 0.00 0.00 3.01
1682 1730 6.069847 TCCCTCCGTTCCAAATATAAGTCTTT 60.070 38.462 0.00 0.00 0.00 2.52
1683 1731 6.038271 CCCTCCGTTCCAAATATAAGTCTTTG 59.962 42.308 0.00 0.00 33.20 2.77
1684 1732 6.598064 CCTCCGTTCCAAATATAAGTCTTTGT 59.402 38.462 0.00 0.00 31.83 2.83
1685 1733 7.767198 CCTCCGTTCCAAATATAAGTCTTTGTA 59.233 37.037 0.00 0.00 31.83 2.41
1686 1734 8.712285 TCCGTTCCAAATATAAGTCTTTGTAG 57.288 34.615 0.00 0.00 31.83 2.74
1687 1735 8.533657 TCCGTTCCAAATATAAGTCTTTGTAGA 58.466 33.333 0.00 0.00 31.83 2.59
1688 1736 8.818057 CCGTTCCAAATATAAGTCTTTGTAGAG 58.182 37.037 0.00 0.00 31.83 2.43
1689 1737 9.582431 CGTTCCAAATATAAGTCTTTGTAGAGA 57.418 33.333 0.00 0.00 31.83 3.10
1701 1749 8.367660 AGTCTTTGTAGAGATTTCACTATGGA 57.632 34.615 0.00 0.00 0.00 3.41
1702 1750 8.254508 AGTCTTTGTAGAGATTTCACTATGGAC 58.745 37.037 0.00 0.00 0.00 4.02
1703 1751 8.254508 GTCTTTGTAGAGATTTCACTATGGACT 58.745 37.037 0.00 0.00 0.00 3.85
1704 1752 9.475620 TCTTTGTAGAGATTTCACTATGGACTA 57.524 33.333 0.00 0.00 0.00 2.59
1705 1753 9.522804 CTTTGTAGAGATTTCACTATGGACTAC 57.477 37.037 0.00 0.00 0.00 2.73
1706 1754 8.589701 TTGTAGAGATTTCACTATGGACTACA 57.410 34.615 0.00 0.00 36.83 2.74
1707 1755 8.768501 TGTAGAGATTTCACTATGGACTACAT 57.231 34.615 0.00 0.00 43.68 2.29
1708 1756 9.862149 TGTAGAGATTTCACTATGGACTACATA 57.138 33.333 0.00 0.00 41.03 2.29
1710 1758 7.877003 AGAGATTTCACTATGGACTACATACG 58.123 38.462 0.00 0.00 41.03 3.06
1711 1759 6.982852 AGATTTCACTATGGACTACATACGG 58.017 40.000 0.00 0.00 41.03 4.02
1712 1760 6.776116 AGATTTCACTATGGACTACATACGGA 59.224 38.462 0.00 0.00 41.03 4.69
1713 1761 6.387041 TTTCACTATGGACTACATACGGAG 57.613 41.667 0.00 0.00 41.03 4.63
1714 1762 3.819337 TCACTATGGACTACATACGGAGC 59.181 47.826 0.00 0.00 41.03 4.70
1715 1763 3.568430 CACTATGGACTACATACGGAGCA 59.432 47.826 0.00 0.00 41.03 4.26
1716 1764 4.037565 CACTATGGACTACATACGGAGCAA 59.962 45.833 0.00 0.00 41.03 3.91
1717 1765 4.647853 ACTATGGACTACATACGGAGCAAA 59.352 41.667 0.00 0.00 41.03 3.68
1718 1766 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
1719 1767 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
1720 1768 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
1721 1769 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
1722 1770 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
1723 1771 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
1724 1772 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
1725 1773 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
1726 1774 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
1727 1775 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
1728 1776 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
1729 1777 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
1730 1778 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
1731 1779 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
1732 1780 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
1733 1781 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
1746 1794 8.430801 AGTGAATCTACACTCTAAAATGCATC 57.569 34.615 0.00 0.00 46.36 3.91
1747 1795 8.263640 AGTGAATCTACACTCTAAAATGCATCT 58.736 33.333 0.00 0.00 46.36 2.90
1748 1796 9.534565 GTGAATCTACACTCTAAAATGCATCTA 57.465 33.333 0.00 0.00 37.73 1.98
1749 1797 9.534565 TGAATCTACACTCTAAAATGCATCTAC 57.465 33.333 0.00 0.00 0.00 2.59
1750 1798 9.534565 GAATCTACACTCTAAAATGCATCTACA 57.465 33.333 0.00 0.00 0.00 2.74
1753 1801 9.967346 TCTACACTCTAAAATGCATCTACATAC 57.033 33.333 0.00 0.00 0.00 2.39
1754 1802 9.750125 CTACACTCTAAAATGCATCTACATACA 57.250 33.333 0.00 0.00 0.00 2.29
1756 1804 9.265901 ACACTCTAAAATGCATCTACATACATC 57.734 33.333 0.00 0.00 0.00 3.06
1757 1805 9.486497 CACTCTAAAATGCATCTACATACATCT 57.514 33.333 0.00 0.00 0.00 2.90
1758 1806 9.486497 ACTCTAAAATGCATCTACATACATCTG 57.514 33.333 0.00 0.00 0.00 2.90
1759 1807 9.486497 CTCTAAAATGCATCTACATACATCTGT 57.514 33.333 0.00 0.00 0.00 3.41
1776 1824 7.898014 ACATCTGTATGTGGTTCATAGTAGA 57.102 36.000 0.00 0.00 44.79 2.59
1777 1825 8.306313 ACATCTGTATGTGGTTCATAGTAGAA 57.694 34.615 0.00 0.00 44.79 2.10
1778 1826 8.928448 ACATCTGTATGTGGTTCATAGTAGAAT 58.072 33.333 0.00 0.00 44.79 2.40
1779 1827 9.416794 CATCTGTATGTGGTTCATAGTAGAATC 57.583 37.037 0.00 0.00 39.36 2.52
1780 1828 8.768501 TCTGTATGTGGTTCATAGTAGAATCT 57.231 34.615 0.00 0.00 39.36 2.40
1781 1829 8.851145 TCTGTATGTGGTTCATAGTAGAATCTC 58.149 37.037 0.00 0.00 39.36 2.75
1782 1830 8.768501 TGTATGTGGTTCATAGTAGAATCTCT 57.231 34.615 0.00 0.00 39.36 3.10
1783 1831 8.851145 TGTATGTGGTTCATAGTAGAATCTCTC 58.149 37.037 0.00 0.00 39.36 3.20
1784 1832 6.716934 TGTGGTTCATAGTAGAATCTCTCC 57.283 41.667 0.00 0.00 29.96 3.71
1785 1833 6.194967 TGTGGTTCATAGTAGAATCTCTCCA 58.805 40.000 0.00 0.00 29.96 3.86
1786 1834 6.667848 TGTGGTTCATAGTAGAATCTCTCCAA 59.332 38.462 0.00 0.00 29.96 3.53
1787 1835 7.180229 TGTGGTTCATAGTAGAATCTCTCCAAA 59.820 37.037 0.00 0.00 29.96 3.28
1788 1836 7.708752 GTGGTTCATAGTAGAATCTCTCCAAAG 59.291 40.741 0.00 0.00 29.96 2.77
1789 1837 7.619698 TGGTTCATAGTAGAATCTCTCCAAAGA 59.380 37.037 0.00 0.00 29.96 2.52
1790 1838 7.923878 GGTTCATAGTAGAATCTCTCCAAAGAC 59.076 40.741 0.00 0.00 0.00 3.01
1791 1839 8.691797 GTTCATAGTAGAATCTCTCCAAAGACT 58.308 37.037 0.00 0.00 0.00 3.24
1792 1840 8.830915 TCATAGTAGAATCTCTCCAAAGACTT 57.169 34.615 0.00 0.00 0.00 3.01
1793 1841 9.922477 TCATAGTAGAATCTCTCCAAAGACTTA 57.078 33.333 0.00 0.00 0.00 2.24
1805 1853 9.250624 CTCTCCAAAGACTTATATTTAGGAACG 57.749 37.037 0.00 0.00 0.00 3.95
1806 1854 8.202137 TCTCCAAAGACTTATATTTAGGAACGG 58.798 37.037 0.00 0.00 0.00 4.44
1807 1855 8.081517 TCCAAAGACTTATATTTAGGAACGGA 57.918 34.615 0.00 0.00 0.00 4.69
1808 1856 8.202137 TCCAAAGACTTATATTTAGGAACGGAG 58.798 37.037 0.00 0.00 0.00 4.63
1809 1857 7.441458 CCAAAGACTTATATTTAGGAACGGAGG 59.559 40.741 0.00 0.00 0.00 4.30
1810 1858 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
1811 1859 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
1812 1860 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
1823 1871 4.761227 GGAACGGAGGGAGTAGTAGAATAG 59.239 50.000 0.00 0.00 0.00 1.73
1844 1892 8.482852 AATAGCATTCTTTGGTAATATGGCTT 57.517 30.769 0.00 0.00 41.39 4.35
1930 1978 9.515226 AATTCTTAACTTGAATTGGTAGCAGTA 57.485 29.630 0.00 0.00 41.06 2.74
1982 2066 3.356529 AACATTTGTTTGGGGTTTGCA 57.643 38.095 0.00 0.00 33.93 4.08
1984 2068 3.895998 ACATTTGTTTGGGGTTTGCATT 58.104 36.364 0.00 0.00 0.00 3.56
1986 2070 4.708909 ACATTTGTTTGGGGTTTGCATTTT 59.291 33.333 0.00 0.00 0.00 1.82
2044 2128 2.526304 TCTCACGCAGCTTTTGTACT 57.474 45.000 0.00 0.00 0.00 2.73
2048 2132 2.055838 CACGCAGCTTTTGTACTACGA 58.944 47.619 0.00 0.00 0.00 3.43
2180 4330 7.839705 TGATTCCTAAGAGAAGCCTACTTTCTA 59.160 37.037 0.00 0.00 35.82 2.10
2183 4392 9.710818 TTCCTAAGAGAAGCCTACTTTCTATAA 57.289 33.333 0.00 0.00 35.82 0.98
2216 4425 6.551736 TGAAGCGCTTATTTAGTCCATTTTC 58.448 36.000 25.11 5.05 0.00 2.29
2280 4489 1.283029 TGCTGCTCTGCCTCCTTTAAT 59.717 47.619 0.00 0.00 0.00 1.40
2346 4555 0.813210 GAGAGCAGGGGAATCAAGCG 60.813 60.000 0.00 0.00 0.00 4.68
2383 4592 4.042809 ACAGGAACCATAGAATGTCAACCA 59.957 41.667 0.00 0.00 0.00 3.67
2384 4593 4.396166 CAGGAACCATAGAATGTCAACCAC 59.604 45.833 0.00 0.00 0.00 4.16
2397 4606 3.684305 TGTCAACCACGAATCTGCAATAG 59.316 43.478 0.00 0.00 0.00 1.73
2479 4692 8.768397 ACTCCAATGGATATACTGTAGTGAAAA 58.232 33.333 0.87 0.00 0.00 2.29
2502 4715 0.468226 TGTCTCGGTTCCAGCAGTTT 59.532 50.000 0.00 0.00 0.00 2.66
2506 4723 2.103432 TCTCGGTTCCAGCAGTTTGTTA 59.897 45.455 0.00 0.00 0.00 2.41
2535 4752 2.906691 TTTCCAAACTGCACAATGGG 57.093 45.000 6.97 0.00 33.66 4.00
2570 4787 5.415701 TGGCTATTGTTCTGTGAGGAATTTC 59.584 40.000 0.00 0.00 0.00 2.17
2575 4792 4.307432 TGTTCTGTGAGGAATTTCGAGAC 58.693 43.478 0.00 0.00 0.00 3.36
2597 4814 3.194861 GGGTTTCAAAGCCTTGTTTGTC 58.805 45.455 11.35 0.00 45.51 3.18
2787 5029 3.263261 TGTCGTGCTACTTGTTTGTTCA 58.737 40.909 0.00 0.00 0.00 3.18
2867 5109 0.518636 CTTGGACAGTGGACGCAATG 59.481 55.000 0.00 0.00 0.00 2.82
2868 5110 1.514678 TTGGACAGTGGACGCAATGC 61.515 55.000 0.00 0.00 0.00 3.56
2869 5111 2.690778 GGACAGTGGACGCAATGCC 61.691 63.158 0.00 0.00 0.00 4.40
2930 5197 2.279120 GGAGCAGGCGAGACGATG 60.279 66.667 0.00 0.00 0.00 3.84
2973 5243 3.018856 GGATGCATTCAGTGTCCATTGA 58.981 45.455 0.00 0.00 0.00 2.57
3149 5535 3.149196 CACAGCCACCATAACTTTGAGT 58.851 45.455 0.00 0.00 0.00 3.41
3167 5553 2.611292 GAGTTCGGCCTCTGAAATGATG 59.389 50.000 0.00 0.00 0.00 3.07
3254 6107 0.459237 CAGACGGTCAGACCTGCATC 60.459 60.000 17.95 9.50 35.66 3.91
3257 6110 0.818296 ACGGTCAGACCTGCATCTAC 59.182 55.000 17.95 0.00 35.66 2.59
3258 6111 0.817654 CGGTCAGACCTGCATCTACA 59.182 55.000 17.95 0.00 35.66 2.74
3259 6112 1.469940 CGGTCAGACCTGCATCTACAC 60.470 57.143 17.95 0.00 35.66 2.90
3260 6113 1.827969 GGTCAGACCTGCATCTACACT 59.172 52.381 12.94 0.00 34.73 3.55
3261 6114 2.159170 GGTCAGACCTGCATCTACACTC 60.159 54.545 12.94 0.00 34.73 3.51
3262 6115 2.757868 GTCAGACCTGCATCTACACTCT 59.242 50.000 0.00 0.00 0.00 3.24
3263 6116 2.757314 TCAGACCTGCATCTACACTCTG 59.243 50.000 0.00 0.00 0.00 3.35
3264 6117 2.757314 CAGACCTGCATCTACACTCTGA 59.243 50.000 0.00 0.00 0.00 3.27
3265 6118 3.194329 CAGACCTGCATCTACACTCTGAA 59.806 47.826 0.00 0.00 0.00 3.02
3266 6119 3.446873 AGACCTGCATCTACACTCTGAAG 59.553 47.826 0.00 0.00 0.00 3.02
3267 6120 3.435275 ACCTGCATCTACACTCTGAAGA 58.565 45.455 0.00 0.00 0.00 2.87
3268 6121 3.194542 ACCTGCATCTACACTCTGAAGAC 59.805 47.826 0.00 0.00 0.00 3.01
3269 6122 3.430098 CCTGCATCTACACTCTGAAGACC 60.430 52.174 0.00 0.00 0.00 3.85
3270 6123 3.435275 TGCATCTACACTCTGAAGACCT 58.565 45.455 0.00 0.00 0.00 3.85
3271 6124 3.834813 TGCATCTACACTCTGAAGACCTT 59.165 43.478 0.00 0.00 0.00 3.50
3272 6125 4.081972 TGCATCTACACTCTGAAGACCTTC 60.082 45.833 2.94 2.94 39.91 3.46
3273 6126 4.081972 GCATCTACACTCTGAAGACCTTCA 60.082 45.833 11.47 11.47 46.27 3.02
3282 6135 3.695830 TGAAGACCTTCATTTAGGCGT 57.304 42.857 8.27 0.00 43.90 5.68
3311 6164 3.099905 TGATCTTGATCCAACGACTCCT 58.900 45.455 7.99 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 7.649306 GCTGACAGATAAAACTGAACATTGTTT 59.351 33.333 6.65 0.00 40.63 2.83
38 40 8.866956 CAGAACTTTTGGATCTTTCATTTATGC 58.133 33.333 0.00 0.00 0.00 3.14
46 48 7.162082 TCTAGTCCAGAACTTTTGGATCTTTC 58.838 38.462 4.41 0.00 45.85 2.62
55 57 5.066593 CCTTGCTTCTAGTCCAGAACTTTT 58.933 41.667 0.00 0.00 38.39 2.27
249 256 7.948278 AGTTACAAGTGTACAATGAGTTCTC 57.052 36.000 14.89 0.00 0.00 2.87
276 283 9.354673 CCCCAATGATGTCACTAATAAAGTAAT 57.645 33.333 0.00 0.00 35.76 1.89
343 350 9.407380 ACAAATGGTGACTGATATGCTTAATTA 57.593 29.630 0.00 0.00 0.00 1.40
377 384 8.814931 AGATTAGCTAGCTTCATGATGAGTAAT 58.185 33.333 24.88 11.46 0.00 1.89
456 464 9.911788 ACAGATGGATAAACAAGACAAAGATAT 57.088 29.630 0.00 0.00 0.00 1.63
459 467 6.072508 GCACAGATGGATAAACAAGACAAAGA 60.073 38.462 0.00 0.00 0.00 2.52
501 516 8.257306 AGAGTTTATGCACCAAGAAAAGAAAAA 58.743 29.630 0.00 0.00 0.00 1.94
502 517 7.781056 AGAGTTTATGCACCAAGAAAAGAAAA 58.219 30.769 0.00 0.00 0.00 2.29
503 518 7.285401 AGAGAGTTTATGCACCAAGAAAAGAAA 59.715 33.333 0.00 0.00 0.00 2.52
504 519 6.772716 AGAGAGTTTATGCACCAAGAAAAGAA 59.227 34.615 0.00 0.00 0.00 2.52
505 520 6.299141 AGAGAGTTTATGCACCAAGAAAAGA 58.701 36.000 0.00 0.00 0.00 2.52
506 521 6.348868 GGAGAGAGTTTATGCACCAAGAAAAG 60.349 42.308 0.00 0.00 0.00 2.27
507 522 5.473504 GGAGAGAGTTTATGCACCAAGAAAA 59.526 40.000 0.00 0.00 0.00 2.29
691 707 7.678947 AATTATGCATGCTGGTTAGAGATAC 57.321 36.000 20.33 0.00 0.00 2.24
700 716 5.113383 CACATGAAAATTATGCATGCTGGT 58.887 37.500 20.33 7.62 42.28 4.00
807 830 3.375699 GGAGAGGGTCCAGAAATAGACA 58.624 50.000 0.00 0.00 46.10 3.41
826 850 8.798402 CCACATACTGTAAATTTACCAAAAGGA 58.202 33.333 22.47 12.11 32.72 3.36
869 893 8.397906 TGGCTGATTAGAATTTCTTACAAATCG 58.602 33.333 3.86 5.92 0.00 3.34
911 936 8.770828 TCTTGACAGAAGAAAAACTTTATACCG 58.229 33.333 0.00 0.00 39.13 4.02
963 990 9.296400 CAACTTTATACTGCTTCTTCTCTACTC 57.704 37.037 0.00 0.00 0.00 2.59
1052 1079 5.415701 TCTTTAGGGCTCATTTGTTGCTAAG 59.584 40.000 0.00 0.00 0.00 2.18
1235 1265 6.849502 ACAGCAATTGATTACTGAAGACATG 58.150 36.000 10.34 0.00 35.29 3.21
1238 1268 5.120830 ACGACAGCAATTGATTACTGAAGAC 59.879 40.000 10.34 2.08 35.29 3.01
1330 1366 2.288763 GCACCAACAATGTACCTTTGGG 60.289 50.000 13.44 7.62 42.49 4.12
1356 1395 3.146066 TCCAACGGTCCAAATTCAGAAG 58.854 45.455 0.00 0.00 0.00 2.85
1524 1568 7.703058 TTCCTCCTAAAATCAAATTCCTCAC 57.297 36.000 0.00 0.00 0.00 3.51
1646 1694 4.161001 TGGAACGGAGGGAGTAGTTATTTC 59.839 45.833 0.00 0.00 0.00 2.17
1654 1702 5.901276 ACTTATATTTGGAACGGAGGGAGTA 59.099 40.000 0.00 0.00 0.00 2.59
1655 1703 4.720273 ACTTATATTTGGAACGGAGGGAGT 59.280 41.667 0.00 0.00 0.00 3.85
1656 1704 5.070580 AGACTTATATTTGGAACGGAGGGAG 59.929 44.000 0.00 0.00 0.00 4.30
1657 1705 4.966805 AGACTTATATTTGGAACGGAGGGA 59.033 41.667 0.00 0.00 0.00 4.20
1658 1706 5.291905 AGACTTATATTTGGAACGGAGGG 57.708 43.478 0.00 0.00 0.00 4.30
1659 1707 6.598064 ACAAAGACTTATATTTGGAACGGAGG 59.402 38.462 3.08 0.00 40.62 4.30
1660 1708 7.611213 ACAAAGACTTATATTTGGAACGGAG 57.389 36.000 3.08 0.00 40.62 4.63
1661 1709 8.533657 TCTACAAAGACTTATATTTGGAACGGA 58.466 33.333 3.08 0.00 40.62 4.69
1662 1710 8.712285 TCTACAAAGACTTATATTTGGAACGG 57.288 34.615 3.08 0.00 40.62 4.44
1663 1711 9.582431 TCTCTACAAAGACTTATATTTGGAACG 57.418 33.333 3.08 0.00 40.62 3.95
1675 1723 8.816894 TCCATAGTGAAATCTCTACAAAGACTT 58.183 33.333 0.00 0.00 0.00 3.01
1676 1724 8.254508 GTCCATAGTGAAATCTCTACAAAGACT 58.745 37.037 0.00 0.00 0.00 3.24
1677 1725 8.254508 AGTCCATAGTGAAATCTCTACAAAGAC 58.745 37.037 0.00 0.00 0.00 3.01
1678 1726 8.367660 AGTCCATAGTGAAATCTCTACAAAGA 57.632 34.615 0.00 0.00 0.00 2.52
1679 1727 9.522804 GTAGTCCATAGTGAAATCTCTACAAAG 57.477 37.037 0.00 0.00 0.00 2.77
1680 1728 9.031537 TGTAGTCCATAGTGAAATCTCTACAAA 57.968 33.333 0.00 0.00 34.46 2.83
1681 1729 8.589701 TGTAGTCCATAGTGAAATCTCTACAA 57.410 34.615 0.00 0.00 34.46 2.41
1682 1730 8.768501 ATGTAGTCCATAGTGAAATCTCTACA 57.231 34.615 0.00 0.00 39.19 2.74
1684 1732 9.000486 CGTATGTAGTCCATAGTGAAATCTCTA 58.000 37.037 0.00 0.00 36.71 2.43
1685 1733 7.040340 CCGTATGTAGTCCATAGTGAAATCTCT 60.040 40.741 0.00 0.00 36.71 3.10
1686 1734 7.040617 TCCGTATGTAGTCCATAGTGAAATCTC 60.041 40.741 0.00 0.00 36.71 2.75
1687 1735 6.776116 TCCGTATGTAGTCCATAGTGAAATCT 59.224 38.462 0.00 0.00 36.71 2.40
1688 1736 6.978338 TCCGTATGTAGTCCATAGTGAAATC 58.022 40.000 0.00 0.00 36.71 2.17
1689 1737 6.516860 GCTCCGTATGTAGTCCATAGTGAAAT 60.517 42.308 0.00 0.00 36.71 2.17
1690 1738 5.221185 GCTCCGTATGTAGTCCATAGTGAAA 60.221 44.000 0.00 0.00 36.71 2.69
1691 1739 4.277672 GCTCCGTATGTAGTCCATAGTGAA 59.722 45.833 0.00 0.00 36.71 3.18
1692 1740 3.819337 GCTCCGTATGTAGTCCATAGTGA 59.181 47.826 0.00 0.00 36.71 3.41
1693 1741 3.568430 TGCTCCGTATGTAGTCCATAGTG 59.432 47.826 0.00 0.00 36.71 2.74
1694 1742 3.828921 TGCTCCGTATGTAGTCCATAGT 58.171 45.455 0.00 0.00 36.71 2.12
1695 1743 4.848562 TTGCTCCGTATGTAGTCCATAG 57.151 45.455 0.00 0.00 36.71 2.23
1696 1744 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
1697 1745 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
1698 1746 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
1699 1747 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
1700 1748 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
1701 1749 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
1702 1750 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
1703 1751 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
1704 1752 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
1705 1753 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
1706 1754 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
1707 1755 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
1708 1756 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
1709 1757 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
1710 1758 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
1711 1759 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
1722 1770 8.430801 AGATGCATTTTAGAGTGTAGATTCAC 57.569 34.615 0.00 0.00 38.46 3.18
1723 1771 9.534565 GTAGATGCATTTTAGAGTGTAGATTCA 57.465 33.333 0.00 0.00 0.00 2.57
1724 1772 9.534565 TGTAGATGCATTTTAGAGTGTAGATTC 57.465 33.333 0.00 0.00 0.00 2.52
1727 1775 9.967346 GTATGTAGATGCATTTTAGAGTGTAGA 57.033 33.333 0.00 0.00 0.00 2.59
1728 1776 9.750125 TGTATGTAGATGCATTTTAGAGTGTAG 57.250 33.333 0.00 0.00 0.00 2.74
1730 1778 9.265901 GATGTATGTAGATGCATTTTAGAGTGT 57.734 33.333 0.00 0.00 35.26 3.55
1731 1779 9.486497 AGATGTATGTAGATGCATTTTAGAGTG 57.514 33.333 0.00 0.00 35.26 3.51
1732 1780 9.486497 CAGATGTATGTAGATGCATTTTAGAGT 57.514 33.333 0.00 0.00 35.26 3.24
1733 1781 9.486497 ACAGATGTATGTAGATGCATTTTAGAG 57.514 33.333 0.00 0.00 35.26 2.43
1750 1798 9.588096 TCTACTATGAACCACATACAGATGTAT 57.412 33.333 0.00 0.00 44.82 2.29
1751 1799 8.990163 TCTACTATGAACCACATACAGATGTA 57.010 34.615 0.00 0.00 44.82 2.29
1753 1801 9.416794 GATTCTACTATGAACCACATACAGATG 57.583 37.037 0.00 0.00 40.07 2.90
1754 1802 9.373450 AGATTCTACTATGAACCACATACAGAT 57.627 33.333 0.00 0.00 40.07 2.90
1755 1803 8.768501 AGATTCTACTATGAACCACATACAGA 57.231 34.615 0.00 0.00 40.07 3.41
1756 1804 8.855110 AGAGATTCTACTATGAACCACATACAG 58.145 37.037 0.00 0.00 40.07 2.74
1757 1805 8.768501 AGAGATTCTACTATGAACCACATACA 57.231 34.615 0.00 0.00 40.07 2.29
1758 1806 8.301002 GGAGAGATTCTACTATGAACCACATAC 58.699 40.741 0.00 0.00 40.07 2.39
1759 1807 8.004801 TGGAGAGATTCTACTATGAACCACATA 58.995 37.037 0.00 0.00 40.07 2.29
1760 1808 6.841229 TGGAGAGATTCTACTATGAACCACAT 59.159 38.462 0.00 0.00 42.39 3.21
1761 1809 6.194967 TGGAGAGATTCTACTATGAACCACA 58.805 40.000 0.00 0.00 0.00 4.17
1762 1810 6.716934 TGGAGAGATTCTACTATGAACCAC 57.283 41.667 0.00 0.00 0.00 4.16
1763 1811 7.619698 TCTTTGGAGAGATTCTACTATGAACCA 59.380 37.037 0.00 0.00 0.00 3.67
1764 1812 7.923878 GTCTTTGGAGAGATTCTACTATGAACC 59.076 40.741 0.00 0.00 31.07 3.62
1765 1813 8.691797 AGTCTTTGGAGAGATTCTACTATGAAC 58.308 37.037 0.00 0.00 31.07 3.18
1766 1814 8.830915 AGTCTTTGGAGAGATTCTACTATGAA 57.169 34.615 0.00 0.00 31.07 2.57
1767 1815 8.830915 AAGTCTTTGGAGAGATTCTACTATGA 57.169 34.615 0.00 0.00 31.07 2.15
1779 1827 9.250624 CGTTCCTAAATATAAGTCTTTGGAGAG 57.749 37.037 0.00 0.00 31.07 3.20
1780 1828 8.202137 CCGTTCCTAAATATAAGTCTTTGGAGA 58.798 37.037 0.00 0.00 0.00 3.71
1781 1829 8.202137 TCCGTTCCTAAATATAAGTCTTTGGAG 58.798 37.037 0.00 0.00 0.00 3.86
1782 1830 8.081517 TCCGTTCCTAAATATAAGTCTTTGGA 57.918 34.615 0.00 0.00 0.00 3.53
1783 1831 7.441458 CCTCCGTTCCTAAATATAAGTCTTTGG 59.559 40.741 0.00 0.00 0.00 3.28
1784 1832 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
1785 1833 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
1786 1834 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
1787 1835 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1788 1836 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
1789 1837 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1790 1838 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1791 1839 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
1792 1840 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
1793 1841 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
1794 1842 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
1795 1843 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
1796 1844 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
1797 1845 3.782523 TCTACTACTCCCTCCGTTCCTAA 59.217 47.826 0.00 0.00 0.00 2.69
1798 1846 3.387962 TCTACTACTCCCTCCGTTCCTA 58.612 50.000 0.00 0.00 0.00 2.94
1799 1847 2.203584 TCTACTACTCCCTCCGTTCCT 58.796 52.381 0.00 0.00 0.00 3.36
1800 1848 2.725221 TCTACTACTCCCTCCGTTCC 57.275 55.000 0.00 0.00 0.00 3.62
1801 1849 4.216042 GCTATTCTACTACTCCCTCCGTTC 59.784 50.000 0.00 0.00 0.00 3.95
1802 1850 4.143543 GCTATTCTACTACTCCCTCCGTT 58.856 47.826 0.00 0.00 0.00 4.44
1803 1851 3.137913 TGCTATTCTACTACTCCCTCCGT 59.862 47.826 0.00 0.00 0.00 4.69
1804 1852 3.752665 TGCTATTCTACTACTCCCTCCG 58.247 50.000 0.00 0.00 0.00 4.63
1805 1853 6.014012 AGAATGCTATTCTACTACTCCCTCC 58.986 44.000 8.93 0.00 0.00 4.30
1806 1854 7.533289 AAGAATGCTATTCTACTACTCCCTC 57.467 40.000 10.51 0.00 0.00 4.30
1807 1855 7.202047 CCAAAGAATGCTATTCTACTACTCCCT 60.202 40.741 10.51 0.00 0.00 4.20
1808 1856 6.931840 CCAAAGAATGCTATTCTACTACTCCC 59.068 42.308 10.51 0.00 0.00 4.30
1809 1857 7.501844 ACCAAAGAATGCTATTCTACTACTCC 58.498 38.462 10.51 0.00 0.00 3.85
1823 1871 5.906073 ACAAGCCATATTACCAAAGAATGC 58.094 37.500 0.00 0.00 0.00 3.56
1990 2074 9.624697 GTTCAGTCAGCATAATTGTTTGAATAA 57.375 29.630 0.00 0.00 0.00 1.40
1993 2077 7.275888 AGTTCAGTCAGCATAATTGTTTGAA 57.724 32.000 0.00 0.00 0.00 2.69
1994 2078 6.882610 AGTTCAGTCAGCATAATTGTTTGA 57.117 33.333 0.00 0.00 0.00 2.69
1995 2079 6.744537 GCTAGTTCAGTCAGCATAATTGTTTG 59.255 38.462 0.00 0.00 35.35 2.93
1998 2082 5.491070 TGCTAGTTCAGTCAGCATAATTGT 58.509 37.500 0.00 0.00 40.26 2.71
2011 2095 4.363138 TGCGTGAGAATATGCTAGTTCAG 58.637 43.478 0.00 0.00 33.75 3.02
2044 2128 5.762045 ACGCTACTTTTACTTCAACTCGTA 58.238 37.500 0.00 0.00 0.00 3.43
2153 4301 6.875972 AAGTAGGCTTCTCTTAGGAATCAA 57.124 37.500 0.00 0.00 0.00 2.57
2166 4314 8.904099 TTTATGGCTTATAGAAAGTAGGCTTC 57.096 34.615 0.00 0.00 33.01 3.86
2180 4330 6.824305 ATAAGCGCTTCATTTATGGCTTAT 57.176 33.333 28.82 6.66 44.09 1.73
2183 4392 5.520376 AAATAAGCGCTTCATTTATGGCT 57.480 34.783 28.82 0.00 0.00 4.75
2196 4405 5.163652 ACAGGAAAATGGACTAAATAAGCGC 60.164 40.000 0.00 0.00 0.00 5.92
2280 4489 6.544564 TGCTGCATCAATTATTGAGAGATTGA 59.455 34.615 13.29 0.00 43.98 2.57
2346 4555 3.250280 GGTTCCTGTTCTTCGTTTTCCTC 59.750 47.826 0.00 0.00 0.00 3.71
2383 4592 6.986231 TGTAACATCATCTATTGCAGATTCGT 59.014 34.615 0.00 0.00 41.49 3.85
2384 4593 7.412137 TGTAACATCATCTATTGCAGATTCG 57.588 36.000 0.00 0.00 41.49 3.34
2397 4606 3.489355 TGCATCCCCATGTAACATCATC 58.511 45.455 0.00 0.00 31.86 2.92
2479 4692 2.154462 CTGCTGGAACCGAGACAAAAT 58.846 47.619 0.00 0.00 0.00 1.82
2502 4715 6.461788 GCAGTTTGGAAAATTACAGGGTAACA 60.462 38.462 0.00 0.00 39.74 2.41
2506 4723 3.964031 TGCAGTTTGGAAAATTACAGGGT 59.036 39.130 0.00 0.00 0.00 4.34
2535 4752 6.541641 ACAGAACAATAGCCAGATTCAAGATC 59.458 38.462 0.00 0.00 0.00 2.75
2570 4787 0.602905 AGGCTTTGAAACCCGTCTCG 60.603 55.000 0.00 0.00 0.00 4.04
2575 4792 2.200899 CAAACAAGGCTTTGAAACCCG 58.799 47.619 16.36 0.00 37.73 5.28
2623 4856 5.909621 AATTCATGTGCTAGTCATGCTTT 57.090 34.783 18.51 13.47 41.40 3.51
2625 4858 5.184479 ACAAAATTCATGTGCTAGTCATGCT 59.816 36.000 18.51 10.06 41.40 3.79
2787 5029 1.613437 CAGGTTTTCCAAAGCGACCAT 59.387 47.619 0.00 0.00 43.73 3.55
2973 5243 3.322254 CCAGAGAACTGTGTTCCACTACT 59.678 47.826 6.80 0.00 42.05 2.57
3068 5454 2.035193 ACACATGTGCCGTTATTTTGCA 59.965 40.909 25.68 0.00 0.00 4.08
3074 5460 3.527533 ACGATAACACATGTGCCGTTAT 58.472 40.909 25.68 20.08 38.27 1.89
3079 5465 2.550978 AGCTACGATAACACATGTGCC 58.449 47.619 25.68 11.26 0.00 5.01
3149 5535 1.339920 TGCATCATTTCAGAGGCCGAA 60.340 47.619 0.00 0.00 44.12 4.30
3167 5553 3.076621 TCTGACATGGATCAACACTTGC 58.923 45.455 0.00 0.00 0.00 4.01
3263 6116 4.454504 TGAAACGCCTAAATGAAGGTCTTC 59.545 41.667 3.91 3.91 39.02 2.87
3264 6117 4.215613 GTGAAACGCCTAAATGAAGGTCTT 59.784 41.667 0.00 0.00 39.02 3.01
3265 6118 3.751698 GTGAAACGCCTAAATGAAGGTCT 59.248 43.478 0.00 0.00 39.02 3.85
3266 6119 3.751698 AGTGAAACGCCTAAATGAAGGTC 59.248 43.478 0.00 0.00 45.86 3.85
3267 6120 3.751518 AGTGAAACGCCTAAATGAAGGT 58.248 40.909 0.00 0.00 45.86 3.50
3268 6121 4.003648 AGAGTGAAACGCCTAAATGAAGG 58.996 43.478 0.00 0.00 45.86 3.46
3269 6122 4.690748 TCAGAGTGAAACGCCTAAATGAAG 59.309 41.667 0.00 0.00 45.86 3.02
3270 6123 4.637276 TCAGAGTGAAACGCCTAAATGAA 58.363 39.130 0.00 0.00 45.86 2.57
3271 6124 4.265904 TCAGAGTGAAACGCCTAAATGA 57.734 40.909 0.00 0.00 45.86 2.57
3272 6125 4.872691 AGATCAGAGTGAAACGCCTAAATG 59.127 41.667 0.00 0.00 45.86 2.32
3273 6126 5.091261 AGATCAGAGTGAAACGCCTAAAT 57.909 39.130 0.00 0.00 45.86 1.40
3274 6127 4.537135 AGATCAGAGTGAAACGCCTAAA 57.463 40.909 0.00 0.00 45.86 1.85
3275 6128 4.021456 TCAAGATCAGAGTGAAACGCCTAA 60.021 41.667 0.00 0.00 45.86 2.69
3276 6129 3.509967 TCAAGATCAGAGTGAAACGCCTA 59.490 43.478 0.00 0.00 45.86 3.93
3277 6130 2.300152 TCAAGATCAGAGTGAAACGCCT 59.700 45.455 0.00 0.00 45.86 5.52
3278 6131 2.688507 TCAAGATCAGAGTGAAACGCC 58.311 47.619 0.00 0.00 45.86 5.68
3279 6132 3.308323 GGATCAAGATCAGAGTGAAACGC 59.692 47.826 11.78 0.00 40.05 4.84
3280 6133 4.498241 TGGATCAAGATCAGAGTGAAACG 58.502 43.478 11.78 0.00 40.05 3.60
3281 6134 5.163913 CGTTGGATCAAGATCAGAGTGAAAC 60.164 44.000 11.78 4.22 39.54 2.78
3282 6135 4.931601 CGTTGGATCAAGATCAGAGTGAAA 59.068 41.667 11.78 0.00 39.54 2.69
3311 6164 5.354513 TCAACATAATTCGCCGGAATAACAA 59.645 36.000 5.05 0.00 41.99 2.83


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

AutoCloner maintained by Alex Coulton.