Multiple sequence alignment - TraesCS4D01G207100

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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 TraesCS4D01G207100 chr4D 100.000 4606 0 0 1 4606 354891700 354887095 0.000000e+00 8506.0
1 TraesCS4D01G207100 chr4D 76.591 1320 267 28 2464 3768 354136506 354137798 0.000000e+00 688.0
2 TraesCS4D01G207100 chr4A 96.738 2330 56 7 2294 4606 109844226 109846552 0.000000e+00 3864.0
3 TraesCS4D01G207100 chr4A 94.542 513 17 5 903 1404 109843048 109843560 0.000000e+00 782.0
4 TraesCS4D01G207100 chr4A 87.619 420 24 11 1886 2278 109843823 109844241 3.250000e-126 462.0
5 TraesCS4D01G207100 chr4A 93.676 253 12 4 983 1233 109787629 109787879 4.350000e-100 375.0
6 TraesCS4D01G207100 chr4A 91.288 264 11 6 1461 1714 109843550 109843811 2.640000e-92 350.0
7 TraesCS4D01G207100 chr4B 94.541 2418 74 10 2225 4606 438381260 438378865 0.000000e+00 3681.0
8 TraesCS4D01G207100 chr4B 93.660 836 31 3 886 1714 438382405 438381585 0.000000e+00 1230.0
9 TraesCS4D01G207100 chr4B 87.470 838 70 20 3 832 438415440 438414630 0.000000e+00 933.0
10 TraesCS4D01G207100 chr4B 76.144 1421 297 31 2363 3768 437949442 437950835 0.000000e+00 708.0
11 TraesCS4D01G207100 chr4B 93.676 253 12 4 983 1233 438607113 438606863 4.350000e-100 375.0
12 TraesCS4D01G207100 chr4B 89.451 237 13 4 1885 2117 438381574 438381346 5.830000e-74 289.0
13 TraesCS4D01G207100 chr2B 79.662 1480 276 17 2338 3798 731250930 731252403 0.000000e+00 1042.0
14 TraesCS4D01G207100 chr2B 89.205 176 18 1 1715 1890 446336174 446336348 7.760000e-53 219.0
15 TraesCS4D01G207100 chr2D 79.324 1480 281 17 2338 3798 601109021 601110494 0.000000e+00 1014.0
16 TraesCS4D01G207100 chr2A 78.919 1480 285 18 2349 3808 734586428 734587900 0.000000e+00 979.0
17 TraesCS4D01G207100 chr2A 84.746 177 23 2 1715 1891 613622002 613622174 1.700000e-39 174.0
18 TraesCS4D01G207100 chr6B 77.919 1490 293 18 2318 3798 647931005 647929543 0.000000e+00 896.0
19 TraesCS4D01G207100 chr6B 76.746 1045 218 13 2361 3382 647708788 647709830 1.120000e-155 560.0
20 TraesCS4D01G207100 chr6B 88.346 266 24 5 970 1229 647837380 647837116 3.460000e-81 313.0
21 TraesCS4D01G207100 chr6B 88.627 255 22 5 984 1233 647691022 647691274 2.080000e-78 303.0
22 TraesCS4D01G207100 chr6B 88.672 256 18 9 984 1232 647588874 647589125 7.490000e-78 302.0
23 TraesCS4D01G207100 chr3D 82.533 916 88 31 3 898 114401544 114400681 0.000000e+00 739.0
24 TraesCS4D01G207100 chr6A 76.689 1051 213 19 2361 3382 574936163 574937210 5.210000e-154 555.0
25 TraesCS4D01G207100 chr6A 76.411 886 174 25 2361 3218 575464803 575465681 3.270000e-121 446.0
26 TraesCS4D01G207100 chr6A 87.970 266 26 3 970 1230 575200279 575200015 4.480000e-80 309.0
27 TraesCS4D01G207100 chr6D 89.328 253 24 2 984 1233 429666501 429666753 9.620000e-82 315.0
28 TraesCS4D01G207100 chr3A 89.205 176 18 1 1715 1890 55492768 55492942 7.760000e-53 219.0
29 TraesCS4D01G207100 chr3B 88.636 176 19 1 1715 1890 570249249 570249075 3.610000e-51 213.0
30 TraesCS4D01G207100 chr3B 84.706 170 23 3 1721 1890 18399374 18399208 2.850000e-37 167.0
31 TraesCS4D01G207100 chr5A 88.304 171 19 1 1720 1890 550794272 550794441 2.170000e-48 204.0
32 TraesCS4D01G207100 chr5D 85.714 175 20 2 1715 1889 118636770 118636601 3.660000e-41 180.0
33 TraesCS4D01G207100 chr1A 83.799 179 25 3 1715 1893 121109384 121109210 2.850000e-37 167.0
34 TraesCS4D01G207100 chr7A 84.706 170 21 3 1721 1890 595831554 595831390 1.030000e-36 165.0
35 TraesCS4D01G207100 chr7B 77.465 142 22 7 13 148 145502882 145503019 4.940000e-10 76.8


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 TraesCS4D01G207100 chr4D 354887095 354891700 4605 True 8506.000000 8506 100.000000 1 4606 1 chr4D.!!$R1 4605
1 TraesCS4D01G207100 chr4D 354136506 354137798 1292 False 688.000000 688 76.591000 2464 3768 1 chr4D.!!$F1 1304
2 TraesCS4D01G207100 chr4A 109843048 109846552 3504 False 1364.500000 3864 92.546750 903 4606 4 chr4A.!!$F2 3703
3 TraesCS4D01G207100 chr4B 438378865 438382405 3540 True 1733.333333 3681 92.550667 886 4606 3 chr4B.!!$R3 3720
4 TraesCS4D01G207100 chr4B 438414630 438415440 810 True 933.000000 933 87.470000 3 832 1 chr4B.!!$R1 829
5 TraesCS4D01G207100 chr4B 437949442 437950835 1393 False 708.000000 708 76.144000 2363 3768 1 chr4B.!!$F1 1405
6 TraesCS4D01G207100 chr2B 731250930 731252403 1473 False 1042.000000 1042 79.662000 2338 3798 1 chr2B.!!$F2 1460
7 TraesCS4D01G207100 chr2D 601109021 601110494 1473 False 1014.000000 1014 79.324000 2338 3798 1 chr2D.!!$F1 1460
8 TraesCS4D01G207100 chr2A 734586428 734587900 1472 False 979.000000 979 78.919000 2349 3808 1 chr2A.!!$F2 1459
9 TraesCS4D01G207100 chr6B 647929543 647931005 1462 True 896.000000 896 77.919000 2318 3798 1 chr6B.!!$R2 1480
10 TraesCS4D01G207100 chr6B 647708788 647709830 1042 False 560.000000 560 76.746000 2361 3382 1 chr6B.!!$F3 1021
11 TraesCS4D01G207100 chr3D 114400681 114401544 863 True 739.000000 739 82.533000 3 898 1 chr3D.!!$R1 895
12 TraesCS4D01G207100 chr6A 574936163 574937210 1047 False 555.000000 555 76.689000 2361 3382 1 chr6A.!!$F1 1021
13 TraesCS4D01G207100 chr6A 575464803 575465681 878 False 446.000000 446 76.411000 2361 3218 1 chr6A.!!$F2 857

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
36 38 0.036875 CAAAGACCAGACCCCCAGTC 59.963 60.000 0.00 0.00 46.71 3.51 F
1259 1303 1.000385 CCTCACGCTGATCTGATCCTC 60.000 57.143 14.71 5.81 0.00 3.71 F
1752 1812 0.251634 AGCAGCTACCCTCAAGAAGC 59.748 55.000 0.00 0.00 35.16 3.86 F
2500 2596 0.178873 TACAGGGGGTTGGAGAAGCT 60.179 55.000 0.00 0.00 0.00 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1733 1793 0.251634 GCTTCTTGAGGGTAGCTGCT 59.748 55.000 7.57 7.57 0.00 4.24 R
2386 2482 1.737029 CGGATGTGTCACTGAATCGCT 60.737 52.381 4.27 0.00 0.00 4.93 R
2927 3049 2.034221 GCCCTCGGGTTGCTTCTT 59.966 61.111 3.54 0.00 37.65 2.52 R
3981 4115 0.934496 CGTTTCTTCTTCACCACGCA 59.066 50.000 0.00 0.00 0.00 5.24 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
26 28 2.917933 TGTTGTGAGGACAAAGACCAG 58.082 47.619 0.00 0.00 43.77 4.00
36 38 0.036875 CAAAGACCAGACCCCCAGTC 59.963 60.000 0.00 0.00 46.71 3.51
51 54 1.974236 CCAGTCAACTCTCCTTCCTGT 59.026 52.381 0.00 0.00 0.00 4.00
61 64 1.111116 TCCTTCCTGTTCGTGTCGGT 61.111 55.000 0.00 0.00 0.00 4.69
92 95 8.158025 TCAAGACAAAGGGGAATAAGAGATAA 57.842 34.615 0.00 0.00 0.00 1.75
109 112 5.705441 AGAGATAAACAGTGGCGAATGAAAA 59.295 36.000 2.36 0.00 0.00 2.29
110 113 5.942872 AGATAAACAGTGGCGAATGAAAAG 58.057 37.500 2.36 0.00 0.00 2.27
117 120 1.628340 TGGCGAATGAAAAGGAGGAGA 59.372 47.619 0.00 0.00 0.00 3.71
122 125 4.065088 CGAATGAAAAGGAGGAGACAACA 58.935 43.478 0.00 0.00 0.00 3.33
153 156 7.839837 GCTCGTATCTTCAACTTATAAAACACG 59.160 37.037 0.00 0.00 0.00 4.49
155 158 6.898189 CGTATCTTCAACTTATAAAACACGGC 59.102 38.462 0.00 0.00 0.00 5.68
157 160 5.310451 TCTTCAACTTATAAAACACGGCCT 58.690 37.500 0.00 0.00 0.00 5.19
205 209 4.097589 ACAAAAATGGCCCAACAAAACATG 59.902 37.500 0.00 0.00 0.00 3.21
212 216 1.470632 CCCAACAAAACATGCACGTGT 60.471 47.619 18.38 0.00 0.00 4.49
248 252 6.071560 ACAAGTGAAGATAGAACATACGACCA 60.072 38.462 0.00 0.00 0.00 4.02
310 325 9.598517 ACAACATTTAAAGTGAACATGTCAAAT 57.401 25.926 0.00 0.00 38.23 2.32
494 526 8.595362 AGAAAAGAAAAGAGAAAAGGAAAGGA 57.405 30.769 0.00 0.00 0.00 3.36
495 527 9.035890 AGAAAAGAAAAGAGAAAAGGAAAGGAA 57.964 29.630 0.00 0.00 0.00 3.36
496 528 9.653287 GAAAAGAAAAGAGAAAAGGAAAGGAAA 57.347 29.630 0.00 0.00 0.00 3.13
500 532 9.823647 AGAAAAGAGAAAAGGAAAGGAAAAATC 57.176 29.630 0.00 0.00 0.00 2.17
501 533 9.599866 GAAAAGAGAAAAGGAAAGGAAAAATCA 57.400 29.630 0.00 0.00 0.00 2.57
502 534 9.958180 AAAAGAGAAAAGGAAAGGAAAAATCAA 57.042 25.926 0.00 0.00 0.00 2.57
503 535 8.948631 AAGAGAAAAGGAAAGGAAAAATCAAC 57.051 30.769 0.00 0.00 0.00 3.18
570 602 9.883142 AACAAGAGGAAAATACACATTCAAAAA 57.117 25.926 0.00 0.00 0.00 1.94
589 621 4.525411 AAACGGTAGAAGACACAAAACG 57.475 40.909 0.00 0.00 0.00 3.60
616 648 3.201266 TGACAGTTTCCCCACAACTAGTT 59.799 43.478 1.12 1.12 32.48 2.24
618 650 5.072600 TGACAGTTTCCCCACAACTAGTTAT 59.927 40.000 8.04 0.00 32.48 1.89
690 722 2.417651 CGAGATACAACCCAACGGCTAA 60.418 50.000 0.00 0.00 0.00 3.09
739 771 1.867233 GCATATACTCTGGCAACACGG 59.133 52.381 0.00 0.00 46.17 4.94
749 781 3.030652 CAACACGGAACAGCCCAC 58.969 61.111 0.00 0.00 0.00 4.61
750 782 2.590575 AACACGGAACAGCCCACG 60.591 61.111 0.00 0.00 0.00 4.94
754 786 1.890510 ACGGAACAGCCCACGAAAC 60.891 57.895 0.00 0.00 0.00 2.78
814 849 7.259290 AGAAACACGACAATACAAAAGACAT 57.741 32.000 0.00 0.00 0.00 3.06
829 864 6.152323 ACAAAAGACATGAATCTTAGCATGCT 59.848 34.615 25.99 25.99 44.30 3.79
834 869 9.736414 AAGACATGAATCTTAGCATGCTATATT 57.264 29.630 27.35 25.86 44.30 1.28
852 889 7.182749 TGCTATATTCAATGGCTAGGGAGTTAT 59.817 37.037 0.00 0.00 0.00 1.89
860 897 5.074746 TGGCTAGGGAGTTATATGTGAGA 57.925 43.478 0.00 0.00 0.00 3.27
864 901 7.178628 TGGCTAGGGAGTTATATGTGAGATAAC 59.821 40.741 0.00 0.00 39.20 1.89
901 938 8.395633 CCACTAGATTTGAAATAGTAAAACCGG 58.604 37.037 0.00 0.00 0.00 5.28
1218 1262 1.031235 TGAACTCCGTCAACACCGTA 58.969 50.000 0.00 0.00 0.00 4.02
1259 1303 1.000385 CCTCACGCTGATCTGATCCTC 60.000 57.143 14.71 5.81 0.00 3.71
1274 1318 2.584835 TCCTCCACCAGTTCAATTGG 57.415 50.000 5.42 0.00 41.60 3.16
1281 1325 2.890311 CACCAGTTCAATTGGCCTACAA 59.110 45.455 3.32 0.00 44.54 2.41
1303 1347 1.028905 GGCCTTGTGTGCTTGTGTTA 58.971 50.000 0.00 0.00 0.00 2.41
1308 1362 4.082787 GCCTTGTGTGCTTGTGTTACATAT 60.083 41.667 0.00 0.00 0.00 1.78
1311 1365 7.188834 CCTTGTGTGCTTGTGTTACATATATG 58.811 38.462 11.29 11.29 0.00 1.78
1406 1460 1.857217 CTTCGTGCTAGCTAGTGCATG 59.143 52.381 21.62 19.09 44.77 4.06
1412 1466 3.623060 GTGCTAGCTAGTGCATGCTAAAA 59.377 43.478 21.62 0.00 40.65 1.52
1419 1473 3.844577 AGTGCATGCTAAAAGCTTCTG 57.155 42.857 20.33 0.00 42.97 3.02
1432 1486 4.322080 AAGCTTCTGTAAAGGCAAAACC 57.678 40.909 0.00 0.00 39.61 3.27
1483 1537 4.870123 AGTGTGCTTGAATTATTGGCAA 57.130 36.364 0.68 0.68 34.65 4.52
1509 1563 5.009210 ACTTCGATCTGCTGTTCTATACTCC 59.991 44.000 0.00 0.00 0.00 3.85
1528 1582 3.777522 CTCCTTAGGTTTCTCAGGTCCAT 59.222 47.826 0.00 0.00 36.15 3.41
1544 1598 1.678635 CATGGGATTGTGCCACGGT 60.679 57.895 0.00 0.00 41.95 4.83
1646 1706 1.437986 CGTTCAGATCCCTCCGTCC 59.562 63.158 0.00 0.00 0.00 4.79
1672 1732 2.421248 CCTTTTTGCCTTGCCCTTTTCA 60.421 45.455 0.00 0.00 0.00 2.69
1714 1774 9.817809 GGATTATCTCATCAACTGTTAAGTACA 57.182 33.333 0.00 0.00 34.77 2.90
1730 1790 8.810427 TGTTAAGTACAGTCAGAAAAAGTTACG 58.190 33.333 0.00 0.00 31.68 3.18
1731 1791 6.839820 AAGTACAGTCAGAAAAAGTTACGG 57.160 37.500 0.00 0.00 0.00 4.02
1732 1792 5.295152 AGTACAGTCAGAAAAAGTTACGGG 58.705 41.667 0.00 0.00 0.00 5.28
1733 1793 4.411256 ACAGTCAGAAAAAGTTACGGGA 57.589 40.909 0.00 0.00 0.00 5.14
1734 1794 4.377897 ACAGTCAGAAAAAGTTACGGGAG 58.622 43.478 0.00 0.00 0.00 4.30
1735 1795 3.186613 CAGTCAGAAAAAGTTACGGGAGC 59.813 47.826 0.00 0.00 0.00 4.70
1736 1796 3.135994 GTCAGAAAAAGTTACGGGAGCA 58.864 45.455 0.00 0.00 0.00 4.26
1737 1797 3.186613 GTCAGAAAAAGTTACGGGAGCAG 59.813 47.826 0.00 0.00 0.00 4.24
1738 1798 2.095718 CAGAAAAAGTTACGGGAGCAGC 60.096 50.000 0.00 0.00 0.00 5.25
1739 1799 2.152016 GAAAAAGTTACGGGAGCAGCT 58.848 47.619 0.00 0.00 0.00 4.24
1740 1800 3.007614 AGAAAAAGTTACGGGAGCAGCTA 59.992 43.478 0.00 0.00 0.00 3.32
1741 1801 2.381725 AAAGTTACGGGAGCAGCTAC 57.618 50.000 0.00 0.00 0.00 3.58
1742 1802 0.535797 AAGTTACGGGAGCAGCTACC 59.464 55.000 14.74 14.74 0.00 3.18
1743 1803 1.143401 GTTACGGGAGCAGCTACCC 59.857 63.158 19.06 17.43 42.43 3.69
1744 1804 1.001248 TTACGGGAGCAGCTACCCT 59.999 57.895 19.06 9.39 43.57 4.34
1745 1805 1.041447 TTACGGGAGCAGCTACCCTC 61.041 60.000 19.06 9.57 43.57 4.30
1746 1806 2.219449 TACGGGAGCAGCTACCCTCA 62.219 60.000 19.06 0.00 43.57 3.86
1747 1807 2.359169 CGGGAGCAGCTACCCTCAA 61.359 63.158 19.06 0.00 43.57 3.02
1748 1808 1.524482 GGGAGCAGCTACCCTCAAG 59.476 63.158 13.67 0.00 42.56 3.02
1749 1809 0.978146 GGGAGCAGCTACCCTCAAGA 60.978 60.000 13.67 0.00 42.56 3.02
1750 1810 0.905357 GGAGCAGCTACCCTCAAGAA 59.095 55.000 0.00 0.00 0.00 2.52
1751 1811 1.134551 GGAGCAGCTACCCTCAAGAAG 60.135 57.143 0.00 0.00 0.00 2.85
1752 1812 0.251634 AGCAGCTACCCTCAAGAAGC 59.748 55.000 0.00 0.00 35.16 3.86
1753 1813 0.251634 GCAGCTACCCTCAAGAAGCT 59.748 55.000 0.00 0.00 45.94 3.74
1755 1815 0.251634 AGCTACCCTCAAGAAGCTGC 59.748 55.000 0.00 0.00 43.46 5.25
1756 1816 1.086634 GCTACCCTCAAGAAGCTGCG 61.087 60.000 0.00 0.00 32.18 5.18
1757 1817 0.460987 CTACCCTCAAGAAGCTGCGG 60.461 60.000 0.00 0.00 0.00 5.69
1758 1818 1.899437 TACCCTCAAGAAGCTGCGGG 61.899 60.000 0.88 0.88 45.44 6.13
1759 1819 2.437359 CCTCAAGAAGCTGCGGGG 60.437 66.667 0.00 0.00 0.00 5.73
1760 1820 2.665000 CTCAAGAAGCTGCGGGGA 59.335 61.111 0.00 0.00 0.00 4.81
1761 1821 1.743252 CTCAAGAAGCTGCGGGGAC 60.743 63.158 0.00 0.00 0.00 4.46
1773 1833 4.452733 GGGGACGGGAGCGTTCAG 62.453 72.222 0.53 0.00 0.00 3.02
1774 1834 3.379445 GGGACGGGAGCGTTCAGA 61.379 66.667 0.53 0.00 0.00 3.27
1775 1835 2.654877 GGACGGGAGCGTTCAGAA 59.345 61.111 0.53 0.00 0.00 3.02
1776 1836 1.005394 GGACGGGAGCGTTCAGAAA 60.005 57.895 0.53 0.00 0.00 2.52
1777 1837 0.601841 GGACGGGAGCGTTCAGAAAA 60.602 55.000 0.53 0.00 0.00 2.29
1778 1838 1.223187 GACGGGAGCGTTCAGAAAAA 58.777 50.000 0.53 0.00 0.00 1.94
1799 1859 6.377327 AAAATTCTACTATGCATCCAACGG 57.623 37.500 0.19 0.00 0.00 4.44
1800 1860 2.526304 TCTACTATGCATCCAACGGC 57.474 50.000 0.19 0.00 0.00 5.68
1801 1861 1.070134 TCTACTATGCATCCAACGGCC 59.930 52.381 0.19 0.00 0.00 6.13
1802 1862 0.833949 TACTATGCATCCAACGGCCA 59.166 50.000 0.19 0.00 0.00 5.36
1803 1863 0.464373 ACTATGCATCCAACGGCCAG 60.464 55.000 0.19 0.00 0.00 4.85
1804 1864 1.152984 TATGCATCCAACGGCCAGG 60.153 57.895 0.19 0.60 0.00 4.45
1805 1865 2.623094 TATGCATCCAACGGCCAGGG 62.623 60.000 0.19 0.00 0.00 4.45
1806 1866 4.424711 GCATCCAACGGCCAGGGA 62.425 66.667 2.24 6.51 34.70 4.20
1807 1867 2.438434 CATCCAACGGCCAGGGAC 60.438 66.667 9.04 0.00 32.60 4.46
1808 1868 2.933287 ATCCAACGGCCAGGGACA 60.933 61.111 9.04 0.00 32.60 4.02
1809 1869 2.971598 ATCCAACGGCCAGGGACAG 61.972 63.158 9.04 0.00 32.60 3.51
1816 1876 4.242602 GCCAGGGACAGCCATAAC 57.757 61.111 0.00 0.00 35.15 1.89
1817 1877 1.819632 GCCAGGGACAGCCATAACG 60.820 63.158 0.00 0.00 35.15 3.18
1818 1878 1.602237 CCAGGGACAGCCATAACGT 59.398 57.895 0.00 0.00 35.15 3.99
1819 1879 0.828022 CCAGGGACAGCCATAACGTA 59.172 55.000 0.00 0.00 35.15 3.57
1820 1880 1.208535 CCAGGGACAGCCATAACGTAA 59.791 52.381 0.00 0.00 35.15 3.18
1821 1881 2.355310 CCAGGGACAGCCATAACGTAAA 60.355 50.000 0.00 0.00 35.15 2.01
1822 1882 3.340034 CAGGGACAGCCATAACGTAAAA 58.660 45.455 0.00 0.00 35.15 1.52
1823 1883 3.945285 CAGGGACAGCCATAACGTAAAAT 59.055 43.478 0.00 0.00 35.15 1.82
1824 1884 4.398044 CAGGGACAGCCATAACGTAAAATT 59.602 41.667 0.00 0.00 35.15 1.82
1825 1885 4.398044 AGGGACAGCCATAACGTAAAATTG 59.602 41.667 0.00 0.00 35.15 2.32
1826 1886 4.439563 GGGACAGCCATAACGTAAAATTGG 60.440 45.833 0.00 0.00 35.15 3.16
1827 1887 4.396790 GGACAGCCATAACGTAAAATTGGA 59.603 41.667 0.00 0.00 0.00 3.53
1828 1888 5.305139 ACAGCCATAACGTAAAATTGGAC 57.695 39.130 0.00 0.00 0.00 4.02
1829 1889 4.762765 ACAGCCATAACGTAAAATTGGACA 59.237 37.500 0.00 0.00 0.00 4.02
1830 1890 5.106317 ACAGCCATAACGTAAAATTGGACAG 60.106 40.000 0.00 0.00 0.00 3.51
1831 1891 4.102649 GCCATAACGTAAAATTGGACAGC 58.897 43.478 0.00 0.00 0.00 4.40
1832 1892 4.142469 GCCATAACGTAAAATTGGACAGCT 60.142 41.667 0.00 0.00 0.00 4.24
1833 1893 5.569413 CCATAACGTAAAATTGGACAGCTC 58.431 41.667 0.00 0.00 0.00 4.09
1834 1894 5.448632 CCATAACGTAAAATTGGACAGCTCC 60.449 44.000 0.00 0.00 37.04 4.70
1835 1895 2.073816 ACGTAAAATTGGACAGCTCCG 58.926 47.619 0.00 0.00 39.88 4.63
1836 1896 1.396996 CGTAAAATTGGACAGCTCCGG 59.603 52.381 0.00 0.00 39.88 5.14
1837 1897 2.706890 GTAAAATTGGACAGCTCCGGA 58.293 47.619 2.93 2.93 39.88 5.14
1838 1898 2.286365 AAAATTGGACAGCTCCGGAA 57.714 45.000 5.23 0.00 39.88 4.30
1839 1899 1.826385 AAATTGGACAGCTCCGGAAG 58.174 50.000 5.23 0.46 39.88 3.46
1850 1910 1.560923 CTCCGGAAGCTGATAACGTG 58.439 55.000 5.23 0.00 0.00 4.49
1851 1911 1.134367 CTCCGGAAGCTGATAACGTGA 59.866 52.381 5.23 0.00 0.00 4.35
1852 1912 1.134367 TCCGGAAGCTGATAACGTGAG 59.866 52.381 0.00 0.00 0.00 3.51
1853 1913 1.560923 CGGAAGCTGATAACGTGAGG 58.439 55.000 0.00 0.00 0.00 3.86
1854 1914 1.802880 CGGAAGCTGATAACGTGAGGG 60.803 57.143 0.00 0.00 0.00 4.30
1855 1915 1.480954 GGAAGCTGATAACGTGAGGGA 59.519 52.381 0.00 0.00 0.00 4.20
1856 1916 2.482142 GGAAGCTGATAACGTGAGGGAG 60.482 54.545 0.00 0.00 0.00 4.30
1857 1917 0.461961 AGCTGATAACGTGAGGGAGC 59.538 55.000 0.00 0.00 0.00 4.70
1858 1918 0.461961 GCTGATAACGTGAGGGAGCT 59.538 55.000 0.00 0.00 0.00 4.09
1859 1919 1.537135 GCTGATAACGTGAGGGAGCTC 60.537 57.143 4.71 4.71 0.00 4.09
1860 1920 1.067821 CTGATAACGTGAGGGAGCTCC 59.932 57.143 25.59 25.59 0.00 4.70
1868 1928 2.041405 AGGGAGCTCCTAGGGTGC 60.041 66.667 31.36 13.49 45.98 5.01
1869 1929 3.164977 GGGAGCTCCTAGGGTGCC 61.165 72.222 31.36 9.17 42.42 5.01
1870 1930 3.164977 GGAGCTCCTAGGGTGCCC 61.165 72.222 26.25 16.56 42.42 5.36
1871 1931 2.365635 GAGCTCCTAGGGTGCCCA 60.366 66.667 19.37 0.00 42.42 5.36
1872 1932 2.366167 AGCTCCTAGGGTGCCCAG 60.366 66.667 19.37 6.35 42.42 4.45
1873 1933 2.689034 GCTCCTAGGGTGCCCAGT 60.689 66.667 9.46 0.00 36.35 4.00
1874 1934 2.301738 GCTCCTAGGGTGCCCAGTT 61.302 63.158 9.46 0.00 36.35 3.16
1875 1935 0.981277 GCTCCTAGGGTGCCCAGTTA 60.981 60.000 9.46 0.00 36.35 2.24
1876 1936 1.807814 CTCCTAGGGTGCCCAGTTAT 58.192 55.000 9.46 0.00 38.92 1.89
1877 1937 2.972348 CTCCTAGGGTGCCCAGTTATA 58.028 52.381 9.46 0.00 38.92 0.98
1878 1938 2.633481 CTCCTAGGGTGCCCAGTTATAC 59.367 54.545 9.46 0.00 38.92 1.47
1879 1939 2.249214 TCCTAGGGTGCCCAGTTATACT 59.751 50.000 9.46 0.00 38.92 2.12
1880 1940 3.468244 TCCTAGGGTGCCCAGTTATACTA 59.532 47.826 9.46 0.00 38.92 1.82
1881 1941 4.109106 TCCTAGGGTGCCCAGTTATACTAT 59.891 45.833 9.46 0.00 38.92 2.12
1882 1942 4.466726 CCTAGGGTGCCCAGTTATACTATC 59.533 50.000 10.26 0.00 38.92 2.08
1883 1943 4.214993 AGGGTGCCCAGTTATACTATCT 57.785 45.455 10.26 0.00 38.92 1.98
2039 2106 8.096414 ACATTGAATGGCTTATTACTTTTGCTT 58.904 29.630 10.27 0.00 33.60 3.91
2040 2107 9.585099 CATTGAATGGCTTATTACTTTTGCTTA 57.415 29.630 0.00 0.00 0.00 3.09
2234 2328 6.381801 AGTTCTGCGAATTGGACTTAAAATG 58.618 36.000 0.00 0.00 0.00 2.32
2269 2363 7.485913 GTGATGCAACTGATACCTAAATTTGTG 59.514 37.037 0.00 0.00 0.00 3.33
2386 2482 0.525761 GCAAAGCGACTTATTGGCCA 59.474 50.000 0.00 0.00 0.00 5.36
2500 2596 0.178873 TACAGGGGGTTGGAGAAGCT 60.179 55.000 0.00 0.00 0.00 3.74
2512 2608 0.514691 GAGAAGCTGTTCGTTGCTGG 59.485 55.000 0.00 0.00 39.71 4.85
3054 3176 0.947244 CGGCATTGACTTCTATGGGC 59.053 55.000 3.38 0.00 31.35 5.36
3153 3275 1.372087 CGATGCCAAGGTGGAGAAGC 61.372 60.000 0.00 0.00 40.96 3.86
3389 3511 3.083293 GCTCGGGGTAGAGATAGTAAGG 58.917 54.545 0.00 0.00 40.57 2.69
3603 3731 0.554792 AGAGCTTAAGGGCATGGCAT 59.445 50.000 22.06 11.91 34.17 4.40
3784 3918 6.426937 TCCGAGGACAAGAAACAAATAAAGAG 59.573 38.462 0.00 0.00 0.00 2.85
3821 3955 9.528018 GAAAATGACAAGGACAAGAAACAAATA 57.472 29.630 0.00 0.00 0.00 1.40
3888 4022 1.740025 GCATGGTAAAGAAGAAGCGCT 59.260 47.619 2.64 2.64 0.00 5.92
3981 4115 0.892063 GAGCAAGGAGGAGTTCGAGT 59.108 55.000 0.00 0.00 0.00 4.18
4126 4280 7.024340 TGGATGCTTAGAGTAGTTACTAACG 57.976 40.000 0.00 0.00 36.50 3.18
4163 4317 2.589720 TCTGGAATGGGCATATGCTTG 58.410 47.619 26.12 8.55 41.70 4.01
4228 4382 8.352201 CAGTTGGGTCATTATACATATTGGTTG 58.648 37.037 0.00 0.00 0.00 3.77
4295 4453 9.412460 TGTAAGCTCATCAAAGATGGAAATATT 57.588 29.630 7.11 0.00 0.00 1.28
4327 4485 5.127682 AGGCTGGAATTCATCATGTAAAACC 59.872 40.000 7.93 0.00 0.00 3.27
4371 4529 3.554324 CCGGTGGTACAAGAAATCATACG 59.446 47.826 0.00 0.00 44.16 3.06
4383 4541 5.057149 AGAAATCATACGTATGGCCAGAAC 58.943 41.667 30.07 11.44 34.50 3.01
4532 4690 9.838339 ATCACGAGAAGAAAACCATATCTATTT 57.162 29.630 0.00 0.00 0.00 1.40
4540 4698 8.958119 AGAAAACCATATCTATTTCGCTTACA 57.042 30.769 0.00 0.00 36.99 2.41
4590 4759 6.038825 TGTTTCAAACTTCACCATCGTGTAAT 59.961 34.615 1.10 0.00 41.09 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 28 0.545548 AGGAGAGTTGACTGGGGGTC 60.546 60.000 0.00 0.00 44.70 4.46
36 38 2.224066 ACACGAACAGGAAGGAGAGTTG 60.224 50.000 0.00 0.00 0.00 3.16
51 54 2.880268 TCTTGAGTAGAACCGACACGAA 59.120 45.455 0.00 0.00 0.00 3.85
61 64 5.843019 ATTCCCCTTTGTCTTGAGTAGAA 57.157 39.130 0.00 0.00 33.81 2.10
92 95 2.554032 CTCCTTTTCATTCGCCACTGTT 59.446 45.455 0.00 0.00 0.00 3.16
109 112 0.398318 GCTGGTTGTTGTCTCCTCCT 59.602 55.000 0.00 0.00 0.00 3.69
110 113 0.398318 AGCTGGTTGTTGTCTCCTCC 59.602 55.000 0.00 0.00 0.00 4.30
117 120 3.244078 TGAAGATACGAGCTGGTTGTTGT 60.244 43.478 6.71 0.00 0.00 3.32
122 125 3.963428 AGTTGAAGATACGAGCTGGTT 57.037 42.857 6.71 0.00 0.00 3.67
173 176 1.805943 GGCCATTTTTGTGTGCAATCC 59.194 47.619 0.00 0.00 34.18 3.01
212 216 2.100749 TCTTCACTTGTCAGCTCGTTCA 59.899 45.455 0.00 0.00 0.00 3.18
248 252 2.878406 CGAGTTGTTTTGTCCCATGTCT 59.122 45.455 0.00 0.00 0.00 3.41
303 318 7.223584 TCATCTAAGTTCTTGACCATTTGACA 58.776 34.615 0.00 0.00 0.00 3.58
310 325 6.611613 ATGTCTCATCTAAGTTCTTGACCA 57.388 37.500 0.00 0.00 0.00 4.02
469 501 8.595362 TCCTTTCCTTTTCTCTTTTCTTTTCT 57.405 30.769 0.00 0.00 0.00 2.52
470 502 9.653287 TTTCCTTTCCTTTTCTCTTTTCTTTTC 57.347 29.630 0.00 0.00 0.00 2.29
475 507 9.599866 TGATTTTTCCTTTCCTTTTCTCTTTTC 57.400 29.630 0.00 0.00 0.00 2.29
557 589 6.762187 TGTCTTCTACCGTTTTTGAATGTGTA 59.238 34.615 0.00 0.00 0.00 2.90
570 602 1.862827 GCGTTTTGTGTCTTCTACCGT 59.137 47.619 0.00 0.00 0.00 4.83
589 621 1.686052 TGTGGGGAAACTGTCATTTGC 59.314 47.619 0.00 0.00 0.00 3.68
666 698 2.533266 CCGTTGGGTTGTATCTCGTAC 58.467 52.381 0.00 0.00 0.00 3.67
672 704 4.271776 GTGTATTAGCCGTTGGGTTGTATC 59.728 45.833 0.00 0.00 34.28 2.24
690 722 5.477607 TTTATCCCCATCGATTCGTGTAT 57.522 39.130 5.89 0.00 0.00 2.29
739 771 2.570442 TTTTGTTTCGTGGGCTGTTC 57.430 45.000 0.00 0.00 0.00 3.18
763 795 1.412079 TGTGGCCAAGCAACTTTGAT 58.588 45.000 7.24 0.00 32.93 2.57
771 803 0.610174 TTGTTTGTTGTGGCCAAGCA 59.390 45.000 7.24 3.62 32.26 3.91
814 849 8.953313 CCATTGAATATAGCATGCTAAGATTCA 58.047 33.333 36.06 36.06 39.92 2.57
834 869 5.843969 TCACATATAACTCCCTAGCCATTGA 59.156 40.000 0.00 0.00 0.00 2.57
875 912 8.395633 CCGGTTTTACTATTTCAAATCTAGTGG 58.604 37.037 0.00 0.00 0.00 4.00
876 913 9.158233 TCCGGTTTTACTATTTCAAATCTAGTG 57.842 33.333 0.00 0.00 0.00 2.74
877 914 9.729281 TTCCGGTTTTACTATTTCAAATCTAGT 57.271 29.630 0.00 0.00 0.00 2.57
1218 1262 6.436532 TGAGGAGTTCTTAGTTCTTACCGAAT 59.563 38.462 0.00 0.00 33.45 3.34
1259 1303 1.818674 GTAGGCCAATTGAACTGGTGG 59.181 52.381 5.01 0.00 36.24 4.61
1281 1325 2.906897 CAAGCACACAAGGCCGGT 60.907 61.111 1.90 0.00 0.00 5.28
1406 1460 4.766404 TGCCTTTACAGAAGCTTTTAGC 57.234 40.909 0.00 0.00 42.84 3.09
1412 1466 3.295973 TGGTTTTGCCTTTACAGAAGCT 58.704 40.909 0.00 0.00 34.33 3.74
1419 1473 3.059166 CAGCACATGGTTTTGCCTTTAC 58.941 45.455 0.00 0.00 39.75 2.01
1483 1537 7.094549 GGAGTATAGAACAGCAGATCGAAGTAT 60.095 40.741 0.00 0.00 0.00 2.12
1509 1563 3.370953 CCCATGGACCTGAGAAACCTAAG 60.371 52.174 15.22 0.00 0.00 2.18
1528 1582 2.282110 CACCGTGGCACAATCCCA 60.282 61.111 19.09 0.00 44.16 4.37
1544 1598 4.994907 ACTGCGGTCTATACATGTAACA 57.005 40.909 10.14 0.00 0.00 2.41
1646 1706 1.543208 GGGCAAGGCAAAAAGGGAAAG 60.543 52.381 0.00 0.00 0.00 2.62
1672 1732 9.246670 TGAGATAATCCTTTCATCACAAACAAT 57.753 29.630 0.00 0.00 0.00 2.71
1714 1774 3.181458 TGCTCCCGTAACTTTTTCTGACT 60.181 43.478 0.00 0.00 0.00 3.41
1715 1775 3.135994 TGCTCCCGTAACTTTTTCTGAC 58.864 45.455 0.00 0.00 0.00 3.51
1716 1776 3.399330 CTGCTCCCGTAACTTTTTCTGA 58.601 45.455 0.00 0.00 0.00 3.27
1717 1777 2.095718 GCTGCTCCCGTAACTTTTTCTG 60.096 50.000 0.00 0.00 0.00 3.02
1719 1779 2.152016 AGCTGCTCCCGTAACTTTTTC 58.848 47.619 0.00 0.00 0.00 2.29
1720 1780 2.271944 AGCTGCTCCCGTAACTTTTT 57.728 45.000 0.00 0.00 0.00 1.94
1721 1781 2.614734 GGTAGCTGCTCCCGTAACTTTT 60.615 50.000 4.91 0.00 0.00 2.27
1723 1783 0.535797 GGTAGCTGCTCCCGTAACTT 59.464 55.000 4.91 0.00 0.00 2.66
1724 1784 1.328430 GGGTAGCTGCTCCCGTAACT 61.328 60.000 17.49 0.00 33.97 2.24
1725 1785 1.143401 GGGTAGCTGCTCCCGTAAC 59.857 63.158 17.49 5.60 33.97 2.50
1726 1786 3.625099 GGGTAGCTGCTCCCGTAA 58.375 61.111 17.49 0.00 33.97 3.18
1730 1790 0.978146 TCTTGAGGGTAGCTGCTCCC 60.978 60.000 22.14 22.14 43.71 4.30
1731 1791 0.905357 TTCTTGAGGGTAGCTGCTCC 59.095 55.000 4.91 7.52 0.00 4.70
1732 1792 1.742071 GCTTCTTGAGGGTAGCTGCTC 60.742 57.143 4.91 0.00 0.00 4.26
1733 1793 0.251634 GCTTCTTGAGGGTAGCTGCT 59.748 55.000 7.57 7.57 0.00 4.24
1734 1794 0.251634 AGCTTCTTGAGGGTAGCTGC 59.748 55.000 0.00 0.00 42.07 5.25
1736 1796 0.251634 GCAGCTTCTTGAGGGTAGCT 59.748 55.000 0.00 0.00 44.34 3.32
1737 1797 1.086634 CGCAGCTTCTTGAGGGTAGC 61.087 60.000 0.00 0.00 0.00 3.58
1738 1798 0.460987 CCGCAGCTTCTTGAGGGTAG 60.461 60.000 0.00 0.00 34.75 3.18
1739 1799 1.596934 CCGCAGCTTCTTGAGGGTA 59.403 57.895 0.00 0.00 34.75 3.69
1740 1800 2.348998 CCGCAGCTTCTTGAGGGT 59.651 61.111 0.00 0.00 34.75 4.34
1742 1802 2.437359 CCCCGCAGCTTCTTGAGG 60.437 66.667 0.00 0.00 37.72 3.86
1743 1803 1.743252 GTCCCCGCAGCTTCTTGAG 60.743 63.158 0.00 0.00 0.00 3.02
1744 1804 2.347490 GTCCCCGCAGCTTCTTGA 59.653 61.111 0.00 0.00 0.00 3.02
1745 1805 3.121030 CGTCCCCGCAGCTTCTTG 61.121 66.667 0.00 0.00 0.00 3.02
1746 1806 4.394712 CCGTCCCCGCAGCTTCTT 62.395 66.667 0.00 0.00 0.00 2.52
1775 1835 6.680378 GCCGTTGGATGCATAGTAGAATTTTT 60.680 38.462 0.00 0.00 0.00 1.94
1776 1836 5.221048 GCCGTTGGATGCATAGTAGAATTTT 60.221 40.000 0.00 0.00 0.00 1.82
1777 1837 4.275936 GCCGTTGGATGCATAGTAGAATTT 59.724 41.667 0.00 0.00 0.00 1.82
1778 1838 3.815401 GCCGTTGGATGCATAGTAGAATT 59.185 43.478 0.00 0.00 0.00 2.17
1779 1839 3.403038 GCCGTTGGATGCATAGTAGAAT 58.597 45.455 0.00 0.00 0.00 2.40
1780 1840 2.484770 GGCCGTTGGATGCATAGTAGAA 60.485 50.000 0.00 0.00 0.00 2.10
1781 1841 1.070134 GGCCGTTGGATGCATAGTAGA 59.930 52.381 0.00 0.00 0.00 2.59
1782 1842 1.202639 TGGCCGTTGGATGCATAGTAG 60.203 52.381 0.00 0.00 0.00 2.57
1783 1843 0.833949 TGGCCGTTGGATGCATAGTA 59.166 50.000 0.00 0.00 0.00 1.82
1784 1844 0.464373 CTGGCCGTTGGATGCATAGT 60.464 55.000 0.00 0.00 0.00 2.12
1785 1845 1.168407 CCTGGCCGTTGGATGCATAG 61.168 60.000 0.00 0.00 0.00 2.23
1786 1846 1.152984 CCTGGCCGTTGGATGCATA 60.153 57.895 0.00 0.00 0.00 3.14
1787 1847 2.440796 CCTGGCCGTTGGATGCAT 60.441 61.111 0.00 0.00 0.00 3.96
1788 1848 4.738998 CCCTGGCCGTTGGATGCA 62.739 66.667 10.40 0.00 0.00 3.96
1789 1849 4.424711 TCCCTGGCCGTTGGATGC 62.425 66.667 10.40 0.00 0.00 3.91
1790 1850 2.438434 GTCCCTGGCCGTTGGATG 60.438 66.667 10.54 0.00 0.00 3.51
1791 1851 2.933287 TGTCCCTGGCCGTTGGAT 60.933 61.111 10.54 0.00 0.00 3.41
1792 1852 3.636231 CTGTCCCTGGCCGTTGGA 61.636 66.667 10.40 7.17 0.00 3.53
1799 1859 1.819632 CGTTATGGCTGTCCCTGGC 60.820 63.158 0.00 0.00 0.00 4.85
1800 1860 0.828022 TACGTTATGGCTGTCCCTGG 59.172 55.000 0.00 0.00 0.00 4.45
1801 1861 2.684001 TTACGTTATGGCTGTCCCTG 57.316 50.000 0.00 0.00 0.00 4.45
1802 1862 3.706600 TTTTACGTTATGGCTGTCCCT 57.293 42.857 0.00 0.00 0.00 4.20
1803 1863 4.439563 CCAATTTTACGTTATGGCTGTCCC 60.440 45.833 0.00 0.00 0.00 4.46
1804 1864 4.396790 TCCAATTTTACGTTATGGCTGTCC 59.603 41.667 0.00 0.00 0.00 4.02
1805 1865 5.106475 TGTCCAATTTTACGTTATGGCTGTC 60.106 40.000 0.00 0.00 0.00 3.51
1806 1866 4.762765 TGTCCAATTTTACGTTATGGCTGT 59.237 37.500 0.00 0.00 0.00 4.40
1807 1867 5.303747 TGTCCAATTTTACGTTATGGCTG 57.696 39.130 0.00 0.00 0.00 4.85
1808 1868 4.142469 GCTGTCCAATTTTACGTTATGGCT 60.142 41.667 0.00 0.00 0.00 4.75
1809 1869 4.102649 GCTGTCCAATTTTACGTTATGGC 58.897 43.478 0.00 0.00 0.00 4.40
1810 1870 5.448632 GGAGCTGTCCAATTTTACGTTATGG 60.449 44.000 0.00 0.00 43.31 2.74
1811 1871 5.569413 GGAGCTGTCCAATTTTACGTTATG 58.431 41.667 0.00 0.00 43.31 1.90
1812 1872 4.331717 CGGAGCTGTCCAATTTTACGTTAT 59.668 41.667 0.00 0.00 44.18 1.89
1813 1873 3.680937 CGGAGCTGTCCAATTTTACGTTA 59.319 43.478 0.00 0.00 44.18 3.18
1814 1874 2.482721 CGGAGCTGTCCAATTTTACGTT 59.517 45.455 0.00 0.00 44.18 3.99
1815 1875 2.073816 CGGAGCTGTCCAATTTTACGT 58.926 47.619 0.00 0.00 44.18 3.57
1816 1876 1.396996 CCGGAGCTGTCCAATTTTACG 59.603 52.381 0.00 0.00 44.18 3.18
1817 1877 2.706890 TCCGGAGCTGTCCAATTTTAC 58.293 47.619 0.00 0.00 44.18 2.01
1818 1878 3.343617 CTTCCGGAGCTGTCCAATTTTA 58.656 45.455 3.34 0.00 44.18 1.52
1819 1879 2.162681 CTTCCGGAGCTGTCCAATTTT 58.837 47.619 3.34 0.00 44.18 1.82
1820 1880 1.826385 CTTCCGGAGCTGTCCAATTT 58.174 50.000 3.34 0.00 44.18 1.82
1821 1881 3.558674 CTTCCGGAGCTGTCCAATT 57.441 52.632 3.34 0.00 44.18 2.32
1831 1891 1.134367 TCACGTTATCAGCTTCCGGAG 59.866 52.381 3.34 0.00 0.00 4.63
1832 1892 1.134367 CTCACGTTATCAGCTTCCGGA 59.866 52.381 0.00 0.00 0.00 5.14
1833 1893 1.560923 CTCACGTTATCAGCTTCCGG 58.439 55.000 0.00 0.00 0.00 5.14
1834 1894 1.560923 CCTCACGTTATCAGCTTCCG 58.439 55.000 0.00 0.00 0.00 4.30
1835 1895 1.480954 TCCCTCACGTTATCAGCTTCC 59.519 52.381 0.00 0.00 0.00 3.46
1836 1896 2.815478 CTCCCTCACGTTATCAGCTTC 58.185 52.381 0.00 0.00 0.00 3.86
1837 1897 1.134670 GCTCCCTCACGTTATCAGCTT 60.135 52.381 0.00 0.00 0.00 3.74
1838 1898 0.461961 GCTCCCTCACGTTATCAGCT 59.538 55.000 0.00 0.00 0.00 4.24
1839 1899 0.461961 AGCTCCCTCACGTTATCAGC 59.538 55.000 0.00 0.00 0.00 4.26
1840 1900 1.067821 GGAGCTCCCTCACGTTATCAG 59.932 57.143 23.19 0.00 39.96 2.90
1841 1901 1.112113 GGAGCTCCCTCACGTTATCA 58.888 55.000 23.19 0.00 39.96 2.15
1842 1902 1.404843 AGGAGCTCCCTCACGTTATC 58.595 55.000 29.54 0.00 43.31 1.75
1843 1903 2.588620 CTAGGAGCTCCCTCACGTTAT 58.411 52.381 29.54 9.89 43.31 1.89
1844 1904 1.409802 CCTAGGAGCTCCCTCACGTTA 60.410 57.143 29.54 12.02 43.31 3.18
1845 1905 0.684805 CCTAGGAGCTCCCTCACGTT 60.685 60.000 29.54 11.45 43.31 3.99
1846 1906 1.076632 CCTAGGAGCTCCCTCACGT 60.077 63.158 29.54 12.24 43.31 4.49
1847 1907 1.830408 CCCTAGGAGCTCCCTCACG 60.830 68.421 29.54 12.07 43.31 4.35
1848 1908 1.045911 CACCCTAGGAGCTCCCTCAC 61.046 65.000 29.54 3.72 43.31 3.51
1849 1909 1.311403 CACCCTAGGAGCTCCCTCA 59.689 63.158 29.54 13.81 43.31 3.86
1850 1910 2.137528 GCACCCTAGGAGCTCCCTC 61.138 68.421 29.54 4.56 43.31 4.30
1852 1912 3.164977 GGCACCCTAGGAGCTCCC 61.165 72.222 29.54 11.72 39.22 4.30
1969 2036 9.282569 GCCATCTTTCCTGGATATATTCATATC 57.717 37.037 0.00 0.00 41.60 1.63
1972 2039 7.036154 TGCCATCTTTCCTGGATATATTCAT 57.964 36.000 0.00 0.00 35.70 2.57
1993 2060 0.383949 TTGCTCGTCAAAAACCTGCC 59.616 50.000 0.00 0.00 0.00 4.85
2128 2222 8.470805 GGATCCTATATGTCATACTCGATGTTT 58.529 37.037 3.84 0.00 36.84 2.83
2221 2315 7.831753 TCACAAAGAACACATTTTAAGTCCAA 58.168 30.769 0.00 0.00 0.00 3.53
2234 2328 4.291540 TCAGTTGCATCACAAAGAACAC 57.708 40.909 0.00 0.00 40.82 3.32
2386 2482 1.737029 CGGATGTGTCACTGAATCGCT 60.737 52.381 4.27 0.00 0.00 4.93
2500 2596 1.895798 AGATCTCTCCAGCAACGAACA 59.104 47.619 0.00 0.00 0.00 3.18
2512 2608 2.699846 AGCAACATGGAGGAGATCTCTC 59.300 50.000 21.81 15.95 42.10 3.20
2904 3023 5.808366 ATGTCACTCTTGTGTCTCCTAAA 57.192 39.130 0.00 0.00 44.14 1.85
2927 3049 2.034221 GCCCTCGGGTTGCTTCTT 59.966 61.111 3.54 0.00 37.65 2.52
3054 3176 4.838152 CCGGGCACGAGTGATGGG 62.838 72.222 11.66 0.37 44.60 4.00
3177 3299 2.788230 ATCCTGGTGGAGCCTCCCAA 62.788 60.000 8.62 0.00 46.91 4.12
3603 3731 5.863935 CGACTTCATATGTCACTTTGAGTCA 59.136 40.000 1.90 0.00 34.37 3.41
3784 3918 8.522830 TGTCCTTGTCATTTTCCATCTTTATTC 58.477 33.333 0.00 0.00 0.00 1.75
3800 3934 8.287439 TCTTTATTTGTTTCTTGTCCTTGTCA 57.713 30.769 0.00 0.00 0.00 3.58
3821 3955 2.171003 CCCTCGCCATTTTCCTTCTTT 58.829 47.619 0.00 0.00 0.00 2.52
3981 4115 0.934496 CGTTTCTTCTTCACCACGCA 59.066 50.000 0.00 0.00 0.00 5.24
4076 4210 2.298163 AGCAAAGGGAGTGCATTGAAAG 59.702 45.455 0.00 0.00 44.74 2.62
4126 4280 3.006967 TCCAGAAGTTGCAGAGAAGTACC 59.993 47.826 0.00 0.00 0.00 3.34
4170 4324 6.403636 GGTTACGAGATCACATGAAGCAAATT 60.404 38.462 0.00 0.00 0.00 1.82
4187 4341 2.346803 CAACTGGACCATGGTTACGAG 58.653 52.381 20.85 15.75 0.00 4.18
4295 4453 1.704628 TGAATTCCAGCCTGTTCCTGA 59.295 47.619 2.27 0.00 32.03 3.86
4327 4485 3.423206 GCTTTGAGTTGCTGTTCGATTTG 59.577 43.478 0.00 0.00 0.00 2.32
4371 4529 1.750778 CCACCAATGTTCTGGCCATAC 59.249 52.381 5.51 8.70 40.45 2.39
4383 4541 1.197721 GACGAACAAGCTCCACCAATG 59.802 52.381 0.00 0.00 0.00 2.82
4532 4690 4.463539 TCATACCTGTAAAGGTGTAAGCGA 59.536 41.667 15.50 0.00 43.03 4.93
4540 4698 9.396022 CAATCTTAATGTCATACCTGTAAAGGT 57.604 33.333 10.20 10.20 45.46 3.50


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

AutoCloner maintained by Alex Coulton.