Multiple sequence alignment - TraesCS5A01G385500

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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 TraesCS5A01G385500 chr5A 100.000 4739 0 0 1 4739 583557170 583561908 0.000000e+00 8752.0
1 TraesCS5A01G385500 chr5A 100.000 572 0 0 5113 5684 583562282 583562853 0.000000e+00 1057.0
2 TraesCS5A01G385500 chr5B 91.656 4506 195 62 313 4729 570066733 570071146 0.000000e+00 6071.0
3 TraesCS5A01G385500 chr5B 93.644 472 16 7 5113 5584 570071222 570071679 0.000000e+00 693.0
4 TraesCS5A01G385500 chr5D 94.264 1883 67 21 2870 4739 463188992 463190846 0.000000e+00 2841.0
5 TraesCS5A01G385500 chr5D 88.306 2001 145 39 1 1935 463185825 463187802 0.000000e+00 2316.0
6 TraesCS5A01G385500 chr5D 90.661 953 55 15 1931 2872 463187903 463188832 0.000000e+00 1236.0
7 TraesCS5A01G385500 chr5D 93.671 395 15 2 5113 5507 463190903 463191287 2.950000e-162 582.0
8 TraesCS5A01G385500 chr6D 90.061 1147 92 12 3276 4417 380980877 380979748 0.000000e+00 1467.0
9 TraesCS5A01G385500 chr6D 89.766 1153 91 15 3270 4417 431261697 431262827 0.000000e+00 1450.0
10 TraesCS5A01G385500 chr1B 92.323 495 30 5 3926 4417 374010955 374010466 0.000000e+00 697.0
11 TraesCS5A01G385500 chr7B 89.691 388 33 5 3826 4211 156916221 156915839 6.620000e-134 488.0
12 TraesCS5A01G385500 chr2B 86.726 113 8 6 2103 2210 446218501 446218611 1.000000e-22 119.0
13 TraesCS5A01G385500 chr2A 83.696 92 13 2 302 392 127151824 127151734 1.010000e-12 86.1


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 TraesCS5A01G385500 chr5A 583557170 583562853 5683 False 4904.50 8752 100.0000 1 5684 2 chr5A.!!$F1 5683
1 TraesCS5A01G385500 chr5B 570066733 570071679 4946 False 3382.00 6071 92.6500 313 5584 2 chr5B.!!$F1 5271
2 TraesCS5A01G385500 chr5D 463185825 463191287 5462 False 1743.75 2841 91.7255 1 5507 4 chr5D.!!$F1 5506
3 TraesCS5A01G385500 chr6D 380979748 380980877 1129 True 1467.00 1467 90.0610 3276 4417 1 chr6D.!!$R1 1141
4 TraesCS5A01G385500 chr6D 431261697 431262827 1130 False 1450.00 1450 89.7660 3270 4417 1 chr6D.!!$F1 1147

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
737 778 0.034186 GCCAAGGACACATCATCCCA 60.034 55.0 0.00 0.00 36.86 4.37 F
1282 1325 0.035343 GGTCCTGCAGGTAGTTTCCC 60.035 60.0 31.58 16.33 36.34 3.97 F
2467 2693 0.035056 GCTATAATCAGCCGGCCCAT 60.035 55.0 26.15 13.01 35.40 4.00 F
3680 4085 0.249398 GCGGTGGATCAGGTACACTT 59.751 55.0 0.00 0.00 41.73 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2448 2673 0.035056 ATGGGCCGGCTGATTATAGC 60.035 55.000 28.56 5.59 42.94 2.97 R
2486 2712 1.743394 GCACCCTTCCGAACCAAATAG 59.257 52.381 0.00 0.00 0.00 1.73 R
3684 4089 1.623811 ACTGCGATGTAAGGGTGAAGT 59.376 47.619 0.00 0.00 0.00 3.01 R
5363 5774 0.462759 GTCGCCATCCTCTTTCCAGG 60.463 60.000 0.00 0.00 34.40 4.45 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
37 38 7.898636 AGTTTTGATGTCCTTATTATTTCCCCA 59.101 33.333 0.00 0.00 0.00 4.96
54 55 3.329520 TCCCCAAGGTGGATTATATTCGG 59.670 47.826 0.00 0.00 40.96 4.30
78 79 9.413048 CGGAAGTCTTATATATTTCCACTCTTC 57.587 37.037 11.80 7.83 37.70 2.87
127 128 5.904362 AACAAATTTCTATCAGACCAGGC 57.096 39.130 0.00 0.00 0.00 4.85
134 135 4.808767 TCTATCAGACCAGGCCTAACTA 57.191 45.455 3.98 0.00 0.00 2.24
156 157 7.339482 ACTAGTTGGAGAGTTATTTTCCATCC 58.661 38.462 0.00 0.00 40.48 3.51
166 167 6.583562 AGTTATTTTCCATCCGAGTAGAAGG 58.416 40.000 0.00 0.00 0.00 3.46
172 173 2.693591 CCATCCGAGTAGAAGGCACTAA 59.306 50.000 0.00 0.00 38.49 2.24
175 176 3.159472 TCCGAGTAGAAGGCACTAACAA 58.841 45.455 0.00 0.00 38.49 2.83
190 191 7.885399 AGGCACTAACAATTTCAATCTTAGAGT 59.115 33.333 0.00 0.00 36.02 3.24
204 205 3.064958 TCTTAGAGTATCGCCAACAGTCG 59.935 47.826 0.00 0.00 42.67 4.18
215 216 4.338964 TCGCCAACAGTCGTCCTATAATAA 59.661 41.667 0.00 0.00 0.00 1.40
217 218 5.598769 GCCAACAGTCGTCCTATAATAAGT 58.401 41.667 0.00 0.00 0.00 2.24
219 220 6.570692 CCAACAGTCGTCCTATAATAAGTGT 58.429 40.000 0.00 0.00 0.00 3.55
225 226 6.827251 AGTCGTCCTATAATAAGTGTGAGTCA 59.173 38.462 0.00 0.00 0.00 3.41
235 236 6.759497 ATAAGTGTGAGTCATTTTTAGGGC 57.241 37.500 0.00 0.00 0.00 5.19
277 280 4.424711 GCCTCCAACCGATGCCCA 62.425 66.667 0.00 0.00 0.00 5.36
280 283 0.684153 CCTCCAACCGATGCCCAATT 60.684 55.000 0.00 0.00 0.00 2.32
284 287 2.025793 TCCAACCGATGCCCAATTCTAA 60.026 45.455 0.00 0.00 0.00 2.10
285 288 2.757868 CCAACCGATGCCCAATTCTAAA 59.242 45.455 0.00 0.00 0.00 1.85
289 293 5.262588 ACCGATGCCCAATTCTAAATTTC 57.737 39.130 0.00 0.00 0.00 2.17
402 407 4.481112 GGCGCCTTCATGCAACCG 62.481 66.667 22.15 0.00 0.00 4.44
403 408 3.430862 GCGCCTTCATGCAACCGA 61.431 61.111 0.00 0.00 0.00 4.69
407 412 1.402720 CGCCTTCATGCAACCGAAAAT 60.403 47.619 0.00 0.00 0.00 1.82
418 423 2.038387 ACCGAAAATCCTTGGATCCG 57.962 50.000 7.39 7.20 0.00 4.18
420 425 2.290705 ACCGAAAATCCTTGGATCCGTT 60.291 45.455 7.39 0.00 0.00 4.44
422 427 2.030457 CGAAAATCCTTGGATCCGTTCG 59.970 50.000 19.16 19.16 0.00 3.95
423 428 2.038387 AAATCCTTGGATCCGTTCGG 57.962 50.000 7.39 4.74 0.00 4.30
424 429 0.909623 AATCCTTGGATCCGTTCGGT 59.090 50.000 7.39 0.00 0.00 4.69
426 431 1.449601 CCTTGGATCCGTTCGGTGG 60.450 63.158 7.39 0.00 0.00 4.61
447 468 2.774633 GGGCCCCCAACCCGAATAT 61.775 63.158 12.23 0.00 37.67 1.28
461 487 1.813092 CGAATATGCTTGCTGCTCCCT 60.813 52.381 0.00 0.00 43.37 4.20
465 491 0.914644 ATGCTTGCTGCTCCCTTCTA 59.085 50.000 0.00 0.00 43.37 2.10
475 501 5.045578 TGCTGCTCCCTTCTAATTTTAGAGT 60.046 40.000 0.00 0.00 40.57 3.24
477 503 6.704050 GCTGCTCCCTTCTAATTTTAGAGTAG 59.296 42.308 0.00 0.00 40.57 2.57
544 579 7.924358 TTATTATAGGGCTACTGTTGGAGAA 57.076 36.000 0.00 0.00 0.00 2.87
549 584 1.362406 GCTACTGTTGGAGAAGGCGC 61.362 60.000 0.00 0.00 0.00 6.53
555 590 1.228245 TTGGAGAAGGCGCTTGCTT 60.228 52.632 7.64 1.33 39.13 3.91
559 594 1.510480 GAGAAGGCGCTTGCTTGTGT 61.510 55.000 7.64 0.00 39.13 3.72
567 602 2.721090 GCGCTTGCTTGTGTAAAAAGAG 59.279 45.455 0.00 0.00 30.71 2.85
583 618 6.968131 AAAAAGAGAAGAAGGTTTTTGTGC 57.032 33.333 0.00 0.00 32.29 4.57
585 620 3.903467 AGAGAAGAAGGTTTTTGTGCCT 58.097 40.909 0.00 0.00 36.51 4.75
586 621 5.048846 AGAGAAGAAGGTTTTTGTGCCTA 57.951 39.130 0.00 0.00 34.15 3.93
590 625 6.749139 AGAAGAAGGTTTTTGTGCCTAATTC 58.251 36.000 0.00 0.00 34.15 2.17
602 640 7.775053 TTGTGCCTAATTCTTTTTACTCCAT 57.225 32.000 0.00 0.00 0.00 3.41
612 650 8.970691 ATTCTTTTTACTCCATCATGTTTTCG 57.029 30.769 0.00 0.00 0.00 3.46
631 672 3.497332 TCGTGCCCTATTATAGAGCTGT 58.503 45.455 7.24 0.00 30.01 4.40
632 673 3.506455 TCGTGCCCTATTATAGAGCTGTC 59.494 47.826 7.24 0.00 30.01 3.51
637 678 4.810790 CCCTATTATAGAGCTGTCGTTGG 58.189 47.826 0.03 0.00 0.00 3.77
638 679 4.523173 CCCTATTATAGAGCTGTCGTTGGA 59.477 45.833 0.03 0.00 0.00 3.53
639 680 5.336055 CCCTATTATAGAGCTGTCGTTGGAG 60.336 48.000 0.03 0.00 0.00 3.86
640 681 5.473846 CCTATTATAGAGCTGTCGTTGGAGA 59.526 44.000 0.03 0.00 0.00 3.71
669 710 0.323302 TGCATTCAGTCCCGCTTGTA 59.677 50.000 0.00 0.00 0.00 2.41
671 712 1.405526 GCATTCAGTCCCGCTTGTAGA 60.406 52.381 0.00 0.00 0.00 2.59
737 778 0.034186 GCCAAGGACACATCATCCCA 60.034 55.000 0.00 0.00 36.86 4.37
750 791 2.275380 ATCCCAAAGCCACGGCAAC 61.275 57.895 11.35 0.00 44.88 4.17
761 802 0.802494 CACGGCAACCTATTGGACAC 59.198 55.000 0.00 0.00 36.23 3.67
762 803 0.322187 ACGGCAACCTATTGGACACC 60.322 55.000 0.00 0.00 36.23 4.16
868 910 9.465985 ACGTCGAAACCACAAAATAAATAAAAT 57.534 25.926 0.00 0.00 0.00 1.82
1029 1071 1.076438 CCTTCTTCTCCACCCCCTTT 58.924 55.000 0.00 0.00 0.00 3.11
1104 1146 1.955080 CCCGCGTAGATTCTAGGTCTT 59.045 52.381 4.92 0.00 0.00 3.01
1282 1325 0.035343 GGTCCTGCAGGTAGTTTCCC 60.035 60.000 31.58 16.33 36.34 3.97
1433 1478 5.047802 AGGTAATTGAACCGACTCGTTTCTA 60.048 40.000 9.75 3.23 44.77 2.10
1655 1729 4.247258 TGAAAAATCATTGTGCATCAGCC 58.753 39.130 0.00 0.00 41.13 4.85
1687 1761 2.618709 AGTTGTTACTGCAAGGTGCTTC 59.381 45.455 1.43 0.00 45.31 3.86
1723 1797 9.586150 CGTATTTTCTTTCTATGTATGATGTGC 57.414 33.333 0.00 0.00 0.00 4.57
1725 1799 8.757982 ATTTTCTTTCTATGTATGATGTGCCT 57.242 30.769 0.00 0.00 0.00 4.75
1745 1819 3.589988 CTCTCATAGAGGTTGTTTGCGT 58.410 45.455 0.00 0.00 38.67 5.24
1746 1820 3.325870 TCTCATAGAGGTTGTTTGCGTG 58.674 45.455 0.00 0.00 0.00 5.34
1747 1821 3.067106 CTCATAGAGGTTGTTTGCGTGT 58.933 45.455 0.00 0.00 0.00 4.49
1750 1824 1.589803 AGAGGTTGTTTGCGTGTACC 58.410 50.000 0.00 0.00 0.00 3.34
1790 1887 4.262164 GCTGTCAATGTTCAGGATTTTGGT 60.262 41.667 9.23 0.00 32.94 3.67
1791 1888 5.048083 GCTGTCAATGTTCAGGATTTTGGTA 60.048 40.000 9.23 0.00 32.94 3.25
1792 1889 6.516527 GCTGTCAATGTTCAGGATTTTGGTAA 60.517 38.462 9.23 0.00 32.94 2.85
1793 1890 6.744112 TGTCAATGTTCAGGATTTTGGTAAC 58.256 36.000 0.00 0.00 0.00 2.50
1794 1891 6.549364 TGTCAATGTTCAGGATTTTGGTAACT 59.451 34.615 0.00 0.00 37.61 2.24
1795 1892 6.863126 GTCAATGTTCAGGATTTTGGTAACTG 59.137 38.462 0.00 0.00 37.61 3.16
1796 1893 6.549364 TCAATGTTCAGGATTTTGGTAACTGT 59.451 34.615 0.00 0.00 37.61 3.55
1797 1894 6.976934 ATGTTCAGGATTTTGGTAACTGTT 57.023 33.333 0.00 0.00 37.61 3.16
1798 1895 8.356657 CAATGTTCAGGATTTTGGTAACTGTTA 58.643 33.333 0.00 0.00 37.61 2.41
1799 1896 7.504924 TGTTCAGGATTTTGGTAACTGTTAG 57.495 36.000 0.00 0.00 37.61 2.34
1800 1897 6.016610 TGTTCAGGATTTTGGTAACTGTTAGC 60.017 38.462 19.82 19.82 37.61 3.09
1801 1898 5.876357 TCAGGATTTTGGTAACTGTTAGCT 58.124 37.500 24.86 9.48 34.81 3.32
1802 1899 5.705441 TCAGGATTTTGGTAACTGTTAGCTG 59.295 40.000 24.86 15.41 34.81 4.24
1803 1900 4.459337 AGGATTTTGGTAACTGTTAGCTGC 59.541 41.667 24.86 13.38 34.81 5.25
1804 1901 4.459337 GGATTTTGGTAACTGTTAGCTGCT 59.541 41.667 24.86 7.57 34.81 4.24
1805 1902 5.048013 GGATTTTGGTAACTGTTAGCTGCTT 60.048 40.000 24.86 11.56 34.81 3.91
1806 1903 4.829064 TTTGGTAACTGTTAGCTGCTTG 57.171 40.909 24.86 0.00 34.81 4.01
1807 1904 2.778299 TGGTAACTGTTAGCTGCTTGG 58.222 47.619 24.86 0.00 34.81 3.61
1808 1905 2.105821 TGGTAACTGTTAGCTGCTTGGT 59.894 45.455 24.86 0.00 34.81 3.67
1809 1906 2.742589 GGTAACTGTTAGCTGCTTGGTC 59.257 50.000 19.46 0.00 0.00 4.02
1810 1907 1.897560 AACTGTTAGCTGCTTGGTCC 58.102 50.000 7.79 0.00 0.00 4.46
1811 1908 0.320771 ACTGTTAGCTGCTTGGTCCG 60.321 55.000 7.79 0.00 0.00 4.79
1812 1909 1.003839 TGTTAGCTGCTTGGTCCGG 60.004 57.895 7.79 0.00 0.00 5.14
1813 1910 1.003718 GTTAGCTGCTTGGTCCGGT 60.004 57.895 7.79 0.00 0.00 5.28
1814 1911 1.003839 TTAGCTGCTTGGTCCGGTG 60.004 57.895 7.79 0.00 0.00 4.94
1815 1912 3.605749 TAGCTGCTTGGTCCGGTGC 62.606 63.158 7.79 0.12 0.00 5.01
1840 1937 3.576982 AGTAGGGATTAATCGGCGAATCA 59.423 43.478 15.93 0.00 34.36 2.57
1841 1938 3.703001 AGGGATTAATCGGCGAATCAT 57.297 42.857 15.93 1.51 34.36 2.45
1844 1941 3.600388 GGATTAATCGGCGAATCATCCT 58.400 45.455 24.12 1.18 34.36 3.24
1874 1971 8.608844 ACTGAATTATCGATAACCCATTTCTC 57.391 34.615 19.73 7.44 0.00 2.87
1897 1994 3.643320 GGTAGGTTAACTAGGGCCGTATT 59.357 47.826 5.45 0.00 30.77 1.89
1903 2000 6.955851 AGGTTAACTAGGGCCGTATTGATATA 59.044 38.462 5.45 0.00 0.00 0.86
1939 2141 4.563580 TGGCAACATACGATGTACTAAACG 59.436 41.667 0.00 0.00 46.17 3.60
1942 2144 5.276067 GCAACATACGATGTACTAAACGTCC 60.276 44.000 0.00 0.00 44.07 4.79
1979 2181 6.239600 CCTGGGCTACATAGTTACATACACAT 60.240 42.308 0.00 0.00 0.00 3.21
1980 2182 6.755206 TGGGCTACATAGTTACATACACATC 58.245 40.000 0.00 0.00 0.00 3.06
1981 2183 6.325286 TGGGCTACATAGTTACATACACATCA 59.675 38.462 0.00 0.00 0.00 3.07
2008 2210 8.252417 CCAATCTTCATAGATCACATAGGAGAG 58.748 40.741 0.00 0.00 40.26 3.20
2023 2225 2.592512 AGGAGAGGGGAGATTACCTTGA 59.407 50.000 0.00 0.00 37.18 3.02
2066 2268 4.488911 AGGGGAGGAGCAGGCGAT 62.489 66.667 0.00 0.00 0.00 4.58
2070 2272 1.221840 GGAGGAGCAGGCGATGAAA 59.778 57.895 0.00 0.00 0.00 2.69
2080 2282 2.813754 CAGGCGATGAAACAGGAAGAAA 59.186 45.455 0.00 0.00 0.00 2.52
2213 2416 3.934962 GCGGATGAGGGAGGCTCC 61.935 72.222 25.80 25.80 35.23 4.70
2308 2511 4.834453 CGGCTGCTGCTCCTCTGG 62.834 72.222 15.64 0.00 39.59 3.86
2398 2622 0.464735 TCCGCCCACCCGATAATTTG 60.465 55.000 0.00 0.00 0.00 2.32
2399 2623 1.358759 CGCCCACCCGATAATTTGC 59.641 57.895 0.00 0.00 0.00 3.68
2400 2624 1.739667 GCCCACCCGATAATTTGCC 59.260 57.895 0.00 0.00 0.00 4.52
2401 2625 1.744320 GCCCACCCGATAATTTGCCC 61.744 60.000 0.00 0.00 0.00 5.36
2402 2626 0.106217 CCCACCCGATAATTTGCCCT 60.106 55.000 0.00 0.00 0.00 5.19
2403 2627 1.687996 CCCACCCGATAATTTGCCCTT 60.688 52.381 0.00 0.00 0.00 3.95
2404 2628 2.107366 CCACCCGATAATTTGCCCTTT 58.893 47.619 0.00 0.00 0.00 3.11
2405 2629 2.499693 CCACCCGATAATTTGCCCTTTT 59.500 45.455 0.00 0.00 0.00 2.27
2406 2630 3.702045 CCACCCGATAATTTGCCCTTTTA 59.298 43.478 0.00 0.00 0.00 1.52
2407 2631 4.343814 CCACCCGATAATTTGCCCTTTTAT 59.656 41.667 0.00 0.00 0.00 1.40
2408 2632 5.163353 CCACCCGATAATTTGCCCTTTTATT 60.163 40.000 0.00 0.00 0.00 1.40
2409 2633 5.752955 CACCCGATAATTTGCCCTTTTATTG 59.247 40.000 0.00 0.00 0.00 1.90
2410 2634 5.163353 ACCCGATAATTTGCCCTTTTATTGG 60.163 40.000 0.00 0.00 36.93 3.16
2419 2643 2.893489 GCCCTTTTATTGGCTATCAGGG 59.107 50.000 13.23 13.23 44.46 4.45
2420 2644 2.893489 CCCTTTTATTGGCTATCAGGGC 59.107 50.000 7.51 0.00 0.00 5.19
2421 2645 3.437052 CCCTTTTATTGGCTATCAGGGCT 60.437 47.826 7.51 0.00 0.00 5.19
2422 2646 4.202567 CCCTTTTATTGGCTATCAGGGCTA 60.203 45.833 7.51 0.00 0.00 3.93
2423 2647 5.517299 CCCTTTTATTGGCTATCAGGGCTAT 60.517 44.000 7.51 0.00 0.00 2.97
2424 2648 6.012745 CCTTTTATTGGCTATCAGGGCTATT 58.987 40.000 0.00 0.00 0.00 1.73
2425 2649 6.494835 CCTTTTATTGGCTATCAGGGCTATTT 59.505 38.462 0.00 0.00 0.00 1.40
2426 2650 6.899393 TTTATTGGCTATCAGGGCTATTTG 57.101 37.500 0.00 0.00 0.00 2.32
2450 2675 3.837355 CCTTTTATTGGCTATCAGGGCT 58.163 45.455 0.00 0.00 0.00 5.19
2467 2693 0.035056 GCTATAATCAGCCGGCCCAT 60.035 55.000 26.15 13.01 35.40 4.00
2720 2952 2.513317 TGGATATGTGGGGATTTCTGCA 59.487 45.455 0.00 0.00 0.00 4.41
2873 3267 2.954318 AGGATGCTCATGCCAATTACAC 59.046 45.455 0.00 0.00 38.71 2.90
3524 3929 6.072286 CCTTATTGATTATGAGGTCATGTGGC 60.072 42.308 2.56 0.00 35.72 5.01
3566 3971 1.187974 CATTTGGCATGCTTCTGGGA 58.812 50.000 18.92 0.00 0.00 4.37
3590 3995 3.325716 ACTTGCTTGCCAGGAAATGAAAT 59.674 39.130 0.00 0.00 28.45 2.17
3597 4002 3.181488 TGCCAGGAAATGAAATATGCACG 60.181 43.478 0.00 0.00 0.00 5.34
3678 4083 1.153429 GGCGGTGGATCAGGTACAC 60.153 63.158 0.00 0.00 41.26 2.90
3679 4084 1.614241 GGCGGTGGATCAGGTACACT 61.614 60.000 0.00 0.00 41.73 3.55
3680 4085 0.249398 GCGGTGGATCAGGTACACTT 59.751 55.000 0.00 0.00 41.73 3.16
3681 4086 1.739371 GCGGTGGATCAGGTACACTTC 60.739 57.143 0.00 0.00 41.73 3.01
3682 4087 1.548719 CGGTGGATCAGGTACACTTCA 59.451 52.381 0.00 0.00 41.73 3.02
3683 4088 2.417379 CGGTGGATCAGGTACACTTCAG 60.417 54.545 0.00 0.00 41.73 3.02
3684 4089 2.832129 GGTGGATCAGGTACACTTCAGA 59.168 50.000 0.00 0.00 41.73 3.27
3759 4164 6.773976 AGGCTTAAAACTGCAATGCTATTA 57.226 33.333 6.82 0.00 0.00 0.98
3760 4165 7.352079 AGGCTTAAAACTGCAATGCTATTAT 57.648 32.000 6.82 0.00 0.00 1.28
3761 4166 7.205297 AGGCTTAAAACTGCAATGCTATTATG 58.795 34.615 6.82 4.58 0.00 1.90
3762 4167 6.980397 GGCTTAAAACTGCAATGCTATTATGT 59.020 34.615 6.82 0.00 0.00 2.29
4297 4704 6.220201 GTGAGTATATCCTGCTTCTCCTTTC 58.780 44.000 0.00 0.00 0.00 2.62
4360 4771 5.814705 TGAAATTTCCTTTGTTTCGTTGCAT 59.185 32.000 15.48 0.00 35.23 3.96
4442 4853 2.480419 CGTCGTTTTCATTCAGAGCCTT 59.520 45.455 0.00 0.00 0.00 4.35
4485 4896 2.286418 CGCATCGCAAGGTAAGAATTCC 60.286 50.000 0.65 0.00 38.47 3.01
4488 4899 1.066430 TCGCAAGGTAAGAATTCCGCT 60.066 47.619 0.65 0.00 38.47 5.52
4690 5101 1.478916 TGACGGATGTTTAGGCGATGA 59.521 47.619 0.00 0.00 0.00 2.92
5192 5603 6.561737 TCTTTTGTATTATGGTTTGCGACA 57.438 33.333 0.00 0.00 0.00 4.35
5243 5654 2.430465 CTCAAGTTGCACAGCATAGGT 58.570 47.619 0.00 0.00 38.76 3.08
5331 5742 9.277783 GTGTATTTCTGTGCTCCATATCTTATT 57.722 33.333 0.00 0.00 0.00 1.40
5342 5753 9.135189 TGCTCCATATCTTATTAATTTGCAAGT 57.865 29.630 0.00 0.00 0.00 3.16
5363 5774 5.533482 AGTTCGTATATCTGAATCCACTGC 58.467 41.667 0.00 0.00 0.00 4.40
5403 5814 3.706373 GGCAGGGAGAAGCGGTCA 61.706 66.667 0.00 0.00 0.00 4.02
5462 5873 0.309922 CGGCTTTGCTATGCCTCATG 59.690 55.000 19.79 3.96 46.42 3.07
5463 5874 0.031721 GGCTTTGCTATGCCTCATGC 59.968 55.000 16.10 0.00 45.26 4.06
5527 5938 4.435651 CGAAGTTTCCAATAAGAACTCGCC 60.436 45.833 0.00 0.00 32.79 5.54
5532 5943 1.006832 CAATAAGAACTCGCCACGGG 58.993 55.000 0.00 0.00 0.00 5.28
5585 5996 1.762708 AAAACGTGGCATCATAGGGG 58.237 50.000 0.00 0.00 0.00 4.79
5586 5997 0.751643 AAACGTGGCATCATAGGGGC 60.752 55.000 0.00 0.00 0.00 5.80
5587 5998 2.666190 CGTGGCATCATAGGGGCG 60.666 66.667 0.00 0.00 0.00 6.13
5588 5999 2.980233 GTGGCATCATAGGGGCGC 60.980 66.667 0.00 0.00 0.00 6.53
5589 6000 3.170672 TGGCATCATAGGGGCGCT 61.171 61.111 7.64 9.68 0.00 5.92
5590 6001 1.841103 TGGCATCATAGGGGCGCTA 60.841 57.895 14.05 14.05 0.00 4.26
5591 6002 1.374947 GGCATCATAGGGGCGCTAA 59.625 57.895 15.66 0.06 0.00 3.09
5592 6003 0.250727 GGCATCATAGGGGCGCTAAA 60.251 55.000 15.66 7.38 0.00 1.85
5593 6004 1.604604 GCATCATAGGGGCGCTAAAA 58.395 50.000 15.66 7.02 0.00 1.52
5594 6005 1.537202 GCATCATAGGGGCGCTAAAAG 59.463 52.381 15.66 8.74 0.00 2.27
5595 6006 2.810400 GCATCATAGGGGCGCTAAAAGA 60.810 50.000 15.66 13.43 0.00 2.52
5596 6007 2.910688 TCATAGGGGCGCTAAAAGAG 57.089 50.000 15.66 4.11 0.00 2.85
5597 6008 1.416401 TCATAGGGGCGCTAAAAGAGG 59.584 52.381 15.66 0.00 0.00 3.69
5598 6009 0.765510 ATAGGGGCGCTAAAAGAGGG 59.234 55.000 15.66 0.00 41.08 4.30
5599 6010 1.342672 TAGGGGCGCTAAAAGAGGGG 61.343 60.000 7.64 0.00 38.55 4.79
5600 6011 2.124278 GGGCGCTAAAAGAGGGGG 60.124 66.667 7.64 0.00 38.55 5.40
5601 6012 2.676265 GGGCGCTAAAAGAGGGGGA 61.676 63.158 7.64 0.00 38.55 4.81
5602 6013 1.153147 GGCGCTAAAAGAGGGGGAG 60.153 63.158 7.64 0.00 38.55 4.30
5603 6014 1.623542 GGCGCTAAAAGAGGGGGAGA 61.624 60.000 7.64 0.00 38.55 3.71
5604 6015 0.470341 GCGCTAAAAGAGGGGGAGAT 59.530 55.000 0.00 0.00 38.55 2.75
5605 6016 1.134068 GCGCTAAAAGAGGGGGAGATT 60.134 52.381 0.00 0.00 38.55 2.40
5606 6017 2.104281 GCGCTAAAAGAGGGGGAGATTA 59.896 50.000 0.00 0.00 38.55 1.75
5607 6018 3.244596 GCGCTAAAAGAGGGGGAGATTAT 60.245 47.826 0.00 0.00 38.55 1.28
5608 6019 4.020485 GCGCTAAAAGAGGGGGAGATTATA 60.020 45.833 0.00 0.00 38.55 0.98
5609 6020 5.512576 GCGCTAAAAGAGGGGGAGATTATAA 60.513 44.000 0.00 0.00 38.55 0.98
5610 6021 6.712276 CGCTAAAAGAGGGGGAGATTATAAT 58.288 40.000 0.00 0.00 34.46 1.28
5611 6022 7.168905 CGCTAAAAGAGGGGGAGATTATAATT 58.831 38.462 0.00 0.00 34.46 1.40
5612 6023 7.665974 CGCTAAAAGAGGGGGAGATTATAATTT 59.334 37.037 0.00 0.00 34.46 1.82
5613 6024 8.797438 GCTAAAAGAGGGGGAGATTATAATTTG 58.203 37.037 0.00 0.00 0.00 2.32
5615 6026 8.768501 AAAAGAGGGGGAGATTATAATTTGAC 57.231 34.615 0.00 0.00 0.00 3.18
5616 6027 6.455690 AGAGGGGGAGATTATAATTTGACC 57.544 41.667 0.00 1.23 0.00 4.02
5617 6028 6.161167 AGAGGGGGAGATTATAATTTGACCT 58.839 40.000 0.00 4.69 0.00 3.85
5618 6029 7.321530 AGAGGGGGAGATTATAATTTGACCTA 58.678 38.462 0.00 0.00 0.00 3.08
5619 6030 7.799583 AGAGGGGGAGATTATAATTTGACCTAA 59.200 37.037 0.00 0.00 0.00 2.69
5620 6031 8.358082 AGGGGGAGATTATAATTTGACCTAAA 57.642 34.615 0.00 0.00 0.00 1.85
5621 6032 8.970813 AGGGGGAGATTATAATTTGACCTAAAT 58.029 33.333 0.00 0.00 40.67 1.40
5641 6052 9.413048 CCTAAATTTAGGTGAGATCGTAGAATC 57.587 37.037 29.13 0.00 44.26 2.52
5642 6053 9.967346 CTAAATTTAGGTGAGATCGTAGAATCA 57.033 33.333 16.19 0.00 43.58 2.57
5644 6055 8.649973 AATTTAGGTGAGATCGTAGAATCAAC 57.350 34.615 0.00 0.00 43.58 3.18
5646 6057 5.508200 AGGTGAGATCGTAGAATCAACTC 57.492 43.478 0.00 0.00 46.77 3.01
5647 6058 4.339814 AGGTGAGATCGTAGAATCAACTCC 59.660 45.833 0.00 0.00 46.77 3.85
5648 6059 4.098044 GGTGAGATCGTAGAATCAACTCCA 59.902 45.833 0.00 0.00 43.58 3.86
5649 6060 5.394224 GGTGAGATCGTAGAATCAACTCCAA 60.394 44.000 0.00 0.00 43.58 3.53
5650 6061 6.100004 GTGAGATCGTAGAATCAACTCCAAA 58.900 40.000 0.00 0.00 43.58 3.28
5651 6062 6.590292 GTGAGATCGTAGAATCAACTCCAAAA 59.410 38.462 0.00 0.00 43.58 2.44
5652 6063 7.278868 GTGAGATCGTAGAATCAACTCCAAAAT 59.721 37.037 0.00 0.00 43.58 1.82
5653 6064 7.824289 TGAGATCGTAGAATCAACTCCAAAATT 59.176 33.333 0.00 0.00 43.58 1.82
5654 6065 8.567285 AGATCGTAGAATCAACTCCAAAATTT 57.433 30.769 0.00 0.00 43.58 1.82
5655 6066 8.669243 AGATCGTAGAATCAACTCCAAAATTTC 58.331 33.333 0.00 0.00 43.58 2.17
5656 6067 7.737972 TCGTAGAATCAACTCCAAAATTTCA 57.262 32.000 0.00 0.00 0.00 2.69
5657 6068 8.335532 TCGTAGAATCAACTCCAAAATTTCAT 57.664 30.769 0.00 0.00 0.00 2.57
5658 6069 9.443323 TCGTAGAATCAACTCCAAAATTTCATA 57.557 29.630 0.00 0.00 0.00 2.15
5665 6076 9.657419 ATCAACTCCAAAATTTCATATTTGACC 57.343 29.630 0.00 0.00 38.50 4.02
5666 6077 8.869109 TCAACTCCAAAATTTCATATTTGACCT 58.131 29.630 0.00 0.00 38.50 3.85
5667 6078 9.492973 CAACTCCAAAATTTCATATTTGACCTT 57.507 29.630 0.00 0.00 38.50 3.50
5668 6079 9.492973 AACTCCAAAATTTCATATTTGACCTTG 57.507 29.630 0.00 0.00 38.50 3.61
5669 6080 7.603784 ACTCCAAAATTTCATATTTGACCTTGC 59.396 33.333 0.00 0.00 38.50 4.01
5670 6081 7.448420 TCCAAAATTTCATATTTGACCTTGCA 58.552 30.769 0.00 0.00 38.50 4.08
5671 6082 7.603404 TCCAAAATTTCATATTTGACCTTGCAG 59.397 33.333 0.00 0.00 38.50 4.41
5672 6083 7.388500 CCAAAATTTCATATTTGACCTTGCAGT 59.612 33.333 0.00 0.00 38.50 4.40
5673 6084 8.776470 CAAAATTTCATATTTGACCTTGCAGTT 58.224 29.630 0.00 0.00 38.50 3.16
5674 6085 9.995003 AAAATTTCATATTTGACCTTGCAGTTA 57.005 25.926 0.00 0.00 0.00 2.24
5675 6086 9.995003 AAATTTCATATTTGACCTTGCAGTTAA 57.005 25.926 0.00 0.00 0.00 2.01
5676 6087 9.643693 AATTTCATATTTGACCTTGCAGTTAAG 57.356 29.630 0.00 0.00 0.00 1.85
5677 6088 7.759489 TTCATATTTGACCTTGCAGTTAAGT 57.241 32.000 0.00 0.00 0.00 2.24
5678 6089 7.759489 TCATATTTGACCTTGCAGTTAAGTT 57.241 32.000 0.00 0.00 0.00 2.66
5679 6090 8.177119 TCATATTTGACCTTGCAGTTAAGTTT 57.823 30.769 0.00 0.00 0.00 2.66
5680 6091 9.290988 TCATATTTGACCTTGCAGTTAAGTTTA 57.709 29.630 0.00 0.00 0.00 2.01
5681 6092 9.341899 CATATTTGACCTTGCAGTTAAGTTTAC 57.658 33.333 0.00 0.00 0.00 2.01
5682 6093 6.761099 TTTGACCTTGCAGTTAAGTTTACA 57.239 33.333 0.00 0.00 0.00 2.41
5683 6094 6.761099 TTGACCTTGCAGTTAAGTTTACAA 57.239 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.416284 GGGGAAATAATAAGGACATCAAAACTA 57.584 33.333 0.00 0.00 0.00 2.24
11 12 7.898636 TGGGGAAATAATAAGGACATCAAAACT 59.101 33.333 0.00 0.00 0.00 2.66
35 36 5.621193 ACTTCCGAATATAATCCACCTTGG 58.379 41.667 0.00 0.00 39.43 3.61
37 38 6.749036 AGACTTCCGAATATAATCCACCTT 57.251 37.500 0.00 0.00 0.00 3.50
127 128 8.319146 TGGAAAATAACTCTCCAACTAGTTAGG 58.681 37.037 8.04 12.09 40.49 2.69
134 135 5.045869 TCGGATGGAAAATAACTCTCCAACT 60.046 40.000 0.00 0.00 42.41 3.16
156 157 5.637810 TGAAATTGTTAGTGCCTTCTACTCG 59.362 40.000 0.00 0.00 0.00 4.18
172 173 7.047891 TGGCGATACTCTAAGATTGAAATTGT 58.952 34.615 0.00 0.00 0.00 2.71
175 176 7.047891 TGTTGGCGATACTCTAAGATTGAAAT 58.952 34.615 0.00 0.00 0.00 2.17
190 191 1.753930 TAGGACGACTGTTGGCGATA 58.246 50.000 0.00 0.00 0.00 2.92
215 216 4.373156 AGCCCTAAAAATGACTCACACT 57.627 40.909 0.00 0.00 0.00 3.55
217 218 5.710099 CCTAAAGCCCTAAAAATGACTCACA 59.290 40.000 0.00 0.00 0.00 3.58
219 220 5.261216 CCCTAAAGCCCTAAAAATGACTCA 58.739 41.667 0.00 0.00 0.00 3.41
225 226 1.754803 GCGCCCTAAAGCCCTAAAAAT 59.245 47.619 0.00 0.00 0.00 1.82
235 236 1.803289 GGCTCTTTGCGCCCTAAAG 59.197 57.895 4.18 8.77 44.05 1.85
269 272 5.232838 GCAAGAAATTTAGAATTGGGCATCG 59.767 40.000 0.00 0.00 0.00 3.84
306 310 1.304617 GCCTCTTTTAGGGCTGCCT 59.695 57.895 19.68 7.25 46.65 4.75
315 319 2.742053 GTCGCACAATGAGCCTCTTTTA 59.258 45.455 0.00 0.00 0.00 1.52
320 325 0.874390 TTTGTCGCACAATGAGCCTC 59.126 50.000 0.00 0.00 38.00 4.70
327 332 1.607767 GCCCCAAATTTGTCGCACAAT 60.608 47.619 16.73 0.00 38.00 2.71
357 362 0.037046 GCCTCATGTTTTTGGGCAGG 60.037 55.000 0.00 0.00 42.08 4.85
398 403 2.290705 ACGGATCCAAGGATTTTCGGTT 60.291 45.455 13.41 3.34 34.60 4.44
402 407 2.354821 CCGAACGGATCCAAGGATTTTC 59.645 50.000 13.41 6.12 37.50 2.29
403 408 2.290705 ACCGAACGGATCCAAGGATTTT 60.291 45.455 20.14 0.00 38.96 1.82
407 412 1.594833 CACCGAACGGATCCAAGGA 59.405 57.895 20.14 0.00 38.96 3.36
431 436 2.200337 GCATATTCGGGTTGGGGGC 61.200 63.158 0.00 0.00 0.00 5.80
434 455 0.385390 GCAAGCATATTCGGGTTGGG 59.615 55.000 6.48 0.00 42.39 4.12
447 468 7.796622 CTAAAATTAGAAGGGAGCAGCAAGCA 61.797 42.308 0.00 0.00 38.19 3.91
461 487 7.549488 GCTCCAACAGCTACTCTAAAATTAGAA 59.451 37.037 4.57 0.00 45.83 2.10
518 553 8.506196 TCTCCAACAGTAGCCCTATAATAAAT 57.494 34.615 0.00 0.00 0.00 1.40
533 568 0.886490 CAAGCGCCTTCTCCAACAGT 60.886 55.000 2.29 0.00 0.00 3.55
544 579 1.028905 TTTTACACAAGCAAGCGCCT 58.971 45.000 2.29 0.00 39.83 5.52
549 584 6.914757 CCTTCTTCTCTTTTTACACAAGCAAG 59.085 38.462 0.00 0.00 0.00 4.01
555 590 8.581578 ACAAAAACCTTCTTCTCTTTTTACACA 58.418 29.630 0.00 0.00 0.00 3.72
559 594 7.039270 GGCACAAAAACCTTCTTCTCTTTTTA 58.961 34.615 0.00 0.00 0.00 1.52
567 602 6.749139 AGAATTAGGCACAAAAACCTTCTTC 58.251 36.000 0.00 0.00 37.50 2.87
586 621 9.410556 CGAAAACATGATGGAGTAAAAAGAATT 57.589 29.630 0.00 0.00 0.00 2.17
590 625 6.088085 GCACGAAAACATGATGGAGTAAAAAG 59.912 38.462 0.00 0.00 0.00 2.27
602 640 6.822442 TCTATAATAGGGCACGAAAACATGA 58.178 36.000 0.00 0.00 0.00 3.07
631 672 2.481969 GCACTATGAGCATCTCCAACGA 60.482 50.000 0.00 0.00 34.92 3.85
632 673 1.863454 GCACTATGAGCATCTCCAACG 59.137 52.381 0.00 0.00 34.92 4.10
669 710 0.737219 GCGGTGTCCACGTATACTCT 59.263 55.000 0.56 0.00 0.00 3.24
671 712 0.966875 TGGCGGTGTCCACGTATACT 60.967 55.000 0.56 0.00 0.00 2.12
694 735 0.314302 GACACTGACACTACCTGCGT 59.686 55.000 0.00 0.00 0.00 5.24
737 778 0.887933 CAATAGGTTGCCGTGGCTTT 59.112 50.000 12.84 0.00 42.51 3.51
750 791 1.813753 CGTGGCGGTGTCCAATAGG 60.814 63.158 0.00 0.00 37.96 2.57
771 812 1.292223 GCCACGTAGACTTCCTGCA 59.708 57.895 0.00 0.00 0.00 4.41
832 873 1.733912 GGTTTCGACGTGGGTTTATCC 59.266 52.381 0.00 0.00 0.00 2.59
868 910 5.408356 GTGCTGACCTTTAATTACGAGAGA 58.592 41.667 0.00 0.00 0.00 3.10
1029 1071 0.395311 CCTGGTAGACGTAGGGCTGA 60.395 60.000 0.00 0.00 0.00 4.26
1056 1098 2.895680 GTGCGAGATGAGGGAGCA 59.104 61.111 0.00 0.00 35.27 4.26
1104 1146 3.833645 CCCCGCGACCTCGAATCA 61.834 66.667 8.23 0.00 43.02 2.57
1142 1184 2.587194 CAATCGGGAGCAGAGCGG 60.587 66.667 0.00 0.00 0.00 5.52
1161 1203 1.360185 ATCAGATCATGAGAGGGGGC 58.640 55.000 0.09 0.00 42.53 5.80
1282 1325 1.812214 GCGAGCGAGAATTAGGCACG 61.812 60.000 9.27 9.27 42.29 5.34
1433 1478 1.273048 TGCAAATTTCAGCCGCAGAAT 59.727 42.857 0.00 0.00 0.00 2.40
1465 1510 2.552599 TTCGGCATGTCACCTTGTTA 57.447 45.000 0.00 0.00 0.00 2.41
1490 1545 3.066760 GCCACATGAATACCAGGCTAAAC 59.933 47.826 0.00 0.00 39.02 2.01
1655 1729 4.210328 TGCAGTAACAACTATCAACACACG 59.790 41.667 0.00 0.00 0.00 4.49
1698 1772 9.884465 GGCACATCATACATAGAAAGAAAATAC 57.116 33.333 0.00 0.00 0.00 1.89
1705 1779 6.519382 TGAGAGGCACATCATACATAGAAAG 58.481 40.000 0.00 0.00 0.00 2.62
1725 1799 3.244078 ACACGCAAACAACCTCTATGAGA 60.244 43.478 0.00 0.00 0.00 3.27
1790 1887 2.611971 CGGACCAAGCAGCTAACAGTTA 60.612 50.000 0.00 0.00 0.00 2.24
1791 1888 1.878102 CGGACCAAGCAGCTAACAGTT 60.878 52.381 0.00 0.00 0.00 3.16
1792 1889 0.320771 CGGACCAAGCAGCTAACAGT 60.321 55.000 0.00 0.00 0.00 3.55
1793 1890 1.021390 CCGGACCAAGCAGCTAACAG 61.021 60.000 0.00 0.00 0.00 3.16
1794 1891 1.003839 CCGGACCAAGCAGCTAACA 60.004 57.895 0.00 0.00 0.00 2.41
1795 1892 1.003718 ACCGGACCAAGCAGCTAAC 60.004 57.895 9.46 0.00 0.00 2.34
1796 1893 1.003839 CACCGGACCAAGCAGCTAA 60.004 57.895 9.46 0.00 0.00 3.09
1797 1894 2.662596 CACCGGACCAAGCAGCTA 59.337 61.111 9.46 0.00 0.00 3.32
1803 1900 2.558554 CTACTCGGCACCGGACCAAG 62.559 65.000 9.46 6.56 40.25 3.61
1804 1901 2.601067 TACTCGGCACCGGACCAA 60.601 61.111 9.46 0.00 40.25 3.67
1805 1902 3.066190 CTACTCGGCACCGGACCA 61.066 66.667 9.46 0.00 40.25 4.02
1806 1903 3.834799 CCTACTCGGCACCGGACC 61.835 72.222 9.46 8.58 40.25 4.46
1807 1904 3.834799 CCCTACTCGGCACCGGAC 61.835 72.222 9.46 0.00 40.25 4.79
1808 1905 2.866523 AATCCCTACTCGGCACCGGA 62.867 60.000 9.46 0.00 40.25 5.14
1809 1906 1.111116 TAATCCCTACTCGGCACCGG 61.111 60.000 9.58 0.00 40.25 5.28
1810 1907 0.748450 TTAATCCCTACTCGGCACCG 59.252 55.000 1.73 1.73 41.35 4.94
1811 1908 2.609737 CGATTAATCCCTACTCGGCACC 60.610 54.545 9.87 0.00 31.02 5.01
1812 1909 2.609737 CCGATTAATCCCTACTCGGCAC 60.610 54.545 9.87 0.00 43.42 5.01
1813 1910 1.616865 CCGATTAATCCCTACTCGGCA 59.383 52.381 9.87 0.00 43.42 5.69
1814 1911 2.365408 CCGATTAATCCCTACTCGGC 57.635 55.000 9.87 0.00 43.42 5.54
1816 1913 1.538512 TCGCCGATTAATCCCTACTCG 59.461 52.381 9.87 4.99 33.64 4.18
1874 1971 0.386838 CGGCCCTAGTTAACCTACCG 59.613 60.000 0.88 5.45 0.00 4.02
1897 1994 5.528337 TGCCATGTAGCCTAGGATATATCA 58.472 41.667 14.75 7.01 0.00 2.15
1903 2000 2.126882 TGTTGCCATGTAGCCTAGGAT 58.873 47.619 14.75 9.51 0.00 3.24
1927 2024 5.688621 TGCATATTCGGACGTTTAGTACATC 59.311 40.000 0.00 0.00 31.45 3.06
1938 2140 1.800586 CCAGGATTGCATATTCGGACG 59.199 52.381 0.00 0.00 0.00 4.79
1939 2141 2.154462 CCCAGGATTGCATATTCGGAC 58.846 52.381 0.00 0.00 0.00 4.79
1942 2144 1.901591 AGCCCAGGATTGCATATTCG 58.098 50.000 0.00 0.00 0.00 3.34
1979 2181 7.510343 TCCTATGTGATCTATGAAGATTGGTGA 59.490 37.037 0.00 0.00 42.73 4.02
1980 2182 7.674120 TCCTATGTGATCTATGAAGATTGGTG 58.326 38.462 0.00 0.00 42.73 4.17
1981 2183 7.732140 TCTCCTATGTGATCTATGAAGATTGGT 59.268 37.037 0.00 0.00 42.73 3.67
2008 2210 3.117888 TCAAGCATCAAGGTAATCTCCCC 60.118 47.826 0.00 0.00 0.00 4.81
2066 2268 5.072741 AGCTTGCTATTTCTTCCTGTTTCA 58.927 37.500 0.00 0.00 0.00 2.69
2070 2272 3.760684 CCAAGCTTGCTATTTCTTCCTGT 59.239 43.478 21.43 0.00 0.00 4.00
2163 2366 2.633509 CCAGCAACAAGGAGCAGCC 61.634 63.158 0.00 0.00 0.00 4.85
2292 2495 4.486503 CCCAGAGGAGCAGCAGCC 62.487 72.222 0.00 0.00 43.56 4.85
2293 2496 4.486503 CCCCAGAGGAGCAGCAGC 62.487 72.222 0.00 0.00 38.24 5.25
2301 2504 4.465446 CTCCCGCTCCCCAGAGGA 62.465 72.222 0.00 0.00 42.17 3.71
2308 2511 3.087906 TTTAGGGCTCCCGCTCCC 61.088 66.667 0.00 0.00 42.94 4.30
2399 2623 2.893489 GCCCTGATAGCCAATAAAAGGG 59.107 50.000 0.27 0.27 40.72 3.95
2400 2624 3.837355 AGCCCTGATAGCCAATAAAAGG 58.163 45.455 0.00 0.00 0.00 3.11
2401 2625 7.373493 CAAATAGCCCTGATAGCCAATAAAAG 58.627 38.462 0.00 0.00 0.00 2.27
2402 2626 6.267471 CCAAATAGCCCTGATAGCCAATAAAA 59.733 38.462 0.00 0.00 0.00 1.52
2403 2627 5.774690 CCAAATAGCCCTGATAGCCAATAAA 59.225 40.000 0.00 0.00 0.00 1.40
2404 2628 5.324409 CCAAATAGCCCTGATAGCCAATAA 58.676 41.667 0.00 0.00 0.00 1.40
2405 2629 4.263905 CCCAAATAGCCCTGATAGCCAATA 60.264 45.833 0.00 0.00 0.00 1.90
2406 2630 3.501019 CCCAAATAGCCCTGATAGCCAAT 60.501 47.826 0.00 0.00 0.00 3.16
2407 2631 2.158475 CCCAAATAGCCCTGATAGCCAA 60.158 50.000 0.00 0.00 0.00 4.52
2408 2632 1.425066 CCCAAATAGCCCTGATAGCCA 59.575 52.381 0.00 0.00 0.00 4.75
2409 2633 1.888391 GCCCAAATAGCCCTGATAGCC 60.888 57.143 0.00 0.00 0.00 3.93
2410 2634 1.539157 GCCCAAATAGCCCTGATAGC 58.461 55.000 0.00 0.00 0.00 2.97
2411 2635 2.206576 GGCCCAAATAGCCCTGATAG 57.793 55.000 0.00 0.00 45.16 2.08
2419 2643 3.466836 GCCAATAAAAGGCCCAAATAGC 58.533 45.455 0.00 0.00 46.50 2.97
2448 2673 0.035056 ATGGGCCGGCTGATTATAGC 60.035 55.000 28.56 5.59 42.94 2.97
2450 2675 2.969821 AAATGGGCCGGCTGATTATA 57.030 45.000 28.56 5.32 0.00 0.98
2467 2693 1.989706 GCCCTATTCGGCCCATTAAA 58.010 50.000 0.00 0.00 43.66 1.52
2486 2712 1.743394 GCACCCTTCCGAACCAAATAG 59.257 52.381 0.00 0.00 0.00 1.73
2556 2788 6.972722 TGTAACACATTGTACCTAAAAAGGC 58.027 36.000 0.00 0.00 0.00 4.35
2915 3309 7.651808 ACAAGTGACAGAATTCTATTTTGGTG 58.348 34.615 7.86 4.39 0.00 4.17
3345 3750 3.300009 GTTCATGCGACTGTTTCAAAGG 58.700 45.455 0.00 0.00 0.00 3.11
3524 3929 2.684881 ACTGAACACAAACTTGCAGGAG 59.315 45.455 1.40 0.00 0.00 3.69
3566 3971 2.699846 TCATTTCCTGGCAAGCAAGTTT 59.300 40.909 0.00 0.00 0.00 2.66
3590 3995 6.871492 TCATCTGTAGAAGAAAAACGTGCATA 59.129 34.615 0.00 0.00 38.79 3.14
3678 4083 4.177026 CGATGTAAGGGTGAAGTCTGAAG 58.823 47.826 0.00 0.00 0.00 3.02
3679 4084 3.616560 GCGATGTAAGGGTGAAGTCTGAA 60.617 47.826 0.00 0.00 0.00 3.02
3680 4085 2.094182 GCGATGTAAGGGTGAAGTCTGA 60.094 50.000 0.00 0.00 0.00 3.27
3681 4086 2.271800 GCGATGTAAGGGTGAAGTCTG 58.728 52.381 0.00 0.00 0.00 3.51
3682 4087 1.899814 TGCGATGTAAGGGTGAAGTCT 59.100 47.619 0.00 0.00 0.00 3.24
3683 4088 2.271800 CTGCGATGTAAGGGTGAAGTC 58.728 52.381 0.00 0.00 0.00 3.01
3684 4089 1.623811 ACTGCGATGTAAGGGTGAAGT 59.376 47.619 0.00 0.00 0.00 3.01
3729 4134 7.707893 AGCATTGCAGTTTTAAGCCTATAATTG 59.292 33.333 11.91 0.00 0.00 2.32
3745 4150 6.764308 ACTCAAACATAATAGCATTGCAGT 57.236 33.333 11.91 0.00 0.00 4.40
3906 4313 2.969821 AGTACTCCCATGCCAACAAA 57.030 45.000 0.00 0.00 0.00 2.83
4103 4510 3.570125 AGAGCAAAAGCTCCCAAAGTTAC 59.430 43.478 13.36 0.00 37.53 2.50
4137 4544 8.193438 GGAGCAAGAATTTTCTGCATTACTAAT 58.807 33.333 13.42 0.00 37.65 1.73
4297 4704 4.404073 ACTGCTCCTCTTGAACTAGTATGG 59.596 45.833 0.00 0.00 0.00 2.74
4442 4853 1.816537 CGAGAGCCGATTGAAGGGA 59.183 57.895 0.00 0.00 41.76 4.20
4488 4899 1.228094 TGGGAAGCGATGTGTTGCA 60.228 52.632 0.00 0.00 37.19 4.08
5116 5527 1.160137 ACAGCTGTGCGATTTCTTCC 58.840 50.000 20.97 0.00 0.00 3.46
5192 5603 1.152963 ACACGAACAAGGGCTGCTT 60.153 52.632 0.00 0.00 0.00 3.91
5335 5746 6.257849 GTGGATTCAGATATACGAACTTGCAA 59.742 38.462 0.00 0.00 0.00 4.08
5342 5753 4.588951 AGGCAGTGGATTCAGATATACGAA 59.411 41.667 0.00 0.00 0.00 3.85
5363 5774 0.462759 GTCGCCATCCTCTTTCCAGG 60.463 60.000 0.00 0.00 34.40 4.45
5419 5830 6.456449 CGGCACATTTTAGATTGGTACAGTAC 60.456 42.308 1.59 1.59 42.39 2.73
5420 5831 5.583061 CGGCACATTTTAGATTGGTACAGTA 59.417 40.000 0.00 0.00 42.39 2.74
5421 5832 4.394920 CGGCACATTTTAGATTGGTACAGT 59.605 41.667 0.00 0.00 42.39 3.55
5422 5833 4.201910 CCGGCACATTTTAGATTGGTACAG 60.202 45.833 0.00 0.00 42.39 2.74
5423 5834 3.692101 CCGGCACATTTTAGATTGGTACA 59.308 43.478 0.00 0.00 0.00 2.90
5462 5873 3.578688 AGAAAGATTTCGGTTGCATTGC 58.421 40.909 0.46 0.46 41.92 3.56
5463 5874 3.848019 CGAGAAAGATTTCGGTTGCATTG 59.152 43.478 0.00 0.00 41.92 2.82
5464 5875 4.083581 CGAGAAAGATTTCGGTTGCATT 57.916 40.909 0.00 0.00 41.92 3.56
5465 5876 3.747099 CGAGAAAGATTTCGGTTGCAT 57.253 42.857 0.00 0.00 41.92 3.96
5576 5987 2.039084 CCTCTTTTAGCGCCCCTATGAT 59.961 50.000 2.29 0.00 0.00 2.45
5579 5990 0.765510 CCCTCTTTTAGCGCCCCTAT 59.234 55.000 2.29 0.00 0.00 2.57
5584 5995 1.153147 CTCCCCCTCTTTTAGCGCC 60.153 63.158 2.29 0.00 0.00 6.53
5585 5996 0.470341 ATCTCCCCCTCTTTTAGCGC 59.530 55.000 0.00 0.00 0.00 5.92
5586 5997 4.625607 ATAATCTCCCCCTCTTTTAGCG 57.374 45.455 0.00 0.00 0.00 4.26
5587 5998 8.797438 CAAATTATAATCTCCCCCTCTTTTAGC 58.203 37.037 0.00 0.00 0.00 3.09
5589 6000 9.862149 GTCAAATTATAATCTCCCCCTCTTTTA 57.138 33.333 0.00 0.00 0.00 1.52
5590 6001 7.785028 GGTCAAATTATAATCTCCCCCTCTTTT 59.215 37.037 0.00 0.00 0.00 2.27
5591 6002 7.131069 AGGTCAAATTATAATCTCCCCCTCTTT 59.869 37.037 0.00 0.00 0.00 2.52
5592 6003 6.625700 AGGTCAAATTATAATCTCCCCCTCTT 59.374 38.462 0.00 0.00 0.00 2.85
5593 6004 6.161167 AGGTCAAATTATAATCTCCCCCTCT 58.839 40.000 0.00 0.00 0.00 3.69
5594 6005 6.455690 AGGTCAAATTATAATCTCCCCCTC 57.544 41.667 0.00 0.00 0.00 4.30
5595 6006 7.964730 TTAGGTCAAATTATAATCTCCCCCT 57.035 36.000 0.00 4.14 0.00 4.79
5596 6007 9.601810 AATTTAGGTCAAATTATAATCTCCCCC 57.398 33.333 0.00 0.00 43.52 5.40
5616 6027 9.967346 TGATTCTACGATCTCACCTAAATTTAG 57.033 33.333 16.90 16.90 0.00 1.85
5618 6029 9.099454 GTTGATTCTACGATCTCACCTAAATTT 57.901 33.333 0.00 0.00 0.00 1.82
5619 6030 8.478877 AGTTGATTCTACGATCTCACCTAAATT 58.521 33.333 0.00 0.00 0.00 1.82
5620 6031 8.012957 AGTTGATTCTACGATCTCACCTAAAT 57.987 34.615 0.00 0.00 0.00 1.40
5621 6032 7.406031 AGTTGATTCTACGATCTCACCTAAA 57.594 36.000 0.00 0.00 0.00 1.85
5622 6033 6.039493 GGAGTTGATTCTACGATCTCACCTAA 59.961 42.308 0.00 0.00 0.00 2.69
5623 6034 5.531659 GGAGTTGATTCTACGATCTCACCTA 59.468 44.000 0.00 0.00 0.00 3.08
5624 6035 4.339814 GGAGTTGATTCTACGATCTCACCT 59.660 45.833 0.00 0.00 0.00 4.00
5625 6036 4.098044 TGGAGTTGATTCTACGATCTCACC 59.902 45.833 0.00 0.00 0.00 4.02
5626 6037 5.250235 TGGAGTTGATTCTACGATCTCAC 57.750 43.478 0.00 0.00 0.00 3.51
5627 6038 5.914898 TTGGAGTTGATTCTACGATCTCA 57.085 39.130 0.00 0.00 0.00 3.27
5628 6039 7.778470 ATTTTGGAGTTGATTCTACGATCTC 57.222 36.000 0.00 0.00 0.00 2.75
5629 6040 8.567285 AAATTTTGGAGTTGATTCTACGATCT 57.433 30.769 0.00 0.00 0.00 2.75
5630 6041 8.450964 TGAAATTTTGGAGTTGATTCTACGATC 58.549 33.333 0.00 0.00 0.00 3.69
5631 6042 8.335532 TGAAATTTTGGAGTTGATTCTACGAT 57.664 30.769 0.00 0.00 0.00 3.73
5632 6043 7.737972 TGAAATTTTGGAGTTGATTCTACGA 57.262 32.000 0.00 0.00 0.00 3.43
5639 6050 9.657419 GGTCAAATATGAAATTTTGGAGTTGAT 57.343 29.630 10.92 0.00 37.30 2.57
5640 6051 8.869109 AGGTCAAATATGAAATTTTGGAGTTGA 58.131 29.630 0.00 0.00 37.30 3.18
5641 6052 9.492973 AAGGTCAAATATGAAATTTTGGAGTTG 57.507 29.630 0.00 0.00 37.30 3.16
5642 6053 9.492973 CAAGGTCAAATATGAAATTTTGGAGTT 57.507 29.630 0.00 0.00 37.30 3.01
5643 6054 7.603784 GCAAGGTCAAATATGAAATTTTGGAGT 59.396 33.333 0.00 0.00 37.30 3.85
5644 6055 7.603404 TGCAAGGTCAAATATGAAATTTTGGAG 59.397 33.333 0.00 0.00 37.30 3.86
5645 6056 7.448420 TGCAAGGTCAAATATGAAATTTTGGA 58.552 30.769 0.00 0.00 37.30 3.53
5646 6057 7.388500 ACTGCAAGGTCAAATATGAAATTTTGG 59.612 33.333 0.00 0.00 39.30 3.28
5647 6058 8.314143 ACTGCAAGGTCAAATATGAAATTTTG 57.686 30.769 0.00 0.00 39.30 2.44
5648 6059 8.907222 AACTGCAAGGTCAAATATGAAATTTT 57.093 26.923 0.00 0.00 39.30 1.82
5649 6060 9.995003 TTAACTGCAAGGTCAAATATGAAATTT 57.005 25.926 0.00 0.00 39.30 1.82
5650 6061 9.643693 CTTAACTGCAAGGTCAAATATGAAATT 57.356 29.630 0.00 0.00 39.30 1.82
5651 6062 8.806146 ACTTAACTGCAAGGTCAAATATGAAAT 58.194 29.630 0.00 0.00 39.30 2.17
5652 6063 8.177119 ACTTAACTGCAAGGTCAAATATGAAA 57.823 30.769 0.00 0.00 39.30 2.69
5653 6064 7.759489 ACTTAACTGCAAGGTCAAATATGAA 57.241 32.000 0.00 0.00 39.30 2.57
5654 6065 7.759489 AACTTAACTGCAAGGTCAAATATGA 57.241 32.000 0.00 0.00 39.30 2.15
5655 6066 9.341899 GTAAACTTAACTGCAAGGTCAAATATG 57.658 33.333 0.00 0.00 39.30 1.78
5656 6067 9.073475 TGTAAACTTAACTGCAAGGTCAAATAT 57.927 29.630 0.00 0.00 39.30 1.28
5657 6068 8.453238 TGTAAACTTAACTGCAAGGTCAAATA 57.547 30.769 0.00 0.00 39.30 1.40
5658 6069 7.341445 TGTAAACTTAACTGCAAGGTCAAAT 57.659 32.000 0.00 0.00 39.30 2.32
5659 6070 6.761099 TGTAAACTTAACTGCAAGGTCAAA 57.239 33.333 0.00 0.00 39.30 2.69
5660 6071 6.761099 TTGTAAACTTAACTGCAAGGTCAA 57.239 33.333 0.00 0.00 39.30 3.18


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

AutoCloner maintained by Alex Coulton.