Multiple sequence alignment - TraesCS6A01G087900

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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 TraesCS6A01G087900 chr6A 100.000 2228 0 0 1 2228 56134110 56131883 0.000000e+00 4115
1 TraesCS6A01G087900 chr6B 91.271 1031 71 11 1191 2208 92619092 92618068 0.000000e+00 1387
2 TraesCS6A01G087900 chr6B 85.816 987 81 30 1 961 92697261 92696308 0.000000e+00 992
3 TraesCS6A01G087900 chr6B 90.726 248 12 8 958 1199 92695774 92695532 9.930000e-84 320
4 TraesCS6A01G087900 chrUn 91.449 421 26 6 7 426 20366804 20366393 8.930000e-159 569
5 TraesCS6A01G087900 chr2B 86.275 255 24 5 631 883 94652715 94652960 1.310000e-67 267
6 TraesCS6A01G087900 chr1D 84.586 266 27 7 631 893 438210953 438211207 3.670000e-63 252
7 TraesCS6A01G087900 chr1D 83.521 267 29 7 631 894 64729518 64729772 3.700000e-58 235
8 TraesCS6A01G087900 chr3B 84.328 268 28 7 631 894 821289835 821290092 1.320000e-62 250
9 TraesCS6A01G087900 chr3B 84.328 268 28 8 631 894 821439256 821439513 1.320000e-62 250
10 TraesCS6A01G087900 chr2A 87.558 217 23 2 631 843 677157854 677158070 4.750000e-62 248
11 TraesCS6A01G087900 chr7B 89.175 194 21 0 631 824 116491564 116491757 2.210000e-60 243
12 TraesCS6A01G087900 chr7D 88.205 195 22 1 631 825 636339640 636339833 4.780000e-57 231
13 TraesCS6A01G087900 chr1B 82.900 269 31 7 631 894 179514068 179513810 6.190000e-56 228
14 TraesCS6A01G087900 chr1B 82.772 267 18 17 631 883 317200790 317201042 1.730000e-51 213
15 TraesCS6A01G087900 chr3A 82.500 280 21 16 631 894 423678569 423678836 1.040000e-53 220
16 TraesCS6A01G087900 chr5B 78.676 272 27 16 631 883 14411795 14411536 3.830000e-33 152
17 TraesCS6A01G087900 chr6D 78.509 228 25 13 669 883 8556665 8556881 6.460000e-26 128


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 TraesCS6A01G087900 chr6A 56131883 56134110 2227 True 4115 4115 100.000 1 2228 1 chr6A.!!$R1 2227
1 TraesCS6A01G087900 chr6B 92618068 92619092 1024 True 1387 1387 91.271 1191 2208 1 chr6B.!!$R1 1017
2 TraesCS6A01G087900 chr6B 92695532 92697261 1729 True 656 992 88.271 1 1199 2 chr6B.!!$R2 1198

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
627 638 0.029989 GGATAAGGAGGGTGGGGTCT 60.03 60.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1451 2027 0.25363 TGTTCTAAGGAGGGGGCCAT 60.254 55.0 4.39 0.0 0.0 4.4 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
28 29 2.966590 GATCGATCCCCTCTCCGC 59.033 66.667 14.76 0.00 0.00 5.54
29 30 2.601966 ATCGATCCCCTCTCCGCC 60.602 66.667 0.00 0.00 0.00 6.13
45 46 3.041469 GCCCCTCTCCTCTGCTTGG 62.041 68.421 0.00 0.00 0.00 3.61
47 48 0.693767 CCCCTCTCCTCTGCTTGGAT 60.694 60.000 0.00 0.00 32.56 3.41
50 51 1.493861 CTCTCCTCTGCTTGGATGGA 58.506 55.000 0.00 0.00 32.56 3.41
155 156 2.315176 TCTTGGGTGGGTGACAAATTG 58.685 47.619 0.00 0.00 0.00 2.32
233 237 5.163395 CGGAGAAATAGGAGGAGTTAGCTTT 60.163 44.000 0.00 0.00 0.00 3.51
247 251 3.256281 GCTTTGGCTTAGGTCTGCT 57.744 52.632 0.00 0.00 35.22 4.24
296 300 1.297598 GACGCGCGGATGGAAATTG 60.298 57.895 35.22 1.22 0.00 2.32
300 304 1.708822 GCGCGGATGGAAATTGTTTT 58.291 45.000 8.83 0.00 0.00 2.43
322 326 0.249405 AAACGGACGCGTACAAGGAA 60.249 50.000 23.49 0.00 0.00 3.36
331 335 3.192001 ACGCGTACAAGGAAACTATCTCA 59.808 43.478 11.67 0.00 42.68 3.27
332 336 4.171005 CGCGTACAAGGAAACTATCTCAA 58.829 43.478 0.00 0.00 42.68 3.02
335 339 5.062308 GCGTACAAGGAAACTATCTCAACAG 59.938 44.000 0.00 0.00 42.68 3.16
336 340 6.157211 CGTACAAGGAAACTATCTCAACAGT 58.843 40.000 0.00 0.00 42.68 3.55
356 360 2.190578 GCCAGGGACGGATTCAGG 59.809 66.667 0.00 0.00 0.00 3.86
361 365 1.382695 GGGACGGATTCAGGGGAGA 60.383 63.158 0.00 0.00 0.00 3.71
362 366 0.981277 GGGACGGATTCAGGGGAGAA 60.981 60.000 0.00 0.00 0.00 2.87
363 367 0.909623 GGACGGATTCAGGGGAGAAA 59.090 55.000 0.00 0.00 0.00 2.52
365 369 2.092375 GGACGGATTCAGGGGAGAAAAT 60.092 50.000 0.00 0.00 0.00 1.82
366 370 3.135895 GGACGGATTCAGGGGAGAAAATA 59.864 47.826 0.00 0.00 0.00 1.40
367 371 4.384868 GGACGGATTCAGGGGAGAAAATAA 60.385 45.833 0.00 0.00 0.00 1.40
368 372 5.187621 ACGGATTCAGGGGAGAAAATAAA 57.812 39.130 0.00 0.00 0.00 1.40
369 373 5.766590 ACGGATTCAGGGGAGAAAATAAAT 58.233 37.500 0.00 0.00 0.00 1.40
375 379 9.987272 GATTCAGGGGAGAAAATAAATAAATGG 57.013 33.333 0.00 0.00 0.00 3.16
379 383 8.204160 CAGGGGAGAAAATAAATAAATGGGAAC 58.796 37.037 0.00 0.00 0.00 3.62
383 387 7.435192 GGAGAAAATAAATAAATGGGAACGCTG 59.565 37.037 0.00 0.00 0.00 5.18
429 433 2.302260 TGGCAAAATGGACGTTTCTCA 58.698 42.857 0.00 0.00 0.00 3.27
442 446 7.156000 TGGACGTTTCTCATTTACATTGTCTA 58.844 34.615 0.00 0.00 0.00 2.59
443 447 7.822334 TGGACGTTTCTCATTTACATTGTCTAT 59.178 33.333 0.00 0.00 0.00 1.98
444 448 8.665685 GGACGTTTCTCATTTACATTGTCTATT 58.334 33.333 0.00 0.00 0.00 1.73
457 461 7.858052 ACATTGTCTATTTTCTTTTTGCGAG 57.142 32.000 0.00 0.00 0.00 5.03
461 465 5.914635 TGTCTATTTTCTTTTTGCGAGCTTG 59.085 36.000 0.00 0.00 0.00 4.01
463 467 7.075741 GTCTATTTTCTTTTTGCGAGCTTGTA 58.924 34.615 2.14 0.00 0.00 2.41
482 486 6.312918 GCTTGTAATTTACATTGTCTCGAGGA 59.687 38.462 13.56 0.00 38.68 3.71
485 489 6.761242 TGTAATTTACATTGTCTCGAGGATGG 59.239 38.462 13.56 1.64 32.89 3.51
500 504 3.629087 AGGATGGCAAATTCCTTCTCAG 58.371 45.455 2.22 0.00 39.36 3.35
508 512 1.270907 ATTCCTTCTCAGAGCACGGT 58.729 50.000 0.00 0.00 0.00 4.83
519 523 0.392461 GAGCACGGTAAATCCTGGCA 60.392 55.000 0.00 0.00 36.04 4.92
556 563 0.811616 GGGTATGCCGTGCTCAAGAG 60.812 60.000 0.00 0.00 34.97 2.85
558 565 1.405526 GGTATGCCGTGCTCAAGAGAA 60.406 52.381 0.32 0.00 0.00 2.87
561 568 1.159285 TGCCGTGCTCAAGAGAATTG 58.841 50.000 0.32 0.00 0.00 2.32
588 599 7.758980 CCAAATAATCAAAATCAATGTCGACCA 59.241 33.333 14.12 1.26 0.00 4.02
596 607 5.567138 AATCAATGTCGACCAATCTTTCC 57.433 39.130 14.12 0.00 0.00 3.13
599 610 5.800296 TCAATGTCGACCAATCTTTCCTTA 58.200 37.500 14.12 0.00 0.00 2.69
601 612 3.581755 TGTCGACCAATCTTTCCTTACG 58.418 45.455 14.12 0.00 0.00 3.18
611 622 1.206371 CTTTCCTTACGGACACGGGAT 59.794 52.381 0.00 0.00 46.48 3.85
618 629 1.041447 ACGGACACGGGATAAGGAGG 61.041 60.000 0.00 0.00 46.48 4.30
620 631 0.690077 GGACACGGGATAAGGAGGGT 60.690 60.000 0.00 0.00 0.00 4.34
626 637 1.060743 GGGATAAGGAGGGTGGGGTC 61.061 65.000 0.00 0.00 0.00 4.46
627 638 0.029989 GGATAAGGAGGGTGGGGTCT 60.030 60.000 0.00 0.00 0.00 3.85
629 640 2.361070 GGATAAGGAGGGTGGGGTCTTA 60.361 54.545 0.00 0.00 0.00 2.10
685 705 8.430801 AGTCTTGCATGTAATTTAGAGATGAC 57.569 34.615 0.00 0.00 0.00 3.06
714 734 8.650143 AAAACATGTCTACAATGGGTTATCTT 57.350 30.769 0.00 0.00 0.00 2.40
719 739 9.396022 CATGTCTACAATGGGTTATCTTTTAGT 57.604 33.333 0.00 0.00 0.00 2.24
721 741 8.822805 TGTCTACAATGGGTTATCTTTTAGTCT 58.177 33.333 0.00 0.00 0.00 3.24
834 854 9.822727 TTTTTATAATTTCTCTCCTTTCCACCT 57.177 29.630 0.00 0.00 0.00 4.00
835 855 9.462606 TTTTATAATTTCTCTCCTTTCCACCTC 57.537 33.333 0.00 0.00 0.00 3.85
836 856 6.642733 ATAATTTCTCTCCTTTCCACCTCA 57.357 37.500 0.00 0.00 0.00 3.86
837 857 5.527026 AATTTCTCTCCTTTCCACCTCAT 57.473 39.130 0.00 0.00 0.00 2.90
838 858 5.527026 ATTTCTCTCCTTTCCACCTCATT 57.473 39.130 0.00 0.00 0.00 2.57
839 859 6.642733 ATTTCTCTCCTTTCCACCTCATTA 57.357 37.500 0.00 0.00 0.00 1.90
840 860 6.642733 TTTCTCTCCTTTCCACCTCATTAT 57.357 37.500 0.00 0.00 0.00 1.28
841 861 6.642733 TTCTCTCCTTTCCACCTCATTATT 57.357 37.500 0.00 0.00 0.00 1.40
842 862 6.642733 TCTCTCCTTTCCACCTCATTATTT 57.357 37.500 0.00 0.00 0.00 1.40
883 903 3.316308 GGCACTCCTAAAATAGCACCATG 59.684 47.826 0.00 0.00 0.00 3.66
884 904 3.243201 GCACTCCTAAAATAGCACCATGC 60.243 47.826 0.00 0.00 45.46 4.06
932 957 1.067199 GCTGCGGAAATTGCTGAACG 61.067 55.000 0.00 0.00 33.64 3.95
952 977 2.359967 GGGTACCGCTCTTCAGGCT 61.360 63.158 5.65 0.00 40.86 4.58
953 978 1.142097 GGTACCGCTCTTCAGGCTC 59.858 63.158 0.00 0.00 0.00 4.70
961 1524 3.067106 CGCTCTTCAGGCTCAAACTAAA 58.933 45.455 0.00 0.00 0.00 1.85
987 1550 1.508088 GAAGGCCATCCAAGTTGCG 59.492 57.895 5.01 0.00 33.74 4.85
1022 1590 1.403382 GGGACGGGTCTACTTCGAAAC 60.403 57.143 0.00 0.00 0.00 2.78
1023 1591 1.270550 GGACGGGTCTACTTCGAAACA 59.729 52.381 0.00 0.00 0.00 2.83
1046 1614 2.234908 ACTGTATGAGTCTTCACCAGGC 59.765 50.000 9.48 0.00 38.78 4.85
1051 1619 2.031163 GTCTTCACCAGGCGCTGT 59.969 61.111 7.64 0.00 0.00 4.40
1069 1637 1.303561 TCAAGCACTGCCATGGACC 60.304 57.895 18.40 0.00 0.00 4.46
1073 1641 4.802051 CACTGCCATGGACCGGGG 62.802 72.222 18.40 0.00 0.00 5.73
1083 1651 4.324991 GACCGGGGTTCGCTTGGT 62.325 66.667 6.32 4.69 37.59 3.67
1197 1765 1.678970 GTTGGCTAAGGCTGGGGTG 60.679 63.158 0.00 0.00 38.73 4.61
1224 1792 3.462021 AGTTCCTGATAGCGAGCAAATC 58.538 45.455 0.00 0.97 0.00 2.17
1236 1804 4.335272 GCGAGCAAATCTAGCTAACAAAC 58.665 43.478 0.00 0.00 43.58 2.93
1241 1809 6.241645 AGCAAATCTAGCTAACAAACTTCCT 58.758 36.000 0.00 0.00 41.32 3.36
1243 1811 6.072452 GCAAATCTAGCTAACAAACTTCCTGT 60.072 38.462 0.00 0.00 0.00 4.00
1245 1813 5.148651 TCTAGCTAACAAACTTCCTGTCC 57.851 43.478 0.00 0.00 0.00 4.02
1256 1824 1.065701 CTTCCTGTCCGATGTACTCCG 59.934 57.143 0.00 0.00 0.00 4.63
1298 1866 0.884704 CCCCCGTAATCTGGAATGCG 60.885 60.000 0.00 0.00 0.00 4.73
1310 1878 0.106918 GGAATGCGGGGTGTTCCATA 60.107 55.000 0.00 0.00 40.82 2.74
1311 1879 1.683629 GGAATGCGGGGTGTTCCATAA 60.684 52.381 0.00 0.00 40.82 1.90
1312 1880 1.676006 GAATGCGGGGTGTTCCATAAG 59.324 52.381 0.00 0.00 37.22 1.73
1313 1881 0.106719 ATGCGGGGTGTTCCATAAGG 60.107 55.000 0.00 0.00 37.22 2.69
1365 1941 7.124347 ACACAAATGATCATGCAAAACATTC 57.876 32.000 9.46 0.00 36.64 2.67
1379 1955 5.697633 GCAAAACATTCACATTTGTCATCCT 59.302 36.000 0.00 0.00 36.63 3.24
1380 1956 6.128742 GCAAAACATTCACATTTGTCATCCTC 60.129 38.462 0.00 0.00 36.63 3.71
1381 1957 5.649782 AACATTCACATTTGTCATCCTCC 57.350 39.130 0.00 0.00 0.00 4.30
1404 1980 4.219115 TCAGCAAAATGTTCCCTGGTTAA 58.781 39.130 0.00 0.00 0.00 2.01
1451 2027 1.292242 AGGGCCTCATAGTCTTCCTCA 59.708 52.381 0.00 0.00 0.00 3.86
1477 2053 4.235372 CCCCCTCCTTAGAACATCTACAT 58.765 47.826 0.00 0.00 0.00 2.29
1481 2057 5.011533 CCCTCCTTAGAACATCTACATCCAG 59.988 48.000 0.00 0.00 0.00 3.86
1499 2075 2.996631 CAGACTTAGCAAATCTGGCCT 58.003 47.619 3.32 0.00 36.92 5.19
1501 2077 2.092699 AGACTTAGCAAATCTGGCCTCC 60.093 50.000 3.32 0.00 0.00 4.30
1506 2082 3.677156 AGCAAATCTGGCCTCCTAAAT 57.323 42.857 3.32 0.00 0.00 1.40
1509 2085 3.181483 GCAAATCTGGCCTCCTAAATGTG 60.181 47.826 3.32 0.00 0.00 3.21
1552 2128 1.311859 ACATGATGCTACAATGGGCG 58.688 50.000 0.00 0.00 0.00 6.13
1599 2175 2.719354 GTGTTGGAACCGGTGCAC 59.281 61.111 16.38 8.80 0.00 4.57
1646 2222 1.274167 TGTTGGAACTGGCTACTACGG 59.726 52.381 0.00 0.00 0.00 4.02
1647 2223 0.899720 TTGGAACTGGCTACTACGGG 59.100 55.000 0.00 0.00 0.00 5.28
1664 2240 1.406069 CGGGTTCTACAAGCTGCTCAT 60.406 52.381 1.00 0.00 29.74 2.90
1665 2241 2.716217 GGGTTCTACAAGCTGCTCATT 58.284 47.619 1.00 0.00 0.00 2.57
1668 2244 1.742761 TCTACAAGCTGCTCATTGGC 58.257 50.000 1.00 0.00 0.00 4.52
1672 2248 2.338015 AAGCTGCTCATTGGCGGTG 61.338 57.895 1.00 0.00 40.42 4.94
1675 2251 1.210931 CTGCTCATTGGCGGTGTTG 59.789 57.895 0.00 0.00 34.21 3.33
1686 2262 2.671963 GGTGTTGGAACCGGCCTC 60.672 66.667 0.00 0.00 0.00 4.70
1702 2278 1.258445 CCTCGTGGGGAGCTACAACT 61.258 60.000 0.00 0.00 41.71 3.16
1712 2288 3.006859 GGGAGCTACAACTGGCAAATTTT 59.993 43.478 0.00 0.00 0.00 1.82
1722 2298 3.119849 ACTGGCAAATTTTAGCGCTACAG 60.120 43.478 18.63 19.39 0.00 2.74
1725 2301 3.171277 GCAAATTTTAGCGCTACAGTGG 58.829 45.455 18.63 4.92 0.00 4.00
1747 2323 0.107508 ACCATCAGATGCTGGAACCG 60.108 55.000 9.59 0.00 35.05 4.44
1749 2325 1.202734 CCATCAGATGCTGGAACCGAT 60.203 52.381 4.68 0.00 33.33 4.18
1798 2374 2.860628 GCGCCGCTACGATGAACTG 61.861 63.158 0.00 0.00 34.06 3.16
1842 2418 1.692519 ACAACGGTAGAAGCTGGAACT 59.307 47.619 0.00 0.00 0.00 3.01
1845 2421 0.741221 CGGTAGAAGCTGGAACTGGC 60.741 60.000 0.00 0.00 0.00 4.85
1848 2426 2.504367 GTAGAAGCTGGAACTGGCAAA 58.496 47.619 0.00 0.00 0.00 3.68
1877 2456 7.920160 TGTTACAATTGATGACAATGAGCTA 57.080 32.000 13.59 0.00 44.67 3.32
1887 2466 0.032678 CAATGAGCTAGGGCGACGAT 59.967 55.000 0.00 0.00 44.37 3.73
1907 2486 2.332654 GGGGTGGTGTCGTGATTGC 61.333 63.158 0.00 0.00 0.00 3.56
1908 2487 2.332654 GGGTGGTGTCGTGATTGCC 61.333 63.158 0.00 0.00 0.00 4.52
1909 2488 1.599518 GGTGGTGTCGTGATTGCCA 60.600 57.895 0.00 0.00 0.00 4.92
1987 2566 3.452627 GGTGGAAGTGATGACCAGTAGAT 59.547 47.826 0.00 0.00 34.21 1.98
1994 2573 4.037327 AGTGATGACCAGTAGATGACGATG 59.963 45.833 0.00 0.00 0.00 3.84
2002 2581 3.980134 CAGTAGATGACGATGATGTGAGC 59.020 47.826 0.00 0.00 0.00 4.26
2004 2583 1.678101 AGATGACGATGATGTGAGCGA 59.322 47.619 0.00 0.00 0.00 4.93
2049 2628 2.475466 CGCTCCCGATGCTGCAATT 61.475 57.895 6.36 0.00 36.29 2.32
2084 2663 4.082523 CGTGGCGGGGATGTGACT 62.083 66.667 0.00 0.00 0.00 3.41
2089 2668 2.954684 GCGGGGATGTGACTGTCCA 61.955 63.158 5.17 3.50 36.19 4.02
2149 2728 3.365535 GCAGGGGCAAACAACGAT 58.634 55.556 0.00 0.00 40.72 3.73
2152 2731 0.893270 CAGGGGCAAACAACGATGGA 60.893 55.000 0.00 0.00 0.00 3.41
2153 2732 0.609131 AGGGGCAAACAACGATGGAG 60.609 55.000 0.00 0.00 0.00 3.86
2178 2757 3.741476 CCTTTGTGCCGCTGGAGC 61.741 66.667 0.00 0.00 37.78 4.70
2208 2788 2.463752 GGGTTTATTTCCCCTTCACCC 58.536 52.381 0.00 0.00 39.08 4.61
2209 2789 2.225420 GGGTTTATTTCCCCTTCACCCA 60.225 50.000 0.00 0.00 41.90 4.51
2210 2790 2.829720 GGTTTATTTCCCCTTCACCCAC 59.170 50.000 0.00 0.00 0.00 4.61
2211 2791 3.501568 GGTTTATTTCCCCTTCACCCACT 60.502 47.826 0.00 0.00 0.00 4.00
2212 2792 4.264038 GGTTTATTTCCCCTTCACCCACTA 60.264 45.833 0.00 0.00 0.00 2.74
2213 2793 4.855298 TTATTTCCCCTTCACCCACTAG 57.145 45.455 0.00 0.00 0.00 2.57
2214 2794 2.127651 TTTCCCCTTCACCCACTAGT 57.872 50.000 0.00 0.00 0.00 2.57
2215 2795 3.278987 TTTCCCCTTCACCCACTAGTA 57.721 47.619 0.00 0.00 0.00 1.82
2216 2796 2.544844 TCCCCTTCACCCACTAGTAG 57.455 55.000 0.00 0.00 0.00 2.57
2217 2797 2.005350 TCCCCTTCACCCACTAGTAGA 58.995 52.381 3.59 0.00 0.00 2.59
2218 2798 2.384375 TCCCCTTCACCCACTAGTAGAA 59.616 50.000 3.59 0.00 0.00 2.10
2219 2799 3.178865 CCCCTTCACCCACTAGTAGAAA 58.821 50.000 3.59 0.00 0.00 2.52
2220 2800 3.585732 CCCCTTCACCCACTAGTAGAAAA 59.414 47.826 3.59 0.00 0.00 2.29
2221 2801 4.042435 CCCCTTCACCCACTAGTAGAAAAA 59.958 45.833 3.59 0.00 0.00 1.94
2222 2802 5.246307 CCCTTCACCCACTAGTAGAAAAAG 58.754 45.833 3.59 0.00 0.00 2.27
2223 2803 5.246307 CCTTCACCCACTAGTAGAAAAAGG 58.754 45.833 3.59 3.25 0.00 3.11
2224 2804 5.012768 CCTTCACCCACTAGTAGAAAAAGGA 59.987 44.000 15.42 0.00 33.05 3.36
2225 2805 5.479124 TCACCCACTAGTAGAAAAAGGAC 57.521 43.478 3.59 0.00 0.00 3.85
2226 2806 4.285260 TCACCCACTAGTAGAAAAAGGACC 59.715 45.833 3.59 0.00 0.00 4.46
2227 2807 4.286291 CACCCACTAGTAGAAAAAGGACCT 59.714 45.833 3.59 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.601966 GGCGGAGAGGGGATCGAT 60.602 66.667 0.00 0.00 0.00 3.59
28 29 0.693767 ATCCAAGCAGAGGAGAGGGG 60.694 60.000 0.00 0.00 38.83 4.79
29 30 0.469070 CATCCAAGCAGAGGAGAGGG 59.531 60.000 0.00 0.00 38.83 4.30
47 48 8.429641 CCAGGAAATAGCTTTAGTATAGTTCCA 58.570 37.037 17.49 0.00 42.99 3.53
155 156 1.079057 GTTTCTCCACCTCCGCCTC 60.079 63.158 0.00 0.00 0.00 4.70
233 237 1.573108 AGCTAAGCAGACCTAAGCCA 58.427 50.000 0.00 0.00 33.63 4.75
242 246 7.268199 CATGAATGGATAAAAGCTAAGCAGA 57.732 36.000 0.00 0.00 0.00 4.26
285 289 4.450757 CCGTTTCCAAAACAATTTCCATCC 59.549 41.667 3.72 0.00 0.00 3.51
296 300 4.199130 CGCGTCCGTTTCCAAAAC 57.801 55.556 0.00 0.00 0.00 2.43
322 326 3.560025 CCTGGCCAACTGTTGAGATAGTT 60.560 47.826 21.49 0.00 37.67 2.24
331 335 2.113139 CGTCCCTGGCCAACTGTT 59.887 61.111 7.01 0.00 0.00 3.16
332 336 3.953775 CCGTCCCTGGCCAACTGT 61.954 66.667 7.01 0.00 0.00 3.55
335 339 1.749258 GAATCCGTCCCTGGCCAAC 60.749 63.158 7.01 0.31 0.00 3.77
336 340 2.196997 CTGAATCCGTCCCTGGCCAA 62.197 60.000 7.01 0.00 0.00 4.52
356 360 6.700081 GCGTTCCCATTTATTTATTTTCTCCC 59.300 38.462 0.00 0.00 0.00 4.30
361 365 7.875554 ACAACAGCGTTCCCATTTATTTATTTT 59.124 29.630 0.00 0.00 0.00 1.82
362 366 7.330700 CACAACAGCGTTCCCATTTATTTATTT 59.669 33.333 0.00 0.00 0.00 1.40
363 367 6.811170 CACAACAGCGTTCCCATTTATTTATT 59.189 34.615 0.00 0.00 0.00 1.40
365 369 5.704888 CACAACAGCGTTCCCATTTATTTA 58.295 37.500 0.00 0.00 0.00 1.40
366 370 4.555262 CACAACAGCGTTCCCATTTATTT 58.445 39.130 0.00 0.00 0.00 1.40
367 371 3.613910 GCACAACAGCGTTCCCATTTATT 60.614 43.478 0.00 0.00 0.00 1.40
368 372 2.094752 GCACAACAGCGTTCCCATTTAT 60.095 45.455 0.00 0.00 0.00 1.40
369 373 1.268352 GCACAACAGCGTTCCCATTTA 59.732 47.619 0.00 0.00 0.00 1.40
375 379 1.279840 GTCAGCACAACAGCGTTCC 59.720 57.895 0.00 0.00 40.15 3.62
379 383 1.083401 GAACGTCAGCACAACAGCG 60.083 57.895 0.00 0.00 40.15 5.18
383 387 1.507141 CCCAGGAACGTCAGCACAAC 61.507 60.000 0.00 0.00 0.00 3.32
442 446 7.713764 AATTACAAGCTCGCAAAAAGAAAAT 57.286 28.000 0.00 0.00 0.00 1.82
443 447 7.532682 AAATTACAAGCTCGCAAAAAGAAAA 57.467 28.000 0.00 0.00 0.00 2.29
444 448 7.702772 TGTAAATTACAAGCTCGCAAAAAGAAA 59.297 29.630 2.97 0.00 35.38 2.52
445 449 7.197017 TGTAAATTACAAGCTCGCAAAAAGAA 58.803 30.769 2.97 0.00 35.38 2.52
446 450 6.730175 TGTAAATTACAAGCTCGCAAAAAGA 58.270 32.000 2.97 0.00 35.38 2.52
447 451 6.984740 TGTAAATTACAAGCTCGCAAAAAG 57.015 33.333 2.97 0.00 35.38 2.27
453 457 5.869350 AGACAATGTAAATTACAAGCTCGC 58.131 37.500 10.09 0.00 42.76 5.03
454 458 6.034577 TCGAGACAATGTAAATTACAAGCTCG 59.965 38.462 25.80 25.80 42.76 5.03
457 461 6.312918 TCCTCGAGACAATGTAAATTACAAGC 59.687 38.462 15.71 0.69 42.76 4.01
461 465 6.292919 GCCATCCTCGAGACAATGTAAATTAC 60.293 42.308 15.71 0.00 0.00 1.89
463 467 4.576463 GCCATCCTCGAGACAATGTAAATT 59.424 41.667 15.71 0.00 0.00 1.82
482 486 3.022406 GCTCTGAGAAGGAATTTGCCAT 58.978 45.455 9.28 0.00 0.00 4.40
485 489 2.159599 CGTGCTCTGAGAAGGAATTTGC 60.160 50.000 9.28 0.00 0.00 3.68
500 504 0.392461 TGCCAGGATTTACCGTGCTC 60.392 55.000 0.00 0.00 44.74 4.26
539 546 2.010145 TTCTCTTGAGCACGGCATAC 57.990 50.000 0.00 0.00 0.00 2.39
546 553 3.648339 TTTGGCAATTCTCTTGAGCAC 57.352 42.857 0.00 0.00 0.00 4.40
558 565 8.605746 CGACATTGATTTTGATTATTTGGCAAT 58.394 29.630 0.00 0.00 0.00 3.56
561 568 7.254084 GGTCGACATTGATTTTGATTATTTGGC 60.254 37.037 18.91 0.00 0.00 4.52
580 591 3.581755 CGTAAGGAAAGATTGGTCGACA 58.418 45.455 18.91 0.00 0.00 4.35
596 607 2.026641 TCCTTATCCCGTGTCCGTAAG 58.973 52.381 0.00 0.00 0.00 2.34
599 610 1.041447 CCTCCTTATCCCGTGTCCGT 61.041 60.000 0.00 0.00 0.00 4.69
601 612 0.690077 ACCCTCCTTATCCCGTGTCC 60.690 60.000 0.00 0.00 0.00 4.02
611 622 3.275497 TGTATAAGACCCCACCCTCCTTA 59.725 47.826 0.00 0.00 0.00 2.69
618 629 3.945640 ACCATTGTATAAGACCCCACC 57.054 47.619 0.00 0.00 0.00 4.61
620 631 5.725551 ATCAACCATTGTATAAGACCCCA 57.274 39.130 0.00 0.00 0.00 4.96
693 713 9.396022 ACTAAAAGATAACCCATTGTAGACATG 57.604 33.333 0.00 0.00 0.00 3.21
810 830 8.611257 TGAGGTGGAAAGGAGAGAAATTATAAA 58.389 33.333 0.00 0.00 0.00 1.40
813 833 6.642733 TGAGGTGGAAAGGAGAGAAATTAT 57.357 37.500 0.00 0.00 0.00 1.28
814 834 6.642733 ATGAGGTGGAAAGGAGAGAAATTA 57.357 37.500 0.00 0.00 0.00 1.40
817 837 6.642733 ATAATGAGGTGGAAAGGAGAGAAA 57.357 37.500 0.00 0.00 0.00 2.52
820 840 6.886459 TGAAAATAATGAGGTGGAAAGGAGAG 59.114 38.462 0.00 0.00 0.00 3.20
821 841 6.789268 TGAAAATAATGAGGTGGAAAGGAGA 58.211 36.000 0.00 0.00 0.00 3.71
825 845 9.880157 AAATGATGAAAATAATGAGGTGGAAAG 57.120 29.630 0.00 0.00 0.00 2.62
837 857 9.077885 GCCACCTAGGATAAATGATGAAAATAA 57.922 33.333 17.98 0.00 41.22 1.40
838 858 8.224025 TGCCACCTAGGATAAATGATGAAAATA 58.776 33.333 17.98 0.00 41.22 1.40
839 859 7.014615 GTGCCACCTAGGATAAATGATGAAAAT 59.985 37.037 17.98 0.00 41.22 1.82
840 860 6.321181 GTGCCACCTAGGATAAATGATGAAAA 59.679 38.462 17.98 0.00 41.22 2.29
841 861 5.827797 GTGCCACCTAGGATAAATGATGAAA 59.172 40.000 17.98 0.00 41.22 2.69
842 862 5.132648 AGTGCCACCTAGGATAAATGATGAA 59.867 40.000 17.98 0.00 41.22 2.57
872 892 2.761786 AGGGAATGCATGGTGCTATT 57.238 45.000 0.00 2.16 45.31 1.73
891 913 1.518774 GACCTCGCCGTTCCCATTA 59.481 57.895 0.00 0.00 0.00 1.90
904 926 1.298859 ATTTCCGCAGCAACGACCTC 61.299 55.000 0.00 0.00 34.06 3.85
913 935 1.067199 CGTTCAGCAATTTCCGCAGC 61.067 55.000 0.00 0.00 0.00 5.25
914 936 0.516877 TCGTTCAGCAATTTCCGCAG 59.483 50.000 0.00 0.00 0.00 5.18
915 937 0.516877 CTCGTTCAGCAATTTCCGCA 59.483 50.000 0.00 0.00 0.00 5.69
916 938 0.179189 CCTCGTTCAGCAATTTCCGC 60.179 55.000 0.00 0.00 0.00 5.54
917 939 0.447801 CCCTCGTTCAGCAATTTCCG 59.552 55.000 0.00 0.00 0.00 4.30
932 957 1.817209 CCTGAAGAGCGGTACCCTC 59.183 63.158 17.92 17.92 0.00 4.30
982 1545 1.094785 ATACCATGCACTTCCGCAAC 58.905 50.000 0.00 0.00 46.87 4.17
987 1550 1.680338 GTCCCATACCATGCACTTCC 58.320 55.000 0.00 0.00 0.00 3.46
1051 1619 1.303561 GGTCCATGGCAGTGCTTGA 60.304 57.895 16.11 3.79 0.00 3.02
1069 1637 1.170290 AGAAAACCAAGCGAACCCCG 61.170 55.000 0.00 0.00 42.21 5.73
1073 1641 2.349532 CGGAAGAGAAAACCAAGCGAAC 60.350 50.000 0.00 0.00 0.00 3.95
1077 1645 0.110192 CGCGGAAGAGAAAACCAAGC 60.110 55.000 0.00 0.00 0.00 4.01
1083 1651 0.250124 TTGCCTCGCGGAAGAGAAAA 60.250 50.000 6.13 0.00 40.10 2.29
1099 1667 5.906073 ACCTAAATGCATGAGGTATTTTGC 58.094 37.500 25.22 0.00 41.91 3.68
1104 1672 7.615365 TCAAAGAAACCTAAATGCATGAGGTAT 59.385 33.333 26.18 16.14 42.93 2.73
1107 1675 6.071728 ACTCAAAGAAACCTAAATGCATGAGG 60.072 38.462 21.21 21.21 35.94 3.86
1140 1708 2.495270 ACAGACCAGAGAGCAGTACATG 59.505 50.000 0.00 0.00 0.00 3.21
1141 1709 2.813907 ACAGACCAGAGAGCAGTACAT 58.186 47.619 0.00 0.00 0.00 2.29
1148 1716 2.364002 GGGAGATTACAGACCAGAGAGC 59.636 54.545 0.00 0.00 0.00 4.09
1197 1765 1.476891 TCGCTATCAGGAACTCCACAC 59.523 52.381 0.00 0.00 34.60 3.82
1224 1792 3.927142 CGGACAGGAAGTTTGTTAGCTAG 59.073 47.826 0.00 0.00 0.00 3.42
1236 1804 1.065701 CGGAGTACATCGGACAGGAAG 59.934 57.143 0.00 0.00 0.00 3.46
1241 1809 0.524414 CACACGGAGTACATCGGACA 59.476 55.000 11.50 0.00 41.61 4.02
1243 1811 1.509463 GCACACGGAGTACATCGGA 59.491 57.895 11.50 0.00 41.61 4.55
1245 1813 1.518572 GGGCACACGGAGTACATCG 60.519 63.158 0.00 0.58 41.61 3.84
1277 1845 1.814248 GCATTCCAGATTACGGGGGAC 60.814 57.143 0.00 0.00 32.37 4.46
1278 1846 0.472471 GCATTCCAGATTACGGGGGA 59.528 55.000 0.00 0.00 32.37 4.81
1282 1850 0.884704 CCCCGCATTCCAGATTACGG 60.885 60.000 0.00 0.00 40.30 4.02
1324 1900 4.927978 TGTGTTTTTCGTGGATGGAAAT 57.072 36.364 0.00 0.00 33.74 2.17
1334 1910 5.288015 TGCATGATCATTTGTGTTTTTCGT 58.712 33.333 5.16 0.00 0.00 3.85
1365 1941 2.681848 GCTGAGGAGGATGACAAATGTG 59.318 50.000 0.00 0.00 0.00 3.21
1379 1955 2.517959 CAGGGAACATTTTGCTGAGGA 58.482 47.619 0.00 0.00 0.00 3.71
1380 1956 1.547372 CCAGGGAACATTTTGCTGAGG 59.453 52.381 0.00 0.00 0.00 3.86
1381 1957 2.242043 ACCAGGGAACATTTTGCTGAG 58.758 47.619 0.00 0.00 0.00 3.35
1422 1998 2.182312 ACTATGAGGCCCTATCCCAAGA 59.818 50.000 0.00 0.00 0.00 3.02
1451 2027 0.253630 TGTTCTAAGGAGGGGGCCAT 60.254 55.000 4.39 0.00 0.00 4.40
1481 2057 2.092699 AGGAGGCCAGATTTGCTAAGTC 60.093 50.000 5.01 0.00 0.00 3.01
1499 2075 1.612199 GGGGTTCGTGCACATTTAGGA 60.612 52.381 18.64 1.26 0.00 2.94
1501 2077 0.808755 GGGGGTTCGTGCACATTTAG 59.191 55.000 18.64 0.00 0.00 1.85
1506 2082 4.263572 CCAGGGGGTTCGTGCACA 62.264 66.667 18.64 0.81 0.00 4.57
1577 2153 2.073716 ACCGGTTCCAACACCTCCA 61.074 57.895 0.00 0.00 34.22 3.86
1584 2160 2.551912 CCTGTGCACCGGTTCCAAC 61.552 63.158 18.45 0.99 0.00 3.77
1599 2175 2.203070 GCCGGTACCAGCATCCTG 60.203 66.667 15.49 0.00 38.85 3.86
1622 2198 0.953960 GTAGCCAGTTCCAACACCCG 60.954 60.000 0.00 0.00 0.00 5.28
1646 2222 2.421424 CCAATGAGCAGCTTGTAGAACC 59.579 50.000 0.00 0.00 0.00 3.62
1647 2223 2.159462 GCCAATGAGCAGCTTGTAGAAC 60.159 50.000 0.00 0.00 0.00 3.01
1672 2248 3.047877 CACGAGGCCGGTTCCAAC 61.048 66.667 1.90 0.00 40.78 3.77
1686 2262 1.079127 CCAGTTGTAGCTCCCCACG 60.079 63.158 0.00 0.00 0.00 4.94
1702 2278 2.817258 ACTGTAGCGCTAAAATTTGCCA 59.183 40.909 20.73 9.27 0.00 4.92
1712 2288 2.577059 GTGCCCACTGTAGCGCTA 59.423 61.111 14.45 14.45 36.57 4.26
1722 2298 1.077212 AGCATCTGATGGTGCCCAC 60.077 57.895 20.49 1.68 42.20 4.61
1747 2323 5.041951 TGGTTGTAGCAAAACAATCGATC 57.958 39.130 0.00 0.00 42.30 3.69
1749 2325 4.517075 TCATGGTTGTAGCAAAACAATCGA 59.483 37.500 0.00 0.00 42.30 3.59
1821 2397 2.104281 AGTTCCAGCTTCTACCGTTGTT 59.896 45.455 0.00 0.00 0.00 2.83
1852 2430 7.400599 AGCTCATTGTCATCAATTGTAACAT 57.599 32.000 5.13 0.00 41.66 2.71
1870 2448 1.662608 CATCGTCGCCCTAGCTCAT 59.337 57.895 0.00 0.00 36.60 2.90
1887 2466 2.150719 AATCACGACACCACCCCCA 61.151 57.895 0.00 0.00 0.00 4.96
1907 2486 1.529226 TTTATGGTTGCTGGTCGTGG 58.471 50.000 0.00 0.00 0.00 4.94
1908 2487 2.668279 GCTTTTATGGTTGCTGGTCGTG 60.668 50.000 0.00 0.00 0.00 4.35
1909 2488 1.539827 GCTTTTATGGTTGCTGGTCGT 59.460 47.619 0.00 0.00 0.00 4.34
1987 2566 1.843992 CATCGCTCACATCATCGTCA 58.156 50.000 0.00 0.00 0.00 4.35
2031 2610 2.475466 AATTGCAGCATCGGGAGCG 61.475 57.895 0.00 0.00 37.01 5.03
2036 2615 1.226859 CCAGCAATTGCAGCATCGG 60.227 57.895 30.89 16.64 45.16 4.18
2039 2618 2.183300 CGCCAGCAATTGCAGCAT 59.817 55.556 31.93 13.71 45.16 3.79
2069 2648 2.927856 ACAGTCACATCCCCGCCA 60.928 61.111 0.00 0.00 0.00 5.69
2081 2660 3.677002 GCTCCTGCTATGGACAGTC 57.323 57.895 0.00 0.00 36.03 3.51
2104 2683 4.681978 GGCTCGGTCGTGGTTGCT 62.682 66.667 0.00 0.00 0.00 3.91
2147 2726 3.873952 GCACAAAGGTGTCTATCTCCATC 59.126 47.826 0.00 0.00 46.95 3.51
2149 2728 2.027192 GGCACAAAGGTGTCTATCTCCA 60.027 50.000 0.00 0.00 46.14 3.86
2178 2757 1.586586 AAATAAACCCCCTCCCCCGG 61.587 60.000 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.