Multiple sequence alignment - TraesCS2A01G448300

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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 TraesCS2A01G448300 chr2A 100.000 3479 0 0 1 3479 697288335 697291813 0.000000e+00 6425.0
1 TraesCS2A01G448300 chr2B 88.742 3562 196 96 3 3473 664932165 664935612 0.000000e+00 4167.0
2 TraesCS2A01G448300 chr2D 88.580 3520 184 92 3 3443 557257146 557260526 0.000000e+00 4072.0
3 TraesCS2A01G448300 chr6A 92.825 223 16 0 1740 1962 488062703 488062481 1.200000e-84 324.0
4 TraesCS2A01G448300 chr6A 88.406 207 22 2 1226 1430 488063009 488062803 7.460000e-62 248.0
5 TraesCS2A01G448300 chr6B 87.324 213 23 4 1220 1430 524064817 524064607 1.250000e-59 241.0
6 TraesCS2A01G448300 chr6D 86.916 214 24 3 1221 1430 354223193 354223406 1.610000e-58 237.0
7 TraesCS2A01G448300 chr7A 82.511 223 37 2 1740 1961 573097002 573096781 9.850000e-46 195.0
8 TraesCS2A01G448300 chr7A 76.829 246 34 15 1740 1963 303102172 303101928 2.190000e-22 117.0
9 TraesCS2A01G448300 chr7D 82.143 224 40 0 1740 1963 505603597 505603374 3.540000e-45 193.0
10 TraesCS2A01G448300 chr7B 82.222 225 38 2 1740 1963 533570540 533570317 3.540000e-45 193.0
11 TraesCS2A01G448300 chr7B 77.236 246 33 15 1740 1963 268454509 268454753 4.720000e-24 122.0
12 TraesCS2A01G448300 chr1D 82.533 229 18 12 1753 1961 275942994 275942768 7.670000e-42 182.0
13 TraesCS2A01G448300 chr1D 79.825 114 17 5 2262 2375 275942634 275942527 1.040000e-10 78.7
14 TraesCS2A01G448300 chr1B 82.533 229 18 13 1753 1961 375257489 375257263 7.670000e-42 182.0
15 TraesCS2A01G448300 chr1B 80.000 115 17 5 2261 2375 375257130 375257022 2.880000e-11 80.5
16 TraesCS2A01G448300 chr1A 81.034 232 19 15 1753 1961 348399582 348399353 9.990000e-36 161.0
17 TraesCS2A01G448300 chr1A 78.986 138 18 9 2262 2399 348399216 348399090 2.230000e-12 84.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G448300 chr2A 697288335 697291813 3478 False 6425 6425 100.0000 1 3479 1 chr2A.!!$F1 3478
1 TraesCS2A01G448300 chr2B 664932165 664935612 3447 False 4167 4167 88.7420 3 3473 1 chr2B.!!$F1 3470
2 TraesCS2A01G448300 chr2D 557257146 557260526 3380 False 4072 4072 88.5800 3 3443 1 chr2D.!!$F1 3440
3 TraesCS2A01G448300 chr6A 488062481 488063009 528 True 286 324 90.6155 1226 1962 2 chr6A.!!$R1 736

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
565 601 0.035630 GACTTCAGTGCTGATGGCCT 60.036 55.0 3.32 0.0 39.64 5.19 F
687 731 0.105778 GAAGCAATCGAGGAGAGGGG 59.894 60.0 0.00 0.0 0.00 4.79 F
688 732 0.325671 AAGCAATCGAGGAGAGGGGA 60.326 55.0 0.00 0.0 0.00 4.81 F
776 820 0.387929 CGGGAGCGGATAAGCAGTTA 59.612 55.0 0.00 0.0 40.15 2.24 F
903 954 0.616679 CCCCTCCCGGTCTACAAAGA 60.617 60.0 0.00 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 1673 1.150536 GGGCTGGAGGACACAACAA 59.849 57.895 0.00 0.0 0.0 2.83 R
1690 1784 1.560146 TCGTCAGAGAGAAGCTAGGGA 59.440 52.381 0.00 0.0 0.0 4.20 R
2090 2192 1.594293 CGTCCACGCCAGAACAGTT 60.594 57.895 0.00 0.0 0.0 3.16 R
2260 2364 1.985116 GGACGGGGAGAAGCTCTGT 60.985 63.158 0.00 0.0 0.0 3.41 R
2763 2898 2.000447 CTAAGAACAACCAGCGCCTAC 59.000 52.381 2.29 0.0 0.0 3.18 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
29 30 4.697828 AGAGAATTTTCCGCTCCTTTTCTC 59.302 41.667 0.00 0.00 38.44 2.87
49 50 0.173708 CCGGGAGAGGAGAAAACTCG 59.826 60.000 0.00 0.00 39.90 4.18
59 60 2.098117 GGAGAAAACTCGGCCATGAATG 59.902 50.000 2.24 0.00 0.00 2.67
183 184 1.157276 CATCCGATCCCTCCCTCCT 59.843 63.158 0.00 0.00 0.00 3.69
197 198 1.000019 CTCCTCCGTCCACTGGGTA 60.000 63.158 0.00 0.00 34.93 3.69
209 210 4.317444 TGGGTACAACGCACCGGG 62.317 66.667 6.32 0.00 36.06 5.73
230 231 2.297701 GTGGACGGCATGGTGATTATT 58.702 47.619 0.00 0.00 0.00 1.40
233 234 3.380004 TGGACGGCATGGTGATTATTTTC 59.620 43.478 0.00 0.00 0.00 2.29
239 240 3.960102 GCATGGTGATTATTTTCCCTCCA 59.040 43.478 0.00 0.00 0.00 3.86
245 246 5.105351 GGTGATTATTTTCCCTCCACCTTTG 60.105 44.000 0.00 0.00 39.41 2.77
246 247 5.714806 GTGATTATTTTCCCTCCACCTTTGA 59.285 40.000 0.00 0.00 0.00 2.69
247 248 5.714806 TGATTATTTTCCCTCCACCTTTGAC 59.285 40.000 0.00 0.00 0.00 3.18
249 250 2.656947 TTTCCCTCCACCTTTGACAG 57.343 50.000 0.00 0.00 0.00 3.51
311 332 1.615107 CCGCGGAGAAAACGTGTCTC 61.615 60.000 24.07 17.31 40.75 3.36
407 428 1.860078 CAAAGCCGAGTGACGAACC 59.140 57.895 0.00 0.00 45.77 3.62
437 458 4.666532 GCACGAAGCACCACGCAC 62.667 66.667 0.00 0.00 46.13 5.34
438 459 4.354212 CACGAAGCACCACGCACG 62.354 66.667 0.00 0.00 46.13 5.34
461 482 4.099824 CGTAAACAAAAACAAACCGAGCT 58.900 39.130 0.00 0.00 0.00 4.09
514 535 0.730265 TTGTTATCGGATGGCAACGC 59.270 50.000 9.69 0.00 42.51 4.84
515 536 1.275657 GTTATCGGATGGCAACGCG 59.724 57.895 3.53 3.53 42.51 6.01
516 537 1.885388 TTATCGGATGGCAACGCGG 60.885 57.895 12.47 0.00 42.51 6.46
565 601 0.035630 GACTTCAGTGCTGATGGCCT 60.036 55.000 3.32 0.00 39.64 5.19
567 603 0.252479 CTTCAGTGCTGATGGCCTCT 59.748 55.000 3.32 0.00 39.64 3.69
600 636 4.873810 TGCCGCTGCCACAACTGT 62.874 61.111 0.00 0.00 36.33 3.55
601 637 3.595758 GCCGCTGCCACAACTGTT 61.596 61.111 0.00 0.00 0.00 3.16
602 638 2.332514 CCGCTGCCACAACTGTTG 59.667 61.111 18.44 18.44 0.00 3.33
603 639 2.353839 CGCTGCCACAACTGTTGC 60.354 61.111 19.82 7.37 37.23 4.17
604 640 2.806929 GCTGCCACAACTGTTGCA 59.193 55.556 19.82 11.55 43.21 4.08
646 690 3.041940 GACAGGACAACACGGCCG 61.042 66.667 26.86 26.86 0.00 6.13
676 720 1.014044 TGAGTCGCCACGAAGCAATC 61.014 55.000 0.00 0.00 37.72 2.67
686 730 3.677002 GAAGCAATCGAGGAGAGGG 57.323 57.895 0.00 0.00 0.00 4.30
687 731 0.105778 GAAGCAATCGAGGAGAGGGG 59.894 60.000 0.00 0.00 0.00 4.79
688 732 0.325671 AAGCAATCGAGGAGAGGGGA 60.326 55.000 0.00 0.00 0.00 4.81
689 733 0.758685 AGCAATCGAGGAGAGGGGAG 60.759 60.000 0.00 0.00 0.00 4.30
690 734 1.753368 GCAATCGAGGAGAGGGGAGG 61.753 65.000 0.00 0.00 0.00 4.30
695 739 2.204705 AGGAGAGGGGAGGAGGGT 60.205 66.667 0.00 0.00 0.00 4.34
707 751 1.003696 GAGGAGGGTCCAAAAGTCCAG 59.996 57.143 0.00 0.00 39.61 3.86
774 818 2.815308 CGGGAGCGGATAAGCAGT 59.185 61.111 0.00 0.00 40.15 4.40
775 819 1.144057 CGGGAGCGGATAAGCAGTT 59.856 57.895 0.00 0.00 40.15 3.16
776 820 0.387929 CGGGAGCGGATAAGCAGTTA 59.612 55.000 0.00 0.00 40.15 2.24
777 821 1.202486 CGGGAGCGGATAAGCAGTTAA 60.202 52.381 0.00 0.00 40.15 2.01
778 822 2.484889 GGGAGCGGATAAGCAGTTAAG 58.515 52.381 0.00 0.00 40.15 1.85
819 863 1.821332 CGCCCCTGAAAGCATCCTC 60.821 63.158 0.00 0.00 0.00 3.71
903 954 0.616679 CCCCTCCCGGTCTACAAAGA 60.617 60.000 0.00 0.00 0.00 2.52
928 979 3.717294 GGCTTTCCTCCGCCTCCA 61.717 66.667 0.00 0.00 42.98 3.86
933 984 0.836400 TTTCCTCCGCCTCCACTTCT 60.836 55.000 0.00 0.00 0.00 2.85
946 997 1.202927 CCACTTCTTCCCTCCAAAGCA 60.203 52.381 0.00 0.00 0.00 3.91
953 1004 2.538141 CCCTCCAAAGCACCCCTCA 61.538 63.158 0.00 0.00 0.00 3.86
998 1049 1.997874 AAATCCTCTGCGCTCCCCT 60.998 57.895 9.73 0.00 0.00 4.79
1126 1177 2.301346 CACATGGTAGCCTCCAAATCC 58.699 52.381 0.00 0.00 41.09 3.01
1155 1207 1.807142 CCTGTTCGCCTTTTCTTCTCC 59.193 52.381 0.00 0.00 0.00 3.71
1174 1226 1.595489 CCGTGCGATTAAATGCTCTGC 60.595 52.381 4.24 0.00 0.00 4.26
1176 1228 2.713011 GTGCGATTAAATGCTCTGCTG 58.287 47.619 4.24 0.00 0.00 4.41
1409 1469 2.687200 TGCCTCGCCTACCACCAT 60.687 61.111 0.00 0.00 0.00 3.55
1461 1521 7.323052 AGAACTAGACCATTTCTTTCCTTCT 57.677 36.000 0.00 0.00 35.55 2.85
1463 1523 6.943899 ACTAGACCATTTCTTTCCTTCTCT 57.056 37.500 0.00 0.00 35.55 3.10
1510 1570 2.184579 CCGGCCGGAGAAGAAGAC 59.815 66.667 41.82 0.00 37.50 3.01
1533 1611 1.134461 TCCCTGTTTCGTTTCCGTTGA 60.134 47.619 0.00 0.00 35.01 3.18
1583 1673 2.862541 TGCTAGATTTGCAGTTGGTGT 58.137 42.857 0.00 0.00 35.31 4.16
1584 1674 3.221771 TGCTAGATTTGCAGTTGGTGTT 58.778 40.909 0.00 0.00 35.31 3.32
1585 1675 3.004629 TGCTAGATTTGCAGTTGGTGTTG 59.995 43.478 0.00 0.00 35.31 3.33
1586 1676 3.004734 GCTAGATTTGCAGTTGGTGTTGT 59.995 43.478 0.00 0.00 0.00 3.32
1587 1677 4.499696 GCTAGATTTGCAGTTGGTGTTGTT 60.500 41.667 0.00 0.00 0.00 2.83
1658 1751 2.027469 ACCCGCCTAACTAACTTCCTTG 60.027 50.000 0.00 0.00 0.00 3.61
1659 1752 2.027469 CCCGCCTAACTAACTTCCTTGT 60.027 50.000 0.00 0.00 0.00 3.16
1661 1754 3.435671 CCGCCTAACTAACTTCCTTGTTG 59.564 47.826 0.00 0.00 0.00 3.33
1687 1781 0.767446 CCCCCTGCTCCATCTCATCT 60.767 60.000 0.00 0.00 0.00 2.90
1689 1783 1.421480 CCCTGCTCCATCTCATCTCA 58.579 55.000 0.00 0.00 0.00 3.27
1690 1784 1.979308 CCCTGCTCCATCTCATCTCAT 59.021 52.381 0.00 0.00 0.00 2.90
1691 1785 2.027929 CCCTGCTCCATCTCATCTCATC 60.028 54.545 0.00 0.00 0.00 2.92
1693 1787 1.976404 TGCTCCATCTCATCTCATCCC 59.024 52.381 0.00 0.00 0.00 3.85
1696 1790 3.448301 GCTCCATCTCATCTCATCCCTAG 59.552 52.174 0.00 0.00 0.00 3.02
1697 1791 3.439154 TCCATCTCATCTCATCCCTAGC 58.561 50.000 0.00 0.00 0.00 3.42
1698 1792 3.077240 TCCATCTCATCTCATCCCTAGCT 59.923 47.826 0.00 0.00 0.00 3.32
1722 1816 5.849510 TCTCTCTGACGATTTTTGTTGGTA 58.150 37.500 0.00 0.00 0.00 3.25
1724 1818 7.608153 TCTCTCTGACGATTTTTGTTGGTATA 58.392 34.615 0.00 0.00 0.00 1.47
1725 1819 8.258007 TCTCTCTGACGATTTTTGTTGGTATAT 58.742 33.333 0.00 0.00 0.00 0.86
1971 2073 2.159085 GGATGCAAGGTACGTAGCTTCT 60.159 50.000 31.42 20.74 41.62 2.85
1972 2074 3.522553 GATGCAAGGTACGTAGCTTCTT 58.477 45.455 31.42 22.96 41.62 2.52
1980 2082 4.954826 AGGTACGTAGCTTCTTCCACTAAT 59.045 41.667 21.15 0.00 0.00 1.73
1981 2083 5.041940 GGTACGTAGCTTCTTCCACTAATG 58.958 45.833 17.27 0.00 0.00 1.90
1982 2084 9.456347 AAGGTACGTAGCTTCTTCCACTAATGG 62.456 44.444 29.31 0.00 42.63 3.16
2028 2130 3.548415 GGTCAACGCCTCTACTAGATTCG 60.548 52.174 0.00 5.88 0.00 3.34
2044 2146 3.743396 AGATTCGTTCAGTTCAGTTCAGC 59.257 43.478 0.00 0.00 0.00 4.26
2090 2192 2.016318 CTGGAGCGGCATTGTGATTTA 58.984 47.619 1.45 0.00 0.00 1.40
2091 2193 2.423185 CTGGAGCGGCATTGTGATTTAA 59.577 45.455 1.45 0.00 0.00 1.52
2092 2194 2.163412 TGGAGCGGCATTGTGATTTAAC 59.837 45.455 1.45 0.00 0.00 2.01
2097 2199 3.608073 GCGGCATTGTGATTTAACTGTTC 59.392 43.478 0.00 0.00 0.00 3.18
2098 2200 4.615912 GCGGCATTGTGATTTAACTGTTCT 60.616 41.667 0.00 0.00 0.00 3.01
2099 2201 4.853196 CGGCATTGTGATTTAACTGTTCTG 59.147 41.667 0.00 0.00 0.00 3.02
2260 2364 1.080772 CGACAAGAGCAGCGTGGTA 60.081 57.895 0.00 0.00 0.00 3.25
2380 2489 3.129462 TCATCGTGGAGTTCTAGAGCAAG 59.871 47.826 9.43 0.00 0.00 4.01
2449 2560 5.543790 ACTGTAGCATACACATCCATCCATA 59.456 40.000 0.00 0.00 46.14 2.74
2451 2562 4.292186 AGCATACACATCCATCCATACC 57.708 45.455 0.00 0.00 0.00 2.73
2471 2582 7.231115 CCATACCTACCTACCTCTAGAGTTTTC 59.769 44.444 18.42 0.00 0.00 2.29
2477 2593 5.246429 ACCTACCTCTAGAGTTTTCCTGTTG 59.754 44.000 18.42 7.96 0.00 3.33
2505 2621 5.422331 TCTGTTCTATACACCAAGGAGAAGG 59.578 44.000 0.00 0.00 32.10 3.46
2506 2622 5.338632 TGTTCTATACACCAAGGAGAAGGA 58.661 41.667 0.00 0.00 0.00 3.36
2515 2631 1.209261 CAAGGAGAAGGAGAAGGAGCC 59.791 57.143 0.00 0.00 0.00 4.70
2622 2743 5.585445 CCACTACTTCGTCATAGTCACTACT 59.415 44.000 0.00 0.00 39.91 2.57
2623 2744 6.760298 CCACTACTTCGTCATAGTCACTACTA 59.240 42.308 0.00 0.00 42.35 1.82
2624 2745 7.254387 CCACTACTTCGTCATAGTCACTACTAC 60.254 44.444 0.00 0.00 40.98 2.73
2625 2746 7.277319 CACTACTTCGTCATAGTCACTACTACA 59.723 40.741 0.00 0.00 40.98 2.74
2626 2747 7.821359 ACTACTTCGTCATAGTCACTACTACAA 59.179 37.037 0.00 0.00 40.98 2.41
2713 2838 5.344066 GGAGGTAGTAGCCGTAGTTTTTAC 58.656 45.833 0.00 0.00 0.00 2.01
2717 2842 7.112779 AGGTAGTAGCCGTAGTTTTTACTCTA 58.887 38.462 0.00 0.00 0.00 2.43
2719 2852 7.859875 GGTAGTAGCCGTAGTTTTTACTCTATG 59.140 40.741 0.00 0.00 0.00 2.23
2731 2864 5.786264 TTTACTCTATGGTGGTAGCTAGC 57.214 43.478 16.08 16.08 0.00 3.42
2732 2865 3.314307 ACTCTATGGTGGTAGCTAGCA 57.686 47.619 21.35 21.35 0.00 3.49
2733 2866 3.226777 ACTCTATGGTGGTAGCTAGCAG 58.773 50.000 25.30 13.53 33.94 4.24
2734 2867 3.226777 CTCTATGGTGGTAGCTAGCAGT 58.773 50.000 25.30 16.20 33.94 4.40
2770 2905 2.152016 ACTTTCTTTCCTTGTAGGCGC 58.848 47.619 0.00 0.00 34.61 6.53
2950 3085 2.443887 TGCTTGCTTGCTTGAATTCC 57.556 45.000 2.27 0.00 0.00 3.01
2966 3101 6.694445 TGAATTCCTCTTCTTCTTCTTCCT 57.306 37.500 2.27 0.00 0.00 3.36
2968 3103 6.500049 TGAATTCCTCTTCTTCTTCTTCCTCT 59.500 38.462 2.27 0.00 0.00 3.69
2970 3105 5.736951 TCCTCTTCTTCTTCTTCCTCTTG 57.263 43.478 0.00 0.00 0.00 3.02
2971 3106 4.020662 TCCTCTTCTTCTTCTTCCTCTTGC 60.021 45.833 0.00 0.00 0.00 4.01
2976 3111 1.056660 TCTTCTTCCTCTTGCCCGTT 58.943 50.000 0.00 0.00 0.00 4.44
2978 3113 1.807142 CTTCTTCCTCTTGCCCGTTTC 59.193 52.381 0.00 0.00 0.00 2.78
2979 3114 0.036306 TCTTCCTCTTGCCCGTTTCC 59.964 55.000 0.00 0.00 0.00 3.13
2980 3115 0.036875 CTTCCTCTTGCCCGTTTCCT 59.963 55.000 0.00 0.00 0.00 3.36
2981 3116 0.476771 TTCCTCTTGCCCGTTTCCTT 59.523 50.000 0.00 0.00 0.00 3.36
2982 3117 1.354101 TCCTCTTGCCCGTTTCCTTA 58.646 50.000 0.00 0.00 0.00 2.69
2992 3127 4.102524 TGCCCGTTTCCTTATATCATCAGT 59.897 41.667 0.00 0.00 0.00 3.41
2993 3128 4.452455 GCCCGTTTCCTTATATCATCAGTG 59.548 45.833 0.00 0.00 0.00 3.66
3038 3183 0.037790 GGAGACCTGTGACTGTGAGC 60.038 60.000 0.00 0.00 0.00 4.26
3096 3241 1.956629 GCGGATTTGGAGGAGACGGA 61.957 60.000 0.00 0.00 0.00 4.69
3138 3283 2.661537 CACCGTCAGCTGCACGAA 60.662 61.111 28.48 4.32 39.75 3.85
3181 3330 1.244019 AACTTGCTTGACCCGCCATC 61.244 55.000 0.00 0.00 0.00 3.51
3191 3340 1.454479 CCCGCCATCCATGAAAGCT 60.454 57.895 0.00 0.00 0.00 3.74
3277 3426 4.101448 CCAGGAACCCTCTGCCCG 62.101 72.222 0.00 0.00 0.00 6.13
3333 3487 4.729918 CTGCCTCTGTGTGCCCCC 62.730 72.222 0.00 0.00 0.00 5.40
3359 3513 2.287915 GTGGCAGTAGCAATGAATACGG 59.712 50.000 0.00 0.00 44.61 4.02
3360 3514 1.264288 GGCAGTAGCAATGAATACGGC 59.736 52.381 10.81 10.81 44.61 5.68
3368 3525 1.800586 CAATGAATACGGCTGGATCGG 59.199 52.381 0.00 0.00 0.00 4.18
3387 3544 1.001406 GGCCGATCTAGGGTTGAGATG 59.999 57.143 0.00 0.00 33.71 2.90
3390 3547 1.001406 CGATCTAGGGTTGAGATGGGC 59.999 57.143 0.00 0.00 33.71 5.36
3402 3559 1.597663 GAGATGGGCCGTACGAAAATG 59.402 52.381 18.76 0.00 0.00 2.32
3450 3613 2.980233 GGCCACGTGCTTCAAGCT 60.980 61.111 11.57 0.00 42.97 3.74
3451 3614 2.558313 GCCACGTGCTTCAAGCTC 59.442 61.111 11.57 6.12 42.97 4.09
3456 3619 4.996976 GTGCTTCAAGCTCGGAGA 57.003 55.556 11.57 0.00 42.97 3.71
3459 3622 2.197577 GTGCTTCAAGCTCGGAGATAC 58.802 52.381 11.57 0.00 42.97 2.24
3460 3623 2.103373 TGCTTCAAGCTCGGAGATACT 58.897 47.619 11.57 0.00 42.97 2.12
3474 3644 3.929094 GAGATACTATCTCGTCTCCCGT 58.071 50.000 9.82 0.00 45.50 5.28
3475 3645 3.928375 GAGATACTATCTCGTCTCCCGTC 59.072 52.174 9.82 0.00 45.50 4.79
3476 3646 3.579586 AGATACTATCTCGTCTCCCGTCT 59.420 47.826 0.00 0.00 33.42 4.18
3477 3647 4.771577 AGATACTATCTCGTCTCCCGTCTA 59.228 45.833 0.00 0.00 33.42 2.59
3478 3648 3.389925 ACTATCTCGTCTCCCGTCTAG 57.610 52.381 0.00 0.00 37.94 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.434702 GAGCGGAAAATTCTCTCCCCTA 59.565 50.000 0.00 0.00 0.00 3.53
1 2 1.210722 GAGCGGAAAATTCTCTCCCCT 59.789 52.381 0.00 0.00 0.00 4.79
29 30 0.537653 GAGTTTTCTCCTCTCCCGGG 59.462 60.000 16.85 16.85 40.79 5.73
162 163 1.535202 AGGGAGGGATCGGATGCTC 60.535 63.158 9.42 5.20 0.00 4.26
183 184 1.808531 CGTTGTACCCAGTGGACGGA 61.809 60.000 11.95 0.00 34.81 4.69
209 210 0.107410 TAATCACCATGCCGTCCACC 60.107 55.000 0.00 0.00 0.00 4.61
217 218 3.960102 TGGAGGGAAAATAATCACCATGC 59.040 43.478 0.00 0.00 0.00 4.06
230 231 1.144913 CCTGTCAAAGGTGGAGGGAAA 59.855 52.381 0.00 0.00 41.74 3.13
233 234 1.380302 CCCTGTCAAAGGTGGAGGG 59.620 63.158 0.00 0.00 45.78 4.30
239 240 1.072331 CAGCACTACCCTGTCAAAGGT 59.928 52.381 0.19 0.19 45.78 3.50
245 246 0.895530 TAGCACAGCACTACCCTGTC 59.104 55.000 0.00 0.00 41.34 3.51
246 247 1.348064 TTAGCACAGCACTACCCTGT 58.652 50.000 0.00 0.00 43.92 4.00
247 248 2.283298 CATTAGCACAGCACTACCCTG 58.717 52.381 0.00 0.00 36.41 4.45
249 250 1.668419 CCATTAGCACAGCACTACCC 58.332 55.000 0.00 0.00 0.00 3.69
250 251 1.017387 GCCATTAGCACAGCACTACC 58.983 55.000 0.00 0.00 42.97 3.18
251 252 0.652592 CGCCATTAGCACAGCACTAC 59.347 55.000 0.00 0.00 44.04 2.73
395 416 1.000607 TCTTTCCTGGTTCGTCACTCG 60.001 52.381 0.00 0.00 41.41 4.18
407 428 1.227999 TTCGTGCGGCTTCTTTCCTG 61.228 55.000 0.00 0.00 0.00 3.86
437 458 2.844804 TCGGTTTGTTTTTGTTTACGCG 59.155 40.909 3.53 3.53 0.00 6.01
438 459 3.301324 GCTCGGTTTGTTTTTGTTTACGC 60.301 43.478 0.00 0.00 0.00 4.42
439 460 4.028026 CAGCTCGGTTTGTTTTTGTTTACG 60.028 41.667 0.00 0.00 0.00 3.18
440 461 4.259650 GCAGCTCGGTTTGTTTTTGTTTAC 60.260 41.667 0.00 0.00 0.00 2.01
461 482 4.081185 TCCTCGCCGATGCTTGCA 62.081 61.111 0.00 0.00 34.43 4.08
471 492 2.099831 CGACTACGTGTCCTCGCC 59.900 66.667 0.00 0.00 42.49 5.54
549 575 0.035725 CAGAGGCCATCAGCACTGAA 60.036 55.000 5.01 0.00 44.64 3.02
646 690 4.436998 CGACTCACCCGGTGGCTC 62.437 72.222 17.76 10.80 33.87 4.70
676 720 2.197324 CCTCCTCCCCTCTCCTCG 59.803 72.222 0.00 0.00 0.00 4.63
686 730 0.328592 GGACTTTTGGACCCTCCTCC 59.671 60.000 0.00 0.00 37.46 4.30
687 731 1.003696 CTGGACTTTTGGACCCTCCTC 59.996 57.143 0.00 0.00 37.46 3.71
688 732 1.068121 CTGGACTTTTGGACCCTCCT 58.932 55.000 0.00 0.00 37.46 3.69
689 733 0.038310 CCTGGACTTTTGGACCCTCC 59.962 60.000 0.00 0.00 36.96 4.30
690 734 0.609406 GCCTGGACTTTTGGACCCTC 60.609 60.000 0.00 0.00 0.00 4.30
695 739 2.434331 CCGGCCTGGACTTTTGGA 59.566 61.111 7.77 0.00 42.00 3.53
753 797 4.664677 CTTATCCGCTCCCGCCCG 62.665 72.222 0.00 0.00 0.00 6.13
771 815 1.447140 TAGCGCCCGTGCTTAACTG 60.447 57.895 8.23 0.00 44.46 3.16
772 816 1.447314 GTAGCGCCCGTGCTTAACT 60.447 57.895 8.23 0.00 44.46 2.24
773 817 2.795389 CGTAGCGCCCGTGCTTAAC 61.795 63.158 8.23 0.71 44.46 2.01
774 818 2.507547 CGTAGCGCCCGTGCTTAA 60.508 61.111 8.23 0.00 44.46 1.85
775 819 4.501714 CCGTAGCGCCCGTGCTTA 62.502 66.667 8.23 0.00 44.46 3.09
819 863 1.908299 GAACCAAACCAGCAGGGGG 60.908 63.158 0.00 0.43 42.91 5.40
928 979 1.202940 GGTGCTTTGGAGGGAAGAAGT 60.203 52.381 0.00 0.00 0.00 3.01
933 984 1.778383 AGGGGTGCTTTGGAGGGAA 60.778 57.895 0.00 0.00 0.00 3.97
946 997 0.547954 GAGGAGAAAGGGTGAGGGGT 60.548 60.000 0.00 0.00 0.00 4.95
953 1004 2.270858 GAGGGAAAGAGGAGAAAGGGT 58.729 52.381 0.00 0.00 0.00 4.34
998 1049 0.757188 GAGGAAGGAGGAGGATGCGA 60.757 60.000 0.00 0.00 0.00 5.10
1002 1053 0.399806 GGCAGAGGAAGGAGGAGGAT 60.400 60.000 0.00 0.00 0.00 3.24
1052 1103 2.126071 CGCCTCGTCGTGGAATGT 60.126 61.111 17.27 0.00 0.00 2.71
1117 1168 0.396278 GGGGAAGCAGGGATTTGGAG 60.396 60.000 0.00 0.00 0.00 3.86
1126 1177 2.747855 GCGAACAGGGGAAGCAGG 60.748 66.667 0.00 0.00 0.00 4.85
1155 1207 1.328680 AGCAGAGCATTTAATCGCACG 59.671 47.619 0.00 0.00 0.00 5.34
1174 1226 4.335400 ACCAAGCAATAAAACCAACCAG 57.665 40.909 0.00 0.00 0.00 4.00
1176 1228 4.956085 AGAACCAAGCAATAAAACCAACC 58.044 39.130 0.00 0.00 0.00 3.77
1434 1494 7.800300 AGGAAAGAAATGGTCTAGTTCTAGT 57.200 36.000 0.00 0.00 42.44 2.57
1436 1496 8.437274 AGAAGGAAAGAAATGGTCTAGTTCTA 57.563 34.615 0.00 0.00 42.44 2.10
1437 1497 7.236640 AGAGAAGGAAAGAAATGGTCTAGTTCT 59.763 37.037 0.00 0.00 44.95 3.01
1438 1498 7.390823 AGAGAAGGAAAGAAATGGTCTAGTTC 58.609 38.462 0.00 0.00 34.56 3.01
1440 1500 6.943899 AGAGAAGGAAAGAAATGGTCTAGT 57.056 37.500 0.00 0.00 34.56 2.57
1451 1511 4.543590 ATGCGAAGAAGAGAAGGAAAGA 57.456 40.909 0.00 0.00 0.00 2.52
1452 1512 4.142730 CCAATGCGAAGAAGAGAAGGAAAG 60.143 45.833 0.00 0.00 0.00 2.62
1461 1521 4.774124 AGATGAATCCAATGCGAAGAAGA 58.226 39.130 0.00 0.00 0.00 2.87
1463 1523 4.943093 TGAAGATGAATCCAATGCGAAGAA 59.057 37.500 0.00 0.00 0.00 2.52
1510 1570 1.866925 GGAAACGAAACAGGGAGCG 59.133 57.895 0.00 0.00 0.00 5.03
1533 1611 1.647084 GACTTTCGTTGGTGCGCTT 59.353 52.632 9.73 0.00 0.00 4.68
1582 1672 1.172812 GGGCTGGAGGACACAACAAC 61.173 60.000 0.00 0.00 0.00 3.32
1583 1673 1.150536 GGGCTGGAGGACACAACAA 59.849 57.895 0.00 0.00 0.00 2.83
1584 1674 2.829384 GGGGCTGGAGGACACAACA 61.829 63.158 0.00 0.00 0.00 3.33
1585 1675 2.034221 GGGGCTGGAGGACACAAC 59.966 66.667 0.00 0.00 0.00 3.32
1586 1676 3.256960 GGGGGCTGGAGGACACAA 61.257 66.667 0.00 0.00 0.00 3.33
1604 1697 2.269241 GGGGAAGAGAGGCCGTTG 59.731 66.667 0.00 0.00 0.00 4.10
1675 1769 3.448301 GCTAGGGATGAGATGAGATGGAG 59.552 52.174 0.00 0.00 0.00 3.86
1687 1781 3.561143 GTCAGAGAGAAGCTAGGGATGA 58.439 50.000 0.00 0.00 0.00 2.92
1689 1783 2.173782 TCGTCAGAGAGAAGCTAGGGAT 59.826 50.000 0.00 0.00 0.00 3.85
1690 1784 1.560146 TCGTCAGAGAGAAGCTAGGGA 59.440 52.381 0.00 0.00 0.00 4.20
1691 1785 2.045561 TCGTCAGAGAGAAGCTAGGG 57.954 55.000 0.00 0.00 0.00 3.53
1693 1787 5.866633 ACAAAAATCGTCAGAGAGAAGCTAG 59.133 40.000 0.00 0.00 0.00 3.42
1696 1790 4.999751 ACAAAAATCGTCAGAGAGAAGC 57.000 40.909 0.00 0.00 0.00 3.86
1697 1791 5.237344 ACCAACAAAAATCGTCAGAGAGAAG 59.763 40.000 0.00 0.00 0.00 2.85
1698 1792 5.123227 ACCAACAAAAATCGTCAGAGAGAA 58.877 37.500 0.00 0.00 0.00 2.87
1847 1949 2.815647 GGGCGCTCGTTGAGGAAG 60.816 66.667 7.64 0.00 0.00 3.46
2028 2130 2.222911 GCTGAGCTGAACTGAACTGAAC 59.777 50.000 0.00 0.00 0.00 3.18
2044 2146 2.183811 CAGTCCAGGCGAGCTGAG 59.816 66.667 0.00 0.00 0.00 3.35
2090 2192 1.594293 CGTCCACGCCAGAACAGTT 60.594 57.895 0.00 0.00 0.00 3.16
2091 2193 2.029073 CGTCCACGCCAGAACAGT 59.971 61.111 0.00 0.00 0.00 3.55
2260 2364 1.985116 GGACGGGGAGAAGCTCTGT 60.985 63.158 0.00 0.00 0.00 3.41
2449 2560 5.255916 AGGAAAACTCTAGAGGTAGGTAGGT 59.744 44.000 23.50 0.00 0.00 3.08
2451 2562 6.189133 ACAGGAAAACTCTAGAGGTAGGTAG 58.811 44.000 23.50 10.65 0.00 3.18
2471 2582 4.091509 GTGTATAGAACAGAACGCAACAGG 59.908 45.833 0.00 0.00 39.29 4.00
2477 2593 3.617263 CCTTGGTGTATAGAACAGAACGC 59.383 47.826 0.00 0.00 39.29 4.84
2622 2743 4.944930 ACCAGCACAGTAACTGTTTTTGTA 59.055 37.500 0.00 0.00 42.59 2.41
2623 2744 3.761752 ACCAGCACAGTAACTGTTTTTGT 59.238 39.130 0.00 1.12 42.59 2.83
2624 2745 4.370364 ACCAGCACAGTAACTGTTTTTG 57.630 40.909 0.00 0.47 42.59 2.44
2625 2746 5.416326 TGTTACCAGCACAGTAACTGTTTTT 59.584 36.000 18.53 0.00 46.31 1.94
2626 2747 4.944930 TGTTACCAGCACAGTAACTGTTTT 59.055 37.500 18.53 0.00 46.31 2.43
2713 2838 3.226777 ACTGCTAGCTACCACCATAGAG 58.773 50.000 17.23 2.46 0.00 2.43
2717 2842 2.166907 AGACTGCTAGCTACCACCAT 57.833 50.000 17.23 0.00 0.00 3.55
2719 2852 2.657143 AGTAGACTGCTAGCTACCACC 58.343 52.381 17.23 0.13 38.14 4.61
2731 2864 7.920738 AGAAAGTTGCAAAACTTAGTAGACTG 58.079 34.615 0.00 0.00 41.76 3.51
2732 2865 8.507524 AAGAAAGTTGCAAAACTTAGTAGACT 57.492 30.769 0.00 0.00 41.76 3.24
2733 2866 9.222916 GAAAGAAAGTTGCAAAACTTAGTAGAC 57.777 33.333 0.00 0.00 41.76 2.59
2734 2867 8.403236 GGAAAGAAAGTTGCAAAACTTAGTAGA 58.597 33.333 0.00 0.00 41.76 2.59
2763 2898 2.000447 CTAAGAACAACCAGCGCCTAC 59.000 52.381 2.29 0.00 0.00 3.18
2770 2905 4.638421 TCAAACACACCTAAGAACAACCAG 59.362 41.667 0.00 0.00 0.00 4.00
2950 3085 4.252878 GGCAAGAGGAAGAAGAAGAAGAG 58.747 47.826 0.00 0.00 0.00 2.85
2966 3101 4.764050 TGATATAAGGAAACGGGCAAGA 57.236 40.909 0.00 0.00 0.00 3.02
2968 3103 5.042463 TGATGATATAAGGAAACGGGCAA 57.958 39.130 0.00 0.00 0.00 4.52
2970 3105 4.452455 CACTGATGATATAAGGAAACGGGC 59.548 45.833 0.00 0.00 0.00 6.13
2971 3106 5.853936 TCACTGATGATATAAGGAAACGGG 58.146 41.667 0.00 0.00 0.00 5.28
2976 3111 8.212995 TCAAGCATTCACTGATGATATAAGGAA 58.787 33.333 0.00 0.00 33.85 3.36
2978 3113 7.974482 TCAAGCATTCACTGATGATATAAGG 57.026 36.000 0.00 0.00 33.85 2.69
2981 3116 9.563748 TCAATTCAAGCATTCACTGATGATATA 57.436 29.630 0.00 0.00 33.85 0.86
2982 3117 8.350722 GTCAATTCAAGCATTCACTGATGATAT 58.649 33.333 0.00 0.00 33.85 1.63
2992 3127 4.587584 TTGCAGTCAATTCAAGCATTCA 57.412 36.364 0.00 0.00 34.87 2.57
2993 3128 4.201685 GCATTGCAGTCAATTCAAGCATTC 60.202 41.667 3.15 0.00 40.74 2.67
3031 3176 2.183811 CCTCTCAGGCGCTCACAG 59.816 66.667 7.64 0.00 0.00 3.66
3032 3177 3.385384 CCCTCTCAGGCGCTCACA 61.385 66.667 7.64 0.00 32.73 3.58
3033 3178 3.386237 ACCCTCTCAGGCGCTCAC 61.386 66.667 7.64 0.00 32.73 3.51
3034 3179 3.385384 CACCCTCTCAGGCGCTCA 61.385 66.667 7.64 0.00 32.73 4.26
3035 3180 4.828925 GCACCCTCTCAGGCGCTC 62.829 72.222 7.64 0.00 32.73 5.03
3038 3183 3.699894 ACAGCACCCTCTCAGGCG 61.700 66.667 0.00 0.00 32.73 5.52
3153 3302 1.136336 GTCAAGCAAGTTAGGCGAACG 60.136 52.381 4.82 0.00 43.37 3.95
3154 3303 1.197036 GGTCAAGCAAGTTAGGCGAAC 59.803 52.381 1.90 1.90 38.44 3.95
3155 3304 1.519408 GGTCAAGCAAGTTAGGCGAA 58.481 50.000 0.00 0.00 36.08 4.70
3156 3305 0.321298 GGGTCAAGCAAGTTAGGCGA 60.321 55.000 0.00 0.00 36.08 5.54
3181 3330 3.830192 GCCCGGCAGCTTTCATGG 61.830 66.667 3.91 0.00 0.00 3.66
3255 3404 1.904032 CAGAGGGTTCCTGGCTCTC 59.096 63.158 0.00 0.00 31.76 3.20
3333 3487 0.723414 CATTGCTACTGCCACAGACG 59.277 55.000 0.78 0.00 38.71 4.18
3368 3525 1.001406 CCATCTCAACCCTAGATCGGC 59.999 57.143 0.00 0.00 31.22 5.54
3387 3544 1.587933 TTGGCATTTTCGTACGGCCC 61.588 55.000 23.78 12.65 43.96 5.80
3390 3547 3.362295 CATCATTGGCATTTTCGTACGG 58.638 45.455 16.52 0.00 0.00 4.02
3402 3559 2.285220 CACGTAGTACAGCATCATTGGC 59.715 50.000 0.38 0.00 41.61 4.52


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

AutoCloner maintained by Alex Coulton.