Multiple sequence alignment - TraesCS4D01G348600

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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 TraesCS4D01G348600 chr4D 100.000 3285 0 0 1 3285 502072491 502075775 0.000000e+00 6067.0
1 TraesCS4D01G348600 chr4D 95.758 660 27 1 2624 3283 495976782 495976124 0.000000e+00 1062.0
2 TraesCS4D01G348600 chr4D 94.753 667 34 1 2620 3285 671464 670798 0.000000e+00 1037.0
3 TraesCS4D01G348600 chr5A 88.148 1679 112 44 947 2578 685004959 685006597 0.000000e+00 1917.0
4 TraesCS4D01G348600 chr5A 90.333 962 58 19 1 947 685003782 685004723 0.000000e+00 1229.0
5 TraesCS4D01G348600 chr5A 82.787 122 12 7 826 947 685004818 685004930 2.090000e-17 100.0
6 TraesCS4D01G348600 chr4B 85.065 1694 135 62 952 2567 646193924 646195577 0.000000e+00 1618.0
7 TraesCS4D01G348600 chr4B 85.099 557 28 19 1 544 646193020 646193534 4.860000e-143 518.0
8 TraesCS4D01G348600 chr4B 79.778 361 50 19 590 945 646193535 646193877 1.180000e-59 241.0
9 TraesCS4D01G348600 chr1D 95.626 663 29 0 2623 3285 455648027 455647365 0.000000e+00 1064.0
10 TraesCS4D01G348600 chr2D 95.023 663 30 2 2623 3285 174244051 174243392 0.000000e+00 1038.0
11 TraesCS4D01G348600 chr2D 94.419 663 36 1 2623 3285 67563922 67564583 0.000000e+00 1018.0
12 TraesCS4D01G348600 chr2D 78.363 171 29 7 1 170 195992321 195992158 1.610000e-18 104.0
13 TraesCS4D01G348600 chr7D 94.872 663 33 1 2623 3285 7423143 7423804 0.000000e+00 1035.0
14 TraesCS4D01G348600 chr7D 94.954 654 33 0 2632 3285 629548043 629547390 0.000000e+00 1026.0
15 TraesCS4D01G348600 chr7D 82.659 173 25 2 1 173 417607888 417608055 7.340000e-32 148.0
16 TraesCS4D01G348600 chr7A 94.570 663 36 0 2623 3285 690927448 690928110 0.000000e+00 1026.0
17 TraesCS4D01G348600 chr6A 94.303 667 34 3 2620 3285 522036146 522035483 0.000000e+00 1018.0
18 TraesCS4D01G348600 chr6A 97.143 35 1 0 1975 2009 616025977 616026011 3.540000e-05 60.2
19 TraesCS4D01G348600 chr5B 90.476 252 17 2 949 1200 707212748 707212504 3.160000e-85 326.0
20 TraesCS4D01G348600 chr3B 83.221 149 19 3 1 149 418884446 418884588 7.400000e-27 132.0
21 TraesCS4D01G348600 chr2B 80.000 170 29 3 1 170 557297011 557296847 1.600000e-23 121.0
22 TraesCS4D01G348600 chr2B 97.143 35 1 0 1975 2009 61181982 61182016 3.540000e-05 60.2
23 TraesCS4D01G348600 chr1B 86.458 96 11 2 1 96 581213658 581213751 1.610000e-18 104.0
24 TraesCS4D01G348600 chr1B 91.045 67 6 0 1 67 416811613 416811547 1.260000e-14 91.6
25 TraesCS4D01G348600 chr3A 85.714 84 12 0 1 84 493744757 493744840 4.510000e-14 89.8
26 TraesCS4D01G348600 chr6D 91.667 60 4 1 1 59 432730206 432730147 7.550000e-12 82.4
27 TraesCS4D01G348600 chr7B 97.143 35 1 0 1975 2009 565763578 565763612 3.540000e-05 60.2
28 TraesCS4D01G348600 chr6B 97.143 35 1 0 1975 2009 675805456 675805490 3.540000e-05 60.2


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 TraesCS4D01G348600 chr4D 502072491 502075775 3284 False 6067.000000 6067 100.000000 1 3285 1 chr4D.!!$F1 3284
1 TraesCS4D01G348600 chr4D 495976124 495976782 658 True 1062.000000 1062 95.758000 2624 3283 1 chr4D.!!$R2 659
2 TraesCS4D01G348600 chr4D 670798 671464 666 True 1037.000000 1037 94.753000 2620 3285 1 chr4D.!!$R1 665
3 TraesCS4D01G348600 chr5A 685003782 685006597 2815 False 1082.000000 1917 87.089333 1 2578 3 chr5A.!!$F1 2577
4 TraesCS4D01G348600 chr4B 646193020 646195577 2557 False 792.333333 1618 83.314000 1 2567 3 chr4B.!!$F1 2566
5 TraesCS4D01G348600 chr1D 455647365 455648027 662 True 1064.000000 1064 95.626000 2623 3285 1 chr1D.!!$R1 662
6 TraesCS4D01G348600 chr2D 174243392 174244051 659 True 1038.000000 1038 95.023000 2623 3285 1 chr2D.!!$R1 662
7 TraesCS4D01G348600 chr2D 67563922 67564583 661 False 1018.000000 1018 94.419000 2623 3285 1 chr2D.!!$F1 662
8 TraesCS4D01G348600 chr7D 7423143 7423804 661 False 1035.000000 1035 94.872000 2623 3285 1 chr7D.!!$F1 662
9 TraesCS4D01G348600 chr7D 629547390 629548043 653 True 1026.000000 1026 94.954000 2632 3285 1 chr7D.!!$R1 653
10 TraesCS4D01G348600 chr7A 690927448 690928110 662 False 1026.000000 1026 94.570000 2623 3285 1 chr7A.!!$F1 662
11 TraesCS4D01G348600 chr6A 522035483 522036146 663 True 1018.000000 1018 94.303000 2620 3285 1 chr6A.!!$R1 665

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
881 898 0.44899 TGCCACGCGTAGTACAGTAG 59.551 55.0 13.44 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2607 2979 0.03601 GGGCCGTGATGATATGGGAG 60.036 60.0 0.0 0.0 0.0 4.3 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
21 22 0.478072 ATCCGCCTCATATTTGGGCA 59.522 50.000 13.25 0.00 45.50 5.36
23 24 1.656441 CGCCTCATATTTGGGCAGC 59.344 57.895 13.25 0.00 45.50 5.25
30 31 4.338012 CTCATATTTGGGCAGCATATGGA 58.662 43.478 4.56 0.00 33.41 3.41
79 80 0.944311 CCGTTTGTGGGTCTCGTCTG 60.944 60.000 0.00 0.00 0.00 3.51
107 108 3.520290 AAATCGTGATAAGAGCGGACA 57.480 42.857 0.00 0.00 0.00 4.02
108 109 2.783828 ATCGTGATAAGAGCGGACAG 57.216 50.000 0.00 0.00 0.00 3.51
114 115 1.476891 GATAAGAGCGGACAGTGACCA 59.523 52.381 12.19 0.00 0.00 4.02
156 157 4.675029 CGGGTTTGAGGCGTCCGT 62.675 66.667 3.56 0.00 36.38 4.69
233 246 2.033299 GCCTTGAGCGCTTGCATATAAA 59.967 45.455 13.26 0.00 42.66 1.40
258 271 3.804325 CAGCCCACACACGAATTATCTAG 59.196 47.826 0.00 0.00 0.00 2.43
450 463 2.394563 GCAGCCGGAGAAGCAGTTC 61.395 63.158 5.05 0.00 0.00 3.01
451 464 1.743252 CAGCCGGAGAAGCAGTTCC 60.743 63.158 5.05 0.00 32.48 3.62
452 465 2.436824 GCCGGAGAAGCAGTTCCC 60.437 66.667 5.05 0.00 32.48 3.97
453 466 2.269241 CCGGAGAAGCAGTTCCCC 59.731 66.667 0.00 0.00 32.48 4.81
454 467 2.294078 CCGGAGAAGCAGTTCCCCT 61.294 63.158 0.00 0.00 32.48 4.79
578 592 4.553547 GCATGCATCTTCGTCTTAATCCAC 60.554 45.833 14.21 0.00 0.00 4.02
580 594 4.433615 TGCATCTTCGTCTTAATCCACTC 58.566 43.478 0.00 0.00 0.00 3.51
582 596 5.359860 TGCATCTTCGTCTTAATCCACTCTA 59.640 40.000 0.00 0.00 0.00 2.43
583 597 6.040955 TGCATCTTCGTCTTAATCCACTCTAT 59.959 38.462 0.00 0.00 0.00 1.98
585 599 6.301687 TCTTCGTCTTAATCCACTCTATCG 57.698 41.667 0.00 0.00 0.00 2.92
586 600 5.238868 TCTTCGTCTTAATCCACTCTATCGG 59.761 44.000 0.00 0.00 0.00 4.18
587 601 4.458397 TCGTCTTAATCCACTCTATCGGT 58.542 43.478 0.00 0.00 0.00 4.69
589 603 4.299978 GTCTTAATCCACTCTATCGGTGC 58.700 47.826 0.00 0.00 33.78 5.01
591 605 4.649674 TCTTAATCCACTCTATCGGTGCTT 59.350 41.667 0.00 0.00 33.78 3.91
592 606 3.460857 AATCCACTCTATCGGTGCTTC 57.539 47.619 0.00 0.00 33.78 3.86
593 607 0.738975 TCCACTCTATCGGTGCTTCG 59.261 55.000 0.00 0.00 33.78 3.79
594 608 0.456221 CCACTCTATCGGTGCTTCGT 59.544 55.000 0.00 0.00 33.78 3.85
595 609 1.534175 CCACTCTATCGGTGCTTCGTC 60.534 57.143 0.00 0.00 33.78 4.20
596 610 1.402259 CACTCTATCGGTGCTTCGTCT 59.598 52.381 0.00 0.00 0.00 4.18
597 611 2.093106 ACTCTATCGGTGCTTCGTCTT 58.907 47.619 0.00 0.00 0.00 3.01
608 622 3.851845 TTCGTCTTGCGTCCCGTGG 62.852 63.158 0.00 0.00 42.13 4.94
684 698 2.843701 CACTCCTGAGCTGACAGTTTT 58.156 47.619 3.99 0.00 36.30 2.43
787 803 2.037136 CCCTGCTTTGCCGACAGAG 61.037 63.158 0.00 0.00 33.10 3.35
795 811 0.458543 TTGCCGACAGAGATTCTCGC 60.459 55.000 8.01 5.89 35.36 5.03
804 820 3.314080 ACAGAGATTCTCGCTGCTAGTAC 59.686 47.826 8.01 0.00 46.24 2.73
805 821 2.546368 AGAGATTCTCGCTGCTAGTACG 59.454 50.000 8.01 0.00 35.36 3.67
864 881 5.050567 CCTCTGCTTTTCTGAATTTTGTTGC 60.051 40.000 0.00 0.00 0.00 4.17
881 898 0.448990 TGCCACGCGTAGTACAGTAG 59.551 55.000 13.44 0.00 0.00 2.57
882 899 0.449388 GCCACGCGTAGTACAGTAGT 59.551 55.000 13.44 0.00 0.00 2.73
906 923 2.165998 GGAAGATTGCAAGCTCTGGTT 58.834 47.619 19.00 0.80 0.00 3.67
914 931 3.225104 TGCAAGCTCTGGTTTTCTGAAT 58.775 40.909 0.00 0.00 0.00 2.57
947 1171 4.688413 GCTTCAGATCGAGTTCAGAAGTTT 59.312 41.667 17.36 0.00 39.86 2.66
950 1174 6.771188 TCAGATCGAGTTCAGAAGTTTTTC 57.229 37.500 0.00 0.00 0.00 2.29
983 1247 7.032580 CGTGCCATTATTAATTTGGAAGTTGA 58.967 34.615 17.12 0.00 31.94 3.18
1003 1267 0.813210 GAGCGCAGGAAGGAAGATGG 60.813 60.000 11.47 0.00 0.00 3.51
1202 1466 1.603236 CTCCTCAAGGTCAGCTCGCT 61.603 60.000 0.00 0.00 36.34 4.93
1203 1467 1.153667 CCTCAAGGTCAGCTCGCTC 60.154 63.158 0.00 0.00 0.00 5.03
1204 1468 1.588597 CTCAAGGTCAGCTCGCTCA 59.411 57.895 0.00 0.00 0.00 4.26
1206 1470 2.091112 CAAGGTCAGCTCGCTCACG 61.091 63.158 0.00 0.00 42.01 4.35
1209 1473 3.474034 GTCAGCTCGCTCACGCAC 61.474 66.667 0.00 0.00 39.84 5.34
1210 1474 3.977244 TCAGCTCGCTCACGCACA 61.977 61.111 0.00 0.00 39.84 4.57
1211 1475 2.812609 CAGCTCGCTCACGCACAT 60.813 61.111 0.00 0.00 39.84 3.21
1212 1476 1.517039 CAGCTCGCTCACGCACATA 60.517 57.895 0.00 0.00 39.84 2.29
1213 1477 1.517257 AGCTCGCTCACGCACATAC 60.517 57.895 0.00 0.00 39.84 2.39
1257 1521 2.290260 TGTAGGCTGCAGCTGTGTTAAT 60.290 45.455 35.82 15.00 41.70 1.40
1260 1524 2.229784 AGGCTGCAGCTGTGTTAATTTC 59.770 45.455 35.82 15.99 41.70 2.17
1270 1534 4.616953 CTGTGTTAATTTCGTTTTGGCCT 58.383 39.130 3.32 0.00 0.00 5.19
1273 1537 3.804873 TGTTAATTTCGTTTTGGCCTTGC 59.195 39.130 3.32 0.00 0.00 4.01
1280 1544 1.632422 GTTTTGGCCTTGCATCGATG 58.368 50.000 21.27 21.27 0.00 3.84
1307 1579 0.320771 AGTGGGTGAACGATCTGCAC 60.321 55.000 0.00 0.00 0.00 4.57
1310 1582 2.740714 GGTGAACGATCTGCACGCC 61.741 63.158 0.00 0.00 33.48 5.68
1448 1740 5.588246 TGTGCTGACTGTTAATTGTTTCTGA 59.412 36.000 0.00 0.00 0.00 3.27
1453 1745 7.166473 GCTGACTGTTAATTGTTTCTGAAACTG 59.834 37.037 27.75 11.57 41.90 3.16
1483 1775 2.047844 AATGCGCTGCTGTCGACT 60.048 55.556 17.92 0.00 0.00 4.18
1511 1803 1.961277 CTGGACCAGTTCGTGTGGC 60.961 63.158 13.84 0.00 38.83 5.01
1570 1864 3.515901 AGATTTAAGCGTCTCACCCTCTT 59.484 43.478 0.00 0.00 0.00 2.85
1571 1865 3.314541 TTTAAGCGTCTCACCCTCTTC 57.685 47.619 0.00 0.00 0.00 2.87
1572 1866 1.183549 TAAGCGTCTCACCCTCTTCC 58.816 55.000 0.00 0.00 0.00 3.46
1597 1891 0.107703 TCCACTCCATTCCATCGTGC 60.108 55.000 0.00 0.00 0.00 5.34
1601 1895 2.804527 CACTCCATTCCATCGTGCATAG 59.195 50.000 0.00 0.00 0.00 2.23
1602 1896 2.435805 ACTCCATTCCATCGTGCATAGT 59.564 45.455 0.00 0.00 0.00 2.12
1603 1897 3.641436 ACTCCATTCCATCGTGCATAGTA 59.359 43.478 0.00 0.00 0.00 1.82
1604 1898 3.990092 TCCATTCCATCGTGCATAGTAC 58.010 45.455 0.00 0.00 0.00 2.73
1620 1914 9.135843 GTGCATAGTACGTATTGATTAGCAATA 57.864 33.333 0.00 0.00 45.16 1.90
1720 2029 3.092511 TGCTGGATGGCCTCCTCC 61.093 66.667 18.49 15.08 45.21 4.30
1746 2055 2.486982 GTGCAAGTCTAGTCGAGGTACA 59.513 50.000 0.00 0.00 0.00 2.90
1752 2061 8.098912 TGCAAGTCTAGTCGAGGTACATATATA 58.901 37.037 0.00 0.00 0.00 0.86
1753 2062 9.111613 GCAAGTCTAGTCGAGGTACATATATAT 57.888 37.037 0.00 0.00 0.00 0.86
1755 2064 8.665643 AGTCTAGTCGAGGTACATATATATGC 57.334 38.462 20.46 7.13 37.19 3.14
1756 2065 8.265764 AGTCTAGTCGAGGTACATATATATGCA 58.734 37.037 20.46 7.07 37.19 3.96
1757 2066 8.336806 GTCTAGTCGAGGTACATATATATGCAC 58.663 40.741 20.46 17.72 37.19 4.57
1759 2068 7.462571 AGTCGAGGTACATATATATGCACAA 57.537 36.000 22.09 6.14 37.19 3.33
1774 2087 4.976224 TGCACAATTTCATCTCATGGAG 57.024 40.909 0.00 0.00 0.00 3.86
1782 2095 4.750021 TTCATCTCATGGAGACTCCTTG 57.250 45.455 24.90 24.90 41.76 3.61
1783 2096 3.717576 TCATCTCATGGAGACTCCTTGT 58.282 45.455 27.80 13.07 41.76 3.16
1785 2098 5.272402 TCATCTCATGGAGACTCCTTGTAA 58.728 41.667 27.80 20.09 41.76 2.41
1786 2099 5.127845 TCATCTCATGGAGACTCCTTGTAAC 59.872 44.000 27.80 2.17 41.76 2.50
1787 2100 4.416516 TCTCATGGAGACTCCTTGTAACA 58.583 43.478 27.80 13.95 41.12 2.41
1788 2101 5.026121 TCTCATGGAGACTCCTTGTAACAT 58.974 41.667 27.80 9.27 41.12 2.71
1798 2118 5.423015 ACTCCTTGTAACATGCTACATGAG 58.577 41.667 22.35 22.35 37.22 2.90
1799 2119 5.046304 ACTCCTTGTAACATGCTACATGAGT 60.046 40.000 23.19 23.19 38.33 3.41
1812 2132 6.846350 TGCTACATGAGTATATGACTGATCG 58.154 40.000 0.00 0.00 39.06 3.69
1835 2157 0.610232 GAGTGGGATTGCAGCTTGGT 60.610 55.000 0.00 0.00 0.00 3.67
1853 2175 3.701664 TGGTGAGCTCAAGAGACTATCA 58.298 45.455 20.19 0.00 0.00 2.15
1909 2231 1.467883 CGCCGACAAATACGAGGTACA 60.468 52.381 0.00 0.00 0.00 2.90
1929 2251 6.366332 GGTACAGTATCATTTTAGATCTGCCG 59.634 42.308 5.18 0.00 31.85 5.69
1946 2268 1.949133 CGCCCACGGACGATGTATG 60.949 63.158 0.00 0.00 34.97 2.39
1948 2270 1.151777 GCCCACGGACGATGTATGTG 61.152 60.000 0.00 0.00 0.00 3.21
1971 2298 9.838339 TGTGAAATTTTAACATAATTTGGTGGT 57.162 25.926 0.00 0.00 35.83 4.16
2093 2432 3.640407 AGCTGGCGCCCAAGAAGA 61.640 61.111 26.77 1.11 36.60 2.87
2185 2530 2.695359 TCACTGACCAATAAACCTCGC 58.305 47.619 0.00 0.00 0.00 5.03
2186 2531 1.737793 CACTGACCAATAAACCTCGCC 59.262 52.381 0.00 0.00 0.00 5.54
2189 2534 2.678336 CTGACCAATAAACCTCGCCTTC 59.322 50.000 0.00 0.00 0.00 3.46
2194 2539 0.824759 ATAAACCTCGCCTTCGCTCT 59.175 50.000 0.00 0.00 35.26 4.09
2195 2540 0.172803 TAAACCTCGCCTTCGCTCTC 59.827 55.000 0.00 0.00 35.26 3.20
2198 2543 1.226831 CCTCGCCTTCGCTCTCTTC 60.227 63.158 0.00 0.00 35.26 2.87
2319 2684 1.773052 ACCATGCATGCTAGTCCAGAT 59.227 47.619 21.69 0.00 0.00 2.90
2417 2786 7.609960 AGCAGTATAGAATGATGATGTCGATT 58.390 34.615 0.00 0.00 0.00 3.34
2470 2839 7.611770 ACATGTACACGGTATATGCTATGAAT 58.388 34.615 15.57 0.00 0.00 2.57
2475 2844 9.932699 GTACACGGTATATGCTATGAATAGTAG 57.067 37.037 0.00 0.00 32.96 2.57
2510 2879 2.687370 TGTCTGGTCGATCATGTGTTG 58.313 47.619 0.00 0.00 0.00 3.33
2518 2887 1.796253 CGATCATGTGTTGGTGCATGC 60.796 52.381 11.82 11.82 41.44 4.06
2543 2915 5.215160 GCTTATATATGCCAACAGTGTTGC 58.785 41.667 27.31 22.06 0.00 4.17
2567 2939 5.390613 CACTTGCGAACCAAAGGTAATAAG 58.609 41.667 0.00 0.00 33.12 1.73
2568 2940 4.457949 ACTTGCGAACCAAAGGTAATAAGG 59.542 41.667 0.00 0.00 33.12 2.69
2578 2950 6.155393 ACCAAAGGTAATAAGGACAGAGAGAG 59.845 42.308 0.00 0.00 32.11 3.20
2579 2951 6.381420 CCAAAGGTAATAAGGACAGAGAGAGA 59.619 42.308 0.00 0.00 0.00 3.10
2580 2952 7.417342 CCAAAGGTAATAAGGACAGAGAGAGAG 60.417 44.444 0.00 0.00 0.00 3.20
2581 2953 6.584471 AGGTAATAAGGACAGAGAGAGAGA 57.416 41.667 0.00 0.00 0.00 3.10
2582 2954 6.601332 AGGTAATAAGGACAGAGAGAGAGAG 58.399 44.000 0.00 0.00 0.00 3.20
2583 2955 6.159751 AGGTAATAAGGACAGAGAGAGAGAGT 59.840 42.308 0.00 0.00 0.00 3.24
2584 2956 7.348801 AGGTAATAAGGACAGAGAGAGAGAGTA 59.651 40.741 0.00 0.00 0.00 2.59
2585 2957 7.443272 GGTAATAAGGACAGAGAGAGAGAGTAC 59.557 44.444 0.00 0.00 0.00 2.73
2586 2958 3.536956 AGGACAGAGAGAGAGAGTACG 57.463 52.381 0.00 0.00 0.00 3.67
2587 2959 1.937899 GGACAGAGAGAGAGAGTACGC 59.062 57.143 0.00 0.00 0.00 4.42
2588 2960 2.623535 GACAGAGAGAGAGAGTACGCA 58.376 52.381 0.00 0.00 0.00 5.24
2589 2961 2.607635 GACAGAGAGAGAGAGTACGCAG 59.392 54.545 0.00 0.00 0.00 5.18
2590 2962 2.235155 ACAGAGAGAGAGAGTACGCAGA 59.765 50.000 0.00 0.00 0.00 4.26
2591 2963 2.866156 CAGAGAGAGAGAGTACGCAGAG 59.134 54.545 0.00 0.00 0.00 3.35
2592 2964 2.158957 AGAGAGAGAGAGTACGCAGAGG 60.159 54.545 0.00 0.00 0.00 3.69
2593 2965 1.557832 AGAGAGAGAGTACGCAGAGGT 59.442 52.381 0.00 0.00 0.00 3.85
2594 2966 2.767394 AGAGAGAGAGTACGCAGAGGTA 59.233 50.000 0.00 0.00 0.00 3.08
2595 2967 3.198200 AGAGAGAGAGTACGCAGAGGTAA 59.802 47.826 0.00 0.00 0.00 2.85
2596 2968 4.131596 GAGAGAGAGTACGCAGAGGTAAT 58.868 47.826 0.00 0.00 0.00 1.89
2597 2969 4.528920 AGAGAGAGTACGCAGAGGTAATT 58.471 43.478 0.00 0.00 0.00 1.40
2598 2970 4.577283 AGAGAGAGTACGCAGAGGTAATTC 59.423 45.833 0.00 0.00 0.00 2.17
2599 2971 4.270834 AGAGAGTACGCAGAGGTAATTCA 58.729 43.478 0.00 0.00 0.00 2.57
2600 2972 4.890581 AGAGAGTACGCAGAGGTAATTCAT 59.109 41.667 0.00 0.00 0.00 2.57
2601 2973 5.361285 AGAGAGTACGCAGAGGTAATTCATT 59.639 40.000 0.00 0.00 0.00 2.57
2602 2974 5.593010 AGAGTACGCAGAGGTAATTCATTC 58.407 41.667 0.00 0.00 0.00 2.67
2603 2975 4.360563 AGTACGCAGAGGTAATTCATTCG 58.639 43.478 0.00 0.00 0.00 3.34
2604 2976 3.247006 ACGCAGAGGTAATTCATTCGT 57.753 42.857 0.00 0.00 0.00 3.85
2605 2977 2.930040 ACGCAGAGGTAATTCATTCGTG 59.070 45.455 0.00 0.00 0.00 4.35
2606 2978 2.285220 CGCAGAGGTAATTCATTCGTGG 59.715 50.000 0.00 0.00 0.00 4.94
2607 2979 2.032178 GCAGAGGTAATTCATTCGTGGC 59.968 50.000 0.00 0.00 0.00 5.01
2608 2980 3.535561 CAGAGGTAATTCATTCGTGGCT 58.464 45.455 0.00 0.00 0.00 4.75
2609 2981 3.557595 CAGAGGTAATTCATTCGTGGCTC 59.442 47.826 0.00 0.00 0.00 4.70
2610 2982 2.872858 GAGGTAATTCATTCGTGGCTCC 59.127 50.000 0.00 0.00 0.00 4.70
2611 2983 1.947456 GGTAATTCATTCGTGGCTCCC 59.053 52.381 0.00 0.00 0.00 4.30
2612 2984 2.639065 GTAATTCATTCGTGGCTCCCA 58.361 47.619 0.00 0.00 0.00 4.37
2613 2985 2.442236 AATTCATTCGTGGCTCCCAT 57.558 45.000 0.00 0.00 35.28 4.00
2614 2986 3.576078 AATTCATTCGTGGCTCCCATA 57.424 42.857 0.00 0.00 35.28 2.74
2615 2987 3.795688 ATTCATTCGTGGCTCCCATAT 57.204 42.857 0.00 0.00 35.28 1.78
2616 2988 2.839486 TCATTCGTGGCTCCCATATC 57.161 50.000 0.00 0.00 35.28 1.63
2617 2989 2.046292 TCATTCGTGGCTCCCATATCA 58.954 47.619 0.00 0.00 35.28 2.15
2618 2990 2.639347 TCATTCGTGGCTCCCATATCAT 59.361 45.455 0.00 0.00 35.28 2.45
2675 3047 3.846430 GCGTAACCCTAGCCCGCT 61.846 66.667 0.00 0.00 41.06 5.52
2710 3082 0.323908 CACCTCTCCTCTCCCTCGTT 60.324 60.000 0.00 0.00 0.00 3.85
2715 3087 1.306141 TCCTCTCCCTCGTTGCCAT 60.306 57.895 0.00 0.00 0.00 4.40
2811 3183 2.355115 GGGCTTTGGATCCGTGGT 59.645 61.111 7.39 0.00 0.00 4.16
2837 3209 2.885644 CGGCTGGTGAATCGACGG 60.886 66.667 0.00 0.00 0.00 4.79
2970 3345 0.539051 CAGATCTGAAGGCCTCCGTT 59.461 55.000 18.34 0.00 0.00 4.44
2992 3367 2.134630 CTTCAACCAGGGCTGCCTCT 62.135 60.000 19.68 11.18 0.00 3.69
3002 3377 1.050988 GGCTGCCTCTGATGGTCCTA 61.051 60.000 12.43 0.00 0.00 2.94
3018 3393 2.040679 GTCCTACTTTGGGTGGCCTTTA 59.959 50.000 3.32 0.00 0.00 1.85
3022 3397 1.074889 ACTTTGGGTGGCCTTTATCGT 59.925 47.619 3.32 0.00 0.00 3.73
3036 3411 4.336433 CCTTTATCGTCGGAGTTGTACCTA 59.664 45.833 0.00 0.00 0.00 3.08
3254 3629 3.112709 GCGTCGTCACCCTCTTGC 61.113 66.667 0.00 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.822637 CCGGCACCCTCCATATGCT 61.823 63.158 0.00 0.00 39.38 3.79
23 24 1.071471 GACCGGCACCCTCCATATG 59.929 63.158 0.00 0.00 0.00 1.78
96 97 0.888619 CTGGTCACTGTCCGCTCTTA 59.111 55.000 0.00 0.00 0.00 2.10
129 130 1.597742 CTCAAACCCGCCTCATATGG 58.402 55.000 2.13 0.00 0.00 2.74
233 246 0.038166 AATTCGTGTGTGGGCTGGAT 59.962 50.000 0.00 0.00 0.00 3.41
258 271 0.317020 GCCGTGAATGGATTTAGCGC 60.317 55.000 0.00 0.00 0.00 5.92
453 466 3.703513 TAGCTGCTGGGGAGGGGAG 62.704 68.421 13.43 0.00 0.00 4.30
454 467 3.267177 TTAGCTGCTGGGGAGGGGA 62.267 63.158 13.43 0.00 0.00 4.81
578 592 2.455032 CAAGACGAAGCACCGATAGAG 58.545 52.381 4.78 0.00 39.76 2.43
580 594 0.924090 GCAAGACGAAGCACCGATAG 59.076 55.000 4.78 0.00 0.00 2.08
582 596 3.876300 GCAAGACGAAGCACCGAT 58.124 55.556 4.78 0.00 0.00 4.18
618 632 3.993614 TAGGCAACAGGCATGGCGG 62.994 63.158 17.64 17.64 46.95 6.13
619 633 1.386525 ATTAGGCAACAGGCATGGCG 61.387 55.000 14.30 11.27 46.95 5.69
684 698 3.440173 GCACAGGCACTTGCTAAAATCTA 59.560 43.478 0.38 0.00 38.66 1.98
823 840 1.078848 GGCCGAAGCAGACATCAGT 60.079 57.895 0.00 0.00 42.56 3.41
864 881 3.310303 GTACTACTGTACTACGCGTGG 57.690 52.381 24.59 23.16 44.08 4.94
881 898 3.373439 CAGAGCTTGCAATCTTCCAGTAC 59.627 47.826 3.98 0.00 0.00 2.73
882 899 3.603532 CAGAGCTTGCAATCTTCCAGTA 58.396 45.455 3.98 0.00 0.00 2.74
884 901 1.743958 CCAGAGCTTGCAATCTTCCAG 59.256 52.381 3.98 0.00 0.00 3.86
886 903 1.831580 ACCAGAGCTTGCAATCTTCC 58.168 50.000 3.98 0.00 0.00 3.46
895 912 6.092670 TCGAATATTCAGAAAACCAGAGCTTG 59.907 38.462 15.57 0.00 0.00 4.01
906 923 5.178061 TGAAGCAGCTCGAATATTCAGAAA 58.822 37.500 15.57 0.00 0.00 2.52
947 1171 5.913137 AATAATGGCACGGAATTCAGAAA 57.087 34.783 12.79 0.00 0.00 2.52
950 1174 7.169645 CCAAATTAATAATGGCACGGAATTCAG 59.830 37.037 7.93 5.85 0.00 3.02
957 1221 5.901552 ACTTCCAAATTAATAATGGCACGG 58.098 37.500 13.07 7.28 34.13 4.94
983 1247 0.177604 CATCTTCCTTCCTGCGCTCT 59.822 55.000 9.73 0.00 0.00 4.09
1202 1466 3.603158 AATGGTACTGTATGTGCGTGA 57.397 42.857 0.00 0.00 31.78 4.35
1203 1467 7.598869 AGATTATAATGGTACTGTATGTGCGTG 59.401 37.037 1.78 0.00 31.78 5.34
1204 1468 7.598869 CAGATTATAATGGTACTGTATGTGCGT 59.401 37.037 1.78 0.00 31.78 5.24
1206 1470 7.604164 AGCAGATTATAATGGTACTGTATGTGC 59.396 37.037 1.78 0.00 0.00 4.57
1209 1473 8.314021 TGGAGCAGATTATAATGGTACTGTATG 58.686 37.037 1.78 0.00 0.00 2.39
1210 1474 8.435931 TGGAGCAGATTATAATGGTACTGTAT 57.564 34.615 1.78 0.00 0.00 2.29
1211 1475 7.849322 TGGAGCAGATTATAATGGTACTGTA 57.151 36.000 1.78 0.00 0.00 2.74
1212 1476 6.747414 TGGAGCAGATTATAATGGTACTGT 57.253 37.500 1.78 0.00 0.00 3.55
1213 1477 7.164122 ACATGGAGCAGATTATAATGGTACTG 58.836 38.462 1.78 5.23 0.00 2.74
1257 1521 1.601663 CGATGCAAGGCCAAAACGAAA 60.602 47.619 5.01 0.00 0.00 3.46
1260 1524 0.171007 ATCGATGCAAGGCCAAAACG 59.829 50.000 5.01 2.95 0.00 3.60
1270 1534 3.784642 TGCAGATCCATCGATGCAA 57.215 47.368 20.25 10.35 45.09 4.08
1273 1537 1.509703 CCACTGCAGATCCATCGATG 58.490 55.000 23.35 18.76 0.00 3.84
1280 1544 1.021390 CGTTCACCCACTGCAGATCC 61.021 60.000 23.35 0.00 0.00 3.36
1382 1654 3.727780 AACGGTAAGAAATTAACGCGG 57.272 42.857 12.47 0.00 40.98 6.46
1448 1740 2.057137 TTCTTGGACTGCAGCAGTTT 57.943 45.000 28.84 7.44 45.44 2.66
1453 1745 1.136147 CGCATTCTTGGACTGCAGC 59.864 57.895 15.27 6.61 37.96 5.25
1511 1803 3.901844 TGGTAAATCCCCGATCTTCCTAG 59.098 47.826 0.00 0.00 34.77 3.02
1601 1895 9.793245 GTTCACATATTGCTAATCAATACGTAC 57.207 33.333 0.00 0.00 46.88 3.67
1602 1896 8.984764 GGTTCACATATTGCTAATCAATACGTA 58.015 33.333 0.00 0.00 46.88 3.57
1603 1897 7.715249 AGGTTCACATATTGCTAATCAATACGT 59.285 33.333 0.00 0.00 46.88 3.57
1604 1898 8.011673 CAGGTTCACATATTGCTAATCAATACG 58.988 37.037 0.10 0.00 46.88 3.06
1620 1914 5.893824 AGAAGAAGAAAAACCAGGTTCACAT 59.106 36.000 4.93 0.00 0.00 3.21
1630 1924 5.289434 CAGCAACAACAGAAGAAGAAAAACC 59.711 40.000 0.00 0.00 0.00 3.27
1693 2002 0.755686 CCATCCAGCAGTAGAGGGAC 59.244 60.000 0.00 0.00 36.00 4.46
1720 2029 1.197036 TCGACTAGACTTGCACAGACG 59.803 52.381 0.00 0.00 0.00 4.18
1752 2061 5.067413 GTCTCCATGAGATGAAATTGTGCAT 59.933 40.000 0.00 0.00 40.98 3.96
1753 2062 4.397103 GTCTCCATGAGATGAAATTGTGCA 59.603 41.667 0.00 0.00 40.98 4.57
1754 2063 4.639310 AGTCTCCATGAGATGAAATTGTGC 59.361 41.667 0.00 0.00 40.98 4.57
1755 2064 5.296283 GGAGTCTCCATGAGATGAAATTGTG 59.704 44.000 14.46 0.00 40.98 3.33
1756 2065 5.191323 AGGAGTCTCCATGAGATGAAATTGT 59.809 40.000 21.26 0.00 40.98 2.71
1757 2066 5.682659 AGGAGTCTCCATGAGATGAAATTG 58.317 41.667 21.26 0.00 40.98 2.32
1759 2068 5.191323 ACAAGGAGTCTCCATGAGATGAAAT 59.809 40.000 26.94 2.87 40.98 2.17
1774 2087 5.419542 TCATGTAGCATGTTACAAGGAGTC 58.580 41.667 23.73 0.00 37.13 3.36
1782 2095 9.133627 CAGTCATATACTCATGTAGCATGTTAC 57.866 37.037 12.39 12.39 35.76 2.50
1783 2096 9.077885 TCAGTCATATACTCATGTAGCATGTTA 57.922 33.333 8.68 0.00 35.76 2.41
1785 2098 7.530426 TCAGTCATATACTCATGTAGCATGT 57.470 36.000 8.68 0.00 35.76 3.21
1786 2099 7.431668 CGATCAGTCATATACTCATGTAGCATG 59.568 40.741 2.93 2.93 35.76 4.06
1787 2100 7.121907 ACGATCAGTCATATACTCATGTAGCAT 59.878 37.037 0.00 0.00 35.76 3.79
1788 2101 6.431234 ACGATCAGTCATATACTCATGTAGCA 59.569 38.462 0.00 0.00 35.76 3.49
1798 2118 5.692204 CCCACTCAAACGATCAGTCATATAC 59.308 44.000 0.00 0.00 0.00 1.47
1799 2119 5.596772 TCCCACTCAAACGATCAGTCATATA 59.403 40.000 0.00 0.00 0.00 0.86
1812 2132 1.251251 AGCTGCAATCCCACTCAAAC 58.749 50.000 1.02 0.00 0.00 2.93
1835 2157 4.382470 GCCTTTGATAGTCTCTTGAGCTCA 60.382 45.833 13.74 13.74 0.00 4.26
1847 2169 3.742640 GCTTCCTCATCGCCTTTGATAGT 60.743 47.826 0.00 0.00 0.00 2.12
1853 2175 2.109126 GCGCTTCCTCATCGCCTTT 61.109 57.895 0.00 0.00 42.71 3.11
1883 2205 1.144496 GTATTTGTCGGCGCCCCTA 59.856 57.895 23.46 5.76 0.00 3.53
1909 2231 4.319177 GGCGGCAGATCTAAAATGATACT 58.681 43.478 3.07 0.00 0.00 2.12
1929 2251 1.143183 ACATACATCGTCCGTGGGC 59.857 57.895 0.00 0.00 0.00 5.36
1964 2286 1.616865 CTCGTCCTACAAGACCACCAA 59.383 52.381 0.00 0.00 32.91 3.67
1967 2294 0.601558 TGCTCGTCCTACAAGACCAC 59.398 55.000 0.00 0.00 32.91 4.16
1970 2297 2.159407 GGTACTGCTCGTCCTACAAGAC 60.159 54.545 0.00 0.00 0.00 3.01
1971 2298 2.089980 GGTACTGCTCGTCCTACAAGA 58.910 52.381 0.00 0.00 0.00 3.02
2185 2530 3.056891 AGAAGAACAGAAGAGAGCGAAGG 60.057 47.826 0.00 0.00 0.00 3.46
2186 2531 3.919804 CAGAAGAACAGAAGAGAGCGAAG 59.080 47.826 0.00 0.00 0.00 3.79
2189 2534 3.241701 GTCAGAAGAACAGAAGAGAGCG 58.758 50.000 0.00 0.00 0.00 5.03
2194 2539 1.964223 AGCCGTCAGAAGAACAGAAGA 59.036 47.619 0.00 0.00 0.00 2.87
2195 2540 2.029470 AGAGCCGTCAGAAGAACAGAAG 60.029 50.000 0.00 0.00 0.00 2.85
2198 2543 1.270826 TCAGAGCCGTCAGAAGAACAG 59.729 52.381 0.00 0.00 0.00 3.16
2286 2645 1.693083 GCATGGTGTAGCGTCCGTTC 61.693 60.000 0.00 0.00 0.00 3.95
2319 2684 1.079127 GAGTTAAGCGGAGGCAGCA 60.079 57.895 0.00 0.00 43.41 4.41
2355 2720 2.251409 ACATCTCGGATTCCATGCTG 57.749 50.000 3.09 0.00 0.00 4.41
2417 2786 6.673106 TGTATAAAAACCGTACGTACAGACA 58.327 36.000 24.50 13.57 0.00 3.41
2460 2829 9.881649 CATGTCCATTACTACTATTCATAGCAT 57.118 33.333 0.00 0.00 33.68 3.79
2493 2862 1.733912 CACCAACACATGATCGACCAG 59.266 52.381 0.00 0.00 0.00 4.00
2518 2887 6.432936 CAACACTGTTGGCATATATAAGCAG 58.567 40.000 13.36 3.85 0.00 4.24
2543 2915 1.600023 TACCTTTGGTTCGCAAGTGG 58.400 50.000 0.00 0.00 37.09 4.00
2567 2939 1.937899 GCGTACTCTCTCTCTCTGTCC 59.062 57.143 0.00 0.00 0.00 4.02
2568 2940 2.607635 CTGCGTACTCTCTCTCTCTGTC 59.392 54.545 0.00 0.00 0.00 3.51
2578 2950 4.634184 TGAATTACCTCTGCGTACTCTC 57.366 45.455 0.00 0.00 0.00 3.20
2579 2951 5.593010 GAATGAATTACCTCTGCGTACTCT 58.407 41.667 0.00 0.00 0.00 3.24
2580 2952 4.441415 CGAATGAATTACCTCTGCGTACTC 59.559 45.833 0.00 0.00 0.00 2.59
2581 2953 4.142227 ACGAATGAATTACCTCTGCGTACT 60.142 41.667 0.00 0.00 0.00 2.73
2582 2954 4.026804 CACGAATGAATTACCTCTGCGTAC 60.027 45.833 0.00 0.00 0.00 3.67
2583 2955 4.109766 CACGAATGAATTACCTCTGCGTA 58.890 43.478 0.00 0.00 0.00 4.42
2584 2956 2.930040 CACGAATGAATTACCTCTGCGT 59.070 45.455 0.00 0.00 0.00 5.24
2585 2957 2.285220 CCACGAATGAATTACCTCTGCG 59.715 50.000 0.00 0.00 0.00 5.18
2586 2958 2.032178 GCCACGAATGAATTACCTCTGC 59.968 50.000 0.00 0.00 0.00 4.26
2587 2959 3.535561 AGCCACGAATGAATTACCTCTG 58.464 45.455 0.00 0.00 0.00 3.35
2588 2960 3.432326 GGAGCCACGAATGAATTACCTCT 60.432 47.826 0.00 0.00 0.00 3.69
2589 2961 2.872858 GGAGCCACGAATGAATTACCTC 59.127 50.000 0.00 0.00 0.00 3.85
2590 2962 2.421529 GGGAGCCACGAATGAATTACCT 60.422 50.000 0.00 0.00 0.00 3.08
2591 2963 1.947456 GGGAGCCACGAATGAATTACC 59.053 52.381 0.00 0.00 0.00 2.85
2592 2964 2.639065 TGGGAGCCACGAATGAATTAC 58.361 47.619 0.00 0.00 0.00 1.89
2593 2965 3.576078 ATGGGAGCCACGAATGAATTA 57.424 42.857 0.00 0.00 35.80 1.40
2594 2966 2.442236 ATGGGAGCCACGAATGAATT 57.558 45.000 0.00 0.00 35.80 2.17
2595 2967 3.072915 TGATATGGGAGCCACGAATGAAT 59.927 43.478 0.00 0.00 35.80 2.57
2596 2968 2.437651 TGATATGGGAGCCACGAATGAA 59.562 45.455 0.00 0.00 35.80 2.57
2597 2969 2.046292 TGATATGGGAGCCACGAATGA 58.954 47.619 0.00 0.00 35.80 2.57
2598 2970 2.549064 TGATATGGGAGCCACGAATG 57.451 50.000 0.00 0.00 35.80 2.67
2599 2971 2.639347 TGATGATATGGGAGCCACGAAT 59.361 45.455 0.00 0.00 35.80 3.34
2600 2972 2.046292 TGATGATATGGGAGCCACGAA 58.954 47.619 0.00 0.00 35.80 3.85
2601 2973 1.344438 GTGATGATATGGGAGCCACGA 59.656 52.381 0.00 0.00 35.80 4.35
2602 2974 1.800805 GTGATGATATGGGAGCCACG 58.199 55.000 0.00 0.00 35.80 4.94
2603 2975 1.609061 CCGTGATGATATGGGAGCCAC 60.609 57.143 0.00 0.00 35.80 5.01
2604 2976 0.686789 CCGTGATGATATGGGAGCCA 59.313 55.000 0.00 0.00 38.19 4.75
2605 2977 0.674895 GCCGTGATGATATGGGAGCC 60.675 60.000 0.00 0.00 0.00 4.70
2606 2978 0.674895 GGCCGTGATGATATGGGAGC 60.675 60.000 0.00 0.00 0.00 4.70
2607 2979 0.036010 GGGCCGTGATGATATGGGAG 60.036 60.000 0.00 0.00 0.00 4.30
2608 2980 1.488705 GGGGCCGTGATGATATGGGA 61.489 60.000 0.00 0.00 0.00 4.37
2609 2981 1.002134 GGGGCCGTGATGATATGGG 60.002 63.158 0.00 0.00 0.00 4.00
2610 2982 1.002134 GGGGGCCGTGATGATATGG 60.002 63.158 0.00 0.00 0.00 2.74
2611 2983 1.375908 CGGGGGCCGTGATGATATG 60.376 63.158 0.00 0.00 42.73 1.78
2612 2984 3.068881 CGGGGGCCGTGATGATAT 58.931 61.111 0.00 0.00 42.73 1.63
2648 3020 4.747529 GGTTACGCCGCCCGAGTT 62.748 66.667 0.65 0.00 41.02 3.01
2817 3189 1.511305 GTCGATTCACCAGCCGAGA 59.489 57.895 0.00 0.00 0.00 4.04
2829 3201 4.814294 GCAGACCCGCCGTCGATT 62.814 66.667 0.00 0.00 46.92 3.34
2970 3345 0.251165 GGCAGCCCTGGTTGAAGTAA 60.251 55.000 0.00 0.00 0.00 2.24
2992 3367 1.633432 CCACCCAAAGTAGGACCATCA 59.367 52.381 0.00 0.00 0.00 3.07
3002 3377 1.074889 ACGATAAAGGCCACCCAAAGT 59.925 47.619 5.01 0.00 0.00 2.66
3018 3393 4.441079 CCAAATAGGTACAACTCCGACGAT 60.441 45.833 0.00 0.00 0.00 3.73
3022 3397 2.417651 CGCCAAATAGGTACAACTCCGA 60.418 50.000 0.00 0.00 40.61 4.55
3036 3411 2.361610 CACCTCCAGCCGCCAAAT 60.362 61.111 0.00 0.00 0.00 2.32
3083 3458 2.359107 CGTCATGGCCAGCACTGT 60.359 61.111 13.05 0.00 0.00 3.55
3254 3629 3.033764 CACCACGAACGACACCCG 61.034 66.667 0.14 0.00 45.44 5.28


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

AutoCloner maintained by Alex Coulton.