Multiple sequence alignment - TraesCS4B01G301500

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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 TraesCS4B01G301500 chr4B 100.000 4455 0 0 1 4455 588200614 588205068 0.000000e+00 8227.0
1 TraesCS4B01G301500 chr4D 90.931 4521 244 70 3 4454 468600114 468604537 0.000000e+00 5925.0
2 TraesCS4B01G301500 chr4A 95.073 893 36 5 3566 4453 2941284 2940395 0.000000e+00 1399.0
3 TraesCS4B01G301500 chr4A 92.808 876 52 9 2698 3571 2942173 2941307 0.000000e+00 1258.0
4 TraesCS4B01G301500 chr4A 86.602 933 71 30 3 909 2943654 2942750 0.000000e+00 981.0
5 TraesCS4B01G301500 chr4A 84.325 504 30 19 2111 2613 2942653 2942198 8.790000e-122 448.0
6 TraesCS4B01G301500 chr3B 87.152 755 55 22 3 736 509971260 509971993 0.000000e+00 819.0
7 TraesCS4B01G301500 chr3B 95.918 49 2 0 1965 2013 99026617 99026665 3.690000e-11 80.5
8 TraesCS4B01G301500 chr1B 86.985 753 64 16 3 739 186140690 186139956 0.000000e+00 817.0
9 TraesCS4B01G301500 chr7B 87.379 721 61 16 3 710 707546759 707547462 0.000000e+00 800.0
10 TraesCS4B01G301500 chr7B 86.842 722 63 16 3 710 669095667 669096370 0.000000e+00 778.0
11 TraesCS4B01G301500 chr6B 87.240 721 61 18 3 710 54643841 54643139 0.000000e+00 793.0
12 TraesCS4B01G301500 chr6B 84.808 757 65 25 3 739 9466088 9465362 0.000000e+00 715.0
13 TraesCS4B01G301500 chrUn 85.972 720 62 14 3 709 65800126 65799433 0.000000e+00 734.0
14 TraesCS4B01G301500 chr5B 85.576 721 72 16 3 710 534718476 534717775 0.000000e+00 726.0
15 TraesCS4B01G301500 chr2B 85.437 721 74 15 3 710 263970214 263969512 0.000000e+00 721.0
16 TraesCS4B01G301500 chr2B 82.906 117 19 1 1934 2050 677350062 677350177 2.190000e-18 104.0
17 TraesCS4B01G301500 chr5D 85.088 114 15 2 1937 2049 231409135 231409023 1.010000e-21 115.0
18 TraesCS4B01G301500 chr5A 83.784 111 17 1 1937 2047 325883014 325883123 2.190000e-18 104.0
19 TraesCS4B01G301500 chr2D 80.909 110 19 2 1937 2046 4186833 4186726 7.940000e-13 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 TraesCS4B01G301500 chr4B 588200614 588205068 4454 False 8227.0 8227 100.000 1 4455 1 chr4B.!!$F1 4454
1 TraesCS4B01G301500 chr4D 468600114 468604537 4423 False 5925.0 5925 90.931 3 4454 1 chr4D.!!$F1 4451
2 TraesCS4B01G301500 chr4A 2940395 2943654 3259 True 1021.5 1399 89.702 3 4453 4 chr4A.!!$R1 4450
3 TraesCS4B01G301500 chr3B 509971260 509971993 733 False 819.0 819 87.152 3 736 1 chr3B.!!$F2 733
4 TraesCS4B01G301500 chr1B 186139956 186140690 734 True 817.0 817 86.985 3 739 1 chr1B.!!$R1 736
5 TraesCS4B01G301500 chr7B 707546759 707547462 703 False 800.0 800 87.379 3 710 1 chr7B.!!$F2 707
6 TraesCS4B01G301500 chr7B 669095667 669096370 703 False 778.0 778 86.842 3 710 1 chr7B.!!$F1 707
7 TraesCS4B01G301500 chr6B 54643139 54643841 702 True 793.0 793 87.240 3 710 1 chr6B.!!$R2 707
8 TraesCS4B01G301500 chr6B 9465362 9466088 726 True 715.0 715 84.808 3 739 1 chr6B.!!$R1 736
9 TraesCS4B01G301500 chrUn 65799433 65800126 693 True 734.0 734 85.972 3 709 1 chrUn.!!$R1 706
10 TraesCS4B01G301500 chr5B 534717775 534718476 701 True 726.0 726 85.576 3 710 1 chr5B.!!$R1 707
11 TraesCS4B01G301500 chr2B 263969512 263970214 702 True 721.0 721 85.437 3 710 1 chr2B.!!$R1 707

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
176 186 0.033504 GCAAGAGACGGAACAGGACA 59.966 55.0 0.0 0.0 0.00 4.02 F
1678 1785 0.029300 ACATGTGTGTTTCGTGCTGC 59.971 50.0 0.0 0.0 34.01 5.25 F
2849 2978 0.392998 ATCTGCTCACCGGCGAAAAT 60.393 50.0 9.3 0.0 34.52 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2218 0.040425 GTGCAAACCAACGTGCTAGG 60.040 55.000 0.0 0.0 41.48 3.02 R
3193 3323 0.540923 GCATCTCAGCCAGACCTTCT 59.459 55.000 0.0 0.0 32.26 2.85 R
3692 3854 1.201769 CCGAACGTTGCATGTTACTCG 60.202 52.381 5.0 0.0 0.00 4.18 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
23 24 4.458295 AGCATCATCTTTCAGTTCAACAGG 59.542 41.667 0.00 0.00 0.00 4.00
24 25 4.456911 GCATCATCTTTCAGTTCAACAGGA 59.543 41.667 0.00 0.00 0.00 3.86
25 26 5.125097 GCATCATCTTTCAGTTCAACAGGAT 59.875 40.000 0.00 0.00 0.00 3.24
26 27 6.349944 GCATCATCTTTCAGTTCAACAGGATT 60.350 38.462 0.00 0.00 0.00 3.01
28 29 8.733458 CATCATCTTTCAGTTCAACAGGATTTA 58.267 33.333 0.00 0.00 0.00 1.40
29 30 8.099364 TCATCTTTCAGTTCAACAGGATTTAC 57.901 34.615 0.00 0.00 0.00 2.01
43 44 5.867716 ACAGGATTTACTACTTGCAGTTACG 59.132 40.000 0.00 0.00 0.00 3.18
57 58 1.548719 AGTTACGGTATGAGCAGCACA 59.451 47.619 0.00 0.00 0.00 4.57
58 59 1.927174 GTTACGGTATGAGCAGCACAG 59.073 52.381 0.00 0.00 0.00 3.66
59 60 1.182667 TACGGTATGAGCAGCACAGT 58.817 50.000 0.00 0.00 0.00 3.55
112 122 3.860641 TGCTGTCTCGCATCAAAAGATA 58.139 40.909 0.00 0.00 34.44 1.98
115 125 4.568359 GCTGTCTCGCATCAAAAGATAGAA 59.432 41.667 0.00 0.00 31.95 2.10
167 177 0.460284 ATTAGCCACGCAAGAGACGG 60.460 55.000 0.00 0.00 43.62 4.79
173 183 1.006102 ACGCAAGAGACGGAACAGG 60.006 57.895 0.00 0.00 43.62 4.00
175 185 1.009389 CGCAAGAGACGGAACAGGAC 61.009 60.000 0.00 0.00 43.02 3.85
176 186 0.033504 GCAAGAGACGGAACAGGACA 59.966 55.000 0.00 0.00 0.00 4.02
208 218 5.231991 ACGCAAAAATCACAAGAAACATGTC 59.768 36.000 0.00 0.00 0.00 3.06
267 277 0.034767 CAGATCAGGCAAGGGAGCAA 60.035 55.000 0.00 0.00 35.83 3.91
271 281 0.478072 TCAGGCAAGGGAGCAAGAAA 59.522 50.000 0.00 0.00 35.83 2.52
278 288 2.494870 CAAGGGAGCAAGAAAAGATGGG 59.505 50.000 0.00 0.00 0.00 4.00
280 290 1.821136 GGGAGCAAGAAAAGATGGGTG 59.179 52.381 0.00 0.00 0.00 4.61
281 291 1.821136 GGAGCAAGAAAAGATGGGTGG 59.179 52.381 0.00 0.00 0.00 4.61
282 292 2.555227 GGAGCAAGAAAAGATGGGTGGA 60.555 50.000 0.00 0.00 0.00 4.02
283 293 3.359950 GAGCAAGAAAAGATGGGTGGAT 58.640 45.455 0.00 0.00 0.00 3.41
424 434 1.001746 CCTCTTGTGCTTCTGCTCAGA 59.998 52.381 0.00 0.00 42.51 3.27
437 453 1.330521 TGCTCAGACGCAAACAAGAAC 59.669 47.619 0.00 0.00 36.89 3.01
440 456 0.934496 CAGACGCAAACAAGAACGGA 59.066 50.000 0.00 0.00 0.00 4.69
474 491 3.918220 GCAGCGAGCGACCGATTG 61.918 66.667 1.05 0.00 0.00 2.67
736 802 2.302587 TGGGATTGGGTTTCTTGGAC 57.697 50.000 0.00 0.00 0.00 4.02
825 891 1.544537 GGGGTTGGGGTTTTTCAATGC 60.545 52.381 0.00 0.00 0.00 3.56
831 897 0.389817 GGGTTTTTCAATGCGCCTCC 60.390 55.000 4.18 0.00 0.00 4.30
832 898 0.603065 GGTTTTTCAATGCGCCTCCT 59.397 50.000 4.18 0.00 0.00 3.69
833 899 1.402852 GGTTTTTCAATGCGCCTCCTC 60.403 52.381 4.18 0.00 0.00 3.71
1013 1079 1.300697 GGTTCGCACGAGTTGACCT 60.301 57.895 4.74 0.00 0.00 3.85
1014 1080 1.557443 GGTTCGCACGAGTTGACCTG 61.557 60.000 4.74 0.00 0.00 4.00
1330 1412 2.979649 GACCCCTCCGTCTTCACC 59.020 66.667 0.00 0.00 0.00 4.02
1349 1431 1.210931 GCCGTACGTGCACACTCTA 59.789 57.895 18.64 0.00 0.00 2.43
1350 1432 0.179145 GCCGTACGTGCACACTCTAT 60.179 55.000 18.64 0.00 0.00 1.98
1351 1433 1.064505 GCCGTACGTGCACACTCTATA 59.935 52.381 18.64 0.00 0.00 1.31
1352 1434 2.853662 GCCGTACGTGCACACTCTATAG 60.854 54.545 18.64 0.00 0.00 1.31
1353 1435 2.353889 CCGTACGTGCACACTCTATAGT 59.646 50.000 18.64 6.32 35.91 2.12
1354 1436 3.557185 CCGTACGTGCACACTCTATAGTA 59.443 47.826 18.64 5.28 33.48 1.82
1355 1437 4.318618 CCGTACGTGCACACTCTATAGTAG 60.319 50.000 18.64 0.00 33.48 2.57
1374 1456 5.415221 AGTAGAGTACTTGCTGAATCAAGC 58.585 41.667 0.00 0.00 45.43 4.01
1375 1457 4.550076 AGAGTACTTGCTGAATCAAGCT 57.450 40.909 0.00 0.00 45.43 3.74
1379 1461 3.911661 ACTTGCTGAATCAAGCTGTTC 57.088 42.857 3.67 0.00 45.43 3.18
1394 1476 4.676546 AGCTGTTCTGCTTTCAGTTTTTC 58.323 39.130 0.00 0.00 40.93 2.29
1401 1483 4.895297 TCTGCTTTCAGTTTTTCCTTCCAT 59.105 37.500 0.00 0.00 41.10 3.41
1402 1484 4.947645 TGCTTTCAGTTTTTCCTTCCATG 58.052 39.130 0.00 0.00 0.00 3.66
1405 1487 2.247358 TCAGTTTTTCCTTCCATGGGC 58.753 47.619 13.02 0.00 0.00 5.36
1406 1488 1.969923 CAGTTTTTCCTTCCATGGGCA 59.030 47.619 13.02 0.00 0.00 5.36
1407 1489 1.970640 AGTTTTTCCTTCCATGGGCAC 59.029 47.619 13.02 0.00 0.00 5.01
1408 1490 1.691434 GTTTTTCCTTCCATGGGCACA 59.309 47.619 13.02 0.00 0.00 4.57
1428 1511 4.034279 CACAAGTTGCTGTTCAAAATTGGG 59.966 41.667 1.81 0.00 37.67 4.12
1454 1537 1.278127 AGGTTCGTGGATTGGTAGTGG 59.722 52.381 0.00 0.00 0.00 4.00
1457 1540 1.195442 TCGTGGATTGGTAGTGGCCA 61.195 55.000 0.00 0.00 36.62 5.36
1458 1541 1.024579 CGTGGATTGGTAGTGGCCAC 61.025 60.000 29.22 29.22 44.18 5.01
1459 1542 0.328258 GTGGATTGGTAGTGGCCACT 59.672 55.000 38.92 38.92 44.23 4.00
1461 1544 1.032114 GGATTGGTAGTGGCCACTGC 61.032 60.000 42.35 39.92 42.52 4.40
1462 1545 0.035056 GATTGGTAGTGGCCACTGCT 60.035 55.000 40.94 28.25 42.56 4.24
1474 1557 2.997897 ACTGCTCCCAGGTCGACC 60.998 66.667 27.67 27.67 43.53 4.79
1482 1565 1.516386 CCAGGTCGACCGTGAATCG 60.516 63.158 28.26 11.73 42.08 3.34
1493 1576 2.095853 ACCGTGAATCGTGATGCATTTC 59.904 45.455 0.00 0.34 37.94 2.17
1511 1594 3.791973 TTCGTGCTTGGTTGTTTGATT 57.208 38.095 0.00 0.00 0.00 2.57
1513 1596 2.948979 TCGTGCTTGGTTGTTTGATTCT 59.051 40.909 0.00 0.00 0.00 2.40
1521 1604 5.181690 TGGTTGTTTGATTCTGTTGTAGC 57.818 39.130 0.00 0.00 0.00 3.58
1526 1609 6.000891 TGTTTGATTCTGTTGTAGCATGAC 57.999 37.500 0.00 0.00 0.00 3.06
1527 1610 5.048782 TGTTTGATTCTGTTGTAGCATGACC 60.049 40.000 0.00 0.00 0.00 4.02
1534 1617 4.081917 TCTGTTGTAGCATGACCGTCATAA 60.082 41.667 13.71 1.91 34.28 1.90
1536 1619 5.182487 TGTTGTAGCATGACCGTCATAAAT 58.818 37.500 13.71 5.76 34.28 1.40
1537 1620 5.293324 TGTTGTAGCATGACCGTCATAAATC 59.707 40.000 13.71 6.40 34.28 2.17
1539 1622 5.670485 TGTAGCATGACCGTCATAAATCTT 58.330 37.500 13.71 0.10 34.28 2.40
1540 1623 6.112734 TGTAGCATGACCGTCATAAATCTTT 58.887 36.000 13.71 0.00 34.28 2.52
1541 1624 6.597672 TGTAGCATGACCGTCATAAATCTTTT 59.402 34.615 13.71 0.00 34.28 2.27
1542 1625 5.883661 AGCATGACCGTCATAAATCTTTTG 58.116 37.500 13.71 1.52 34.28 2.44
1543 1626 5.415701 AGCATGACCGTCATAAATCTTTTGT 59.584 36.000 13.71 0.00 34.28 2.83
1544 1627 5.739161 GCATGACCGTCATAAATCTTTTGTC 59.261 40.000 13.71 0.00 34.28 3.18
1545 1628 6.622679 GCATGACCGTCATAAATCTTTTGTCA 60.623 38.462 13.71 0.00 34.28 3.58
1546 1629 6.869315 TGACCGTCATAAATCTTTTGTCAA 57.131 33.333 0.00 0.00 0.00 3.18
1547 1630 6.664515 TGACCGTCATAAATCTTTTGTCAAC 58.335 36.000 0.00 0.00 0.00 3.18
1548 1631 6.485313 TGACCGTCATAAATCTTTTGTCAACT 59.515 34.615 0.00 0.00 0.00 3.16
1549 1632 7.658167 TGACCGTCATAAATCTTTTGTCAACTA 59.342 33.333 0.00 0.00 0.00 2.24
1550 1633 8.385898 ACCGTCATAAATCTTTTGTCAACTAA 57.614 30.769 0.00 0.00 0.00 2.24
1551 1634 9.010029 ACCGTCATAAATCTTTTGTCAACTAAT 57.990 29.630 0.00 0.00 0.00 1.73
1572 1655 9.226606 ACTAATAATATTTATGCTGCCGCTTAA 57.773 29.630 0.70 2.98 34.95 1.85
1586 1669 6.598753 TGCCGCTTAAATAAGAACTATGAC 57.401 37.500 4.39 0.00 35.33 3.06
1623 1724 1.926511 GAATGCACCAAGCTGGACGG 61.927 60.000 8.91 0.18 45.94 4.79
1624 1725 3.925630 ATGCACCAAGCTGGACGGG 62.926 63.158 8.91 0.00 45.94 5.28
1628 1729 0.251916 CACCAAGCTGGACGGGATTA 59.748 55.000 8.91 0.00 40.96 1.75
1636 1737 0.390603 TGGACGGGATTAGCAACACG 60.391 55.000 0.00 0.00 38.94 4.49
1637 1738 1.087771 GGACGGGATTAGCAACACGG 61.088 60.000 0.00 0.00 37.23 4.94
1677 1784 2.473530 AACATGTGTGTTTCGTGCTG 57.526 45.000 0.00 0.00 46.07 4.41
1678 1785 0.029300 ACATGTGTGTTTCGTGCTGC 59.971 50.000 0.00 0.00 34.01 5.25
1718 1827 4.187694 GAGAGGGCTTGAGAATGTGTTAG 58.812 47.826 0.00 0.00 0.00 2.34
1719 1828 3.840666 AGAGGGCTTGAGAATGTGTTAGA 59.159 43.478 0.00 0.00 0.00 2.10
1720 1829 4.081198 AGAGGGCTTGAGAATGTGTTAGAG 60.081 45.833 0.00 0.00 0.00 2.43
1734 1843 1.134371 GTTAGAGGCGGCCAAGAGAAT 60.134 52.381 23.09 0.00 0.00 2.40
1765 1874 8.136165 ACAGTAAAGAAGATCATATACACGTCC 58.864 37.037 0.00 0.00 0.00 4.79
1827 1936 5.934043 CAGATGAGACACAGGTGAAATTGTA 59.066 40.000 6.40 0.00 0.00 2.41
1828 1937 6.091849 CAGATGAGACACAGGTGAAATTGTAG 59.908 42.308 6.40 0.00 0.00 2.74
1831 1940 7.004555 TGAGACACAGGTGAAATTGTAGTAT 57.995 36.000 6.40 0.00 0.00 2.12
1871 1980 5.685511 GCTTTGTCGTTTTTCATCTTGCTAA 59.314 36.000 0.00 0.00 0.00 3.09
1938 2047 3.078837 GGCACGGATTTTTAGGTCTTCA 58.921 45.455 0.00 0.00 0.00 3.02
1947 2056 8.512138 CGGATTTTTAGGTCTTCAAATGTAGTT 58.488 33.333 0.00 0.00 0.00 2.24
2059 2168 2.563179 CGGAGGGAGTATGTCCTTATGG 59.437 54.545 0.00 0.00 46.06 2.74
2077 2186 6.755141 CCTTATGGATGATTTTTGAGCAACAG 59.245 38.462 0.00 0.00 34.57 3.16
2103 2212 4.347000 TGGTTGTTAGTTCTGTTCTAGGCT 59.653 41.667 0.00 0.00 0.00 4.58
2104 2213 5.541101 TGGTTGTTAGTTCTGTTCTAGGCTA 59.459 40.000 0.00 0.00 0.00 3.93
2105 2214 6.100668 GGTTGTTAGTTCTGTTCTAGGCTAG 58.899 44.000 15.56 15.56 0.00 3.42
2106 2215 5.326200 TGTTAGTTCTGTTCTAGGCTAGC 57.674 43.478 16.85 6.04 0.00 3.42
2107 2216 4.770531 TGTTAGTTCTGTTCTAGGCTAGCA 59.229 41.667 18.24 8.96 0.00 3.49
2108 2217 5.105716 TGTTAGTTCTGTTCTAGGCTAGCAG 60.106 44.000 18.24 17.52 0.00 4.24
2109 2218 2.167487 AGTTCTGTTCTAGGCTAGCAGC 59.833 50.000 18.24 9.31 41.46 5.25
2170 2299 9.976511 TTTACTTGGTCTATATACTTGATTCCG 57.023 33.333 0.00 0.00 0.00 4.30
2252 2381 3.245229 TGGTCACTGGTGCTATTTCCAAT 60.245 43.478 0.00 0.00 33.06 3.16
2253 2382 3.129287 GGTCACTGGTGCTATTTCCAATG 59.871 47.826 0.00 0.00 33.05 2.82
2284 2413 2.831685 TGTACAGTAACACCCAGCTG 57.168 50.000 6.78 6.78 35.31 4.24
2334 2463 5.337578 AATTGGGGTATTGAACGATTTGG 57.662 39.130 0.00 0.00 0.00 3.28
2338 2467 3.119280 GGGGTATTGAACGATTTGGGTTG 60.119 47.826 0.00 0.00 0.00 3.77
2382 2511 0.915904 CACAAACTGCGCAAACTGTG 59.084 50.000 22.98 22.98 0.00 3.66
2384 2513 1.405105 ACAAACTGCGCAAACTGTGAT 59.595 42.857 13.05 0.00 0.00 3.06
2595 2724 2.642311 TGTATGAGAACCTTCTTGCCCA 59.358 45.455 0.00 0.00 37.73 5.36
2596 2725 3.266772 TGTATGAGAACCTTCTTGCCCAT 59.733 43.478 0.00 0.00 37.73 4.00
2597 2726 2.205022 TGAGAACCTTCTTGCCCATG 57.795 50.000 0.00 0.00 37.73 3.66
2598 2727 1.704628 TGAGAACCTTCTTGCCCATGA 59.295 47.619 0.00 0.00 37.73 3.07
2599 2728 2.108075 TGAGAACCTTCTTGCCCATGAA 59.892 45.455 0.00 0.00 37.73 2.57
2600 2729 3.245371 TGAGAACCTTCTTGCCCATGAAT 60.245 43.478 0.00 0.00 37.73 2.57
2601 2730 4.018506 TGAGAACCTTCTTGCCCATGAATA 60.019 41.667 0.00 0.00 37.73 1.75
2602 2731 4.934356 AGAACCTTCTTGCCCATGAATAA 58.066 39.130 0.00 0.00 32.55 1.40
2603 2732 5.332743 AGAACCTTCTTGCCCATGAATAAA 58.667 37.500 0.00 0.00 32.55 1.40
2604 2733 5.960202 AGAACCTTCTTGCCCATGAATAAAT 59.040 36.000 0.00 0.00 32.55 1.40
2605 2734 5.859205 ACCTTCTTGCCCATGAATAAATC 57.141 39.130 0.00 0.00 0.00 2.17
2606 2735 5.271598 ACCTTCTTGCCCATGAATAAATCA 58.728 37.500 0.00 0.00 43.67 2.57
2849 2978 0.392998 ATCTGCTCACCGGCGAAAAT 60.393 50.000 9.30 0.00 34.52 1.82
3019 3148 4.341863 ACCCTGTATGTCCCAGTACTTA 57.658 45.455 0.00 0.00 0.00 2.24
3145 3275 2.483876 AGACATCAATGGGCGTATTCG 58.516 47.619 0.00 0.00 40.37 3.34
3193 3323 4.518970 GGCTACAATCCAAGAAACTTGACA 59.481 41.667 12.25 0.50 0.00 3.58
3274 3404 8.418597 AGTGTTCTACTCTGTTATTACTTCCA 57.581 34.615 0.00 0.00 33.17 3.53
3316 3446 6.101332 TGTAGACCGTCATGTTTTATGTACC 58.899 40.000 0.40 0.00 0.00 3.34
3342 3473 9.603298 CAAATCATTGACATGTATATACTGCAC 57.397 33.333 13.89 8.14 38.94 4.57
3351 3482 5.799827 TGTATATACTGCACTATGCCACA 57.200 39.130 13.89 0.00 44.23 4.17
3352 3483 5.538118 TGTATATACTGCACTATGCCACAC 58.462 41.667 13.89 0.00 44.23 3.82
3378 3509 7.216494 TGTCTTGTTGTATCAAGTTGAGATGA 58.784 34.615 11.91 0.00 43.44 2.92
3421 3554 9.396022 GTCCATATTCAGATAAAGGAAGAAACA 57.604 33.333 0.00 0.00 31.68 2.83
3458 3591 8.206189 TCTGATACTGTTTGATTCTATGCATGA 58.794 33.333 10.16 1.87 0.00 3.07
3571 3732 4.951254 TGTGTCAGACGAATACTTTGGAA 58.049 39.130 0.00 0.00 0.00 3.53
3595 3756 7.649533 ACAATCCATGCTTTGATCAAGATAA 57.350 32.000 8.41 0.00 33.80 1.75
3605 3766 7.092716 GCTTTGATCAAGATAACAAACATGGT 58.907 34.615 8.41 0.00 33.80 3.55
3610 3771 6.480524 TCAAGATAACAAACATGGTCTTCG 57.519 37.500 0.00 0.00 0.00 3.79
3634 3796 7.832187 TCGGAATACAGTTCCCTATTGAAATTT 59.168 33.333 0.00 0.00 35.17 1.82
3692 3854 8.721478 TGCTGAGACAAAGAAAGATAATAACAC 58.279 33.333 0.00 0.00 0.00 3.32
3707 3869 2.941891 AACACGAGTAACATGCAACG 57.058 45.000 0.00 0.00 0.00 4.10
3711 3873 1.454276 ACGAGTAACATGCAACGTTCG 59.546 47.619 8.04 8.83 0.00 3.95
3753 3918 5.163457 TGCTGGATAATCGATGTACAACAGA 60.163 40.000 0.00 0.00 0.00 3.41
3849 4014 8.149647 AGTTTTGCTGAATCAAATAATCAACCA 58.850 29.630 0.00 0.00 36.04 3.67
4083 4248 3.243301 GGCATACCTGACAATCATTGCAG 60.243 47.826 12.40 12.40 35.78 4.41
4147 4312 9.140286 GGAAAATAAGTTCAATAAAACAGGCTC 57.860 33.333 0.00 0.00 0.00 4.70
4303 4468 3.490759 GTCTGTGCATGACCGCCG 61.491 66.667 10.54 0.00 0.00 6.46
4411 4576 1.355381 TGCACCATCTTCTTGTCCCAT 59.645 47.619 0.00 0.00 0.00 4.00
4428 4593 5.417894 TGTCCCATACTACAGTAAGTCAGTG 59.582 44.000 0.00 0.00 33.76 3.66
4450 4615 5.297029 GTGATTGCCAGTTTAGGATACCTTC 59.703 44.000 0.00 0.00 34.61 3.46
4454 4619 5.192927 TGCCAGTTTAGGATACCTTCAATG 58.807 41.667 0.00 0.00 34.61 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.458295 CCTGTTGAACTGAAAGATGATGCT 59.542 41.667 3.64 0.00 37.43 3.79
1 2 4.456911 TCCTGTTGAACTGAAAGATGATGC 59.543 41.667 3.64 0.00 37.43 3.91
11 12 6.426937 GCAAGTAGTAAATCCTGTTGAACTGA 59.573 38.462 3.64 0.00 0.00 3.41
94 104 7.433708 TTTTTCTATCTTTTGATGCGAGACA 57.566 32.000 0.00 0.00 39.88 3.41
115 125 4.560108 GCTGTGAGATGGCAACTGATTTTT 60.560 41.667 0.51 0.00 37.61 1.94
162 172 1.201647 CATACGTGTCCTGTTCCGTCT 59.798 52.381 0.00 0.00 34.95 4.18
208 218 9.657419 GGGGAAATGCTTATAATGAATAAATGG 57.343 33.333 0.00 0.00 29.59 3.16
267 277 2.003072 ACCCATCCACCCATCTTTTCT 58.997 47.619 0.00 0.00 0.00 2.52
271 281 0.552367 TCCACCCATCCACCCATCTT 60.552 55.000 0.00 0.00 0.00 2.40
278 288 0.178981 CCATCCATCCACCCATCCAC 60.179 60.000 0.00 0.00 0.00 4.02
280 290 1.078955 ATCCATCCATCCACCCATCC 58.921 55.000 0.00 0.00 0.00 3.51
281 291 2.025887 GGTATCCATCCATCCACCCATC 60.026 54.545 0.00 0.00 0.00 3.51
282 292 1.995542 GGTATCCATCCATCCACCCAT 59.004 52.381 0.00 0.00 0.00 4.00
283 293 1.060640 AGGTATCCATCCATCCACCCA 60.061 52.381 0.00 0.00 0.00 4.51
424 434 2.923605 TTTTCCGTTCTTGTTTGCGT 57.076 40.000 0.00 0.00 0.00 5.24
437 453 2.788786 GCCATTAATCGTGCATTTTCCG 59.211 45.455 0.00 0.00 0.00 4.30
440 456 3.189285 GCTGCCATTAATCGTGCATTTT 58.811 40.909 0.00 0.00 32.53 1.82
497 517 4.847444 GCCGCCTTCTCTCCCTGC 62.847 72.222 0.00 0.00 0.00 4.85
498 518 4.521062 CGCCGCCTTCTCTCCCTG 62.521 72.222 0.00 0.00 0.00 4.45
499 519 4.761058 TCGCCGCCTTCTCTCCCT 62.761 66.667 0.00 0.00 0.00 4.20
714 780 3.195610 GTCCAAGAAACCCAATCCCATTC 59.804 47.826 0.00 0.00 0.00 2.67
715 781 3.173151 GTCCAAGAAACCCAATCCCATT 58.827 45.455 0.00 0.00 0.00 3.16
716 782 2.820178 GTCCAAGAAACCCAATCCCAT 58.180 47.619 0.00 0.00 0.00 4.00
757 823 0.037160 TAAACCCACGCCTTCCCTTC 59.963 55.000 0.00 0.00 0.00 3.46
758 824 0.479378 TTAAACCCACGCCTTCCCTT 59.521 50.000 0.00 0.00 0.00 3.95
759 825 0.037734 CTTAAACCCACGCCTTCCCT 59.962 55.000 0.00 0.00 0.00 4.20
760 826 1.592400 GCTTAAACCCACGCCTTCCC 61.592 60.000 0.00 0.00 0.00 3.97
914 980 2.352814 CGGTCCAGAGAAATGTCTTCGT 60.353 50.000 0.00 0.00 32.80 3.85
916 982 2.622436 CCGGTCCAGAGAAATGTCTTC 58.378 52.381 0.00 0.00 32.80 2.87
942 1008 0.378257 CTCTCTCACTGAGCGAGCTC 59.622 60.000 17.42 17.42 42.38 4.09
985 1051 4.920112 TGCGAACCACCCACCACG 62.920 66.667 0.00 0.00 0.00 4.94
986 1052 3.284449 GTGCGAACCACCCACCAC 61.284 66.667 0.00 0.00 38.55 4.16
987 1053 4.920112 CGTGCGAACCACCCACCA 62.920 66.667 0.00 0.00 41.53 4.17
988 1054 4.612412 TCGTGCGAACCACCCACC 62.612 66.667 0.00 0.00 41.53 4.61
989 1055 3.041940 CTCGTGCGAACCACCCAC 61.042 66.667 0.00 0.00 41.53 4.61
990 1056 3.096633 AACTCGTGCGAACCACCCA 62.097 57.895 0.00 0.00 41.53 4.51
991 1057 2.280592 AACTCGTGCGAACCACCC 60.281 61.111 0.00 0.00 41.53 4.61
992 1058 1.593209 TCAACTCGTGCGAACCACC 60.593 57.895 0.00 0.00 41.53 4.61
993 1059 1.563173 GTCAACTCGTGCGAACCAC 59.437 57.895 0.00 0.00 41.15 4.16
1000 1066 2.280797 TGCCAGGTCAACTCGTGC 60.281 61.111 0.00 0.00 0.00 5.34
1013 1079 2.350895 CCGATCCAACCACTGCCA 59.649 61.111 0.00 0.00 0.00 4.92
1014 1080 3.134127 GCCGATCCAACCACTGCC 61.134 66.667 0.00 0.00 0.00 4.85
1067 1149 4.838152 CACCCTCATGTCGGCCGG 62.838 72.222 27.83 9.38 0.00 6.13
1068 1150 4.838152 CCACCCTCATGTCGGCCG 62.838 72.222 22.12 22.12 0.00 6.13
1069 1151 3.717294 ACCACCCTCATGTCGGCC 61.717 66.667 0.00 0.00 0.00 6.13
1346 1428 9.628500 TTGATTCAGCAAGTACTCTACTATAGA 57.372 33.333 6.78 0.00 38.26 1.98
1349 1431 7.069331 AGCTTGATTCAGCAAGTACTCTACTAT 59.931 37.037 6.67 0.00 45.41 2.12
1350 1432 6.378564 AGCTTGATTCAGCAAGTACTCTACTA 59.621 38.462 6.67 0.00 45.41 1.82
1351 1433 5.186797 AGCTTGATTCAGCAAGTACTCTACT 59.813 40.000 6.67 0.00 45.41 2.57
1352 1434 5.290643 CAGCTTGATTCAGCAAGTACTCTAC 59.709 44.000 6.67 0.00 45.41 2.59
1353 1435 5.047021 ACAGCTTGATTCAGCAAGTACTCTA 60.047 40.000 6.67 0.00 45.41 2.43
1354 1436 4.252073 CAGCTTGATTCAGCAAGTACTCT 58.748 43.478 6.67 0.00 45.41 3.24
1355 1437 3.999663 ACAGCTTGATTCAGCAAGTACTC 59.000 43.478 6.67 0.00 45.41 2.59
1374 1456 5.254339 AGGAAAAACTGAAAGCAGAACAG 57.746 39.130 0.00 0.00 45.17 3.16
1375 1457 5.394115 GGAAGGAAAAACTGAAAGCAGAACA 60.394 40.000 0.00 0.00 45.17 3.18
1387 1469 1.970640 GTGCCCATGGAAGGAAAAACT 59.029 47.619 15.22 0.00 0.00 2.66
1389 1471 2.094100 TGTGCCCATGGAAGGAAAAA 57.906 45.000 15.22 0.00 0.00 1.94
1394 1476 0.604578 CAACTTGTGCCCATGGAAGG 59.395 55.000 15.22 0.00 0.00 3.46
1405 1487 4.034279 CCCAATTTTGAACAGCAACTTGTG 59.966 41.667 0.00 0.00 35.91 3.33
1406 1488 4.190772 CCCAATTTTGAACAGCAACTTGT 58.809 39.130 0.00 0.00 35.91 3.16
1407 1489 4.034279 CACCCAATTTTGAACAGCAACTTG 59.966 41.667 0.00 0.00 35.91 3.16
1408 1490 4.081198 TCACCCAATTTTGAACAGCAACTT 60.081 37.500 0.00 0.00 35.91 2.66
1419 1502 3.255642 ACGAACCTGATCACCCAATTTTG 59.744 43.478 0.00 0.00 0.00 2.44
1428 1511 2.009774 CCAATCCACGAACCTGATCAC 58.990 52.381 0.00 0.00 0.00 3.06
1454 1537 4.767255 CGACCTGGGAGCAGTGGC 62.767 72.222 0.00 0.00 41.61 5.01
1457 1540 2.997897 GGTCGACCTGGGAGCAGT 60.998 66.667 27.64 0.00 32.38 4.40
1458 1541 4.135153 CGGTCGACCTGGGAGCAG 62.135 72.222 30.92 10.14 32.38 4.24
1459 1542 4.988716 ACGGTCGACCTGGGAGCA 62.989 66.667 30.92 0.00 32.38 4.26
1461 1544 1.605058 ATTCACGGTCGACCTGGGAG 61.605 60.000 30.92 17.90 0.00 4.30
1462 1545 1.601419 GATTCACGGTCGACCTGGGA 61.601 60.000 30.92 26.04 0.00 4.37
1493 1576 3.044986 CAGAATCAAACAACCAAGCACG 58.955 45.455 0.00 0.00 0.00 5.34
1511 1594 1.616374 TGACGGTCATGCTACAACAGA 59.384 47.619 6.76 0.00 0.00 3.41
1513 1596 2.760634 ATGACGGTCATGCTACAACA 57.239 45.000 22.09 0.00 35.43 3.33
1521 1604 6.841119 TGACAAAAGATTTATGACGGTCATG 58.159 36.000 29.02 15.44 37.70 3.07
1541 1624 8.503196 CGGCAGCATAAATATTATTAGTTGACA 58.497 33.333 0.00 0.00 0.00 3.58
1542 1625 7.481798 GCGGCAGCATAAATATTATTAGTTGAC 59.518 37.037 3.18 0.00 44.35 3.18
1543 1626 7.526608 GCGGCAGCATAAATATTATTAGTTGA 58.473 34.615 3.18 0.00 44.35 3.18
1544 1627 7.725610 GCGGCAGCATAAATATTATTAGTTG 57.274 36.000 3.18 0.00 44.35 3.16
1566 1649 8.197988 AGTTGGTCATAGTTCTTATTTAAGCG 57.802 34.615 0.00 0.00 33.40 4.68
1595 1678 5.764686 CCAGCTTGGTGCATTCATAGTTATA 59.235 40.000 0.00 0.00 45.94 0.98
1607 1708 4.641645 CCCGTCCAGCTTGGTGCA 62.642 66.667 0.00 0.00 45.94 4.57
1623 1724 1.135689 CACTTGCCGTGTTGCTAATCC 60.136 52.381 0.00 0.00 38.84 3.01
1624 1725 1.804151 TCACTTGCCGTGTTGCTAATC 59.196 47.619 3.56 0.00 44.16 1.75
1628 1729 1.032014 ATTTCACTTGCCGTGTTGCT 58.968 45.000 3.56 0.00 44.16 3.91
1636 1737 9.855021 ATGTTTAGTAATACAATTTCACTTGCC 57.145 29.630 0.00 0.00 0.00 4.52
1669 1776 1.065491 ACCTGATAATGGCAGCACGAA 60.065 47.619 0.00 0.00 32.06 3.85
1670 1777 0.541392 ACCTGATAATGGCAGCACGA 59.459 50.000 0.00 0.00 32.06 4.35
1671 1778 0.940126 GACCTGATAATGGCAGCACG 59.060 55.000 0.00 0.00 32.06 5.34
1673 1780 2.804986 TTGACCTGATAATGGCAGCA 57.195 45.000 0.00 0.00 32.06 4.41
1674 1781 2.954318 ACATTGACCTGATAATGGCAGC 59.046 45.455 0.00 0.00 38.33 5.25
1675 1782 4.201657 TCACATTGACCTGATAATGGCAG 58.798 43.478 0.00 0.00 38.33 4.85
1676 1783 4.080413 TCTCACATTGACCTGATAATGGCA 60.080 41.667 0.00 0.00 38.33 4.92
1677 1784 4.454678 TCTCACATTGACCTGATAATGGC 58.545 43.478 0.00 0.00 38.33 4.40
1678 1785 5.061853 CCTCTCACATTGACCTGATAATGG 58.938 45.833 0.00 0.00 38.33 3.16
1718 1827 2.476320 GCATTCTCTTGGCCGCCTC 61.476 63.158 11.61 0.00 0.00 4.70
1719 1828 2.439156 GCATTCTCTTGGCCGCCT 60.439 61.111 11.61 0.00 0.00 5.52
1720 1829 3.521796 GGCATTCTCTTGGCCGCC 61.522 66.667 1.04 1.04 38.04 6.13
1734 1843 3.953712 TGATCTTCTTTACTGTCGGCA 57.046 42.857 0.00 0.00 0.00 5.69
1765 1874 1.493311 GCCAAGTGCGAAGAACGAG 59.507 57.895 0.00 0.00 45.77 4.18
1831 1940 9.865321 AACGACAAAGCTAATACAGTTCTATAA 57.135 29.630 0.00 0.00 0.00 0.98
1835 1944 7.492352 AAAACGACAAAGCTAATACAGTTCT 57.508 32.000 0.00 0.00 0.00 3.01
1846 1955 4.044426 GCAAGATGAAAAACGACAAAGCT 58.956 39.130 0.00 0.00 0.00 3.74
2003 2112 1.133730 TCGGGCACAGGTTTTTAGGTT 60.134 47.619 0.00 0.00 0.00 3.50
2012 2121 3.321111 CAGTATATTAGTCGGGCACAGGT 59.679 47.826 0.00 0.00 0.00 4.00
2015 2124 3.319972 GGTCAGTATATTAGTCGGGCACA 59.680 47.826 0.00 0.00 0.00 4.57
2077 2186 5.179555 CCTAGAACAGAACTAACAACCAAGC 59.820 44.000 0.00 0.00 0.00 4.01
2086 2195 4.142138 GCTGCTAGCCTAGAACAGAACTAA 60.142 45.833 13.29 0.00 34.48 2.24
2103 2212 1.218047 CCAACGTGCTAGGCTGCTA 59.782 57.895 0.00 0.00 0.00 3.49
2104 2213 2.046892 CCAACGTGCTAGGCTGCT 60.047 61.111 0.00 0.00 0.00 4.24
2105 2214 1.515521 AAACCAACGTGCTAGGCTGC 61.516 55.000 0.00 0.00 0.00 5.25
2106 2215 0.238289 CAAACCAACGTGCTAGGCTG 59.762 55.000 0.00 0.00 0.00 4.85
2107 2216 1.515521 GCAAACCAACGTGCTAGGCT 61.516 55.000 0.00 0.00 37.78 4.58
2108 2217 1.081442 GCAAACCAACGTGCTAGGC 60.081 57.895 0.00 0.00 37.78 3.93
2109 2218 0.040425 GTGCAAACCAACGTGCTAGG 60.040 55.000 0.00 0.00 41.48 3.02
2168 2297 2.432444 TCTACCCTTGCAATTTGACGG 58.568 47.619 0.00 0.00 0.00 4.79
2170 2299 8.854614 ATATCTATCTACCCTTGCAATTTGAC 57.145 34.615 0.00 0.00 0.00 3.18
2201 2330 5.711976 AGTTAGGTTTCCAGATTTGACCATG 59.288 40.000 0.00 0.00 32.81 3.66
2252 2381 6.018262 GTGTTACTGTACAAGCAGAATTGTCA 60.018 38.462 0.00 0.00 42.33 3.58
2253 2382 6.363473 GTGTTACTGTACAAGCAGAATTGTC 58.637 40.000 0.00 0.00 42.33 3.18
2334 2463 5.859495 AGCTCTGCCTAAATATAGACAACC 58.141 41.667 0.00 0.00 0.00 3.77
2338 2467 7.135467 GCAAAAAGCTCTGCCTAAATATAGAC 58.865 38.462 4.46 0.00 41.15 2.59
2372 2501 5.591643 ACTTAGTTGTATCACAGTTTGCG 57.408 39.130 0.00 0.00 0.00 4.85
2635 2764 1.913403 GCGCTGTGTTTTATGCATCAC 59.087 47.619 0.19 5.83 0.00 3.06
2768 2897 1.647213 CCACTAACAACATCGTCGACG 59.353 52.381 31.30 31.30 41.45 5.12
3050 3179 3.758554 AGGATGGACTGTATGCAAACAAC 59.241 43.478 0.00 0.00 29.34 3.32
3145 3275 3.518634 TCCCTTTTTGCTTTGTCACAC 57.481 42.857 0.00 0.00 0.00 3.82
3193 3323 0.540923 GCATCTCAGCCAGACCTTCT 59.459 55.000 0.00 0.00 32.26 2.85
3202 3332 2.292845 GAGCCATAAAAGCATCTCAGCC 59.707 50.000 0.00 0.00 34.23 4.85
3287 3417 7.389330 ACATAAAACATGACGGTCTACATGAAA 59.611 33.333 13.35 0.00 44.28 2.69
3316 3446 9.603298 GTGCAGTATATACATGTCAATGATTTG 57.397 33.333 15.18 1.32 37.24 2.32
3342 3473 3.141398 ACAACAAGACAGTGTGGCATAG 58.859 45.455 0.00 0.00 0.00 2.23
3351 3482 6.582636 TCTCAACTTGATACAACAAGACAGT 58.417 36.000 14.00 0.00 46.85 3.55
3352 3483 7.386025 TCATCTCAACTTGATACAACAAGACAG 59.614 37.037 14.00 7.30 46.85 3.51
3546 3679 5.995282 TCCAAAGTATTCGTCTGACACAATT 59.005 36.000 8.73 0.00 0.00 2.32
3547 3680 5.547465 TCCAAAGTATTCGTCTGACACAAT 58.453 37.500 8.73 7.74 0.00 2.71
3571 3732 7.123098 TGTTATCTTGATCAAAGCATGGATTGT 59.877 33.333 9.88 0.00 35.69 2.71
3595 3756 4.647611 TGTATTCCGAAGACCATGTTTGT 58.352 39.130 3.51 0.00 0.00 2.83
3605 3766 5.659525 TCAATAGGGAACTGTATTCCGAAGA 59.340 40.000 0.00 0.00 43.88 2.87
3610 3771 8.129211 CGAAATTTCAATAGGGAACTGTATTCC 58.871 37.037 17.99 0.00 43.88 3.01
3634 3796 3.693578 TGAGTTTCAATATGGCATTGCGA 59.306 39.130 4.78 0.00 0.00 5.10
3692 3854 1.201769 CCGAACGTTGCATGTTACTCG 60.202 52.381 5.00 0.00 0.00 4.18
3707 3869 5.560953 GCACTTATTTATGAGATGGCCGAAC 60.561 44.000 0.00 0.00 0.00 3.95
3711 3873 4.217118 CCAGCACTTATTTATGAGATGGCC 59.783 45.833 0.00 0.00 0.00 5.36
3849 4014 7.611855 CCTGATATCCTGACTGTTTACCTTTTT 59.388 37.037 0.00 0.00 0.00 1.94
3860 4025 3.784511 ATTGGCCTGATATCCTGACTG 57.215 47.619 3.32 0.00 0.00 3.51
3862 4027 4.363991 AGAATTGGCCTGATATCCTGAC 57.636 45.455 3.32 0.00 0.00 3.51
4075 4240 6.878389 TGTACACTAAATCACATCTGCAATGA 59.122 34.615 13.53 4.44 0.00 2.57
4147 4312 2.276732 TTTCTTGAGAAGCACAGGGG 57.723 50.000 0.00 0.00 35.21 4.79
4172 4337 6.819397 AAAAGAGGAAGGTAAGTAATGTGC 57.181 37.500 0.00 0.00 0.00 4.57
4303 4468 5.215252 TCTACCCATTGATACTTGCTAGC 57.785 43.478 8.10 8.10 0.00 3.42
4411 4576 5.479027 TGGCAATCACTGACTTACTGTAGTA 59.521 40.000 0.00 0.00 32.26 1.82
4428 4593 5.437060 TGAAGGTATCCTAAACTGGCAATC 58.563 41.667 0.00 0.00 31.13 2.67


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

AutoCloner maintained by Alex Coulton.