Multiple sequence alignment - TraesCS2D01G557700

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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 TraesCS2D01G557700 chr2D 100.000 2312 0 0 1 2312 630516214 630518525 0.000000e+00 4270.0
1 TraesCS2D01G557700 chr2D 88.779 811 74 12 1 801 615923694 615922891 0.000000e+00 977.0
2 TraesCS2D01G557700 chr2D 87.808 812 80 13 1 801 631917162 631917965 0.000000e+00 933.0
3 TraesCS2D01G557700 chr2D 91.034 145 13 0 2167 2311 630518230 630518374 1.810000e-46 196.0
4 TraesCS2D01G557700 chr2D 91.034 145 13 0 2017 2161 630518380 630518524 1.810000e-46 196.0
5 TraesCS2D01G557700 chr7D 89.552 804 73 6 7 802 405218061 405217261 0.000000e+00 1009.0
6 TraesCS2D01G557700 chr7D 80.142 141 17 8 1443 1574 566258969 566259107 6.800000e-16 95.3
7 TraesCS2D01G557700 chr6D 88.765 810 79 7 1 801 465607005 465607811 0.000000e+00 981.0
8 TraesCS2D01G557700 chr5D 88.807 813 73 14 1 801 564577107 564577913 0.000000e+00 981.0
9 TraesCS2D01G557700 chr5D 86.139 404 43 2 1765 2166 250406078 250405686 7.640000e-115 424.0
10 TraesCS2D01G557700 chr5D 90.345 145 14 0 2167 2311 250405835 250405691 8.430000e-45 191.0
11 TraesCS2D01G557700 chr5D 80.255 157 25 6 1423 1573 481520454 481520610 1.880000e-21 113.0
12 TraesCS2D01G557700 chr3D 88.698 814 76 11 3 807 143427917 143427111 0.000000e+00 979.0
13 TraesCS2D01G557700 chr3D 87.160 810 91 9 1 801 31210238 31209433 0.000000e+00 907.0
14 TraesCS2D01G557700 chr3D 86.700 812 96 9 1 803 54075823 54076631 0.000000e+00 891.0
15 TraesCS2D01G557700 chr3D 84.579 428 49 7 1738 2161 179163794 179163380 2.140000e-110 409.0
16 TraesCS2D01G557700 chr3D 84.461 399 49 4 1764 2161 556621193 556620807 4.660000e-102 381.0
17 TraesCS2D01G557700 chr3D 85.034 147 21 1 2167 2312 179163525 179163379 5.150000e-32 148.0
18 TraesCS2D01G557700 chr3D 78.528 163 29 5 1418 1574 489528215 489528377 4.060000e-18 102.0
19 TraesCS2D01G557700 chr3D 80.147 136 19 5 1429 1556 515225443 515225578 6.800000e-16 95.3
20 TraesCS2D01G557700 chrUn 86.609 814 96 8 1 803 320054742 320053931 0.000000e+00 887.0
21 TraesCS2D01G557700 chrUn 80.000 150 22 8 1439 1580 220050222 220050073 1.130000e-18 104.0
22 TraesCS2D01G557700 chr2B 81.533 796 80 39 960 1731 773424056 773424808 5.500000e-166 593.0
23 TraesCS2D01G557700 chr2B 83.565 432 58 10 1732 2161 142605545 142605125 2.150000e-105 392.0
24 TraesCS2D01G557700 chr2B 84.383 397 48 5 1764 2158 728624006 728624390 6.030000e-101 377.0
25 TraesCS2D01G557700 chr2B 91.083 157 13 1 802 958 773423258 773423413 6.470000e-51 211.0
26 TraesCS2D01G557700 chr2B 81.560 141 18 7 1421 1554 793813310 793813449 2.430000e-20 110.0
27 TraesCS2D01G557700 chr2A 93.503 354 23 0 961 1314 760621810 760622163 5.660000e-146 527.0
28 TraesCS2D01G557700 chr2A 93.038 158 9 2 802 958 760621249 760621405 1.790000e-56 230.0
29 TraesCS2D01G557700 chr2A 89.231 130 9 3 1598 1726 760622317 760622442 8.550000e-35 158.0
30 TraesCS2D01G557700 chr3B 85.629 501 46 11 1735 2234 718700073 718699598 9.530000e-139 503.0
31 TraesCS2D01G557700 chr3B 89.552 67 5 1 2017 2083 718699663 718699599 1.470000e-12 84.2
32 TraesCS2D01G557700 chr3B 92.857 56 4 0 2257 2312 718699604 718699549 5.290000e-12 82.4
33 TraesCS2D01G557700 chr7B 88.119 404 46 1 1765 2166 23593860 23593457 1.610000e-131 479.0
34 TraesCS2D01G557700 chr7B 83.459 399 50 5 1764 2158 539991443 539991829 7.860000e-95 357.0
35 TraesCS2D01G557700 chr7A 85.714 434 61 1 1734 2166 670516443 670516010 7.530000e-125 457.0
36 TraesCS2D01G557700 chr1D 84.289 401 48 6 1764 2161 411723218 411723606 6.030000e-101 377.0
37 TraesCS2D01G557700 chr5A 82.663 398 54 6 1764 2158 24767538 24767923 2.850000e-89 339.0
38 TraesCS2D01G557700 chr6B 83.571 140 21 2 2174 2312 180960695 180960557 1.860000e-26 130.0
39 TraesCS2D01G557700 chr4A 80.000 150 22 8 1439 1580 705954584 705954435 1.130000e-18 104.0
40 TraesCS2D01G557700 chr4A 80.000 150 22 8 1439 1580 706090560 706090411 1.130000e-18 104.0
41 TraesCS2D01G557700 chr6A 90.476 63 5 1 1513 1574 64507665 64507603 5.290000e-12 82.4


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 TraesCS2D01G557700 chr2D 630516214 630518525 2311 False 1554.0 4270 94.022667 1 2312 3 chr2D.!!$F2 2311
1 TraesCS2D01G557700 chr2D 615922891 615923694 803 True 977.0 977 88.779000 1 801 1 chr2D.!!$R1 800
2 TraesCS2D01G557700 chr2D 631917162 631917965 803 False 933.0 933 87.808000 1 801 1 chr2D.!!$F1 800
3 TraesCS2D01G557700 chr7D 405217261 405218061 800 True 1009.0 1009 89.552000 7 802 1 chr7D.!!$R1 795
4 TraesCS2D01G557700 chr6D 465607005 465607811 806 False 981.0 981 88.765000 1 801 1 chr6D.!!$F1 800
5 TraesCS2D01G557700 chr5D 564577107 564577913 806 False 981.0 981 88.807000 1 801 1 chr5D.!!$F2 800
6 TraesCS2D01G557700 chr3D 143427111 143427917 806 True 979.0 979 88.698000 3 807 1 chr3D.!!$R2 804
7 TraesCS2D01G557700 chr3D 31209433 31210238 805 True 907.0 907 87.160000 1 801 1 chr3D.!!$R1 800
8 TraesCS2D01G557700 chr3D 54075823 54076631 808 False 891.0 891 86.700000 1 803 1 chr3D.!!$F1 802
9 TraesCS2D01G557700 chrUn 320053931 320054742 811 True 887.0 887 86.609000 1 803 1 chrUn.!!$R2 802
10 TraesCS2D01G557700 chr2B 773423258 773424808 1550 False 402.0 593 86.308000 802 1731 2 chr2B.!!$F3 929
11 TraesCS2D01G557700 chr2A 760621249 760622442 1193 False 305.0 527 91.924000 802 1726 3 chr2A.!!$F1 924
12 TraesCS2D01G557700 chr3B 718699549 718700073 524 True 223.2 503 89.346000 1735 2312 3 chr3B.!!$R1 577

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
883 898 0.03438 GAGGGGGTTTGAGGGTTAGC 60.034 60.0 0.0 0.0 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 2903 0.106116 AGTAGGTAGAGGGGGCGAAG 60.106 60.0 0.0 0.0 0.0 3.79 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
78 79 2.034687 GCTTCTTGGAGCCAGGCA 59.965 61.111 15.80 0.00 36.66 4.75
344 348 1.553704 GCCCTTCTCGGAGGAAGTAAA 59.446 52.381 4.96 0.00 40.56 2.01
395 399 3.120477 TCGATTGGTTTATGCGTGTGAAC 60.120 43.478 0.00 0.00 0.00 3.18
410 414 1.673337 GAACGTTACAGGGGGTGCC 60.673 63.158 0.00 0.00 0.00 5.01
489 501 4.515944 CGTTACAAGGGGTTCAATGTACAA 59.484 41.667 0.00 0.00 0.00 2.41
564 578 1.089920 GACTACGGAGTGAACGCCTA 58.910 55.000 4.10 0.00 45.73 3.93
601 615 6.260493 GCTAGTCGACTCCTAGTCTTCAATAA 59.740 42.308 23.89 0.00 42.92 1.40
607 621 7.086230 GACTCCTAGTCTTCAATAAGTCGAA 57.914 40.000 0.00 0.00 41.88 3.71
640 654 1.736586 GTCGAGTGATCGCAGGGAT 59.263 57.895 9.33 0.00 38.35 3.85
663 677 2.990066 GGATCTCCGAGTGATTGGTT 57.010 50.000 0.00 0.00 0.00 3.67
678 692 4.405680 TGATTGGTTAGTCGAGTGGATGAT 59.594 41.667 2.10 0.00 0.00 2.45
699 713 2.030562 CGACGTCTTGGTTGGGCT 59.969 61.111 14.70 0.00 0.00 5.19
717 732 2.037772 GGCTCTCTCTGTTGTCCTTTGA 59.962 50.000 0.00 0.00 0.00 2.69
720 735 4.021894 GCTCTCTCTGTTGTCCTTTGAGTA 60.022 45.833 0.00 0.00 0.00 2.59
721 736 5.455056 TCTCTCTGTTGTCCTTTGAGTAC 57.545 43.478 0.00 0.00 0.00 2.73
747 762 5.178096 TGCTTCTTTGATAATGACCCTGA 57.822 39.130 0.00 0.00 0.00 3.86
782 797 0.104934 CAGGCCTATGACCCTACCCT 60.105 60.000 3.98 0.00 0.00 4.34
804 819 3.311990 AGGTCTATGTCATCATCAGCCA 58.688 45.455 0.00 0.00 35.70 4.75
864 879 0.757188 AGGCTGGTCCGGACAGATAG 60.757 60.000 34.40 24.85 40.77 2.08
880 895 2.206223 GATAGAGGGGGTTTGAGGGTT 58.794 52.381 0.00 0.00 0.00 4.11
883 898 0.034380 GAGGGGGTTTGAGGGTTAGC 60.034 60.000 0.00 0.00 0.00 3.09
887 902 1.162698 GGGTTTGAGGGTTAGCGTTC 58.837 55.000 0.00 0.00 0.00 3.95
914 929 8.962884 ATTGAAAACTTTAAATTCTGTTGCCT 57.037 26.923 0.00 0.00 0.00 4.75
958 973 4.489771 GCCACCTGGTCCCATCGG 62.490 72.222 0.00 0.00 37.57 4.18
1004 1664 3.933955 CCTCTTGAAGCAGAGACAATGAG 59.066 47.826 0.48 0.00 42.81 2.90
1024 1684 0.586319 GCTGCAAACGCAACTACTCA 59.414 50.000 0.00 0.00 39.39 3.41
1041 1701 2.575279 ACTCATCTTGGCTTCCATCACT 59.425 45.455 0.00 0.00 31.53 3.41
1061 1721 0.883370 GCAGCGATGATCATGAGCCA 60.883 55.000 22.12 5.77 0.00 4.75
1064 1724 0.598419 GCGATGATCATGAGCCACGA 60.598 55.000 23.57 1.57 0.00 4.35
1095 1755 2.998480 ACCACCCACGCGATACCA 60.998 61.111 15.93 0.00 0.00 3.25
1105 1765 2.506217 CGATACCAGTGCGCACGT 60.506 61.111 32.94 26.88 36.20 4.49
1108 1768 0.921347 GATACCAGTGCGCACGTTAG 59.079 55.000 32.94 23.90 36.20 2.34
1122 1782 3.515286 TTAGGCGGCGTCGAGGAG 61.515 66.667 16.53 2.99 39.00 3.69
1315 1975 3.336566 GCCGCGGGCGTTAATTAT 58.663 55.556 29.38 0.00 39.62 1.28
1325 1985 5.005490 GCGGGCGTTAATTATCTTATCTAGC 59.995 44.000 0.00 0.00 0.00 3.42
1357 2017 1.298953 TCCTATTTGCTTCCCTGGCT 58.701 50.000 0.00 0.00 0.00 4.75
1394 2074 9.520515 GTGGAGATTATGAAATGTGGGTTATAT 57.479 33.333 0.00 0.00 0.00 0.86
1412 2092 9.959749 GGGTTATATATGTATTTGTGTTGTTGG 57.040 33.333 0.00 0.00 0.00 3.77
1416 2096 6.811253 ATATGTATTTGTGTTGTTGGACGT 57.189 33.333 0.00 0.00 0.00 4.34
1417 2097 4.280101 TGTATTTGTGTTGTTGGACGTG 57.720 40.909 0.00 0.00 0.00 4.49
1418 2098 3.939592 TGTATTTGTGTTGTTGGACGTGA 59.060 39.130 0.00 0.00 0.00 4.35
1419 2099 4.576873 TGTATTTGTGTTGTTGGACGTGAT 59.423 37.500 0.00 0.00 0.00 3.06
1420 2100 3.412981 TTTGTGTTGTTGGACGTGATG 57.587 42.857 0.00 0.00 0.00 3.07
1421 2101 2.317530 TGTGTTGTTGGACGTGATGA 57.682 45.000 0.00 0.00 0.00 2.92
1422 2102 2.844946 TGTGTTGTTGGACGTGATGAT 58.155 42.857 0.00 0.00 0.00 2.45
1423 2103 3.210227 TGTGTTGTTGGACGTGATGATT 58.790 40.909 0.00 0.00 0.00 2.57
1424 2104 3.249799 TGTGTTGTTGGACGTGATGATTC 59.750 43.478 0.00 0.00 0.00 2.52
1425 2105 3.498397 GTGTTGTTGGACGTGATGATTCT 59.502 43.478 0.00 0.00 0.00 2.40
1426 2106 3.745975 TGTTGTTGGACGTGATGATTCTC 59.254 43.478 0.00 0.00 0.00 2.87
1427 2107 2.972625 TGTTGGACGTGATGATTCTCC 58.027 47.619 0.00 0.00 0.00 3.71
1428 2108 1.927174 GTTGGACGTGATGATTCTCCG 59.073 52.381 0.00 0.00 0.00 4.63
1429 2109 0.459899 TGGACGTGATGATTCTCCGG 59.540 55.000 0.00 0.00 0.00 5.14
1430 2110 0.460311 GGACGTGATGATTCTCCGGT 59.540 55.000 0.00 0.00 0.00 5.28
1434 2114 3.021695 ACGTGATGATTCTCCGGTCTTA 58.978 45.455 0.00 0.00 0.00 2.10
1437 2117 5.301045 ACGTGATGATTCTCCGGTCTTAATA 59.699 40.000 0.00 0.00 0.00 0.98
1464 2144 4.385358 TTTTCTTCTTGGCTGGTGTTTC 57.615 40.909 0.00 0.00 0.00 2.78
1465 2145 2.727123 TCTTCTTGGCTGGTGTTTCA 57.273 45.000 0.00 0.00 0.00 2.69
1476 2156 3.253188 GCTGGTGTTTCATTGTGCTAAGA 59.747 43.478 0.00 0.00 0.00 2.10
1477 2157 4.082571 GCTGGTGTTTCATTGTGCTAAGAT 60.083 41.667 0.00 0.00 0.00 2.40
1478 2158 5.123820 GCTGGTGTTTCATTGTGCTAAGATA 59.876 40.000 0.00 0.00 0.00 1.98
1479 2159 6.676456 GCTGGTGTTTCATTGTGCTAAGATAG 60.676 42.308 0.00 0.00 0.00 2.08
1489 2169 2.250348 GCTAAGATAGCGCTCTACCG 57.750 55.000 16.34 0.00 42.62 4.02
1490 2170 1.536331 GCTAAGATAGCGCTCTACCGT 59.464 52.381 16.34 2.41 42.62 4.83
1492 2172 3.550436 GCTAAGATAGCGCTCTACCGTTT 60.550 47.826 16.34 2.76 42.62 3.60
1493 2173 2.778187 AGATAGCGCTCTACCGTTTC 57.222 50.000 16.34 0.00 0.00 2.78
1494 2174 1.337387 AGATAGCGCTCTACCGTTTCC 59.663 52.381 16.34 0.00 0.00 3.13
1497 2177 1.180029 AGCGCTCTACCGTTTCCTTA 58.820 50.000 2.64 0.00 0.00 2.69
1498 2178 1.134560 AGCGCTCTACCGTTTCCTTAG 59.865 52.381 2.64 0.00 0.00 2.18
1499 2179 1.557651 CGCTCTACCGTTTCCTTAGC 58.442 55.000 0.00 0.00 0.00 3.09
1505 2186 2.180432 ACCGTTTCCTTAGCCTTGTC 57.820 50.000 0.00 0.00 0.00 3.18
1506 2187 1.418637 ACCGTTTCCTTAGCCTTGTCA 59.581 47.619 0.00 0.00 0.00 3.58
1514 2195 4.638304 TCCTTAGCCTTGTCAGTGTTTAC 58.362 43.478 0.00 0.00 0.00 2.01
1518 2199 2.159014 AGCCTTGTCAGTGTTTACGTGA 60.159 45.455 0.00 0.00 0.00 4.35
1519 2200 2.033151 GCCTTGTCAGTGTTTACGTGAC 60.033 50.000 0.00 0.00 40.89 3.67
1525 2206 4.799949 TGTCAGTGTTTACGTGACTTGTAC 59.200 41.667 0.00 0.00 41.06 2.90
1529 2210 8.017373 GTCAGTGTTTACGTGACTTGTACTATA 58.983 37.037 0.00 0.00 38.06 1.31
1539 2220 9.128404 ACGTGACTTGTACTATAATCCTTATGA 57.872 33.333 0.00 0.00 0.00 2.15
1610 2298 6.400568 GGAACAATGATGTGTTTGGATGAAT 58.599 36.000 0.00 0.00 41.78 2.57
1611 2299 6.875195 GGAACAATGATGTGTTTGGATGAATT 59.125 34.615 0.00 0.00 41.78 2.17
1656 2347 5.799827 TTTTGTTATTGGTTTCCAGGAGG 57.200 39.130 0.00 0.00 33.81 4.30
1705 2397 7.507733 AGCTAATTTAGGAATCTCTTGCATG 57.492 36.000 5.61 0.00 0.00 4.06
1713 2405 0.251354 ATCTCTTGCATGCACCTCGT 59.749 50.000 22.58 3.91 0.00 4.18
1714 2406 0.035317 TCTCTTGCATGCACCTCGTT 59.965 50.000 22.58 0.00 0.00 3.85
1726 2418 6.360681 GCATGCACCTCGTTAATTAATCAATC 59.639 38.462 14.21 0.00 0.00 2.67
1731 2423 9.944663 GCACCTCGTTAATTAATCAATCAATTA 57.055 29.630 0.31 0.00 0.00 1.40
1786 2478 1.739035 GCATAACTGCCACACGAGCTA 60.739 52.381 0.00 0.00 42.88 3.32
1795 2487 0.522180 CACACGAGCTAGGAGACGTT 59.478 55.000 0.00 0.00 36.86 3.99
1809 2501 0.914551 GACGTTGGATCACGATCACG 59.085 55.000 12.06 14.72 43.15 4.35
1825 2517 2.100797 CGCGATCGAACCGGTACA 59.899 61.111 21.57 0.00 38.10 2.90
1859 2552 1.848886 AAACAGATCGGACCCCACCC 61.849 60.000 0.00 0.00 0.00 4.61
1861 2554 1.075525 CAGATCGGACCCCACCCTA 60.076 63.158 0.00 0.00 0.00 3.53
1881 2574 5.501156 CCTAAGGAGAAAACCAATAGTGCT 58.499 41.667 0.00 0.00 0.00 4.40
1891 2584 3.725634 ACCAATAGTGCTACCCTCTCTT 58.274 45.455 0.00 0.00 0.00 2.85
1893 2586 3.243569 CCAATAGTGCTACCCTCTCTTCG 60.244 52.174 0.00 0.00 0.00 3.79
1896 2589 0.179124 GTGCTACCCTCTCTTCGCTG 60.179 60.000 0.00 0.00 0.00 5.18
1917 2610 0.601311 CCTCGCTTCGATCCCCATTC 60.601 60.000 0.00 0.00 34.61 2.67
1918 2611 0.601311 CTCGCTTCGATCCCCATTCC 60.601 60.000 0.00 0.00 34.61 3.01
1921 2614 0.181350 GCTTCGATCCCCATTCCAGT 59.819 55.000 0.00 0.00 0.00 4.00
1924 2617 1.595382 CGATCCCCATTCCAGTCGC 60.595 63.158 0.00 0.00 0.00 5.19
1996 2689 4.477119 GGAGGCTCCTACCCCCGT 62.477 72.222 26.44 0.00 32.53 5.28
2043 2736 4.825679 CTCCCCCTCCACCTCCCC 62.826 77.778 0.00 0.00 0.00 4.81
2048 2741 2.689034 CCTCCACCTCCCCAGACC 60.689 72.222 0.00 0.00 0.00 3.85
2057 2750 0.995024 CTCCCCAGACCAGGTCAATT 59.005 55.000 22.31 0.00 34.60 2.32
2059 2752 1.075374 TCCCCAGACCAGGTCAATTTG 59.925 52.381 22.31 10.72 34.60 2.32
2060 2753 0.890683 CCCAGACCAGGTCAATTTGC 59.109 55.000 22.31 0.00 34.60 3.68
2061 2754 0.523072 CCAGACCAGGTCAATTTGCG 59.477 55.000 22.31 2.17 34.60 4.85
2062 2755 0.109597 CAGACCAGGTCAATTTGCGC 60.110 55.000 22.31 0.00 34.60 6.09
2063 2756 1.212751 GACCAGGTCAATTTGCGCC 59.787 57.895 15.43 0.00 32.09 6.53
2064 2757 2.179018 CCAGGTCAATTTGCGCCG 59.821 61.111 4.18 0.00 0.00 6.46
2065 2758 2.504681 CAGGTCAATTTGCGCCGC 60.505 61.111 4.18 0.00 0.00 6.53
2066 2759 3.747976 AGGTCAATTTGCGCCGCC 61.748 61.111 6.63 0.00 0.00 6.13
2067 2760 4.794439 GGTCAATTTGCGCCGCCC 62.794 66.667 6.63 0.00 0.00 6.13
2068 2761 4.794439 GTCAATTTGCGCCGCCCC 62.794 66.667 6.63 0.00 0.00 5.80
2070 2763 4.067913 CAATTTGCGCCGCCCCTT 62.068 61.111 6.63 0.00 0.00 3.95
2071 2764 3.758931 AATTTGCGCCGCCCCTTC 61.759 61.111 6.63 0.00 0.00 3.46
2072 2765 4.740822 ATTTGCGCCGCCCCTTCT 62.741 61.111 6.63 0.00 0.00 2.85
2073 2766 2.830186 AATTTGCGCCGCCCCTTCTA 62.830 55.000 6.63 0.00 0.00 2.10
2074 2767 4.770874 TTGCGCCGCCCCTTCTAC 62.771 66.667 6.63 0.00 0.00 2.59
2077 2770 4.222847 CGCCGCCCCTTCTACCTC 62.223 72.222 0.00 0.00 0.00 3.85
2078 2771 3.862991 GCCGCCCCTTCTACCTCC 61.863 72.222 0.00 0.00 0.00 4.30
2079 2772 2.041819 CCGCCCCTTCTACCTCCT 60.042 66.667 0.00 0.00 0.00 3.69
2080 2773 2.435693 CCGCCCCTTCTACCTCCTG 61.436 68.421 0.00 0.00 0.00 3.86
2081 2774 2.911928 GCCCCTTCTACCTCCTGC 59.088 66.667 0.00 0.00 0.00 4.85
2147 2840 3.489277 GACGTTGTCCGGTGTCCGT 62.489 63.158 0.00 6.52 46.80 4.69
2149 2842 2.732094 GTTGTCCGGTGTCCGTCG 60.732 66.667 0.00 0.00 46.80 5.12
2163 2856 4.309950 GTCGTGGACTGGCCCGTT 62.310 66.667 0.00 0.00 34.97 4.44
2210 2903 1.593265 CCAGACCAGGCCAATTTGC 59.407 57.895 5.01 0.00 0.00 3.68
2211 2904 0.901580 CCAGACCAGGCCAATTTGCT 60.902 55.000 5.01 0.00 0.00 3.91
2221 2914 1.512694 CAATTTGCTTCGCCCCCTC 59.487 57.895 0.00 0.00 0.00 4.30
2222 2915 0.967380 CAATTTGCTTCGCCCCCTCT 60.967 55.000 0.00 0.00 0.00 3.69
2223 2916 0.623723 AATTTGCTTCGCCCCCTCTA 59.376 50.000 0.00 0.00 0.00 2.43
2224 2917 0.107165 ATTTGCTTCGCCCCCTCTAC 60.107 55.000 0.00 0.00 0.00 2.59
2225 2918 2.193087 TTTGCTTCGCCCCCTCTACC 62.193 60.000 0.00 0.00 0.00 3.18
2226 2919 2.764547 GCTTCGCCCCCTCTACCT 60.765 66.667 0.00 0.00 0.00 3.08
2227 2920 1.457079 GCTTCGCCCCCTCTACCTA 60.457 63.158 0.00 0.00 0.00 3.08
2228 2921 1.746322 GCTTCGCCCCCTCTACCTAC 61.746 65.000 0.00 0.00 0.00 3.18
2229 2922 0.106116 CTTCGCCCCCTCTACCTACT 60.106 60.000 0.00 0.00 0.00 2.57
2230 2923 0.396695 TTCGCCCCCTCTACCTACTG 60.397 60.000 0.00 0.00 0.00 2.74
2231 2924 2.499827 CGCCCCCTCTACCTACTGC 61.500 68.421 0.00 0.00 0.00 4.40
2232 2925 2.499827 GCCCCCTCTACCTACTGCG 61.500 68.421 0.00 0.00 0.00 5.18
2233 2926 1.229359 CCCCCTCTACCTACTGCGA 59.771 63.158 0.00 0.00 0.00 5.10
2234 2927 0.824182 CCCCCTCTACCTACTGCGAG 60.824 65.000 0.00 0.00 0.00 5.03
2235 2928 1.457009 CCCCTCTACCTACTGCGAGC 61.457 65.000 0.00 0.00 0.00 5.03
2236 2929 1.457009 CCCTCTACCTACTGCGAGCC 61.457 65.000 0.00 0.00 0.00 4.70
2237 2930 1.649815 CTCTACCTACTGCGAGCCG 59.350 63.158 0.00 0.00 0.00 5.52
2253 2946 3.803082 CGCCACGAGCCAACCATG 61.803 66.667 0.00 0.00 38.78 3.66
2254 2947 4.120331 GCCACGAGCCAACCATGC 62.120 66.667 0.00 0.00 34.35 4.06
2255 2948 3.803082 CCACGAGCCAACCATGCG 61.803 66.667 0.00 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 4.373116 GACGTTGAGGCGCTCCCA 62.373 66.667 7.64 0.00 35.39 4.37
344 348 2.416432 GCTCCGAGACGTAGGGCTT 61.416 63.158 0.00 0.00 0.00 4.35
395 399 1.969589 GTTGGCACCCCCTGTAACG 60.970 63.158 0.00 0.00 0.00 3.18
489 501 1.142262 ACCAGTAACGGCCTGTCTTTT 59.858 47.619 0.00 0.00 0.00 2.27
601 615 5.983720 CGACCATATAAAGAACCATTCGACT 59.016 40.000 0.00 0.00 34.02 4.18
607 621 6.479972 TCACTCGACCATATAAAGAACCAT 57.520 37.500 0.00 0.00 0.00 3.55
678 692 0.599558 CCCAACCAAGACGTCGAGTA 59.400 55.000 10.46 0.00 0.00 2.59
687 701 0.979665 CAGAGAGAGCCCAACCAAGA 59.020 55.000 0.00 0.00 0.00 3.02
699 713 4.281182 GGTACTCAAAGGACAACAGAGAGA 59.719 45.833 0.00 0.00 0.00 3.10
720 735 5.185828 GGGTCATTATCAAAGAAGCAAAGGT 59.814 40.000 0.00 0.00 0.00 3.50
721 736 5.420104 AGGGTCATTATCAAAGAAGCAAAGG 59.580 40.000 0.00 0.00 0.00 3.11
747 762 4.704403 AGGCCTGATCTATAAGCCCTATT 58.296 43.478 3.11 0.00 45.00 1.73
761 776 1.485210 GGGTAGGGTCATAGGCCTGAT 60.485 57.143 17.99 1.82 0.00 2.90
782 797 4.482990 TGGCTGATGATGACATAGACCTA 58.517 43.478 0.00 0.00 36.82 3.08
864 879 0.034380 GCTAACCCTCAAACCCCCTC 60.034 60.000 0.00 0.00 0.00 4.30
880 895 9.109533 GAATTTAAAGTTTTCAATCGAACGCTA 57.890 29.630 0.00 0.00 0.00 4.26
883 898 8.953990 ACAGAATTTAAAGTTTTCAATCGAACG 58.046 29.630 0.00 0.00 0.00 3.95
887 902 8.003784 GGCAACAGAATTTAAAGTTTTCAATCG 58.996 33.333 0.00 0.00 0.00 3.34
914 929 3.738830 AACACTAACGCTACCTCACAA 57.261 42.857 0.00 0.00 0.00 3.33
972 1632 1.584380 CTTCAAGAGGTGCTGCTGCC 61.584 60.000 13.47 3.35 38.71 4.85
984 1644 3.867600 GCCTCATTGTCTCTGCTTCAAGA 60.868 47.826 0.00 0.00 0.00 3.02
1024 1684 1.005097 TGCAGTGATGGAAGCCAAGAT 59.995 47.619 0.00 0.00 36.95 2.40
1041 1701 0.883370 GGCTCATGATCATCGCTGCA 60.883 55.000 20.10 0.00 0.00 4.41
1105 1765 3.515286 CTCCTCGACGCCGCCTAA 61.515 66.667 0.00 0.00 35.37 2.69
1154 1814 4.853142 TCCTCCGCGGGTATGCCT 62.853 66.667 27.83 0.00 34.45 4.75
1314 1974 7.397761 GGAATGGTAGTACCTGCTAGATAAGAT 59.602 40.741 20.07 0.00 39.58 2.40
1315 1975 6.720288 GGAATGGTAGTACCTGCTAGATAAGA 59.280 42.308 20.07 0.00 39.58 2.10
1325 1985 5.930135 AGCAAATAGGAATGGTAGTACCTG 58.070 41.667 20.07 7.82 39.58 4.00
1335 1995 2.363359 GCCAGGGAAGCAAATAGGAATG 59.637 50.000 0.00 0.00 0.00 2.67
1357 2017 4.099419 TCATAATCTCCACGCAGCTTCTTA 59.901 41.667 0.00 0.00 0.00 2.10
1394 2074 5.758784 TCACGTCCAACAACACAAATACATA 59.241 36.000 0.00 0.00 0.00 2.29
1412 2092 1.405821 AGACCGGAGAATCATCACGTC 59.594 52.381 9.46 0.00 36.25 4.34
1414 2094 2.586258 AAGACCGGAGAATCATCACG 57.414 50.000 9.46 0.00 36.25 4.35
1415 2095 6.750148 ACTATTAAGACCGGAGAATCATCAC 58.250 40.000 9.46 0.00 36.25 3.06
1416 2096 6.978674 ACTATTAAGACCGGAGAATCATCA 57.021 37.500 9.46 0.00 36.25 3.07
1417 2097 9.930693 AATTACTATTAAGACCGGAGAATCATC 57.069 33.333 9.46 0.00 36.25 2.92
1434 2114 8.306761 CACCAGCCAAGAAGAAAAATTACTATT 58.693 33.333 0.00 0.00 0.00 1.73
1437 2117 5.598417 ACACCAGCCAAGAAGAAAAATTACT 59.402 36.000 0.00 0.00 0.00 2.24
1450 2130 2.746269 CACAATGAAACACCAGCCAAG 58.254 47.619 0.00 0.00 0.00 3.61
1476 2156 1.400737 AGGAAACGGTAGAGCGCTAT 58.599 50.000 11.50 10.93 0.00 2.97
1477 2157 1.180029 AAGGAAACGGTAGAGCGCTA 58.820 50.000 11.50 0.00 0.00 4.26
1478 2158 1.134560 CTAAGGAAACGGTAGAGCGCT 59.865 52.381 11.27 11.27 0.00 5.92
1479 2159 1.557651 CTAAGGAAACGGTAGAGCGC 58.442 55.000 0.00 0.00 0.00 5.92
1480 2160 1.557651 GCTAAGGAAACGGTAGAGCG 58.442 55.000 0.00 0.00 0.00 5.03
1481 2161 1.481363 AGGCTAAGGAAACGGTAGAGC 59.519 52.381 0.00 0.00 0.00 4.09
1482 2162 3.056035 ACAAGGCTAAGGAAACGGTAGAG 60.056 47.826 0.00 0.00 0.00 2.43
1483 2163 2.901839 ACAAGGCTAAGGAAACGGTAGA 59.098 45.455 0.00 0.00 0.00 2.59
1484 2164 3.259902 GACAAGGCTAAGGAAACGGTAG 58.740 50.000 0.00 0.00 0.00 3.18
1485 2165 2.633967 TGACAAGGCTAAGGAAACGGTA 59.366 45.455 0.00 0.00 0.00 4.02
1486 2166 1.418637 TGACAAGGCTAAGGAAACGGT 59.581 47.619 0.00 0.00 0.00 4.83
1487 2167 2.076863 CTGACAAGGCTAAGGAAACGG 58.923 52.381 0.00 0.00 0.00 4.44
1489 2169 3.477530 ACACTGACAAGGCTAAGGAAAC 58.522 45.455 0.00 0.00 0.00 2.78
1490 2170 3.857157 ACACTGACAAGGCTAAGGAAA 57.143 42.857 0.00 0.00 0.00 3.13
1492 2172 3.857157 AAACACTGACAAGGCTAAGGA 57.143 42.857 0.00 0.00 0.00 3.36
1493 2173 3.432252 CGTAAACACTGACAAGGCTAAGG 59.568 47.826 0.00 0.00 0.00 2.69
1494 2174 4.056050 ACGTAAACACTGACAAGGCTAAG 58.944 43.478 0.00 0.00 0.00 2.18
1497 2177 2.159014 TCACGTAAACACTGACAAGGCT 60.159 45.455 0.00 0.00 0.00 4.58
1498 2178 2.033151 GTCACGTAAACACTGACAAGGC 60.033 50.000 0.00 0.00 35.39 4.35
1499 2179 3.454375 AGTCACGTAAACACTGACAAGG 58.546 45.455 9.43 0.00 37.39 3.61
1505 2186 8.732413 TTATAGTACAAGTCACGTAAACACTG 57.268 34.615 0.00 0.00 0.00 3.66
1506 2187 9.565213 GATTATAGTACAAGTCACGTAAACACT 57.435 33.333 0.00 0.00 0.00 3.55
1542 2223 8.618702 TTTCAGGGTAATACACGTTTCATTTA 57.381 30.769 0.00 0.00 0.00 1.40
1545 2226 7.513371 TTTTTCAGGGTAATACACGTTTCAT 57.487 32.000 0.00 0.00 0.00 2.57
1546 2227 6.939132 TTTTTCAGGGTAATACACGTTTCA 57.061 33.333 0.00 0.00 0.00 2.69
1579 2260 2.892852 ACACATCATTGTTCCCACAAGG 59.107 45.455 0.00 0.00 46.25 3.61
1580 2261 4.589216 AACACATCATTGTTCCCACAAG 57.411 40.909 0.00 0.00 46.25 3.16
1586 2274 5.389859 TCATCCAAACACATCATTGTTCC 57.610 39.130 0.00 0.00 38.82 3.62
1594 2282 8.309163 TGCTTAAAAATTCATCCAAACACATC 57.691 30.769 0.00 0.00 0.00 3.06
1705 2397 8.856490 AATTGATTGATTAATTAACGAGGTGC 57.144 30.769 0.00 0.00 0.00 5.01
1731 2423 6.339730 TCGGTTACCACATACATATTTCGTT 58.660 36.000 1.13 0.00 0.00 3.85
1732 2424 5.904941 TCGGTTACCACATACATATTTCGT 58.095 37.500 1.13 0.00 0.00 3.85
1733 2425 6.831727 TTCGGTTACCACATACATATTTCG 57.168 37.500 1.13 0.00 0.00 3.46
1769 2461 0.530744 CCTAGCTCGTGTGGCAGTTA 59.469 55.000 0.00 0.00 0.00 2.24
1786 2478 1.405821 GATCGTGATCCAACGTCTCCT 59.594 52.381 5.60 0.00 43.96 3.69
1809 2501 1.138047 CTGTGTACCGGTTCGATCGC 61.138 60.000 15.04 6.24 0.00 4.58
1835 2527 0.676782 GGGTCCGATCTGTTTGGGTG 60.677 60.000 0.00 0.00 0.00 4.61
1836 2528 1.683441 GGGTCCGATCTGTTTGGGT 59.317 57.895 0.00 0.00 0.00 4.51
1837 2529 1.077716 GGGGTCCGATCTGTTTGGG 60.078 63.158 0.00 0.00 0.00 4.12
1839 2531 0.676782 GGTGGGGTCCGATCTGTTTG 60.677 60.000 0.00 0.00 0.00 2.93
1840 2532 1.683441 GGTGGGGTCCGATCTGTTT 59.317 57.895 0.00 0.00 0.00 2.83
1859 2552 6.539103 GGTAGCACTATTGGTTTTCTCCTTAG 59.461 42.308 0.00 0.00 34.50 2.18
1861 2554 5.254115 GGTAGCACTATTGGTTTTCTCCTT 58.746 41.667 0.00 0.00 34.50 3.36
1881 2574 0.331954 AGGTCAGCGAAGAGAGGGTA 59.668 55.000 0.00 0.00 0.00 3.69
1891 2584 2.324332 GATCGAAGCGAGGTCAGCGA 62.324 60.000 0.00 0.00 39.91 4.93
1893 2586 1.590259 GGATCGAAGCGAGGTCAGC 60.590 63.158 0.00 0.00 39.91 4.26
1896 2589 1.749334 ATGGGGATCGAAGCGAGGTC 61.749 60.000 0.00 0.00 39.91 3.85
1940 2633 4.489771 GGGGAGCGACCATGGTGG 62.490 72.222 25.52 23.35 45.02 4.61
1976 2669 4.153330 GGGGTAGGAGCCTCCGGA 62.153 72.222 2.93 2.93 42.75 5.14
2017 2710 4.410400 GAGGGGGAGTGTTGGCGG 62.410 72.222 0.00 0.00 0.00 6.13
2043 2736 0.109597 GCGCAAATTGACCTGGTCTG 60.110 55.000 26.03 17.08 33.15 3.51
2048 2741 2.504681 GCGGCGCAAATTGACCTG 60.505 61.111 29.21 0.00 0.00 4.00
2057 2750 4.770874 GTAGAAGGGGCGGCGCAA 62.771 66.667 34.36 6.29 0.00 4.85
2060 2753 4.222847 GAGGTAGAAGGGGCGGCG 62.223 72.222 0.51 0.51 0.00 6.46
2061 2754 3.862991 GGAGGTAGAAGGGGCGGC 61.863 72.222 0.00 0.00 0.00 6.53
2062 2755 2.041819 AGGAGGTAGAAGGGGCGG 60.042 66.667 0.00 0.00 0.00 6.13
2063 2756 3.095347 GCAGGAGGTAGAAGGGGCG 62.095 68.421 0.00 0.00 0.00 6.13
2064 2757 2.911928 GCAGGAGGTAGAAGGGGC 59.088 66.667 0.00 0.00 0.00 5.80
2065 2758 3.095347 GCGCAGGAGGTAGAAGGGG 62.095 68.421 0.30 0.00 0.00 4.79
2066 2759 2.501610 GCGCAGGAGGTAGAAGGG 59.498 66.667 0.30 0.00 0.00 3.95
2067 2760 2.105128 CGCGCAGGAGGTAGAAGG 59.895 66.667 8.75 0.00 0.00 3.46
2068 2761 2.583593 GCGCGCAGGAGGTAGAAG 60.584 66.667 29.10 0.00 0.00 2.85
2069 2762 4.143333 GGCGCGCAGGAGGTAGAA 62.143 66.667 34.42 0.00 0.00 2.10
2109 2802 2.054140 CTCGTCCTCTGGCTAGTCGC 62.054 65.000 0.00 0.00 38.13 5.19
2110 2803 1.440938 CCTCGTCCTCTGGCTAGTCG 61.441 65.000 0.00 0.00 0.00 4.18
2147 2840 4.308458 CAACGGGCCAGTCCACGA 62.308 66.667 9.62 0.00 36.21 4.35
2149 2842 2.358737 CTCAACGGGCCAGTCCAC 60.359 66.667 9.62 0.00 36.21 4.02
2161 2854 1.172812 GGGAGTGTTGGTGGCTCAAC 61.173 60.000 14.29 14.29 45.13 3.18
2163 2856 2.829384 GGGGAGTGTTGGTGGCTCA 61.829 63.158 0.00 0.00 0.00 4.26
2210 2903 0.106116 AGTAGGTAGAGGGGGCGAAG 60.106 60.000 0.00 0.00 0.00 3.79
2211 2904 0.396695 CAGTAGGTAGAGGGGGCGAA 60.397 60.000 0.00 0.00 0.00 4.70
2236 2929 3.803082 CATGGTTGGCTCGTGGCG 61.803 66.667 6.55 0.00 42.94 5.69
2237 2930 4.120331 GCATGGTTGGCTCGTGGC 62.120 66.667 3.80 3.80 40.90 5.01
2238 2931 3.803082 CGCATGGTTGGCTCGTGG 61.803 66.667 0.00 0.00 0.00 4.94
2239 2932 4.465512 GCGCATGGTTGGCTCGTG 62.466 66.667 0.30 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.