Multiple sequence alignment - TraesCS3B01G436900

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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 TraesCS3B01G436900 chr3B 100.000 3819 0 0 1 3819 675283266 675279448 0.000000e+00 7053.0
1 TraesCS3B01G436900 chr3D 90.287 2090 105 38 1 2019 512708819 512706757 0.000000e+00 2645.0
2 TraesCS3B01G436900 chr3D 92.735 1817 82 24 2024 3817 512706702 512704913 0.000000e+00 2579.0
3 TraesCS3B01G436900 chr3A 90.437 1830 77 45 2021 3808 648311175 648309402 0.000000e+00 2320.0
4 TraesCS3B01G436900 chr3A 86.465 1980 108 63 160 2019 648313164 648311225 0.000000e+00 2025.0
5 TraesCS3B01G436900 chr1D 92.776 263 15 4 1346 1606 355698587 355698327 1.000000e-100 377.0
6 TraesCS3B01G436900 chr1D 91.429 175 14 1 1082 1255 355698831 355698657 4.930000e-59 239.0
7 TraesCS3B01G436900 chr1A 92.776 263 15 4 1346 1606 456323326 456323066 1.000000e-100 377.0
8 TraesCS3B01G436900 chr1A 90.857 175 15 1 1082 1255 456323587 456323413 2.290000e-57 233.0
9 TraesCS3B01G436900 chr1B 92.395 263 16 4 1346 1606 478583492 478583232 4.660000e-99 372.0
10 TraesCS3B01G436900 chr1B 92.000 175 13 1 1082 1255 478583757 478583583 1.060000e-60 244.0
11 TraesCS3B01G436900 chr7D 86.429 280 33 4 1346 1621 401093668 401093390 6.200000e-78 302.0
12 TraesCS3B01G436900 chr7D 88.415 164 15 4 1096 1258 401094034 401093874 1.080000e-45 195.0
13 TraesCS3B01G436900 chr7D 86.486 74 6 4 1110 1181 34151675 34151604 1.140000e-10 78.7
14 TraesCS3B01G436900 chr7A 86.429 280 33 4 1346 1621 458934572 458934294 6.200000e-78 302.0
15 TraesCS3B01G436900 chr7A 88.415 164 15 4 1096 1258 458934934 458934774 1.080000e-45 195.0
16 TraesCS3B01G436900 chr7B 85.714 280 35 4 1346 1621 410620575 410620297 1.340000e-74 291.0
17 TraesCS3B01G436900 chr7B 87.805 164 16 4 1096 1258 410620942 410620782 5.040000e-44 189.0
18 TraesCS3B01G436900 chr5A 75.417 240 47 10 1360 1590 666525277 666525041 5.220000e-19 106.0
19 TraesCS3B01G436900 chr5A 77.686 121 27 0 36 156 423039539 423039419 1.470000e-09 75.0
20 TraesCS3B01G436900 chr5B 79.339 121 24 1 36 156 377311315 377311196 2.440000e-12 84.2
21 TraesCS3B01G436900 chr2D 78.070 114 21 3 26 137 398690821 398690932 6.850000e-08 69.4
22 TraesCS3B01G436900 chr5D 76.515 132 26 5 33 161 324906048 324905919 2.460000e-07 67.6


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 TraesCS3B01G436900 chr3B 675279448 675283266 3818 True 7053.0 7053 100.0000 1 3819 1 chr3B.!!$R1 3818
1 TraesCS3B01G436900 chr3D 512704913 512708819 3906 True 2612.0 2645 91.5110 1 3817 2 chr3D.!!$R1 3816
2 TraesCS3B01G436900 chr3A 648309402 648313164 3762 True 2172.5 2320 88.4510 160 3808 2 chr3A.!!$R1 3648
3 TraesCS3B01G436900 chr1D 355698327 355698831 504 True 308.0 377 92.1025 1082 1606 2 chr1D.!!$R1 524
4 TraesCS3B01G436900 chr1A 456323066 456323587 521 True 305.0 377 91.8165 1082 1606 2 chr1A.!!$R1 524
5 TraesCS3B01G436900 chr1B 478583232 478583757 525 True 308.0 372 92.1975 1082 1606 2 chr1B.!!$R1 524
6 TraesCS3B01G436900 chr7D 401093390 401094034 644 True 248.5 302 87.4220 1096 1621 2 chr7D.!!$R2 525
7 TraesCS3B01G436900 chr7A 458934294 458934934 640 True 248.5 302 87.4220 1096 1621 2 chr7A.!!$R1 525
8 TraesCS3B01G436900 chr7B 410620297 410620942 645 True 240.0 291 86.7595 1096 1621 2 chr7B.!!$R1 525

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
766 838 0.248289 TCACGCTAGGTAAAGCCACC 59.752 55.0 0.00 0.0 39.43 4.61 F
2058 2410 0.109179 TCGCATGCCACATTTGCTTC 60.109 50.0 13.15 0.0 34.23 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2573 0.109342 CCCTTGTCTGTTGTCCTGCT 59.891 55.0 0.0 0.0 0.00 4.24 R
3476 3858 0.034059 AAGAGAACACAGTGCTCCCG 59.966 55.0 0.0 0.0 38.94 5.14 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
34 35 0.772124 AAGCCAAAGAGTCCCCTCCA 60.772 55.000 0.00 0.00 38.58 3.86
82 83 7.504574 ACCATTTGATGATCAAGCATAGATTCA 59.495 33.333 8.01 0.00 37.70 2.57
83 84 8.523658 CCATTTGATGATCAAGCATAGATTCAT 58.476 33.333 8.01 0.00 37.70 2.57
134 143 4.526650 CCCAAGGCTTTTAGGTTTACACAT 59.473 41.667 0.00 0.00 0.00 3.21
232 241 5.163163 TGGACTTATGGAGATGCTAGCAAAT 60.163 40.000 23.54 13.40 0.00 2.32
233 242 5.180868 GGACTTATGGAGATGCTAGCAAATG 59.819 44.000 23.54 7.08 0.00 2.32
234 243 5.933617 ACTTATGGAGATGCTAGCAAATGA 58.066 37.500 23.54 5.38 0.00 2.57
248 265 3.057315 AGCAAATGACAATGCCACACTAC 60.057 43.478 11.69 0.00 43.57 2.73
258 275 7.094975 TGACAATGCCACACTACAGTTATTTAC 60.095 37.037 0.00 0.00 0.00 2.01
277 294 6.528537 TTTACGCCAGTAGAGTAATAACCA 57.471 37.500 0.00 0.00 33.87 3.67
283 301 5.462398 GCCAGTAGAGTAATAACCACATTCG 59.538 44.000 0.00 0.00 0.00 3.34
331 349 5.302568 TGGTGCAACATGAGAAGAAGAAAAT 59.697 36.000 0.00 0.00 39.98 1.82
332 350 5.632347 GGTGCAACATGAGAAGAAGAAAATG 59.368 40.000 0.00 0.00 39.98 2.32
333 351 5.118203 GTGCAACATGAGAAGAAGAAAATGC 59.882 40.000 0.00 0.00 36.32 3.56
334 352 5.221283 TGCAACATGAGAAGAAGAAAATGCA 60.221 36.000 0.00 0.00 36.65 3.96
340 367 2.746362 AGAAGAAGAAAATGCAGCGGAG 59.254 45.455 0.00 0.00 0.00 4.63
418 469 2.105128 CAAGAGAGTAGCCGGGCG 59.895 66.667 14.39 0.00 0.00 6.13
419 470 3.148279 AAGAGAGTAGCCGGGCGG 61.148 66.667 14.39 0.00 38.57 6.13
436 487 1.378646 GGGCCCAAGGAAGCTACAC 60.379 63.158 19.95 0.00 0.00 2.90
437 488 1.745489 GGCCCAAGGAAGCTACACG 60.745 63.158 0.00 0.00 0.00 4.49
440 491 1.439679 CCCAAGGAAGCTACACGAAC 58.560 55.000 0.00 0.00 0.00 3.95
468 519 2.653726 AGCCACCGCATTAATCAATGA 58.346 42.857 0.00 0.00 43.67 2.57
717 775 2.287373 CGTAGACTAGTGGTTAGAGCGG 59.713 54.545 0.00 0.00 33.39 5.52
736 794 4.227134 CAGTAGCAGCCGCCCGAT 62.227 66.667 0.00 0.00 39.83 4.18
766 838 0.248289 TCACGCTAGGTAAAGCCACC 59.752 55.000 0.00 0.00 39.43 4.61
772 844 2.224305 GCTAGGTAAAGCCACCATCGAT 60.224 50.000 0.00 0.00 41.40 3.59
790 862 5.801350 TCGATTAATCCTTGTGCTTTCTG 57.199 39.130 9.87 0.00 0.00 3.02
803 875 9.376075 CCTTGTGCTTTCTGATCGATATATATT 57.624 33.333 0.00 0.00 0.00 1.28
805 877 8.189709 TGTGCTTTCTGATCGATATATATTGC 57.810 34.615 0.00 0.00 0.00 3.56
806 878 7.278646 TGTGCTTTCTGATCGATATATATTGCC 59.721 37.037 0.00 1.44 0.00 4.52
807 879 6.763135 TGCTTTCTGATCGATATATATTGCCC 59.237 38.462 0.00 1.14 0.00 5.36
809 881 6.806668 TTCTGATCGATATATATTGCCCCA 57.193 37.500 0.00 3.01 0.00 4.96
810 882 6.410942 TCTGATCGATATATATTGCCCCAG 57.589 41.667 0.00 10.66 0.00 4.45
812 884 6.040955 TCTGATCGATATATATTGCCCCAGAC 59.959 42.308 16.46 0.00 0.00 3.51
814 886 5.339008 TCGATATATATTGCCCCAGACAC 57.661 43.478 5.20 0.00 0.00 3.67
829 901 4.656112 CCCAGACACCACTAATCTTATCCT 59.344 45.833 0.00 0.00 0.00 3.24
1067 1156 2.345991 GGGAGCTGGCGTGTGTAA 59.654 61.111 0.00 0.00 0.00 2.41
1071 1160 2.561569 GGAGCTGGCGTGTGTAATATT 58.438 47.619 0.00 0.00 0.00 1.28
1167 1256 2.034053 GGAGCTGATCGAGTTCTACCTG 59.966 54.545 0.00 0.00 32.59 4.00
1353 1600 4.569023 CCGGCGATCGCAGCACTA 62.569 66.667 38.00 0.00 44.11 2.74
1648 1898 9.699410 ATTCTAGCTATATTCTAGCATCTCACT 57.301 33.333 6.98 0.00 42.68 3.41
1671 1921 4.284490 TGAAATTCCCCTCCTGATCTATCG 59.716 45.833 0.00 0.00 0.00 2.92
1677 1927 3.308760 CCCCTCCTGATCTATCGATCTGA 60.309 52.174 13.61 1.91 45.10 3.27
1688 1938 6.190954 TCTATCGATCTGAACAAGAAACGA 57.809 37.500 0.00 0.00 45.07 3.85
1691 1944 2.989840 CGATCTGAACAAGAAACGAGCT 59.010 45.455 0.00 0.00 39.49 4.09
1694 1947 2.158957 TCTGAACAAGAAACGAGCTGGT 60.159 45.455 0.00 0.00 29.54 4.00
1695 1948 2.614057 CTGAACAAGAAACGAGCTGGTT 59.386 45.455 8.47 8.47 32.34 3.67
1697 1950 4.193090 TGAACAAGAAACGAGCTGGTTTA 58.807 39.130 24.41 6.71 40.05 2.01
1699 1952 4.547406 ACAAGAAACGAGCTGGTTTAAC 57.453 40.909 24.41 14.33 40.05 2.01
1704 1957 7.012989 ACAAGAAACGAGCTGGTTTAACTAATT 59.987 33.333 24.41 11.14 40.05 1.40
1726 1979 8.947055 AATTTGCAGGTAATTTAATTAGCAGG 57.053 30.769 23.21 17.02 43.67 4.85
1727 1980 7.475137 TTTGCAGGTAATTTAATTAGCAGGT 57.525 32.000 23.21 5.73 43.67 4.00
1747 2000 4.042934 AGGTATGAACTAGGGTTTGTGCTT 59.957 41.667 0.00 0.00 35.58 3.91
1755 2008 1.008538 GGTTTGTGCTTCGCCTGTG 60.009 57.895 0.00 0.00 0.00 3.66
1756 2009 1.724582 GGTTTGTGCTTCGCCTGTGT 61.725 55.000 0.00 0.00 0.00 3.72
1773 2040 5.120830 GCCTGTGTACTAGTTCTTTGATGTG 59.879 44.000 0.00 0.00 0.00 3.21
1776 2043 5.071250 TGTGTACTAGTTCTTTGATGTGGGT 59.929 40.000 0.00 0.00 0.00 4.51
1779 2046 7.117379 GTGTACTAGTTCTTTGATGTGGGTTAC 59.883 40.741 0.00 0.00 0.00 2.50
1790 2057 7.604657 TTGATGTGGGTTACTACCAATTTTT 57.395 32.000 0.00 0.00 46.96 1.94
1814 2081 7.903995 TGGGCATCTAATTTTCAAATTGTTC 57.096 32.000 7.63 0.00 38.90 3.18
1816 2083 7.603404 TGGGCATCTAATTTTCAAATTGTTCTG 59.397 33.333 7.63 2.55 38.90 3.02
1825 2102 7.712264 TTTTCAAATTGTTCTGCTTATGGTG 57.288 32.000 0.00 0.00 0.00 4.17
1826 2103 4.808558 TCAAATTGTTCTGCTTATGGTGC 58.191 39.130 0.00 0.00 0.00 5.01
1841 2118 0.451783 GGTGCATACGCCTTTTCAGG 59.548 55.000 0.00 0.00 43.60 3.86
1845 2122 1.398390 GCATACGCCTTTTCAGGTCTG 59.602 52.381 0.00 0.00 43.18 3.51
1851 2128 1.683385 GCCTTTTCAGGTCTGCAAGTT 59.317 47.619 0.00 0.00 43.18 2.66
1853 2130 3.317993 GCCTTTTCAGGTCTGCAAGTTAA 59.682 43.478 0.00 0.00 43.18 2.01
1854 2131 4.021981 GCCTTTTCAGGTCTGCAAGTTAAT 60.022 41.667 0.00 0.00 43.18 1.40
1855 2132 5.703876 CCTTTTCAGGTCTGCAAGTTAATC 58.296 41.667 0.00 0.00 35.06 1.75
1883 2163 6.765915 AGGGCTTCAATCTTTTGTATCTTC 57.234 37.500 0.00 0.00 34.32 2.87
1893 2176 5.869579 TCTTTTGTATCTTCTCTTGCACCT 58.130 37.500 0.00 0.00 0.00 4.00
1896 2179 4.623932 TGTATCTTCTCTTGCACCTTGT 57.376 40.909 0.00 0.00 0.00 3.16
1902 2185 2.997980 TCTCTTGCACCTTGTTGTTCA 58.002 42.857 0.00 0.00 0.00 3.18
1911 2194 2.964464 ACCTTGTTGTTCATGCCATGAA 59.036 40.909 15.94 15.94 46.30 2.57
1921 2204 4.310357 TCATGCCATGAACAACATATGC 57.690 40.909 4.55 0.00 37.46 3.14
1930 2215 6.183360 CCATGAACAACATATGCACAACCTAT 60.183 38.462 1.58 0.00 37.46 2.57
1950 2235 3.667497 TGCACTCGATTGGATATCTCC 57.333 47.619 4.82 0.00 42.45 3.71
1957 2242 5.890985 ACTCGATTGGATATCTCCCTAGATG 59.109 44.000 2.05 0.00 42.60 2.90
1982 2272 5.557576 AGCTAGCATCTGGAACATATGAA 57.442 39.130 18.83 0.00 44.32 2.57
1988 2284 5.104193 AGCATCTGGAACATATGAAGAACCT 60.104 40.000 10.38 5.05 44.32 3.50
1989 2285 6.100279 AGCATCTGGAACATATGAAGAACCTA 59.900 38.462 10.38 0.00 44.32 3.08
2012 2308 9.278011 CCTATAGAATTCCATCCTAGATTCCTT 57.722 37.037 0.00 0.00 0.00 3.36
2016 2312 8.574309 AGAATTCCATCCTAGATTCCTTAACT 57.426 34.615 0.65 0.00 0.00 2.24
2019 2315 9.634021 AATTCCATCCTAGATTCCTTAACTTTC 57.366 33.333 0.00 0.00 0.00 2.62
2020 2316 7.749377 TCCATCCTAGATTCCTTAACTTTCA 57.251 36.000 0.00 0.00 0.00 2.69
2021 2317 7.796054 TCCATCCTAGATTCCTTAACTTTCAG 58.204 38.462 0.00 0.00 0.00 3.02
2022 2318 6.484977 CCATCCTAGATTCCTTAACTTTCAGC 59.515 42.308 0.00 0.00 0.00 4.26
2054 2406 2.350899 TTCTTCGCATGCCACATTTG 57.649 45.000 13.15 0.00 0.00 2.32
2058 2410 0.109179 TCGCATGCCACATTTGCTTC 60.109 50.000 13.15 0.00 34.23 3.86
2069 2426 3.309138 CACATTTGCTTCTCGATCCTCAG 59.691 47.826 0.00 0.00 0.00 3.35
2070 2427 3.055530 ACATTTGCTTCTCGATCCTCAGT 60.056 43.478 0.00 0.00 0.00 3.41
2071 2428 2.949451 TTGCTTCTCGATCCTCAGTC 57.051 50.000 0.00 0.00 0.00 3.51
2072 2429 1.107114 TGCTTCTCGATCCTCAGTCC 58.893 55.000 0.00 0.00 0.00 3.85
2074 2431 1.336755 GCTTCTCGATCCTCAGTCCTC 59.663 57.143 0.00 0.00 0.00 3.71
2075 2432 2.649190 CTTCTCGATCCTCAGTCCTCA 58.351 52.381 0.00 0.00 0.00 3.86
2076 2433 2.045561 TCTCGATCCTCAGTCCTCAC 57.954 55.000 0.00 0.00 0.00 3.51
2077 2434 0.660488 CTCGATCCTCAGTCCTCACG 59.340 60.000 0.00 0.00 0.00 4.35
2088 2447 0.806868 GTCCTCACGTACGTCCATGA 59.193 55.000 19.94 11.95 0.00 3.07
2089 2448 1.200716 GTCCTCACGTACGTCCATGAA 59.799 52.381 19.94 0.00 0.00 2.57
2090 2449 2.097036 TCCTCACGTACGTCCATGAAT 58.903 47.619 19.94 0.00 0.00 2.57
2091 2450 2.494471 TCCTCACGTACGTCCATGAATT 59.506 45.455 19.94 0.00 0.00 2.17
2092 2451 3.695556 TCCTCACGTACGTCCATGAATTA 59.304 43.478 19.94 0.00 0.00 1.40
2104 2463 5.516339 CGTCCATGAATTAAATTTGCAGACC 59.484 40.000 0.00 0.00 0.00 3.85
2281 2640 2.707849 GCCGACTCCGTCCAAGCTA 61.708 63.158 0.00 0.00 0.00 3.32
2284 2643 0.456312 CGACTCCGTCCAAGCTACAC 60.456 60.000 0.00 0.00 0.00 2.90
2290 2649 1.404315 CCGTCCAAGCTACACCTTCTC 60.404 57.143 0.00 0.00 0.00 2.87
2338 2700 1.884464 CATGACCGATCACGCCCAG 60.884 63.158 0.00 0.00 37.79 4.45
2422 2784 4.082679 GGCTCAATAGGATACCTACAGTCG 60.083 50.000 0.00 0.00 39.10 4.18
2427 2789 1.211457 AGGATACCTACAGTCGACCGT 59.789 52.381 13.01 11.26 28.47 4.83
2428 2790 2.019984 GGATACCTACAGTCGACCGTT 58.980 52.381 13.01 0.00 0.00 4.44
2807 3169 2.185867 GAGATTACGGTGGCGCCA 59.814 61.111 29.03 29.03 36.97 5.69
2838 3200 1.524849 GGATCAAGAGGGAAGCGCC 60.525 63.158 2.29 0.00 0.00 6.53
2881 3243 2.042259 GTGCATGGCTAGCTGTGCA 61.042 57.895 30.26 30.26 44.50 4.57
2882 3244 1.303480 TGCATGGCTAGCTGTGCAA 60.303 52.632 31.16 20.45 43.83 4.08
2883 3245 0.681887 TGCATGGCTAGCTGTGCAAT 60.682 50.000 31.16 10.13 43.83 3.56
2884 3246 0.458669 GCATGGCTAGCTGTGCAATT 59.541 50.000 28.03 0.74 37.52 2.32
2915 3288 0.613777 CTCCACCTTGTACACCTCCC 59.386 60.000 0.00 0.00 0.00 4.30
2919 3292 1.978580 CACCTTGTACACCTCCCTCTT 59.021 52.381 0.00 0.00 0.00 2.85
3003 3377 9.632638 ACAATTAGACCATTATAGCATTCTTGT 57.367 29.630 0.00 0.00 0.00 3.16
3008 3382 5.380043 ACCATTATAGCATTCTTGTCCAGG 58.620 41.667 0.00 0.00 0.00 4.45
3024 3398 8.125081 TCTTGTCCAGGTCCATATATAGATCAT 58.875 37.037 0.00 0.00 0.00 2.45
3034 3408 8.592809 GTCCATATATAGATCATCCCATCTTCC 58.407 40.741 0.00 0.00 34.75 3.46
3111 3492 9.860898 CTGATGAGTTCCATATAATAACATCGA 57.139 33.333 0.00 0.00 35.17 3.59
3133 3514 6.363357 TCGATCGATTTGACATGATACACATC 59.637 38.462 15.15 4.36 37.07 3.06
3269 3650 1.755395 GCCAGCTGCATGATTGGGA 60.755 57.895 8.66 0.00 40.77 4.37
3324 3706 4.919510 TGATTAGGAGAGAGAGAGAGGGAT 59.080 45.833 0.00 0.00 0.00 3.85
3360 3742 2.738480 GTGCTGTCGGGGTGTACA 59.262 61.111 0.00 0.00 0.00 2.90
3477 3859 2.295692 GCTCTCTGCATGTACAGCG 58.704 57.895 0.33 0.00 42.31 5.18
3497 3879 1.202698 GGGAGCACTGTGTTCTCTTGT 60.203 52.381 21.32 0.00 0.00 3.16
3503 3885 3.732212 CACTGTGTTCTCTTGTCATGGA 58.268 45.455 0.00 0.00 0.00 3.41
3506 3888 5.934043 CACTGTGTTCTCTTGTCATGGATTA 59.066 40.000 0.00 0.00 0.00 1.75
3525 3907 7.901029 TGGATTATTGGATTTTTGTTAGTGCA 58.099 30.769 0.00 0.00 0.00 4.57
3547 3933 5.047590 GCAATCATGGATTATTGGATGAGCA 60.048 40.000 6.90 0.00 34.37 4.26
3577 3972 2.736719 CGTGTCATGGACTCACTCATCC 60.737 54.545 0.00 0.00 33.15 3.51
3601 3996 1.256361 TGGATGGTACGTACGGCCAA 61.256 55.000 28.60 15.57 35.74 4.52
3606 4001 3.061231 TACGTACGGCCAAGCGGA 61.061 61.111 21.06 0.00 33.14 5.54
3610 4005 3.766691 TACGGCCAAGCGGAGTCC 61.767 66.667 2.24 0.00 33.14 3.85
3613 4008 4.785453 GGCCAAGCGGAGTCCCAG 62.785 72.222 2.80 0.00 0.00 4.45
3614 4009 4.021925 GCCAAGCGGAGTCCCAGT 62.022 66.667 2.80 0.00 0.00 4.00
3615 4010 2.750350 CCAAGCGGAGTCCCAGTT 59.250 61.111 2.80 0.00 0.00 3.16
3660 4056 2.447443 GGATGGAAAGGGAGGTGAAAC 58.553 52.381 0.00 0.00 0.00 2.78
3664 4060 1.314730 GAAAGGGAGGTGAAACGCAA 58.685 50.000 0.00 0.00 38.12 4.85
3665 4061 1.886542 GAAAGGGAGGTGAAACGCAAT 59.113 47.619 0.00 0.00 38.12 3.56
3704 4100 6.184789 GGGAGATAAGATACCTCCTGTCTAG 58.815 48.000 0.00 0.00 44.43 2.43
3714 4113 3.181448 ACCTCCTGTCTAGCTAGCTACTC 60.181 52.174 20.67 15.55 0.00 2.59
3743 4147 3.243873 TGCATGAGATCGATACCTTGGAC 60.244 47.826 0.00 0.00 0.00 4.02
3818 4222 8.972127 TGCTGATCTTGGTACTATATTAGATCC 58.028 37.037 13.17 3.52 38.01 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.020128 GTGGTGGAGGATCTTTAACACTCT 60.020 45.833 4.60 0.00 31.76 3.24
134 143 3.244422 ACGTCTGGTGAAATGGAAGCTTA 60.244 43.478 0.00 0.00 0.00 3.09
232 241 2.928801 ACTGTAGTGTGGCATTGTCA 57.071 45.000 0.00 0.00 0.00 3.58
233 242 5.880054 AATAACTGTAGTGTGGCATTGTC 57.120 39.130 0.00 0.00 0.00 3.18
234 243 6.128391 CGTAAATAACTGTAGTGTGGCATTGT 60.128 38.462 0.00 0.00 0.00 2.71
248 265 9.740239 TTATTACTCTACTGGCGTAAATAACTG 57.260 33.333 0.00 0.00 0.00 3.16
258 275 4.380841 TGTGGTTATTACTCTACTGGCG 57.619 45.455 0.00 0.00 0.00 5.69
277 294 6.889198 TCCTCCTTAATTTCATCTCGAATGT 58.111 36.000 7.24 0.00 32.32 2.71
331 349 3.838244 AATATAAGTTCCTCCGCTGCA 57.162 42.857 0.00 0.00 0.00 4.41
332 350 4.261197 CCAAAATATAAGTTCCTCCGCTGC 60.261 45.833 0.00 0.00 0.00 5.25
333 351 4.881850 ACCAAAATATAAGTTCCTCCGCTG 59.118 41.667 0.00 0.00 0.00 5.18
334 352 5.112129 ACCAAAATATAAGTTCCTCCGCT 57.888 39.130 0.00 0.00 0.00 5.52
418 469 1.378646 GTGTAGCTTCCTTGGGCCC 60.379 63.158 17.59 17.59 0.00 5.80
419 470 1.745489 CGTGTAGCTTCCTTGGGCC 60.745 63.158 0.00 0.00 0.00 5.80
420 471 0.321298 TTCGTGTAGCTTCCTTGGGC 60.321 55.000 0.00 0.00 0.00 5.36
421 472 1.002087 AGTTCGTGTAGCTTCCTTGGG 59.998 52.381 0.00 0.00 0.00 4.12
422 473 2.288825 TGAGTTCGTGTAGCTTCCTTGG 60.289 50.000 0.00 0.00 0.00 3.61
423 474 2.731976 GTGAGTTCGTGTAGCTTCCTTG 59.268 50.000 0.00 0.00 0.00 3.61
426 477 1.000506 TGGTGAGTTCGTGTAGCTTCC 59.999 52.381 0.00 0.00 0.00 3.46
429 480 2.755650 CTTTGGTGAGTTCGTGTAGCT 58.244 47.619 0.00 0.00 0.00 3.32
430 481 1.194772 GCTTTGGTGAGTTCGTGTAGC 59.805 52.381 0.00 0.00 0.00 3.58
431 482 1.798813 GGCTTTGGTGAGTTCGTGTAG 59.201 52.381 0.00 0.00 0.00 2.74
436 487 1.841663 CGGTGGCTTTGGTGAGTTCG 61.842 60.000 0.00 0.00 0.00 3.95
437 488 1.949257 CGGTGGCTTTGGTGAGTTC 59.051 57.895 0.00 0.00 0.00 3.01
440 491 1.526575 AATGCGGTGGCTTTGGTGAG 61.527 55.000 0.00 0.00 40.82 3.51
733 791 5.147865 CCTAGCGTGAGTATTAACTGATCG 58.852 45.833 0.00 0.00 35.56 3.69
734 792 6.074544 ACCTAGCGTGAGTATTAACTGATC 57.925 41.667 0.00 0.00 35.56 2.92
735 793 7.578310 TTACCTAGCGTGAGTATTAACTGAT 57.422 36.000 0.00 0.00 35.56 2.90
736 794 7.395190 TTTACCTAGCGTGAGTATTAACTGA 57.605 36.000 0.00 0.00 35.56 3.41
766 838 6.037500 TCAGAAAGCACAAGGATTAATCGATG 59.962 38.462 9.32 12.21 0.00 3.84
772 844 5.487433 TCGATCAGAAAGCACAAGGATTAA 58.513 37.500 0.00 0.00 0.00 1.40
790 862 5.986135 GTGTCTGGGGCAATATATATCGATC 59.014 44.000 0.00 0.00 0.00 3.69
803 875 0.618458 GATTAGTGGTGTCTGGGGCA 59.382 55.000 0.00 0.00 0.00 5.36
804 876 0.912486 AGATTAGTGGTGTCTGGGGC 59.088 55.000 0.00 0.00 0.00 5.80
805 877 4.202367 GGATAAGATTAGTGGTGTCTGGGG 60.202 50.000 0.00 0.00 0.00 4.96
806 878 4.656112 AGGATAAGATTAGTGGTGTCTGGG 59.344 45.833 0.00 0.00 0.00 4.45
807 879 5.878406 AGGATAAGATTAGTGGTGTCTGG 57.122 43.478 0.00 0.00 0.00 3.86
809 881 5.367060 GGGAAGGATAAGATTAGTGGTGTCT 59.633 44.000 0.00 0.00 0.00 3.41
810 882 5.454897 GGGGAAGGATAAGATTAGTGGTGTC 60.455 48.000 0.00 0.00 0.00 3.67
812 884 4.202472 GGGGGAAGGATAAGATTAGTGGTG 60.202 50.000 0.00 0.00 0.00 4.17
814 886 4.642466 GGGGGAAGGATAAGATTAGTGG 57.358 50.000 0.00 0.00 0.00 4.00
841 915 1.860950 CGTATGCAAGTGGAGAATCGG 59.139 52.381 0.00 0.00 34.37 4.18
875 950 2.742372 GCGAAAAGGAGCTCGGCA 60.742 61.111 7.83 0.00 35.60 5.69
980 1066 2.190578 CTCCTCCCCAATCCGCAC 59.809 66.667 0.00 0.00 0.00 5.34
985 1071 0.110104 CTCATGCCTCCTCCCCAATC 59.890 60.000 0.00 0.00 0.00 2.67
1063 1152 2.289195 CGCCGCCCTCCTTAATATTACA 60.289 50.000 0.00 0.00 0.00 2.41
1067 1156 1.677552 CCGCCGCCCTCCTTAATAT 59.322 57.895 0.00 0.00 0.00 1.28
1353 1600 3.391665 CTTCTCCCCAATCGCCGCT 62.392 63.158 0.00 0.00 0.00 5.52
1434 1681 4.789075 CAGTACCCCGACGCCGTG 62.789 72.222 0.00 0.00 0.00 4.94
1624 1874 8.325046 TCAGTGAGATGCTAGAATATAGCTAGA 58.675 37.037 8.43 0.00 40.95 2.43
1647 1897 5.568423 CGATAGATCAGGAGGGGAATTTCAG 60.568 48.000 0.00 0.00 39.76 3.02
1648 1898 4.284490 CGATAGATCAGGAGGGGAATTTCA 59.716 45.833 0.00 0.00 39.76 2.69
1671 1921 3.124297 CCAGCTCGTTTCTTGTTCAGATC 59.876 47.826 0.00 0.00 0.00 2.75
1677 1927 4.638865 AGTTAAACCAGCTCGTTTCTTGTT 59.361 37.500 12.96 0.00 37.20 2.83
1688 1938 4.832823 ACCTGCAAATTAGTTAAACCAGCT 59.167 37.500 0.00 0.00 0.00 4.24
1704 1957 8.629158 CATACCTGCTAATTAAATTACCTGCAA 58.371 33.333 0.00 0.00 0.00 4.08
1717 1970 6.576778 AACCCTAGTTCATACCTGCTAATT 57.423 37.500 0.00 0.00 0.00 1.40
1723 1976 3.689649 GCACAAACCCTAGTTCATACCTG 59.310 47.826 0.00 0.00 34.19 4.00
1726 1979 4.092968 CGAAGCACAAACCCTAGTTCATAC 59.907 45.833 0.00 0.00 34.19 2.39
1727 1980 4.250464 CGAAGCACAAACCCTAGTTCATA 58.750 43.478 0.00 0.00 34.19 2.15
1747 2000 3.570975 TCAAAGAACTAGTACACAGGCGA 59.429 43.478 0.00 0.00 0.00 5.54
1755 2008 7.384477 AGTAACCCACATCAAAGAACTAGTAC 58.616 38.462 0.00 0.00 0.00 2.73
1756 2009 7.549147 AGTAACCCACATCAAAGAACTAGTA 57.451 36.000 0.00 0.00 0.00 1.82
1790 2057 7.603404 CAGAACAATTTGAAAATTAGATGCCCA 59.397 33.333 2.79 0.00 36.52 5.36
1805 2072 4.558178 TGCACCATAAGCAGAACAATTTG 58.442 39.130 0.00 0.00 37.02 2.32
1806 2073 4.870123 TGCACCATAAGCAGAACAATTT 57.130 36.364 0.00 0.00 37.02 1.82
1807 2074 5.449041 CGTATGCACCATAAGCAGAACAATT 60.449 40.000 0.00 0.00 46.36 2.32
1808 2075 4.035558 CGTATGCACCATAAGCAGAACAAT 59.964 41.667 0.00 0.00 46.36 2.71
1811 2078 2.286418 GCGTATGCACCATAAGCAGAAC 60.286 50.000 15.05 0.00 45.89 3.01
1816 2083 1.308998 AAGGCGTATGCACCATAAGC 58.691 50.000 9.59 12.60 45.88 3.09
1820 2087 1.745087 CTGAAAAGGCGTATGCACCAT 59.255 47.619 9.59 0.00 45.35 3.55
1822 2089 0.451783 CCTGAAAAGGCGTATGCACC 59.548 55.000 9.59 0.00 45.35 5.01
1825 2102 1.398390 CAGACCTGAAAAGGCGTATGC 59.602 52.381 0.00 0.00 41.71 3.14
1826 2103 1.398390 GCAGACCTGAAAAGGCGTATG 59.602 52.381 0.47 0.00 0.00 2.39
1834 2111 5.278463 GCTGATTAACTTGCAGACCTGAAAA 60.278 40.000 0.47 0.00 0.00 2.29
1841 2118 3.873952 CCCTAGCTGATTAACTTGCAGAC 59.126 47.826 0.00 0.00 0.00 3.51
1851 2128 8.018286 ACAAAAGATTGAAGCCCTAGCTGATTA 61.018 37.037 0.00 0.00 43.77 1.75
1853 2130 5.809040 ACAAAAGATTGAAGCCCTAGCTGAT 60.809 40.000 0.00 0.00 43.77 2.90
1854 2131 4.507335 ACAAAAGATTGAAGCCCTAGCTGA 60.507 41.667 0.00 0.00 43.77 4.26
1855 2132 3.760684 ACAAAAGATTGAAGCCCTAGCTG 59.239 43.478 0.00 0.00 43.77 4.24
1874 2154 4.973168 ACAAGGTGCAAGAGAAGATACAA 58.027 39.130 0.00 0.00 0.00 2.41
1876 2156 4.757149 ACAACAAGGTGCAAGAGAAGATAC 59.243 41.667 0.00 0.00 0.00 2.24
1883 2163 3.635331 CATGAACAACAAGGTGCAAGAG 58.365 45.455 0.00 0.00 28.00 2.85
1902 2185 3.447944 TGTGCATATGTTGTTCATGGCAT 59.552 39.130 4.29 0.00 43.97 4.40
1911 2194 4.015764 TGCATAGGTTGTGCATATGTTGT 58.984 39.130 4.29 0.00 46.76 3.32
1912 2195 4.635833 TGCATAGGTTGTGCATATGTTG 57.364 40.909 4.29 0.00 46.76 3.33
1920 2203 1.656652 ATCGAGTGCATAGGTTGTGC 58.343 50.000 0.00 0.00 42.81 4.57
1921 2204 2.352651 CCAATCGAGTGCATAGGTTGTG 59.647 50.000 7.49 0.00 0.00 3.33
1930 2215 2.300152 GGGAGATATCCAATCGAGTGCA 59.700 50.000 7.49 0.00 0.00 4.57
1982 2272 9.851267 AATCTAGGATGGAATTCTATAGGTTCT 57.149 33.333 4.04 1.46 32.90 3.01
2012 2308 4.890158 TGAGGATGTCTGCTGAAAGTTA 57.110 40.909 0.00 0.00 35.30 2.24
2015 2311 4.942483 AGAATTGAGGATGTCTGCTGAAAG 59.058 41.667 0.00 0.00 0.00 2.62
2016 2312 4.914983 AGAATTGAGGATGTCTGCTGAAA 58.085 39.130 0.00 0.00 0.00 2.69
2019 2315 3.309138 CGAAGAATTGAGGATGTCTGCTG 59.691 47.826 0.00 0.00 0.00 4.41
2020 2316 3.529533 CGAAGAATTGAGGATGTCTGCT 58.470 45.455 0.00 0.00 0.00 4.24
2021 2317 2.031437 GCGAAGAATTGAGGATGTCTGC 59.969 50.000 0.00 0.00 0.00 4.26
2022 2318 3.264947 TGCGAAGAATTGAGGATGTCTG 58.735 45.455 0.00 0.00 0.00 3.51
2054 2406 1.336755 GAGGACTGAGGATCGAGAAGC 59.663 57.143 0.00 0.00 38.61 3.86
2058 2410 0.660488 CGTGAGGACTGAGGATCGAG 59.340 60.000 0.00 0.00 38.61 4.04
2069 2426 0.806868 TCATGGACGTACGTGAGGAC 59.193 55.000 28.16 10.76 43.21 3.85
2070 2427 1.536940 TTCATGGACGTACGTGAGGA 58.463 50.000 28.16 15.96 37.65 3.71
2071 2428 2.579207 ATTCATGGACGTACGTGAGG 57.421 50.000 28.16 13.76 37.65 3.86
2072 2429 6.583912 ATTTAATTCATGGACGTACGTGAG 57.416 37.500 28.16 12.28 37.65 3.51
2074 2431 6.021782 GCAAATTTAATTCATGGACGTACGTG 60.022 38.462 28.16 14.19 0.00 4.49
2075 2432 6.025280 GCAAATTTAATTCATGGACGTACGT 58.975 36.000 23.04 23.04 0.00 3.57
2076 2433 6.024664 TGCAAATTTAATTCATGGACGTACG 58.975 36.000 15.01 15.01 0.00 3.67
2077 2434 7.218204 GTCTGCAAATTTAATTCATGGACGTAC 59.782 37.037 0.00 0.00 0.00 3.67
2088 2447 7.830739 AGAGATTTCGGTCTGCAAATTTAATT 58.169 30.769 0.00 0.00 0.00 1.40
2089 2448 7.337942 AGAGAGATTTCGGTCTGCAAATTTAAT 59.662 33.333 0.00 0.00 0.00 1.40
2090 2449 6.655003 AGAGAGATTTCGGTCTGCAAATTTAA 59.345 34.615 0.00 0.00 0.00 1.52
2091 2450 6.173339 AGAGAGATTTCGGTCTGCAAATTTA 58.827 36.000 0.00 0.00 0.00 1.40
2092 2451 5.006386 AGAGAGATTTCGGTCTGCAAATTT 58.994 37.500 0.00 0.00 0.00 1.82
2104 2463 1.205485 CGCGGCAGAGAGAGATTTCG 61.205 60.000 0.00 0.00 0.00 3.46
2205 2564 1.895231 TTGTCCTGCTGTGCTGCTG 60.895 57.895 0.00 2.47 0.00 4.41
2206 2565 1.895707 GTTGTCCTGCTGTGCTGCT 60.896 57.895 0.00 0.00 0.00 4.24
2207 2566 2.126417 CTGTTGTCCTGCTGTGCTGC 62.126 60.000 0.00 0.00 0.00 5.25
2208 2567 0.533531 TCTGTTGTCCTGCTGTGCTG 60.534 55.000 0.00 0.00 0.00 4.41
2209 2568 0.533755 GTCTGTTGTCCTGCTGTGCT 60.534 55.000 0.00 0.00 0.00 4.40
2214 2573 0.109342 CCCTTGTCTGTTGTCCTGCT 59.891 55.000 0.00 0.00 0.00 4.24
2272 2631 1.623811 TGGAGAAGGTGTAGCTTGGAC 59.376 52.381 0.45 0.00 0.00 4.02
2281 2640 1.073897 GCCTGCTTGGAGAAGGTGT 59.926 57.895 3.96 0.00 43.47 4.16
2284 2643 1.449246 CTCGCCTGCTTGGAGAAGG 60.449 63.158 0.00 0.00 44.47 3.46
2290 2649 3.730761 GTGCACTCGCCTGCTTGG 61.731 66.667 10.32 0.00 38.07 3.61
2405 2767 3.072184 ACGGTCGACTGTAGGTATCCTAT 59.928 47.826 28.22 0.00 38.48 2.57
2440 2802 0.250381 CTCCCTCCTGCTGATGATGC 60.250 60.000 0.00 0.00 0.00 3.91
2578 2940 3.619767 ACCAGCGTGCTCAGCTCA 61.620 61.111 0.00 0.00 44.06 4.26
2743 3105 1.573108 TCCAGTCCCAGATCTTGTCC 58.427 55.000 0.00 0.00 0.00 4.02
2784 3146 1.904771 CCACCGTAATCTCTGCCCA 59.095 57.895 0.00 0.00 0.00 5.36
2807 3169 2.300152 TCTTGATCCGTCACTTGAAGCT 59.700 45.455 0.00 0.00 33.11 3.74
2838 3200 2.390599 ATACACTGTTGCCGCGCAG 61.391 57.895 8.75 5.07 40.61 5.18
2881 3243 5.530176 AGGTGGAGTGGTACCAATTAATT 57.470 39.130 18.31 0.00 39.46 1.40
2882 3244 5.222254 ACAAGGTGGAGTGGTACCAATTAAT 60.222 40.000 18.31 0.00 39.46 1.40
2883 3245 4.105057 ACAAGGTGGAGTGGTACCAATTAA 59.895 41.667 18.31 4.89 39.46 1.40
2884 3246 3.653836 ACAAGGTGGAGTGGTACCAATTA 59.346 43.478 18.31 6.14 39.46 1.40
2915 3288 4.878397 GGAGAGAGTGAGAGAGAGAAAGAG 59.122 50.000 0.00 0.00 0.00 2.85
2919 3292 4.104086 AGAGGAGAGAGTGAGAGAGAGAA 58.896 47.826 0.00 0.00 0.00 2.87
3003 3377 6.067661 TGGGATGATCTATATATGGACCTGGA 60.068 42.308 0.00 0.00 0.00 3.86
3008 3382 8.592809 GGAAGATGGGATGATCTATATATGGAC 58.407 40.741 0.20 0.00 32.11 4.02
3024 3398 1.344087 GGAGTACCTGGGAAGATGGGA 60.344 57.143 0.00 0.00 0.00 4.37
3034 3408 4.895889 TCTTGATCATACTGGAGTACCTGG 59.104 45.833 0.00 0.00 39.06 4.45
3107 3488 6.215845 TGTGTATCATGTCAAATCGATCGAT 58.784 36.000 24.60 24.60 36.23 3.59
3111 3492 6.290605 TGGATGTGTATCATGTCAAATCGAT 58.709 36.000 0.00 0.00 36.83 3.59
3269 3650 2.748798 GCAATCTCTGCCATGGTCATCT 60.749 50.000 14.67 0.00 46.13 2.90
3324 3706 2.668632 CCCGGCCTGCAAGTTCTA 59.331 61.111 0.00 0.00 0.00 2.10
3360 3742 1.273606 CATCTCTGACACGGTCCTGTT 59.726 52.381 2.23 0.00 0.00 3.16
3476 3858 0.034059 AAGAGAACACAGTGCTCCCG 59.966 55.000 0.00 0.00 38.94 5.14
3477 3859 1.202698 ACAAGAGAACACAGTGCTCCC 60.203 52.381 0.00 0.00 38.94 4.30
3503 3885 9.941325 TGATTGCACTAACAAAAATCCAATAAT 57.059 25.926 0.00 0.00 32.27 1.28
3506 3888 7.334921 CCATGATTGCACTAACAAAAATCCAAT 59.665 33.333 0.00 0.00 32.27 3.16
3525 3907 6.724441 ACATGCTCATCCAATAATCCATGATT 59.276 34.615 0.00 0.00 36.20 2.57
3547 3933 0.897621 TCCATGACACGCTCTGACAT 59.102 50.000 0.00 0.00 35.89 3.06
3577 3972 1.438814 GTACGTACCATCCACCGGG 59.561 63.158 15.00 0.00 0.00 5.73
3601 3996 0.537371 CCAAAAACTGGGACTCCGCT 60.537 55.000 0.00 0.00 42.17 5.52
3610 4005 2.146073 CTGCGAGGCCCAAAAACTGG 62.146 60.000 0.00 0.00 45.97 4.00
3611 4006 1.172180 TCTGCGAGGCCCAAAAACTG 61.172 55.000 0.00 0.00 0.00 3.16
3612 4007 0.251341 ATCTGCGAGGCCCAAAAACT 60.251 50.000 0.00 0.00 0.00 2.66
3613 4008 0.109132 CATCTGCGAGGCCCAAAAAC 60.109 55.000 0.00 0.00 0.00 2.43
3614 4009 0.539438 ACATCTGCGAGGCCCAAAAA 60.539 50.000 0.00 0.00 0.00 1.94
3615 4010 1.074775 ACATCTGCGAGGCCCAAAA 59.925 52.632 0.00 0.00 0.00 2.44
3660 4056 0.791422 CACACCAATTTGGCATTGCG 59.209 50.000 15.49 0.00 42.67 4.85
3664 4060 0.178909 TCCCCACACCAATTTGGCAT 60.179 50.000 15.49 0.65 42.67 4.40
3665 4061 0.831288 CTCCCCACACCAATTTGGCA 60.831 55.000 15.49 0.00 42.67 4.92
3704 4100 3.217743 ACGGGCCGAGTAGCTAGC 61.218 66.667 35.78 6.62 0.00 3.42
3714 4113 2.969238 GATCTCATGCACGGGCCG 60.969 66.667 27.06 27.06 40.13 6.13
3743 4147 2.814919 CCTACGAGTATAGACTGCCCTG 59.185 54.545 0.00 0.00 35.45 4.45
3747 4151 2.485038 GCTCCCTACGAGTATAGACTGC 59.515 54.545 0.00 0.00 41.10 4.40


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

AutoCloner maintained by Alex Coulton.