Multiple sequence alignment - TraesCS4D01G185300

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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 TraesCS4D01G185300 chr4D 100.000 3099 0 0 676 3774 323351585 323354683 0.000000e+00 5723.0
1 TraesCS4D01G185300 chr4D 100.000 415 0 0 1 415 323350910 323351324 0.000000e+00 767.0
2 TraesCS4D01G185300 chr4A 90.529 1911 115 26 1919 3774 148759901 148758002 0.000000e+00 2466.0
3 TraesCS4D01G185300 chr4A 93.474 521 24 5 1154 1674 148762053 148761543 0.000000e+00 765.0
4 TraesCS4D01G185300 chr4A 88.454 485 32 7 689 1154 148762595 148762116 7.080000e-157 564.0
5 TraesCS4D01G185300 chr4A 90.950 221 18 2 1671 1890 148761518 148761299 2.850000e-76 296.0
6 TraesCS4D01G185300 chr4A 88.636 44 4 1 1874 1917 544173338 544173380 7.000000e-03 52.8
7 TraesCS4D01G185300 chr4A 92.105 38 2 1 1879 1915 679449546 679449583 7.000000e-03 52.8
8 TraesCS4D01G185300 chr4B 92.182 793 41 9 2358 3134 403623017 403623804 0.000000e+00 1101.0
9 TraesCS4D01G185300 chr4B 86.283 678 30 28 3118 3774 403623894 403624529 0.000000e+00 678.0
10 TraesCS4D01G185300 chr4B 90.361 415 40 0 1 415 403620005 403620419 2.560000e-151 545.0
11 TraesCS4D01G185300 chr4B 96.800 250 5 3 907 1154 403621558 403621806 7.540000e-112 414.0
12 TraesCS4D01G185300 chr4B 87.467 375 19 10 2007 2359 403622566 403622934 1.260000e-109 407.0
13 TraesCS4D01G185300 chr4B 88.102 353 23 11 1661 2012 403622183 403622517 5.870000e-108 401.0
14 TraesCS4D01G185300 chr4B 94.902 255 13 0 1154 1408 403621870 403622124 2.110000e-107 399.0
15 TraesCS4D01G185300 chr4B 90.598 234 16 5 676 909 403620469 403620696 4.740000e-79 305.0
16 TraesCS4D01G185300 chr4B 96.591 88 2 1 3321 3407 413498631 413498544 1.090000e-30 145.0
17 TraesCS4D01G185300 chr6D 95.699 93 3 1 3311 3403 17887815 17887724 8.450000e-32 148.0
18 TraesCS4D01G185300 chr6D 100.000 30 0 0 1886 1915 27459800 27459829 5.270000e-04 56.5
19 TraesCS4D01G185300 chr6A 96.629 89 3 0 3311 3399 18580880 18580792 8.450000e-32 148.0
20 TraesCS4D01G185300 chr6A 100.000 30 0 0 1886 1915 4956301 4956330 5.270000e-04 56.5
21 TraesCS4D01G185300 chr6B 93.137 102 4 3 3311 3411 32019419 32019320 3.040000e-31 147.0
22 TraesCS4D01G185300 chr3A 94.624 93 4 1 3309 3401 25367995 25368086 3.930000e-30 143.0
23 TraesCS4D01G185300 chr3B 92.000 100 6 2 3300 3398 5587441 5587343 5.080000e-29 139.0
24 TraesCS4D01G185300 chr3B 92.079 101 4 3 3310 3408 16445206 16445108 5.080000e-29 139.0
25 TraesCS4D01G185300 chr3B 92.105 38 1 2 1890 1925 448777369 448777332 7.000000e-03 52.8
26 TraesCS4D01G185300 chr2D 82.927 123 14 7 3654 3774 13229045 13228928 1.850000e-18 104.0
27 TraesCS4D01G185300 chr2A 82.927 123 14 6 3654 3774 15270378 15270261 1.850000e-18 104.0
28 TraesCS4D01G185300 chr2B 82.114 123 15 6 3654 3774 23878495 23878378 8.630000e-17 99.0
29 TraesCS4D01G185300 chr2B 100.000 28 0 0 1890 1917 404186978 404187005 7.000000e-03 52.8
30 TraesCS4D01G185300 chr7D 97.143 35 0 1 1883 1917 3404994 3405027 1.460000e-04 58.4
31 TraesCS4D01G185300 chr7D 97.143 35 0 1 1881 1915 115212334 115212301 1.460000e-04 58.4
32 TraesCS4D01G185300 chr7A 100.000 31 0 0 1885 1915 120137590 120137560 1.460000e-04 58.4
33 TraesCS4D01G185300 chr1A 100.000 30 0 0 1886 1915 32425313 32425342 5.270000e-04 56.5
34 TraesCS4D01G185300 chr1A 100.000 30 0 0 1886 1915 41071984 41071955 5.270000e-04 56.5


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 TraesCS4D01G185300 chr4D 323350910 323354683 3773 False 3245.00 5723 100.000000 1 3774 2 chr4D.!!$F1 3773
1 TraesCS4D01G185300 chr4A 148758002 148762595 4593 True 1022.75 2466 90.851750 689 3774 4 chr4A.!!$R1 3085
2 TraesCS4D01G185300 chr4B 403620005 403624529 4524 False 531.25 1101 90.836875 1 3774 8 chr4B.!!$F1 3773

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
697 698 0.319641 GGCCTTGTCTCGAACGAGTT 60.320 55.0 20.76 0.0 42.49 3.01 F
1756 2716 0.035820 TTCCGTGGTCAAGGGCATAC 60.036 55.0 3.29 0.0 33.54 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2231 4646 0.463204 CCATGTCCGAGCTGTCTGAT 59.537 55.0 0.0 0.0 0.0 2.90 R
3039 5557 0.179032 TGCAGCCGAGGTTTTCAGAA 60.179 50.0 0.0 0.0 0.0 3.02 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
53 54 2.547218 GGTAAGACGCAACTCACCTTGA 60.547 50.000 0.00 0.00 0.00 3.02
73 74 1.002430 AGAAGACAATGGCGAGCTCAA 59.998 47.619 15.40 0.00 0.00 3.02
82 83 3.068881 CGAGCTCAAAGGGGTCCA 58.931 61.111 15.40 0.00 0.00 4.02
91 92 1.167033 AAAGGGGTCCAGGGAAACAT 58.833 50.000 0.00 0.00 0.00 2.71
106 107 3.259123 GGAAACATGATGAATATGGGGCC 59.741 47.826 0.00 0.00 0.00 5.80
113 114 0.396974 TGAATATGGGGCCAAGGTGC 60.397 55.000 4.39 0.00 0.00 5.01
120 121 2.263540 GGCCAAGGTGCAAGCATG 59.736 61.111 0.00 0.00 36.26 4.06
265 266 4.373116 GCGACCTCGTTGCCCTCA 62.373 66.667 0.00 0.00 42.22 3.86
273 274 2.616330 CGTTGCCCTCACGCATGTT 61.616 57.895 0.00 0.00 38.87 2.71
274 275 1.210155 GTTGCCCTCACGCATGTTC 59.790 57.895 0.00 0.00 38.87 3.18
280 281 0.803768 CCTCACGCATGTTCTCTCCG 60.804 60.000 0.00 0.00 0.00 4.63
304 305 1.927174 CACGACATCCTCGATTTGGTC 59.073 52.381 0.00 0.00 46.14 4.02
305 306 1.134788 ACGACATCCTCGATTTGGTCC 60.135 52.381 0.00 0.00 46.14 4.46
333 334 2.997315 CTCTCCCACGGTGGCTCA 60.997 66.667 21.88 6.59 35.79 4.26
697 698 0.319641 GGCCTTGTCTCGAACGAGTT 60.320 55.000 20.76 0.00 42.49 3.01
734 735 0.320771 ACGTGAGCTCGCCAAGATTT 60.321 50.000 21.21 0.00 0.00 2.17
749 750 1.888512 AGATTTGTGCAATGGCTTCGT 59.111 42.857 0.00 0.00 41.91 3.85
752 753 2.177394 TTGTGCAATGGCTTCGTAGA 57.823 45.000 0.00 0.00 41.91 2.59
753 754 2.177394 TGTGCAATGGCTTCGTAGAA 57.823 45.000 0.00 0.00 39.24 2.10
778 779 1.078143 ACGGAGCAGCCAGATTTCC 60.078 57.895 0.00 0.00 35.94 3.13
783 784 3.093278 CAGCCAGATTTCCGACGC 58.907 61.111 0.00 0.00 0.00 5.19
786 787 2.517450 GCCAGATTTCCGACGCTCG 61.517 63.158 0.00 1.17 40.07 5.03
801 802 4.548346 CGACGCTCGGAAGTTATCATTTTC 60.548 45.833 0.00 0.00 36.00 2.29
868 869 4.108336 CCTCCACGAATATGATAGCATCG 58.892 47.826 0.00 0.00 35.94 3.84
893 894 6.477033 GCGACAATCTACACACAAGATAAGAT 59.523 38.462 0.00 0.00 33.32 2.40
905 906 8.281194 CACACAAGATAAGATACTCATCAATGC 58.719 37.037 0.00 0.00 33.21 3.56
1237 2168 2.893637 AGCATCGCTAACCTTACACTG 58.106 47.619 0.00 0.00 36.99 3.66
1238 2169 1.327764 GCATCGCTAACCTTACACTGC 59.672 52.381 0.00 0.00 0.00 4.40
1255 2186 2.306805 ACTGCCAGTGGATCTTGATTCA 59.693 45.455 15.20 0.00 0.00 2.57
1293 2224 3.382865 TGCACTGACTTAGATGAGCTAGG 59.617 47.826 0.00 0.00 32.75 3.02
1334 2265 7.233553 TCTGTGGTCTGAGAAGAAGAAAAGATA 59.766 37.037 0.00 0.00 0.00 1.98
1337 2268 8.524487 GTGGTCTGAGAAGAAGAAAAGATAGTA 58.476 37.037 0.00 0.00 0.00 1.82
1347 2278 6.621514 AGAAGAAAAGATAGTATGGGTGGGAT 59.378 38.462 0.00 0.00 0.00 3.85
1386 2317 4.374843 TGTGTTGATCCATTTAGCATGC 57.625 40.909 10.51 10.51 0.00 4.06
1465 2396 2.500910 CCTGGAATGCTTATTTTGGCCA 59.499 45.455 0.00 0.00 0.00 5.36
1466 2397 3.055240 CCTGGAATGCTTATTTTGGCCAA 60.055 43.478 16.05 16.05 0.00 4.52
1481 2412 1.877443 GGCCAACGCTTAGACTTTCAA 59.123 47.619 0.00 0.00 34.44 2.69
1514 2445 1.135939 GAAACGGCATGGTTACGGC 59.864 57.895 0.00 0.00 0.00 5.68
1583 2514 1.786937 TGCCATGGTGGTTTTGAAGT 58.213 45.000 14.67 0.00 40.46 3.01
1584 2515 1.411977 TGCCATGGTGGTTTTGAAGTG 59.588 47.619 14.67 0.00 40.46 3.16
1587 2518 2.546373 CCATGGTGGTTTTGAAGTGCAG 60.546 50.000 2.57 0.00 31.35 4.41
1588 2519 1.846007 TGGTGGTTTTGAAGTGCAGT 58.154 45.000 0.00 0.00 0.00 4.40
1589 2520 3.006112 TGGTGGTTTTGAAGTGCAGTA 57.994 42.857 0.00 0.00 0.00 2.74
1590 2521 3.561143 TGGTGGTTTTGAAGTGCAGTAT 58.439 40.909 0.00 0.00 0.00 2.12
1591 2522 3.317711 TGGTGGTTTTGAAGTGCAGTATG 59.682 43.478 0.00 0.00 40.87 2.39
1592 2523 3.305335 GGTGGTTTTGAAGTGCAGTATGG 60.305 47.826 0.00 0.00 35.86 2.74
1593 2524 3.317993 GTGGTTTTGAAGTGCAGTATGGT 59.682 43.478 0.00 0.00 35.86 3.55
1665 2596 5.026462 CGACAGAATTTGCTGCTCAATTAG 58.974 41.667 0.00 5.10 39.51 1.73
1756 2716 0.035820 TTCCGTGGTCAAGGGCATAC 60.036 55.000 3.29 0.00 33.54 2.39
1757 2717 1.451387 CCGTGGTCAAGGGCATACC 60.451 63.158 0.00 0.00 40.67 2.73
1810 2770 3.438781 GGCGATTTCCTGTCATGTTTACA 59.561 43.478 0.00 0.00 0.00 2.41
1811 2771 4.096382 GGCGATTTCCTGTCATGTTTACAT 59.904 41.667 0.00 0.00 36.96 2.29
1881 2841 3.708403 TGATGCACAGAGAAGGAACAT 57.292 42.857 0.00 0.00 0.00 2.71
1884 2844 5.559770 TGATGCACAGAGAAGGAACATTAA 58.440 37.500 0.00 0.00 0.00 1.40
1890 2850 7.094634 TGCACAGAGAAGGAACATTAATTCTTC 60.095 37.037 0.00 0.00 32.31 2.87
1891 2851 7.094634 GCACAGAGAAGGAACATTAATTCTTCA 60.095 37.037 14.60 0.00 32.31 3.02
1893 2853 8.160106 ACAGAGAAGGAACATTAATTCTTCAGT 58.840 33.333 14.60 9.81 32.31 3.41
1894 2854 9.007901 CAGAGAAGGAACATTAATTCTTCAGTT 57.992 33.333 14.60 4.23 32.31 3.16
1895 2855 9.579932 AGAGAAGGAACATTAATTCTTCAGTTT 57.420 29.630 14.60 4.52 32.31 2.66
1898 2858 8.593492 AAGGAACATTAATTCTTCAGTTTTGC 57.407 30.769 5.41 0.00 0.00 3.68
1899 2859 7.955918 AGGAACATTAATTCTTCAGTTTTGCT 58.044 30.769 5.41 0.00 0.00 3.91
1900 2860 9.077885 AGGAACATTAATTCTTCAGTTTTGCTA 57.922 29.630 5.41 0.00 0.00 3.49
1901 2861 9.691362 GGAACATTAATTCTTCAGTTTTGCTAA 57.309 29.630 5.41 0.00 0.00 3.09
1904 2864 9.196552 ACATTAATTCTTCAGTTTTGCTAAAGC 57.803 29.630 0.00 0.00 42.50 3.51
2021 4414 8.130671 ACTCTGCATTAGTACTTGGTACTTAA 57.869 34.615 14.27 8.25 45.68 1.85
2036 4429 4.142469 GGTACTTAATTGGCGCTTGATTGT 60.142 41.667 7.64 1.49 0.00 2.71
2039 4432 4.022416 ACTTAATTGGCGCTTGATTGTTGA 60.022 37.500 7.64 0.00 0.00 3.18
2040 4433 3.383620 AATTGGCGCTTGATTGTTGAA 57.616 38.095 7.64 0.00 0.00 2.69
2077 4470 9.339850 AGACGTCATATACTTCACTAATGTAGT 57.660 33.333 19.50 0.00 39.54 2.73
2078 4471 9.947669 GACGTCATATACTTCACTAATGTAGTT 57.052 33.333 11.55 0.00 37.59 2.24
2098 4491 8.395633 TGTAGTTTCTTGCTTGTTTTCTAAGAC 58.604 33.333 0.00 0.00 0.00 3.01
2103 4496 7.346751 TCTTGCTTGTTTTCTAAGACCAATT 57.653 32.000 0.00 0.00 0.00 2.32
2105 4498 6.959639 TGCTTGTTTTCTAAGACCAATTCT 57.040 33.333 0.00 0.00 35.32 2.40
2106 4499 6.738114 TGCTTGTTTTCTAAGACCAATTCTG 58.262 36.000 0.00 0.00 33.46 3.02
2119 4512 3.329520 ACCAATTCTGCAGTGGTTACCTA 59.670 43.478 19.09 0.00 43.19 3.08
2120 4513 3.689649 CCAATTCTGCAGTGGTTACCTAC 59.310 47.826 14.67 0.00 0.00 3.18
2130 4545 6.597672 TGCAGTGGTTACCTACATGAAATAAG 59.402 38.462 2.07 0.00 0.00 1.73
2132 4547 7.499232 GCAGTGGTTACCTACATGAAATAAGAT 59.501 37.037 2.07 0.00 0.00 2.40
2282 4697 1.090728 GTGGCTTGGCTTCTCTTAGC 58.909 55.000 0.00 0.00 40.48 3.09
2345 4760 1.947456 GTTGATCTGGCCGGTATTTCC 59.053 52.381 12.43 0.00 0.00 3.13
2378 4877 7.563924 AGTTCTAATATGGAGTACTGCAGGTTA 59.436 37.037 22.09 19.26 33.50 2.85
2385 4886 4.160439 TGGAGTACTGCAGGTTAATCTCTG 59.840 45.833 19.93 0.00 0.00 3.35
2386 4887 4.160626 GGAGTACTGCAGGTTAATCTCTGT 59.839 45.833 19.93 0.00 33.81 3.41
2393 4894 4.515191 TGCAGGTTAATCTCTGTCAAACAC 59.485 41.667 0.00 0.00 33.81 3.32
2395 4896 5.334414 GCAGGTTAATCTCTGTCAAACACTG 60.334 44.000 0.00 0.00 33.81 3.66
2396 4897 4.757149 AGGTTAATCTCTGTCAAACACTGC 59.243 41.667 0.00 0.00 0.00 4.40
2404 4905 3.066621 TCTGTCAAACACTGCCACAATTC 59.933 43.478 0.00 0.00 0.00 2.17
2430 4933 6.543735 ACAACCTTAGAGTGCTAAAGGATTT 58.456 36.000 15.57 3.01 43.42 2.17
2432 4935 8.161425 ACAACCTTAGAGTGCTAAAGGATTTTA 58.839 33.333 15.57 0.00 40.09 1.52
2467 4970 2.239654 TCTTATGGCCAGGTTTCTCCAG 59.760 50.000 13.05 0.00 39.02 3.86
2471 4974 1.682257 GCCAGGTTTCTCCAGAGCT 59.318 57.895 0.00 0.00 39.02 4.09
2553 5056 4.092968 CGTGTACCAGGATAGTTTTGCTTC 59.907 45.833 0.00 0.00 0.00 3.86
2700 5210 2.229792 GCCACCTGATGTTGTCAAGAA 58.770 47.619 0.00 0.00 36.14 2.52
2783 5293 1.517257 CAGTCCTAAGCGGCGACTG 60.517 63.158 12.98 17.25 45.33 3.51
2825 5342 4.804139 CGTTACTTGGACGAAATAGATGCT 59.196 41.667 0.00 0.00 42.82 3.79
2877 5395 3.519510 CCCCTGTATCTTGGTTTCTCTGA 59.480 47.826 0.00 0.00 0.00 3.27
2998 5516 2.194201 ACACCGTGGAATTACTTGGG 57.806 50.000 3.03 0.00 0.00 4.12
3039 5557 5.465724 GTCGGTTTAGTGTTCAGTCTTTCAT 59.534 40.000 0.00 0.00 0.00 2.57
3040 5558 6.018180 GTCGGTTTAGTGTTCAGTCTTTCATT 60.018 38.462 0.00 0.00 0.00 2.57
3059 5577 0.179032 TCTGAAAACCTCGGCTGCAA 60.179 50.000 0.50 0.00 0.00 4.08
3082 5600 6.920569 ATGTCGGTATAGATGTTTTTGTCC 57.079 37.500 0.00 0.00 0.00 4.02
3181 5805 2.837532 ATGTTGCCATGTGAAAACCC 57.162 45.000 0.00 0.00 0.00 4.11
3199 5823 2.290464 CCCAAACGTCACAACCAGTTA 58.710 47.619 0.00 0.00 0.00 2.24
3202 5826 3.242608 CCAAACGTCACAACCAGTTACTG 60.243 47.826 5.22 5.22 0.00 2.74
3230 5855 5.597182 ACAGTACGTCATATGACCCTACATT 59.403 40.000 26.33 14.48 41.86 2.71
3280 5911 6.247229 AGTAAAAGCAAAGGGGAAAAACAT 57.753 33.333 0.00 0.00 0.00 2.71
3283 5914 9.095700 AGTAAAAGCAAAGGGGAAAAACATATA 57.904 29.630 0.00 0.00 0.00 0.86
3404 6049 0.110056 CGCCACTCTGATTTGTGTGC 60.110 55.000 0.00 0.00 32.17 4.57
3408 6053 4.191544 GCCACTCTGATTTGTGTGCTATA 58.808 43.478 0.00 0.00 32.17 1.31
3411 6056 6.146837 GCCACTCTGATTTGTGTGCTATATAG 59.853 42.308 5.30 5.30 32.17 1.31
3416 6061 8.877808 TCTGATTTGTGTGCTATATAGTTGAG 57.122 34.615 11.38 0.00 0.00 3.02
3417 6062 8.478066 TCTGATTTGTGTGCTATATAGTTGAGT 58.522 33.333 11.38 0.00 0.00 3.41
3418 6063 8.424274 TGATTTGTGTGCTATATAGTTGAGTG 57.576 34.615 11.38 0.00 0.00 3.51
3420 6065 5.276461 TGTGTGCTATATAGTTGAGTGGG 57.724 43.478 11.38 0.00 0.00 4.61
3421 6066 4.058817 GTGTGCTATATAGTTGAGTGGGC 58.941 47.826 11.38 0.00 0.00 5.36
3425 6070 5.010719 GTGCTATATAGTTGAGTGGGCACTA 59.989 44.000 11.38 0.00 42.66 2.74
3435 6081 4.269183 TGAGTGGGCACTAATTAACATGG 58.731 43.478 0.00 0.00 42.66 3.66
3437 6083 4.270008 AGTGGGCACTAATTAACATGGTC 58.730 43.478 0.00 0.00 40.43 4.02
3438 6084 4.013728 GTGGGCACTAATTAACATGGTCA 58.986 43.478 0.00 0.00 0.00 4.02
3445 6091 5.294306 CACTAATTAACATGGTCACTCGCAT 59.706 40.000 0.00 0.00 0.00 4.73
3460 6106 4.751600 CACTCGCATCTTGCCTTGATAATA 59.248 41.667 0.00 0.00 41.12 0.98
3540 6186 6.934561 AACAAATCTTTGCTCGCTTTATTC 57.065 33.333 2.63 0.00 41.79 1.75
3549 6195 4.006989 TGCTCGCTTTATTCTAAGCCAAA 58.993 39.130 0.00 0.00 46.06 3.28
3551 6197 4.142687 GCTCGCTTTATTCTAAGCCAAACA 60.143 41.667 0.00 0.00 46.06 2.83
3575 6221 9.220767 ACAAAATAAAGCAACAAACCAAACTTA 57.779 25.926 0.00 0.00 0.00 2.24
3613 6259 2.032528 TGCCACGCAAGCTAAGCT 59.967 55.556 9.12 0.00 42.56 3.74
3614 6260 2.034879 TGCCACGCAAGCTAAGCTC 61.035 57.895 9.12 0.00 38.25 4.09
3653 6313 2.125350 GAAGACGGCAGGAGCAGG 60.125 66.667 0.00 0.00 44.61 4.85
3654 6314 4.400961 AAGACGGCAGGAGCAGGC 62.401 66.667 0.00 0.00 45.11 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.877649 CCCTTCGGATCGATGCACAG 60.878 60.000 17.54 11.00 35.23 3.66
14 15 2.066999 CCTCCTTCCTCCCCTTCGG 61.067 68.421 0.00 0.00 0.00 4.30
53 54 0.610174 TGAGCTCGCCATTGTCTTCT 59.390 50.000 9.64 0.00 0.00 2.85
59 60 1.660560 CCCCTTTGAGCTCGCCATTG 61.661 60.000 9.64 0.00 0.00 2.82
73 74 0.409484 CATGTTTCCCTGGACCCCTT 59.591 55.000 0.00 0.00 0.00 3.95
82 83 4.744237 CCCCATATTCATCATGTTTCCCT 58.256 43.478 0.00 0.00 0.00 4.20
91 92 1.858910 ACCTTGGCCCCATATTCATCA 59.141 47.619 0.00 0.00 0.00 3.07
102 103 2.999063 ATGCTTGCACCTTGGCCC 60.999 61.111 0.00 0.00 0.00 5.80
106 107 1.290955 CACCCATGCTTGCACCTTG 59.709 57.895 0.00 0.00 0.00 3.61
113 114 2.658422 GGTTGCCACCCATGCTTG 59.342 61.111 0.00 0.00 37.03 4.01
131 132 2.432628 GTCGCACAACGGAGGAGG 60.433 66.667 0.00 0.00 43.89 4.30
137 138 1.298157 ATCATGGTGTCGCACAACGG 61.298 55.000 11.20 1.68 39.05 4.44
220 221 2.051518 TGGTTTCATGGGATGCGCC 61.052 57.895 4.18 0.00 0.00 6.53
221 222 1.139520 GTGGTTTCATGGGATGCGC 59.860 57.895 0.00 0.00 0.00 6.09
230 231 1.876497 GCATGTGCGGGTGGTTTCAT 61.876 55.000 0.00 0.00 0.00 2.57
231 232 2.560119 GCATGTGCGGGTGGTTTCA 61.560 57.895 0.00 0.00 0.00 2.69
265 266 2.125512 GGCGGAGAGAACATGCGT 60.126 61.111 0.00 0.00 33.65 5.24
274 275 4.498520 ATGTCGTGCGGCGGAGAG 62.499 66.667 9.78 2.80 41.72 3.20
295 296 2.106683 GCTCCACCGGACCAAATCG 61.107 63.158 9.46 0.00 0.00 3.34
348 349 4.351938 CGTTCCCGTGGCTGTCGA 62.352 66.667 0.00 0.00 0.00 4.20
384 385 4.753877 CGAGGAGTTCACGCGCGA 62.754 66.667 39.36 13.15 0.00 5.87
697 698 1.595328 CGTTGACACGTCATCACCAAA 59.405 47.619 0.00 0.00 41.84 3.28
734 735 2.177394 TTCTACGAAGCCATTGCACA 57.823 45.000 0.00 0.00 41.13 4.57
749 750 1.470979 GCTGCTCCGTCCGAATTTCTA 60.471 52.381 0.00 0.00 0.00 2.10
752 753 1.745489 GGCTGCTCCGTCCGAATTT 60.745 57.895 0.00 0.00 0.00 1.82
753 754 2.125106 GGCTGCTCCGTCCGAATT 60.125 61.111 0.00 0.00 0.00 2.17
778 779 2.121116 ATGATAACTTCCGAGCGTCG 57.879 50.000 0.00 0.00 40.07 5.12
839 840 6.073548 GCTATCATATTCGTGGAGGTTTCAAG 60.074 42.308 0.00 0.00 0.00 3.02
840 841 5.758296 GCTATCATATTCGTGGAGGTTTCAA 59.242 40.000 0.00 0.00 0.00 2.69
841 842 5.163353 TGCTATCATATTCGTGGAGGTTTCA 60.163 40.000 0.00 0.00 0.00 2.69
842 843 5.297547 TGCTATCATATTCGTGGAGGTTTC 58.702 41.667 0.00 0.00 0.00 2.78
868 869 5.805486 TCTTATCTTGTGTGTAGATTGTCGC 59.195 40.000 0.00 0.00 34.35 5.19
926 1791 7.439157 TGGAGTTTCTGTGAACATTAGAATG 57.561 36.000 0.61 0.61 42.10 2.67
927 1792 7.667219 ACATGGAGTTTCTGTGAACATTAGAAT 59.333 33.333 0.00 0.00 31.21 2.40
928 1793 6.998074 ACATGGAGTTTCTGTGAACATTAGAA 59.002 34.615 0.00 0.00 31.94 2.10
1050 1917 1.365999 CGTGGCCCGCTCATACATA 59.634 57.895 0.00 0.00 0.00 2.29
1188 2119 1.131638 AGGAGCCGCTCAATCCAATA 58.868 50.000 21.76 0.00 35.45 1.90
1237 2168 2.941720 GTCTGAATCAAGATCCACTGGC 59.058 50.000 0.00 0.00 0.00 4.85
1238 2169 4.190001 CAGTCTGAATCAAGATCCACTGG 58.810 47.826 0.00 0.00 0.00 4.00
1255 2186 1.064060 GTGCAAAAAGTCACGCAGTCT 59.936 47.619 0.00 0.00 41.61 3.24
1334 2265 4.447762 GCCTTATGAAATCCCACCCATACT 60.448 45.833 0.00 0.00 0.00 2.12
1337 2268 2.519691 AGCCTTATGAAATCCCACCCAT 59.480 45.455 0.00 0.00 0.00 4.00
1347 2278 6.939730 TCAACACATTCAGTAGCCTTATGAAA 59.060 34.615 0.00 0.00 36.59 2.69
1386 2317 3.837213 AATCTCCACAAATCTTGCACG 57.163 42.857 0.00 0.00 0.00 5.34
1399 2330 2.449464 CAGCAATCCCACAAATCTCCA 58.551 47.619 0.00 0.00 0.00 3.86
1436 2367 2.270434 AAGCATTCCAGGTCCTCCTA 57.730 50.000 0.00 0.00 43.07 2.94
1437 2368 2.270434 TAAGCATTCCAGGTCCTCCT 57.730 50.000 0.00 0.00 46.37 3.69
1438 2369 3.584733 AATAAGCATTCCAGGTCCTCC 57.415 47.619 0.00 0.00 0.00 4.30
1465 2396 4.196971 AGTTGGTTGAAAGTCTAAGCGTT 58.803 39.130 0.00 0.00 0.00 4.84
1466 2397 3.805207 AGTTGGTTGAAAGTCTAAGCGT 58.195 40.909 0.00 0.00 0.00 5.07
1481 2412 3.751698 GCCGTTTCTCAGATTAAGTTGGT 59.248 43.478 0.00 0.00 0.00 3.67
1514 2445 3.485463 TCACACTCCAGGTTTGGTAAG 57.515 47.619 0.00 0.00 45.26 2.34
1539 2470 2.033424 GTCCCAGCACACTTTCAGTTTC 59.967 50.000 0.00 0.00 0.00 2.78
1583 2514 4.079980 ACAAACACTGTACCATACTGCA 57.920 40.909 0.00 0.00 36.10 4.41
1584 2515 4.755123 AGAACAAACACTGTACCATACTGC 59.245 41.667 0.00 0.00 37.23 4.40
1587 2518 7.435068 AATCAGAACAAACACTGTACCATAC 57.565 36.000 0.00 0.00 37.23 2.39
1588 2519 7.822334 CCTAATCAGAACAAACACTGTACCATA 59.178 37.037 0.00 0.00 37.23 2.74
1589 2520 6.655003 CCTAATCAGAACAAACACTGTACCAT 59.345 38.462 0.00 0.00 37.23 3.55
1590 2521 5.995282 CCTAATCAGAACAAACACTGTACCA 59.005 40.000 0.00 0.00 37.23 3.25
1591 2522 6.228258 TCCTAATCAGAACAAACACTGTACC 58.772 40.000 0.00 0.00 37.23 3.34
1592 2523 7.387948 ACATCCTAATCAGAACAAACACTGTAC 59.612 37.037 0.00 0.00 37.23 2.90
1593 2524 7.450074 ACATCCTAATCAGAACAAACACTGTA 58.550 34.615 0.00 0.00 37.23 2.74
1610 2541 9.561069 GAATTTCAATCCTAGCTAACATCCTAA 57.439 33.333 0.00 0.00 0.00 2.69
1756 2716 9.137459 TGAACTAGACTATTCAATAAGGAGAGG 57.863 37.037 0.00 0.00 31.95 3.69
1757 2717 9.959749 GTGAACTAGACTATTCAATAAGGAGAG 57.040 37.037 0.00 0.00 36.62 3.20
1765 2725 6.989169 GCCATGAGTGAACTAGACTATTCAAT 59.011 38.462 0.00 0.00 36.62 2.57
1810 2770 6.034898 GCAAGTAACAAAAAGCATCGCATTAT 59.965 34.615 0.00 0.00 0.00 1.28
1811 2771 5.344665 GCAAGTAACAAAAAGCATCGCATTA 59.655 36.000 0.00 0.00 0.00 1.90
1853 2813 4.629200 CCTTCTCTGTGCATCAAGAAGTAC 59.371 45.833 22.65 0.00 38.31 2.73
1930 4273 4.485024 TTTAAATGAAGCGCACCGTTTA 57.515 36.364 11.47 15.22 29.28 2.01
1937 4280 9.449550 CAATAATAGACATTTAAATGAAGCGCA 57.550 29.630 30.18 13.68 39.67 6.09
1939 4282 9.398170 CCCAATAATAGACATTTAAATGAAGCG 57.602 33.333 30.18 7.91 39.67 4.68
1986 4329 9.603189 AAGTACTAATGCAGAGTAATACCCTAT 57.397 33.333 11.73 0.00 31.33 2.57
2021 4414 3.243839 ACTTTCAACAATCAAGCGCCAAT 60.244 39.130 2.29 0.00 0.00 3.16
2040 4433 9.953697 GAAGTATATGACGTCTGAATCTAACTT 57.046 33.333 17.92 13.88 34.09 2.66
2077 4470 6.767524 TGGTCTTAGAAAACAAGCAAGAAA 57.232 33.333 0.00 0.00 0.00 2.52
2078 4471 6.767524 TTGGTCTTAGAAAACAAGCAAGAA 57.232 33.333 0.00 0.00 0.00 2.52
2079 4472 6.959639 ATTGGTCTTAGAAAACAAGCAAGA 57.040 33.333 0.00 0.00 0.00 3.02
2080 4473 7.380602 CAGAATTGGTCTTAGAAAACAAGCAAG 59.619 37.037 0.00 0.00 32.70 4.01
2084 4477 6.738114 TGCAGAATTGGTCTTAGAAAACAAG 58.262 36.000 0.00 0.00 32.70 3.16
2098 4491 2.795329 AGGTAACCACTGCAGAATTGG 58.205 47.619 23.35 20.12 34.74 3.16
2103 4496 3.169908 TCATGTAGGTAACCACTGCAGA 58.830 45.455 23.35 0.00 34.13 4.26
2105 4498 4.359434 TTTCATGTAGGTAACCACTGCA 57.641 40.909 0.00 0.00 35.10 4.41
2106 4499 6.821665 TCTTATTTCATGTAGGTAACCACTGC 59.178 38.462 0.00 0.00 37.17 4.40
2229 4644 1.931841 CATGTCCGAGCTGTCTGATTG 59.068 52.381 0.00 0.00 0.00 2.67
2231 4646 0.463204 CCATGTCCGAGCTGTCTGAT 59.537 55.000 0.00 0.00 0.00 2.90
2282 4697 2.662006 TGAACCAAGAGAGCTCATCG 57.338 50.000 17.77 0.79 0.00 3.84
2345 4760 4.235372 ACTCCATATTAGAACTGAGGGGG 58.765 47.826 0.00 0.00 0.00 5.40
2378 4877 3.213206 TGGCAGTGTTTGACAGAGATT 57.787 42.857 0.00 0.00 40.88 2.40
2385 4886 3.715628 AGAATTGTGGCAGTGTTTGAC 57.284 42.857 0.00 0.00 34.37 3.18
2386 4887 4.203226 TGTAGAATTGTGGCAGTGTTTGA 58.797 39.130 0.00 0.00 0.00 2.69
2393 4894 5.245531 TCTAAGGTTGTAGAATTGTGGCAG 58.754 41.667 0.00 0.00 0.00 4.85
2395 4896 5.122396 CACTCTAAGGTTGTAGAATTGTGGC 59.878 44.000 0.00 0.00 29.74 5.01
2396 4897 5.122396 GCACTCTAAGGTTGTAGAATTGTGG 59.878 44.000 0.00 0.00 30.28 4.17
2404 4905 6.282199 TCCTTTAGCACTCTAAGGTTGTAG 57.718 41.667 9.88 0.00 36.27 2.74
2432 4935 8.109634 CCTGGCCATAAGAATAATACCATAGTT 58.890 37.037 5.51 0.00 0.00 2.24
2447 4950 2.239654 TCTGGAGAAACCTGGCCATAAG 59.760 50.000 5.51 0.00 39.86 1.73
2553 5056 5.582665 GTCTTGTTACCTTCTTCTATGCAGG 59.417 44.000 0.00 0.00 0.00 4.85
2594 5097 1.341156 CCCCATCTCTGACAGGTCCC 61.341 65.000 1.81 0.00 0.00 4.46
2794 5304 1.957186 TCCAAGTAACGCACGGTGC 60.957 57.895 22.78 22.78 40.69 5.01
2799 5309 3.922240 TCTATTTCGTCCAAGTAACGCAC 59.078 43.478 0.00 0.00 39.90 5.34
2803 5320 5.502544 GCAGCATCTATTTCGTCCAAGTAAC 60.503 44.000 0.00 0.00 0.00 2.50
2825 5342 1.412079 AAAATGCTGAACCCACTGCA 58.588 45.000 0.00 0.00 45.48 4.41
2877 5395 2.487762 CAGGTTATTGCACGGTGTTCAT 59.512 45.455 10.24 2.44 0.00 2.57
2998 5516 3.619929 ACCGACAAAAACATCTATACCGC 59.380 43.478 0.00 0.00 0.00 5.68
3039 5557 0.179032 TGCAGCCGAGGTTTTCAGAA 60.179 50.000 0.00 0.00 0.00 3.02
3040 5558 0.179032 TTGCAGCCGAGGTTTTCAGA 60.179 50.000 0.00 0.00 0.00 3.27
3059 5577 5.522460 CGGACAAAAACATCTATACCGACAT 59.478 40.000 0.00 0.00 40.16 3.06
3082 5600 6.959361 AGAAGCCAGCATAAAAATACATACG 58.041 36.000 0.00 0.00 0.00 3.06
3137 5761 4.959631 TTCAGTTCGCTACAAACTTACG 57.040 40.909 0.00 0.00 34.79 3.18
3181 5805 3.619483 TCAGTAACTGGTTGTGACGTTTG 59.381 43.478 0.00 0.00 35.16 2.93
3199 5823 6.360844 GTCATATGACGTACTGTACTCAGT 57.639 41.667 19.63 6.55 44.52 3.41
3202 5826 4.820716 AGGGTCATATGACGTACTGTACTC 59.179 45.833 25.65 10.43 45.65 2.59
3230 5855 3.909776 CAGCATGCTCTTTCAGAAACA 57.090 42.857 19.68 0.00 0.00 2.83
3322 5967 5.279506 GGATCGAAACCTGGCTCTGATATTA 60.280 44.000 0.00 0.00 0.00 0.98
3408 6053 6.717289 TGTTAATTAGTGCCCACTCAACTAT 58.283 36.000 3.88 0.00 42.54 2.12
3411 6056 5.393027 CCATGTTAATTAGTGCCCACTCAAC 60.393 44.000 3.88 6.28 42.54 3.18
3416 6061 4.013728 TGACCATGTTAATTAGTGCCCAC 58.986 43.478 0.00 0.00 0.00 4.61
3417 6062 4.013728 GTGACCATGTTAATTAGTGCCCA 58.986 43.478 0.00 0.00 0.00 5.36
3418 6063 4.270008 AGTGACCATGTTAATTAGTGCCC 58.730 43.478 0.00 0.00 0.00 5.36
3420 6065 4.494199 GCGAGTGACCATGTTAATTAGTGC 60.494 45.833 0.00 0.00 0.00 4.40
3421 6066 4.629634 TGCGAGTGACCATGTTAATTAGTG 59.370 41.667 0.00 0.00 0.00 2.74
3425 6070 4.517285 AGATGCGAGTGACCATGTTAATT 58.483 39.130 0.00 0.00 0.00 1.40
3430 6076 1.730501 CAAGATGCGAGTGACCATGT 58.269 50.000 0.00 0.00 0.00 3.21
3435 6081 0.445436 CAAGGCAAGATGCGAGTGAC 59.555 55.000 0.00 0.00 46.21 3.67
3437 6083 1.376543 ATCAAGGCAAGATGCGAGTG 58.623 50.000 0.00 0.00 46.21 3.51
3438 6084 2.988010 TATCAAGGCAAGATGCGAGT 57.012 45.000 2.43 0.00 46.21 4.18
3445 6091 9.440773 GTGTGATATCATATTATCAAGGCAAGA 57.559 33.333 9.02 0.00 39.61 3.02
3460 6106 7.904558 TTAGGAGTTCTGAGTGTGATATCAT 57.095 36.000 9.02 0.00 0.00 2.45
3540 6186 7.475771 TGTTGCTTTATTTTGTTTGGCTTAG 57.524 32.000 0.00 0.00 0.00 2.18
3549 6195 7.680442 AGTTTGGTTTGTTGCTTTATTTTGT 57.320 28.000 0.00 0.00 0.00 2.83
3575 6221 0.899717 ATTGGCATCTTGGGCGTGTT 60.900 50.000 0.00 0.00 35.84 3.32
3613 6259 3.673956 ATTGCCGGCCGTCATTCGA 62.674 57.895 26.77 1.66 42.86 3.71
3614 6260 3.202001 ATTGCCGGCCGTCATTCG 61.202 61.111 26.77 8.60 39.52 3.34
3654 6314 3.181967 GACAGCTAGCCGTGCGTG 61.182 66.667 8.68 2.86 35.28 5.34


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

AutoCloner maintained by Alex Coulton.