Multiple sequence alignment - TraesCS2A01G379000

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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 TraesCS2A01G379000 chr2A 100.000 3047 0 0 1 3047 621919598 621922644 0.000000e+00 5627.0
1 TraesCS2A01G379000 chr2A 100.000 642 0 0 3363 4004 621922960 621923601 0.000000e+00 1186.0
2 TraesCS2A01G379000 chr2A 88.816 152 14 3 1 151 621913795 621913944 2.460000e-42 183.0
3 TraesCS2A01G379000 chr2A 87.500 152 16 3 1 151 621911011 621911160 5.320000e-39 172.0
4 TraesCS2A01G379000 chr2D 91.643 2094 92 33 151 2202 479178363 479180415 0.000000e+00 2820.0
5 TraesCS2A01G379000 chr2D 95.360 819 32 3 2197 3011 479180443 479181259 0.000000e+00 1297.0
6 TraesCS2A01G379000 chr2D 94.717 530 24 4 3363 3892 479181330 479181855 0.000000e+00 821.0
7 TraesCS2A01G379000 chr2B 92.082 1604 75 14 151 1728 562216511 562218088 0.000000e+00 2211.0
8 TraesCS2A01G379000 chr2B 95.770 851 29 5 2197 3047 562218572 562219415 0.000000e+00 1365.0
9 TraesCS2A01G379000 chr2B 93.925 642 33 4 3363 4004 562219468 562220103 0.000000e+00 965.0
10 TraesCS2A01G379000 chr2B 96.606 442 9 4 1761 2202 562218094 562218529 0.000000e+00 728.0
11 TraesCS2A01G379000 chr4D 88.147 464 46 7 1028 1491 441900908 441901362 9.790000e-151 544.0
12 TraesCS2A01G379000 chr4D 89.840 374 32 5 2200 2571 441901420 441901789 3.620000e-130 475.0
13 TraesCS2A01G379000 chr4D 89.873 237 24 0 2727 2963 441901781 441902017 5.030000e-79 305.0
14 TraesCS2A01G379000 chr4A 87.284 464 50 6 1028 1491 25497771 25497317 4.590000e-144 521.0
15 TraesCS2A01G379000 chr4A 90.054 372 37 0 2200 2571 25497257 25496886 2.160000e-132 483.0
16 TraesCS2A01G379000 chr4A 88.048 251 26 3 2730 2978 25496891 25496643 1.090000e-75 294.0
17 TraesCS2A01G379000 chr4B 86.853 464 52 6 1028 1491 548766813 548767267 9.930000e-141 510.0
18 TraesCS2A01G379000 chr4B 90.323 372 33 3 2200 2571 548767325 548767693 6.020000e-133 484.0
19 TraesCS2A01G379000 chr4B 89.867 375 29 6 1120 1494 659689552 659689187 1.300000e-129 473.0
20 TraesCS2A01G379000 chr4B 87.786 393 38 7 1107 1494 660089991 660090378 6.100000e-123 451.0
21 TraesCS2A01G379000 chr4B 87.464 351 33 4 2229 2578 660090483 660090823 1.040000e-105 394.0
22 TraesCS2A01G379000 chr4B 85.638 376 48 5 2201 2576 659689157 659688788 1.350000e-104 390.0
23 TraesCS2A01G379000 chr4B 89.451 237 25 0 2727 2963 548767685 548767921 2.340000e-77 300.0
24 TraesCS2A01G379000 chr5A 82.617 512 70 13 991 1488 698888608 698889114 6.150000e-118 435.0
25 TraesCS2A01G379000 chr5A 90.535 243 23 0 2720 2962 698889653 698889895 4.990000e-84 322.0
26 TraesCS2A01G379000 chr5A 89.344 244 23 3 2720 2962 698896128 698896369 1.810000e-78 303.0
27 TraesCS2A01G379000 chr5A 88.742 151 17 0 1290 1440 698820530 698820680 6.830000e-43 185.0
28 TraesCS2A01G379000 chr6B 81.341 343 51 12 2233 2573 468010423 468010092 2.370000e-67 267.0
29 TraesCS2A01G379000 chr6D 81.050 343 52 12 2233 2573 302249725 302249394 1.100000e-65 261.0
30 TraesCS2A01G379000 chr7A 91.667 60 5 0 2720 2779 135533711 135533770 2.560000e-12 84.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G379000 chr2A 621919598 621923601 4003 False 3406.500000 5627 100.000000 1 4004 2 chr2A.!!$F2 4003
1 TraesCS2A01G379000 chr2D 479178363 479181855 3492 False 1646.000000 2820 93.906667 151 3892 3 chr2D.!!$F1 3741
2 TraesCS2A01G379000 chr2B 562216511 562220103 3592 False 1317.250000 2211 94.595750 151 4004 4 chr2B.!!$F1 3853
3 TraesCS2A01G379000 chr4D 441900908 441902017 1109 False 441.333333 544 89.286667 1028 2963 3 chr4D.!!$F1 1935
4 TraesCS2A01G379000 chr4A 25496643 25497771 1128 True 432.666667 521 88.462000 1028 2978 3 chr4A.!!$R1 1950
5 TraesCS2A01G379000 chr4B 659688788 659689552 764 True 431.500000 473 87.752500 1120 2576 2 chr4B.!!$R1 1456
6 TraesCS2A01G379000 chr4B 548766813 548767921 1108 False 431.333333 510 88.875667 1028 2963 3 chr4B.!!$F1 1935
7 TraesCS2A01G379000 chr4B 660089991 660090823 832 False 422.500000 451 87.625000 1107 2578 2 chr4B.!!$F2 1471
8 TraesCS2A01G379000 chr5A 698888608 698889895 1287 False 378.500000 435 86.576000 991 2962 2 chr5A.!!$F3 1971

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
130 131 0.033642 TGCAAACGGGTCATGACGTA 59.966 50.0 19.33 1.45 43.31 3.57 F
149 150 0.036875 AGTACCTTTGTCCCTGCTGC 59.963 55.0 0.00 0.00 0.00 5.25 F
812 849 0.681564 ATATAGGCCTCTCGCTCCCG 60.682 60.0 9.68 0.00 37.74 5.14 F
979 1022 0.801067 CGCACGTGTCTAAGCTACCC 60.801 60.0 18.38 0.00 0.00 3.69 F
1756 1838 1.092345 GGAAGAAGATGGAGGCACGC 61.092 60.0 0.00 0.00 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 2056 0.963962 GACACTGTACACGGAAGGGA 59.036 55.00 0.00 0.0 38.45 4.20 R
2148 2241 5.401531 AAATTCTCGCCTAGTGTGACTAA 57.598 39.13 0.00 0.0 29.00 2.24 R
2613 2773 1.247567 CTTGGTCAAAACTCCGGCAT 58.752 50.00 0.00 0.0 0.00 4.40 R
2650 2810 1.389555 AGTACCATCTGATGCGACGA 58.610 50.00 12.17 0.0 0.00 4.20 R
3492 3675 0.822121 AGGGACAAACAAACGGGAGC 60.822 55.00 0.00 0.0 0.00 4.70 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 6.158023 ACCGATCTAATGGAAATCGTTAGT 57.842 37.500 0.00 0.00 42.63 2.24
24 25 6.214399 ACCGATCTAATGGAAATCGTTAGTC 58.786 40.000 0.00 0.00 42.63 2.59
25 26 6.040616 ACCGATCTAATGGAAATCGTTAGTCT 59.959 38.462 0.00 0.00 42.63 3.24
26 27 7.230108 ACCGATCTAATGGAAATCGTTAGTCTA 59.770 37.037 0.00 0.00 42.63 2.59
27 28 8.080417 CCGATCTAATGGAAATCGTTAGTCTAA 58.920 37.037 0.00 0.00 42.63 2.10
28 29 9.459640 CGATCTAATGGAAATCGTTAGTCTAAA 57.540 33.333 0.00 0.00 42.63 1.85
32 33 7.541122 AATGGAAATCGTTAGTCTAAAGAGC 57.459 36.000 12.77 6.05 30.10 4.09
33 34 6.032956 TGGAAATCGTTAGTCTAAAGAGCA 57.967 37.500 12.77 0.00 30.10 4.26
34 35 6.460781 TGGAAATCGTTAGTCTAAAGAGCAA 58.539 36.000 12.77 0.00 30.10 3.91
35 36 7.103641 TGGAAATCGTTAGTCTAAAGAGCAAT 58.896 34.615 12.77 1.28 30.10 3.56
36 37 7.277981 TGGAAATCGTTAGTCTAAAGAGCAATC 59.722 37.037 12.77 8.40 30.10 2.67
37 38 7.492994 GGAAATCGTTAGTCTAAAGAGCAATCT 59.507 37.037 12.77 0.00 30.10 2.40
38 39 7.995463 AATCGTTAGTCTAAAGAGCAATCTC 57.005 36.000 12.77 0.00 39.65 2.75
47 48 2.675519 GAGCAATCTCTGTCGGCTG 58.324 57.895 0.00 0.00 36.42 4.85
48 49 0.108424 GAGCAATCTCTGTCGGCTGT 60.108 55.000 0.00 0.00 36.42 4.40
49 50 0.108424 AGCAATCTCTGTCGGCTGTC 60.108 55.000 0.00 0.00 32.76 3.51
50 51 0.390340 GCAATCTCTGTCGGCTGTCA 60.390 55.000 0.00 0.00 0.00 3.58
51 52 1.941209 GCAATCTCTGTCGGCTGTCAA 60.941 52.381 0.00 0.00 0.00 3.18
52 53 1.728971 CAATCTCTGTCGGCTGTCAAC 59.271 52.381 0.00 0.00 0.00 3.18
53 54 0.247736 ATCTCTGTCGGCTGTCAACC 59.752 55.000 0.00 0.00 0.00 3.77
54 55 1.374758 CTCTGTCGGCTGTCAACCC 60.375 63.158 0.00 0.00 0.00 4.11
55 56 2.738521 CTGTCGGCTGTCAACCCG 60.739 66.667 5.46 5.46 45.64 5.28
56 57 4.980805 TGTCGGCTGTCAACCCGC 62.981 66.667 6.70 3.88 44.01 6.13
62 63 4.308458 CTGTCAACCCGCCCACGA 62.308 66.667 0.00 0.00 43.93 4.35
63 64 4.308458 TGTCAACCCGCCCACGAG 62.308 66.667 0.00 0.00 43.93 4.18
74 75 4.431131 CCACGAGGGCCCAGCAAT 62.431 66.667 27.56 0.88 0.00 3.56
75 76 3.136123 CACGAGGGCCCAGCAATG 61.136 66.667 27.56 12.57 0.00 2.82
77 78 4.809496 CGAGGGCCCAGCAATGCT 62.809 66.667 27.56 0.00 40.77 3.79
103 104 4.061570 GCAGCATTGCTCAAATTTGAAC 57.938 40.909 20.82 17.08 46.95 3.18
104 105 3.422603 GCAGCATTGCTCAAATTTGAACG 60.423 43.478 20.82 11.91 46.95 3.95
105 106 3.122278 CAGCATTGCTCAAATTTGAACGG 59.878 43.478 20.82 11.24 36.40 4.44
106 107 2.159801 GCATTGCTCAAATTTGAACGGC 60.160 45.455 20.82 19.76 36.64 5.68
107 108 2.879002 TTGCTCAAATTTGAACGGCA 57.121 40.000 22.62 22.62 36.64 5.69
108 109 2.879002 TGCTCAAATTTGAACGGCAA 57.121 40.000 23.65 12.27 34.35 4.52
109 110 2.741612 TGCTCAAATTTGAACGGCAAG 58.258 42.857 23.65 12.22 37.87 4.01
110 111 2.360483 TGCTCAAATTTGAACGGCAAGA 59.640 40.909 23.65 7.80 37.87 3.02
111 112 3.005684 TGCTCAAATTTGAACGGCAAGAT 59.994 39.130 23.65 0.00 37.87 2.40
112 113 3.365820 GCTCAAATTTGAACGGCAAGATG 59.634 43.478 20.82 7.25 37.87 2.90
113 114 3.316283 TCAAATTTGAACGGCAAGATGC 58.684 40.909 18.45 0.00 37.87 3.91
114 115 3.243670 TCAAATTTGAACGGCAAGATGCA 60.244 39.130 18.45 0.00 38.65 3.96
115 116 4.738839 TCAAATTTGAACGGCAAGATGCAA 60.739 37.500 18.45 0.00 38.65 4.08
116 117 6.195082 TCAAATTTGAACGGCAAGATGCAAA 61.195 36.000 18.45 0.00 38.65 3.68
117 118 8.145106 TCAAATTTGAACGGCAAGATGCAAAC 62.145 38.462 18.45 0.00 38.65 2.93
122 123 4.868195 GCAAGATGCAAACGGGTC 57.132 55.556 0.00 0.00 44.26 4.46
123 124 1.956043 GCAAGATGCAAACGGGTCA 59.044 52.632 0.00 0.00 44.26 4.02
124 125 0.527565 GCAAGATGCAAACGGGTCAT 59.472 50.000 0.00 0.00 44.26 3.06
125 126 1.733389 GCAAGATGCAAACGGGTCATG 60.733 52.381 0.00 0.00 44.26 3.07
126 127 1.811965 CAAGATGCAAACGGGTCATGA 59.188 47.619 0.00 0.00 0.00 3.07
127 128 1.453155 AGATGCAAACGGGTCATGAC 58.547 50.000 17.91 17.91 0.00 3.06
128 129 0.096976 GATGCAAACGGGTCATGACG 59.903 55.000 19.33 11.71 0.00 4.35
129 130 0.605319 ATGCAAACGGGTCATGACGT 60.605 50.000 19.33 12.39 46.48 4.34
130 131 0.033642 TGCAAACGGGTCATGACGTA 59.966 50.000 19.33 1.45 43.31 3.57
131 132 0.719465 GCAAACGGGTCATGACGTAG 59.281 55.000 19.33 14.56 43.31 3.51
146 147 1.274447 ACGTAGTACCTTTGTCCCTGC 59.726 52.381 0.00 0.00 41.94 4.85
147 148 1.549170 CGTAGTACCTTTGTCCCTGCT 59.451 52.381 0.00 0.00 0.00 4.24
148 149 2.674177 CGTAGTACCTTTGTCCCTGCTG 60.674 54.545 0.00 0.00 0.00 4.41
149 150 0.036875 AGTACCTTTGTCCCTGCTGC 59.963 55.000 0.00 0.00 0.00 5.25
162 163 5.104527 TGTCCCTGCTGCTAATTAACACTAT 60.105 40.000 0.00 0.00 0.00 2.12
193 194 1.202268 GCAACCATCATGCTTGAGCTC 60.202 52.381 6.82 6.82 42.66 4.09
229 230 2.225491 CACTCGAGATAGAGCCAGCTAC 59.775 54.545 21.68 0.00 41.77 3.58
230 231 1.463056 CTCGAGATAGAGCCAGCTACG 59.537 57.143 6.58 0.00 0.00 3.51
252 253 2.438411 AGAAGCTGTGCGAGTAGTACT 58.562 47.619 1.37 1.37 36.37 2.73
253 254 3.607741 AGAAGCTGTGCGAGTAGTACTA 58.392 45.455 1.88 0.00 36.37 1.82
254 255 3.623960 AGAAGCTGTGCGAGTAGTACTAG 59.376 47.826 1.87 4.26 36.37 2.57
255 256 2.988570 AGCTGTGCGAGTAGTACTAGT 58.011 47.619 10.09 10.09 36.37 2.57
256 257 4.134379 AGCTGTGCGAGTAGTACTAGTA 57.866 45.455 10.28 0.00 36.37 1.82
257 258 3.870419 AGCTGTGCGAGTAGTACTAGTAC 59.130 47.826 23.03 23.03 37.08 2.73
298 299 6.071952 ACGGAATGATCAAAATTGCACTTACT 60.072 34.615 0.00 0.00 0.00 2.24
299 300 7.120579 ACGGAATGATCAAAATTGCACTTACTA 59.879 33.333 0.00 0.00 0.00 1.82
300 301 7.429340 CGGAATGATCAAAATTGCACTTACTAC 59.571 37.037 0.00 0.00 0.00 2.73
309 310 2.232399 TGCACTTACTACCTGTCGTCA 58.768 47.619 0.00 0.00 0.00 4.35
313 314 4.558095 GCACTTACTACCTGTCGTCAGAAA 60.558 45.833 11.41 0.00 43.76 2.52
314 315 5.710984 CACTTACTACCTGTCGTCAGAAAT 58.289 41.667 11.41 0.00 43.76 2.17
315 316 6.157211 CACTTACTACCTGTCGTCAGAAATT 58.843 40.000 11.41 0.00 43.76 1.82
376 377 9.186323 CATACAGTAGTACATCAACATTAGAGC 57.814 37.037 2.52 0.00 31.96 4.09
397 402 1.661463 AGTGCCATGGAGAAGAAGGA 58.339 50.000 18.40 0.00 0.00 3.36
431 437 3.607422 TGTGCATCTCAAGAAACAACG 57.393 42.857 0.00 0.00 0.00 4.10
446 452 8.869897 CAAGAAACAACGAGTAGCTATGAATTA 58.130 33.333 0.00 0.00 0.00 1.40
464 470 1.504359 TAGGACCTTTTGCAACGTCG 58.496 50.000 0.00 0.00 0.00 5.12
561 571 1.082756 GTTGCGCGGTCAAAGACAG 60.083 57.895 8.83 0.00 33.68 3.51
648 665 2.351336 ATCGCTCGAAACGGCTAGGG 62.351 60.000 7.56 0.00 0.00 3.53
809 846 5.860611 TCTCTATATATAGGCCTCTCGCTC 58.139 45.833 9.68 0.00 37.74 5.03
812 849 0.681564 ATATAGGCCTCTCGCTCCCG 60.682 60.000 9.68 0.00 37.74 5.14
828 865 1.676529 TCCCGAGATCTTTCGTAGCAG 59.323 52.381 0.00 0.00 38.88 4.24
872 909 4.514577 CGAGCGGCCCAGTGGTAG 62.515 72.222 8.74 0.00 0.00 3.18
873 910 4.840005 GAGCGGCCCAGTGGTAGC 62.840 72.222 8.74 10.34 36.73 3.58
959 1002 2.409651 GCTAGCTAGACGCACGCT 59.590 61.111 25.15 0.00 42.61 5.07
972 1015 2.640989 ACGCTCGCACGTGTCTAA 59.359 55.556 18.38 0.00 46.28 2.10
979 1022 0.801067 CGCACGTGTCTAAGCTACCC 60.801 60.000 18.38 0.00 0.00 3.69
1555 1637 2.300152 CCCTGCTTACTCTGTCAGACAA 59.700 50.000 4.41 0.00 0.00 3.18
1571 1653 2.157668 AGACAATTAGCGAACGTGCTTG 59.842 45.455 5.64 1.53 44.46 4.01
1573 1655 2.096417 ACAATTAGCGAACGTGCTTGAC 60.096 45.455 5.64 0.00 44.46 3.18
1576 1658 2.933495 TAGCGAACGTGCTTGACTAT 57.067 45.000 5.64 0.00 44.46 2.12
1682 1764 3.126957 GCGCGCGATCGTTAGTAG 58.873 61.111 37.18 0.00 38.14 2.57
1753 1835 1.561542 GAAGGGAAGAAGATGGAGGCA 59.438 52.381 0.00 0.00 0.00 4.75
1756 1838 1.092345 GGAAGAAGATGGAGGCACGC 61.092 60.000 0.00 0.00 0.00 5.34
1778 1861 3.303791 CGGCAAACTTTCCTGTCAACTAC 60.304 47.826 0.00 0.00 0.00 2.73
1926 2009 2.391972 CCTACCAACCCCATCCCCC 61.392 68.421 0.00 0.00 0.00 5.40
1944 2027 2.978978 CCCCAGGACCATGATACATACA 59.021 50.000 0.00 0.00 0.00 2.29
1973 2056 1.398958 AATTTGTGTGCTGCGGGGTT 61.399 50.000 0.00 0.00 0.00 4.11
2096 2179 7.675270 GCATGAGCACTTGTTTCAATATTAG 57.325 36.000 0.00 0.00 41.58 1.73
2127 2220 7.716560 TGACCATGAATCTAATCTGGTTACATG 59.283 37.037 0.00 0.00 40.22 3.21
2398 2550 3.065306 CTCAACAGGTACCCGGCA 58.935 61.111 8.74 0.00 0.00 5.69
2613 2773 6.734137 CGTTTTACCCCATATACGTACTACA 58.266 40.000 0.00 0.00 0.00 2.74
2650 2810 0.033011 AGCAGAGAGGTGTACCCGAT 60.033 55.000 0.00 0.00 38.74 4.18
2708 2869 3.791353 CGCATTTTTCGCCTTCTTATTCC 59.209 43.478 0.00 0.00 0.00 3.01
2709 2870 4.674101 CGCATTTTTCGCCTTCTTATTCCA 60.674 41.667 0.00 0.00 0.00 3.53
2998 3181 2.420547 GCCATGAATCACAGCCTCTGTA 60.421 50.000 0.00 0.00 43.43 2.74
3008 3191 2.626743 ACAGCCTCTGTACTTAACACGT 59.373 45.455 0.00 0.00 43.46 4.49
3010 3193 4.164294 CAGCCTCTGTACTTAACACGTAC 58.836 47.826 0.00 0.00 38.13 3.67
3011 3194 3.822735 AGCCTCTGTACTTAACACGTACA 59.177 43.478 6.16 6.16 43.41 2.90
3019 3202 7.962964 TGTACTTAACACGTACAGTAGTACT 57.037 36.000 19.13 0.00 41.47 2.73
3020 3203 7.796838 TGTACTTAACACGTACAGTAGTACTG 58.203 38.462 25.56 25.56 41.47 2.74
3021 3204 7.441157 TGTACTTAACACGTACAGTAGTACTGT 59.559 37.037 32.60 32.60 46.63 3.55
3391 3574 9.204570 TCTGTTTCTATTCTAGTTTTCTTTCGG 57.795 33.333 0.00 0.00 0.00 4.30
3492 3675 0.752658 TGATACGTCTGCCCATCTGG 59.247 55.000 0.00 0.00 37.09 3.86
3508 3691 0.310854 CTGGCTCCCGTTTGTTTGTC 59.689 55.000 0.00 0.00 0.00 3.18
3535 3718 3.720949 TCCTTCTTTTCGTCTTGTCGA 57.279 42.857 0.00 0.00 38.08 4.20
3626 3809 9.462174 TGTTTTCACTAGACAAGCATATTTTTG 57.538 29.630 0.00 0.00 0.00 2.44
3817 4000 5.763876 AGTTAGAGAGGGTTTTGCATAGT 57.236 39.130 0.00 0.00 0.00 2.12
3896 4079 8.691797 TGGCCATTCTGTTAGGAATATTTTTAC 58.308 33.333 0.00 0.00 34.59 2.01
3898 4081 7.860872 GCCATTCTGTTAGGAATATTTTTACCG 59.139 37.037 0.00 0.00 34.59 4.02
3919 4102 2.544694 GGACATGCTGATCCACTACTCG 60.545 54.545 0.00 0.00 34.87 4.18
3933 4116 4.695455 CCACTACTCGTTGATGGAATGTTT 59.305 41.667 0.00 0.00 31.69 2.83
3949 4132 8.755696 TGGAATGTTTTGCATTTCAATACTAC 57.244 30.769 0.00 0.00 46.91 2.73
3950 4133 8.363390 TGGAATGTTTTGCATTTCAATACTACA 58.637 29.630 0.00 0.00 46.91 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.040616 AGACTAACGATTTCCATTAGATCGGT 59.959 38.462 9.39 5.48 45.00 4.69
1 2 6.448006 AGACTAACGATTTCCATTAGATCGG 58.552 40.000 9.39 0.00 45.00 4.18
6 7 8.756864 GCTCTTTAGACTAACGATTTCCATTAG 58.243 37.037 2.18 0.00 33.08 1.73
7 8 8.255206 TGCTCTTTAGACTAACGATTTCCATTA 58.745 33.333 2.18 0.00 0.00 1.90
8 9 7.103641 TGCTCTTTAGACTAACGATTTCCATT 58.896 34.615 2.18 0.00 0.00 3.16
9 10 6.640518 TGCTCTTTAGACTAACGATTTCCAT 58.359 36.000 2.18 0.00 0.00 3.41
10 11 6.032956 TGCTCTTTAGACTAACGATTTCCA 57.967 37.500 2.18 0.00 0.00 3.53
11 12 6.963049 TTGCTCTTTAGACTAACGATTTCC 57.037 37.500 2.18 0.00 0.00 3.13
12 13 8.413899 AGATTGCTCTTTAGACTAACGATTTC 57.586 34.615 2.18 0.00 0.00 2.17
13 14 8.413899 GAGATTGCTCTTTAGACTAACGATTT 57.586 34.615 2.18 0.00 38.16 2.17
14 15 7.995463 GAGATTGCTCTTTAGACTAACGATT 57.005 36.000 2.18 0.00 38.16 3.34
29 30 0.108424 ACAGCCGACAGAGATTGCTC 60.108 55.000 0.00 0.00 41.62 4.26
30 31 0.108424 GACAGCCGACAGAGATTGCT 60.108 55.000 0.00 0.00 0.00 3.91
31 32 0.390340 TGACAGCCGACAGAGATTGC 60.390 55.000 0.00 0.00 0.00 3.56
32 33 1.728971 GTTGACAGCCGACAGAGATTG 59.271 52.381 0.00 0.00 0.00 2.67
33 34 1.338200 GGTTGACAGCCGACAGAGATT 60.338 52.381 0.00 0.00 0.00 2.40
34 35 0.247736 GGTTGACAGCCGACAGAGAT 59.752 55.000 0.00 0.00 0.00 2.75
35 36 1.666011 GGTTGACAGCCGACAGAGA 59.334 57.895 0.00 0.00 0.00 3.10
36 37 1.374758 GGGTTGACAGCCGACAGAG 60.375 63.158 1.86 0.00 0.00 3.35
37 38 2.741092 GGGTTGACAGCCGACAGA 59.259 61.111 1.86 0.00 0.00 3.41
45 46 4.308458 TCGTGGGCGGGTTGACAG 62.308 66.667 0.00 0.00 38.89 3.51
46 47 4.308458 CTCGTGGGCGGGTTGACA 62.308 66.667 0.00 0.00 38.89 3.58
57 58 4.431131 ATTGCTGGGCCCTCGTGG 62.431 66.667 25.70 9.02 37.09 4.94
58 59 3.136123 CATTGCTGGGCCCTCGTG 61.136 66.667 25.70 13.30 0.00 4.35
60 61 4.809496 AGCATTGCTGGGCCCTCG 62.809 66.667 25.70 15.49 37.57 4.63
83 84 3.122278 CCGTTCAAATTTGAGCAATGCTG 59.878 43.478 27.66 14.26 39.88 4.41
84 85 3.319755 CCGTTCAAATTTGAGCAATGCT 58.680 40.909 27.66 7.79 43.88 3.79
85 86 2.159801 GCCGTTCAAATTTGAGCAATGC 60.160 45.455 27.66 22.69 38.17 3.56
86 87 3.058450 TGCCGTTCAAATTTGAGCAATG 58.942 40.909 27.66 18.52 38.17 2.82
87 88 3.383620 TGCCGTTCAAATTTGAGCAAT 57.616 38.095 27.66 0.00 38.17 3.56
88 89 2.879002 TGCCGTTCAAATTTGAGCAA 57.121 40.000 27.66 14.24 38.17 3.91
89 90 2.360483 TCTTGCCGTTCAAATTTGAGCA 59.640 40.909 27.66 25.10 38.17 4.26
90 91 3.011949 TCTTGCCGTTCAAATTTGAGC 57.988 42.857 21.30 21.30 38.61 4.26
91 92 3.365820 GCATCTTGCCGTTCAAATTTGAG 59.634 43.478 19.64 10.66 37.42 3.02
92 93 3.243670 TGCATCTTGCCGTTCAAATTTGA 60.244 39.130 16.91 16.91 44.23 2.69
93 94 3.058450 TGCATCTTGCCGTTCAAATTTG 58.942 40.909 12.15 12.15 44.23 2.32
94 95 3.383620 TGCATCTTGCCGTTCAAATTT 57.616 38.095 0.00 0.00 44.23 1.82
95 96 3.383620 TTGCATCTTGCCGTTCAAATT 57.616 38.095 0.00 0.00 44.23 1.82
96 97 3.059166 GTTTGCATCTTGCCGTTCAAAT 58.941 40.909 0.00 0.00 44.23 2.32
97 98 2.468831 GTTTGCATCTTGCCGTTCAAA 58.531 42.857 0.00 0.00 44.23 2.69
98 99 1.599171 CGTTTGCATCTTGCCGTTCAA 60.599 47.619 0.00 0.00 44.23 2.69
99 100 0.040514 CGTTTGCATCTTGCCGTTCA 60.041 50.000 0.00 0.00 44.23 3.18
100 101 0.729140 CCGTTTGCATCTTGCCGTTC 60.729 55.000 0.00 0.00 44.23 3.95
101 102 1.285641 CCGTTTGCATCTTGCCGTT 59.714 52.632 0.00 0.00 44.23 4.44
102 103 2.625823 CCCGTTTGCATCTTGCCGT 61.626 57.895 0.00 0.00 44.23 5.68
103 104 2.179018 CCCGTTTGCATCTTGCCG 59.821 61.111 0.00 0.00 44.23 5.69
104 105 1.212751 GACCCGTTTGCATCTTGCC 59.787 57.895 0.00 0.00 44.23 4.52
105 106 0.527565 ATGACCCGTTTGCATCTTGC 59.472 50.000 0.00 0.00 45.29 4.01
106 107 1.811965 TCATGACCCGTTTGCATCTTG 59.188 47.619 0.00 0.00 0.00 3.02
107 108 1.812571 GTCATGACCCGTTTGCATCTT 59.187 47.619 15.31 0.00 0.00 2.40
108 109 1.453155 GTCATGACCCGTTTGCATCT 58.547 50.000 15.31 0.00 0.00 2.90
109 110 0.096976 CGTCATGACCCGTTTGCATC 59.903 55.000 20.03 0.00 0.00 3.91
110 111 0.605319 ACGTCATGACCCGTTTGCAT 60.605 50.000 20.03 0.00 32.50 3.96
111 112 0.033642 TACGTCATGACCCGTTTGCA 59.966 50.000 20.03 0.00 38.43 4.08
112 113 0.719465 CTACGTCATGACCCGTTTGC 59.281 55.000 20.03 0.00 38.43 3.68
113 114 2.074547 ACTACGTCATGACCCGTTTG 57.925 50.000 20.03 13.17 38.43 2.93
114 115 2.094545 GGTACTACGTCATGACCCGTTT 60.095 50.000 20.03 8.64 38.43 3.60
115 116 1.474077 GGTACTACGTCATGACCCGTT 59.526 52.381 20.03 4.50 38.43 4.44
116 117 1.098050 GGTACTACGTCATGACCCGT 58.902 55.000 20.03 17.14 40.87 5.28
117 118 1.386533 AGGTACTACGTCATGACCCG 58.613 55.000 20.03 12.00 36.02 5.28
118 119 3.056322 ACAAAGGTACTACGTCATGACCC 60.056 47.826 20.03 13.56 38.49 4.46
119 120 4.171754 GACAAAGGTACTACGTCATGACC 58.828 47.826 20.03 4.81 38.49 4.02
120 121 4.171754 GGACAAAGGTACTACGTCATGAC 58.828 47.826 16.21 16.21 40.28 3.06
121 122 3.194116 GGGACAAAGGTACTACGTCATGA 59.806 47.826 0.00 0.00 40.28 3.07
122 123 3.194968 AGGGACAAAGGTACTACGTCATG 59.805 47.826 0.00 0.00 40.28 3.07
123 124 3.194968 CAGGGACAAAGGTACTACGTCAT 59.805 47.826 0.00 0.00 40.28 3.06
124 125 2.559668 CAGGGACAAAGGTACTACGTCA 59.440 50.000 0.00 0.00 40.28 4.35
125 126 2.673326 GCAGGGACAAAGGTACTACGTC 60.673 54.545 0.00 0.00 38.49 4.34
126 127 1.274447 GCAGGGACAAAGGTACTACGT 59.726 52.381 0.00 0.00 38.49 3.57
127 128 1.549170 AGCAGGGACAAAGGTACTACG 59.451 52.381 0.00 0.00 38.49 3.51
128 129 2.935676 GCAGCAGGGACAAAGGTACTAC 60.936 54.545 0.00 0.00 38.49 2.73
129 130 1.278127 GCAGCAGGGACAAAGGTACTA 59.722 52.381 0.00 0.00 38.49 1.82
131 132 0.036875 AGCAGCAGGGACAAAGGTAC 59.963 55.000 0.00 0.00 0.00 3.34
132 133 1.651737 TAGCAGCAGGGACAAAGGTA 58.348 50.000 0.00 0.00 0.00 3.08
133 134 0.771127 TTAGCAGCAGGGACAAAGGT 59.229 50.000 0.00 0.00 0.00 3.50
134 135 2.134789 ATTAGCAGCAGGGACAAAGG 57.865 50.000 0.00 0.00 0.00 3.11
135 136 4.458989 TGTTAATTAGCAGCAGGGACAAAG 59.541 41.667 0.00 0.00 0.00 2.77
136 137 4.217550 GTGTTAATTAGCAGCAGGGACAAA 59.782 41.667 1.81 0.00 0.00 2.83
137 138 3.756434 GTGTTAATTAGCAGCAGGGACAA 59.244 43.478 1.81 0.00 0.00 3.18
138 139 3.009033 AGTGTTAATTAGCAGCAGGGACA 59.991 43.478 1.81 0.00 0.00 4.02
139 140 3.610911 AGTGTTAATTAGCAGCAGGGAC 58.389 45.455 1.81 0.00 0.00 4.46
140 141 5.630415 ATAGTGTTAATTAGCAGCAGGGA 57.370 39.130 1.81 0.00 0.00 4.20
141 142 9.102757 CATATATAGTGTTAATTAGCAGCAGGG 57.897 37.037 1.81 0.00 0.00 4.45
142 143 9.102757 CCATATATAGTGTTAATTAGCAGCAGG 57.897 37.037 1.81 0.00 0.00 4.85
143 144 9.658799 ACCATATATAGTGTTAATTAGCAGCAG 57.341 33.333 1.81 0.00 0.00 4.24
144 145 9.435688 CACCATATATAGTGTTAATTAGCAGCA 57.564 33.333 1.81 0.00 0.00 4.41
145 146 8.883731 CCACCATATATAGTGTTAATTAGCAGC 58.116 37.037 9.93 0.00 31.88 5.25
146 147 9.944376 ACCACCATATATAGTGTTAATTAGCAG 57.056 33.333 9.93 0.00 31.88 4.24
147 148 9.719355 CACCACCATATATAGTGTTAATTAGCA 57.281 33.333 9.93 0.00 31.88 3.49
148 149 8.665685 GCACCACCATATATAGTGTTAATTAGC 58.334 37.037 9.93 0.00 31.88 3.09
149 150 9.719355 TGCACCACCATATATAGTGTTAATTAG 57.281 33.333 9.93 0.00 31.88 1.73
193 194 5.817988 TCTCGAGTGGTTAATTAGATGACG 58.182 41.667 13.13 0.00 0.00 4.35
229 230 1.130749 ACTACTCGCACAGCTTCTACG 59.869 52.381 0.00 0.00 0.00 3.51
230 231 2.923605 ACTACTCGCACAGCTTCTAC 57.076 50.000 0.00 0.00 0.00 2.59
239 240 4.872691 TCTTGGTACTAGTACTACTCGCAC 59.127 45.833 27.71 12.38 36.36 5.34
272 273 4.487948 AGTGCAATTTTGATCATTCCGTG 58.512 39.130 0.00 0.00 0.00 4.94
274 275 6.324819 AGTAAGTGCAATTTTGATCATTCCG 58.675 36.000 4.05 0.00 0.00 4.30
298 299 3.394674 TGCAATTTCTGACGACAGGTA 57.605 42.857 14.76 3.96 43.60 3.08
299 300 2.254546 TGCAATTTCTGACGACAGGT 57.745 45.000 14.76 0.00 43.60 4.00
300 301 3.837213 AATGCAATTTCTGACGACAGG 57.163 42.857 14.76 0.00 43.60 4.00
313 314 7.718525 TGCATGTATGACTCAATTAATGCAAT 58.281 30.769 14.70 0.00 44.32 3.56
314 315 7.098074 TGCATGTATGACTCAATTAATGCAA 57.902 32.000 14.70 4.71 44.32 4.08
315 316 6.459985 GGTGCATGTATGACTCAATTAATGCA 60.460 38.462 13.73 13.73 44.88 3.96
332 333 0.323302 TGTATCGTGTGGGTGCATGT 59.677 50.000 0.00 0.00 0.00 3.21
376 377 2.089980 CCTTCTTCTCCATGGCACTTG 58.910 52.381 6.96 0.00 0.00 3.16
397 402 3.628942 AGATGCACATCACGCAATATTGT 59.371 39.130 16.61 0.00 43.84 2.71
431 437 7.041712 GCAAAAGGTCCTAATTCATAGCTACTC 60.042 40.741 0.00 0.00 0.00 2.59
446 452 1.782028 GCGACGTTGCAAAAGGTCCT 61.782 55.000 23.02 0.00 34.96 3.85
539 549 1.092921 TCTTTGACCGCGCAACTTGT 61.093 50.000 8.75 0.00 0.00 3.16
561 571 1.758122 CAGCAAGTTATGGGGGCCC 60.758 63.158 15.76 15.76 0.00 5.80
648 665 0.033090 GACGGTGGATCGGGGAATAC 59.967 60.000 0.00 0.00 0.00 1.89
669 686 1.523032 CCCGGCCGCCTTTACTTAG 60.523 63.158 22.85 0.90 0.00 2.18
809 846 1.866063 GCTGCTACGAAAGATCTCGGG 60.866 57.143 8.95 3.21 43.22 5.14
812 849 0.849579 GCGCTGCTACGAAAGATCTC 59.150 55.000 0.00 0.00 34.06 2.75
873 910 3.770666 TCACTTGCTTAGCTTAGCTACG 58.229 45.455 23.89 13.25 41.12 3.51
959 1002 0.169672 GGTAGCTTAGACACGTGCGA 59.830 55.000 17.22 1.84 0.00 5.10
972 1015 0.468400 GACGGAGGAGATGGGTAGCT 60.468 60.000 0.00 0.00 0.00 3.32
979 1022 1.818363 TCGGTCGACGGAGGAGATG 60.818 63.158 20.54 0.00 44.45 2.90
1555 1637 2.080286 AGTCAAGCACGTTCGCTAAT 57.920 45.000 0.23 0.00 42.89 1.73
1615 1697 5.334414 CGTCCTTGGACTCTCAAATGAAAAG 60.334 44.000 16.60 0.00 0.00 2.27
1626 1708 2.698797 TGTTCTTTCGTCCTTGGACTCT 59.301 45.455 16.60 0.00 0.00 3.24
1645 1727 5.499652 CGCGCGTAATAACTATCAAAAGTGT 60.500 40.000 24.19 0.00 0.00 3.55
1677 1759 5.217393 CGGCAGCAAACGAATATACTACTA 58.783 41.667 0.00 0.00 0.00 1.82
1678 1760 4.049186 CGGCAGCAAACGAATATACTACT 58.951 43.478 0.00 0.00 0.00 2.57
1679 1761 3.183775 CCGGCAGCAAACGAATATACTAC 59.816 47.826 0.00 0.00 0.00 2.73
1680 1762 3.386486 CCGGCAGCAAACGAATATACTA 58.614 45.455 0.00 0.00 0.00 1.82
1681 1763 2.210116 CCGGCAGCAAACGAATATACT 58.790 47.619 0.00 0.00 0.00 2.12
1682 1764 1.333791 GCCGGCAGCAAACGAATATAC 60.334 52.381 24.80 0.00 42.97 1.47
1725 1807 7.222180 TCCATCTTCTTCCCTTCTACTACTA 57.778 40.000 0.00 0.00 0.00 1.82
1726 1808 6.093617 TCCATCTTCTTCCCTTCTACTACT 57.906 41.667 0.00 0.00 0.00 2.57
1727 1809 5.303333 CCTCCATCTTCTTCCCTTCTACTAC 59.697 48.000 0.00 0.00 0.00 2.73
1753 1835 1.782028 GACAGGAAAGTTTGCCGCGT 61.782 55.000 4.92 0.00 0.00 6.01
1756 1838 1.676006 AGTTGACAGGAAAGTTTGCCG 59.324 47.619 3.17 0.00 0.00 5.69
1778 1861 5.285134 CCAAACAAAGCCGAATTAATGTACG 59.715 40.000 0.00 0.00 0.00 3.67
1926 2009 3.320826 TCGGTGTATGTATCATGGTCCTG 59.679 47.826 0.00 0.00 0.00 3.86
1944 2027 5.339990 GCAGCACACAAATTAATATTCGGT 58.660 37.500 0.00 0.00 0.00 4.69
1973 2056 0.963962 GACACTGTACACGGAAGGGA 59.036 55.000 0.00 0.00 38.45 4.20
2083 2166 9.898152 TCATGGTCATGTACTAATATTGAAACA 57.102 29.630 10.32 0.00 39.72 2.83
2093 2176 9.987272 CAGATTAGATTCATGGTCATGTACTAA 57.013 33.333 10.32 15.31 39.72 2.24
2096 2179 7.220030 ACCAGATTAGATTCATGGTCATGTAC 58.780 38.462 10.32 0.00 40.16 2.90
2148 2241 5.401531 AAATTCTCGCCTAGTGTGACTAA 57.598 39.130 0.00 0.00 29.00 2.24
2238 2381 2.124983 CCACCTCCTGCATCACGG 60.125 66.667 0.00 0.00 0.00 4.94
2613 2773 1.247567 CTTGGTCAAAACTCCGGCAT 58.752 50.000 0.00 0.00 0.00 4.40
2650 2810 1.389555 AGTACCATCTGATGCGACGA 58.610 50.000 12.17 0.00 0.00 4.20
3014 3197 9.209175 GTGAGATTTGAGTATTTCAACAGTACT 57.791 33.333 0.00 0.00 45.22 2.73
3016 3199 7.330946 CGGTGAGATTTGAGTATTTCAACAGTA 59.669 37.037 0.00 0.00 45.22 2.74
3017 3200 6.147821 CGGTGAGATTTGAGTATTTCAACAGT 59.852 38.462 0.00 0.00 45.22 3.55
3018 3201 6.147821 ACGGTGAGATTTGAGTATTTCAACAG 59.852 38.462 0.00 0.00 45.22 3.16
3019 3202 5.995282 ACGGTGAGATTTGAGTATTTCAACA 59.005 36.000 0.00 0.00 45.22 3.33
3020 3203 6.481954 ACGGTGAGATTTGAGTATTTCAAC 57.518 37.500 0.00 0.00 45.22 3.18
3021 3204 7.608153 TCTACGGTGAGATTTGAGTATTTCAA 58.392 34.615 0.00 0.00 43.92 2.69
3368 3551 7.242079 GGCCGAAAGAAAACTAGAATAGAAAC 58.758 38.462 0.00 0.00 42.77 2.78
3427 3610 6.175471 TCCATTGATTCCTCCATCATTATCG 58.825 40.000 0.00 0.00 33.07 2.92
3492 3675 0.822121 AGGGACAAACAAACGGGAGC 60.822 55.000 0.00 0.00 0.00 4.70
3508 3691 2.067013 GACGAAAAGAAGGAACGAGGG 58.933 52.381 0.00 0.00 0.00 4.30
3535 3718 2.666619 CGTTTGTTCCTCGTAGTACGCT 60.667 50.000 17.90 0.00 42.21 5.07
3677 3860 9.258826 CCAGTTCAAACAAATGAAAATATGACA 57.741 29.630 0.00 0.00 40.76 3.58
3747 3930 8.291740 GCAAATCTTTATGCCTTTGAAATTTGT 58.708 29.630 0.00 0.00 36.56 2.83
3896 4079 0.752658 TAGTGGATCAGCATGTCCGG 59.247 55.000 0.00 0.00 38.56 5.14
3898 4081 2.544694 CGAGTAGTGGATCAGCATGTCC 60.545 54.545 0.00 0.00 36.99 4.02
3933 4116 9.237187 TGGATACTTTGTAGTATTGAAATGCAA 57.763 29.630 0.00 0.00 45.43 4.08
3946 4129 3.064958 TCGCGAGTCTGGATACTTTGTAG 59.935 47.826 3.71 0.00 37.61 2.74
3947 4130 3.011818 TCGCGAGTCTGGATACTTTGTA 58.988 45.455 3.71 0.00 37.61 2.41
3948 4131 1.816835 TCGCGAGTCTGGATACTTTGT 59.183 47.619 3.71 0.00 37.61 2.83
3949 4132 2.186076 GTCGCGAGTCTGGATACTTTG 58.814 52.381 10.24 0.00 37.61 2.77
3950 4133 1.202154 CGTCGCGAGTCTGGATACTTT 60.202 52.381 10.24 0.00 37.61 2.66


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

AutoCloner maintained by Alex Coulton.