Multiple sequence alignment - TraesCS5B01G391700

Loading Multiple Alignment...

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 TraesCS5B01G391700 chr5B 100.000 4667 0 0 1 4667 570923074 570927740 0.000000e+00 8619.0
1 TraesCS5B01G391700 chr5B 100.000 1951 0 0 5051 7001 570928124 570930074 0.000000e+00 3603.0
2 TraesCS5B01G391700 chr5B 98.551 552 3 4 1 547 641105661 641106212 0.000000e+00 970.0
3 TraesCS5B01G391700 chr5B 98.370 552 4 4 1 547 700993934 700994485 0.000000e+00 965.0
4 TraesCS5B01G391700 chr5B 87.037 54 7 0 5482 5535 543285173 543285120 2.110000e-05 62.1
5 TraesCS5B01G391700 chr5A 92.249 4167 238 39 556 4665 584449196 584453334 0.000000e+00 5827.0
6 TraesCS5B01G391700 chr5A 91.895 1974 111 23 5051 7001 584453486 584455433 0.000000e+00 2713.0
7 TraesCS5B01G391700 chr5A 86.036 222 27 4 593 812 559787423 559787642 1.170000e-57 235.0
8 TraesCS5B01G391700 chr5D 93.297 2730 116 29 1969 4665 464067604 464070299 0.000000e+00 3965.0
9 TraesCS5B01G391700 chr5D 93.539 1981 74 23 5051 7001 464070452 464072408 0.000000e+00 2900.0
10 TraesCS5B01G391700 chr5D 90.627 1355 92 18 556 1906 464066286 464067609 0.000000e+00 1766.0
11 TraesCS5B01G391700 chr5D 100.000 28 0 0 5505 5532 250068602 250068575 1.300000e-02 52.8
12 TraesCS5B01G391700 chr2B 98.907 549 4 1 1 547 340548127 340548675 0.000000e+00 979.0
13 TraesCS5B01G391700 chr7B 98.545 550 5 2 1 547 152068338 152068887 0.000000e+00 968.0
14 TraesCS5B01G391700 chr7B 98.545 550 5 3 1 547 636443815 636444364 0.000000e+00 968.0
15 TraesCS5B01G391700 chr6B 98.367 551 5 3 1 547 80812571 80813121 0.000000e+00 965.0
16 TraesCS5B01G391700 chr1B 98.364 550 6 2 1 547 404479678 404480227 0.000000e+00 963.0
17 TraesCS5B01G391700 chr1B 98.195 554 3 5 1 547 57742562 57742009 0.000000e+00 961.0
18 TraesCS5B01G391700 chr1B 83.673 98 8 3 5051 5148 252288714 252288803 1.250000e-12 86.1
19 TraesCS5B01G391700 chr4B 98.358 548 8 1 1 547 347640727 347640180 0.000000e+00 961.0
20 TraesCS5B01G391700 chr6A 86.283 226 27 4 596 818 46549072 46548848 7.020000e-60 243.0
21 TraesCS5B01G391700 chr6A 86.697 218 27 2 596 812 422776035 422776251 2.520000e-59 241.0
22 TraesCS5B01G391700 chr6A 87.952 83 10 0 5453 5535 66388164 66388082 1.610000e-16 99.0
23 TraesCS5B01G391700 chr3A 86.425 221 26 4 596 814 597887811 597888029 9.080000e-59 239.0
24 TraesCS5B01G391700 chr3A 97.436 39 1 0 5454 5492 516801682 516801720 4.530000e-07 67.6
25 TraesCS5B01G391700 chr7A 85.455 220 30 2 596 814 32629320 32629538 1.960000e-55 228.0
26 TraesCS5B01G391700 chr7A 100.000 38 0 0 5498 5535 127774909 127774872 3.500000e-08 71.3
27 TraesCS5B01G391700 chr1D 85.714 217 29 2 596 811 100879619 100879404 1.960000e-55 228.0
28 TraesCS5B01G391700 chr1D 96.774 31 1 0 5505 5535 423055818 423055788 1.300000e-02 52.8
29 TraesCS5B01G391700 chr6D 85.068 221 31 2 598 817 470623793 470624012 2.540000e-54 224.0
30 TraesCS5B01G391700 chr3D 88.372 86 8 1 5455 5538 370115798 370115713 1.240000e-17 102.0
31 TraesCS5B01G391700 chr7D 87.654 81 10 0 5455 5535 623531465 623531385 2.080000e-15 95.3
32 TraesCS5B01G391700 chr1A 82.051 78 7 5 5462 5535 300771548 300771474 7.580000e-05 60.2
33 TraesCS5B01G391700 chr2D 90.698 43 4 0 5493 5535 14814243 14814285 2.730000e-04 58.4
34 TraesCS5B01G391700 chrUn 96.774 31 1 0 5505 5535 65584307 65584277 1.300000e-02 52.8


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 TraesCS5B01G391700 chr5B 570923074 570930074 7000 False 6111 8619 100.000000 1 7001 2 chr5B.!!$F3 7000
1 TraesCS5B01G391700 chr5B 641105661 641106212 551 False 970 970 98.551000 1 547 1 chr5B.!!$F1 546
2 TraesCS5B01G391700 chr5B 700993934 700994485 551 False 965 965 98.370000 1 547 1 chr5B.!!$F2 546
3 TraesCS5B01G391700 chr5A 584449196 584455433 6237 False 4270 5827 92.072000 556 7001 2 chr5A.!!$F2 6445
4 TraesCS5B01G391700 chr5D 464066286 464072408 6122 False 2877 3965 92.487667 556 7001 3 chr5D.!!$F1 6445
5 TraesCS5B01G391700 chr2B 340548127 340548675 548 False 979 979 98.907000 1 547 1 chr2B.!!$F1 546
6 TraesCS5B01G391700 chr7B 152068338 152068887 549 False 968 968 98.545000 1 547 1 chr7B.!!$F1 546
7 TraesCS5B01G391700 chr7B 636443815 636444364 549 False 968 968 98.545000 1 547 1 chr7B.!!$F2 546
8 TraesCS5B01G391700 chr6B 80812571 80813121 550 False 965 965 98.367000 1 547 1 chr6B.!!$F1 546
9 TraesCS5B01G391700 chr1B 404479678 404480227 549 False 963 963 98.364000 1 547 1 chr1B.!!$F2 546
10 TraesCS5B01G391700 chr1B 57742009 57742562 553 True 961 961 98.195000 1 547 1 chr1B.!!$R1 546
11 TraesCS5B01G391700 chr4B 347640180 347640727 547 True 961 961 98.358000 1 547 1 chr4B.!!$R1 546

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
637 647 0.721154 GATGCGCGTTCAATGTGAGA 59.279 50.000 8.43 0.0 0.00 3.27 F
1494 1516 1.214062 CTGCGAGTGACAGAGGACC 59.786 63.158 0.00 0.0 37.32 4.46 F
2140 2169 0.251341 GTTGCCACTCCCAGGTCAAT 60.251 55.000 0.00 0.0 0.00 2.57 F
3654 3706 2.595750 TTAGTGGTCAATGGGTTGGG 57.404 50.000 0.00 0.0 35.99 4.12 F
4348 4445 0.625849 AAGGAGGCGAATGGTTCCAT 59.374 50.000 0.00 0.0 32.02 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1503 1525 0.244450 GCACCATCCACCAACATGTG 59.756 55.000 0.00 0.00 35.98 3.21 R
3399 3450 0.751277 CACCAGTCCAGCCACAACAA 60.751 55.000 0.00 0.00 0.00 2.83 R
4101 4168 3.436015 GCATAGCACATGATCATGAGGAC 59.564 47.826 36.37 22.53 41.20 3.85 R
5210 5313 0.246086 TGCCTTTGCTTATTTGGCGG 59.754 50.000 0.00 0.00 45.90 6.13 R
6071 6191 0.524862 CCAGCTCAACCAAGATGCAC 59.475 55.000 0.00 0.00 31.30 4.57 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
222 223 6.310941 TGGGAATTGGTTATCTTGTCTTCAA 58.689 36.000 0.00 0.00 0.00 2.69
315 317 1.135344 TGTTATGCACTAGCGCGTGTA 60.135 47.619 15.40 12.08 46.23 2.90
557 566 3.155344 CGTTGCAACGTGTTCTTCTAG 57.845 47.619 37.16 10.63 46.63 2.43
567 576 6.525578 ACGTGTTCTTCTAGTATGGATTGA 57.474 37.500 0.00 0.00 0.00 2.57
606 616 7.601856 TCGCAACAAAATCAGGATTTATTTCT 58.398 30.769 7.62 0.00 39.88 2.52
608 618 7.541783 CGCAACAAAATCAGGATTTATTTCTGA 59.458 33.333 7.62 0.00 39.88 3.27
633 643 2.098298 GCGATGCGCGTTCAATGT 59.902 55.556 8.43 0.00 44.55 2.71
637 647 0.721154 GATGCGCGTTCAATGTGAGA 59.279 50.000 8.43 0.00 0.00 3.27
676 686 2.047560 GGCGCCTACGGTGACTTT 60.048 61.111 22.15 0.00 38.38 2.66
687 697 6.620089 GCCTACGGTGACTTTTAAAATCTCAC 60.620 42.308 20.66 20.66 0.00 3.51
708 718 2.227626 CGATGATATGTCGGCTCAGTCT 59.772 50.000 0.00 0.00 35.55 3.24
711 721 3.291584 TGATATGTCGGCTCAGTCTCTT 58.708 45.455 0.00 0.00 0.00 2.85
716 726 1.673920 GTCGGCTCAGTCTCTTAGAGG 59.326 57.143 9.58 0.00 0.00 3.69
718 728 2.504585 TCGGCTCAGTCTCTTAGAGGTA 59.495 50.000 9.58 0.00 0.00 3.08
745 755 4.158949 ACACAGTTAGGATATGCGTGTGTA 59.841 41.667 18.82 0.00 43.85 2.90
746 756 5.163447 ACACAGTTAGGATATGCGTGTGTAT 60.163 40.000 18.82 3.95 43.85 2.29
756 766 6.312918 GGATATGCGTGTGTATGTTTATAGGG 59.687 42.308 0.00 0.00 0.00 3.53
807 817 5.052633 GCTTGCGTTTGTACTGTGTTAAAAG 60.053 40.000 0.00 0.00 0.00 2.27
811 821 7.082602 TGCGTTTGTACTGTGTTAAAAGAAAA 58.917 30.769 0.00 0.00 0.00 2.29
812 822 7.594015 TGCGTTTGTACTGTGTTAAAAGAAAAA 59.406 29.630 0.00 0.00 0.00 1.94
949 963 4.776647 GTGGCCCGTGCAAATCGC 62.777 66.667 0.00 0.00 40.13 4.58
994 1008 8.680001 ACGTAATAATAATCACAGGGGAAAAAC 58.320 33.333 0.00 0.00 0.00 2.43
1238 1255 1.940613 CCTTACTGGCTTCCGTATTGC 59.059 52.381 0.00 0.00 0.00 3.56
1333 1350 2.436542 CCCATGGTGATGATTTTGCCAT 59.563 45.455 11.73 0.00 40.22 4.40
1334 1351 3.642377 CCCATGGTGATGATTTTGCCATA 59.358 43.478 11.73 0.00 37.80 2.74
1336 1353 4.501915 CCATGGTGATGATTTTGCCATACC 60.502 45.833 2.57 0.00 37.80 2.73
1431 1453 1.361204 TGCTTTCCATCCTGACTCCA 58.639 50.000 0.00 0.00 0.00 3.86
1477 1499 3.245158 TGTCGACCCCGAGATATAATCCT 60.245 47.826 14.12 0.00 46.52 3.24
1494 1516 1.214062 CTGCGAGTGACAGAGGACC 59.786 63.158 0.00 0.00 37.32 4.46
1503 1525 2.743928 CAGAGGACCGGCTGTTGC 60.744 66.667 0.00 0.00 38.76 4.17
1505 1527 3.050275 GAGGACCGGCTGTTGCAC 61.050 66.667 0.00 0.00 41.91 4.57
1509 1531 2.203337 ACCGGCTGTTGCACATGT 60.203 55.556 0.00 0.00 41.91 3.21
1543 1566 3.709987 CTTCTCAAGCTTGTTTTGTGGG 58.290 45.455 25.19 0.00 0.00 4.61
1590 1613 1.619654 CAGGCATTTTGGGTCAGACA 58.380 50.000 2.17 0.00 0.00 3.41
1607 1630 5.415701 GTCAGACAAAAGGGCAGATCAAATA 59.584 40.000 0.00 0.00 0.00 1.40
1786 1809 3.504134 GGTTCTGCTTCCTTCCTCTTTTC 59.496 47.826 0.00 0.00 0.00 2.29
1793 1816 4.584743 GCTTCCTTCCTCTTTTCCTTCAAA 59.415 41.667 0.00 0.00 0.00 2.69
1798 1821 6.611236 TCCTTCCTCTTTTCCTTCAAATTGTT 59.389 34.615 0.00 0.00 0.00 2.83
1844 1867 8.947115 GGATACAAGACTTTTAACTAGTGCATT 58.053 33.333 0.00 0.00 0.00 3.56
1875 1898 9.720667 CATGTTATGTCATGTTTGGTAGTTATG 57.279 33.333 0.00 0.00 39.93 1.90
1949 1972 3.945640 AGTCCAAACTTGGTAGGTTGT 57.054 42.857 8.32 0.00 45.75 3.32
1950 1973 5.221702 GGTAGTCCAAACTTGGTAGGTTGTA 60.222 44.000 8.32 0.00 45.75 2.41
1956 1979 5.300792 CCAAACTTGGTAGGTTGTACAACAT 59.699 40.000 33.42 30.26 45.75 2.71
1960 1983 7.069877 ACTTGGTAGGTTGTACAACATCTTA 57.930 36.000 33.42 19.38 42.85 2.10
1972 1995 9.616156 TTGTACAACATCTTACTTTTAACCTGA 57.384 29.630 3.59 0.00 0.00 3.86
1989 2012 3.015327 CCTGATTCTGCTTCCTTCCTTG 58.985 50.000 0.00 0.00 0.00 3.61
2048 2077 4.689062 TCAGTTAGTTCTCCTCCCTGATT 58.311 43.478 0.00 0.00 29.67 2.57
2056 2085 4.934797 TCTCCTCCCTGATTGAAATGTT 57.065 40.909 0.00 0.00 0.00 2.71
2089 2118 9.678941 GCCTACTGCCTTTATACATTTAATTTC 57.321 33.333 0.00 0.00 0.00 2.17
2140 2169 0.251341 GTTGCCACTCCCAGGTCAAT 60.251 55.000 0.00 0.00 0.00 2.57
2414 2445 6.663953 AGCCTGGTATTACTCGTGTGATATAT 59.336 38.462 5.54 0.00 29.41 0.86
2587 2619 3.281727 TTGGCAGTTATCCCATCTGTC 57.718 47.619 0.00 0.00 34.84 3.51
2956 3004 3.729108 TGTCAGAGAGAAGGAATGGGAT 58.271 45.455 0.00 0.00 0.00 3.85
3067 3115 7.242322 TCAAATGATTGATCCAAATGAACCA 57.758 32.000 0.00 0.00 40.59 3.67
3490 3541 6.372659 AGGATTATGTGCTCACTGTTTTACTG 59.627 38.462 1.47 0.00 0.00 2.74
3491 3542 6.149474 GGATTATGTGCTCACTGTTTTACTGT 59.851 38.462 1.47 0.00 0.00 3.55
3492 3543 6.935741 TTATGTGCTCACTGTTTTACTGTT 57.064 33.333 1.47 0.00 0.00 3.16
3493 3544 8.615878 ATTATGTGCTCACTGTTTTACTGTTA 57.384 30.769 1.47 0.00 0.00 2.41
3496 3547 8.615878 ATGTGCTCACTGTTTTACTGTTATTA 57.384 30.769 1.47 0.00 0.00 0.98
3520 3571 3.912248 ACTAGGATGTAACATCGGACCT 58.088 45.455 0.00 0.00 0.00 3.85
3538 3589 5.126067 GGACCTGTCAATGTATATGCTTGT 58.874 41.667 0.00 0.00 0.00 3.16
3543 3594 5.331098 TGTCAATGTATATGCTTGTTTGCG 58.669 37.500 0.00 0.00 35.36 4.85
3551 3602 6.592220 TGTATATGCTTGTTTGCGTTCTCTAA 59.408 34.615 0.00 0.00 35.36 2.10
3556 3607 5.034797 GCTTGTTTGCGTTCTCTAAAACTT 58.965 37.500 0.00 0.00 34.39 2.66
3557 3608 5.052370 GCTTGTTTGCGTTCTCTAAAACTTG 60.052 40.000 0.00 0.00 34.39 3.16
3648 3700 7.012704 CAGTGGAATAGAATTAGTGGTCAATGG 59.987 40.741 0.00 0.00 0.00 3.16
3654 3706 2.595750 TTAGTGGTCAATGGGTTGGG 57.404 50.000 0.00 0.00 35.99 4.12
3660 3712 2.636893 TGGTCAATGGGTTGGGATTTTG 59.363 45.455 0.00 0.00 35.99 2.44
3665 3717 2.685106 TGGGTTGGGATTTTGCACTA 57.315 45.000 0.00 0.00 0.00 2.74
3759 3825 6.915349 TGGTACAATTTCCAGAATTTTACCG 58.085 36.000 16.12 0.00 31.92 4.02
4011 4077 9.625747 TTTTTATGATGCACTGGATACTATTCA 57.374 29.630 0.00 0.00 37.61 2.57
4017 4083 9.797642 TGATGCACTGGATACTATTCATAAAAT 57.202 29.630 0.00 0.00 37.61 1.82
4101 4168 7.391275 TGGTTGTATATCATATTGGTGCATCAG 59.609 37.037 0.00 0.00 0.00 2.90
4163 4258 5.537188 CGAAGGAAAAACATTGGAATTCCA 58.463 37.500 23.63 23.63 45.94 3.53
4184 4279 9.657419 ATTCCAAAAACATTAGATAAAAGGCAG 57.343 29.630 0.00 0.00 0.00 4.85
4191 4286 8.593945 AACATTAGATAAAAGGCAGAATGGAA 57.406 30.769 0.00 0.00 35.86 3.53
4262 4358 9.769093 GCTTGTTATCGTATGATTTACTTTTGT 57.231 29.630 2.02 0.00 35.99 2.83
4293 4390 9.030452 GTTATATGAAGGTCATCCATCTCTACT 57.970 37.037 0.00 0.00 38.26 2.57
4348 4445 0.625849 AAGGAGGCGAATGGTTCCAT 59.374 50.000 0.00 0.00 32.02 3.41
4455 4552 5.497474 TCTCCTAAATTGGTAAGAGGCAAC 58.503 41.667 0.00 0.00 0.00 4.17
4511 4610 3.814005 ACCTTATCACGTAAATCGCCT 57.186 42.857 0.00 0.00 44.19 5.52
4561 4660 9.615295 AAATGTGAATTTGTATAACCGTGTTAC 57.385 29.630 0.00 0.00 0.00 2.50
4625 4725 5.254339 AGTGCAAACTTTCCTTTTCAGAG 57.746 39.130 0.00 0.00 0.00 3.35
4632 4733 6.396829 AACTTTCCTTTTCAGAGAACCATG 57.603 37.500 0.00 0.00 0.00 3.66
4654 4755 7.230712 CCATGTAACTTAGTCCTTCAAAACCTT 59.769 37.037 0.00 0.00 0.00 3.50
5137 5239 1.601759 CACCTGGTGTGGGAGCTTG 60.602 63.158 18.76 0.00 41.52 4.01
5148 5250 2.820037 GAGCTTGTAGCACCGGGC 60.820 66.667 6.32 6.61 45.56 6.13
5155 5257 1.602605 GTAGCACCGGGCCTGTTTT 60.603 57.895 11.58 0.00 46.50 2.43
5260 5363 2.358737 CAGACCCAAGGCACCGAC 60.359 66.667 0.00 0.00 0.00 4.79
5272 5375 2.814410 CACCGACAGTGTACAGCTG 58.186 57.895 13.48 13.48 41.93 4.24
5298 5401 7.337942 GGAATTAAGCTTATCCAGGGACATATG 59.662 40.741 17.67 0.00 32.08 1.78
5301 5404 5.495926 AGCTTATCCAGGGACATATGAAG 57.504 43.478 10.38 0.26 0.00 3.02
5326 5444 9.314321 AGGAATCATGATTGTTAACTAGTAACG 57.686 33.333 25.37 0.00 44.46 3.18
5373 5491 7.008332 AGGCCCTATAATTAATTACCCAACAC 58.992 38.462 10.07 0.03 0.00 3.32
5378 5496 8.357402 CCTATAATTAATTACCCAACACAAGCC 58.643 37.037 10.07 0.00 0.00 4.35
5415 5533 4.324563 CCCACATGACATCCTTCTTTACCT 60.325 45.833 0.00 0.00 0.00 3.08
5439 5557 7.419518 CCTCTCTCTTCAAAATCTAATAGCCCA 60.420 40.741 0.00 0.00 0.00 5.36
5535 5655 9.542462 CGTTTTATATTTTGATACAGAGGGAGA 57.458 33.333 0.00 0.00 0.00 3.71
5589 5709 3.500448 TTTCCTCACATGTACCTGCAA 57.500 42.857 0.00 0.00 0.00 4.08
5592 5712 2.571202 TCCTCACATGTACCTGCAATCA 59.429 45.455 0.00 0.00 0.00 2.57
5622 5742 1.376037 CGTCCCTTGAAGTCAGCCC 60.376 63.158 0.00 0.00 0.00 5.19
5628 5748 1.479389 CCTTGAAGTCAGCCCCTTGTT 60.479 52.381 0.00 0.00 0.00 2.83
5629 5749 2.310538 CTTGAAGTCAGCCCCTTGTTT 58.689 47.619 0.00 0.00 0.00 2.83
5708 5828 0.317020 GTTTGCTCGCCAGTGTTGAC 60.317 55.000 0.00 0.00 0.00 3.18
5838 5958 4.497473 TCAATTTGTAAGGAGGCGTTTG 57.503 40.909 0.00 0.00 0.00 2.93
5889 6009 0.881796 TATATGCTGGAGAGGACGCG 59.118 55.000 3.53 3.53 0.00 6.01
5967 6087 5.504010 CGCCGCAAACAATCTATCATAGTTT 60.504 40.000 0.00 0.00 33.09 2.66
5990 6110 3.050835 AGGTGTTGGTAACCTGGTAACT 58.949 45.455 0.00 0.00 46.51 2.24
6002 6122 8.733458 GGTAACCTGGTAACTATTTTACTTTGG 58.267 37.037 0.00 0.00 37.61 3.28
6052 6172 0.452987 TTTGCTCGCATGATTCTGCC 59.547 50.000 0.00 0.00 39.00 4.85
6066 6186 0.913934 TCTGCCCCTGAGCACCATTA 60.914 55.000 0.00 0.00 38.00 1.90
6090 6213 0.524862 GTGCATCTTGGTTGAGCTGG 59.475 55.000 0.00 0.00 0.00 4.85
6186 6312 4.271696 TCTCCCTGTTTCACATGTGTAG 57.728 45.455 24.63 17.19 0.00 2.74
6237 6370 8.562892 GTTGCTGCTGTATATCTACAAATGATT 58.437 33.333 0.00 0.00 37.41 2.57
6240 6373 8.777413 GCTGCTGTATATCTACAAATGATTTGA 58.223 33.333 23.37 7.27 43.26 2.69
6256 6389 9.857656 AAATGATTTGATAGTACATCCAGACAT 57.142 29.630 0.00 0.00 0.00 3.06
6393 6526 0.815734 ACCACTCGTACTTGGATCCG 59.184 55.000 7.39 0.00 36.28 4.18
6402 6535 1.452108 CTTGGATCCGGGGCTGAAC 60.452 63.158 7.39 0.00 0.00 3.18
6420 6553 0.522180 ACACGTACAGCTCCTCGAAG 59.478 55.000 7.73 0.00 0.00 3.79
6500 6633 5.611796 TCCACAAGAATTTCATCAGTTCG 57.388 39.130 0.00 0.00 0.00 3.95
6510 6643 2.677199 TCATCAGTTCGTCAGTTCAGC 58.323 47.619 0.00 0.00 0.00 4.26
6512 6645 2.140065 TCAGTTCGTCAGTTCAGCTG 57.860 50.000 7.63 7.63 46.34 4.24
6516 6649 2.159099 AGTTCGTCAGTTCAGCTGTGAA 60.159 45.455 14.67 0.00 45.23 3.18
6517 6650 2.802816 GTTCGTCAGTTCAGCTGTGAAT 59.197 45.455 14.67 0.00 44.58 2.57
6541 6674 3.250762 TGTGATCCTTCTTCAGTTTTGCG 59.749 43.478 0.00 0.00 0.00 4.85
6566 6699 0.809385 CACGTACCCTGTCGATGACT 59.191 55.000 0.00 0.00 33.15 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
222 223 8.774890 TGCATTAATAAACAAATGTTCTGCAT 57.225 26.923 0.00 0.00 37.25 3.96
315 317 6.591935 ACCATAATCCATCTATTTCACACGT 58.408 36.000 0.00 0.00 0.00 4.49
547 556 6.672218 TCCCTTCAATCCATACTAGAAGAACA 59.328 38.462 0.00 0.00 38.30 3.18
548 557 6.987404 GTCCCTTCAATCCATACTAGAAGAAC 59.013 42.308 0.00 0.00 38.30 3.01
549 558 6.903534 AGTCCCTTCAATCCATACTAGAAGAA 59.096 38.462 0.00 0.00 38.30 2.52
550 559 6.444704 AGTCCCTTCAATCCATACTAGAAGA 58.555 40.000 0.00 0.00 38.30 2.87
551 560 6.739331 AGTCCCTTCAATCCATACTAGAAG 57.261 41.667 0.00 0.00 36.38 2.85
552 561 7.130099 TGTAGTCCCTTCAATCCATACTAGAA 58.870 38.462 0.00 0.00 0.00 2.10
553 562 6.679542 TGTAGTCCCTTCAATCCATACTAGA 58.320 40.000 0.00 0.00 0.00 2.43
554 563 6.978674 TGTAGTCCCTTCAATCCATACTAG 57.021 41.667 0.00 0.00 0.00 2.57
557 566 7.254795 CGATTTTGTAGTCCCTTCAATCCATAC 60.255 40.741 0.00 0.00 0.00 2.39
567 576 3.482436 TGTTGCGATTTTGTAGTCCCTT 58.518 40.909 0.00 0.00 0.00 3.95
606 616 3.097672 CGCATCGCCGGAAATTCA 58.902 55.556 5.05 0.00 0.00 2.57
665 675 6.215121 TCGTGAGATTTTAAAAGTCACCGTA 58.785 36.000 25.82 16.19 34.63 4.02
687 697 2.227626 AGACTGAGCCGACATATCATCG 59.772 50.000 0.00 0.00 39.33 3.84
708 718 5.944599 CCTAACTGTGTGAGTACCTCTAAGA 59.055 44.000 0.00 0.00 33.09 2.10
711 721 5.509832 TCCTAACTGTGTGAGTACCTCTA 57.490 43.478 0.00 0.00 33.09 2.43
716 726 4.976731 CGCATATCCTAACTGTGTGAGTAC 59.023 45.833 0.00 0.00 33.09 2.73
718 728 3.447586 ACGCATATCCTAACTGTGTGAGT 59.552 43.478 0.00 0.00 35.94 3.41
723 733 3.521560 ACACACGCATATCCTAACTGTG 58.478 45.455 0.00 0.00 34.90 3.66
725 735 5.289595 ACATACACACGCATATCCTAACTG 58.710 41.667 0.00 0.00 0.00 3.16
745 755 5.621193 GCATACACTCACCCCTATAAACAT 58.379 41.667 0.00 0.00 0.00 2.71
746 756 4.442332 CGCATACACTCACCCCTATAAACA 60.442 45.833 0.00 0.00 0.00 2.83
756 766 5.751509 TCATATAAACACGCATACACTCACC 59.248 40.000 0.00 0.00 0.00 4.02
812 822 7.278203 ACGGGTGTTTTCGTTGATTTTATTTTT 59.722 29.630 0.00 0.00 36.04 1.94
813 823 6.757478 ACGGGTGTTTTCGTTGATTTTATTTT 59.243 30.769 0.00 0.00 36.04 1.82
814 824 6.274579 ACGGGTGTTTTCGTTGATTTTATTT 58.725 32.000 0.00 0.00 36.04 1.40
817 827 4.897025 ACGGGTGTTTTCGTTGATTTTA 57.103 36.364 0.00 0.00 36.04 1.52
825 835 4.609947 GGATTTTTAACGGGTGTTTTCGT 58.390 39.130 0.00 0.00 39.54 3.85
949 963 5.277857 ACGTCATTAATCTGGTTAGGAGG 57.722 43.478 0.00 3.91 0.00 4.30
978 992 3.903530 AGAGGTTTTTCCCCTGTGATT 57.096 42.857 0.00 0.00 36.75 2.57
985 999 2.724454 GCTAGGAAGAGGTTTTTCCCC 58.276 52.381 0.62 0.00 44.19 4.81
994 1008 2.036604 GGGAAATCTCGCTAGGAAGAGG 59.963 54.545 0.00 0.00 35.34 3.69
1096 1110 2.406616 AATTGCCATGCCGGTCGAC 61.407 57.895 7.13 7.13 36.97 4.20
1238 1255 1.880340 GGTGCTCGAATCTGCGGAG 60.880 63.158 0.00 0.00 0.00 4.63
1388 1410 6.566197 AAATTCACTCTCCACAATGACTTC 57.434 37.500 0.00 0.00 0.00 3.01
1389 1411 6.736794 GCAAAATTCACTCTCCACAATGACTT 60.737 38.462 0.00 0.00 0.00 3.01
1431 1453 7.506938 ACAATTAAAGCATGGCCAGATTACTAT 59.493 33.333 13.05 0.00 0.00 2.12
1477 1499 2.626780 CGGTCCTCTGTCACTCGCA 61.627 63.158 0.00 0.00 0.00 5.10
1503 1525 0.244450 GCACCATCCACCAACATGTG 59.756 55.000 0.00 0.00 35.98 3.21
1505 1527 1.203052 GAAGCACCATCCACCAACATG 59.797 52.381 0.00 0.00 0.00 3.21
1509 1531 0.770499 TGAGAAGCACCATCCACCAA 59.230 50.000 0.00 0.00 0.00 3.67
1568 1591 0.899720 CTGACCCAAAATGCCTGCAT 59.100 50.000 0.00 0.00 38.46 3.96
1590 1613 5.832060 CAGGAGATATTTGATCTGCCCTTTT 59.168 40.000 2.83 0.00 37.22 2.27
1786 1809 8.567948 TCTTTAAGCTACAGAACAATTTGAAGG 58.432 33.333 2.79 0.00 0.00 3.46
1822 1845 9.116067 TGTAAATGCACTAGTTAAAAGTCTTGT 57.884 29.630 0.00 0.00 0.00 3.16
1826 1849 9.329913 CATGTGTAAATGCACTAGTTAAAAGTC 57.670 33.333 0.00 0.00 39.89 3.01
1875 1898 3.697619 AGCAACCCTGGAGTAACTAAC 57.302 47.619 0.00 0.00 0.00 2.34
1906 1929 5.880054 ACCGGACAAAATGATCAAGTTAG 57.120 39.130 9.46 0.00 0.00 2.34
1944 1967 8.843262 AGGTTAAAAGTAAGATGTTGTACAACC 58.157 33.333 30.68 18.81 40.46 3.77
1945 1968 9.659830 CAGGTTAAAAGTAAGATGTTGTACAAC 57.340 33.333 28.13 28.13 41.50 3.32
1946 1969 9.616156 TCAGGTTAAAAGTAAGATGTTGTACAA 57.384 29.630 3.59 3.59 0.00 2.41
1947 1970 9.787435 ATCAGGTTAAAAGTAAGATGTTGTACA 57.213 29.630 0.00 0.00 0.00 2.90
1950 1973 9.574516 AGAATCAGGTTAAAAGTAAGATGTTGT 57.425 29.630 0.00 0.00 0.00 3.32
1956 1979 7.390718 GGAAGCAGAATCAGGTTAAAAGTAAGA 59.609 37.037 0.00 0.00 0.00 2.10
1960 1983 5.635120 AGGAAGCAGAATCAGGTTAAAAGT 58.365 37.500 0.00 0.00 0.00 2.66
1972 1995 4.379302 AGTTCAAGGAAGGAAGCAGAAT 57.621 40.909 0.00 0.00 0.00 2.40
1989 2012 6.403636 CCATTATGTTGCAGGACTACAAGTTC 60.404 42.308 0.00 0.00 37.55 3.01
2048 2077 4.002982 CAGTAGGCACTAGCAACATTTCA 58.997 43.478 0.00 0.00 44.14 2.69
2056 2085 0.984230 AAAGGCAGTAGGCACTAGCA 59.016 50.000 0.00 0.00 44.14 3.49
2089 2118 9.449719 AGTTAACTAAGATAACCACCAGAAATG 57.550 33.333 6.26 0.00 34.50 2.32
2309 2340 7.766219 TTTGTATTAATTACTCGGTGCTCTC 57.234 36.000 0.00 0.00 0.00 3.20
2378 2409 7.095187 CGAGTAATACCAGGCTTTTCATATTCC 60.095 40.741 0.00 0.00 0.00 3.01
2414 2445 2.171659 TGACAGTTTAACAGCTGGGTGA 59.828 45.455 19.93 0.00 37.07 4.02
2430 2461 4.639310 AGGCTTCTTGCTTCAATATGACAG 59.361 41.667 0.00 0.00 42.39 3.51
2630 2663 7.484140 TGGCTCTCTATCTGTATAATAATGCG 58.516 38.462 0.00 0.00 0.00 4.73
2818 2866 5.010282 GGAGGTATTTTTCCTTCTGCAAGA 58.990 41.667 0.00 0.00 44.68 3.02
2956 3004 3.859248 CCATACCTCTCTCCCTATCCCTA 59.141 52.174 0.00 0.00 0.00 3.53
3067 3115 5.952387 ACCTGGTGGCATATACAATATGTT 58.048 37.500 0.00 0.00 36.63 2.71
3110 3158 4.431416 TGCAAGTACCGGGAATATGAAT 57.569 40.909 6.32 0.00 0.00 2.57
3192 3243 9.439500 CACCATATGAAACCTGAAAATCAATTT 57.561 29.630 3.65 0.00 0.00 1.82
3399 3450 0.751277 CACCAGTCCAGCCACAACAA 60.751 55.000 0.00 0.00 0.00 2.83
3493 3544 8.529476 GGTCCGATGTTACATCCTAGTAATAAT 58.471 37.037 18.33 0.00 36.47 1.28
3496 3547 6.015350 CAGGTCCGATGTTACATCCTAGTAAT 60.015 42.308 18.33 0.00 36.47 1.89
3517 3568 6.625740 GCAAACAAGCATATACATTGACAGGT 60.626 38.462 0.00 0.00 0.00 4.00
3520 3571 5.106357 ACGCAAACAAGCATATACATTGACA 60.106 36.000 0.00 0.00 0.00 3.58
3538 3589 4.796312 GCAACAAGTTTTAGAGAACGCAAA 59.204 37.500 0.00 0.00 34.74 3.68
3543 3594 8.634475 AGAAATTGCAACAAGTTTTAGAGAAC 57.366 30.769 0.00 0.00 0.00 3.01
3551 3602 8.730680 ACGATATCTAGAAATTGCAACAAGTTT 58.269 29.630 0.00 0.00 0.00 2.66
3575 3626 8.064222 CCAACTTCTAATTGCTCATGTTATACG 58.936 37.037 0.00 0.00 0.00 3.06
3648 3700 6.098266 AGGAATTATAGTGCAAAATCCCAACC 59.902 38.462 0.00 0.00 0.00 3.77
3734 3786 7.027161 CGGTAAAATTCTGGAAATTGTACCAG 58.973 38.462 21.37 15.90 44.89 4.00
4017 4083 9.396022 GGATGATTGTGAAGGTTTCTTTATCTA 57.604 33.333 0.00 0.00 32.52 1.98
4079 4146 7.038088 AGGACTGATGCACCAATATGATATACA 60.038 37.037 0.00 0.00 0.00 2.29
4101 4168 3.436015 GCATAGCACATGATCATGAGGAC 59.564 47.826 36.37 22.53 41.20 3.85
4158 4253 9.657419 CTGCCTTTTATCTAATGTTTTTGGAAT 57.343 29.630 0.00 0.00 0.00 3.01
4159 4254 8.865090 TCTGCCTTTTATCTAATGTTTTTGGAA 58.135 29.630 0.00 0.00 0.00 3.53
4160 4255 8.415950 TCTGCCTTTTATCTAATGTTTTTGGA 57.584 30.769 0.00 0.00 0.00 3.53
4161 4256 9.657419 ATTCTGCCTTTTATCTAATGTTTTTGG 57.343 29.630 0.00 0.00 0.00 3.28
4163 4258 9.657419 CCATTCTGCCTTTTATCTAATGTTTTT 57.343 29.630 0.00 0.00 0.00 1.94
4164 4259 9.034800 TCCATTCTGCCTTTTATCTAATGTTTT 57.965 29.630 0.00 0.00 0.00 2.43
4165 4260 8.593945 TCCATTCTGCCTTTTATCTAATGTTT 57.406 30.769 0.00 0.00 0.00 2.83
4166 4261 8.470002 GTTCCATTCTGCCTTTTATCTAATGTT 58.530 33.333 0.00 0.00 0.00 2.71
4167 4262 7.068716 GGTTCCATTCTGCCTTTTATCTAATGT 59.931 37.037 0.00 0.00 0.00 2.71
4168 4263 7.428826 GGTTCCATTCTGCCTTTTATCTAATG 58.571 38.462 0.00 0.00 0.00 1.90
4169 4264 6.551227 GGGTTCCATTCTGCCTTTTATCTAAT 59.449 38.462 0.00 0.00 0.00 1.73
4170 4265 5.891551 GGGTTCCATTCTGCCTTTTATCTAA 59.108 40.000 0.00 0.00 0.00 2.10
4171 4266 5.193728 AGGGTTCCATTCTGCCTTTTATCTA 59.806 40.000 0.00 0.00 0.00 1.98
4172 4267 4.017130 AGGGTTCCATTCTGCCTTTTATCT 60.017 41.667 0.00 0.00 0.00 1.98
4173 4268 4.281657 AGGGTTCCATTCTGCCTTTTATC 58.718 43.478 0.00 0.00 0.00 1.75
4174 4269 4.337264 AGGGTTCCATTCTGCCTTTTAT 57.663 40.909 0.00 0.00 0.00 1.40
4184 4279 5.557866 ACACTACTTTGTAGGGTTCCATTC 58.442 41.667 6.80 0.00 0.00 2.67
4191 4286 3.389983 TGCAAGACACTACTTTGTAGGGT 59.610 43.478 11.83 11.83 33.17 4.34
4225 4320 4.503910 ACGATAACAAGCATCAGCACTTA 58.496 39.130 0.00 0.00 45.49 2.24
4232 4327 8.887036 AGTAAATCATACGATAACAAGCATCA 57.113 30.769 0.00 0.00 0.00 3.07
4262 4358 8.274322 AGATGGATGACCTTCATATAACAAACA 58.726 33.333 0.00 0.00 37.20 2.83
4277 4374 4.040217 AGCAATCAGTAGAGATGGATGACC 59.960 45.833 0.00 0.00 0.00 4.02
4293 4390 7.706179 GGCAAGCATATAAAAAGTTAGCAATCA 59.294 33.333 0.00 0.00 0.00 2.57
4348 4445 0.669619 TCAGACCAACGCACGAGTAA 59.330 50.000 0.00 0.00 0.00 2.24
4455 4552 6.103997 TCTACAGATTTAAAGCGGTTGGTAG 58.896 40.000 14.20 12.86 0.00 3.18
4625 4725 7.739498 TTTGAAGGACTAAGTTACATGGTTC 57.261 36.000 0.00 0.00 0.00 3.62
4632 4733 7.797038 TCAAGGTTTTGAAGGACTAAGTTAC 57.203 36.000 0.00 0.00 40.26 2.50
5137 5239 1.176619 AAAAACAGGCCCGGTGCTAC 61.177 55.000 13.58 0.02 40.92 3.58
5209 5312 0.246360 GCCTTTGCTTATTTGGCGGT 59.754 50.000 0.00 0.00 33.96 5.68
5210 5313 0.246086 TGCCTTTGCTTATTTGGCGG 59.754 50.000 0.00 0.00 45.90 6.13
5260 5363 4.256920 AGCTTAATTCCAGCTGTACACTG 58.743 43.478 13.81 14.75 46.25 3.66
5272 5375 5.048846 TGTCCCTGGATAAGCTTAATTCC 57.951 43.478 16.27 16.27 0.00 3.01
5290 5393 7.756395 ACAATCATGATTCCTTCATATGTCC 57.244 36.000 18.16 0.00 43.40 4.02
5301 5404 8.062448 GCGTTACTAGTTAACAATCATGATTCC 58.938 37.037 18.16 4.56 40.30 3.01
5326 5444 3.591196 TTATGTGAAATTGCAGTGGGC 57.409 42.857 0.00 0.00 45.13 5.36
5368 5486 4.869297 TGTTTTTCTCAATGGCTTGTGTTG 59.131 37.500 0.00 0.00 33.87 3.33
5373 5491 3.181467 TGGGTGTTTTTCTCAATGGCTTG 60.181 43.478 0.00 0.00 0.00 4.01
5378 5496 4.984161 GTCATGTGGGTGTTTTTCTCAATG 59.016 41.667 0.00 0.00 0.00 2.82
5415 5533 7.275920 GTGGGCTATTAGATTTTGAAGAGAGA 58.724 38.462 0.00 0.00 0.00 3.10
5439 5557 3.775316 AGGGAGTATTGAATTCCAGTCGT 59.225 43.478 2.27 0.00 32.50 4.34
5512 5632 9.847224 GGTTCTCCCTCTGTATCAAAATATAAA 57.153 33.333 0.00 0.00 0.00 1.40
5535 5655 1.674817 CGGCGATTGACTACCAAGGTT 60.675 52.381 0.00 0.00 38.31 3.50
5622 5742 5.394115 CCCAAGAATTATCCCGAAAACAAGG 60.394 44.000 0.00 0.00 0.00 3.61
5628 5748 3.054948 ACGACCCAAGAATTATCCCGAAA 60.055 43.478 0.00 0.00 0.00 3.46
5629 5749 2.502538 ACGACCCAAGAATTATCCCGAA 59.497 45.455 0.00 0.00 0.00 4.30
5724 5844 2.046217 GGAAAGTCTGGGCCGACC 60.046 66.667 19.96 8.91 40.81 4.79
5838 5958 5.240844 ACCAAAATAAGACCACACTGTAAGC 59.759 40.000 0.00 0.00 37.60 3.09
5913 6033 0.748005 ACAACAGAACACGCCAAGCT 60.748 50.000 0.00 0.00 0.00 3.74
5990 6110 9.661563 AATAGACATCACGACCAAAGTAAAATA 57.338 29.630 0.00 0.00 0.00 1.40
6002 6122 4.348656 TGACGCTTAATAGACATCACGAC 58.651 43.478 0.00 0.00 0.00 4.34
6052 6172 2.267174 CCAGATAATGGTGCTCAGGG 57.733 55.000 0.00 0.00 44.91 4.45
6066 6186 2.719739 CTCAACCAAGATGCACCAGAT 58.280 47.619 0.00 0.00 0.00 2.90
6071 6191 0.524862 CCAGCTCAACCAAGATGCAC 59.475 55.000 0.00 0.00 31.30 4.57
6079 6199 2.401699 CTGCACCTCCAGCTCAACCA 62.402 60.000 0.00 0.00 0.00 3.67
6080 6200 1.673665 CTGCACCTCCAGCTCAACC 60.674 63.158 0.00 0.00 0.00 3.77
6207 6333 8.956533 TTTGTAGATATACAGCAGCAACAATA 57.043 30.769 0.00 0.00 0.00 1.90
6208 6334 7.864108 TTTGTAGATATACAGCAGCAACAAT 57.136 32.000 0.00 0.00 0.00 2.71
6237 6370 5.876651 AGCATGTCTGGATGTACTATCAA 57.123 39.130 0.00 0.00 0.00 2.57
6240 6373 5.337894 GGCATAGCATGTCTGGATGTACTAT 60.338 44.000 0.00 0.00 30.66 2.12
6241 6374 4.021104 GGCATAGCATGTCTGGATGTACTA 60.021 45.833 0.00 0.00 30.66 1.82
6242 6375 3.244353 GGCATAGCATGTCTGGATGTACT 60.244 47.826 0.00 0.00 30.66 2.73
6256 6389 1.064758 CCCAAACCTGTAGGCATAGCA 60.065 52.381 0.00 0.00 39.32 3.49
6393 6526 4.278956 CTGTACGTGTTCAGCCCC 57.721 61.111 0.00 0.00 0.00 5.80
6402 6535 0.798771 GCTTCGAGGAGCTGTACGTG 60.799 60.000 0.00 0.00 39.57 4.49
6488 6621 3.494626 GCTGAACTGACGAACTGATGAAA 59.505 43.478 0.00 0.00 0.00 2.69
6510 6643 6.206243 ACTGAAGAAGGATCACAAATTCACAG 59.794 38.462 0.00 0.00 35.97 3.66
6512 6645 6.566197 ACTGAAGAAGGATCACAAATTCAC 57.434 37.500 0.00 0.00 0.00 3.18
6516 6649 6.218746 GCAAAACTGAAGAAGGATCACAAAT 58.781 36.000 0.00 0.00 0.00 2.32
6517 6650 5.591099 GCAAAACTGAAGAAGGATCACAAA 58.409 37.500 0.00 0.00 0.00 2.83
6566 6699 4.329545 GCGCCCAGGGAGTTCACA 62.330 66.667 10.89 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.