Multiple sequence alignment - TraesCS2A01G254400

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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 TraesCS2A01G254400 chr2A 100.000 4038 0 0 1 4038 387646073 387642036 0.000000e+00 7457.0
1 TraesCS2A01G254400 chr2A 98.413 63 1 0 3648 3710 387642363 387642301 1.190000e-20 111.0
2 TraesCS2A01G254400 chr2A 98.413 63 1 0 3711 3773 387642426 387642364 1.190000e-20 111.0
3 TraesCS2A01G254400 chr2A 95.556 45 2 0 3520 3564 154126209 154126253 5.600000e-09 73.1
4 TraesCS2A01G254400 chr2A 95.652 46 1 1 3519 3564 196519521 196519565 5.600000e-09 73.1
5 TraesCS2A01G254400 chr2A 93.750 48 2 1 3523 3569 734989363 734989410 2.010000e-08 71.3
6 TraesCS2A01G254400 chr2A 100.000 29 0 0 147 175 387645899 387645871 2.000000e-03 54.7
7 TraesCS2A01G254400 chr2A 100.000 29 0 0 175 203 387645927 387645899 2.000000e-03 54.7
8 TraesCS2A01G254400 chr2D 96.478 2442 64 12 1207 3635 307027070 307024638 0.000000e+00 4013.0
9 TraesCS2A01G254400 chr2D 90.346 549 19 12 1 547 307027602 307027086 0.000000e+00 689.0
10 TraesCS2A01G254400 chr2D 94.578 332 8 5 3711 4038 307024663 307024338 4.660000e-139 505.0
11 TraesCS2A01G254400 chr2D 97.101 69 2 0 3642 3710 307024669 307024601 2.550000e-22 117.0
12 TraesCS2A01G254400 chr2B 96.078 1938 53 10 1381 3298 360978271 360980205 0.000000e+00 3136.0
13 TraesCS2A01G254400 chr2B 94.263 1377 28 11 1 1369 360973144 360974477 0.000000e+00 2058.0
14 TraesCS2A01G254400 chr2B 87.278 1462 140 30 181 1622 23109371 23107936 0.000000e+00 1628.0
15 TraesCS2A01G254400 chr2B 88.102 353 38 3 1730 2082 23107937 23107589 2.250000e-112 416.0
16 TraesCS2A01G254400 chr2B 94.239 243 13 1 3279 3520 360980216 360980458 1.770000e-98 370.0
17 TraesCS2A01G254400 chr2B 86.018 329 26 10 3711 4035 360980487 360980799 6.470000e-88 335.0
18 TraesCS2A01G254400 chr2B 92.537 134 10 0 2280 2413 23107219 23107086 4.120000e-45 193.0
19 TraesCS2A01G254400 chr2B 79.032 186 25 10 1 175 23109531 23109349 9.170000e-22 115.0
20 TraesCS2A01G254400 chr2B 91.667 72 3 1 3642 3710 360980481 360980552 3.320000e-16 97.1
21 TraesCS2A01G254400 chr1D 88.235 1462 117 27 190 1622 457975335 457973900 0.000000e+00 1696.0
22 TraesCS2A01G254400 chr1D 76.034 1160 160 75 2115 3212 457973344 457972241 1.010000e-135 494.0
23 TraesCS2A01G254400 chr1D 89.076 357 39 0 1730 2086 457973901 457973545 1.030000e-120 444.0
24 TraesCS2A01G254400 chr1D 97.727 44 0 1 3520 3563 201519309 201519267 1.560000e-09 75.0
25 TraesCS2A01G254400 chr1A 87.577 1465 121 29 181 1622 550445038 550443612 0.000000e+00 1640.0
26 TraesCS2A01G254400 chr1A 75.669 1159 154 74 2114 3211 550442951 550441860 1.020000e-125 460.0
27 TraesCS2A01G254400 chr1A 82.889 450 52 14 2726 3163 560850064 560850500 8.190000e-102 381.0
28 TraesCS2A01G254400 chr1A 81.933 476 53 16 2209 2663 560845104 560845567 4.930000e-99 372.0
29 TraesCS2A01G254400 chr1A 84.046 351 39 8 1734 2081 560844518 560844854 5.030000e-84 322.0
30 TraesCS2A01G254400 chr1B 87.440 1465 118 31 181 1622 628053461 628052040 0.000000e+00 1626.0
31 TraesCS2A01G254400 chr1B 87.989 358 40 2 1730 2086 628052041 628051686 1.740000e-113 420.0
32 TraesCS2A01G254400 chr1B 86.014 286 30 7 2134 2412 628051457 628051175 8.480000e-77 298.0
33 TraesCS2A01G254400 chr7D 92.562 121 4 3 1614 1734 310990308 310990193 6.940000e-38 169.0
34 TraesCS2A01G254400 chr7D 92.241 116 5 3 1617 1732 236821646 236821535 1.160000e-35 161.0
35 TraesCS2A01G254400 chr7B 91.379 116 6 2 1617 1732 213457682 213457571 5.400000e-34 156.0
36 TraesCS2A01G254400 chr6D 90.083 121 6 5 1621 1740 391925879 391925994 6.990000e-33 152.0
37 TraesCS2A01G254400 chr7A 90.517 116 7 3 1617 1732 252178508 252178397 2.510000e-32 150.0
38 TraesCS2A01G254400 chr3D 89.167 120 9 1 1614 1733 536330570 536330685 3.250000e-31 147.0
39 TraesCS2A01G254400 chr6B 88.983 118 9 1 1615 1732 93568342 93568455 4.210000e-30 143.0
40 TraesCS2A01G254400 chr3B 94.000 50 3 0 3515 3564 690430213 690430262 4.330000e-10 76.8
41 TraesCS2A01G254400 chr3B 90.385 52 3 2 3520 3569 430939811 430939862 2.600000e-07 67.6
42 TraesCS2A01G254400 chr3A 95.745 47 2 0 3523 3569 648496523 648496477 4.330000e-10 76.8
43 TraesCS2A01G254400 chr5D 89.286 56 5 1 3517 3572 133859094 133859148 7.240000e-08 69.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G254400 chr2A 387642036 387646073 4037 True 1557.680000 7457 99.365200 1 4038 5 chr2A.!!$R1 4037
1 TraesCS2A01G254400 chr2D 307024338 307027602 3264 True 1331.000000 4013 94.625750 1 4038 4 chr2D.!!$R1 4037
2 TraesCS2A01G254400 chr2B 360973144 360980799 7655 False 1199.220000 3136 92.453000 1 4035 5 chr2B.!!$F1 4034
3 TraesCS2A01G254400 chr2B 23107086 23109531 2445 True 588.000000 1628 86.737250 1 2413 4 chr2B.!!$R1 2412
4 TraesCS2A01G254400 chr1D 457972241 457975335 3094 True 878.000000 1696 84.448333 190 3212 3 chr1D.!!$R2 3022
5 TraesCS2A01G254400 chr1A 550441860 550445038 3178 True 1050.000000 1640 81.623000 181 3211 2 chr1A.!!$R1 3030
6 TraesCS2A01G254400 chr1A 560844518 560845567 1049 False 347.000000 372 82.989500 1734 2663 2 chr1A.!!$F2 929
7 TraesCS2A01G254400 chr1B 628051175 628053461 2286 True 781.333333 1626 87.147667 181 2412 3 chr1B.!!$R1 2231

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
174 184 0.106708 GACAACCTGAGTCACCTGCA 59.893 55.000 0.00 0.0 36.06 4.41 F
175 185 0.767375 ACAACCTGAGTCACCTGCAT 59.233 50.000 0.00 0.0 0.00 3.96 F
994 1020 1.413445 AGCACTTGCAAAAATGCCTGA 59.587 42.857 20.53 0.0 45.16 3.86 F
2578 6790 0.598065 AGTCGGAAAAGGCATTGCAC 59.402 50.000 11.39 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 1060 1.398390 GTGGCAGTAGAAAATCCAGCG 59.602 52.381 0.00 0.0 0.00 5.18 R
1933 5758 2.365293 ACCAAATGGCAAGGAACAGAAC 59.635 45.455 10.45 0.0 39.32 3.01 R
2965 7210 0.250234 TGCTCTGGATTCCACTTCCG 59.750 55.000 0.00 0.0 35.94 4.30 R
3632 7932 0.031178 GTGCCGTTACCGATACCGAT 59.969 55.000 0.00 0.0 38.22 4.18 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
36 37 6.012113 TGTTCTTTTCATGTCTGATTCCCAT 58.988 36.000 0.00 0.00 0.00 4.00
44 45 7.862274 TCATGTCTGATTCCCATATAGAACT 57.138 36.000 0.00 0.00 0.00 3.01
152 162 8.728098 AGTCCCTGGAGAGCTTTTTAATATTAT 58.272 33.333 0.00 0.00 0.00 1.28
171 181 6.875972 ATTATAAGACAACCTGAGTCACCT 57.124 37.500 0.00 0.00 38.46 4.00
172 182 2.918712 AAGACAACCTGAGTCACCTG 57.081 50.000 0.00 0.00 38.46 4.00
173 183 0.394565 AGACAACCTGAGTCACCTGC 59.605 55.000 0.00 0.00 38.46 4.85
174 184 0.106708 GACAACCTGAGTCACCTGCA 59.893 55.000 0.00 0.00 36.06 4.41
175 185 0.767375 ACAACCTGAGTCACCTGCAT 59.233 50.000 0.00 0.00 0.00 3.96
176 186 1.977854 ACAACCTGAGTCACCTGCATA 59.022 47.619 0.00 0.00 0.00 3.14
177 187 2.573462 ACAACCTGAGTCACCTGCATAT 59.427 45.455 0.00 0.00 0.00 1.78
178 188 3.009473 ACAACCTGAGTCACCTGCATATT 59.991 43.478 0.00 0.00 0.00 1.28
179 189 4.225042 ACAACCTGAGTCACCTGCATATTA 59.775 41.667 0.00 0.00 0.00 0.98
333 356 7.363268 GCTTCCATTCAATTTGAGTTCATAGGT 60.363 37.037 0.00 0.00 0.00 3.08
392 415 9.122779 GTTCATCTTTAGTCTAGCCTTAGTCTA 57.877 37.037 0.00 0.00 0.00 2.59
393 416 9.696572 TTCATCTTTAGTCTAGCCTTAGTCTAA 57.303 33.333 0.00 0.00 36.44 2.10
435 459 5.067674 ACCGCTGCATGACAATACATTAATT 59.932 36.000 0.00 0.00 0.00 1.40
547 573 3.452474 CAGAGTACCAGCTCATTGTAGC 58.548 50.000 0.00 0.00 43.11 3.58
628 654 3.731216 CGTGATAAGTATCGGCTGAAGTG 59.269 47.826 0.00 0.00 35.48 3.16
675 701 2.163818 TCCGATTGATTATGCCCGTC 57.836 50.000 0.00 0.00 0.00 4.79
895 921 5.640147 TGATTTTGTTGAGGGTAGAATGGT 58.360 37.500 0.00 0.00 0.00 3.55
994 1020 1.413445 AGCACTTGCAAAAATGCCTGA 59.587 42.857 20.53 0.00 45.16 3.86
1029 1057 7.915923 CAGTTACTTGGAGGAAAGAAGAAAAAC 59.084 37.037 0.00 0.00 0.00 2.43
1032 1060 5.594725 ACTTGGAGGAAAGAAGAAAAACCTC 59.405 40.000 0.00 0.00 41.90 3.85
1175 1205 4.764172 ACTCTAGCAGCAAGAATCGATTT 58.236 39.130 12.81 0.00 0.00 2.17
1316 1346 4.283722 AGACTCCGAGCCTAAAAAGAAGAA 59.716 41.667 0.00 0.00 0.00 2.52
1374 1408 8.360390 AGGTAAGCTTTTCTCAACTATTTTTGG 58.640 33.333 3.20 0.00 0.00 3.28
1434 5250 8.865590 TTTGTTTCTTGAACTACTTATTTGCC 57.134 30.769 0.00 0.00 39.08 4.52
1721 5540 4.574892 TGAGCGACAAGTAATTTGGATCA 58.425 39.130 0.00 0.00 41.25 2.92
1933 5758 5.878116 TCCCACAGTATCTTATTTTGTTCCG 59.122 40.000 0.00 0.00 0.00 4.30
1987 5812 9.046296 GCATAAAGCACATCACTACTAATTAGT 57.954 33.333 21.35 21.35 41.86 2.24
2013 5838 3.620821 GCAATAGAGGTCTTCTGCACTTC 59.379 47.826 7.69 0.00 36.61 3.01
2019 5844 3.501349 AGGTCTTCTGCACTTCTACTCA 58.499 45.455 0.00 0.00 0.00 3.41
2256 6426 7.601856 TGTTTCTATTTCAATTCATGACCACC 58.398 34.615 0.00 0.00 37.92 4.61
2578 6790 0.598065 AGTCGGAAAAGGCATTGCAC 59.402 50.000 11.39 0.00 0.00 4.57
2723 6959 4.041075 TCTTGTAAACCAGGTGCTGTATGA 59.959 41.667 0.00 0.00 0.00 2.15
3020 7265 0.301687 CGGCACATTTTCTCGGATCG 59.698 55.000 0.00 0.00 0.00 3.69
3095 7348 3.750371 ACGATGATTGTTTCTTGGTCCA 58.250 40.909 0.00 0.00 0.00 4.02
3365 7658 6.262273 GGAATTACCTTGTCTGAAACTGTTGA 59.738 38.462 0.00 0.00 35.41 3.18
3415 7708 0.671781 CAACCGAGTTGAGCTCCAGG 60.672 60.000 12.15 9.61 45.28 4.45
3468 7762 7.816640 TGAGGAAATAATTTTTCTCCGAAGTG 58.183 34.615 4.69 0.00 44.03 3.16
3521 7815 4.132336 CAATGTAGACTGCATGGTGCTAT 58.868 43.478 6.82 0.00 45.31 2.97
3535 7829 5.294734 TGGTGCTATCACATGACATATGT 57.705 39.130 8.43 8.43 44.87 2.29
3541 7835 6.930722 TGCTATCACATGACATATGTGGTAAG 59.069 38.462 14.43 13.18 46.78 2.34
3557 7851 7.055667 TGTGGTAAGCAATCCAAACAATTTA 57.944 32.000 0.00 0.00 35.38 1.40
3595 7895 3.144506 AGGTGCTGATATTACATGCTGC 58.855 45.455 0.00 0.00 0.00 5.25
3603 7903 2.634982 ATTACATGCTGCGGTGTTTG 57.365 45.000 14.27 0.00 0.00 2.93
3604 7904 0.595588 TTACATGCTGCGGTGTTTGG 59.404 50.000 14.27 0.00 0.00 3.28
3605 7905 0.536233 TACATGCTGCGGTGTTTGGT 60.536 50.000 14.27 0.00 0.00 3.67
3606 7906 0.536233 ACATGCTGCGGTGTTTGGTA 60.536 50.000 4.87 0.00 0.00 3.25
3607 7907 0.595588 CATGCTGCGGTGTTTGGTAA 59.404 50.000 0.00 0.00 0.00 2.85
3608 7908 1.202114 CATGCTGCGGTGTTTGGTAAT 59.798 47.619 0.00 0.00 0.00 1.89
3609 7909 0.595588 TGCTGCGGTGTTTGGTAATG 59.404 50.000 0.00 0.00 0.00 1.90
3610 7910 0.109319 GCTGCGGTGTTTGGTAATGG 60.109 55.000 0.00 0.00 0.00 3.16
3611 7911 0.109319 CTGCGGTGTTTGGTAATGGC 60.109 55.000 0.00 0.00 0.00 4.40
3612 7912 0.823769 TGCGGTGTTTGGTAATGGCA 60.824 50.000 0.00 0.00 0.00 4.92
3613 7913 0.388006 GCGGTGTTTGGTAATGGCAC 60.388 55.000 0.00 0.00 0.00 5.01
3614 7914 0.109964 CGGTGTTTGGTAATGGCACG 60.110 55.000 0.00 0.00 0.00 5.34
3615 7915 1.240256 GGTGTTTGGTAATGGCACGA 58.760 50.000 0.00 0.00 0.00 4.35
3616 7916 1.068816 GGTGTTTGGTAATGGCACGAC 60.069 52.381 0.00 0.00 0.00 4.34
3617 7917 1.068816 GTGTTTGGTAATGGCACGACC 60.069 52.381 11.79 11.79 39.84 4.79
3625 7925 2.832498 TGGCACGACCATGAACCA 59.168 55.556 0.00 0.00 46.36 3.67
3626 7926 1.302431 TGGCACGACCATGAACCAG 60.302 57.895 0.00 0.00 46.36 4.00
3627 7927 1.302511 GGCACGACCATGAACCAGT 60.303 57.895 0.00 0.00 38.86 4.00
3628 7928 0.036765 GGCACGACCATGAACCAGTA 60.037 55.000 0.00 0.00 38.86 2.74
3629 7929 1.609580 GGCACGACCATGAACCAGTAA 60.610 52.381 0.00 0.00 38.86 2.24
3630 7930 2.147958 GCACGACCATGAACCAGTAAA 58.852 47.619 0.00 0.00 0.00 2.01
3631 7931 2.747446 GCACGACCATGAACCAGTAAAT 59.253 45.455 0.00 0.00 0.00 1.40
3632 7932 3.936453 GCACGACCATGAACCAGTAAATA 59.064 43.478 0.00 0.00 0.00 1.40
3633 7933 4.574828 GCACGACCATGAACCAGTAAATAT 59.425 41.667 0.00 0.00 0.00 1.28
3634 7934 5.277345 GCACGACCATGAACCAGTAAATATC 60.277 44.000 0.00 0.00 0.00 1.63
3635 7935 5.047847 ACGACCATGAACCAGTAAATATCG 58.952 41.667 0.00 0.00 0.00 2.92
3636 7936 4.447724 CGACCATGAACCAGTAAATATCGG 59.552 45.833 0.00 0.00 0.00 4.18
3637 7937 5.365619 GACCATGAACCAGTAAATATCGGT 58.634 41.667 0.00 0.00 0.00 4.69
3638 7938 6.488769 ACCATGAACCAGTAAATATCGGTA 57.511 37.500 0.00 0.00 0.00 4.02
3639 7939 7.074653 ACCATGAACCAGTAAATATCGGTAT 57.925 36.000 0.00 0.00 0.00 2.73
3640 7940 7.159372 ACCATGAACCAGTAAATATCGGTATC 58.841 38.462 0.00 0.00 0.00 2.24
3706 8006 8.462143 TTTCTTACTTTTGTACTAGATCAGCG 57.538 34.615 0.00 0.00 34.15 5.18
3707 8007 7.154435 TCTTACTTTTGTACTAGATCAGCGT 57.846 36.000 0.00 0.00 34.15 5.07
3708 8008 7.249147 TCTTACTTTTGTACTAGATCAGCGTC 58.751 38.462 0.00 0.00 34.15 5.19
3709 8009 5.386958 ACTTTTGTACTAGATCAGCGTCA 57.613 39.130 0.00 0.00 0.00 4.35
3710 8010 5.403246 ACTTTTGTACTAGATCAGCGTCAG 58.597 41.667 0.00 0.00 0.00 3.51
3711 8011 4.371855 TTTGTACTAGATCAGCGTCAGG 57.628 45.455 0.00 0.00 0.00 3.86
3712 8012 1.676529 TGTACTAGATCAGCGTCAGGC 59.323 52.381 0.00 0.00 44.05 4.85
3721 8021 2.821366 GCGTCAGGCAGGACCATG 60.821 66.667 0.00 0.00 43.14 3.66
3722 8022 2.981302 CGTCAGGCAGGACCATGA 59.019 61.111 0.00 0.00 43.14 3.07
3723 8023 1.296392 CGTCAGGCAGGACCATGAA 59.704 57.895 0.00 0.00 43.14 2.57
3724 8024 1.021390 CGTCAGGCAGGACCATGAAC 61.021 60.000 0.00 0.00 43.14 3.18
3725 8025 0.678048 GTCAGGCAGGACCATGAACC 60.678 60.000 0.00 0.00 43.14 3.62
3726 8026 1.133181 TCAGGCAGGACCATGAACCA 61.133 55.000 0.00 0.00 43.14 3.67
3727 8027 0.679002 CAGGCAGGACCATGAACCAG 60.679 60.000 0.00 0.00 43.14 4.00
3728 8028 1.136329 AGGCAGGACCATGAACCAGT 61.136 55.000 0.00 0.00 43.14 4.00
3729 8029 0.618458 GGCAGGACCATGAACCAGTA 59.382 55.000 0.00 0.00 38.86 2.74
3730 8030 1.004277 GGCAGGACCATGAACCAGTAA 59.996 52.381 0.00 0.00 38.86 2.24
3731 8031 2.554344 GGCAGGACCATGAACCAGTAAA 60.554 50.000 0.00 0.00 38.86 2.01
3732 8032 3.356290 GCAGGACCATGAACCAGTAAAT 58.644 45.455 0.00 0.00 0.00 1.40
3733 8033 4.523083 GCAGGACCATGAACCAGTAAATA 58.477 43.478 0.00 0.00 0.00 1.40
3734 8034 5.133221 GCAGGACCATGAACCAGTAAATAT 58.867 41.667 0.00 0.00 0.00 1.28
3735 8035 5.239525 GCAGGACCATGAACCAGTAAATATC 59.760 44.000 0.00 0.00 0.00 1.63
3736 8036 6.595682 CAGGACCATGAACCAGTAAATATCT 58.404 40.000 0.00 0.00 0.00 1.98
3737 8037 7.056635 CAGGACCATGAACCAGTAAATATCTT 58.943 38.462 0.00 0.00 0.00 2.40
3738 8038 7.557719 CAGGACCATGAACCAGTAAATATCTTT 59.442 37.037 0.00 0.00 0.00 2.52
3739 8039 7.775561 AGGACCATGAACCAGTAAATATCTTTC 59.224 37.037 0.00 0.00 0.00 2.62
3740 8040 7.556275 GGACCATGAACCAGTAAATATCTTTCA 59.444 37.037 0.00 0.00 0.00 2.69
3741 8041 8.877864 ACCATGAACCAGTAAATATCTTTCAA 57.122 30.769 0.00 0.00 0.00 2.69
3742 8042 8.960591 ACCATGAACCAGTAAATATCTTTCAAG 58.039 33.333 0.00 0.00 0.00 3.02
3743 8043 8.960591 CCATGAACCAGTAAATATCTTTCAAGT 58.039 33.333 0.00 0.00 0.00 3.16
3787 8090 2.872245 AGCGTCAATTAACATGGATCGG 59.128 45.455 0.00 0.00 0.00 4.18
3788 8091 2.612212 GCGTCAATTAACATGGATCGGT 59.388 45.455 0.00 0.00 0.00 4.69
3789 8092 3.546020 GCGTCAATTAACATGGATCGGTG 60.546 47.826 0.00 0.00 0.00 4.94
3790 8093 3.002246 CGTCAATTAACATGGATCGGTGG 59.998 47.826 0.00 0.00 0.00 4.61
3791 8094 3.315191 GTCAATTAACATGGATCGGTGGG 59.685 47.826 0.00 0.00 0.00 4.61
3792 8095 3.201045 TCAATTAACATGGATCGGTGGGA 59.799 43.478 0.00 0.00 0.00 4.37
3917 8220 4.035112 TCGAGGCTATTTTTAGGGGAAGA 58.965 43.478 0.00 0.00 0.00 2.87
3939 8242 2.145397 TCTCCAGGCCACTACAGTAG 57.855 55.000 5.01 6.00 0.00 2.57
4035 8342 1.135689 CAATTACGACAAGCCCACTGC 60.136 52.381 0.00 0.00 41.71 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 7.171678 CCATTTGCACCCTACGAAAAATTTAAA 59.828 33.333 0.00 0.00 0.00 1.52
47 48 4.994217 CCATTTGCACCCTACGAAAAATTT 59.006 37.500 0.00 0.00 0.00 1.82
50 51 3.223435 TCCATTTGCACCCTACGAAAAA 58.777 40.909 0.00 0.00 0.00 1.94
52 53 2.039216 TCTCCATTTGCACCCTACGAAA 59.961 45.455 0.00 0.00 0.00 3.46
56 57 6.715347 AAAATATCTCCATTTGCACCCTAC 57.285 37.500 0.00 0.00 0.00 3.18
152 162 2.037251 GCAGGTGACTCAGGTTGTCTTA 59.963 50.000 0.00 0.00 40.21 2.10
153 163 1.202698 GCAGGTGACTCAGGTTGTCTT 60.203 52.381 0.00 0.00 40.21 3.01
154 164 0.394565 GCAGGTGACTCAGGTTGTCT 59.605 55.000 0.00 0.00 40.21 3.41
155 165 0.106708 TGCAGGTGACTCAGGTTGTC 59.893 55.000 0.00 0.00 40.21 3.18
156 166 0.767375 ATGCAGGTGACTCAGGTTGT 59.233 50.000 0.00 0.00 40.21 3.32
157 167 2.768253 TATGCAGGTGACTCAGGTTG 57.232 50.000 0.00 0.00 40.21 3.77
158 168 5.636903 ATAATATGCAGGTGACTCAGGTT 57.363 39.130 0.00 0.00 40.21 3.50
159 169 6.554982 TCTTATAATATGCAGGTGACTCAGGT 59.445 38.462 0.00 0.00 40.21 4.00
160 170 6.870965 GTCTTATAATATGCAGGTGACTCAGG 59.129 42.308 0.00 0.00 40.21 3.86
161 171 7.436933 TGTCTTATAATATGCAGGTGACTCAG 58.563 38.462 0.00 0.00 40.21 3.35
162 172 7.360113 TGTCTTATAATATGCAGGTGACTCA 57.640 36.000 0.00 0.00 40.21 3.41
163 173 7.171678 GGTTGTCTTATAATATGCAGGTGACTC 59.828 40.741 0.00 0.00 40.21 3.36
164 174 6.992715 GGTTGTCTTATAATATGCAGGTGACT 59.007 38.462 0.00 0.00 46.44 3.41
165 175 6.992715 AGGTTGTCTTATAATATGCAGGTGAC 59.007 38.462 0.00 0.00 0.00 3.67
166 176 6.992123 CAGGTTGTCTTATAATATGCAGGTGA 59.008 38.462 0.00 0.00 0.00 4.02
167 177 6.992123 TCAGGTTGTCTTATAATATGCAGGTG 59.008 38.462 0.00 0.00 0.00 4.00
168 178 7.136822 TCAGGTTGTCTTATAATATGCAGGT 57.863 36.000 0.00 0.00 0.00 4.00
169 179 7.220030 ACTCAGGTTGTCTTATAATATGCAGG 58.780 38.462 0.00 0.00 0.00 4.85
170 180 7.928167 TGACTCAGGTTGTCTTATAATATGCAG 59.072 37.037 0.00 0.00 35.63 4.41
171 181 7.710907 GTGACTCAGGTTGTCTTATAATATGCA 59.289 37.037 0.00 0.00 35.63 3.96
172 182 7.171678 GGTGACTCAGGTTGTCTTATAATATGC 59.828 40.741 0.00 0.00 35.63 3.14
173 183 8.424918 AGGTGACTCAGGTTGTCTTATAATATG 58.575 37.037 0.00 0.00 32.90 1.78
174 184 8.424918 CAGGTGACTCAGGTTGTCTTATAATAT 58.575 37.037 0.00 0.00 40.21 1.28
175 185 7.632898 GCAGGTGACTCAGGTTGTCTTATAATA 60.633 40.741 0.00 0.00 40.21 0.98
176 186 6.644347 CAGGTGACTCAGGTTGTCTTATAAT 58.356 40.000 0.00 0.00 40.21 1.28
177 187 5.568825 GCAGGTGACTCAGGTTGTCTTATAA 60.569 44.000 0.00 0.00 40.21 0.98
178 188 4.081642 GCAGGTGACTCAGGTTGTCTTATA 60.082 45.833 0.00 0.00 40.21 0.98
179 189 3.307059 GCAGGTGACTCAGGTTGTCTTAT 60.307 47.826 0.00 0.00 40.21 1.73
333 356 2.103094 CCCTATGGACTCAAATCGCAGA 59.897 50.000 0.00 0.00 45.75 4.26
435 459 1.164411 CGCAGCAAATGGACCTGTAA 58.836 50.000 0.00 0.00 0.00 2.41
547 573 9.608617 CAATATCTACTGATAAAGCATTGCAAG 57.391 33.333 11.91 0.00 38.50 4.01
628 654 2.040412 ACAAGGGATTCCAGTTCAGGAC 59.960 50.000 4.80 0.00 37.42 3.85
675 701 5.582269 TCTCATTGGCGATCTTCTTAACAAG 59.418 40.000 0.00 0.00 0.00 3.16
895 921 3.886505 AGAAAGGTTTGGTGCGATGTAAA 59.113 39.130 0.00 0.00 0.00 2.01
994 1020 4.074970 CCTCCAAGTAACTGAACATTGCT 58.925 43.478 0.00 0.00 0.00 3.91
1029 1057 1.936547 GCAGTAGAAAATCCAGCGAGG 59.063 52.381 0.00 0.00 39.47 4.63
1032 1060 1.398390 GTGGCAGTAGAAAATCCAGCG 59.602 52.381 0.00 0.00 0.00 5.18
1175 1205 4.361783 TCCAGTTGGATCACCTCTAATCA 58.638 43.478 0.00 0.00 39.78 2.57
1333 1363 9.665719 AAAAGCTTACCTTTCTTTCATTTTTCA 57.334 25.926 0.00 0.00 42.82 2.69
1434 5250 5.428496 TGAATCAAGTTTCAGCACAGAAG 57.572 39.130 0.00 0.00 32.07 2.85
1695 5514 4.576873 TCCAAATTACTTGTCGCTCAAACA 59.423 37.500 0.00 0.00 35.48 2.83
1721 5540 6.602803 GTGTAGCTAAACTAACTACTCCCTCT 59.397 42.308 6.82 0.00 37.70 3.69
1933 5758 2.365293 ACCAAATGGCAAGGAACAGAAC 59.635 45.455 10.45 0.00 39.32 3.01
1987 5812 2.418746 GCAGAAGACCTCTATTGCCGAA 60.419 50.000 0.00 0.00 32.58 4.30
2256 6426 2.931969 TGCAGTGCGTGATATCAAGAAG 59.068 45.455 20.98 8.28 0.00 2.85
2331 6522 0.817634 TGTTGCACCACTGCTACCAC 60.818 55.000 5.10 0.00 45.41 4.16
2578 6790 5.571277 CAGCAAAAAGACAAAAACAATGGG 58.429 37.500 0.00 0.00 0.00 4.00
2723 6959 3.149196 CATGGTCCAAACTAACAGCAGT 58.851 45.455 0.00 0.00 0.00 4.40
2854 7098 6.881602 AGAGATTTCATGTGGTTAACCTCTTC 59.118 38.462 24.78 12.92 36.82 2.87
2965 7210 0.250234 TGCTCTGGATTCCACTTCCG 59.750 55.000 0.00 0.00 35.94 4.30
3020 7265 1.875488 TTCTAACCTCCAGGCCTACC 58.125 55.000 3.98 0.00 39.32 3.18
3095 7348 3.516300 TGCAGAATGGGATGAAATTGCTT 59.484 39.130 0.00 0.00 35.86 3.91
3343 7636 7.823745 ATTCAACAGTTTCAGACAAGGTAAT 57.176 32.000 0.00 0.00 0.00 1.89
3344 7637 7.201785 GGAATTCAACAGTTTCAGACAAGGTAA 60.202 37.037 7.93 0.00 0.00 2.85
3345 7638 6.262273 GGAATTCAACAGTTTCAGACAAGGTA 59.738 38.462 7.93 0.00 0.00 3.08
3346 7639 5.067805 GGAATTCAACAGTTTCAGACAAGGT 59.932 40.000 7.93 0.00 0.00 3.50
3415 7708 7.035840 AGGTCAATCACAATTATCATCTTGC 57.964 36.000 0.00 0.00 0.00 4.01
3535 7829 8.964476 TTTTAAATTGTTTGGATTGCTTACCA 57.036 26.923 0.00 0.00 0.00 3.25
3595 7895 0.109964 CGTGCCATTACCAAACACCG 60.110 55.000 0.00 0.00 0.00 4.94
3609 7909 0.036765 TACTGGTTCATGGTCGTGCC 60.037 55.000 0.00 0.00 37.90 5.01
3610 7910 1.803334 TTACTGGTTCATGGTCGTGC 58.197 50.000 0.00 0.00 0.00 5.34
3611 7911 5.051039 CGATATTTACTGGTTCATGGTCGTG 60.051 44.000 0.00 0.00 0.00 4.35
3612 7912 5.047847 CGATATTTACTGGTTCATGGTCGT 58.952 41.667 0.00 0.00 0.00 4.34
3613 7913 4.447724 CCGATATTTACTGGTTCATGGTCG 59.552 45.833 0.00 0.00 0.00 4.79
3614 7914 5.365619 ACCGATATTTACTGGTTCATGGTC 58.634 41.667 0.00 0.00 0.00 4.02
3615 7915 5.367945 ACCGATATTTACTGGTTCATGGT 57.632 39.130 0.00 0.00 0.00 3.55
3616 7916 6.310467 CGATACCGATATTTACTGGTTCATGG 59.690 42.308 0.00 0.00 38.22 3.66
3617 7917 6.310467 CCGATACCGATATTTACTGGTTCATG 59.690 42.308 0.00 0.00 38.22 3.07
3618 7918 6.014840 ACCGATACCGATATTTACTGGTTCAT 60.015 38.462 0.00 0.00 38.22 2.57
3619 7919 5.302568 ACCGATACCGATATTTACTGGTTCA 59.697 40.000 0.00 0.00 38.22 3.18
3620 7920 5.776744 ACCGATACCGATATTTACTGGTTC 58.223 41.667 0.00 0.00 38.22 3.62
3621 7921 5.796424 ACCGATACCGATATTTACTGGTT 57.204 39.130 0.00 0.00 38.22 3.67
3622 7922 6.568462 CGTTACCGATACCGATATTTACTGGT 60.568 42.308 0.00 0.00 38.22 4.00
3623 7923 5.796935 CGTTACCGATACCGATATTTACTGG 59.203 44.000 0.00 0.00 38.22 4.00
3624 7924 5.796935 CCGTTACCGATACCGATATTTACTG 59.203 44.000 0.00 0.00 38.22 2.74
3625 7925 5.619981 GCCGTTACCGATACCGATATTTACT 60.620 44.000 0.00 0.00 38.22 2.24
3626 7926 4.558860 GCCGTTACCGATACCGATATTTAC 59.441 45.833 0.00 0.00 38.22 2.01
3627 7927 4.217334 TGCCGTTACCGATACCGATATTTA 59.783 41.667 0.00 0.00 38.22 1.40
3628 7928 3.005684 TGCCGTTACCGATACCGATATTT 59.994 43.478 0.00 0.00 38.22 1.40
3629 7929 2.557924 TGCCGTTACCGATACCGATATT 59.442 45.455 0.00 0.00 38.22 1.28
3630 7930 2.095059 GTGCCGTTACCGATACCGATAT 60.095 50.000 0.00 0.00 38.22 1.63
3631 7931 1.266718 GTGCCGTTACCGATACCGATA 59.733 52.381 0.00 0.00 38.22 2.92
3632 7932 0.031178 GTGCCGTTACCGATACCGAT 59.969 55.000 0.00 0.00 38.22 4.18
3633 7933 1.433064 GTGCCGTTACCGATACCGA 59.567 57.895 0.00 0.00 38.22 4.69
3634 7934 1.940758 CGTGCCGTTACCGATACCG 60.941 63.158 0.00 0.00 35.63 4.02
3635 7935 0.867329 GTCGTGCCGTTACCGATACC 60.867 60.000 0.00 0.00 35.63 2.73
3636 7936 0.867329 GGTCGTGCCGTTACCGATAC 60.867 60.000 0.00 0.00 35.63 2.24
3637 7937 1.311651 TGGTCGTGCCGTTACCGATA 61.312 55.000 0.00 0.00 41.21 2.92
3638 7938 1.952102 ATGGTCGTGCCGTTACCGAT 61.952 55.000 0.00 0.00 41.21 4.18
3639 7939 2.638354 ATGGTCGTGCCGTTACCGA 61.638 57.895 0.00 0.00 41.21 4.69
3640 7940 2.125832 ATGGTCGTGCCGTTACCG 60.126 61.111 0.00 0.00 41.21 4.02
3681 7981 8.086522 ACGCTGATCTAGTACAAAAGTAAGAAA 58.913 33.333 0.00 0.00 0.00 2.52
3682 7982 7.600065 ACGCTGATCTAGTACAAAAGTAAGAA 58.400 34.615 0.00 0.00 0.00 2.52
3683 7983 7.094506 TGACGCTGATCTAGTACAAAAGTAAGA 60.095 37.037 0.00 0.00 0.00 2.10
3684 7984 7.027760 TGACGCTGATCTAGTACAAAAGTAAG 58.972 38.462 0.00 0.00 0.00 2.34
3685 7985 6.916440 TGACGCTGATCTAGTACAAAAGTAA 58.084 36.000 0.00 0.00 0.00 2.24
3686 7986 6.404403 CCTGACGCTGATCTAGTACAAAAGTA 60.404 42.308 0.00 0.00 0.00 2.24
3687 7987 5.386958 TGACGCTGATCTAGTACAAAAGT 57.613 39.130 0.00 0.00 0.00 2.66
3688 7988 4.800993 CCTGACGCTGATCTAGTACAAAAG 59.199 45.833 0.00 0.00 0.00 2.27
3689 7989 4.744570 CCTGACGCTGATCTAGTACAAAA 58.255 43.478 0.00 0.00 0.00 2.44
3690 7990 3.428999 GCCTGACGCTGATCTAGTACAAA 60.429 47.826 0.00 0.00 0.00 2.83
3691 7991 2.099263 GCCTGACGCTGATCTAGTACAA 59.901 50.000 0.00 0.00 0.00 2.41
3692 7992 1.676529 GCCTGACGCTGATCTAGTACA 59.323 52.381 0.00 0.00 0.00 2.90
3693 7993 1.676529 TGCCTGACGCTGATCTAGTAC 59.323 52.381 0.00 0.00 38.78 2.73
3694 7994 1.950216 CTGCCTGACGCTGATCTAGTA 59.050 52.381 0.00 0.00 38.65 1.82
3695 7995 0.743688 CTGCCTGACGCTGATCTAGT 59.256 55.000 0.00 0.00 38.65 2.57
3696 7996 0.031857 CCTGCCTGACGCTGATCTAG 59.968 60.000 0.00 0.00 38.65 2.43
3697 7997 0.395724 TCCTGCCTGACGCTGATCTA 60.396 55.000 0.00 0.00 38.65 1.98
3698 7998 1.683707 TCCTGCCTGACGCTGATCT 60.684 57.895 0.00 0.00 38.65 2.75
3699 7999 1.520342 GTCCTGCCTGACGCTGATC 60.520 63.158 0.00 0.00 38.65 2.92
3700 8000 2.581354 GTCCTGCCTGACGCTGAT 59.419 61.111 0.00 0.00 38.65 2.90
3701 8001 3.695606 GGTCCTGCCTGACGCTGA 61.696 66.667 0.00 0.00 38.65 4.26
3702 8002 3.320879 ATGGTCCTGCCTGACGCTG 62.321 63.158 0.00 0.00 38.78 5.18
3703 8003 3.005539 ATGGTCCTGCCTGACGCT 61.006 61.111 0.00 0.00 38.78 5.07
3704 8004 2.803155 TTCATGGTCCTGCCTGACGC 62.803 60.000 0.00 0.00 38.35 5.19
3705 8005 1.021390 GTTCATGGTCCTGCCTGACG 61.021 60.000 0.00 0.00 38.35 4.35
3706 8006 0.678048 GGTTCATGGTCCTGCCTGAC 60.678 60.000 0.00 0.00 38.35 3.51
3707 8007 1.133181 TGGTTCATGGTCCTGCCTGA 61.133 55.000 0.00 0.00 38.35 3.86
3708 8008 0.679002 CTGGTTCATGGTCCTGCCTG 60.679 60.000 0.00 0.00 38.35 4.85
3709 8009 1.136329 ACTGGTTCATGGTCCTGCCT 61.136 55.000 11.54 0.00 38.35 4.75
3710 8010 0.618458 TACTGGTTCATGGTCCTGCC 59.382 55.000 11.54 0.00 37.90 4.85
3711 8011 2.489938 TTACTGGTTCATGGTCCTGC 57.510 50.000 11.54 0.00 0.00 4.85
3712 8012 6.595682 AGATATTTACTGGTTCATGGTCCTG 58.404 40.000 0.00 2.88 0.00 3.86
3713 8013 6.831664 AGATATTTACTGGTTCATGGTCCT 57.168 37.500 0.00 0.00 0.00 3.85
3714 8014 7.556275 TGAAAGATATTTACTGGTTCATGGTCC 59.444 37.037 0.00 0.00 0.00 4.46
3715 8015 8.506168 TGAAAGATATTTACTGGTTCATGGTC 57.494 34.615 0.00 0.00 0.00 4.02
3716 8016 8.877864 TTGAAAGATATTTACTGGTTCATGGT 57.122 30.769 0.00 0.00 0.00 3.55
3717 8017 8.960591 ACTTGAAAGATATTTACTGGTTCATGG 58.039 33.333 0.00 0.00 0.00 3.66
3743 8043 8.922676 CGCTGATCTAGTACAAAAGTAAGAAAA 58.077 33.333 0.00 0.00 0.00 2.29
3787 8090 1.939980 AGAACTACTCCCACTCCCAC 58.060 55.000 0.00 0.00 0.00 4.61
3788 8091 2.715763 AAGAACTACTCCCACTCCCA 57.284 50.000 0.00 0.00 0.00 4.37
3789 8092 4.041815 AGAAAAAGAACTACTCCCACTCCC 59.958 45.833 0.00 0.00 0.00 4.30
3790 8093 4.998033 CAGAAAAAGAACTACTCCCACTCC 59.002 45.833 0.00 0.00 0.00 3.85
3791 8094 5.855045 TCAGAAAAAGAACTACTCCCACTC 58.145 41.667 0.00 0.00 0.00 3.51
3792 8095 5.602978 TCTCAGAAAAAGAACTACTCCCACT 59.397 40.000 0.00 0.00 0.00 4.00
3917 8220 2.269940 ACTGTAGTGGCCTGGAGATTT 58.730 47.619 3.32 0.00 0.00 2.17
3939 8242 5.163854 CGATTGGGTTTGTCTTCATCAGTAC 60.164 44.000 0.00 0.00 0.00 2.73
4009 8316 0.179163 GCTTGTCGTAATTGGGCTGC 60.179 55.000 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.