Multiple sequence alignment - TraesCS3B01G085800

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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 TraesCS3B01G085800 chr3B 100.000 4134 0 0 1 4134 54329415 54325282 0.000000e+00 7635.0
1 TraesCS3B01G085800 chr3B 95.918 931 37 1 1 931 53972099 53971170 0.000000e+00 1507.0
2 TraesCS3B01G085800 chr3B 89.682 785 62 5 1035 1813 53964039 53963268 0.000000e+00 983.0
3 TraesCS3B01G085800 chr3B 87.517 745 70 9 1077 1818 54506024 54505300 0.000000e+00 839.0
4 TraesCS3B01G085800 chr3B 87.458 590 53 10 2029 2613 54504814 54504241 0.000000e+00 660.0
5 TraesCS3B01G085800 chr3B 84.630 514 44 17 2637 3140 54504270 54503782 2.890000e-131 479.0
6 TraesCS3B01G085800 chr3B 96.071 280 11 0 932 1211 53964184 53963905 1.350000e-124 457.0
7 TraesCS3B01G085800 chr3B 89.908 327 27 4 3491 3815 54503504 54503182 2.300000e-112 416.0
8 TraesCS3B01G085800 chr3B 95.367 259 9 1 3852 4107 53961356 53961098 3.850000e-110 409.0
9 TraesCS3B01G085800 chr3B 94.141 256 14 1 3852 4106 54503064 54502809 5.010000e-104 388.0
10 TraesCS3B01G085800 chr3B 81.106 434 46 16 2782 3209 53962589 53962186 8.630000e-82 315.0
11 TraesCS3B01G085800 chr3B 88.593 263 23 5 3577 3838 53961720 53961464 3.100000e-81 313.0
12 TraesCS3B01G085800 chr3B 84.817 191 23 6 1853 2038 54505052 54504863 1.960000e-43 187.0
13 TraesCS3B01G085800 chr3B 85.965 171 12 5 3241 3411 54503659 54503501 5.490000e-39 172.0
14 TraesCS3B01G085800 chr3B 97.872 94 1 1 3405 3497 777762474 777762567 1.190000e-35 161.0
15 TraesCS3B01G085800 chr3B 95.918 98 2 2 3406 3502 52905260 52905164 1.540000e-34 158.0
16 TraesCS3B01G085800 chr3B 89.831 118 9 3 3403 3519 44751049 44750934 9.260000e-32 148.0
17 TraesCS3B01G085800 chr3D 91.720 2198 123 20 1045 3220 31806980 31804820 0.000000e+00 2996.0
18 TraesCS3B01G085800 chr3D 87.201 711 50 27 2715 3405 31964286 31964975 0.000000e+00 771.0
19 TraesCS3B01G085800 chr3D 88.235 357 35 4 3491 3845 31804640 31804289 1.780000e-113 420.0
20 TraesCS3B01G085800 chr3D 80.524 611 64 32 703 1307 31962852 31963413 6.390000e-113 418.0
21 TraesCS3B01G085800 chr3D 94.510 255 14 0 3852 4106 31804185 31803931 1.080000e-105 394.0
22 TraesCS3B01G085800 chr3D 85.194 412 30 13 2029 2420 31963682 31964082 1.080000e-105 394.0
23 TraesCS3B01G085800 chr3D 94.118 255 15 0 3852 4106 31965201 31965455 5.010000e-104 388.0
24 TraesCS3B01G085800 chr3D 81.641 463 42 14 755 1211 31807281 31806856 1.100000e-90 344.0
25 TraesCS3B01G085800 chr3D 94.545 165 7 2 2464 2626 31964096 31964260 1.910000e-63 254.0
26 TraesCS3B01G085800 chr3D 87.442 215 26 1 1587 1801 31963410 31963623 3.190000e-61 246.0
27 TraesCS3B01G085800 chr3D 90.511 137 12 1 3491 3627 31848681 31848546 3.280000e-41 180.0
28 TraesCS3B01G085800 chr3D 100.000 39 0 0 1986 2024 31963619 31963657 5.730000e-09 73.1
29 TraesCS3B01G085800 chr2A 82.286 1400 122 55 713 2038 528103961 528105308 0.000000e+00 1096.0
30 TraesCS3B01G085800 chr2A 91.453 585 43 5 2026 2604 528105354 528105937 0.000000e+00 797.0
31 TraesCS3B01G085800 chr2A 89.655 348 30 4 3492 3838 528106631 528106973 4.910000e-119 438.0
32 TraesCS3B01G085800 chr2A 96.471 255 9 0 3852 4106 528107081 528107335 4.940000e-114 422.0
33 TraesCS3B01G085800 chr2A 82.579 442 50 16 2965 3405 528106212 528106627 8.450000e-97 364.0
34 TraesCS3B01G085800 chr2A 89.744 78 5 1 2676 2753 528105943 528106017 3.400000e-16 97.1
35 TraesCS3B01G085800 chr2B 85.895 475 38 18 2768 3231 227310766 227311222 2.890000e-131 479.0
36 TraesCS3B01G085800 chr2B 82.697 393 49 16 2236 2621 227310295 227310675 8.570000e-87 331.0
37 TraesCS3B01G085800 chr4A 80.921 456 44 19 762 1211 515589547 515589129 1.850000e-83 320.0
38 TraesCS3B01G085800 chr4A 100.000 90 0 0 3408 3497 603462434 603462345 2.560000e-37 167.0
39 TraesCS3B01G085800 chr4A 98.913 92 0 1 3404 3494 603501363 603501454 3.310000e-36 163.0
40 TraesCS3B01G085800 chrUn 98.913 92 0 1 3405 3495 27476045 27475954 3.310000e-36 163.0
41 TraesCS3B01G085800 chr7A 96.875 96 2 1 3405 3499 579199550 579199455 4.280000e-35 159.0
42 TraesCS3B01G085800 chr1B 97.849 93 0 2 3402 3494 402103312 402103402 4.280000e-35 159.0
43 TraesCS3B01G085800 chr1B 92.523 107 6 2 3404 3509 400719129 400719234 7.160000e-33 152.0
44 TraesCS3B01G085800 chr6A 83.784 111 18 0 3712 3822 50118372 50118262 5.650000e-19 106.0


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 TraesCS3B01G085800 chr3B 54325282 54329415 4133 True 7635.000000 7635 100.000000 1 4134 1 chr3B.!!$R4 4133
1 TraesCS3B01G085800 chr3B 53971170 53972099 929 True 1507.000000 1507 95.918000 1 931 1 chr3B.!!$R3 930
2 TraesCS3B01G085800 chr3B 53961098 53964184 3086 True 495.400000 983 90.163800 932 4107 5 chr3B.!!$R5 3175
3 TraesCS3B01G085800 chr3B 54502809 54506024 3215 True 448.714286 839 87.776571 1077 4106 7 chr3B.!!$R6 3029
4 TraesCS3B01G085800 chr3D 31803931 31807281 3350 True 1038.500000 2996 89.026500 755 4106 4 chr3D.!!$R2 3351
5 TraesCS3B01G085800 chr3D 31962852 31965455 2603 False 363.442857 771 89.860571 703 4106 7 chr3D.!!$F1 3403
6 TraesCS3B01G085800 chr2A 528103961 528107335 3374 False 535.683333 1096 88.698000 713 4106 6 chr2A.!!$F1 3393
7 TraesCS3B01G085800 chr2B 227310295 227311222 927 False 405.000000 479 84.296000 2236 3231 2 chr2B.!!$F1 995

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
115 116 0.244450 ACATGGTTCGCAAGCAATGG 59.756 50.0 0.00 2.32 42.83 3.16 F
140 141 0.534203 TCTTGAACCAGGCAACGACC 60.534 55.0 0.00 0.00 46.39 4.79 F
326 327 0.539051 AGAAGGGAGGCAATGAGACG 59.461 55.0 0.00 0.00 0.00 4.18 F
1865 2196 0.613292 TCAGAGGAGTGAGGCCTGAC 60.613 60.0 15.42 15.42 35.44 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1958 0.179108 AGGCTTCGCATCCGTTACTC 60.179 55.0 0.00 0.0 35.54 2.59 R
1889 2220 1.231221 AAATTTGACACGCGGCTGTA 58.769 45.0 12.47 0.0 0.00 2.74 R
2261 2749 2.380064 ATGGTGTTTTTGCTCCCAGA 57.620 45.0 0.00 0.0 0.00 3.86 R
3862 4767 0.037447 GAGCTTCTCCCCTGCTTGTT 59.963 55.0 0.00 0.0 37.16 2.83 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
26 27 3.120792 CCAGACGATAATGGTAACCACG 58.879 50.000 0.00 0.00 35.80 4.94
78 79 1.623557 CCCTCTCATCCTCCCTCAACA 60.624 57.143 0.00 0.00 0.00 3.33
96 97 1.102154 CAGTTTGACCAAGCCACACA 58.898 50.000 0.00 0.00 0.00 3.72
107 108 2.551006 GCCACACACATGGTTCGCA 61.551 57.895 0.00 0.00 42.28 5.10
115 116 0.244450 ACATGGTTCGCAAGCAATGG 59.756 50.000 0.00 2.32 42.83 3.16
135 136 1.165907 CGCACTCTTGAACCAGGCAA 61.166 55.000 0.00 0.00 0.00 4.52
140 141 0.534203 TCTTGAACCAGGCAACGACC 60.534 55.000 0.00 0.00 46.39 4.79
157 158 2.105128 CCGCGAGTGATGGAGACC 59.895 66.667 8.23 0.00 0.00 3.85
182 183 4.875713 GATCGGTGCCGGCCCAAT 62.876 66.667 26.77 15.82 40.25 3.16
199 200 1.678627 CAATCGTCGACCATCCTCTCT 59.321 52.381 10.58 0.00 0.00 3.10
303 304 0.905357 AGACAGATGGGGGTTTCTCG 59.095 55.000 0.00 0.00 0.00 4.04
305 306 0.613777 ACAGATGGGGGTTTCTCGAC 59.386 55.000 0.00 0.00 0.00 4.20
309 310 0.613853 ATGGGGGTTTCTCGACGAGA 60.614 55.000 23.27 23.27 36.86 4.04
320 321 0.970937 TCGACGAGAAGGGAGGCAAT 60.971 55.000 0.00 0.00 0.00 3.56
326 327 0.539051 AGAAGGGAGGCAATGAGACG 59.461 55.000 0.00 0.00 0.00 4.18
436 437 4.873129 CCCACGACGGCGATCCTG 62.873 72.222 22.49 4.34 41.64 3.86
458 459 0.751643 GTGTGGTGCCAAACTGGAGT 60.752 55.000 4.34 0.00 40.96 3.85
473 474 1.216678 TGGAGTGTGGGTTGTTTCCAT 59.783 47.619 0.00 0.00 36.58 3.41
480 481 5.423931 AGTGTGGGTTGTTTCCATAAAAAGT 59.576 36.000 0.00 0.00 36.58 2.66
487 488 5.068215 TGTTTCCATAAAAAGTGAGGGGA 57.932 39.130 0.00 0.00 0.00 4.81
488 489 5.076873 TGTTTCCATAAAAAGTGAGGGGAG 58.923 41.667 0.00 0.00 0.00 4.30
489 490 4.316025 TTCCATAAAAAGTGAGGGGAGG 57.684 45.455 0.00 0.00 0.00 4.30
533 534 2.579201 CACCGGGGTGCTCTACTG 59.421 66.667 6.32 0.00 39.39 2.74
539 540 1.668101 GGGGTGCTCTACTGTCGAGG 61.668 65.000 10.83 0.00 0.00 4.63
574 575 7.647907 GGTACCATAGAATGTTACGTATTGG 57.352 40.000 7.15 0.00 29.87 3.16
637 638 2.038820 ACCAAATCATTGTGGGCCAAAG 59.961 45.455 8.40 0.00 39.39 2.77
753 754 3.717707 TCGAGCATAATTTCTTCCGGAG 58.282 45.455 3.34 0.00 0.00 4.63
815 816 8.800370 TTTAACATGAAGATGGTGTGCTAATA 57.200 30.769 0.00 0.00 33.39 0.98
1167 1214 4.320456 CACCACCACCTCGCTGCT 62.320 66.667 0.00 0.00 0.00 4.24
1298 1402 4.090588 GGATGACGCCACGGGGAA 62.091 66.667 8.67 0.00 35.59 3.97
1462 1566 3.113386 CTCATCGACGAGCTCGCCA 62.113 63.158 34.83 19.47 42.62 5.69
1481 1585 4.379813 CGCCAGTAATAATCCATGGATTGC 60.380 45.833 39.01 30.86 43.75 3.56
1484 1588 6.243900 CCAGTAATAATCCATGGATTGCTCT 58.756 40.000 39.01 28.49 43.75 4.09
1503 1607 4.118410 CTCTTGCTGTGAGCTCGATAATT 58.882 43.478 9.64 0.00 42.97 1.40
1547 1653 7.392494 TGTTAATTGTTGTGTTGTTACCTGA 57.608 32.000 0.00 0.00 0.00 3.86
1636 1742 2.008329 CAGAGGCTCATTGCTGAACTC 58.992 52.381 18.26 0.00 42.39 3.01
1674 1780 1.066908 GCTCGAGTGGAAGATGGAGAG 59.933 57.143 15.13 0.00 0.00 3.20
1706 1812 1.127343 GCAGGAGCTGGAGAAGGTAT 58.873 55.000 0.00 0.00 36.52 2.73
1746 1856 3.376546 CCTGAACTCTAAAATGCTGGCTC 59.623 47.826 0.00 0.00 0.00 4.70
1747 1857 3.002791 TGAACTCTAAAATGCTGGCTCG 58.997 45.455 0.00 0.00 0.00 5.03
1793 1903 7.801716 TTACACAGCTCTACAATGTCTTTTT 57.198 32.000 0.00 0.00 0.00 1.94
1827 1958 4.393062 CACCAGCATCAGTACCTAACAAAG 59.607 45.833 0.00 0.00 0.00 2.77
1831 1962 6.351033 CCAGCATCAGTACCTAACAAAGAGTA 60.351 42.308 0.00 0.00 0.00 2.59
1865 2196 0.613292 TCAGAGGAGTGAGGCCTGAC 60.613 60.000 15.42 15.42 35.44 3.51
1876 2207 1.000938 GAGGCCTGACTTGCAAGTTTG 60.001 52.381 31.58 24.56 39.88 2.93
1889 2220 6.657117 ACTTGCAAGTTTGTACCCAAAATTTT 59.343 30.769 26.36 0.00 44.00 1.82
1895 2226 6.285224 AGTTTGTACCCAAAATTTTACAGCC 58.715 36.000 2.44 0.03 41.99 4.85
1915 2246 2.722116 CCGCGTGTCAAATTTTGTTACC 59.278 45.455 4.92 4.08 0.00 2.85
1949 2280 8.441608 GCATCAACATCATATATGTCAAGAGAC 58.558 37.037 12.42 0.00 45.19 3.36
2127 2613 1.494721 TCAAGTCTGGCTGAAAAGGGT 59.505 47.619 0.00 0.00 0.00 4.34
2239 2727 9.255304 GTTATCAAAATGAAGCTTACAACCAAA 57.745 29.630 0.00 0.00 0.00 3.28
2261 2749 6.573664 AAACAACACAGTGTACATATGCAT 57.426 33.333 6.63 3.79 0.00 3.96
2460 2953 1.134946 CCGGCTGGGCTTGAAATAAAG 59.865 52.381 2.57 0.00 0.00 1.85
2960 3559 9.515020 ACATAGTCTTGTGTTGTTTTATTGTTG 57.485 29.630 0.00 0.00 0.00 3.33
3008 3629 0.252421 ACATGGCAGGTGGAGAGAGA 60.252 55.000 3.00 0.00 0.00 3.10
3103 3725 9.651718 CTCTGTAACATGTTTACTTTCAGTTTC 57.348 33.333 17.78 0.00 0.00 2.78
3111 3733 6.411376 TGTTTACTTTCAGTTTCCAGAGTGA 58.589 36.000 0.00 0.00 0.00 3.41
3210 3832 0.944386 GATGGTAATGCCGAATGCGT 59.056 50.000 0.00 0.00 45.60 5.24
3267 3939 4.010349 GAGTACTTGCCCTGCTTTACAAT 58.990 43.478 0.00 0.00 0.00 2.71
3283 3955 7.448777 TGCTTTACAATCCAAAACATGTAGGTA 59.551 33.333 0.00 0.00 30.64 3.08
3301 3973 7.737869 TGTAGGTAGGAGTTAAAACAATGTGA 58.262 34.615 0.00 0.00 0.00 3.58
3415 4087 3.664240 CCCCCAAAACAGTACTCCC 57.336 57.895 0.00 0.00 0.00 4.30
3416 4088 1.073098 CCCCCAAAACAGTACTCCCT 58.927 55.000 0.00 0.00 0.00 4.20
3417 4089 1.004394 CCCCCAAAACAGTACTCCCTC 59.996 57.143 0.00 0.00 0.00 4.30
3418 4090 1.004394 CCCCAAAACAGTACTCCCTCC 59.996 57.143 0.00 0.00 0.00 4.30
3419 4091 1.338769 CCCAAAACAGTACTCCCTCCG 60.339 57.143 0.00 0.00 0.00 4.63
3420 4092 1.346722 CCAAAACAGTACTCCCTCCGT 59.653 52.381 0.00 0.00 0.00 4.69
3421 4093 2.564062 CCAAAACAGTACTCCCTCCGTA 59.436 50.000 0.00 0.00 0.00 4.02
3422 4094 3.007182 CCAAAACAGTACTCCCTCCGTAA 59.993 47.826 0.00 0.00 0.00 3.18
3423 4095 4.503643 CCAAAACAGTACTCCCTCCGTAAA 60.504 45.833 0.00 0.00 0.00 2.01
3424 4096 3.949842 AACAGTACTCCCTCCGTAAAC 57.050 47.619 0.00 0.00 0.00 2.01
3425 4097 3.166560 ACAGTACTCCCTCCGTAAACT 57.833 47.619 0.00 0.00 0.00 2.66
3426 4098 4.307032 ACAGTACTCCCTCCGTAAACTA 57.693 45.455 0.00 0.00 0.00 2.24
3427 4099 4.666512 ACAGTACTCCCTCCGTAAACTAA 58.333 43.478 0.00 0.00 0.00 2.24
3428 4100 5.267587 ACAGTACTCCCTCCGTAAACTAAT 58.732 41.667 0.00 0.00 0.00 1.73
3429 4101 6.426587 ACAGTACTCCCTCCGTAAACTAATA 58.573 40.000 0.00 0.00 0.00 0.98
3430 4102 7.065504 ACAGTACTCCCTCCGTAAACTAATAT 58.934 38.462 0.00 0.00 0.00 1.28
3431 4103 8.220559 ACAGTACTCCCTCCGTAAACTAATATA 58.779 37.037 0.00 0.00 0.00 0.86
3432 4104 9.071276 CAGTACTCCCTCCGTAAACTAATATAA 57.929 37.037 0.00 0.00 0.00 0.98
3433 4105 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
3434 4106 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
3435 4107 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
3436 4108 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
3437 4109 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
3438 4110 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
3439 4111 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
3440 4112 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
3441 4113 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
3442 4114 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
3443 4115 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
3457 4129 9.570488 AAGAGCGTTTAGAATACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
3458 4130 8.954350 AGAGCGTTTAGAATACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
3459 4131 9.733219 GAGCGTTTAGAATACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
3460 4132 9.733219 AGCGTTTAGAATACTAAAGTAGTGATC 57.267 33.333 0.00 0.00 45.42 2.92
3461 4133 9.733219 GCGTTTAGAATACTAAAGTAGTGATCT 57.267 33.333 0.00 4.67 45.42 2.75
3502 4181 7.190501 AGTTTACAGAGGGAGTATTAGGAAGT 58.809 38.462 0.00 0.00 0.00 3.01
3544 4224 8.777865 TTCAGTGGAAACTCTAGACAAATATG 57.222 34.615 0.00 0.00 31.78 1.78
3550 4230 4.965200 ACTCTAGACAAATATGGGCTCC 57.035 45.455 0.00 0.00 0.00 4.70
3613 4418 0.535102 CTCCACCGCAATATGACCCC 60.535 60.000 0.00 0.00 0.00 4.95
3627 4432 1.271163 TGACCCCGTTCATGTCCTTTC 60.271 52.381 0.00 0.00 0.00 2.62
3649 4455 1.276622 TGGTCTTAGCAGAACTCCCC 58.723 55.000 0.00 0.00 37.67 4.81
3650 4456 1.203313 TGGTCTTAGCAGAACTCCCCT 60.203 52.381 0.00 0.00 37.67 4.79
3651 4457 2.043939 TGGTCTTAGCAGAACTCCCCTA 59.956 50.000 0.00 0.00 37.67 3.53
3652 4458 2.696187 GGTCTTAGCAGAACTCCCCTAG 59.304 54.545 0.00 0.00 33.35 3.02
3723 4529 0.536006 AAGAGTGCAAGGTGGCTGAC 60.536 55.000 0.00 0.00 34.04 3.51
3780 4586 8.499967 GTTTCTTCTTCTCTTTGATAGGACAAC 58.500 37.037 0.00 0.00 0.00 3.32
3781 4587 7.546250 TCTTCTTCTCTTTGATAGGACAACT 57.454 36.000 0.00 0.00 0.00 3.16
3801 4607 4.633175 ACTGATAAGCTCATCTGCATCAG 58.367 43.478 3.73 12.27 43.70 2.90
3845 4653 4.383173 CAGCTGACCATGCTATTCATACA 58.617 43.478 8.42 0.00 38.92 2.29
3846 4654 4.818005 CAGCTGACCATGCTATTCATACAA 59.182 41.667 8.42 0.00 38.92 2.41
3847 4655 5.297527 CAGCTGACCATGCTATTCATACAAA 59.702 40.000 8.42 0.00 38.92 2.83
3848 4656 5.887598 AGCTGACCATGCTATTCATACAAAA 59.112 36.000 0.00 0.00 39.21 2.44
3849 4657 6.548622 AGCTGACCATGCTATTCATACAAAAT 59.451 34.615 0.00 0.00 39.21 1.82
3850 4658 7.720957 AGCTGACCATGCTATTCATACAAAATA 59.279 33.333 0.00 0.00 39.21 1.40
3989 4894 4.397417 CCATTGCTAGACCTCTTCAAAAGG 59.603 45.833 0.00 0.00 39.96 3.11
4113 5022 6.410942 CTCATTGGGAGGAGTTTTCTTTTT 57.589 37.500 0.00 0.00 40.13 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 1.102978 GTGTGTGGCTTGGTCAAACT 58.897 50.000 0.00 0.00 0.00 2.66
96 97 0.244450 CCATTGCTTGCGAACCATGT 59.756 50.000 0.00 0.00 0.00 3.21
107 108 0.890542 TCAAGAGTGCGCCATTGCTT 60.891 50.000 4.18 0.00 35.36 3.91
115 116 2.970974 GCCTGGTTCAAGAGTGCGC 61.971 63.158 0.00 0.00 0.00 6.09
135 136 4.129737 CCATCACTCGCGGGTCGT 62.130 66.667 9.74 0.00 39.67 4.34
140 141 1.949847 AAGGTCTCCATCACTCGCGG 61.950 60.000 6.13 0.00 0.00 6.46
157 158 1.811266 CGGCACCGATCCACTCAAG 60.811 63.158 2.01 0.00 42.83 3.02
182 183 0.252197 TGAGAGAGGATGGTCGACGA 59.748 55.000 9.92 5.99 0.00 4.20
199 200 3.489229 CGATAGCGAAGACCAATGAGTGA 60.489 47.826 0.00 0.00 40.82 3.41
303 304 0.537188 TCATTGCCTCCCTTCTCGTC 59.463 55.000 0.00 0.00 0.00 4.20
305 306 0.826715 TCTCATTGCCTCCCTTCTCG 59.173 55.000 0.00 0.00 0.00 4.04
309 310 0.909610 TCCGTCTCATTGCCTCCCTT 60.910 55.000 0.00 0.00 0.00 3.95
320 321 0.919710 TCCCATCTCTCTCCGTCTCA 59.080 55.000 0.00 0.00 0.00 3.27
326 327 1.063266 ACTCCACTCCCATCTCTCTCC 60.063 57.143 0.00 0.00 0.00 3.71
408 409 3.948719 TCGTGGGCCCACTTGTCC 61.949 66.667 43.90 23.62 44.16 4.02
436 437 1.355210 CAGTTTGGCACCACACGTC 59.645 57.895 0.49 0.00 32.45 4.34
473 474 3.497942 GCAGAACCTCCCCTCACTTTTTA 60.498 47.826 0.00 0.00 0.00 1.52
480 481 0.850100 TTTTGCAGAACCTCCCCTCA 59.150 50.000 0.00 0.00 0.00 3.86
520 521 1.668101 CCTCGACAGTAGAGCACCCC 61.668 65.000 5.17 0.00 34.56 4.95
533 534 2.421399 CCCTTACGGTCCCCTCGAC 61.421 68.421 0.00 0.00 41.15 4.20
539 540 1.966354 CTATGGTACCCTTACGGTCCC 59.034 57.143 10.07 0.00 43.58 4.46
573 574 9.383462 CACTACGATATGATCTTTATATACGCC 57.617 37.037 0.00 0.00 0.00 5.68
574 575 9.932699 ACACTACGATATGATCTTTATATACGC 57.067 33.333 0.00 0.00 0.00 4.42
606 607 5.280945 CACAATGATTTGGTTCGACAACTT 58.719 37.500 0.00 0.00 37.15 2.66
637 638 3.882888 TCACATGTTTGGTCCTTCAAGTC 59.117 43.478 0.00 0.00 0.00 3.01
669 670 1.383523 CTTCCAAGGCCTCGAATTCC 58.616 55.000 5.23 0.00 0.00 3.01
671 672 0.329596 AGCTTCCAAGGCCTCGAATT 59.670 50.000 5.23 0.00 0.00 2.17
753 754 7.873739 AAGCTATTTTAATCACTGTTGTTGC 57.126 32.000 0.00 0.00 0.00 4.17
792 793 8.800370 TTTATTAGCACACCATCTTCATGTTA 57.200 30.769 0.00 0.00 0.00 2.41
1252 1356 0.184692 TGCATGAAGTGGTGGTGGAA 59.815 50.000 0.00 0.00 0.00 3.53
1339 1443 4.139420 CGCGTCGTACTCGTCGGT 62.139 66.667 0.00 0.00 45.21 4.69
1462 1566 6.208204 GCAAGAGCAATCCATGGATTATTACT 59.792 38.462 34.23 27.27 42.30 2.24
1481 1585 2.859526 TATCGAGCTCACAGCAAGAG 57.140 50.000 15.40 0.00 45.56 2.85
1484 1588 5.693555 CAGATAATTATCGAGCTCACAGCAA 59.306 40.000 15.40 0.16 39.63 3.91
1547 1653 5.182950 CGTCAGATATGATCCTTAGCTCTGT 59.817 44.000 0.00 0.00 32.49 3.41
1595 1701 0.325671 TTCTGCTCCTCCGGATCCTT 60.326 55.000 3.57 0.00 0.00 3.36
1626 1732 1.954146 GTGGCGTCGAGTTCAGCAA 60.954 57.895 0.00 0.00 0.00 3.91
1627 1733 2.355837 GTGGCGTCGAGTTCAGCA 60.356 61.111 0.00 0.00 0.00 4.41
1636 1742 2.426183 CTCTTTCGTCGTGGCGTCG 61.426 63.158 2.23 2.23 39.38 5.12
1747 1857 3.911661 AAAGTTCAGCACTCTTCATGC 57.088 42.857 0.00 0.00 43.74 4.06
1793 1903 6.892658 ACTGATGCTGGTGTTAATTTGTAA 57.107 33.333 0.00 0.00 0.00 2.41
1802 1912 3.326588 TGTTAGGTACTGATGCTGGTGTT 59.673 43.478 0.00 0.00 41.52 3.32
1827 1958 0.179108 AGGCTTCGCATCCGTTACTC 60.179 55.000 0.00 0.00 35.54 2.59
1831 1962 1.448540 CTGAGGCTTCGCATCCGTT 60.449 57.895 0.00 0.00 38.67 4.44
1851 2182 1.376553 GCAAGTCAGGCCTCACTCC 60.377 63.158 10.81 0.00 0.00 3.85
1865 2196 6.676237 AAATTTTGGGTACAAACTTGCAAG 57.324 33.333 24.84 24.84 45.64 4.01
1876 2207 3.247442 GCGGCTGTAAAATTTTGGGTAC 58.753 45.455 13.76 4.29 0.00 3.34
1889 2220 1.231221 AAATTTGACACGCGGCTGTA 58.769 45.000 12.47 0.00 0.00 2.74
1895 2226 2.399102 CGGTAACAAAATTTGACACGCG 59.601 45.455 13.19 3.53 0.00 6.01
1915 2246 5.919272 ATATGATGTTGATGCTCACTTCG 57.081 39.130 0.00 0.00 0.00 3.79
1943 2274 4.454678 TGCTTCATTTCAGTGTGTCTCTT 58.545 39.130 0.00 0.00 0.00 2.85
1949 2280 3.713858 TGGTTGCTTCATTTCAGTGTG 57.286 42.857 0.00 0.00 0.00 3.82
1950 2281 4.081752 TGTTTGGTTGCTTCATTTCAGTGT 60.082 37.500 0.00 0.00 0.00 3.55
1951 2282 4.268405 GTGTTTGGTTGCTTCATTTCAGTG 59.732 41.667 0.00 0.00 0.00 3.66
2127 2613 8.778358 GGGTAATTTGTAAAAATGCATTTCACA 58.222 29.630 24.28 24.55 0.00 3.58
2239 2727 5.939883 AGATGCATATGTACACTGTGTTGTT 59.060 36.000 19.73 6.59 0.00 2.83
2261 2749 2.380064 ATGGTGTTTTTGCTCCCAGA 57.620 45.000 0.00 0.00 0.00 3.86
2355 2844 5.534407 TCTGCAAAACGACACTATGAAGTA 58.466 37.500 0.00 0.00 33.48 2.24
2705 3203 7.531857 TTCAGGCAGTGGACAATTAATAAAA 57.468 32.000 0.00 0.00 0.00 1.52
2822 3380 9.804758 AGTATCACTGTACATCTAGCTAAAAAC 57.195 33.333 0.00 0.00 0.00 2.43
2960 3559 0.690762 TGACCTCCAAAGCACCCTAC 59.309 55.000 0.00 0.00 0.00 3.18
3103 3725 5.005740 TGAGGTGAAAATTCATCACTCTGG 58.994 41.667 18.45 0.00 45.13 3.86
3111 3733 8.571336 CACTCTAAAGTTGAGGTGAAAATTCAT 58.429 33.333 0.00 0.00 36.03 2.57
3180 3802 4.876107 CGGCATTACCATCTGTAACTTCTT 59.124 41.667 0.00 0.00 42.06 2.52
3181 3803 4.161565 TCGGCATTACCATCTGTAACTTCT 59.838 41.667 0.00 0.00 42.06 2.85
3221 3844 8.286191 TCTCTGAGCATATGATATACATTCGT 57.714 34.615 6.97 0.00 40.07 3.85
3231 3854 5.279406 GGCAAGTACTCTCTGAGCATATGAT 60.279 44.000 6.97 0.00 32.04 2.45
3233 3856 4.305769 GGCAAGTACTCTCTGAGCATATG 58.694 47.826 0.00 0.00 32.04 1.78
3235 3858 2.695666 GGGCAAGTACTCTCTGAGCATA 59.304 50.000 0.00 0.00 32.04 3.14
3236 3859 1.484240 GGGCAAGTACTCTCTGAGCAT 59.516 52.381 0.00 0.00 32.04 3.79
3237 3860 0.898320 GGGCAAGTACTCTCTGAGCA 59.102 55.000 0.00 0.00 32.04 4.26
3238 3861 1.134848 CAGGGCAAGTACTCTCTGAGC 60.135 57.143 5.68 0.00 32.04 4.26
3267 3939 5.836024 AACTCCTACCTACATGTTTTGGA 57.164 39.130 2.30 4.38 0.00 3.53
3283 3955 8.912988 TCTGAATTTCACATTGTTTTAACTCCT 58.087 29.630 0.00 0.00 0.00 3.69
3401 4073 2.833631 ACGGAGGGAGTACTGTTTTG 57.166 50.000 0.00 0.00 0.00 2.44
3405 4077 3.166560 AGTTTACGGAGGGAGTACTGT 57.833 47.619 0.00 0.00 0.00 3.55
3406 4078 5.848833 ATTAGTTTACGGAGGGAGTACTG 57.151 43.478 0.00 0.00 0.00 2.74
3407 4079 9.294614 CTTATATTAGTTTACGGAGGGAGTACT 57.705 37.037 0.00 0.00 0.00 2.73
3408 4080 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
3409 4081 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
3410 4082 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
3411 4083 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
3412 4084 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
3413 4085 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
3414 4086 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
3415 4087 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
3416 4088 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
3417 4089 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
3431 4103 9.570488 CACTACTTTAGTATTCTAAACGCTCTT 57.430 33.333 0.76 0.00 40.05 2.85
3432 4104 8.954350 TCACTACTTTAGTATTCTAAACGCTCT 58.046 33.333 0.76 0.00 40.05 4.09
3433 4105 9.733219 ATCACTACTTTAGTATTCTAAACGCTC 57.267 33.333 0.76 0.00 40.05 5.03
3434 4106 9.733219 GATCACTACTTTAGTATTCTAAACGCT 57.267 33.333 0.76 0.00 40.05 5.07
3435 4107 9.733219 AGATCACTACTTTAGTATTCTAAACGC 57.267 33.333 0.76 0.00 40.05 4.84
3464 4136 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
3465 4137 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
3466 4138 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
3474 4146 9.725206 TTCCTAATACTCCCTCTGTAAACTAAT 57.275 33.333 0.00 0.00 0.00 1.73
3475 4147 9.198475 CTTCCTAATACTCCCTCTGTAAACTAA 57.802 37.037 0.00 0.00 0.00 2.24
3476 4148 8.342270 ACTTCCTAATACTCCCTCTGTAAACTA 58.658 37.037 0.00 0.00 0.00 2.24
3477 4149 7.124448 CACTTCCTAATACTCCCTCTGTAAACT 59.876 40.741 0.00 0.00 0.00 2.66
3478 4150 7.093421 ACACTTCCTAATACTCCCTCTGTAAAC 60.093 40.741 0.00 0.00 0.00 2.01
3479 4151 6.958192 ACACTTCCTAATACTCCCTCTGTAAA 59.042 38.462 0.00 0.00 0.00 2.01
3480 4152 6.500336 ACACTTCCTAATACTCCCTCTGTAA 58.500 40.000 0.00 0.00 0.00 2.41
3481 4153 6.088541 ACACTTCCTAATACTCCCTCTGTA 57.911 41.667 0.00 0.00 0.00 2.74
3482 4154 4.949121 ACACTTCCTAATACTCCCTCTGT 58.051 43.478 0.00 0.00 0.00 3.41
3483 4155 4.956700 TGACACTTCCTAATACTCCCTCTG 59.043 45.833 0.00 0.00 0.00 3.35
3484 4156 5.205056 CTGACACTTCCTAATACTCCCTCT 58.795 45.833 0.00 0.00 0.00 3.69
3485 4157 4.202172 GCTGACACTTCCTAATACTCCCTC 60.202 50.000 0.00 0.00 0.00 4.30
3486 4158 3.707102 GCTGACACTTCCTAATACTCCCT 59.293 47.826 0.00 0.00 0.00 4.20
3487 4159 3.707102 AGCTGACACTTCCTAATACTCCC 59.293 47.826 0.00 0.00 0.00 4.30
3488 4160 5.346181 AAGCTGACACTTCCTAATACTCC 57.654 43.478 0.00 0.00 0.00 3.85
3489 4161 7.703197 GTCTTAAGCTGACACTTCCTAATACTC 59.297 40.741 0.00 0.00 34.80 2.59
3502 4181 4.686091 CACTGAAATCGTCTTAAGCTGACA 59.314 41.667 0.00 0.00 34.37 3.58
3565 4245 7.836842 TCAGTCTGTTAGTTATGAATGTAGCA 58.163 34.615 0.00 0.00 0.00 3.49
3613 4418 4.759782 AGACCATAGAAAGGACATGAACG 58.240 43.478 0.00 0.00 0.00 3.95
3627 4432 3.070302 GGGGAGTTCTGCTAAGACCATAG 59.930 52.174 0.00 0.00 29.98 2.23
3649 4455 3.738281 GCACCCTGTGTATGTGTAGCTAG 60.738 52.174 0.00 0.00 35.75 3.42
3650 4456 2.167693 GCACCCTGTGTATGTGTAGCTA 59.832 50.000 0.00 0.00 35.75 3.32
3651 4457 1.066143 GCACCCTGTGTATGTGTAGCT 60.066 52.381 0.00 0.00 35.75 3.32
3652 4458 1.066143 AGCACCCTGTGTATGTGTAGC 60.066 52.381 0.00 0.00 35.75 3.58
3732 4538 3.056678 CCTTGTGGTTTTCATGCAGCATA 60.057 43.478 7.82 0.00 0.00 3.14
3780 4586 4.884247 TCTGATGCAGATGAGCTTATCAG 58.116 43.478 19.58 13.14 42.53 2.90
3781 4587 4.950205 TCTGATGCAGATGAGCTTATCA 57.050 40.909 19.58 1.24 43.70 2.15
3801 4607 5.061853 TGCTTGATGGAGCTGATAAGAATC 58.938 41.667 0.00 0.00 43.11 2.52
3845 4653 7.439056 CCTGCTTGTTGTTTCATGTTCTATTTT 59.561 33.333 0.00 0.00 0.00 1.82
3846 4654 6.925165 CCTGCTTGTTGTTTCATGTTCTATTT 59.075 34.615 0.00 0.00 0.00 1.40
3847 4655 6.449698 CCTGCTTGTTGTTTCATGTTCTATT 58.550 36.000 0.00 0.00 0.00 1.73
3848 4656 5.047802 CCCTGCTTGTTGTTTCATGTTCTAT 60.048 40.000 0.00 0.00 0.00 1.98
3849 4657 4.278170 CCCTGCTTGTTGTTTCATGTTCTA 59.722 41.667 0.00 0.00 0.00 2.10
3850 4658 3.068590 CCCTGCTTGTTGTTTCATGTTCT 59.931 43.478 0.00 0.00 0.00 3.01
3862 4767 0.037447 GAGCTTCTCCCCTGCTTGTT 59.963 55.000 0.00 0.00 37.16 2.83
3989 4894 4.704833 TCGCTGTTGGCCTGCTCC 62.705 66.667 3.32 0.00 37.74 4.70
4005 4910 2.200899 GCGATTCTCTTGGAGCTCTTC 58.799 52.381 14.64 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.