Multiple sequence alignment - TraesCS4B01G086300

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 TraesCS4B01G086300 chr4B 100.000 2356 0 0 2049 4404 86141022 86138667 0.000000e+00 4351.0
1 TraesCS4B01G086300 chr4B 100.000 1823 0 0 1 1823 86143070 86141248 0.000000e+00 3367.0
2 TraesCS4B01G086300 chr4B 100.000 46 0 0 838 883 103805713 103805668 7.850000e-13 86.1
3 TraesCS4B01G086300 chr4B 100.000 46 0 0 838 883 447451797 447451752 7.850000e-13 86.1
4 TraesCS4B01G086300 chr4A 93.033 1823 90 17 5 1823 539126464 539128253 0.000000e+00 2628.0
5 TraesCS4B01G086300 chr4A 93.309 1674 69 25 2054 3709 539128322 539129970 0.000000e+00 2431.0
6 TraesCS4B01G086300 chr4A 90.233 215 20 1 3865 4079 539132030 539132243 3.350000e-71 279.0
7 TraesCS4B01G086300 chr4A 91.200 125 6 3 4281 4404 539132420 539132540 9.800000e-37 165.0
8 TraesCS4B01G086300 chr4A 86.842 114 15 0 3844 3957 235649660 235649547 1.290000e-25 128.0
9 TraesCS4B01G086300 chr4A 100.000 33 0 0 3543 3575 539129859 539129891 1.320000e-05 62.1
10 TraesCS4B01G086300 chr4D 93.416 1777 58 18 2050 3803 57836774 57838514 0.000000e+00 2579.0
11 TraesCS4B01G086300 chr4D 95.965 917 33 1 883 1799 57835675 57836587 0.000000e+00 1485.0
12 TraesCS4B01G086300 chr4D 92.826 683 28 5 2 668 57834120 57834797 0.000000e+00 970.0
13 TraesCS4B01G086300 chr4D 90.608 181 16 1 3806 3985 57838705 57838885 5.690000e-59 239.0
14 TraesCS4B01G086300 chr4D 94.253 87 5 0 757 843 57835591 57835677 2.760000e-27 134.0
15 TraesCS4B01G086300 chr4D 85.965 114 14 2 3844 3957 230472962 230472851 2.150000e-23 121.0
16 TraesCS4B01G086300 chr4D 100.000 46 0 0 838 883 426846059 426846104 7.850000e-13 86.1
17 TraesCS4B01G086300 chr7D 89.844 128 10 3 3837 3964 34373348 34373472 1.270000e-35 161.0
18 TraesCS4B01G086300 chr3A 89.683 126 11 2 3837 3962 378814138 378814015 4.560000e-35 159.0
19 TraesCS4B01G086300 chr6B 89.076 119 12 1 3844 3962 298824902 298824785 3.550000e-31 147.0
20 TraesCS4B01G086300 chr5B 87.302 126 15 1 3844 3969 217613145 217613269 4.590000e-30 143.0
21 TraesCS4B01G086300 chr7A 87.719 114 13 1 3844 3956 674819341 674819454 9.940000e-27 132.0
22 TraesCS4B01G086300 chr3D 100.000 48 0 0 841 888 260332621 260332574 6.070000e-14 89.8
23 TraesCS4B01G086300 chrUn 96.154 52 1 1 841 891 253929081 253929132 2.820000e-12 84.2
24 TraesCS4B01G086300 chr2D 96.154 52 1 1 841 891 44215323 44215374 2.820000e-12 84.2
25 TraesCS4B01G086300 chr2D 96.154 52 1 1 841 891 44236494 44236545 2.820000e-12 84.2
26 TraesCS4B01G086300 chr2B 91.525 59 2 2 826 881 790113044 790112986 1.310000e-10 78.7


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 TraesCS4B01G086300 chr4B 86138667 86143070 4403 True 3859.00 4351 100.0000 1 4404 2 chr4B.!!$R3 4403
1 TraesCS4B01G086300 chr4A 539126464 539132540 6076 False 1113.02 2628 93.5550 5 4404 5 chr4A.!!$F1 4399
2 TraesCS4B01G086300 chr4D 57834120 57838885 4765 False 1081.40 2579 93.4136 2 3985 5 chr4D.!!$F2 3983

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
606 623 0.460311 CCTCGGCTTCTGTCCGTTAT 59.540 55.0 1.22 0.00 46.49 1.89 F
1308 2067 0.935898 GCATGACTTCGCTGGATCTG 59.064 55.0 0.00 0.00 0.00 2.90 F
2464 3225 0.745845 ATCTGATGACGGCAACAGGC 60.746 55.0 26.26 0.22 43.02 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2454 3215 0.179174 GGTAAAATCGCCTGTTGCCG 60.179 55.0 0.00 0.0 36.24 5.69 R
3082 3843 0.035439 CTGGGGCCTTTGATACACGT 60.035 55.0 0.84 0.0 0.00 4.49 R
4211 7099 0.110486 TTTGGAGCCCAGTTCTCACC 59.890 55.0 0.00 0.0 33.81 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.446272 CGTTCTCCTTCCGCTCACC 60.446 63.158 0.00 0.00 0.00 4.02
48 49 0.788391 CGCTCACCGTTTAGTTGACC 59.212 55.000 0.00 0.00 0.00 4.02
97 98 2.608988 AGTGGGCCCCAGTCTCAG 60.609 66.667 22.27 0.00 30.18 3.35
450 466 3.296709 ATCCGCGCTCTCACCGTTT 62.297 57.895 5.56 0.00 0.00 3.60
479 495 0.964358 GCCAGCAACTCAGCTTCCAT 60.964 55.000 0.00 0.00 43.70 3.41
484 500 1.065564 GCAACTCAGCTTCCATCCTCT 60.066 52.381 0.00 0.00 0.00 3.69
542 559 6.144402 CGATTTCACTTTCCCTGATTTGTTTG 59.856 38.462 0.00 0.00 0.00 2.93
586 603 1.599606 AATCCGAGTCTCGCTGCAGT 61.600 55.000 17.02 0.00 38.82 4.40
606 623 0.460311 CCTCGGCTTCTGTCCGTTAT 59.540 55.000 1.22 0.00 46.49 1.89
649 666 1.079317 GGTTTGCCAACGCGTTGTTT 61.079 50.000 40.30 13.43 39.29 2.83
669 686 9.710900 GTTGTTTTGATCCAGATTCCTTTTATT 57.289 29.630 0.00 0.00 0.00 1.40
670 687 9.927668 TTGTTTTGATCCAGATTCCTTTTATTC 57.072 29.630 0.00 0.00 0.00 1.75
680 697 7.153985 CAGATTCCTTTTATTCAGTTTTGCCA 58.846 34.615 0.00 0.00 0.00 4.92
763 1488 3.433615 GCTCATTCGGATACATTAGTGCC 59.566 47.826 0.00 0.00 0.00 5.01
774 1499 2.509548 ACATTAGTGCCAGGGCTCATTA 59.490 45.455 12.19 0.00 42.51 1.90
840 1565 4.574674 TCAGTATGCTCTGTTGGGATTT 57.425 40.909 0.00 0.00 36.85 2.17
841 1566 5.692115 TCAGTATGCTCTGTTGGGATTTA 57.308 39.130 0.00 0.00 36.85 1.40
842 1567 5.428253 TCAGTATGCTCTGTTGGGATTTAC 58.572 41.667 0.00 0.00 36.85 2.01
843 1568 5.189736 TCAGTATGCTCTGTTGGGATTTACT 59.810 40.000 0.00 0.00 36.85 2.24
844 1569 5.525378 CAGTATGCTCTGTTGGGATTTACTC 59.475 44.000 0.00 0.00 0.00 2.59
845 1570 3.350219 TGCTCTGTTGGGATTTACTCC 57.650 47.619 0.00 0.00 44.11 3.85
857 1582 5.349061 GGATTTACTCCCTCCGTAAAGAA 57.651 43.478 0.00 0.00 39.40 2.52
858 1583 5.737860 GGATTTACTCCCTCCGTAAAGAAA 58.262 41.667 0.00 0.00 39.40 2.52
859 1584 6.354938 GGATTTACTCCCTCCGTAAAGAAAT 58.645 40.000 0.00 0.00 39.40 2.17
860 1585 7.503549 GGATTTACTCCCTCCGTAAAGAAATA 58.496 38.462 0.00 0.00 39.40 1.40
861 1586 8.155510 GGATTTACTCCCTCCGTAAAGAAATAT 58.844 37.037 0.00 0.00 39.40 1.28
865 1590 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
866 1591 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
867 1592 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
868 1593 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
869 1594 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
870 1595 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
871 1596 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
872 1597 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
873 1598 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
874 1599 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
953 1712 4.431416 TGTTTCCTTTTAGGCACTGAGA 57.569 40.909 0.00 0.00 41.52 3.27
964 1723 2.039480 AGGCACTGAGAAAGCTTCATGA 59.961 45.455 0.00 0.00 37.18 3.07
973 1732 7.333921 ACTGAGAAAGCTTCATGATAAACTCTG 59.666 37.037 0.00 8.01 0.00 3.35
988 1747 3.919223 ACTCTGGACGTTGAAGTAGAC 57.081 47.619 0.00 0.00 0.00 2.59
1125 1884 2.028420 TGAAGGCATCAGTTGATCCG 57.972 50.000 0.00 0.00 33.04 4.18
1135 1894 2.548057 TCAGTTGATCCGAACAACAAGC 59.452 45.455 20.00 0.00 46.58 4.01
1178 1937 5.359009 ACAACAAAGAAGGATCCATATGCAG 59.641 40.000 15.82 0.43 0.00 4.41
1308 2067 0.935898 GCATGACTTCGCTGGATCTG 59.064 55.000 0.00 0.00 0.00 2.90
1401 2160 8.856153 TTGATCTCTCGTATAATAGCTTCTCT 57.144 34.615 0.00 0.00 0.00 3.10
1440 2199 3.733224 CGCTAGCTAACTGCACTTATCTG 59.267 47.826 13.93 0.00 45.94 2.90
1458 2217 8.993121 ACTTATCTGAATGTTGTCAGTTTACAG 58.007 33.333 2.38 0.00 44.56 2.74
1564 2323 1.003349 CAGGCCAGATCCCATCATCTC 59.997 57.143 5.01 0.00 30.07 2.75
1566 2325 2.113233 AGGCCAGATCCCATCATCTCTA 59.887 50.000 5.01 0.00 30.07 2.43
1751 2510 2.125952 GCGGAAAATGCCTGCCAC 60.126 61.111 0.00 0.00 0.00 5.01
2113 2872 4.680237 TGTCGCGTCTTGCCCCAG 62.680 66.667 5.77 0.00 42.08 4.45
2262 3021 7.933577 TGCCTTGAAGAATAACCTGTATCATAG 59.066 37.037 0.00 0.00 0.00 2.23
2263 3022 7.389053 GCCTTGAAGAATAACCTGTATCATAGG 59.611 40.741 0.00 0.00 41.22 2.57
2264 3023 8.651389 CCTTGAAGAATAACCTGTATCATAGGA 58.349 37.037 0.00 0.00 38.71 2.94
2265 3024 9.703892 CTTGAAGAATAACCTGTATCATAGGAG 57.296 37.037 0.00 0.00 38.71 3.69
2266 3025 8.783660 TGAAGAATAACCTGTATCATAGGAGT 57.216 34.615 0.00 0.00 38.71 3.85
2267 3026 9.877222 TGAAGAATAACCTGTATCATAGGAGTA 57.123 33.333 0.00 0.00 38.71 2.59
2464 3225 0.745845 ATCTGATGACGGCAACAGGC 60.746 55.000 26.26 0.22 43.02 4.85
2566 3327 2.026915 TGCTATCAAGAGGCTGCAAGAA 60.027 45.455 0.50 0.00 34.07 2.52
2644 3405 2.602217 GCAACGCAACTTAGTTCCACTG 60.602 50.000 0.00 0.00 0.00 3.66
2653 3414 6.653740 GCAACTTAGTTCCACTGTTAGGTTAT 59.346 38.462 0.00 0.00 0.00 1.89
2656 3417 7.742767 ACTTAGTTCCACTGTTAGGTTATTGT 58.257 34.615 0.00 0.00 0.00 2.71
2830 3591 2.063015 ATCACAGTTGCAACCCCCGA 62.063 55.000 25.62 16.83 0.00 5.14
2896 3657 7.609097 TGATGACTATGAGCCTAAGATTTCT 57.391 36.000 0.00 0.00 0.00 2.52
2929 3690 4.032310 TGGCAAGGCTTATGAATCCAATT 58.968 39.130 0.00 0.00 0.00 2.32
3059 3820 9.841295 ATAGTTTTGGTGTAGTCTTACTTGAAA 57.159 29.630 0.00 0.00 0.00 2.69
3082 3843 2.847234 ACCGGTGAAGAGCCCACA 60.847 61.111 6.12 0.00 36.31 4.17
3154 3915 7.990886 TGGATAACATACCTATCAAACAACTCC 59.009 37.037 0.00 0.00 0.00 3.85
3414 4175 1.406539 GGCGAAATAGACGGGTCTGTA 59.593 52.381 11.47 0.00 40.71 2.74
3469 4230 7.567458 TCTTGTGAATGATCAGGTTGATATGA 58.433 34.615 0.09 0.00 37.20 2.15
3496 4269 7.355101 AGTAATGTACTATCTGGACTCCTTCA 58.645 38.462 0.00 0.00 37.23 3.02
3497 4270 6.723298 AATGTACTATCTGGACTCCTTCAG 57.277 41.667 0.00 0.00 0.00 3.02
3648 4426 1.006102 CTGGTGTGTGAGACGGACC 60.006 63.158 0.00 0.00 0.00 4.46
3653 4431 1.289380 GTGTGAGACGGACCACCTC 59.711 63.158 3.75 3.75 32.61 3.85
3736 4519 4.842531 AAAAATTCCTTATGGCCCTTGG 57.157 40.909 0.00 0.00 0.00 3.61
3737 4520 3.774842 AAATTCCTTATGGCCCTTGGA 57.225 42.857 0.00 0.00 0.00 3.53
3749 4543 2.224967 GGCCCTTGGAGATAGCATGATT 60.225 50.000 0.00 0.00 0.00 2.57
3750 4544 2.818432 GCCCTTGGAGATAGCATGATTG 59.182 50.000 0.00 0.00 0.00 2.67
3757 4551 4.103627 TGGAGATAGCATGATTGGACACAT 59.896 41.667 0.00 0.00 0.00 3.21
3791 4585 0.321919 TGAGGAAGACACATGCAGCC 60.322 55.000 0.00 0.00 0.00 4.85
3803 4597 4.171005 CACATGCAGCCTGAAACAATTAG 58.829 43.478 4.47 0.00 0.00 1.73
3804 4598 3.184541 CATGCAGCCTGAAACAATTAGC 58.815 45.455 0.00 0.00 0.00 3.09
3815 4797 8.899771 GCCTGAAACAATTAGCCTATAAACTTA 58.100 33.333 0.00 0.00 0.00 2.24
3848 4830 7.070821 ACTCCCTCTGTTCACTAACTTCTTTTA 59.929 37.037 0.00 0.00 36.51 1.52
3893 6781 6.919721 ACATGTTTTACTGTGTTTGTTCAGT 58.080 32.000 0.00 0.00 45.21 3.41
3904 6792 5.647658 TGTGTTTGTTCAGTCATTTCAGTCT 59.352 36.000 0.00 0.00 0.00 3.24
3969 6857 3.751175 TGAACGGAGGAAGTAGCAAATTG 59.249 43.478 0.00 0.00 0.00 2.32
4025 6913 7.801716 TTTAGGAACAAGATATGTATGTGCC 57.198 36.000 0.00 0.00 42.99 5.01
4038 6926 4.435425 TGTATGTGCCGTATTTGAGGTAC 58.565 43.478 0.00 0.00 42.35 3.34
4149 7037 7.463961 TCGAAGTTCTAGATTTGTCCTAAGT 57.536 36.000 0.56 0.00 0.00 2.24
4150 7038 7.893658 TCGAAGTTCTAGATTTGTCCTAAGTT 58.106 34.615 0.56 0.00 0.00 2.66
4192 7080 9.618890 TGATCAAGTCTATAGAAAATTTCAGGG 57.381 33.333 3.40 0.00 0.00 4.45
4193 7081 8.986929 ATCAAGTCTATAGAAAATTTCAGGGG 57.013 34.615 3.40 0.00 0.00 4.79
4195 7083 6.582929 AGTCTATAGAAAATTTCAGGGGCT 57.417 37.500 3.40 0.00 0.00 5.19
4196 7084 6.360618 AGTCTATAGAAAATTTCAGGGGCTG 58.639 40.000 3.40 0.00 0.00 4.85
4198 7086 6.261158 GTCTATAGAAAATTTCAGGGGCTGAC 59.739 42.308 3.40 3.71 40.46 3.51
4199 7087 2.529632 AGAAAATTTCAGGGGCTGACC 58.470 47.619 8.55 0.00 40.46 4.02
4213 7101 3.299503 GGCTGACCCATGAATTATTGGT 58.700 45.455 0.00 0.00 37.51 3.67
4214 7102 3.068590 GGCTGACCCATGAATTATTGGTG 59.931 47.826 0.00 1.16 35.08 4.17
4215 7103 3.953612 GCTGACCCATGAATTATTGGTGA 59.046 43.478 0.00 0.00 35.08 4.02
4216 7104 4.037208 GCTGACCCATGAATTATTGGTGAG 59.963 45.833 0.00 0.00 38.38 3.51
4217 7105 5.439721 CTGACCCATGAATTATTGGTGAGA 58.560 41.667 0.00 0.00 37.82 3.27
4221 7109 5.653769 ACCCATGAATTATTGGTGAGAACTG 59.346 40.000 0.00 0.00 33.74 3.16
4222 7110 5.068198 CCCATGAATTATTGGTGAGAACTGG 59.932 44.000 0.00 0.00 0.00 4.00
4223 7111 5.068198 CCATGAATTATTGGTGAGAACTGGG 59.932 44.000 0.00 0.00 0.00 4.45
4224 7112 4.016444 TGAATTATTGGTGAGAACTGGGC 58.984 43.478 0.00 0.00 0.00 5.36
4225 7113 4.263905 TGAATTATTGGTGAGAACTGGGCT 60.264 41.667 0.00 0.00 0.00 5.19
4226 7114 3.350219 TTATTGGTGAGAACTGGGCTC 57.650 47.619 0.00 0.00 0.00 4.70
4227 7115 0.329596 ATTGGTGAGAACTGGGCTCC 59.670 55.000 0.00 0.00 0.00 4.70
4228 7116 1.059584 TTGGTGAGAACTGGGCTCCA 61.060 55.000 0.00 0.00 0.00 3.86
4229 7117 1.059584 TGGTGAGAACTGGGCTCCAA 61.060 55.000 0.00 0.00 30.80 3.53
4231 7119 1.478654 GGTGAGAACTGGGCTCCAAAA 60.479 52.381 0.00 0.00 30.80 2.44
4232 7120 1.609072 GTGAGAACTGGGCTCCAAAAC 59.391 52.381 0.00 0.00 30.80 2.43
4234 7122 1.882623 GAGAACTGGGCTCCAAAACTG 59.117 52.381 0.00 0.00 30.80 3.16
4236 7124 0.469892 AACTGGGCTCCAAAACTGGG 60.470 55.000 0.00 0.00 30.80 4.45
4237 7125 1.607467 CTGGGCTCCAAAACTGGGG 60.607 63.158 0.00 0.00 30.80 4.96
4240 7128 2.997315 GCTCCAAAACTGGGGGCC 60.997 66.667 0.00 0.00 46.58 5.80
4241 7129 2.283894 CTCCAAAACTGGGGGCCC 60.284 66.667 15.76 15.76 0.00 5.80
4242 7130 3.113477 TCCAAAACTGGGGGCCCA 61.113 61.111 26.86 9.85 45.02 5.36
4243 7131 2.122636 CCAAAACTGGGGGCCCAA 60.123 61.111 26.86 13.71 46.63 4.12
4244 7132 2.515979 CCAAAACTGGGGGCCCAAC 61.516 63.158 26.86 17.00 46.63 3.77
4245 7133 1.459348 CAAAACTGGGGGCCCAACT 60.459 57.895 26.86 0.00 46.63 3.16
4246 7134 0.178947 CAAAACTGGGGGCCCAACTA 60.179 55.000 26.86 3.60 46.63 2.24
4247 7135 0.114364 AAAACTGGGGGCCCAACTAG 59.886 55.000 26.86 17.00 46.63 2.57
4248 7136 1.071909 AAACTGGGGGCCCAACTAGT 61.072 55.000 26.86 17.73 46.63 2.57
4249 7137 1.789576 AACTGGGGGCCCAACTAGTG 61.790 60.000 26.86 2.66 46.63 2.74
4250 7138 1.923395 CTGGGGGCCCAACTAGTGA 60.923 63.158 26.86 0.00 46.63 3.41
4251 7139 1.464395 TGGGGGCCCAACTAGTGAA 60.464 57.895 26.86 0.00 44.12 3.18
4252 7140 1.068943 TGGGGGCCCAACTAGTGAAA 61.069 55.000 26.86 0.00 44.12 2.69
4253 7141 0.113580 GGGGGCCCAACTAGTGAAAA 59.886 55.000 26.86 0.00 35.81 2.29
4254 7142 1.254026 GGGGCCCAACTAGTGAAAAC 58.746 55.000 26.86 0.00 0.00 2.43
4255 7143 0.879090 GGGCCCAACTAGTGAAAACG 59.121 55.000 19.95 0.00 0.00 3.60
4262 7150 3.186613 CCAACTAGTGAAAACGGAGCTTC 59.813 47.826 0.00 0.00 0.00 3.86
4263 7151 3.746045 ACTAGTGAAAACGGAGCTTCA 57.254 42.857 0.00 0.00 31.48 3.02
4265 7153 4.448210 ACTAGTGAAAACGGAGCTTCAAA 58.552 39.130 0.00 0.00 35.02 2.69
4266 7154 3.971032 AGTGAAAACGGAGCTTCAAAG 57.029 42.857 0.00 0.00 35.02 2.77
4309 7197 5.104776 TCAATGGAATGGAGAGAGTACCTTG 60.105 44.000 0.00 0.00 0.00 3.61
4310 7198 3.107601 TGGAATGGAGAGAGTACCTTGG 58.892 50.000 0.00 0.00 0.00 3.61
4314 7202 3.474798 TGGAGAGAGTACCTTGGATGT 57.525 47.619 0.00 0.00 0.00 3.06
4315 7203 4.603094 TGGAGAGAGTACCTTGGATGTA 57.397 45.455 0.00 0.00 0.00 2.29
4316 7204 4.942944 TGGAGAGAGTACCTTGGATGTAA 58.057 43.478 0.00 0.00 0.00 2.41
4346 7234 4.821260 TCCCCATGAATTATCGACACAATG 59.179 41.667 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.904136 ACGAGGAAATTTCACAGCTTG 57.096 42.857 19.49 12.68 0.00 4.01
36 37 3.370978 CACCTATGCTGGTCAACTAAACG 59.629 47.826 0.00 0.00 38.45 3.60
48 49 2.301346 GGATTTGGACCACCTATGCTG 58.699 52.381 0.00 0.00 37.04 4.41
128 139 0.528684 GAGCGTGGACTGGACTATGC 60.529 60.000 0.00 0.00 34.32 3.14
419 435 0.870307 CGCGGATGAAGGTTACCTCG 60.870 60.000 3.62 4.61 30.89 4.63
479 495 1.601759 GTGGCAGCAAAGCAGAGGA 60.602 57.895 0.00 0.00 35.83 3.71
542 559 4.465512 CCGCGGCACAGAACATGC 62.466 66.667 14.67 0.00 42.62 4.06
563 580 0.108615 CAGCGAGACTCGGATTTGGT 60.109 55.000 25.31 0.00 40.84 3.67
649 666 8.884124 AACTGAATAAAAGGAATCTGGATCAA 57.116 30.769 0.00 0.00 0.00 2.57
669 686 2.655090 TCAGTGGATGGCAAAACTGA 57.345 45.000 19.99 19.99 45.04 3.41
670 687 3.087031 AGATCAGTGGATGGCAAAACTG 58.913 45.455 16.91 16.91 41.11 3.16
680 697 2.125233 ACTGCATGGAGATCAGTGGAT 58.875 47.619 22.24 0.00 39.36 3.41
840 1565 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
841 1566 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
842 1567 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
843 1568 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
844 1569 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
845 1570 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
846 1571 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
847 1572 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
848 1573 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
859 1584 9.551734 TGTAGTAGTGATCTAAACGCTCTTATA 57.448 33.333 0.00 0.00 0.00 0.98
860 1585 8.447924 TGTAGTAGTGATCTAAACGCTCTTAT 57.552 34.615 0.00 0.00 0.00 1.73
861 1586 7.854557 TGTAGTAGTGATCTAAACGCTCTTA 57.145 36.000 0.00 0.00 0.00 2.10
862 1587 6.754702 TGTAGTAGTGATCTAAACGCTCTT 57.245 37.500 0.00 0.00 0.00 2.85
863 1588 6.319152 ACATGTAGTAGTGATCTAAACGCTCT 59.681 38.462 0.00 0.00 0.00 4.09
864 1589 6.496571 ACATGTAGTAGTGATCTAAACGCTC 58.503 40.000 0.00 0.00 0.00 5.03
865 1590 6.452494 ACATGTAGTAGTGATCTAAACGCT 57.548 37.500 0.00 0.00 0.00 5.07
866 1591 7.391786 CAAACATGTAGTAGTGATCTAAACGC 58.608 38.462 0.00 0.00 0.00 4.84
867 1592 7.544566 ACCAAACATGTAGTAGTGATCTAAACG 59.455 37.037 0.00 0.00 0.00 3.60
868 1593 8.773404 ACCAAACATGTAGTAGTGATCTAAAC 57.227 34.615 0.00 0.00 0.00 2.01
869 1594 9.787435 AAACCAAACATGTAGTAGTGATCTAAA 57.213 29.630 0.00 0.00 0.00 1.85
871 1596 9.865321 GTAAACCAAACATGTAGTAGTGATCTA 57.135 33.333 0.00 0.00 0.00 1.98
872 1597 8.372459 TGTAAACCAAACATGTAGTAGTGATCT 58.628 33.333 0.00 0.00 0.00 2.75
873 1598 8.542497 TGTAAACCAAACATGTAGTAGTGATC 57.458 34.615 0.00 0.00 0.00 2.92
953 1712 5.352569 CGTCCAGAGTTTATCATGAAGCTTT 59.647 40.000 0.00 0.00 0.00 3.51
964 1723 6.015688 TGTCTACTTCAACGTCCAGAGTTTAT 60.016 38.462 0.00 0.00 0.00 1.40
973 1732 2.059541 GTGCTGTCTACTTCAACGTCC 58.940 52.381 0.00 0.00 0.00 4.79
988 1747 2.590007 GGCCATCCTAGCGTGCTG 60.590 66.667 4.25 0.00 0.00 4.41
1125 1884 2.223782 TGTCCAATGCAGCTTGTTGTTC 60.224 45.455 0.00 0.00 0.00 3.18
1135 1894 4.443913 TGTCATCAAATGTCCAATGCAG 57.556 40.909 0.00 0.00 0.00 4.41
1178 1937 0.939419 ACACTCCACGCCGTTAAAAC 59.061 50.000 0.00 0.00 0.00 2.43
1308 2067 0.040067 CGGAAAGGCTGTTGCTTGAC 60.040 55.000 0.00 0.00 39.59 3.18
1401 2160 0.469917 GCGATTCTGGAATCTCCCCA 59.530 55.000 17.62 0.00 43.71 4.96
1440 2199 9.944663 TTGTTATTCTGTAAACTGACAACATTC 57.055 29.630 12.85 0.00 33.37 2.67
1458 2217 5.689383 TTGCTCCAGTCAACTTGTTATTC 57.311 39.130 0.00 0.00 0.00 1.75
1564 2323 9.245962 GAAATTGGATGATGAGAATTTGCTTAG 57.754 33.333 0.00 0.00 30.11 2.18
1566 2325 6.755141 CGAAATTGGATGATGAGAATTTGCTT 59.245 34.615 0.00 0.00 30.11 3.91
1620 2379 1.745115 GGCAGTGCAATCACCGCTA 60.745 57.895 18.61 0.00 44.06 4.26
1751 2510 3.832527 TCCAGGTCCTTTTCCTTCTTTG 58.167 45.455 0.00 0.00 32.37 2.77
2057 2816 4.929819 ACAAAGGACGGCTAACATTTTT 57.070 36.364 0.00 0.00 0.00 1.94
2058 2817 4.929819 AACAAAGGACGGCTAACATTTT 57.070 36.364 0.00 0.00 0.00 1.82
2113 2872 9.520204 TCTTCACAAAGATGAAACATCTTTTTC 57.480 29.630 26.55 5.45 43.52 2.29
2454 3215 0.179174 GGTAAAATCGCCTGTTGCCG 60.179 55.000 0.00 0.00 36.24 5.69
2464 3225 8.868916 CCAATAATGTTTTCCTTGGTAAAATCG 58.131 33.333 0.00 0.00 33.29 3.34
2558 3319 3.501062 TCTGAATGCTGAGTTTCTTGCAG 59.499 43.478 0.00 0.00 38.87 4.41
2566 3327 1.627329 TGGCTCTCTGAATGCTGAGTT 59.373 47.619 7.42 0.00 40.03 3.01
2653 3414 6.054860 AGCCTCTCTTTCTTAGCAATACAA 57.945 37.500 0.00 0.00 0.00 2.41
2791 3552 3.850098 AAGCCACGCCAACCCTCTG 62.850 63.158 0.00 0.00 0.00 3.35
2830 3591 5.239525 GGAGCTAATATTGCGGTGAAGAATT 59.760 40.000 0.00 0.00 35.28 2.17
2896 3657 0.396060 GCCTTGCCAACCCAAAATCA 59.604 50.000 0.00 0.00 0.00 2.57
2929 3690 1.418097 ATGTGCTCAGGTGGGTGTCA 61.418 55.000 0.00 0.00 0.00 3.58
3052 3813 1.142060 TCACCGGTGACCATTTCAAGT 59.858 47.619 33.23 0.00 35.39 3.16
3059 3820 1.296715 GCTCTTCACCGGTGACCAT 59.703 57.895 36.40 0.00 39.66 3.55
3082 3843 0.035439 CTGGGGCCTTTGATACACGT 60.035 55.000 0.84 0.00 0.00 4.49
3154 3915 2.609459 GTCCACCGCATCTTGAAGTATG 59.391 50.000 0.00 0.00 0.00 2.39
3280 4041 1.404851 GCTCTCAGAAGCTGGTACACC 60.405 57.143 0.00 0.00 39.27 4.16
3414 4175 2.092968 ACACCGAGCATCAATGTACCAT 60.093 45.455 0.00 0.00 31.73 3.55
3430 4191 4.804608 TCACAAGATACAACAAACACCG 57.195 40.909 0.00 0.00 0.00 4.94
3496 4269 2.688958 AGCTTCCGATAGTTTCGCTACT 59.311 45.455 0.00 0.00 46.71 2.57
3497 4270 3.044286 GAGCTTCCGATAGTTTCGCTAC 58.956 50.000 0.00 0.00 46.71 3.58
3587 4360 4.216472 CACTACAGACTGAGCAAGTACAGA 59.784 45.833 10.08 0.00 40.07 3.41
3648 4426 5.332055 CGTACTTCTACAAAAACGTGAGGTG 60.332 44.000 0.00 0.00 0.00 4.00
3653 4431 6.738352 ACTACGTACTTCTACAAAAACGTG 57.262 37.500 8.42 2.20 42.80 4.49
3715 4498 4.434195 TCCAAGGGCCATAAGGAATTTTT 58.566 39.130 6.18 0.00 36.89 1.94
3716 4499 4.033009 CTCCAAGGGCCATAAGGAATTTT 58.967 43.478 6.18 0.00 36.89 1.82
3717 4500 3.272020 TCTCCAAGGGCCATAAGGAATTT 59.728 43.478 6.18 0.00 36.89 1.82
3718 4501 2.858768 TCTCCAAGGGCCATAAGGAATT 59.141 45.455 6.18 0.00 36.89 2.17
3719 4502 2.502745 TCTCCAAGGGCCATAAGGAAT 58.497 47.619 6.18 0.00 36.89 3.01
3720 4503 1.979809 TCTCCAAGGGCCATAAGGAA 58.020 50.000 6.18 2.41 36.89 3.36
3722 4505 2.290577 GCTATCTCCAAGGGCCATAAGG 60.291 54.545 6.18 3.28 38.23 2.69
3723 4506 2.373169 TGCTATCTCCAAGGGCCATAAG 59.627 50.000 6.18 0.00 0.00 1.73
3727 4510 0.475475 CATGCTATCTCCAAGGGCCA 59.525 55.000 6.18 0.00 0.00 5.36
3728 4511 0.767375 TCATGCTATCTCCAAGGGCC 59.233 55.000 0.00 0.00 0.00 5.80
3729 4512 2.818432 CAATCATGCTATCTCCAAGGGC 59.182 50.000 0.00 0.00 0.00 5.19
3730 4513 3.073503 TCCAATCATGCTATCTCCAAGGG 59.926 47.826 0.00 0.00 0.00 3.95
3731 4514 4.070716 GTCCAATCATGCTATCTCCAAGG 58.929 47.826 0.00 0.00 0.00 3.61
3735 4518 4.077300 TGTGTCCAATCATGCTATCTCC 57.923 45.455 0.00 0.00 0.00 3.71
3736 4519 7.918536 AATATGTGTCCAATCATGCTATCTC 57.081 36.000 0.00 0.00 0.00 2.75
3737 4520 8.701908 AAAATATGTGTCCAATCATGCTATCT 57.298 30.769 0.00 0.00 0.00 1.98
3749 4543 9.695526 CTCAAAAATGAAGAAAATATGTGTCCA 57.304 29.630 0.00 0.00 0.00 4.02
3750 4544 9.143631 CCTCAAAAATGAAGAAAATATGTGTCC 57.856 33.333 0.00 0.00 0.00 4.02
3757 4551 9.965824 GTGTCTTCCTCAAAAATGAAGAAAATA 57.034 29.630 3.01 0.00 44.27 1.40
3803 4597 8.975663 AGGGAGTAACATTTAAGTTTATAGGC 57.024 34.615 0.00 0.00 33.07 3.93
3815 4797 5.568620 AGTGAACAGAGGGAGTAACATTT 57.431 39.130 0.00 0.00 0.00 2.32
3818 4800 5.145564 AGTTAGTGAACAGAGGGAGTAACA 58.854 41.667 0.00 0.00 38.10 2.41
3848 4830 8.753133 ACATGTATATACACATCCGATTCAGAT 58.247 33.333 17.69 0.00 39.30 2.90
3873 6761 8.460831 AAATGACTGAACAAACACAGTAAAAC 57.539 30.769 0.00 0.00 45.54 2.43
3879 6767 5.883661 ACTGAAATGACTGAACAAACACAG 58.116 37.500 0.00 0.00 39.65 3.66
4009 6897 7.360353 CCTCAAATACGGCACATACATATCTTG 60.360 40.741 0.00 0.00 0.00 3.02
4013 6901 5.865085 ACCTCAAATACGGCACATACATAT 58.135 37.500 0.00 0.00 0.00 1.78
4017 6905 3.488310 CGTACCTCAAATACGGCACATAC 59.512 47.826 0.00 0.00 41.33 2.39
4038 6926 5.227908 TCCTTCTAGAAAAACTGCACTACG 58.772 41.667 6.63 0.00 0.00 3.51
4119 7007 9.535878 AGGACAAATCTAGAACTTCGAATATTC 57.464 33.333 12.26 12.26 0.00 1.75
4126 7014 9.804758 ATAACTTAGGACAAATCTAGAACTTCG 57.195 33.333 0.00 0.00 0.00 3.79
4169 7057 6.828785 GCCCCTGAAATTTTCTATAGACTTGA 59.171 38.462 0.67 0.00 0.00 3.02
4192 7080 3.068590 CACCAATAATTCATGGGTCAGCC 59.931 47.826 12.61 0.00 39.15 4.85
4193 7081 3.953612 TCACCAATAATTCATGGGTCAGC 59.046 43.478 12.61 0.00 39.15 4.26
4195 7083 5.449297 TCTCACCAATAATTCATGGGTCA 57.551 39.130 12.61 0.00 39.15 4.02
4196 7084 5.888161 AGTTCTCACCAATAATTCATGGGTC 59.112 40.000 12.61 0.00 39.15 4.46
4198 7086 5.068198 CCAGTTCTCACCAATAATTCATGGG 59.932 44.000 12.61 1.81 41.17 4.00
4199 7087 5.068198 CCCAGTTCTCACCAATAATTCATGG 59.932 44.000 7.67 7.67 42.60 3.66
4202 7090 4.016444 GCCCAGTTCTCACCAATAATTCA 58.984 43.478 0.00 0.00 0.00 2.57
4203 7091 4.273318 AGCCCAGTTCTCACCAATAATTC 58.727 43.478 0.00 0.00 0.00 2.17
4205 7093 3.372025 GGAGCCCAGTTCTCACCAATAAT 60.372 47.826 0.00 0.00 32.38 1.28
4206 7094 2.026262 GGAGCCCAGTTCTCACCAATAA 60.026 50.000 0.00 0.00 32.38 1.40
4207 7095 1.559682 GGAGCCCAGTTCTCACCAATA 59.440 52.381 0.00 0.00 32.38 1.90
4209 7097 1.059584 TGGAGCCCAGTTCTCACCAA 61.060 55.000 0.00 0.00 32.38 3.67
4211 7099 0.110486 TTTGGAGCCCAGTTCTCACC 59.890 55.000 0.00 0.00 33.81 4.02
4212 7100 1.609072 GTTTTGGAGCCCAGTTCTCAC 59.391 52.381 0.00 0.00 33.81 3.51
4213 7101 1.494721 AGTTTTGGAGCCCAGTTCTCA 59.505 47.619 0.00 0.00 33.81 3.27
4214 7102 1.882623 CAGTTTTGGAGCCCAGTTCTC 59.117 52.381 0.00 0.00 33.81 2.87
4215 7103 1.986882 CAGTTTTGGAGCCCAGTTCT 58.013 50.000 0.00 0.00 33.81 3.01
4234 7122 0.113580 TTTTCACTAGTTGGGCCCCC 59.886 55.000 22.27 10.32 0.00 5.40
4236 7124 0.879090 CGTTTTCACTAGTTGGGCCC 59.121 55.000 17.59 17.59 0.00 5.80
4237 7125 0.879090 CCGTTTTCACTAGTTGGGCC 59.121 55.000 0.00 0.00 0.00 5.80
4239 7127 1.804748 GCTCCGTTTTCACTAGTTGGG 59.195 52.381 0.00 0.00 0.00 4.12
4240 7128 2.767505 AGCTCCGTTTTCACTAGTTGG 58.232 47.619 0.00 0.00 0.00 3.77
4241 7129 3.807622 TGAAGCTCCGTTTTCACTAGTTG 59.192 43.478 0.00 0.00 0.00 3.16
4242 7130 4.067972 TGAAGCTCCGTTTTCACTAGTT 57.932 40.909 0.00 0.00 0.00 2.24
4243 7131 3.746045 TGAAGCTCCGTTTTCACTAGT 57.254 42.857 0.00 0.00 0.00 2.57
4244 7132 5.023551 CTTTGAAGCTCCGTTTTCACTAG 57.976 43.478 0.00 0.00 33.36 2.57
4246 7134 3.971032 CTTTGAAGCTCCGTTTTCACT 57.029 42.857 0.00 0.00 33.36 3.41
4262 7150 8.633075 TGAAGTTCAACTATTTTTCAGCTTTG 57.367 30.769 2.20 0.00 0.00 2.77
4263 7151 9.822185 ATTGAAGTTCAACTATTTTTCAGCTTT 57.178 25.926 20.26 0.00 39.45 3.51
4265 7153 7.869429 CCATTGAAGTTCAACTATTTTTCAGCT 59.131 33.333 20.26 0.00 39.45 4.24
4266 7154 7.867403 TCCATTGAAGTTCAACTATTTTTCAGC 59.133 33.333 20.26 0.00 39.45 4.26
4267 7155 9.748708 TTCCATTGAAGTTCAACTATTTTTCAG 57.251 29.630 20.26 1.30 39.45 3.02
4270 7158 9.492973 CCATTCCATTGAAGTTCAACTATTTTT 57.507 29.630 20.26 0.08 39.45 1.94
4272 7160 8.421249 TCCATTCCATTGAAGTTCAACTATTT 57.579 30.769 20.26 1.58 39.45 1.40
4275 7163 6.778821 TCTCCATTCCATTGAAGTTCAACTA 58.221 36.000 20.26 6.38 39.45 2.24
4276 7164 5.634118 TCTCCATTCCATTGAAGTTCAACT 58.366 37.500 20.26 7.46 39.45 3.16
4277 7165 5.707298 TCTCTCCATTCCATTGAAGTTCAAC 59.293 40.000 20.26 0.00 39.45 3.18
4279 7167 5.013495 ACTCTCTCCATTCCATTGAAGTTCA 59.987 40.000 0.08 0.08 33.05 3.18
4309 7197 5.310409 TCATGGGGAAGAGAATTACATCC 57.690 43.478 0.00 0.00 0.00 3.51
4310 7198 7.830099 AATTCATGGGGAAGAGAATTACATC 57.170 36.000 0.00 0.00 38.51 3.06
4314 7202 7.878127 GTCGATAATTCATGGGGAAGAGAATTA 59.122 37.037 0.00 0.00 43.19 1.40
4315 7203 6.712547 GTCGATAATTCATGGGGAAGAGAATT 59.287 38.462 0.00 0.00 41.83 2.17
4316 7204 6.183361 TGTCGATAATTCATGGGGAAGAGAAT 60.183 38.462 0.00 0.00 39.30 2.40


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

AutoCloner maintained by Alex Coulton.