Multiple sequence alignment - TraesCS2B01G505800

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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 TraesCS2B01G505800 chr2B 100.000 6225 0 0 1 6225 701100784 701094560 0.000000e+00 11496.0
1 TraesCS2B01G505800 chr2B 77.047 1429 209 70 2941 4311 701761578 701762945 0.000000e+00 712.0
2 TraesCS2B01G505800 chr2B 82.383 193 27 6 211 402 701757655 701757841 1.800000e-35 161.0
3 TraesCS2B01G505800 chr2D 95.758 6176 143 35 1 6092 582030078 582023938 0.000000e+00 9843.0
4 TraesCS2B01G505800 chr2D 77.419 1426 206 66 2941 4311 582707067 582708431 0.000000e+00 743.0
5 TraesCS2B01G505800 chr2D 95.082 122 3 1 6105 6223 582018592 582018471 8.240000e-44 189.0
6 TraesCS2B01G505800 chr2D 82.653 196 22 9 211 405 582703279 582703463 4.990000e-36 163.0
7 TraesCS2B01G505800 chr2D 94.118 51 3 0 6170 6220 96081152 96081102 1.860000e-10 78.7
8 TraesCS2B01G505800 chr2D 94.118 51 3 0 6170 6220 96290638 96290588 1.860000e-10 78.7
9 TraesCS2B01G505800 chr2D 100.000 34 0 0 1524 1557 582029019 582028986 5.210000e-06 63.9
10 TraesCS2B01G505800 chr3D 76.475 1424 211 73 2941 4311 577912161 577910809 0.000000e+00 660.0
11 TraesCS2B01G505800 chr3D 79.048 630 108 12 4794 5409 577908988 577909607 1.620000e-110 411.0
12 TraesCS2B01G505800 chr3D 83.929 112 15 1 1843 1951 577913028 577912917 3.070000e-18 104.0
13 TraesCS2B01G505800 chr3D 96.296 54 2 0 6170 6223 55752228 55752175 8.600000e-14 89.8
14 TraesCS2B01G505800 chr3D 96.296 54 2 0 6170 6223 610873305 610873358 8.600000e-14 89.8
15 TraesCS2B01G505800 chr3D 100.000 31 0 0 2492 2522 577912588 577912558 2.420000e-04 58.4
16 TraesCS2B01G505800 chr3B 75.949 1422 229 64 2941 4311 771000124 771001483 1.470000e-175 627.0
17 TraesCS2B01G505800 chr3B 75.105 1430 223 74 2941 4311 771005141 771003786 4.240000e-151 545.0
18 TraesCS2B01G505800 chr3B 74.282 1427 219 80 2941 4311 770985737 770984403 3.400000e-127 466.0
19 TraesCS2B01G505800 chr3B 78.297 599 108 10 4824 5409 770983988 770983399 3.550000e-97 366.0
20 TraesCS2B01G505800 chr3B 76.879 346 35 23 2941 3262 770980507 770980831 3.010000e-33 154.0
21 TraesCS2B01G505800 chr3B 86.607 112 12 2 1843 1951 770979320 770979431 3.050000e-23 121.0
22 TraesCS2B01G505800 chr3B 85.455 110 13 2 1845 1951 770999014 770999123 1.830000e-20 111.0
23 TraesCS2B01G505800 chr3B 91.525 59 5 0 6165 6223 826368496 826368438 1.440000e-11 82.4
24 TraesCS2B01G505800 chr2A 75.698 1218 196 58 3448 4590 690317176 690315984 9.250000e-143 518.0
25 TraesCS2B01G505800 chr2A 77.793 707 99 32 4795 5481 690315797 690315129 3.520000e-102 383.0
26 TraesCS2B01G505800 chr5A 94.545 55 3 0 6169 6223 12047933 12047987 1.110000e-12 86.1
27 TraesCS2B01G505800 chr4B 96.154 52 2 0 6170 6221 635048950 635048899 1.110000e-12 86.1
28 TraesCS2B01G505800 chr6A 92.453 53 4 0 6171 6223 390367948 390367896 6.690000e-10 76.8
29 TraesCS2B01G505800 chr5D 97.059 34 1 0 4228 4261 287579841 287579874 2.420000e-04 58.4
30 TraesCS2B01G505800 chr5D 97.059 34 1 0 4228 4261 287579920 287579953 2.420000e-04 58.4
31 TraesCS2B01G505800 chr4A 97.059 34 1 0 4228 4261 370570274 370570307 2.420000e-04 58.4


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 TraesCS2B01G505800 chr2B 701094560 701100784 6224 True 11496.000000 11496 100.000000 1 6225 1 chr2B.!!$R1 6224
1 TraesCS2B01G505800 chr2B 701757655 701762945 5290 False 436.500000 712 79.715000 211 4311 2 chr2B.!!$F1 4100
2 TraesCS2B01G505800 chr2D 582023938 582030078 6140 True 4953.450000 9843 97.879000 1 6092 2 chr2D.!!$R4 6091
3 TraesCS2B01G505800 chr2D 582703279 582708431 5152 False 453.000000 743 80.036000 211 4311 2 chr2D.!!$F1 4100
4 TraesCS2B01G505800 chr3D 577908988 577909607 619 False 411.000000 411 79.048000 4794 5409 1 chr3D.!!$F1 615
5 TraesCS2B01G505800 chr3D 577910809 577913028 2219 True 274.133333 660 86.801333 1843 4311 3 chr3D.!!$R2 2468
6 TraesCS2B01G505800 chr3B 771003786 771005141 1355 True 545.000000 545 75.105000 2941 4311 1 chr3B.!!$R1 1370
7 TraesCS2B01G505800 chr3B 770983399 770985737 2338 True 416.000000 466 76.289500 2941 5409 2 chr3B.!!$R3 2468
8 TraesCS2B01G505800 chr3B 770999014 771001483 2469 False 369.000000 627 80.702000 1845 4311 2 chr3B.!!$F2 2466
9 TraesCS2B01G505800 chr2A 690315129 690317176 2047 True 450.500000 518 76.745500 3448 5481 2 chr2A.!!$R1 2033

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
993 1242 0.555769 TTTCTTTGCTCACCCCACCT 59.444 50.000 0.0 0.0 0.00 4.00 F
2240 4699 0.105246 TTTGGTGGTTCTGGGGCATT 60.105 50.000 0.0 0.0 0.00 3.56 F
3010 5628 1.004610 CTGCCGTAGAAATGCATCGTG 60.005 52.381 0.0 0.0 33.97 4.35 F
4154 6851 0.396811 CCGAGTGGAGAACCCTTGTT 59.603 55.000 0.0 0.0 37.49 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 4721 1.144708 ACATCACATGTGTGGTTGGGA 59.855 47.619 24.63 3.87 45.65 4.37 R
3511 6151 1.629043 GCCAATGGCCTCATCATCAT 58.371 50.000 14.47 0.00 44.06 2.45 R
4629 7379 1.669211 GGGAACAACTCGAGAACGGAG 60.669 57.143 21.68 4.34 40.21 4.63 R
6139 8942 0.179018 AACAGCCGGCAGTCTTCTTT 60.179 50.000 31.54 7.60 0.00 2.52 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
68 69 8.728833 CAAATGCTCAGAAGATTCTAAGTTCTT 58.271 33.333 0.00 0.00 35.34 2.52
94 95 4.463539 TGCACATTTGGCAGAAATACTCAT 59.536 37.500 0.00 0.00 36.11 2.90
97 98 6.183360 GCACATTTGGCAGAAATACTCATTTG 60.183 38.462 0.00 0.00 34.44 2.32
101 102 2.101415 GGCAGAAATACTCATTTGGCCC 59.899 50.000 0.00 0.00 41.27 5.80
108 109 1.821332 CTCATTTGGCCCGCCTCTC 60.821 63.158 7.35 0.00 36.94 3.20
134 135 1.402968 CAGCCTGTCATTGCACCATAC 59.597 52.381 0.00 0.00 0.00 2.39
171 172 1.891150 AGCCATGCAAAGACTTTGAGG 59.109 47.619 28.15 24.03 43.26 3.86
183 184 5.808366 AGACTTTGAGGACTGTGATTGTA 57.192 39.130 0.00 0.00 0.00 2.41
294 295 8.883731 ACACAGCTACTCACATATGTTTATTTC 58.116 33.333 5.37 0.00 0.00 2.17
317 318 5.302059 TCTCTCTAGTCTAGCTCTCTGTCTC 59.698 48.000 1.60 0.00 0.00 3.36
397 406 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
398 407 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
557 791 3.307059 CGTCCCTCTCTCTGTTTCCAATT 60.307 47.826 0.00 0.00 0.00 2.32
598 840 6.563422 TCTTGCAATGCATTGTTAGTTATCC 58.437 36.000 33.67 17.91 38.76 2.59
653 895 6.424509 GCAGATCTAGAGATTTCATCCAAGTG 59.575 42.308 0.00 0.00 34.37 3.16
720 968 7.062957 TCCTCCTCTCATTTTTCTTGTTTTCT 58.937 34.615 0.00 0.00 0.00 2.52
833 1081 4.807443 GTTAGTCACCTCTAACAGTCCAC 58.193 47.826 10.46 0.00 45.07 4.02
834 1082 2.249139 AGTCACCTCTAACAGTCCACC 58.751 52.381 0.00 0.00 0.00 4.61
835 1083 2.158295 AGTCACCTCTAACAGTCCACCT 60.158 50.000 0.00 0.00 0.00 4.00
836 1084 2.231721 GTCACCTCTAACAGTCCACCTC 59.768 54.545 0.00 0.00 0.00 3.85
837 1085 2.110188 TCACCTCTAACAGTCCACCTCT 59.890 50.000 0.00 0.00 0.00 3.69
838 1086 2.494073 CACCTCTAACAGTCCACCTCTC 59.506 54.545 0.00 0.00 0.00 3.20
839 1087 2.380590 ACCTCTAACAGTCCACCTCTCT 59.619 50.000 0.00 0.00 0.00 3.10
840 1088 3.020984 CCTCTAACAGTCCACCTCTCTC 58.979 54.545 0.00 0.00 0.00 3.20
841 1089 3.308832 CCTCTAACAGTCCACCTCTCTCT 60.309 52.174 0.00 0.00 0.00 3.10
842 1090 4.340617 CTCTAACAGTCCACCTCTCTCTT 58.659 47.826 0.00 0.00 0.00 2.85
843 1091 4.082845 TCTAACAGTCCACCTCTCTCTTG 58.917 47.826 0.00 0.00 0.00 3.02
844 1092 0.972883 ACAGTCCACCTCTCTCTTGC 59.027 55.000 0.00 0.00 0.00 4.01
845 1093 0.972134 CAGTCCACCTCTCTCTTGCA 59.028 55.000 0.00 0.00 0.00 4.08
846 1094 1.067000 CAGTCCACCTCTCTCTTGCAG 60.067 57.143 0.00 0.00 0.00 4.41
847 1095 1.203112 AGTCCACCTCTCTCTTGCAGA 60.203 52.381 0.00 0.00 0.00 4.26
848 1096 1.830477 GTCCACCTCTCTCTTGCAGAT 59.170 52.381 0.00 0.00 0.00 2.90
849 1097 2.106566 TCCACCTCTCTCTTGCAGATC 58.893 52.381 0.00 0.00 0.00 2.75
850 1098 2.109774 CCACCTCTCTCTTGCAGATCT 58.890 52.381 0.00 0.00 0.00 2.75
851 1099 3.053320 TCCACCTCTCTCTTGCAGATCTA 60.053 47.826 0.00 0.00 0.00 1.98
852 1100 3.318839 CCACCTCTCTCTTGCAGATCTAG 59.681 52.174 0.00 0.00 0.00 2.43
853 1101 4.206375 CACCTCTCTCTTGCAGATCTAGA 58.794 47.826 0.00 0.00 0.00 2.43
854 1102 4.276678 CACCTCTCTCTTGCAGATCTAGAG 59.723 50.000 12.95 12.95 43.21 2.43
855 1103 4.165950 ACCTCTCTCTTGCAGATCTAGAGA 59.834 45.833 18.49 18.49 46.42 3.10
900 1148 5.175859 TCATCGTGTTGAGGTTTCTTATCC 58.824 41.667 0.00 0.00 0.00 2.59
993 1242 0.555769 TTTCTTTGCTCACCCCACCT 59.444 50.000 0.00 0.00 0.00 4.00
1008 1257 1.683385 CCACCTCTACAGATGCATCGA 59.317 52.381 20.67 10.97 0.00 3.59
1031 1280 2.806288 CGAAACGCTTGGTGGAATAG 57.194 50.000 0.00 0.00 0.00 1.73
1033 1282 2.739913 CGAAACGCTTGGTGGAATAGAA 59.260 45.455 0.00 0.00 0.00 2.10
1055 1304 2.926200 CAGATGGTGCTGAAACTCGTAG 59.074 50.000 0.00 0.00 38.14 3.51
1161 1411 7.618964 TTCGTCAATTATTATGTAGACGCTC 57.381 36.000 7.79 0.00 45.82 5.03
1186 1436 8.474831 TCGAAGGACAGAGACAATTCAATATTA 58.525 33.333 0.00 0.00 0.00 0.98
1230 1480 2.351726 ACTCAGAACTGCACGAAACAAC 59.648 45.455 0.00 0.00 0.00 3.32
1276 1531 5.474876 ACTGAGCAGTGCTTAGCTTAAAAAT 59.525 36.000 30.80 10.94 44.50 1.82
1302 1557 6.320164 ACCAACAGTTTCAATTTAGTAGTGCA 59.680 34.615 0.00 0.00 0.00 4.57
1909 4099 6.581919 TGTTATGATTTTGTCAACGAGCATTG 59.418 34.615 4.71 0.00 40.97 2.82
2218 4676 1.410517 CATGCATCCGAGTACTCCACT 59.589 52.381 17.23 0.00 41.47 4.00
2239 4698 0.542702 CTTTGGTGGTTCTGGGGCAT 60.543 55.000 0.00 0.00 0.00 4.40
2240 4699 0.105246 TTTGGTGGTTCTGGGGCATT 60.105 50.000 0.00 0.00 0.00 3.56
2262 4721 2.704572 CCATCGAAGAGGCTTTCAGTT 58.295 47.619 0.00 0.00 43.63 3.16
2352 4814 5.116180 CAATCGTGAACCATATGTACCACT 58.884 41.667 1.24 0.00 31.94 4.00
2415 4877 7.824779 AGACCAAGAGTTTAGCTAAGTTTATGG 59.175 37.037 19.71 19.71 0.00 2.74
2434 4896 1.974543 CAAAGAATGGTGGGGGCAC 59.025 57.895 0.00 0.00 0.00 5.01
2549 5011 5.220931 GCTGGTGCTATAGAAGGAAATTGTG 60.221 44.000 3.21 0.00 36.03 3.33
2578 5040 1.531578 GTCTTCGCCAAGTGAACCTTC 59.468 52.381 0.00 0.00 0.00 3.46
2609 5071 3.867493 TCGCATGTCTTGATCAGATGTTC 59.133 43.478 0.00 0.00 32.60 3.18
2615 5077 4.043310 TGTCTTGATCAGATGTTCCCCTTT 59.957 41.667 0.00 0.00 32.60 3.11
2630 5092 2.420022 CCCCTTTGCTAAGAACACATCG 59.580 50.000 9.62 0.00 32.92 3.84
2828 5319 6.219473 GCCACCAGCTAGTATATATATGCAG 58.781 44.000 12.61 8.92 38.99 4.41
3010 5628 1.004610 CTGCCGTAGAAATGCATCGTG 60.005 52.381 0.00 0.00 33.97 4.35
3273 5909 4.663636 AAACTAGACCGAAATTTCTGCG 57.336 40.909 15.92 3.85 0.00 5.18
3509 6149 6.350200 GTTTGTTAAAACCTTCGAGTACGAG 58.650 40.000 0.00 0.00 43.07 4.18
3511 6151 7.167468 GTTTGTTAAAACCTTCGAGTACGAGTA 59.833 37.037 0.00 0.00 43.07 2.59
3521 6161 5.847670 TCGAGTACGAGTATGATGATGAG 57.152 43.478 0.00 0.00 43.81 2.90
4009 6703 0.744414 TCGGAGCTTGCCAACTATGC 60.744 55.000 0.00 0.00 0.00 3.14
4084 6781 1.800655 CGGGAGAGAAAGAGACATGCG 60.801 57.143 0.00 0.00 0.00 4.73
4154 6851 0.396811 CCGAGTGGAGAACCCTTGTT 59.603 55.000 0.00 0.00 37.49 2.83
4171 6868 4.222588 CCTTGTTGATCTTCTCCTCTCAGT 59.777 45.833 0.00 0.00 0.00 3.41
4389 7121 0.473755 ATTCGGGTATGCATGCAGGA 59.526 50.000 26.69 13.76 0.00 3.86
4484 7225 3.308530 CACTGCCGAAGAAAAATTGGAC 58.691 45.455 0.00 0.00 0.00 4.02
4581 7328 1.371595 TCGCTACCCGGCATTTAAAC 58.628 50.000 0.00 0.00 37.59 2.01
4629 7379 4.744570 TGAACTAGAACGTGACCATGATC 58.255 43.478 0.00 0.00 0.00 2.92
4638 7388 2.796383 CGTGACCATGATCTCCGTTCTC 60.796 54.545 0.00 0.00 0.00 2.87
5185 7948 2.113860 TCCAATTGTGGCTAGCTCAC 57.886 50.000 22.21 22.21 45.54 3.51
5311 8087 1.202302 TGAGATCGACGGCAATGTCTC 60.202 52.381 0.00 0.00 36.71 3.36
5390 8168 1.516386 CTGCGTCGCTTGTATCGGT 60.516 57.895 19.50 0.00 0.00 4.69
5424 8202 5.278364 CCATGTATCGAACCTACACCTCTAC 60.278 48.000 0.00 0.00 32.24 2.59
5662 8463 1.264288 GTTGACTTTTCTGTCCGCTGG 59.736 52.381 0.00 0.00 36.21 4.85
5699 8500 0.250901 AGTGGTGTTGGGATGACAGC 60.251 55.000 0.00 0.00 43.74 4.40
5775 8576 7.659390 GCATCCTTAGACTAAATACAAGAGCAT 59.341 37.037 0.00 0.00 0.00 3.79
5998 8799 4.218417 CGGTGGGAACAATTCAAGATTTCT 59.782 41.667 0.00 0.00 46.06 2.52
6118 8921 7.541916 AAAAACCTCTCTACTAACTAGCACT 57.458 36.000 0.00 0.00 0.00 4.40
6119 8922 6.762702 AAACCTCTCTACTAACTAGCACTC 57.237 41.667 0.00 0.00 0.00 3.51
6120 8923 5.438698 ACCTCTCTACTAACTAGCACTCA 57.561 43.478 0.00 0.00 0.00 3.41
6121 8924 5.433526 ACCTCTCTACTAACTAGCACTCAG 58.566 45.833 0.00 0.00 0.00 3.35
6122 8925 5.045432 ACCTCTCTACTAACTAGCACTCAGT 60.045 44.000 0.00 0.00 0.00 3.41
6123 8926 6.156602 ACCTCTCTACTAACTAGCACTCAGTA 59.843 42.308 0.00 0.00 0.00 2.74
6124 8927 7.147444 ACCTCTCTACTAACTAGCACTCAGTAT 60.147 40.741 0.00 0.00 0.00 2.12
6125 8928 7.172532 CCTCTCTACTAACTAGCACTCAGTATG 59.827 44.444 0.00 0.00 37.54 2.39
6138 8941 3.232213 TCAGTATGAGAAACGTGAGGC 57.768 47.619 0.00 0.00 42.56 4.70
6139 8942 2.560981 TCAGTATGAGAAACGTGAGGCA 59.439 45.455 0.00 0.00 42.56 4.75
6140 8943 3.006430 TCAGTATGAGAAACGTGAGGCAA 59.994 43.478 0.00 0.00 42.56 4.52
6141 8944 3.745975 CAGTATGAGAAACGTGAGGCAAA 59.254 43.478 0.00 0.00 39.69 3.68
6142 8945 3.997021 AGTATGAGAAACGTGAGGCAAAG 59.003 43.478 0.00 0.00 0.00 2.77
6143 8946 2.613026 TGAGAAACGTGAGGCAAAGA 57.387 45.000 0.00 0.00 0.00 2.52
6144 8947 2.912771 TGAGAAACGTGAGGCAAAGAA 58.087 42.857 0.00 0.00 0.00 2.52
6145 8948 2.872245 TGAGAAACGTGAGGCAAAGAAG 59.128 45.455 0.00 0.00 0.00 2.85
6146 8949 3.131396 GAGAAACGTGAGGCAAAGAAGA 58.869 45.455 0.00 0.00 0.00 2.87
6147 8950 2.872858 AGAAACGTGAGGCAAAGAAGAC 59.127 45.455 0.00 0.00 0.00 3.01
6148 8951 2.622064 AACGTGAGGCAAAGAAGACT 57.378 45.000 0.00 0.00 0.00 3.24
6149 8952 1.871080 ACGTGAGGCAAAGAAGACTG 58.129 50.000 0.00 0.00 0.00 3.51
6150 8953 0.514691 CGTGAGGCAAAGAAGACTGC 59.485 55.000 0.00 0.00 37.86 4.40
6154 8957 2.563427 GCAAAGAAGACTGCCGGC 59.437 61.111 22.73 22.73 32.18 6.13
6155 8958 1.968540 GCAAAGAAGACTGCCGGCT 60.969 57.895 29.70 8.29 32.18 5.52
6156 8959 1.871772 CAAAGAAGACTGCCGGCTG 59.128 57.895 29.48 29.48 0.00 4.85
6157 8960 0.886490 CAAAGAAGACTGCCGGCTGT 60.886 55.000 35.60 35.60 0.00 4.40
6158 8961 0.179018 AAAGAAGACTGCCGGCTGTT 60.179 50.000 35.37 23.31 0.00 3.16
6159 8962 0.179018 AAGAAGACTGCCGGCTGTTT 60.179 50.000 35.37 28.63 0.00 2.83
6160 8963 0.886490 AGAAGACTGCCGGCTGTTTG 60.886 55.000 35.37 18.71 0.00 2.93
6161 8964 2.463675 GAAGACTGCCGGCTGTTTGC 62.464 60.000 35.37 26.61 41.94 3.68
6170 8973 2.671619 GCTGTTTGCCGCCTACCA 60.672 61.111 0.00 0.00 35.15 3.25
6171 8974 2.690778 GCTGTTTGCCGCCTACCAG 61.691 63.158 0.00 0.00 35.15 4.00
6172 8975 2.033448 TGTTTGCCGCCTACCAGG 59.967 61.111 0.00 0.00 38.80 4.45
6173 8976 2.750237 GTTTGCCGCCTACCAGGG 60.750 66.667 0.00 0.00 35.37 4.45
6180 8983 3.712907 GCCTACCAGGGCCGTTGA 61.713 66.667 3.14 0.00 45.92 3.18
6181 8984 3.074281 CCTACCAGGGCCGTTGAA 58.926 61.111 3.14 0.00 0.00 2.69
6182 8985 1.078426 CCTACCAGGGCCGTTGAAG 60.078 63.158 3.14 3.03 0.00 3.02
6183 8986 1.078426 CTACCAGGGCCGTTGAAGG 60.078 63.158 3.14 0.50 0.00 3.46
6184 8987 2.536997 CTACCAGGGCCGTTGAAGGG 62.537 65.000 3.14 0.00 0.00 3.95
6190 8993 3.365265 GCCGTTGAAGGGCCTGTG 61.365 66.667 17.54 0.00 42.98 3.66
6191 8994 3.365265 CCGTTGAAGGGCCTGTGC 61.365 66.667 6.92 0.00 0.00 4.57
6192 8995 3.726517 CGTTGAAGGGCCTGTGCG 61.727 66.667 6.92 6.22 38.85 5.34
6193 8996 2.281484 GTTGAAGGGCCTGTGCGA 60.281 61.111 6.92 0.00 38.85 5.10
6194 8997 2.032528 TTGAAGGGCCTGTGCGAG 59.967 61.111 6.92 0.00 38.85 5.03
6195 8998 4.704833 TGAAGGGCCTGTGCGAGC 62.705 66.667 6.92 0.00 38.85 5.03
6196 8999 4.400961 GAAGGGCCTGTGCGAGCT 62.401 66.667 6.92 0.00 38.85 4.09
6197 9000 4.711949 AAGGGCCTGTGCGAGCTG 62.712 66.667 6.92 0.00 38.85 4.24
6200 9003 4.996434 GGCCTGTGCGAGCTGTGT 62.996 66.667 0.00 0.00 38.85 3.72
6201 9004 3.720193 GCCTGTGCGAGCTGTGTG 61.720 66.667 0.00 0.00 0.00 3.82
6202 9005 3.720193 CCTGTGCGAGCTGTGTGC 61.720 66.667 0.00 0.00 43.29 4.57
6219 9022 4.659172 CTCGCACAGGGCCCCAAA 62.659 66.667 21.43 0.00 40.31 3.28
6220 9023 4.211330 TCGCACAGGGCCCCAAAA 62.211 61.111 21.43 0.00 40.31 2.44
6221 9024 3.230245 CGCACAGGGCCCCAAAAA 61.230 61.111 21.43 0.00 40.31 1.94
6222 9025 2.582493 CGCACAGGGCCCCAAAAAT 61.582 57.895 21.43 0.00 40.31 1.82
6223 9026 1.760527 GCACAGGGCCCCAAAAATT 59.239 52.632 21.43 0.00 36.11 1.82
6224 9027 0.321564 GCACAGGGCCCCAAAAATTC 60.322 55.000 21.43 0.00 36.11 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.374220 TCTGAGCATTTGTTTTGGCAG 57.626 42.857 0.00 0.00 0.00 4.85
68 69 3.965379 ATTTCTGCCAAATGTGCATCA 57.035 38.095 0.00 0.00 38.22 3.07
94 95 3.717294 GAGGAGAGGCGGGCCAAA 61.717 66.667 12.97 0.00 38.92 3.28
101 102 4.527583 GGCTGCAGAGGAGAGGCG 62.528 72.222 20.43 0.00 0.00 5.52
108 109 1.654954 GCAATGACAGGCTGCAGAGG 61.655 60.000 20.43 8.08 36.09 3.69
134 135 2.486203 TGGCTGCTATACAAAAACCGTG 59.514 45.455 0.00 0.00 0.00 4.94
171 172 4.399004 AGGAGCATCTACAATCACAGTC 57.601 45.455 0.00 0.00 33.73 3.51
183 184 7.397761 ACTTGTACTAGTAAAGAAGGAGCATCT 59.602 37.037 21.50 2.51 33.73 2.90
294 295 5.303078 AGAGACAGAGAGCTAGACTAGAGAG 59.697 48.000 13.91 0.00 0.00 3.20
301 302 2.542595 GCGTAGAGACAGAGAGCTAGAC 59.457 54.545 0.00 0.00 0.00 2.59
317 318 8.085296 AGTGGAGAGAAATAAATATGAGCGTAG 58.915 37.037 0.00 0.00 0.00 3.51
397 406 8.078060 TGATATAACTGATGTTTGGTCAGAGA 57.922 34.615 9.86 0.00 44.57 3.10
398 407 8.200120 TCTGATATAACTGATGTTTGGTCAGAG 58.800 37.037 9.86 0.00 44.57 3.35
598 840 4.226168 AGATGGAAAAGAGGGACTGTTAGG 59.774 45.833 0.00 0.00 42.78 2.69
609 851 5.243981 TCTGCAAGAAGAGATGGAAAAGAG 58.756 41.667 0.00 0.00 42.31 2.85
730 978 8.630037 CCCTAAACCATAATCCAAAACTATGAC 58.370 37.037 0.00 0.00 0.00 3.06
736 984 7.123697 AGCTAACCCTAAACCATAATCCAAAAC 59.876 37.037 0.00 0.00 0.00 2.43
840 1088 5.537722 AGCAGGGATCTCTAGATCTGCAAG 61.538 50.000 24.54 12.10 46.49 4.01
841 1089 3.693653 AGCAGGGATCTCTAGATCTGCAA 60.694 47.826 24.54 0.00 46.49 4.08
842 1090 2.158340 AGCAGGGATCTCTAGATCTGCA 60.158 50.000 24.54 0.00 46.49 4.41
847 1095 3.326946 ACACAGCAGGGATCTCTAGAT 57.673 47.619 0.00 0.00 37.51 1.98
848 1096 2.762887 CAACACAGCAGGGATCTCTAGA 59.237 50.000 0.00 0.00 0.00 2.43
849 1097 2.499289 ACAACACAGCAGGGATCTCTAG 59.501 50.000 0.00 0.00 0.00 2.43
850 1098 2.234661 CACAACACAGCAGGGATCTCTA 59.765 50.000 0.00 0.00 0.00 2.43
851 1099 1.002888 CACAACACAGCAGGGATCTCT 59.997 52.381 0.00 0.00 0.00 3.10
852 1100 1.002430 TCACAACACAGCAGGGATCTC 59.998 52.381 0.00 0.00 0.00 2.75
853 1101 1.059098 TCACAACACAGCAGGGATCT 58.941 50.000 0.00 0.00 0.00 2.75
854 1102 2.119801 ATCACAACACAGCAGGGATC 57.880 50.000 0.00 0.00 0.00 3.36
855 1103 2.592102 AATCACAACACAGCAGGGAT 57.408 45.000 0.00 0.00 0.00 3.85
900 1148 1.202132 CGAAGAGAGAGGAGCACGAAG 60.202 57.143 0.00 0.00 0.00 3.79
993 1242 0.030773 GCGGTCGATGCATCTGTAGA 59.969 55.000 23.73 11.15 0.00 2.59
1028 1277 5.171339 AGTTTCAGCACCATCTGTTCTAT 57.829 39.130 0.00 0.00 35.63 1.98
1030 1279 3.406764 GAGTTTCAGCACCATCTGTTCT 58.593 45.455 0.00 0.00 35.63 3.01
1031 1280 2.158449 CGAGTTTCAGCACCATCTGTTC 59.842 50.000 0.00 0.00 35.63 3.18
1033 1282 1.070758 ACGAGTTTCAGCACCATCTGT 59.929 47.619 0.00 0.00 35.63 3.41
1055 1304 7.224167 AGAGTTTGCTGTAGTTTGTACTAACAC 59.776 37.037 19.88 15.55 38.55 3.32
1090 1339 9.504708 CTAATGCATCCATAGAAAGAGAGAAAT 57.495 33.333 0.00 0.00 0.00 2.17
1161 1411 7.545362 AATATTGAATTGTCTCTGTCCTTCG 57.455 36.000 0.00 0.00 0.00 3.79
1209 1459 2.309528 TGTTTCGTGCAGTTCTGAGT 57.690 45.000 3.84 0.00 0.00 3.41
1258 1508 7.367285 TGTTGGTATTTTTAAGCTAAGCACTG 58.633 34.615 0.00 0.00 0.00 3.66
1266 1521 9.830975 AATTGAAACTGTTGGTATTTTTAAGCT 57.169 25.926 0.00 0.00 0.00 3.74
1276 1531 7.499563 TGCACTACTAAATTGAAACTGTTGGTA 59.500 33.333 0.00 0.00 0.00 3.25
1302 1557 6.895782 TGTAGTAGTTGGCATTTTAGGCTAT 58.104 36.000 0.00 0.00 34.73 2.97
1366 1621 6.490040 TGCTAAGCACTTCTAAATTGGAGTTT 59.510 34.615 0.00 0.00 31.71 2.66
1424 1679 9.503399 AGCTTATTTTTACACTAAGCACTACTT 57.497 29.630 13.99 0.00 46.20 2.24
2218 4676 1.152567 CCCCAGAACCACCAAAGCA 60.153 57.895 0.00 0.00 0.00 3.91
2262 4721 1.144708 ACATCACATGTGTGGTTGGGA 59.855 47.619 24.63 3.87 45.65 4.37
2352 4814 1.559368 AACAGCAATGCATGGCCTAA 58.441 45.000 22.73 0.00 0.00 2.69
2415 4877 1.912763 TGCCCCCACCATTCTTTGC 60.913 57.895 0.00 0.00 0.00 3.68
2434 4896 2.473816 TCACGAGCTTGTGAAGTTCTG 58.526 47.619 30.61 6.00 45.40 3.02
2578 5040 1.332686 CAAGACATGCGATGGATGGTG 59.667 52.381 3.38 0.00 33.60 4.17
2587 5049 3.531934 ACATCTGATCAAGACATGCGA 57.468 42.857 0.00 0.00 37.88 5.10
2609 5071 2.420022 CGATGTGTTCTTAGCAAAGGGG 59.580 50.000 0.00 0.00 33.22 4.79
2615 5077 6.220930 AGAGTTAAACGATGTGTTCTTAGCA 58.779 36.000 0.00 0.00 40.84 3.49
2630 5092 8.148807 AGAAGCTCAAAGAGAAAGAGTTAAAC 57.851 34.615 0.00 0.00 0.00 2.01
2995 5613 8.076714 TGATAGAATTCACGATGCATTTCTAC 57.923 34.615 15.20 11.12 0.00 2.59
3509 6149 2.490903 GCCAATGGCCTCATCATCATAC 59.509 50.000 14.47 0.00 44.06 2.39
3511 6151 1.629043 GCCAATGGCCTCATCATCAT 58.371 50.000 14.47 0.00 44.06 2.45
3907 6573 3.490078 GCGTGATCCCAAAGAAACACAAA 60.490 43.478 0.00 0.00 36.37 2.83
4084 6781 4.159506 TGGTTACAAAATCCATAAGCTGCC 59.840 41.667 0.00 0.00 0.00 4.85
4154 6851 3.245407 TGGTCACTGAGAGGAGAAGATCA 60.245 47.826 0.00 0.00 0.00 2.92
4191 6888 3.657634 AGCTGTGTTATGAGATATGGCG 58.342 45.455 0.00 0.00 0.00 5.69
4389 7121 9.668497 GTAATAAGAATCAACTCTAAGTGGGTT 57.332 33.333 0.00 0.00 0.00 4.11
4466 7207 2.288152 GCAGTCCAATTTTTCTTCGGCA 60.288 45.455 0.00 0.00 0.00 5.69
4484 7225 4.480667 CCATGTGGAGAGCTACAAAGCAG 61.481 52.174 0.00 0.00 44.44 4.24
4581 7328 2.345641 CGAAGTCATGCAAGAAGTACCG 59.654 50.000 0.00 0.00 0.00 4.02
4629 7379 1.669211 GGGAACAACTCGAGAACGGAG 60.669 57.143 21.68 4.34 40.21 4.63
4702 7455 3.318275 GTCCCTGTTTTCTTTGAGTTCCC 59.682 47.826 0.00 0.00 0.00 3.97
4773 7526 2.412591 ACTCCCATCATTAGGGTCCTG 58.587 52.381 0.00 0.00 46.82 3.86
5185 7948 8.044060 ACATAGACACATGGATAAACAAACAG 57.956 34.615 0.00 0.00 0.00 3.16
5311 8087 1.002134 AGACCAACCCAATGGCTCG 60.002 57.895 0.00 0.00 44.75 5.03
5390 8168 5.362717 AGGTTCGATACATGGTCACATAGAA 59.637 40.000 0.00 0.00 34.99 2.10
5424 8202 3.873952 AGCGCTAGAATAAAGCCAGAAAG 59.126 43.478 8.99 0.00 36.60 2.62
5662 8463 0.813210 CTGGAGAGCCGAGCCATTTC 60.813 60.000 0.00 0.00 36.79 2.17
5699 8500 1.878522 GTGTGTGAGCTATCCGGCG 60.879 63.158 0.00 0.00 37.29 6.46
5998 8799 3.986996 TGAGAACAGCCATCATGAAGA 57.013 42.857 0.00 0.00 0.00 2.87
6094 8897 7.232941 TGAGTGCTAGTTAGTAGAGAGGTTTTT 59.767 37.037 0.00 0.00 0.00 1.94
6095 8898 6.720288 TGAGTGCTAGTTAGTAGAGAGGTTTT 59.280 38.462 0.00 0.00 0.00 2.43
6096 8899 6.246919 TGAGTGCTAGTTAGTAGAGAGGTTT 58.753 40.000 0.00 0.00 0.00 3.27
6097 8900 5.817784 TGAGTGCTAGTTAGTAGAGAGGTT 58.182 41.667 0.00 0.00 0.00 3.50
6098 8901 5.045432 ACTGAGTGCTAGTTAGTAGAGAGGT 60.045 44.000 0.00 0.00 0.00 3.85
6099 8902 5.433526 ACTGAGTGCTAGTTAGTAGAGAGG 58.566 45.833 0.00 0.00 0.00 3.69
6100 8903 7.929245 TCATACTGAGTGCTAGTTAGTAGAGAG 59.071 40.741 0.00 0.00 0.00 3.20
6101 8904 7.793036 TCATACTGAGTGCTAGTTAGTAGAGA 58.207 38.462 0.00 0.00 0.00 3.10
6102 8905 7.929245 TCTCATACTGAGTGCTAGTTAGTAGAG 59.071 40.741 0.00 0.00 44.58 2.43
6103 8906 7.793036 TCTCATACTGAGTGCTAGTTAGTAGA 58.207 38.462 0.00 0.00 44.58 2.59
6104 8907 8.439993 TTCTCATACTGAGTGCTAGTTAGTAG 57.560 38.462 0.00 0.00 44.58 2.57
6105 8908 8.675504 GTTTCTCATACTGAGTGCTAGTTAGTA 58.324 37.037 0.00 0.00 44.58 1.82
6106 8909 7.540299 GTTTCTCATACTGAGTGCTAGTTAGT 58.460 38.462 0.00 0.00 44.58 2.24
6107 8910 6.689241 CGTTTCTCATACTGAGTGCTAGTTAG 59.311 42.308 0.00 0.00 44.58 2.34
6108 8911 6.150641 ACGTTTCTCATACTGAGTGCTAGTTA 59.849 38.462 0.00 0.00 44.58 2.24
6109 8912 5.047943 ACGTTTCTCATACTGAGTGCTAGTT 60.048 40.000 0.00 0.00 44.58 2.24
6110 8913 4.459685 ACGTTTCTCATACTGAGTGCTAGT 59.540 41.667 0.00 0.00 44.58 2.57
6111 8914 4.795795 CACGTTTCTCATACTGAGTGCTAG 59.204 45.833 0.00 0.00 44.58 3.42
6112 8915 4.457949 TCACGTTTCTCATACTGAGTGCTA 59.542 41.667 0.00 0.00 44.58 3.49
6113 8916 3.255888 TCACGTTTCTCATACTGAGTGCT 59.744 43.478 0.00 0.00 44.58 4.40
6114 8917 3.575630 TCACGTTTCTCATACTGAGTGC 58.424 45.455 0.00 0.00 44.58 4.40
6115 8918 4.169508 CCTCACGTTTCTCATACTGAGTG 58.830 47.826 0.00 0.00 44.58 3.51
6116 8919 3.367498 GCCTCACGTTTCTCATACTGAGT 60.367 47.826 4.21 0.00 44.58 3.41
6117 8920 3.182967 GCCTCACGTTTCTCATACTGAG 58.817 50.000 0.00 0.00 45.59 3.35
6118 8921 2.560981 TGCCTCACGTTTCTCATACTGA 59.439 45.455 0.00 0.00 0.00 3.41
6119 8922 2.959516 TGCCTCACGTTTCTCATACTG 58.040 47.619 0.00 0.00 0.00 2.74
6120 8923 3.678056 TTGCCTCACGTTTCTCATACT 57.322 42.857 0.00 0.00 0.00 2.12
6121 8924 3.994392 TCTTTGCCTCACGTTTCTCATAC 59.006 43.478 0.00 0.00 0.00 2.39
6122 8925 4.265904 TCTTTGCCTCACGTTTCTCATA 57.734 40.909 0.00 0.00 0.00 2.15
6123 8926 3.126001 TCTTTGCCTCACGTTTCTCAT 57.874 42.857 0.00 0.00 0.00 2.90
6124 8927 2.613026 TCTTTGCCTCACGTTTCTCA 57.387 45.000 0.00 0.00 0.00 3.27
6125 8928 3.059529 GTCTTCTTTGCCTCACGTTTCTC 60.060 47.826 0.00 0.00 0.00 2.87
6126 8929 2.872858 GTCTTCTTTGCCTCACGTTTCT 59.127 45.455 0.00 0.00 0.00 2.52
6127 8930 2.872858 AGTCTTCTTTGCCTCACGTTTC 59.127 45.455 0.00 0.00 0.00 2.78
6128 8931 2.614057 CAGTCTTCTTTGCCTCACGTTT 59.386 45.455 0.00 0.00 0.00 3.60
6129 8932 2.213499 CAGTCTTCTTTGCCTCACGTT 58.787 47.619 0.00 0.00 0.00 3.99
6130 8933 1.871080 CAGTCTTCTTTGCCTCACGT 58.129 50.000 0.00 0.00 0.00 4.49
6131 8934 0.514691 GCAGTCTTCTTTGCCTCACG 59.485 55.000 0.00 0.00 34.28 4.35
6137 8940 1.968540 AGCCGGCAGTCTTCTTTGC 60.969 57.895 31.54 0.00 39.56 3.68
6138 8941 0.886490 ACAGCCGGCAGTCTTCTTTG 60.886 55.000 31.54 17.15 0.00 2.77
6139 8942 0.179018 AACAGCCGGCAGTCTTCTTT 60.179 50.000 31.54 7.60 0.00 2.52
6140 8943 0.179018 AAACAGCCGGCAGTCTTCTT 60.179 50.000 31.54 15.13 0.00 2.52
6141 8944 0.886490 CAAACAGCCGGCAGTCTTCT 60.886 55.000 31.54 8.89 0.00 2.85
6142 8945 1.576421 CAAACAGCCGGCAGTCTTC 59.424 57.895 31.54 0.00 0.00 2.87
6143 8946 2.555547 GCAAACAGCCGGCAGTCTT 61.556 57.895 31.54 19.47 37.23 3.01
6144 8947 2.980233 GCAAACAGCCGGCAGTCT 60.980 61.111 31.54 11.60 37.23 3.24
6153 8956 2.671619 TGGTAGGCGGCAAACAGC 60.672 61.111 13.08 3.41 44.65 4.40
6154 8957 2.040544 CCTGGTAGGCGGCAAACAG 61.041 63.158 13.08 15.10 0.00 3.16
6155 8958 2.033448 CCTGGTAGGCGGCAAACA 59.967 61.111 13.08 5.50 0.00 2.83
6156 8959 2.750237 CCCTGGTAGGCGGCAAAC 60.750 66.667 13.08 8.96 32.73 2.93
6157 8960 4.733542 GCCCTGGTAGGCGGCAAA 62.734 66.667 13.08 0.00 44.57 3.68
6164 8967 1.078426 CTTCAACGGCCCTGGTAGG 60.078 63.158 0.00 0.00 34.30 3.18
6165 8968 1.078426 CCTTCAACGGCCCTGGTAG 60.078 63.158 0.00 0.00 0.00 3.18
6166 8969 2.598787 CCCTTCAACGGCCCTGGTA 61.599 63.158 0.00 0.00 0.00 3.25
6167 8970 3.966543 CCCTTCAACGGCCCTGGT 61.967 66.667 0.00 0.00 0.00 4.00
6173 8976 3.365265 CACAGGCCCTTCAACGGC 61.365 66.667 0.00 0.00 46.29 5.68
6174 8977 3.365265 GCACAGGCCCTTCAACGG 61.365 66.667 0.00 0.00 0.00 4.44
6175 8978 3.726517 CGCACAGGCCCTTCAACG 61.727 66.667 0.00 0.00 36.38 4.10
6176 8979 2.281484 TCGCACAGGCCCTTCAAC 60.281 61.111 0.00 0.00 36.38 3.18
6177 8980 2.032528 CTCGCACAGGCCCTTCAA 59.967 61.111 0.00 0.00 36.38 2.69
6178 8981 4.704833 GCTCGCACAGGCCCTTCA 62.705 66.667 0.00 0.00 36.38 3.02
6179 8982 4.400961 AGCTCGCACAGGCCCTTC 62.401 66.667 0.00 0.00 36.38 3.46
6180 8983 4.711949 CAGCTCGCACAGGCCCTT 62.712 66.667 0.00 0.00 36.38 3.95
6183 8986 4.996434 ACACAGCTCGCACAGGCC 62.996 66.667 0.00 0.00 36.38 5.19
6184 8987 3.720193 CACACAGCTCGCACAGGC 61.720 66.667 0.00 0.00 0.00 4.85
6185 8988 3.720193 GCACACAGCTCGCACAGG 61.720 66.667 0.00 0.00 41.15 4.00
6202 9005 4.659172 TTTGGGGCCCTGTGCGAG 62.659 66.667 25.93 0.00 42.61 5.03
6203 9006 3.740495 TTTTTGGGGCCCTGTGCGA 62.740 57.895 25.93 0.69 42.61 5.10
6204 9007 2.110757 AATTTTTGGGGCCCTGTGCG 62.111 55.000 25.93 0.00 42.61 5.34
6205 9008 0.321564 GAATTTTTGGGGCCCTGTGC 60.322 55.000 25.93 5.04 40.16 4.57
6206 9009 3.933879 GAATTTTTGGGGCCCTGTG 57.066 52.632 25.93 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.