Multiple sequence alignment - TraesCS3B01G418900

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 TraesCS3B01G418900 chr3B 100.000 3603 0 0 916 4518 655630068 655626466 0.000000e+00 6654
1 TraesCS3B01G418900 chr3B 100.000 496 0 0 1 496 655630983 655630488 0.000000e+00 917
2 TraesCS3B01G418900 chr3B 98.347 121 2 0 1 121 405940738 405940858 3.540000e-51 213
3 TraesCS3B01G418900 chr3A 95.706 2608 88 8 1785 4389 638207213 638209799 0.000000e+00 4174
4 TraesCS3B01G418900 chr3A 91.388 987 61 11 965 1928 638206317 638207302 0.000000e+00 1330
5 TraesCS3B01G418900 chr3A 89.501 381 24 8 120 496 638205651 638206019 6.840000e-128 468
6 TraesCS3B01G418900 chr3A 97.183 71 2 0 4448 4518 638209801 638209871 2.210000e-23 121
7 TraesCS3B01G418900 chr3D 94.011 2755 114 18 1785 4516 496676358 496673632 0.000000e+00 4126
8 TraesCS3B01G418900 chr3D 91.393 1034 57 18 916 1928 496677291 496676269 0.000000e+00 1387
9 TraesCS3B01G418900 chr3D 88.295 393 23 8 110 496 496678051 496677676 2.480000e-122 449
10 TraesCS3B01G418900 chr2B 96.694 121 3 1 1 121 153123357 153123238 2.760000e-47 200
11 TraesCS3B01G418900 chr1B 96.694 121 3 1 1 121 679597261 679597380 2.760000e-47 200
12 TraesCS3B01G418900 chr7D 92.500 120 7 2 1 120 616512776 616512893 2.160000e-38 171
13 TraesCS3B01G418900 chr7B 91.667 120 8 2 1 120 93323788 93323671 1.010000e-36 165
14 TraesCS3B01G418900 chr5A 91.667 120 8 2 1 120 345752804 345752921 1.010000e-36 165
15 TraesCS3B01G418900 chr5A 91.667 120 8 2 1 120 669591499 669591382 1.010000e-36 165
16 TraesCS3B01G418900 chr4B 91.667 120 8 2 1 120 175555725 175555608 1.010000e-36 165
17 TraesCS3B01G418900 chr1A 91.667 120 8 2 1 120 74100750 74100633 1.010000e-36 165


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 TraesCS3B01G418900 chr3B 655626466 655630983 4517 True 3785.500000 6654 100.0000 1 4518 2 chr3B.!!$R1 4517
1 TraesCS3B01G418900 chr3A 638205651 638209871 4220 False 1523.250000 4174 93.4445 120 4518 4 chr3A.!!$F1 4398
2 TraesCS3B01G418900 chr3D 496673632 496678051 4419 True 1987.333333 4126 91.2330 110 4516 3 chr3D.!!$R1 4406

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
156 157 0.252012 TTCCCCACATTTCCCGCATT 60.252 50.0 0.0 0.0 0.0 3.56 F
1412 1461 0.104671 GGCTCTCTCTGATCACAGGC 59.895 60.0 0.0 0.0 43.6 4.85 F
1881 1935 0.473117 AAGGTCGGGGTGAGGAAGAA 60.473 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 1959 0.108898 CCTGACCTTCTGACTGCTCG 60.109 60.000 0.00 0.00 0.00 5.03 R
2580 2688 5.188434 TCAGCATTTCTATTCTCAACTGGG 58.812 41.667 0.00 0.00 0.00 4.45 R
3857 3967 0.606944 GACCATGCCACGGTTAACCA 60.607 55.000 24.14 4.72 36.69 3.67 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
25 26 7.545362 AACACTATTGCAAGATCTACATCAC 57.455 36.000 4.94 0.00 0.00 3.06
26 27 6.643388 ACACTATTGCAAGATCTACATCACA 58.357 36.000 4.94 0.00 0.00 3.58
27 28 7.278135 ACACTATTGCAAGATCTACATCACAT 58.722 34.615 4.94 0.00 0.00 3.21
28 29 7.772292 ACACTATTGCAAGATCTACATCACATT 59.228 33.333 4.94 0.00 0.00 2.71
29 30 8.618677 CACTATTGCAAGATCTACATCACATTT 58.381 33.333 4.94 0.00 0.00 2.32
30 31 9.182214 ACTATTGCAAGATCTACATCACATTTT 57.818 29.630 4.94 0.00 0.00 1.82
32 33 8.697846 ATTGCAAGATCTACATCACATTTTTG 57.302 30.769 4.94 0.00 0.00 2.44
33 34 6.623486 TGCAAGATCTACATCACATTTTTGG 58.377 36.000 0.00 0.00 0.00 3.28
34 35 6.209192 TGCAAGATCTACATCACATTTTTGGT 59.791 34.615 0.00 0.00 0.00 3.67
35 36 7.092716 GCAAGATCTACATCACATTTTTGGTT 58.907 34.615 0.00 0.00 0.00 3.67
36 37 7.062605 GCAAGATCTACATCACATTTTTGGTTG 59.937 37.037 0.00 0.00 0.00 3.77
37 38 7.161773 AGATCTACATCACATTTTTGGTTGG 57.838 36.000 0.00 0.00 0.00 3.77
38 39 6.721208 AGATCTACATCACATTTTTGGTTGGT 59.279 34.615 0.00 0.00 0.00 3.67
39 40 7.888021 AGATCTACATCACATTTTTGGTTGGTA 59.112 33.333 0.00 0.00 0.00 3.25
40 41 8.593945 ATCTACATCACATTTTTGGTTGGTAT 57.406 30.769 0.00 0.00 0.00 2.73
41 42 8.415950 TCTACATCACATTTTTGGTTGGTATT 57.584 30.769 0.00 0.00 0.00 1.89
42 43 8.865090 TCTACATCACATTTTTGGTTGGTATTT 58.135 29.630 0.00 0.00 0.00 1.40
43 44 9.487790 CTACATCACATTTTTGGTTGGTATTTT 57.512 29.630 0.00 0.00 0.00 1.82
57 58 9.841295 TGGTTGGTATTTTATACTGACTAATCC 57.159 33.333 0.00 0.00 0.00 3.01
58 59 9.281371 GGTTGGTATTTTATACTGACTAATCCC 57.719 37.037 0.00 0.00 0.00 3.85
59 60 9.841295 GTTGGTATTTTATACTGACTAATCCCA 57.159 33.333 0.00 0.00 0.00 4.37
66 67 9.967451 TTTTATACTGACTAATCCCATGTTCAA 57.033 29.630 0.00 0.00 0.00 2.69
67 68 9.967451 TTTATACTGACTAATCCCATGTTCAAA 57.033 29.630 0.00 0.00 0.00 2.69
68 69 9.967451 TTATACTGACTAATCCCATGTTCAAAA 57.033 29.630 0.00 0.00 0.00 2.44
69 70 8.877864 ATACTGACTAATCCCATGTTCAAAAA 57.122 30.769 0.00 0.00 0.00 1.94
91 92 7.707624 AAAAATGTCATGGCTATTCTCTTGA 57.292 32.000 0.00 0.00 0.00 3.02
92 93 7.893124 AAAATGTCATGGCTATTCTCTTGAT 57.107 32.000 0.00 0.00 0.00 2.57
93 94 8.985315 AAAATGTCATGGCTATTCTCTTGATA 57.015 30.769 0.00 0.00 0.00 2.15
94 95 8.618702 AAATGTCATGGCTATTCTCTTGATAG 57.381 34.615 0.00 0.00 0.00 2.08
95 96 5.545588 TGTCATGGCTATTCTCTTGATAGC 58.454 41.667 0.00 7.41 41.71 2.97
96 97 5.306419 TGTCATGGCTATTCTCTTGATAGCT 59.694 40.000 13.79 0.00 42.01 3.32
97 98 6.494835 TGTCATGGCTATTCTCTTGATAGCTA 59.505 38.462 13.79 9.59 42.01 3.32
98 99 7.015584 TGTCATGGCTATTCTCTTGATAGCTAA 59.984 37.037 13.79 5.64 42.01 3.09
99 100 7.875041 GTCATGGCTATTCTCTTGATAGCTAAA 59.125 37.037 13.79 0.00 42.01 1.85
100 101 8.600668 TCATGGCTATTCTCTTGATAGCTAAAT 58.399 33.333 13.79 0.00 42.01 1.40
101 102 9.881649 CATGGCTATTCTCTTGATAGCTAAATA 57.118 33.333 13.79 0.00 42.01 1.40
103 104 9.881649 TGGCTATTCTCTTGATAGCTAAATATG 57.118 33.333 13.79 0.00 42.01 1.78
104 105 9.883142 GGCTATTCTCTTGATAGCTAAATATGT 57.117 33.333 13.79 0.00 42.01 2.29
136 137 2.493907 TTACCCGCAAATTTGGCCGC 62.494 55.000 19.47 4.31 0.00 6.53
156 157 0.252012 TTCCCCACATTTCCCGCATT 60.252 50.000 0.00 0.00 0.00 3.56
162 163 1.203052 CACATTTCCCGCATTGAAGCT 59.797 47.619 0.00 0.00 0.00 3.74
227 228 2.018515 TCACAGTTTGAAACCGAACCC 58.981 47.619 4.14 0.00 0.00 4.11
230 231 2.686405 ACAGTTTGAAACCGAACCCTTC 59.314 45.455 4.14 0.00 0.00 3.46
253 254 2.425312 AGTTTTGACATTGACAACGGCA 59.575 40.909 1.00 0.00 0.00 5.69
254 255 2.772568 TTTGACATTGACAACGGCAG 57.227 45.000 1.00 0.00 0.00 4.85
255 256 0.950836 TTGACATTGACAACGGCAGG 59.049 50.000 0.00 0.00 0.00 4.85
256 257 1.210155 GACATTGACAACGGCAGGC 59.790 57.895 0.00 0.00 0.00 4.85
257 258 1.514678 GACATTGACAACGGCAGGCA 61.515 55.000 0.00 0.00 0.00 4.75
364 374 1.729276 CATGAATCGCCGTGCCAAT 59.271 52.632 0.00 0.00 0.00 3.16
406 418 0.391927 CGCGATACAAAACCCAGGGA 60.392 55.000 14.54 0.00 0.00 4.20
436 460 2.041405 CTCCACCTCCTCCTCCCC 60.041 72.222 0.00 0.00 0.00 4.81
437 461 3.695825 TCCACCTCCTCCTCCCCC 61.696 72.222 0.00 0.00 0.00 5.40
1136 1160 4.657824 CGTCGTTGCGTCCTGGGT 62.658 66.667 0.00 0.00 0.00 4.51
1231 1260 0.533032 CTCTTCCGTCCCTGAACTCC 59.467 60.000 0.00 0.00 0.00 3.85
1240 1269 2.043992 TCCCTGAACTCCGAAGTTTCA 58.956 47.619 0.00 0.00 45.80 2.69
1244 1273 3.467803 CTGAACTCCGAAGTTTCACCTT 58.532 45.455 0.00 0.00 45.80 3.50
1245 1274 4.502604 CCTGAACTCCGAAGTTTCACCTTA 60.503 45.833 0.00 0.00 45.80 2.69
1246 1275 5.223449 TGAACTCCGAAGTTTCACCTTAT 57.777 39.130 0.00 0.00 45.80 1.73
1247 1276 4.994852 TGAACTCCGAAGTTTCACCTTATG 59.005 41.667 0.00 0.00 45.80 1.90
1248 1277 4.884668 ACTCCGAAGTTTCACCTTATGA 57.115 40.909 0.00 0.00 34.65 2.15
1249 1278 5.422214 ACTCCGAAGTTTCACCTTATGAT 57.578 39.130 0.00 0.00 37.11 2.45
1314 1354 2.097466 CGGTAGATGTTTGGTGGATTGC 59.903 50.000 0.00 0.00 0.00 3.56
1394 1439 2.097538 CGTATGCGGTTGTTGCGG 59.902 61.111 0.00 0.00 34.24 5.69
1395 1440 2.202427 GTATGCGGTTGTTGCGGC 60.202 61.111 0.00 0.00 34.24 6.53
1396 1441 2.359354 TATGCGGTTGTTGCGGCT 60.359 55.556 0.00 0.00 35.98 5.52
1397 1442 2.395360 TATGCGGTTGTTGCGGCTC 61.395 57.895 0.00 0.00 35.98 4.70
1398 1443 2.796483 TATGCGGTTGTTGCGGCTCT 62.796 55.000 0.00 0.00 35.98 4.09
1399 1444 4.090057 GCGGTTGTTGCGGCTCTC 62.090 66.667 0.00 0.00 0.00 3.20
1400 1445 2.357517 CGGTTGTTGCGGCTCTCT 60.358 61.111 0.00 0.00 0.00 3.10
1401 1446 2.383527 CGGTTGTTGCGGCTCTCTC 61.384 63.158 0.00 0.00 0.00 3.20
1412 1461 0.104671 GGCTCTCTCTGATCACAGGC 59.895 60.000 0.00 0.00 43.60 4.85
1449 1499 1.681825 GTTGCCGAAATTTCCACGTC 58.318 50.000 12.54 0.00 0.00 4.34
1459 1510 1.563111 TTTCCACGTCGTGTTCTGTC 58.437 50.000 23.01 0.00 0.00 3.51
1535 1589 4.984295 TGACTGGGATCACATTTTCTTCA 58.016 39.130 0.00 0.00 0.00 3.02
1537 1591 6.012113 TGACTGGGATCACATTTTCTTCATT 58.988 36.000 0.00 0.00 0.00 2.57
1563 1617 1.229625 TGCAGATGGTGGAGACCCT 60.230 57.895 0.00 0.00 42.34 4.34
1659 1713 2.372264 GAGCATGAGGAGAATTTGGCA 58.628 47.619 0.00 0.00 0.00 4.92
1691 1745 5.518812 TGACACATGTGTAAAACTTGATGC 58.481 37.500 30.63 14.17 45.05 3.91
1735 1789 1.467734 CAGTGCTGCAGGAAGATGAAC 59.532 52.381 17.12 0.00 0.00 3.18
1741 1795 2.740981 CTGCAGGAAGATGAACTGTGTC 59.259 50.000 5.57 0.00 34.79 3.67
1753 1807 3.843619 TGAACTGTGTCCCAAGGATGATA 59.156 43.478 0.00 0.00 32.73 2.15
1755 1809 2.505819 ACTGTGTCCCAAGGATGATACC 59.494 50.000 0.00 0.00 32.73 2.73
1756 1810 1.843851 TGTGTCCCAAGGATGATACCC 59.156 52.381 0.00 0.00 32.73 3.69
1757 1811 1.843851 GTGTCCCAAGGATGATACCCA 59.156 52.381 0.00 0.00 32.73 4.51
1777 1831 3.128242 CCAAAGTGATGACATGGAAGCTC 59.872 47.826 0.00 0.00 34.69 4.09
1781 1835 5.627182 AGTGATGACATGGAAGCTCTAAT 57.373 39.130 0.00 0.00 0.00 1.73
1782 1836 6.737720 AGTGATGACATGGAAGCTCTAATA 57.262 37.500 0.00 0.00 0.00 0.98
1783 1837 6.757237 AGTGATGACATGGAAGCTCTAATAG 58.243 40.000 0.00 0.00 0.00 1.73
1793 1847 5.417266 TGGAAGCTCTAATAGAGGATGATCG 59.583 44.000 17.99 0.00 42.54 3.69
1800 1854 7.701924 GCTCTAATAGAGGATGATCGAATTGAG 59.298 40.741 17.99 0.00 42.54 3.02
1806 1860 2.474359 GGATGATCGAATTGAGCTGTCG 59.526 50.000 0.00 0.00 32.98 4.35
1819 1873 2.525629 TGTCGGAAGGTCAGGGCA 60.526 61.111 0.00 0.00 0.00 5.36
1821 1875 1.376037 GTCGGAAGGTCAGGGCAAG 60.376 63.158 0.00 0.00 0.00 4.01
1831 1885 1.609072 GTCAGGGCAAGGAACAAACTC 59.391 52.381 0.00 0.00 0.00 3.01
1838 1892 3.826729 GGCAAGGAACAAACTCTAACCAT 59.173 43.478 0.00 0.00 0.00 3.55
1880 1934 0.903454 GAAGGTCGGGGTGAGGAAGA 60.903 60.000 0.00 0.00 0.00 2.87
1881 1935 0.473117 AAGGTCGGGGTGAGGAAGAA 60.473 55.000 0.00 0.00 0.00 2.52
1883 1937 1.192803 GGTCGGGGTGAGGAAGAAGT 61.193 60.000 0.00 0.00 0.00 3.01
1888 1942 1.003696 GGGGTGAGGAAGAAGTTCTGG 59.996 57.143 6.06 0.00 32.72 3.86
1905 1959 3.559069 TCTGGCCAAGGATGATCAAATC 58.441 45.455 7.01 0.00 0.00 2.17
1916 2024 3.874392 TGATCAAATCGAGCAGTCAGA 57.126 42.857 0.00 0.00 34.35 3.27
2020 2128 1.675310 CCAGCAAGATTGGCACGGA 60.675 57.895 0.00 0.00 0.00 4.69
2031 2139 1.749258 GGCACGGATTGTTCCTCCC 60.749 63.158 0.00 0.00 40.17 4.30
2097 2205 2.237392 GGATGCCTCTAGTCAAACTGGT 59.763 50.000 0.00 0.00 0.00 4.00
2580 2688 5.220567 GGAAAAGATGCTCGAGAACTTGATC 60.221 44.000 18.75 16.52 0.00 2.92
3168 3278 5.104259 AGACCAACTTGTCCTGGATAATC 57.896 43.478 6.33 1.46 35.83 1.75
3189 3299 7.559590 AATCTCATACTCAGGTTTGTATTGC 57.440 36.000 0.00 0.00 0.00 3.56
3219 3329 2.231964 AGTTTCATGGATTTGCATGCGT 59.768 40.909 14.09 0.88 0.00 5.24
3227 3337 5.422666 TGGATTTGCATGCGTATTAAGAG 57.577 39.130 14.09 0.00 0.00 2.85
3252 3362 4.455533 GCATGATATTGCTTGGGACGATTA 59.544 41.667 0.00 0.00 39.57 1.75
3521 3631 7.773224 CCTCCATTTTGGTAATACAGTGATGTA 59.227 37.037 0.00 0.00 39.03 2.29
3665 3775 7.120716 TCATCATTGATCTCAAATTTGGAGGA 58.879 34.615 17.90 13.40 39.55 3.71
3722 3832 4.870363 TGAAGTCATTTTAAAGGTGCAGC 58.130 39.130 8.11 8.11 0.00 5.25
3831 3941 1.086696 CTACCTGGAAACCATGTGCG 58.913 55.000 0.00 0.00 34.41 5.34
3857 3967 1.002888 CTGGAGCCGGCAATCATAGAT 59.997 52.381 31.54 3.33 0.00 1.98
4033 4160 4.022068 CCTCCACATTGTGTTGCTTACAAT 60.022 41.667 15.34 7.62 46.54 2.71
4034 4161 5.509501 CCTCCACATTGTGTTGCTTACAATT 60.510 40.000 15.34 2.61 44.04 2.32
4035 4162 6.294453 CCTCCACATTGTGTTGCTTACAATTA 60.294 38.462 15.34 0.00 44.04 1.40
4036 4163 6.442952 TCCACATTGTGTTGCTTACAATTAC 58.557 36.000 15.34 0.00 44.04 1.89
4037 4164 6.039829 TCCACATTGTGTTGCTTACAATTACA 59.960 34.615 15.34 0.00 44.04 2.41
4038 4165 6.699204 CCACATTGTGTTGCTTACAATTACAA 59.301 34.615 15.34 11.37 44.04 2.41
4039 4166 7.384660 CCACATTGTGTTGCTTACAATTACAAT 59.615 33.333 15.34 13.74 46.26 2.71
4040 4167 8.763356 CACATTGTGTTGCTTACAATTACAATT 58.237 29.630 8.69 9.11 44.81 2.32
4041 4168 9.323985 ACATTGTGTTGCTTACAATTACAATTT 57.676 25.926 15.53 10.52 44.81 1.82
4044 4171 9.803315 TTGTGTTGCTTACAATTACAATTTACA 57.197 25.926 7.19 0.00 39.09 2.41
4045 4172 9.803315 TGTGTTGCTTACAATTACAATTTACAA 57.197 25.926 0.00 0.00 38.80 2.41
4047 4174 9.469807 TGTTGCTTACAATTACAATTTACAAGG 57.530 29.630 0.00 0.00 38.27 3.61
4048 4175 8.432359 GTTGCTTACAATTACAATTTACAAGGC 58.568 33.333 0.00 0.00 38.27 4.35
4049 4176 7.661968 TGCTTACAATTACAATTTACAAGGCA 58.338 30.769 0.00 0.00 0.00 4.75
4050 4177 7.812191 TGCTTACAATTACAATTTACAAGGCAG 59.188 33.333 0.00 0.00 0.00 4.85
4051 4178 7.812669 GCTTACAATTACAATTTACAAGGCAGT 59.187 33.333 0.00 0.00 0.00 4.40
4100 4227 1.282157 GGAAGGCACCATTGGTACTCT 59.718 52.381 8.31 3.63 32.11 3.24
4190 4320 5.760253 GCCACATATGTACAGCTGTTCTTAT 59.240 40.000 27.06 22.43 0.00 1.73
4262 4403 3.505293 AGCTTCTCAGTTGGAATTTCTGC 59.495 43.478 0.00 0.00 0.00 4.26
4263 4404 3.669023 GCTTCTCAGTTGGAATTTCTGCG 60.669 47.826 0.00 0.00 0.00 5.18
4264 4405 3.126001 TCTCAGTTGGAATTTCTGCGT 57.874 42.857 0.00 0.00 0.00 5.24
4265 4406 4.265904 TCTCAGTTGGAATTTCTGCGTA 57.734 40.909 0.00 0.00 0.00 4.42
4266 4407 4.832248 TCTCAGTTGGAATTTCTGCGTAT 58.168 39.130 0.00 0.00 0.00 3.06
4267 4408 5.972935 TCTCAGTTGGAATTTCTGCGTATA 58.027 37.500 0.00 0.00 0.00 1.47
4268 4409 6.582636 TCTCAGTTGGAATTTCTGCGTATAT 58.417 36.000 0.00 0.00 0.00 0.86
4269 4410 6.701841 TCTCAGTTGGAATTTCTGCGTATATC 59.298 38.462 0.00 0.00 0.00 1.63
4270 4411 6.582636 TCAGTTGGAATTTCTGCGTATATCT 58.417 36.000 0.00 0.00 0.00 1.98
4271 4412 7.722363 TCAGTTGGAATTTCTGCGTATATCTA 58.278 34.615 0.00 0.00 0.00 1.98
4356 4497 7.495901 TGGCATTGAAAAATACTTTTGTCTGA 58.504 30.769 0.00 0.00 34.83 3.27
4426 4567 0.321919 TCCTGCTCAGTTGACCATGC 60.322 55.000 0.00 0.00 0.00 4.06
4431 4572 2.813754 TGCTCAGTTGACCATGCTTTAC 59.186 45.455 0.00 0.00 0.00 2.01
4433 4574 3.253188 GCTCAGTTGACCATGCTTTACAA 59.747 43.478 0.00 0.00 0.00 2.41
4442 4583 4.057432 ACCATGCTTTACAATGTGCAAAC 58.943 39.130 1.06 0.00 38.96 2.93
4480 4624 2.627945 TGGATATCCACAGTTTCACGC 58.372 47.619 20.98 0.00 42.01 5.34
4482 4626 1.593006 GATATCCACAGTTTCACGCGG 59.407 52.381 12.47 0.00 0.00 6.46
4483 4627 1.017177 TATCCACAGTTTCACGCGGC 61.017 55.000 12.47 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.105588 TGTGATGTAGATCTTGCAATAGTGTT 58.894 34.615 0.00 0.00 0.00 3.32
2 3 6.643388 TGTGATGTAGATCTTGCAATAGTGT 58.357 36.000 0.00 0.00 0.00 3.55
4 5 8.743085 AAATGTGATGTAGATCTTGCAATAGT 57.257 30.769 0.00 0.00 0.00 2.12
6 7 9.791820 CAAAAATGTGATGTAGATCTTGCAATA 57.208 29.630 0.00 0.00 0.00 1.90
7 8 7.762615 CCAAAAATGTGATGTAGATCTTGCAAT 59.237 33.333 0.00 0.00 0.00 3.56
8 9 7.092079 CCAAAAATGTGATGTAGATCTTGCAA 58.908 34.615 0.00 0.00 0.00 4.08
9 10 6.209192 ACCAAAAATGTGATGTAGATCTTGCA 59.791 34.615 0.00 0.84 0.00 4.08
10 11 6.624423 ACCAAAAATGTGATGTAGATCTTGC 58.376 36.000 0.00 0.00 0.00 4.01
11 12 7.543172 CCAACCAAAAATGTGATGTAGATCTTG 59.457 37.037 0.00 0.00 0.00 3.02
12 13 7.233348 ACCAACCAAAAATGTGATGTAGATCTT 59.767 33.333 0.00 0.00 0.00 2.40
13 14 6.721208 ACCAACCAAAAATGTGATGTAGATCT 59.279 34.615 0.00 0.00 0.00 2.75
14 15 6.924111 ACCAACCAAAAATGTGATGTAGATC 58.076 36.000 0.00 0.00 0.00 2.75
15 16 6.916360 ACCAACCAAAAATGTGATGTAGAT 57.084 33.333 0.00 0.00 0.00 1.98
16 17 8.415950 AATACCAACCAAAAATGTGATGTAGA 57.584 30.769 0.00 0.00 0.00 2.59
17 18 9.487790 AAAATACCAACCAAAAATGTGATGTAG 57.512 29.630 0.00 0.00 0.00 2.74
31 32 9.841295 GGATTAGTCAGTATAAAATACCAACCA 57.159 33.333 0.00 0.00 0.00 3.67
32 33 9.281371 GGGATTAGTCAGTATAAAATACCAACC 57.719 37.037 0.00 0.00 31.82 3.77
33 34 9.841295 TGGGATTAGTCAGTATAAAATACCAAC 57.159 33.333 0.00 0.00 37.55 3.77
40 41 9.967451 TTGAACATGGGATTAGTCAGTATAAAA 57.033 29.630 0.00 0.00 0.00 1.52
41 42 9.967451 TTTGAACATGGGATTAGTCAGTATAAA 57.033 29.630 0.00 0.00 0.00 1.40
42 43 9.967451 TTTTGAACATGGGATTAGTCAGTATAA 57.033 29.630 0.00 0.00 0.00 0.98
43 44 9.967451 TTTTTGAACATGGGATTAGTCAGTATA 57.033 29.630 0.00 0.00 0.00 1.47
44 45 8.877864 TTTTTGAACATGGGATTAGTCAGTAT 57.122 30.769 0.00 0.00 0.00 2.12
67 68 7.707624 TCAAGAGAATAGCCATGACATTTTT 57.292 32.000 0.00 0.00 0.00 1.94
68 69 7.893124 ATCAAGAGAATAGCCATGACATTTT 57.107 32.000 0.00 0.00 0.00 1.82
69 70 7.174599 GCTATCAAGAGAATAGCCATGACATTT 59.825 37.037 0.00 0.00 37.80 2.32
70 71 6.654161 GCTATCAAGAGAATAGCCATGACATT 59.346 38.462 0.00 0.00 37.80 2.71
71 72 6.013553 AGCTATCAAGAGAATAGCCATGACAT 60.014 38.462 10.62 0.00 43.01 3.06
72 73 5.306419 AGCTATCAAGAGAATAGCCATGACA 59.694 40.000 10.62 0.00 43.01 3.58
73 74 5.792741 AGCTATCAAGAGAATAGCCATGAC 58.207 41.667 10.62 0.00 43.01 3.06
74 75 7.544804 TTAGCTATCAAGAGAATAGCCATGA 57.455 36.000 10.62 0.00 43.01 3.07
75 76 8.789825 ATTTAGCTATCAAGAGAATAGCCATG 57.210 34.615 10.62 0.00 43.01 3.66
77 78 9.881649 CATATTTAGCTATCAAGAGAATAGCCA 57.118 33.333 10.62 0.00 43.01 4.75
78 79 9.883142 ACATATTTAGCTATCAAGAGAATAGCC 57.117 33.333 10.62 0.00 43.01 3.93
99 100 9.290988 TGCGGGTAAAATGAAATATGTACATAT 57.709 29.630 20.49 20.49 35.63 1.78
100 101 8.678593 TGCGGGTAAAATGAAATATGTACATA 57.321 30.769 17.65 17.65 0.00 2.29
101 102 7.575414 TGCGGGTAAAATGAAATATGTACAT 57.425 32.000 13.93 13.93 0.00 2.29
102 103 7.392494 TTGCGGGTAAAATGAAATATGTACA 57.608 32.000 0.00 0.00 0.00 2.90
103 104 8.865590 ATTTGCGGGTAAAATGAAATATGTAC 57.134 30.769 0.00 0.00 0.00 2.90
104 105 9.877178 AAATTTGCGGGTAAAATGAAATATGTA 57.123 25.926 0.00 0.00 0.00 2.29
105 106 8.663911 CAAATTTGCGGGTAAAATGAAATATGT 58.336 29.630 5.01 0.00 0.00 2.29
106 107 8.121708 CCAAATTTGCGGGTAAAATGAAATATG 58.878 33.333 12.92 0.00 0.00 1.78
107 108 7.201688 GCCAAATTTGCGGGTAAAATGAAATAT 60.202 33.333 12.92 0.00 0.00 1.28
108 109 6.092807 GCCAAATTTGCGGGTAAAATGAAATA 59.907 34.615 12.92 0.00 0.00 1.40
109 110 5.106357 GCCAAATTTGCGGGTAAAATGAAAT 60.106 36.000 12.92 0.00 0.00 2.17
110 111 4.214332 GCCAAATTTGCGGGTAAAATGAAA 59.786 37.500 12.92 0.00 0.00 2.69
111 112 3.748568 GCCAAATTTGCGGGTAAAATGAA 59.251 39.130 12.92 0.00 0.00 2.57
112 113 3.330267 GCCAAATTTGCGGGTAAAATGA 58.670 40.909 12.92 0.00 0.00 2.57
113 114 2.418280 GGCCAAATTTGCGGGTAAAATG 59.582 45.455 12.92 0.00 0.00 2.32
114 115 2.705730 GGCCAAATTTGCGGGTAAAAT 58.294 42.857 12.92 0.00 0.00 1.82
115 116 1.605712 CGGCCAAATTTGCGGGTAAAA 60.606 47.619 12.92 0.00 0.00 1.52
118 119 2.995872 GCGGCCAAATTTGCGGGTA 61.996 57.895 12.92 0.00 0.00 3.69
136 137 0.684153 ATGCGGGAAATGTGGGGAAG 60.684 55.000 0.00 0.00 0.00 3.46
162 163 2.841881 ACGGGGTAGAATAGAAAGCCAA 59.158 45.455 0.00 0.00 32.32 4.52
171 172 3.644738 GGGAGAAATCACGGGGTAGAATA 59.355 47.826 0.00 0.00 0.00 1.75
209 210 2.430248 AGGGTTCGGTTTCAAACTGT 57.570 45.000 8.99 0.00 38.89 3.55
227 228 4.666176 CGTTGTCAATGTCAAAACTCGAAG 59.334 41.667 0.00 0.00 0.00 3.79
230 231 3.288242 CCGTTGTCAATGTCAAAACTCG 58.712 45.455 4.13 0.00 0.00 4.18
242 243 2.192861 CCTTGCCTGCCGTTGTCAA 61.193 57.895 0.00 0.00 0.00 3.18
255 256 4.056125 GAAACCCCGCTGCCTTGC 62.056 66.667 0.00 0.00 0.00 4.01
256 257 2.282462 AGAAACCCCGCTGCCTTG 60.282 61.111 0.00 0.00 0.00 3.61
257 258 2.282462 CAGAAACCCCGCTGCCTT 60.282 61.111 0.00 0.00 0.00 4.35
364 374 1.004560 CTCTTGTCGGCTTCCAGCA 60.005 57.895 0.00 0.00 44.75 4.41
369 380 1.833860 CGAGATCTCTTGTCGGCTTC 58.166 55.000 20.26 0.00 0.00 3.86
436 460 4.179599 GGAGGAGGAGGGGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
437 461 3.368501 TGGAGGAGGAGGGGAGGG 61.369 72.222 0.00 0.00 0.00 4.30
438 462 2.041405 GTGGAGGAGGAGGGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
439 463 2.041405 GGTGGAGGAGGAGGGGAG 60.041 72.222 0.00 0.00 0.00 4.30
440 464 2.540910 AGGTGGAGGAGGAGGGGA 60.541 66.667 0.00 0.00 0.00 4.81
441 465 2.366167 CAGGTGGAGGAGGAGGGG 60.366 72.222 0.00 0.00 0.00 4.79
442 466 3.086600 GCAGGTGGAGGAGGAGGG 61.087 72.222 0.00 0.00 0.00 4.30
443 467 3.086600 GGCAGGTGGAGGAGGAGG 61.087 72.222 0.00 0.00 0.00 4.30
444 468 1.614824 AAGGCAGGTGGAGGAGGAG 60.615 63.158 0.00 0.00 0.00 3.69
445 469 1.613630 GAAGGCAGGTGGAGGAGGA 60.614 63.158 0.00 0.00 0.00 3.71
446 470 2.674220 GGAAGGCAGGTGGAGGAGG 61.674 68.421 0.00 0.00 0.00 4.30
447 471 1.277580 ATGGAAGGCAGGTGGAGGAG 61.278 60.000 0.00 0.00 0.00 3.69
448 472 1.229951 ATGGAAGGCAGGTGGAGGA 60.230 57.895 0.00 0.00 0.00 3.71
477 501 2.363975 AAACGGCCGGAGCTCCATA 61.364 57.895 31.67 0.00 39.73 2.74
992 1016 1.002366 CGACTTCTGCATTTCTCCCG 58.998 55.000 0.00 0.00 0.00 5.14
1136 1160 2.052104 TTGAGGATGAGGAGCGCGA 61.052 57.895 12.10 0.00 0.00 5.87
1231 1260 8.338259 CAGGATTAATCATAAGGTGAAACTTCG 58.662 37.037 17.07 0.00 40.97 3.79
1240 1269 4.141482 ACGGCACAGGATTAATCATAAGGT 60.141 41.667 17.07 2.04 0.00 3.50
1244 1273 3.138304 GCACGGCACAGGATTAATCATA 58.862 45.455 17.07 0.00 0.00 2.15
1245 1274 1.949525 GCACGGCACAGGATTAATCAT 59.050 47.619 17.07 7.33 0.00 2.45
1246 1275 1.065491 AGCACGGCACAGGATTAATCA 60.065 47.619 17.07 0.00 0.00 2.57
1247 1276 1.331756 CAGCACGGCACAGGATTAATC 59.668 52.381 6.93 6.93 0.00 1.75
1248 1277 1.382522 CAGCACGGCACAGGATTAAT 58.617 50.000 0.00 0.00 0.00 1.40
1249 1278 1.305219 GCAGCACGGCACAGGATTAA 61.305 55.000 0.00 0.00 0.00 1.40
1362 1404 3.850273 CGCATACGGATTACGGATCTAAC 59.150 47.826 0.00 0.00 44.68 2.34
1394 1439 1.113788 AGCCTGTGATCAGAGAGAGC 58.886 55.000 20.90 15.09 43.76 4.09
1395 1440 1.202440 GCAGCCTGTGATCAGAGAGAG 60.202 57.143 20.90 10.49 43.76 3.20
1396 1441 0.822811 GCAGCCTGTGATCAGAGAGA 59.177 55.000 20.90 0.00 43.76 3.10
1397 1442 0.825410 AGCAGCCTGTGATCAGAGAG 59.175 55.000 20.90 11.83 43.76 3.20
1398 1443 0.535797 CAGCAGCCTGTGATCAGAGA 59.464 55.000 20.90 0.00 43.76 3.10
1399 1444 0.462225 CCAGCAGCCTGTGATCAGAG 60.462 60.000 12.86 12.86 43.76 3.35
1400 1445 1.196766 ACCAGCAGCCTGTGATCAGA 61.197 55.000 0.00 0.00 43.76 3.27
1401 1446 0.322277 AACCAGCAGCCTGTGATCAG 60.322 55.000 0.00 0.00 41.01 2.90
1412 1461 1.442769 ACGCATCTAACAACCAGCAG 58.557 50.000 0.00 0.00 0.00 4.24
1449 1499 6.030849 CAGTAAATCTAGGAGACAGAACACG 58.969 44.000 0.00 0.00 0.00 4.49
1459 1510 4.339814 AGGAGCGTTCAGTAAATCTAGGAG 59.660 45.833 0.53 0.00 0.00 3.69
1511 1565 6.012113 TGAAGAAAATGTGATCCCAGTCAAT 58.988 36.000 0.00 0.00 0.00 2.57
1535 1589 4.346730 TCCACCATCTGCAGAAATCAAAT 58.653 39.130 22.50 0.00 0.00 2.32
1537 1591 3.009363 TCTCCACCATCTGCAGAAATCAA 59.991 43.478 22.50 4.27 0.00 2.57
1667 1721 5.626543 GCATCAAGTTTTACACATGTGTCAG 59.373 40.000 33.72 15.83 43.74 3.51
1691 1745 4.813161 TCTCTTCTGAAAGCAAGACACTTG 59.187 41.667 7.07 7.07 30.62 3.16
1735 1789 2.158755 GGGTATCATCCTTGGGACACAG 60.159 54.545 0.00 0.00 39.29 3.66
1741 1795 3.053693 TCACTTTGGGTATCATCCTTGGG 60.054 47.826 0.00 0.00 0.00 4.12
1753 1807 3.424703 CTTCCATGTCATCACTTTGGGT 58.575 45.455 0.00 0.00 31.09 4.51
1755 1809 3.087031 AGCTTCCATGTCATCACTTTGG 58.913 45.455 0.00 0.00 0.00 3.28
1756 1810 4.008330 AGAGCTTCCATGTCATCACTTTG 58.992 43.478 0.00 0.00 0.00 2.77
1757 1811 4.298103 AGAGCTTCCATGTCATCACTTT 57.702 40.909 0.00 0.00 0.00 2.66
1777 1831 7.488792 CAGCTCAATTCGATCATCCTCTATTAG 59.511 40.741 0.00 0.00 0.00 1.73
1781 1835 4.586421 ACAGCTCAATTCGATCATCCTCTA 59.414 41.667 0.00 0.00 0.00 2.43
1782 1836 3.387374 ACAGCTCAATTCGATCATCCTCT 59.613 43.478 0.00 0.00 0.00 3.69
1783 1837 3.726607 ACAGCTCAATTCGATCATCCTC 58.273 45.455 0.00 0.00 0.00 3.71
1793 1847 2.003301 GACCTTCCGACAGCTCAATTC 58.997 52.381 0.00 0.00 0.00 2.17
1800 1854 2.266055 CCCTGACCTTCCGACAGC 59.734 66.667 0.00 0.00 0.00 4.40
1806 1860 0.609406 GTTCCTTGCCCTGACCTTCC 60.609 60.000 0.00 0.00 0.00 3.46
1819 1873 5.319043 TCCATGGTTAGAGTTTGTTCCTT 57.681 39.130 12.58 0.00 0.00 3.36
1821 1875 5.253330 TCATCCATGGTTAGAGTTTGTTCC 58.747 41.667 12.58 0.00 0.00 3.62
1831 1885 6.548622 AGGTGAATTTGATCATCCATGGTTAG 59.451 38.462 12.58 3.01 30.40 2.34
1838 1892 4.920999 TGACAGGTGAATTTGATCATCCA 58.079 39.130 0.00 0.00 30.40 3.41
1868 1922 1.003696 CCAGAACTTCTTCCTCACCCC 59.996 57.143 0.00 0.00 0.00 4.95
1880 1934 2.309755 TGATCATCCTTGGCCAGAACTT 59.690 45.455 5.11 0.00 0.00 2.66
1881 1935 1.918262 TGATCATCCTTGGCCAGAACT 59.082 47.619 5.11 0.00 0.00 3.01
1883 1937 3.454719 TTTGATCATCCTTGGCCAGAA 57.545 42.857 5.11 0.00 0.00 3.02
1888 1942 2.031333 GCTCGATTTGATCATCCTTGGC 60.031 50.000 0.00 0.00 0.00 4.52
1905 1959 0.108898 CCTGACCTTCTGACTGCTCG 60.109 60.000 0.00 0.00 0.00 5.03
1916 2024 0.489567 AGGACTCTCACCCTGACCTT 59.510 55.000 0.00 0.00 0.00 3.50
2097 2205 0.541392 CCCTTCGGTGGATCACATGA 59.459 55.000 0.00 0.00 35.86 3.07
2253 2361 7.016957 AGCTCTATGATGACATATTTTCCCTCA 59.983 37.037 0.00 0.00 38.17 3.86
2580 2688 5.188434 TCAGCATTTCTATTCTCAACTGGG 58.812 41.667 0.00 0.00 0.00 4.45
3168 3278 8.668510 AATAGCAATACAAACCTGAGTATGAG 57.331 34.615 0.00 0.00 31.68 2.90
3244 3354 8.826710 TGATGATTCACAAAGTTATAATCGTCC 58.173 33.333 11.16 0.00 39.89 4.79
3252 3362 7.400599 ACAGCATGATGATTCACAAAGTTAT 57.599 32.000 19.60 0.00 39.69 1.89
3447 3557 2.291282 ACAAGCCATCCGGATTTTACCA 60.291 45.455 16.19 0.00 37.78 3.25
3521 3631 6.460261 CCGCGATTATATGGAGATGAGTACAT 60.460 42.308 8.23 0.00 39.67 2.29
3665 3775 4.935205 GCACACTTTGTTCCTTTCCTTTTT 59.065 37.500 0.00 0.00 0.00 1.94
3722 3832 9.669887 TTCTAGACTTTACTACTTCTAGTCTGG 57.330 37.037 12.04 9.67 43.80 3.86
3758 3868 1.203441 AGGCATGGACCAGAGCAGAA 61.203 55.000 19.79 0.00 0.00 3.02
3857 3967 0.606944 GACCATGCCACGGTTAACCA 60.607 55.000 24.14 4.72 36.69 3.67
4033 4160 6.096987 TGGACAAACTGCCTTGTAAATTGTAA 59.903 34.615 0.00 0.00 39.63 2.41
4034 4161 5.594725 TGGACAAACTGCCTTGTAAATTGTA 59.405 36.000 0.00 0.00 39.63 2.41
4035 4162 4.404073 TGGACAAACTGCCTTGTAAATTGT 59.596 37.500 0.00 0.00 39.63 2.71
4036 4163 4.942852 TGGACAAACTGCCTTGTAAATTG 58.057 39.130 0.00 0.00 39.63 2.32
4037 4164 5.806654 ATGGACAAACTGCCTTGTAAATT 57.193 34.783 0.00 0.00 39.63 1.82
4038 4165 5.806654 AATGGACAAACTGCCTTGTAAAT 57.193 34.783 0.00 0.00 39.63 1.40
4039 4166 5.105146 ACAAATGGACAAACTGCCTTGTAAA 60.105 36.000 0.00 0.00 39.63 2.01
4040 4167 4.404073 ACAAATGGACAAACTGCCTTGTAA 59.596 37.500 0.00 0.00 39.63 2.41
4041 4168 3.957497 ACAAATGGACAAACTGCCTTGTA 59.043 39.130 0.00 0.00 39.63 2.41
4042 4169 2.765699 ACAAATGGACAAACTGCCTTGT 59.234 40.909 0.00 0.00 42.23 3.16
4043 4170 3.457610 ACAAATGGACAAACTGCCTTG 57.542 42.857 0.00 0.00 0.00 3.61
4044 4171 4.441792 GAAACAAATGGACAAACTGCCTT 58.558 39.130 0.00 0.00 0.00 4.35
4045 4172 3.181466 GGAAACAAATGGACAAACTGCCT 60.181 43.478 0.00 0.00 0.00 4.75
4046 4173 3.130633 GGAAACAAATGGACAAACTGCC 58.869 45.455 0.00 0.00 0.00 4.85
4047 4174 3.555547 GTGGAAACAAATGGACAAACTGC 59.444 43.478 0.00 0.00 46.06 4.40
4048 4175 5.009854 AGTGGAAACAAATGGACAAACTG 57.990 39.130 0.00 0.00 46.06 3.16
4049 4176 5.675684 AAGTGGAAACAAATGGACAAACT 57.324 34.783 0.00 0.00 46.06 2.66
4050 4177 5.293324 GGAAAGTGGAAACAAATGGACAAAC 59.707 40.000 0.00 0.00 46.06 2.93
4051 4178 5.046304 TGGAAAGTGGAAACAAATGGACAAA 60.046 36.000 0.00 0.00 46.06 2.83
4121 4248 5.559770 TGATGAGCCATTGACTTCAGTTTA 58.440 37.500 0.00 0.00 0.00 2.01
4208 4339 7.335422 TGGAAGCAATAGAAAAACTTGCAAAAA 59.665 29.630 0.00 0.00 45.93 1.94
4271 4412 9.630098 CAACTATCACAAATAGCTTGTTCAAAT 57.370 29.630 0.00 0.00 46.49 2.32
4356 4497 2.752030 TGGCTAGCTAACCAGATGTCT 58.248 47.619 15.72 0.00 0.00 3.41
4415 4556 4.559300 GCACATTGTAAAGCATGGTCAACT 60.559 41.667 0.00 0.00 0.00 3.16
4426 4567 2.725723 CCGCAGTTTGCACATTGTAAAG 59.274 45.455 1.69 0.00 45.36 1.85
4431 4572 1.522258 GAAACCGCAGTTTGCACATTG 59.478 47.619 2.00 0.00 46.25 2.82
4433 4574 1.032014 AGAAACCGCAGTTTGCACAT 58.968 45.000 2.00 0.00 46.25 3.21
4442 4583 0.169672 CATCCAGCAAGAAACCGCAG 59.830 55.000 0.00 0.00 0.00 5.18
4480 4624 1.069823 AGCTGACATAGGAGAATGCCG 59.930 52.381 0.00 0.00 0.00 5.69
4482 4626 3.801698 TGAAGCTGACATAGGAGAATGC 58.198 45.455 0.00 0.00 0.00 3.56
4483 4627 5.608449 TGATGAAGCTGACATAGGAGAATG 58.392 41.667 6.64 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.