Multiple sequence alignment - TraesCS2B01G625400

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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 TraesCS2B01G625400 chr2B 100.000 6367 0 0 1 6367 798160197 798153831 0.000000e+00 11758.0
1 TraesCS2B01G625400 chr2B 85.656 2217 267 24 3325 5534 798331021 798328849 0.000000e+00 2285.0
2 TraesCS2B01G625400 chr2B 84.563 2222 286 29 3324 5534 798193076 798190901 0.000000e+00 2150.0
3 TraesCS2B01G625400 chr2B 84.857 2133 263 36 3324 5443 798226513 798224428 0.000000e+00 2095.0
4 TraesCS2B01G625400 chr2B 83.221 1186 155 28 668 1824 798195676 798194506 0.000000e+00 1048.0
5 TraesCS2B01G625400 chr2B 87.230 509 49 10 5810 6312 798184071 798183573 3.330000e-157 566.0
6 TraesCS2B01G625400 chr2B 77.881 859 148 21 1068 1902 798334231 798333391 4.430000e-136 496.0
7 TraesCS2B01G625400 chr2B 89.041 292 31 1 905 1196 798256646 798256356 1.690000e-95 361.0
8 TraesCS2B01G625400 chr2B 89.041 292 31 1 905 1196 798266424 798266134 1.690000e-95 361.0
9 TraesCS2B01G625400 chr2B 86.547 223 23 6 5810 6026 798328651 798328430 8.250000e-59 239.0
10 TraesCS2B01G625400 chr2B 88.060 201 19 3 660 855 798256838 798256638 3.840000e-57 233.0
11 TraesCS2B01G625400 chr2B 88.060 201 19 3 660 855 798266616 798266416 3.840000e-57 233.0
12 TraesCS2B01G625400 chr2B 75.436 574 87 25 2543 3096 798194050 798193511 4.970000e-56 230.0
13 TraesCS2B01G625400 chr2B 75.385 260 38 15 2146 2401 798194300 798194063 1.130000e-17 102.0
14 TraesCS2B01G625400 chr2B 95.556 45 1 1 858 902 610020593 610020636 3.180000e-08 71.3
15 TraesCS2B01G625400 chr2A 95.363 3062 115 17 3133 6175 764726070 764723017 0.000000e+00 4843.0
16 TraesCS2B01G625400 chr2A 97.304 2485 54 6 660 3131 764728849 764726365 0.000000e+00 4205.0
17 TraesCS2B01G625400 chr2A 92.113 355 21 6 313 664 764729228 764728878 1.590000e-135 494.0
18 TraesCS2B01G625400 chr2A 93.272 327 16 4 1 322 764729569 764729244 1.610000e-130 477.0
19 TraesCS2B01G625400 chr2A 93.925 214 12 1 1934 2147 95604633 95604421 7.960000e-84 322.0
20 TraesCS2B01G625400 chr2A 92.991 214 15 0 1934 2147 23755085 23754872 4.790000e-81 313.0
21 TraesCS2B01G625400 chr2A 90.625 192 10 3 6172 6357 764722709 764722520 1.370000e-61 248.0
22 TraesCS2B01G625400 chr2A 88.108 185 21 1 5960 6143 764770147 764769963 1.070000e-52 219.0
23 TraesCS2B01G625400 chr2A 82.716 162 23 2 5740 5899 764770312 764770154 8.610000e-29 139.0
24 TraesCS2B01G625400 chr2A 74.926 339 44 19 6007 6318 764783699 764783375 4.030000e-22 117.0
25 TraesCS2B01G625400 chr2A 86.585 82 7 4 6254 6332 764648086 764648006 3.160000e-13 87.9
26 TraesCS2B01G625400 chr2D 82.623 2981 387 75 3324 6278 638864166 638861291 0.000000e+00 2514.0
27 TraesCS2B01G625400 chr2D 90.944 1579 115 6 3131 4705 639090287 639088733 0.000000e+00 2098.0
28 TraesCS2B01G625400 chr2D 82.016 2391 341 51 3324 5676 639362125 639359786 0.000000e+00 1951.0
29 TraesCS2B01G625400 chr2D 81.719 2385 337 58 3324 5676 639137010 639134693 0.000000e+00 1897.0
30 TraesCS2B01G625400 chr2D 89.956 1135 63 10 2002 3134 639091431 639090346 0.000000e+00 1417.0
31 TraesCS2B01G625400 chr2D 91.452 971 80 3 968 1937 639092543 639091575 0.000000e+00 1330.0
32 TraesCS2B01G625400 chr2D 83.046 1392 192 21 3324 4705 639278610 639277253 0.000000e+00 1223.0
33 TraesCS2B01G625400 chr2D 84.074 1193 152 22 660 1824 639364422 639363240 0.000000e+00 1116.0
34 TraesCS2B01G625400 chr2D 80.214 1400 201 45 4746 6126 639277101 639275759 0.000000e+00 981.0
35 TraesCS2B01G625400 chr2D 77.860 1617 240 72 4746 6318 639088581 639087039 0.000000e+00 894.0
36 TraesCS2B01G625400 chr2D 81.818 880 141 12 960 1828 638876115 638875244 0.000000e+00 721.0
37 TraesCS2B01G625400 chr2D 81.401 828 137 9 1010 1827 639279723 639278903 0.000000e+00 660.0
38 TraesCS2B01G625400 chr2D 80.612 882 144 13 961 1824 639148131 639147259 0.000000e+00 656.0
39 TraesCS2B01G625400 chr2D 89.834 482 40 5 5838 6317 639151606 639151132 1.520000e-170 610.0
40 TraesCS2B01G625400 chr2D 80.731 711 92 27 5616 6318 639134691 639134018 4.400000e-141 512.0
41 TraesCS2B01G625400 chr2D 89.205 352 33 3 5828 6177 639359555 639359207 9.800000e-118 435.0
42 TraesCS2B01G625400 chr2D 87.606 355 38 6 5960 6311 638889055 638888704 2.140000e-109 407.0
43 TraesCS2B01G625400 chr2D 80.460 261 38 8 2146 2401 639138408 639138156 3.030000e-43 187.0
44 TraesCS2B01G625400 chr2D 80.488 123 17 6 1020 1138 639163421 639163302 3.160000e-13 87.9
45 TraesCS2B01G625400 chr2D 95.918 49 0 2 617 664 638876528 638876481 1.900000e-10 78.7
46 TraesCS2B01G625400 chr2D 92.857 42 3 0 811 852 639092646 639092605 1.920000e-05 62.1
47 TraesCS2B01G625400 chr3A 96.226 212 8 0 1936 2147 198839191 198839402 1.310000e-91 348.0
48 TraesCS2B01G625400 chr1A 95.327 214 10 0 1934 2147 62247296 62247509 2.200000e-89 340.0
49 TraesCS2B01G625400 chr1A 92.991 214 15 0 1934 2147 62247858 62248071 4.790000e-81 313.0
50 TraesCS2B01G625400 chr3B 95.939 197 8 0 1951 2147 243808991 243808795 2.860000e-83 320.0
51 TraesCS2B01G625400 chr4D 94.231 208 11 1 1934 2141 304361951 304362157 3.700000e-82 316.0
52 TraesCS2B01G625400 chr1D 70.909 990 223 43 3535 4496 12534221 12535173 8.490000e-39 172.0
53 TraesCS2B01G625400 chr7B 91.781 73 6 0 1566 1638 734078041 734077969 1.130000e-17 102.0
54 TraesCS2B01G625400 chr7A 74.494 247 51 10 996 1236 634922133 634921893 5.250000e-16 97.1
55 TraesCS2B01G625400 chr7A 97.619 42 0 1 862 903 705502267 705502307 3.180000e-08 71.3
56 TraesCS2B01G625400 chr7A 95.122 41 1 1 863 903 67682635 67682674 5.330000e-06 63.9
57 TraesCS2B01G625400 chr6A 78.676 136 27 2 1573 1707 4596935 4596801 8.790000e-14 89.8
58 TraesCS2B01G625400 chr6D 97.619 42 0 1 862 903 320198091 320198051 3.180000e-08 71.3
59 TraesCS2B01G625400 chr7D 95.238 42 1 1 862 903 613714900 613714940 1.480000e-06 65.8


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 TraesCS2B01G625400 chr2B 798153831 798160197 6366 True 11758.000000 11758 100.000000 1 6367 1 chr2B.!!$R1 6366
1 TraesCS2B01G625400 chr2B 798224428 798226513 2085 True 2095.000000 2095 84.857000 3324 5443 1 chr2B.!!$R3 2119
2 TraesCS2B01G625400 chr2B 798328430 798334231 5801 True 1006.666667 2285 83.361333 1068 6026 3 chr2B.!!$R7 4958
3 TraesCS2B01G625400 chr2B 798190901 798195676 4775 True 882.500000 2150 79.651250 668 5534 4 chr2B.!!$R4 4866
4 TraesCS2B01G625400 chr2A 764722520 764729569 7049 True 2053.400000 4843 93.735400 1 6357 5 chr2A.!!$R5 6356
5 TraesCS2B01G625400 chr2D 638861291 638864166 2875 True 2514.000000 2514 82.623000 3324 6278 1 chr2D.!!$R1 2954
6 TraesCS2B01G625400 chr2D 639359207 639364422 5215 True 1167.333333 1951 85.098333 660 6177 3 chr2D.!!$R9 5517
7 TraesCS2B01G625400 chr2D 639087039 639092646 5607 True 1160.220000 2098 88.613800 811 6318 5 chr2D.!!$R5 5507
8 TraesCS2B01G625400 chr2D 639275759 639279723 3964 True 954.666667 1223 81.553667 1010 6126 3 chr2D.!!$R8 5116
9 TraesCS2B01G625400 chr2D 639134018 639138408 4390 True 865.333333 1897 80.970000 2146 6318 3 chr2D.!!$R6 4172
10 TraesCS2B01G625400 chr2D 639147259 639151606 4347 True 633.000000 656 85.223000 961 6317 2 chr2D.!!$R7 5356
11 TraesCS2B01G625400 chr2D 638875244 638876528 1284 True 399.850000 721 88.868000 617 1828 2 chr2D.!!$R4 1211
12 TraesCS2B01G625400 chr1A 62247296 62248071 775 False 326.500000 340 94.159000 1934 2147 2 chr1A.!!$F1 213

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
60 61 0.106569 TACCCGGTATCGAGCTCCAA 60.107 55.000 8.47 0.00 39.00 3.53 F
460 493 0.597637 AACGAGTGAACAGGAGTGCG 60.598 55.000 0.00 0.00 0.00 5.34 F
730 812 2.683768 CCCCCTCACTACTCATTAGCT 58.316 52.381 0.00 0.00 0.00 3.32 F
1110 3626 2.689646 CAAAAGGTCGAGTCCTTCTCC 58.310 52.381 7.71 0.00 45.79 3.71 F
2265 5469 1.201647 TGTCAGCACGCCTACTTCTAC 59.798 52.381 0.00 0.00 0.00 2.59 F
2980 6650 2.031314 CAGTGGAATGCGCTGTAATCTG 59.969 50.000 9.73 7.33 0.00 2.90 F
3970 9051 0.261696 AAAGGTCAAACCAGCCCACT 59.738 50.000 0.00 0.00 41.95 4.00 F
3977 9058 0.396974 AAACCAGCCCACTTGCAGAA 60.397 50.000 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 3710 2.550208 CCTAACTTCGTCAGCCCAAACT 60.550 50.000 0.00 0.0 0.00 2.66 R
1281 3809 3.920231 AGCCTGTTCTGCTCATCATTA 57.080 42.857 0.00 0.0 32.41 1.90 R
1879 4511 4.321718 CGTCAGGATTGATGCTATGGATT 58.678 43.478 0.00 0.0 35.39 3.01 R
2964 6511 2.208431 AGAGCAGATTACAGCGCATTC 58.792 47.619 11.47 0.0 33.76 2.67 R
3217 8193 0.179187 CGGTACTGACTCTCACAGCG 60.179 60.000 0.00 0.0 38.74 5.18 R
4515 9608 0.667993 ACAACACTGGACGGCAATTG 59.332 50.000 0.00 0.0 0.00 2.32 R
5135 10354 0.947244 GAACCATTGGCATAGCTCCG 59.053 55.000 1.54 0.0 0.00 4.63 R
5410 10646 1.217942 AGCCAAAAGAAACAGGGGACT 59.782 47.619 0.00 0.0 46.44 3.85 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 1.477685 ATGTGGACTTCGTTCGGGGT 61.478 55.000 0.00 0.00 0.00 4.95
37 38 1.037493 GTTCGGGGTTGCTTTTCCTT 58.963 50.000 0.00 0.00 0.00 3.36
60 61 0.106569 TACCCGGTATCGAGCTCCAA 60.107 55.000 8.47 0.00 39.00 3.53
106 107 6.828785 CCTTAATGGTTATTCTTAGCAGTGGT 59.171 38.462 0.00 0.00 0.00 4.16
107 108 7.990886 CCTTAATGGTTATTCTTAGCAGTGGTA 59.009 37.037 0.00 0.00 0.00 3.25
119 120 2.958355 AGCAGTGGTAGTGTTTTTGCAT 59.042 40.909 0.00 0.00 32.79 3.96
152 153 4.919774 TGAAGGCATTACTTGGAGGTTA 57.080 40.909 0.00 0.00 0.00 2.85
195 199 5.773239 AAACACATGATACGACCTTTACG 57.227 39.130 0.00 0.00 0.00 3.18
209 213 3.150767 CCTTTACGGGTTGGATTTGACA 58.849 45.455 0.00 0.00 0.00 3.58
227 231 2.163412 GACAACAAAGACACAAGGTGCA 59.837 45.455 0.00 0.00 36.98 4.57
253 257 1.528129 CTTTCCTGGAGGTGTTGCTC 58.472 55.000 0.00 0.00 36.34 4.26
285 289 1.747709 TCTCTCGTAGTAGTGTGGCC 58.252 55.000 0.00 0.00 0.00 5.36
286 290 0.739561 CTCTCGTAGTAGTGTGGCCC 59.260 60.000 0.00 0.00 0.00 5.80
344 376 1.884075 ATGGCTGTGTGCATGCTTGG 61.884 55.000 20.33 5.86 45.15 3.61
363 395 5.691754 GCTTGGTGTCTTGAATAACTTTTGG 59.308 40.000 0.00 0.00 0.00 3.28
364 396 6.460953 GCTTGGTGTCTTGAATAACTTTTGGA 60.461 38.462 0.00 0.00 0.00 3.53
383 415 9.831737 CTTTTGGAAGTGTGTTATTATTGAGAG 57.168 33.333 0.00 0.00 0.00 3.20
392 424 6.101150 TGTGTTATTATTGAGAGGCCAGGTAT 59.899 38.462 5.01 0.00 0.00 2.73
397 429 9.739276 TTATTATTGAGAGGCCAGGTATAATTG 57.261 33.333 5.01 0.00 0.00 2.32
460 493 0.597637 AACGAGTGAACAGGAGTGCG 60.598 55.000 0.00 0.00 0.00 5.34
481 514 3.467803 GTCCGGTTTCCTCTTATCCATG 58.532 50.000 0.00 0.00 0.00 3.66
482 515 3.134081 GTCCGGTTTCCTCTTATCCATGA 59.866 47.826 0.00 0.00 0.00 3.07
502 535 8.380867 TCCATGAGTCTTCGGTCTTAGTATATA 58.619 37.037 0.00 0.00 0.00 0.86
730 812 2.683768 CCCCCTCACTACTCATTAGCT 58.316 52.381 0.00 0.00 0.00 3.32
1110 3626 2.689646 CAAAAGGTCGAGTCCTTCTCC 58.310 52.381 7.71 0.00 45.79 3.71
1283 3811 3.074281 CTGCGACCCCAACCCTAA 58.926 61.111 0.00 0.00 0.00 2.69
1879 4511 4.301628 CACGCAAGATACATCTATGCAGA 58.698 43.478 18.12 0.00 39.08 4.26
2265 5469 1.201647 TGTCAGCACGCCTACTTCTAC 59.798 52.381 0.00 0.00 0.00 2.59
2361 5566 4.201871 TGCTCTAAACAACCGACACTTTTG 60.202 41.667 0.00 0.00 0.00 2.44
2587 6120 9.837525 GATAGACATGCATTTCTATTTCCATTC 57.162 33.333 27.82 15.53 35.57 2.67
2980 6650 2.031314 CAGTGGAATGCGCTGTAATCTG 59.969 50.000 9.73 7.33 0.00 2.90
3090 7763 2.300152 AGGCGATCTTTGTGACAAGAGA 59.700 45.455 10.87 10.87 0.00 3.10
3126 7801 2.686915 AGTGCATTGGCTCTAATTGCTC 59.313 45.455 0.00 0.00 41.75 4.26
3217 8193 6.771076 TGTGATAATACGATTCAAAGTGTGC 58.229 36.000 0.00 0.00 0.00 4.57
3578 8627 6.606395 TGAAATCTCTCTCTGATGATGACTCA 59.394 38.462 0.00 0.00 35.41 3.41
3965 9046 3.634910 TCCAAGTAAAAGGTCAAACCAGC 59.365 43.478 0.00 0.00 41.95 4.85
3966 9047 3.243737 CCAAGTAAAAGGTCAAACCAGCC 60.244 47.826 0.00 0.00 41.95 4.85
3967 9048 2.594131 AGTAAAAGGTCAAACCAGCCC 58.406 47.619 0.00 0.00 41.95 5.19
3968 9049 2.091555 AGTAAAAGGTCAAACCAGCCCA 60.092 45.455 0.00 0.00 41.95 5.36
3969 9050 1.119684 AAAAGGTCAAACCAGCCCAC 58.880 50.000 0.00 0.00 41.95 4.61
3970 9051 0.261696 AAAGGTCAAACCAGCCCACT 59.738 50.000 0.00 0.00 41.95 4.00
3971 9052 0.261696 AAGGTCAAACCAGCCCACTT 59.738 50.000 0.00 0.00 41.95 3.16
3972 9053 0.468029 AGGTCAAACCAGCCCACTTG 60.468 55.000 0.00 0.00 41.95 3.16
3973 9054 1.363807 GTCAAACCAGCCCACTTGC 59.636 57.895 0.00 0.00 0.00 4.01
3974 9055 1.076412 TCAAACCAGCCCACTTGCA 60.076 52.632 0.00 0.00 0.00 4.08
3975 9056 1.108727 TCAAACCAGCCCACTTGCAG 61.109 55.000 0.00 0.00 0.00 4.41
3976 9057 1.108727 CAAACCAGCCCACTTGCAGA 61.109 55.000 0.00 0.00 0.00 4.26
3977 9058 0.396974 AAACCAGCCCACTTGCAGAA 60.397 50.000 0.00 0.00 0.00 3.02
3978 9059 0.396974 AACCAGCCCACTTGCAGAAA 60.397 50.000 0.00 0.00 0.00 2.52
3979 9060 0.396974 ACCAGCCCACTTGCAGAAAA 60.397 50.000 0.00 0.00 0.00 2.29
3980 9061 0.971386 CCAGCCCACTTGCAGAAAAT 59.029 50.000 0.00 0.00 0.00 1.82
3981 9062 1.067354 CCAGCCCACTTGCAGAAAATC 60.067 52.381 0.00 0.00 0.00 2.17
3982 9063 1.614903 CAGCCCACTTGCAGAAAATCA 59.385 47.619 0.00 0.00 0.00 2.57
3983 9064 2.036217 CAGCCCACTTGCAGAAAATCAA 59.964 45.455 0.00 0.00 0.00 2.57
3984 9065 2.036346 AGCCCACTTGCAGAAAATCAAC 59.964 45.455 0.00 0.00 0.00 3.18
3985 9066 2.867647 GCCCACTTGCAGAAAATCAACC 60.868 50.000 0.00 0.00 0.00 3.77
3986 9067 2.629617 CCCACTTGCAGAAAATCAACCT 59.370 45.455 0.00 0.00 0.00 3.50
3987 9068 3.826157 CCCACTTGCAGAAAATCAACCTA 59.174 43.478 0.00 0.00 0.00 3.08
3988 9069 4.082571 CCCACTTGCAGAAAATCAACCTAG 60.083 45.833 0.00 0.00 0.00 3.02
4157 9244 9.447040 GAAAACTTTGTTACTGTATTGGACTTC 57.553 33.333 0.00 0.00 0.00 3.01
4177 9264 2.303022 TCATCAAGGGAGACACACCTTC 59.697 50.000 0.00 0.00 44.98 3.46
4307 9397 3.769844 GTCCCTCTGTCAGTAAGATTCCA 59.230 47.826 0.00 0.00 0.00 3.53
4955 10165 5.464069 TCCTACCTTGATCTAACTGCCATA 58.536 41.667 0.00 0.00 0.00 2.74
5029 10248 0.946221 GTCTCCCTTGACACACGCAG 60.946 60.000 0.00 0.00 36.97 5.18
5102 10321 1.953311 GCGAGGGTATGCCTTTTCCAA 60.953 52.381 0.00 0.00 34.45 3.53
5114 10333 9.569122 GTATGCCTTTTCCAAGGAATTATACTA 57.431 33.333 5.13 0.00 45.60 1.82
5135 10354 2.836944 GAACCCTACGTTCCAGCAC 58.163 57.895 0.00 0.00 44.46 4.40
5162 10381 1.212751 GCCAATGGTTCAACGCCTC 59.787 57.895 0.00 0.00 0.00 4.70
5215 10434 2.095718 GTCCCGACTTCAATTTGAGCAC 60.096 50.000 0.00 0.00 0.00 4.40
5406 10642 5.963176 TGCTTCTGCATTTAGTTCAATGA 57.037 34.783 0.00 0.00 45.31 2.57
5407 10643 6.519679 TGCTTCTGCATTTAGTTCAATGAT 57.480 33.333 0.00 0.00 45.31 2.45
5408 10644 6.927416 TGCTTCTGCATTTAGTTCAATGATT 58.073 32.000 0.00 0.00 45.31 2.57
5409 10645 6.809689 TGCTTCTGCATTTAGTTCAATGATTG 59.190 34.615 0.00 0.00 45.31 2.67
5410 10646 7.031372 GCTTCTGCATTTAGTTCAATGATTGA 58.969 34.615 3.29 3.29 36.39 2.57
5431 10668 1.613925 GTCCCCTGTTTCTTTTGGCTC 59.386 52.381 0.00 0.00 0.00 4.70
5495 10732 1.130373 GCCGAGCGATGAACAAAATCA 59.870 47.619 0.00 0.00 0.00 2.57
5528 10765 8.141298 TCAAGGTACTAATTGTATCCAGTTGA 57.859 34.615 0.00 0.00 38.49 3.18
5585 10828 2.939103 ACTCGCATTATTCCTTCAGCAC 59.061 45.455 0.00 0.00 0.00 4.40
5599 10842 1.001746 TCAGCACCTTCTTCAGCTCTG 59.998 52.381 0.00 0.00 34.61 3.35
5607 10850 1.043022 TCTTCAGCTCTGCACTGTCA 58.957 50.000 3.05 0.00 36.50 3.58
5676 10981 5.850557 TTTGTCTCTGCCTTTGATTTCAA 57.149 34.783 0.00 0.00 0.00 2.69
5713 11022 4.193334 TCGGCGGCATCGACTCTG 62.193 66.667 10.53 0.00 43.49 3.35
5746 11055 2.022428 TCCATCTTCCTAGCCCCAGTTA 60.022 50.000 0.00 0.00 0.00 2.24
5764 11073 4.034510 CAGTTACATGCTTTCGATCTTCCC 59.965 45.833 0.00 0.00 0.00 3.97
5771 11080 3.454447 TGCTTTCGATCTTCCCCATCTTA 59.546 43.478 0.00 0.00 0.00 2.10
5864 11204 3.128589 TGAACCAACTTGTTTGCTCAGTC 59.871 43.478 0.00 0.00 33.34 3.51
5888 11232 3.449746 AATAAGGCTAGTTTGGTGGCA 57.550 42.857 0.00 0.00 0.00 4.92
5967 11311 1.160329 GGTGTGCGTTGAACTCAGCT 61.160 55.000 0.00 0.00 0.00 4.24
5980 11324 5.734720 TGAACTCAGCTAACCTATTTCCAG 58.265 41.667 0.00 0.00 0.00 3.86
6218 11888 4.078537 TGTACACTACTACCGGCTTGTTA 58.921 43.478 0.00 0.00 0.00 2.41
6272 11945 6.451064 TTTCAGACTCCTTTTTGTCTTTCC 57.549 37.500 0.00 0.00 41.06 3.13
6351 12026 3.816994 TCATTCCCAATGAGCTGATCTG 58.183 45.455 0.00 0.00 42.69 2.90
6352 12027 2.048444 TTCCCAATGAGCTGATCTGC 57.952 50.000 16.18 16.18 0.00 4.26
6353 12028 0.913924 TCCCAATGAGCTGATCTGCA 59.086 50.000 24.33 7.17 34.99 4.41
6354 12029 1.282738 TCCCAATGAGCTGATCTGCAA 59.717 47.619 24.33 13.62 34.99 4.08
6355 12030 2.092049 TCCCAATGAGCTGATCTGCAAT 60.092 45.455 24.33 15.12 34.99 3.56
6356 12031 2.693591 CCCAATGAGCTGATCTGCAATT 59.306 45.455 24.33 19.27 34.99 2.32
6357 12032 3.490933 CCCAATGAGCTGATCTGCAATTG 60.491 47.826 27.76 27.76 38.18 2.32
6358 12033 3.130516 CCAATGAGCTGATCTGCAATTGT 59.869 43.478 29.72 14.17 37.46 2.71
6359 12034 4.381612 CCAATGAGCTGATCTGCAATTGTT 60.382 41.667 29.72 16.65 37.46 2.83
6360 12035 5.168569 CAATGAGCTGATCTGCAATTGTTT 58.831 37.500 27.08 10.72 35.96 2.83
6361 12036 6.327154 CAATGAGCTGATCTGCAATTGTTTA 58.673 36.000 27.08 9.28 35.96 2.01
6362 12037 5.300969 TGAGCTGATCTGCAATTGTTTAC 57.699 39.130 24.33 6.59 34.99 2.01
6363 12038 5.005740 TGAGCTGATCTGCAATTGTTTACT 58.994 37.500 24.33 1.69 34.99 2.24
6364 12039 5.474532 TGAGCTGATCTGCAATTGTTTACTT 59.525 36.000 24.33 1.19 34.99 2.24
6365 12040 5.947443 AGCTGATCTGCAATTGTTTACTTC 58.053 37.500 24.33 0.00 34.99 3.01
6366 12041 5.474532 AGCTGATCTGCAATTGTTTACTTCA 59.525 36.000 24.33 3.13 34.99 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.500229 CGGGTACTCAAGGAAAAGCAA 58.500 47.619 0.00 0.00 0.00 3.91
37 38 0.182061 AGCTCGATACCGGGTACTCA 59.818 55.000 9.50 0.00 38.83 3.41
60 61 0.698818 CAGGCCTAGGGTTTTCACCT 59.301 55.000 3.98 3.26 43.65 4.00
96 97 3.948473 TGCAAAAACACTACCACTGCTAA 59.052 39.130 0.00 0.00 0.00 3.09
106 107 7.897575 ACAAGAAAACAATGCAAAAACACTA 57.102 28.000 0.00 0.00 0.00 2.74
107 108 6.799926 ACAAGAAAACAATGCAAAAACACT 57.200 29.167 0.00 0.00 0.00 3.55
119 120 6.872920 AGTAATGCCTTCAACAAGAAAACAA 58.127 32.000 0.00 0.00 35.40 2.83
195 199 4.142049 TGTCTTTGTTGTCAAATCCAACCC 60.142 41.667 0.00 0.00 41.77 4.11
209 213 3.195396 ACAATGCACCTTGTGTCTTTGTT 59.805 39.130 4.90 0.00 37.93 2.83
212 216 3.181476 GGAACAATGCACCTTGTGTCTTT 60.181 43.478 6.46 0.00 39.25 2.52
227 231 2.447047 ACACCTCCAGGAAAGGAACAAT 59.553 45.455 0.00 0.00 37.20 2.71
279 283 4.697756 GCAGCTACACGGGCCACA 62.698 66.667 4.39 0.00 0.00 4.17
285 289 0.723414 CACATCAAGCAGCTACACGG 59.277 55.000 0.00 0.00 0.00 4.94
286 290 0.723414 CCACATCAAGCAGCTACACG 59.277 55.000 0.00 0.00 0.00 4.49
319 323 3.700539 AGCATGCACACAGCCATATTAAA 59.299 39.130 21.98 0.00 44.83 1.52
344 376 7.432252 CACACTTCCAAAAGTTATTCAAGACAC 59.568 37.037 0.00 0.00 43.28 3.67
363 395 5.880332 TGGCCTCTCAATAATAACACACTTC 59.120 40.000 3.32 0.00 0.00 3.01
364 396 5.815581 TGGCCTCTCAATAATAACACACTT 58.184 37.500 3.32 0.00 0.00 3.16
383 415 9.905713 TCAAGAATATATCAATTATACCTGGCC 57.094 33.333 0.00 0.00 0.00 5.36
444 477 0.667792 GGACGCACTCCTGTTCACTC 60.668 60.000 0.00 0.00 35.89 3.51
460 493 3.134081 TCATGGATAAGAGGAAACCGGAC 59.866 47.826 9.46 0.00 0.00 4.79
506 539 7.402054 AGCCGATCAATTGTATATATTGGGAA 58.598 34.615 5.13 0.00 34.51 3.97
508 541 6.018751 CGAGCCGATCAATTGTATATATTGGG 60.019 42.308 5.13 0.00 34.51 4.12
730 812 3.390311 AGAGCTGTATCATCCTGATGCAA 59.610 43.478 8.81 0.00 46.11 4.08
864 946 8.674263 TGTGGTTAGCAAAATCAAAAATTCAT 57.326 26.923 0.00 0.00 0.00 2.57
866 948 8.558700 ACATGTGGTTAGCAAAATCAAAAATTC 58.441 29.630 0.00 0.00 0.00 2.17
868 950 8.449251 AACATGTGGTTAGCAAAATCAAAAAT 57.551 26.923 0.00 0.00 38.15 1.82
1188 3710 2.550208 CCTAACTTCGTCAGCCCAAACT 60.550 50.000 0.00 0.00 0.00 2.66
1281 3809 3.920231 AGCCTGTTCTGCTCATCATTA 57.080 42.857 0.00 0.00 32.41 1.90
1700 4250 8.426881 AAAGAGAAGATCGCTTAATACTTTCC 57.573 34.615 0.00 0.00 35.47 3.13
1879 4511 4.321718 CGTCAGGATTGATGCTATGGATT 58.678 43.478 0.00 0.00 35.39 3.01
1920 4554 6.151648 CCTTTCTCCATGCTTTTTATCTGACA 59.848 38.462 0.00 0.00 0.00 3.58
2172 5372 6.697641 AGAGACCTGGTGTTTTTCCTTATA 57.302 37.500 2.82 0.00 0.00 0.98
2265 5469 4.323562 CCAAGGTAGGTACTGGGAGAAAAG 60.324 50.000 0.00 0.00 41.52 2.27
2519 6052 7.759489 ACAGTGTAGATTTGCCATAGAAAAA 57.241 32.000 0.00 0.00 0.00 1.94
2863 6408 4.445385 GTCCATGAAAACAAATGTGCTGAC 59.555 41.667 0.00 0.00 0.00 3.51
2913 6459 5.088680 TCGGGGTTTCTTCGTACAAATAT 57.911 39.130 0.00 0.00 0.00 1.28
2964 6511 2.208431 AGAGCAGATTACAGCGCATTC 58.792 47.619 11.47 0.00 33.76 2.67
2980 6650 7.160049 GGAACTTATACCCCTAATACAAGAGC 58.840 42.308 0.00 0.00 0.00 4.09
3013 6683 3.434940 ACCACCTTAAGCCAAACTAGG 57.565 47.619 0.00 0.00 31.24 3.02
3090 7763 3.275617 TGCACTAGGGCGATACATTTT 57.724 42.857 13.37 0.00 36.28 1.82
3126 7801 5.456497 CGCTACCACATTCAATGCATAAAAG 59.544 40.000 0.00 0.00 0.00 2.27
3217 8193 0.179187 CGGTACTGACTCTCACAGCG 60.179 60.000 0.00 0.00 38.74 5.18
3884 8935 6.073873 GGTCTCTGCTAATTTGATGATCTTCG 60.074 42.308 4.32 0.00 0.00 3.79
3965 9046 2.629617 AGGTTGATTTTCTGCAAGTGGG 59.370 45.455 0.00 0.00 33.76 4.61
3966 9047 4.520492 ACTAGGTTGATTTTCTGCAAGTGG 59.480 41.667 0.00 0.00 33.76 4.00
3967 9048 5.471456 AGACTAGGTTGATTTTCTGCAAGTG 59.529 40.000 0.00 0.00 33.76 3.16
3968 9049 5.625150 AGACTAGGTTGATTTTCTGCAAGT 58.375 37.500 0.00 0.00 33.76 3.16
3969 9050 5.123027 GGAGACTAGGTTGATTTTCTGCAAG 59.877 44.000 0.00 0.00 0.00 4.01
3970 9051 5.003804 GGAGACTAGGTTGATTTTCTGCAA 58.996 41.667 0.00 0.00 0.00 4.08
3971 9052 4.287067 AGGAGACTAGGTTGATTTTCTGCA 59.713 41.667 0.00 0.00 40.61 4.41
3972 9053 4.837972 AGGAGACTAGGTTGATTTTCTGC 58.162 43.478 0.00 0.00 40.61 4.26
3973 9054 6.467677 TCAAGGAGACTAGGTTGATTTTCTG 58.532 40.000 0.00 0.00 42.68 3.02
3974 9055 6.688073 TCAAGGAGACTAGGTTGATTTTCT 57.312 37.500 0.00 0.00 42.68 2.52
3975 9056 5.352846 GCTCAAGGAGACTAGGTTGATTTTC 59.647 44.000 0.00 0.00 42.68 2.29
3976 9057 5.013599 AGCTCAAGGAGACTAGGTTGATTTT 59.986 40.000 0.00 0.00 42.68 1.82
3977 9058 4.534103 AGCTCAAGGAGACTAGGTTGATTT 59.466 41.667 0.00 0.00 42.68 2.17
3978 9059 4.100373 AGCTCAAGGAGACTAGGTTGATT 58.900 43.478 0.00 0.00 42.68 2.57
3979 9060 3.718723 AGCTCAAGGAGACTAGGTTGAT 58.281 45.455 0.00 0.00 42.68 2.57
3980 9061 3.176924 AGCTCAAGGAGACTAGGTTGA 57.823 47.619 0.00 0.00 42.68 3.18
3981 9062 3.594134 CAAGCTCAAGGAGACTAGGTTG 58.406 50.000 0.00 0.00 43.84 3.77
3982 9063 2.569404 CCAAGCTCAAGGAGACTAGGTT 59.431 50.000 0.00 0.00 42.68 3.50
3983 9064 2.183679 CCAAGCTCAAGGAGACTAGGT 58.816 52.381 0.00 0.00 42.68 3.08
3984 9065 2.461695 TCCAAGCTCAAGGAGACTAGG 58.538 52.381 0.00 0.00 42.68 3.02
4121 9208 6.194692 CAGTAACAAAGTTTTCTTCGCTTGAC 59.805 38.462 0.00 0.00 39.48 3.18
4157 9244 2.704572 GAAGGTGTGTCTCCCTTGATG 58.295 52.381 0.00 0.00 41.13 3.07
4307 9397 8.233190 CGCAAAACTTGAAATCTAGAAAGAGAT 58.767 33.333 8.56 0.00 37.81 2.75
4515 9608 0.667993 ACAACACTGGACGGCAATTG 59.332 50.000 0.00 0.00 0.00 2.32
4955 10165 3.509575 GGATATCTCTGGATCGCACTTCT 59.490 47.826 2.05 0.00 33.71 2.85
5077 10296 3.546009 GGCATACCCTCGCCTGTA 58.454 61.111 0.00 0.00 45.29 2.74
5087 10306 6.731292 ATAATTCCTTGGAAAAGGCATACC 57.269 37.500 6.16 0.00 39.80 2.73
5102 10321 7.065504 ACGTAGGGTTCACTAGTATAATTCCT 58.934 38.462 0.00 7.45 0.00 3.36
5132 10351 1.650912 CATTGGCATAGCTCCGTGC 59.349 57.895 9.47 9.47 43.29 5.34
5135 10354 0.947244 GAACCATTGGCATAGCTCCG 59.053 55.000 1.54 0.00 0.00 4.63
5403 10639 4.664688 AAGAAACAGGGGACTCAATCAT 57.335 40.909 0.00 0.00 40.21 2.45
5404 10640 4.453480 AAAGAAACAGGGGACTCAATCA 57.547 40.909 0.00 0.00 40.21 2.57
5405 10641 4.021981 CCAAAAGAAACAGGGGACTCAATC 60.022 45.833 0.00 0.00 40.21 2.67
5406 10642 3.897505 CCAAAAGAAACAGGGGACTCAAT 59.102 43.478 0.00 0.00 40.21 2.57
5407 10643 3.295973 CCAAAAGAAACAGGGGACTCAA 58.704 45.455 0.00 0.00 40.21 3.02
5408 10644 2.944129 CCAAAAGAAACAGGGGACTCA 58.056 47.619 0.00 0.00 40.21 3.41
5409 10645 1.613925 GCCAAAAGAAACAGGGGACTC 59.386 52.381 0.00 0.00 40.21 3.36
5410 10646 1.217942 AGCCAAAAGAAACAGGGGACT 59.782 47.619 0.00 0.00 46.44 3.85
5495 10732 6.374417 ACAATTAGTACCTTGAGGACACAT 57.626 37.500 3.59 0.00 38.94 3.21
5528 10765 5.294306 CCTAACACATGCGTGATGTAGAAAT 59.706 40.000 14.17 1.22 46.80 2.17
5585 10828 1.270732 ACAGTGCAGAGCTGAAGAAGG 60.271 52.381 9.59 0.00 37.40 3.46
5599 10842 3.202906 TGGTGAAGTAAACTGACAGTGC 58.797 45.455 9.33 3.03 0.00 4.40
5607 10850 6.599638 GCATAAGGAAGATGGTGAAGTAAACT 59.400 38.462 0.00 0.00 0.00 2.66
5676 10981 2.839228 AGGAAATCACCTCCTGCTAGT 58.161 47.619 0.00 0.00 41.96 2.57
5713 11022 4.205587 AGGAAGATGGAGATTTGCATGAC 58.794 43.478 0.00 0.00 35.28 3.06
5746 11055 1.281867 TGGGGAAGATCGAAAGCATGT 59.718 47.619 0.00 0.00 0.00 3.21
5764 11073 7.056635 ACAGAGGGTACATGAATTTAAGATGG 58.943 38.462 0.00 0.00 0.00 3.51
5771 11080 6.931281 CGATGATACAGAGGGTACATGAATTT 59.069 38.462 0.00 0.00 34.07 1.82
5864 11204 4.335594 GCCACCAAACTAGCCTTATTACAG 59.664 45.833 0.00 0.00 0.00 2.74
5919 11263 2.431057 CCCTCTAGTTACATTCGCTGGT 59.569 50.000 0.00 0.00 0.00 4.00
5967 11311 9.226606 CACAACAATAGAACTGGAAATAGGTTA 57.773 33.333 0.00 0.00 0.00 2.85
5980 11324 7.387948 AGACAGTATTCCACACAACAATAGAAC 59.612 37.037 0.00 0.00 0.00 3.01
6272 11945 5.665916 AGGGCTTCACTTATTGATTTTGG 57.334 39.130 0.00 0.00 32.84 3.28
6328 12003 4.643334 CAGATCAGCTCATTGGGAATGAAA 59.357 41.667 0.00 0.00 46.49 2.69
6332 12007 2.092049 TGCAGATCAGCTCATTGGGAAT 60.092 45.455 11.68 0.00 34.99 3.01
6343 12018 5.702865 TGAAGTAAACAATTGCAGATCAGC 58.297 37.500 5.05 2.62 0.00 4.26


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

AutoCloner maintained by Alex Coulton.