Multiple sequence alignment - TraesCS5B01G159200

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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 TraesCS5B01G159200 chr5B 100.000 4423 0 0 1 4423 293554360 293549938 0.000000e+00 8168.0
1 TraesCS5B01G159200 chr5B 83.559 444 69 4 1 442 53238043 53237602 3.180000e-111 412.0
2 TraesCS5B01G159200 chr5B 82.243 214 31 1 3571 3777 293550537 293550324 1.260000e-40 178.0
3 TraesCS5B01G159200 chr5B 82.243 214 31 1 3824 4037 293550790 293550584 1.260000e-40 178.0
4 TraesCS5B01G159200 chr5B 93.000 100 5 1 4322 4421 694234438 694234535 1.280000e-30 145.0
5 TraesCS5B01G159200 chr5B 80.000 125 13 9 2285 2400 391644737 391644616 1.020000e-11 82.4
6 TraesCS5B01G159200 chr5D 92.081 4407 229 36 1 4329 260788119 260792483 0.000000e+00 6095.0
7 TraesCS5B01G159200 chr5D 81.879 447 79 2 2 447 63768889 63768444 4.180000e-100 375.0
8 TraesCS5B01G159200 chr5D 82.199 191 27 1 3824 4014 260791742 260791925 1.650000e-34 158.0
9 TraesCS5B01G159200 chr5D 89.394 66 3 4 2335 2398 334702867 334702804 3.670000e-11 80.5
10 TraesCS5B01G159200 chr5D 100.000 30 0 0 2369 2398 332406936 332406965 6.180000e-04 56.5
11 TraesCS5B01G159200 chr5A 91.297 3792 196 49 623 4332 344549835 344546096 0.000000e+00 5051.0
12 TraesCS5B01G159200 chr5A 86.335 161 22 0 3571 3731 344546603 344546443 4.550000e-40 176.0
13 TraesCS5B01G159200 chr6B 84.424 443 68 1 1 442 355184137 355184579 6.790000e-118 435.0
14 TraesCS5B01G159200 chr6B 85.841 113 13 3 1932 2043 54661388 54661278 2.800000e-22 117.0
15 TraesCS5B01G159200 chr4D 84.424 443 68 1 1 442 226265032 226265474 6.790000e-118 435.0
16 TraesCS5B01G159200 chr1D 84.199 443 68 2 1 442 168382010 168382451 3.160000e-116 429.0
17 TraesCS5B01G159200 chr6A 82.247 445 76 2 1 442 237567790 237568234 8.980000e-102 381.0
18 TraesCS5B01G159200 chr6A 92.233 103 5 2 4322 4423 591407609 591407709 4.610000e-30 143.0
19 TraesCS5B01G159200 chr4B 82.207 444 75 4 1 442 60379767 60380208 3.230000e-101 379.0
20 TraesCS5B01G159200 chr4B 92.308 104 5 2 4319 4421 86056560 86056661 1.280000e-30 145.0
21 TraesCS5B01G159200 chr2D 82.529 435 71 4 11 442 419994176 419994608 1.160000e-100 377.0
22 TraesCS5B01G159200 chr3B 94.845 97 3 1 4325 4421 736841329 736841423 2.760000e-32 150.0
23 TraesCS5B01G159200 chr3B 90.654 107 7 2 4317 4423 505837029 505837132 5.970000e-29 139.0
24 TraesCS5B01G159200 chr2A 94.845 97 3 2 4325 4421 765824526 765824620 2.760000e-32 150.0
25 TraesCS5B01G159200 chr2A 93.939 99 4 1 4325 4423 80849297 80849393 9.910000e-32 148.0
26 TraesCS5B01G159200 chr7B 94.000 100 3 2 4322 4421 735948766 735948862 9.910000e-32 148.0
27 TraesCS5B01G159200 chr3A 90.566 106 8 1 4316 4421 729354233 729354336 5.970000e-29 139.0
28 TraesCS5B01G159200 chr3D 91.071 56 3 2 2050 2105 30982639 30982692 1.710000e-09 75.0
29 TraesCS5B01G159200 chr2B 77.181 149 20 11 2260 2399 728629221 728629364 1.710000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G159200 chr5B 293549938 293554360 4422 True 8168.0 8168 100.000 1 4423 1 chr5B.!!$R2 4422
1 TraesCS5B01G159200 chr5D 260788119 260792483 4364 False 3126.5 6095 87.140 1 4329 2 chr5D.!!$F2 4328
2 TraesCS5B01G159200 chr5A 344546096 344549835 3739 True 2613.5 5051 88.816 623 4332 2 chr5A.!!$R1 3709

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
908 914 0.036388 TCCTTCACAGATCCAACGGC 60.036 55.0 0.00 0.0 0.00 5.68 F
1272 1327 0.035739 TACCGGGGTGTTGCTTCTTC 59.964 55.0 6.32 0.0 0.00 2.87 F
1274 1329 0.323629 CCGGGGTGTTGCTTCTTCTA 59.676 55.0 0.00 0.0 0.00 2.10 F
3283 3368 0.749454 CCTGAGGCTACAATGGCACC 60.749 60.0 0.00 0.0 34.73 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2137 2195 1.287425 GCCGTTTCTAACCGATCCTG 58.713 55.000 0.00 0.00 0.00 3.86 R
3160 3245 0.953727 TGGCATGTCACTTGCTGTTC 59.046 50.000 14.82 0.00 40.03 3.18 R
3312 3397 2.520536 ATCCATAGCAGGGACGCCC 61.521 63.158 6.80 6.80 45.90 6.13 R
4360 4472 0.168128 AACAGACTAATTTGCGGCGC 59.832 50.000 27.44 27.44 0.00 6.53 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
70 72 2.327343 GCAGCATCAAGACCACGCA 61.327 57.895 0.00 0.00 0.00 5.24
76 78 2.395988 ATCAAGACCACGCACTGCCA 62.396 55.000 0.00 0.00 0.00 4.92
109 111 2.027625 CGGACGTCAAGACCAAGCC 61.028 63.158 18.91 0.00 34.24 4.35
170 172 2.359975 CCTTCACCCCGGAACTGC 60.360 66.667 0.73 0.00 0.00 4.40
172 174 3.530910 CTTCACCCCGGAACTGCGT 62.531 63.158 0.73 0.00 0.00 5.24
183 185 3.851845 AACTGCGTCGCGTTGCCTA 62.852 57.895 20.86 4.50 0.00 3.93
209 211 2.716217 GCAAGTTCAAGCCAGACCTAT 58.284 47.619 0.00 0.00 0.00 2.57
210 212 3.084786 GCAAGTTCAAGCCAGACCTATT 58.915 45.455 0.00 0.00 0.00 1.73
211 213 3.119708 GCAAGTTCAAGCCAGACCTATTG 60.120 47.826 0.00 0.00 0.00 1.90
220 222 1.070758 CCAGACCTATTGCCACGCTAT 59.929 52.381 0.00 0.00 0.00 2.97
232 234 4.910585 CGCTATGACGGCACCCCC 62.911 72.222 0.00 0.00 0.00 5.40
306 308 1.523154 GACGGCAAGGTCATGGCAAA 61.523 55.000 0.00 0.00 45.50 3.68
351 353 4.899239 CGTGCGCTCCTGGATCCC 62.899 72.222 9.90 0.00 0.00 3.85
388 390 5.280419 GGGATTAATCTCCTCTTGGGATGAG 60.280 48.000 14.95 0.00 44.15 2.90
600 602 7.917720 CATCAACGATGAAAATGATGCATAA 57.082 32.000 0.00 0.00 42.09 1.90
742 747 6.327626 TCAATAATTCCCTGGTTTTGTTTCCA 59.672 34.615 0.00 0.00 0.00 3.53
743 748 6.950860 ATAATTCCCTGGTTTTGTTTCCAT 57.049 33.333 0.00 0.00 33.01 3.41
794 800 9.796120 TTTTGTTGTATTTCTACACTTTTCCAG 57.204 29.630 0.00 0.00 37.58 3.86
816 822 4.768968 AGTTACTGCATTTCAAATCTGGCT 59.231 37.500 0.00 0.00 0.00 4.75
874 880 3.071892 ACACAAGAAATTAGACACCGGGA 59.928 43.478 6.32 0.00 0.00 5.14
908 914 0.036388 TCCTTCACAGATCCAACGGC 60.036 55.000 0.00 0.00 0.00 5.68
911 917 1.488705 TTCACAGATCCAACGGCCCT 61.489 55.000 0.00 0.00 0.00 5.19
947 953 1.549203 GAAGCTTTGCTGATTCCCCA 58.451 50.000 0.00 0.00 39.62 4.96
949 955 2.242882 AGCTTTGCTGATTCCCCATT 57.757 45.000 0.00 0.00 37.57 3.16
1012 1065 4.776322 CAGCAATGTCGGGGCGGA 62.776 66.667 0.00 0.00 0.00 5.54
1071 1124 2.515523 GCGGACCAGCTGATGCAT 60.516 61.111 17.39 0.00 42.74 3.96
1180 1233 0.674895 CCCTTTTCCGCCTCTCTGTG 60.675 60.000 0.00 0.00 0.00 3.66
1199 1252 1.600107 GCACCCGAATCCCAGTGTA 59.400 57.895 0.00 0.00 32.75 2.90
1200 1253 0.180406 GCACCCGAATCCCAGTGTAT 59.820 55.000 0.00 0.00 32.75 2.29
1201 1254 1.810412 GCACCCGAATCCCAGTGTATC 60.810 57.143 0.00 0.00 32.75 2.24
1202 1255 1.762957 CACCCGAATCCCAGTGTATCT 59.237 52.381 0.00 0.00 0.00 1.98
1203 1256 1.762957 ACCCGAATCCCAGTGTATCTG 59.237 52.381 0.00 0.00 43.27 2.90
1204 1257 1.762957 CCCGAATCCCAGTGTATCTGT 59.237 52.381 0.00 0.00 42.19 3.41
1213 1267 3.753272 CCCAGTGTATCTGTTTGGTTCAG 59.247 47.826 0.00 0.00 42.19 3.02
1231 1285 5.952033 GTTCAGTAACCTCGAATACTGTCT 58.048 41.667 22.11 1.27 45.83 3.41
1246 1300 2.499289 ACTGTCTCAGAGATCGGCATTT 59.501 45.455 2.64 0.00 35.18 2.32
1248 1302 3.937706 CTGTCTCAGAGATCGGCATTTTT 59.062 43.478 2.64 0.00 32.44 1.94
1251 1305 5.105351 TGTCTCAGAGATCGGCATTTTTCTA 60.105 40.000 2.64 0.00 0.00 2.10
1252 1306 5.988561 GTCTCAGAGATCGGCATTTTTCTAT 59.011 40.000 2.64 0.00 0.00 1.98
1253 1307 6.481644 GTCTCAGAGATCGGCATTTTTCTATT 59.518 38.462 2.64 0.00 0.00 1.73
1255 1309 7.653713 TCTCAGAGATCGGCATTTTTCTATTAC 59.346 37.037 0.00 0.00 0.00 1.89
1257 1311 5.696724 AGAGATCGGCATTTTTCTATTACCG 59.303 40.000 0.00 0.00 40.47 4.02
1258 1312 4.755123 AGATCGGCATTTTTCTATTACCGG 59.245 41.667 0.00 0.00 39.59 5.28
1259 1313 3.207778 TCGGCATTTTTCTATTACCGGG 58.792 45.455 6.32 0.00 39.59 5.73
1272 1327 0.035739 TACCGGGGTGTTGCTTCTTC 59.964 55.000 6.32 0.00 0.00 2.87
1273 1328 1.073199 CCGGGGTGTTGCTTCTTCT 59.927 57.895 0.00 0.00 0.00 2.85
1274 1329 0.323629 CCGGGGTGTTGCTTCTTCTA 59.676 55.000 0.00 0.00 0.00 2.10
1275 1330 1.271163 CCGGGGTGTTGCTTCTTCTAA 60.271 52.381 0.00 0.00 0.00 2.10
1276 1331 2.618045 CCGGGGTGTTGCTTCTTCTAAT 60.618 50.000 0.00 0.00 0.00 1.73
1277 1332 2.420022 CGGGGTGTTGCTTCTTCTAATG 59.580 50.000 0.00 0.00 0.00 1.90
1278 1333 3.421844 GGGGTGTTGCTTCTTCTAATGT 58.578 45.455 0.00 0.00 0.00 2.71
1279 1334 3.440522 GGGGTGTTGCTTCTTCTAATGTC 59.559 47.826 0.00 0.00 0.00 3.06
1339 1394 1.132643 AGTTGGTCGATCGACACTAGC 59.867 52.381 39.98 28.30 46.20 3.42
1380 1435 2.094026 GGTTCCAAGGACATGATTTGGC 60.094 50.000 17.15 8.61 40.87 4.52
1381 1436 2.827921 GTTCCAAGGACATGATTTGGCT 59.172 45.455 17.15 0.00 40.87 4.75
1496 1554 2.046120 AGGAAGAGCAGCAGCAGC 60.046 61.111 3.17 0.46 45.49 5.25
1497 1555 2.359602 GGAAGAGCAGCAGCAGCA 60.360 61.111 12.92 0.00 45.49 4.41
1498 1556 2.400158 GGAAGAGCAGCAGCAGCAG 61.400 63.158 12.92 0.00 45.49 4.24
1504 1562 3.128188 CAGCAGCAGCAGCAGGAG 61.128 66.667 12.92 0.00 45.49 3.69
1505 1563 3.320014 AGCAGCAGCAGCAGGAGA 61.320 61.111 12.92 0.00 45.49 3.71
1529 1587 2.159170 CCTAAAGTGAGCTCCCTTCTCG 60.159 54.545 12.08 3.93 33.41 4.04
1533 1591 0.820871 GTGAGCTCCCTTCTCGATGT 59.179 55.000 12.15 0.00 33.41 3.06
1539 1597 3.054802 AGCTCCCTTCTCGATGTCATTTT 60.055 43.478 0.00 0.00 0.00 1.82
1540 1598 3.064545 GCTCCCTTCTCGATGTCATTTTG 59.935 47.826 0.00 0.00 0.00 2.44
1546 1604 3.402110 TCTCGATGTCATTTTGTGTGCT 58.598 40.909 0.00 0.00 0.00 4.40
1571 1629 2.418628 CTCACACGTGTGGTTCTTGTTT 59.581 45.455 39.88 4.93 45.65 2.83
1586 1644 8.405531 TGGTTCTTGTTTCTGATTAGTTTTCAG 58.594 33.333 0.00 0.00 41.61 3.02
1651 1709 7.604657 AACACAATTAACCTTTATGTTCCCA 57.395 32.000 0.00 0.00 0.00 4.37
1659 1717 9.990868 ATTAACCTTTATGTTCCCAATCTTACT 57.009 29.630 0.00 0.00 0.00 2.24
1722 1780 5.064707 AGTGACAACATGTACACAGTTTGAC 59.935 40.000 22.99 9.09 33.74 3.18
1800 1858 6.041296 GGAGGGATGCATTTCATTTCATAACT 59.959 38.462 0.00 0.00 35.05 2.24
1964 2022 3.774216 GCATCTCTAGCAGATCCCCTATT 59.226 47.826 0.00 0.00 40.20 1.73
2048 2106 8.511748 TTTTCTAAATCTAGCAGATCCCCTAT 57.488 34.615 0.00 0.00 32.89 2.57
2130 2188 5.473504 TGAGCAGAATTTTTGTAGGGACTTC 59.526 40.000 0.00 0.00 41.75 3.01
2508 2593 8.821147 TTCACGAAAAAGCTATCTAGTGTTAA 57.179 30.769 10.09 0.00 0.00 2.01
2614 2699 4.724399 TGCTGTTGATTTCTTCACCCTTA 58.276 39.130 0.00 0.00 32.84 2.69
2693 2778 3.991121 TCGATGCGTTCTTGACATACAAA 59.009 39.130 0.00 0.00 38.08 2.83
2729 2814 4.505313 AAAAGCCAGAGGAAAACGAATC 57.495 40.909 0.00 0.00 0.00 2.52
2845 2930 4.470602 CCTTTTTAACCCTGTCTGGTTCT 58.529 43.478 0.00 0.00 45.51 3.01
2847 2932 5.362717 CCTTTTTAACCCTGTCTGGTTCTTT 59.637 40.000 0.00 0.00 45.51 2.52
2970 3055 5.719085 TGAATTGTTGGGTAGCCAAATATGT 59.281 36.000 27.24 12.16 0.00 2.29
3069 3154 7.420002 TCAGCTGTTGTGATATAATTTCATGC 58.580 34.615 14.67 0.00 0.00 4.06
3092 3177 3.778954 AGCTCTAAACTGAGGCTTTGT 57.221 42.857 0.00 0.00 34.82 2.83
3137 3222 3.090952 TGGTGTGTAATGCAGCAAAAC 57.909 42.857 0.00 0.79 40.72 2.43
3148 3233 0.848305 CAGCAAAACGAAGCAGCAAC 59.152 50.000 0.00 0.00 0.00 4.17
3160 3245 2.031516 CAGCAACCTCTGAGGCACG 61.032 63.158 23.43 12.73 39.63 5.34
3283 3368 0.749454 CCTGAGGCTACAATGGCACC 60.749 60.000 0.00 0.00 34.73 5.01
3312 3397 4.036262 CAGCTACAGGAACTAGTAGAGCAG 59.964 50.000 3.59 0.00 40.16 4.24
3429 3514 0.687757 AGGAAGCGGCTGAGTGGATA 60.688 55.000 1.81 0.00 0.00 2.59
3469 3554 5.514136 CCCCACTTAACTGGTGATGTTTCTA 60.514 44.000 1.13 0.00 36.89 2.10
3531 3624 4.841443 TTGCTACGAGTGAGTAACTTCA 57.159 40.909 0.00 0.00 40.07 3.02
3551 3644 5.294734 TCATATCTCTTGCCATACTTGCA 57.705 39.130 0.00 0.00 36.84 4.08
3563 3658 4.807304 GCCATACTTGCATTTTGGATTCAG 59.193 41.667 8.86 0.00 0.00 3.02
3566 3661 6.350361 CCATACTTGCATTTTGGATTCAGTGA 60.350 38.462 0.00 0.00 0.00 3.41
3584 3679 5.582269 TCAGTGATAAATGCTTGCTGTAGAC 59.418 40.000 0.00 0.00 0.00 2.59
3605 3700 6.091437 AGACTTTACGATTTCCTTAGTCGTG 58.909 40.000 9.59 0.00 46.70 4.35
3612 3707 4.092821 CGATTTCCTTAGTCGTGAATGCAA 59.907 41.667 0.00 0.00 0.00 4.08
3618 3713 5.407387 TCCTTAGTCGTGAATGCAAAAGTAC 59.593 40.000 0.00 0.00 0.00 2.73
3803 3898 4.101741 GGATGGACCTACTGTCTGCTTATT 59.898 45.833 0.00 0.00 43.89 1.40
3859 3954 2.713863 TACGGTTTCCTTGGTTGTGT 57.286 45.000 0.00 0.00 0.00 3.72
3862 3957 1.262151 CGGTTTCCTTGGTTGTGTACG 59.738 52.381 0.00 0.00 0.00 3.67
3876 3971 1.003223 GTGTACGCAAAAGTGTGGTCC 60.003 52.381 0.39 0.00 39.72 4.46
3891 3986 0.942252 GGTCCAGTTTGAACGGTGAC 59.058 55.000 0.00 6.91 0.00 3.67
3988 4083 2.863740 GTTTTGTTTGCACCAAGCCTAC 59.136 45.455 0.00 0.00 44.83 3.18
4090 4190 9.884465 CTATACAAGCTTTTTATCCATACAAGC 57.116 33.333 0.00 0.00 0.00 4.01
4091 4191 5.965922 ACAAGCTTTTTATCCATACAAGCC 58.034 37.500 0.00 0.00 0.00 4.35
4198 4305 0.813210 GACAGGCAGGCACATAGCTC 60.813 60.000 0.00 0.00 44.79 4.09
4199 4306 1.886313 CAGGCAGGCACATAGCTCG 60.886 63.158 0.00 0.00 44.79 5.03
4243 4350 3.932710 GTCGTCTGAAGTATTGGCAATGA 59.067 43.478 22.57 7.25 0.00 2.57
4306 4418 5.470098 AGTTAACACAGCACAGATAGTTTGG 59.530 40.000 8.61 0.00 0.00 3.28
4308 4420 2.153645 CACAGCACAGATAGTTTGGCA 58.846 47.619 0.00 0.00 0.00 4.92
4329 4441 5.861491 CAAGCGCTATTTGCATTTAAGAG 57.139 39.130 12.05 0.00 43.06 2.85
4332 4444 4.037208 AGCGCTATTTGCATTTAAGAGCAT 59.963 37.500 8.99 2.21 40.94 3.79
4333 4445 4.380974 GCGCTATTTGCATTTAAGAGCATC 59.619 41.667 14.61 4.16 40.94 3.91
4334 4446 5.755813 CGCTATTTGCATTTAAGAGCATCT 58.244 37.500 14.61 0.00 46.55 2.90
4335 4447 5.850128 CGCTATTTGCATTTAAGAGCATCTC 59.150 40.000 14.61 0.00 44.40 2.75
4336 4448 6.148264 GCTATTTGCATTTAAGAGCATCTCC 58.852 40.000 10.56 0.00 43.80 3.71
4337 4449 6.238842 GCTATTTGCATTTAAGAGCATCTCCA 60.239 38.462 10.56 0.00 43.80 3.86
4338 4450 7.682741 GCTATTTGCATTTAAGAGCATCTCCAA 60.683 37.037 10.56 0.00 43.80 3.53
4344 4456 3.805267 GAGCATCTCCAACAGCCG 58.195 61.111 0.00 0.00 0.00 5.52
4345 4457 2.437359 AGCATCTCCAACAGCCGC 60.437 61.111 0.00 0.00 0.00 6.53
4346 4458 3.869272 GCATCTCCAACAGCCGCG 61.869 66.667 0.00 0.00 0.00 6.46
4347 4459 3.869272 CATCTCCAACAGCCGCGC 61.869 66.667 0.00 0.00 0.00 6.86
4348 4460 4.087892 ATCTCCAACAGCCGCGCT 62.088 61.111 5.56 0.00 40.77 5.92
4349 4461 2.721167 ATCTCCAACAGCCGCGCTA 61.721 57.895 5.56 0.00 36.40 4.26
4350 4462 2.238847 ATCTCCAACAGCCGCGCTAA 62.239 55.000 5.56 0.00 36.40 3.09
4351 4463 2.031314 TCCAACAGCCGCGCTAAA 59.969 55.556 5.56 0.00 36.40 1.85
4352 4464 2.175811 CCAACAGCCGCGCTAAAC 59.824 61.111 5.56 0.00 36.40 2.01
4353 4465 2.325082 CCAACAGCCGCGCTAAACT 61.325 57.895 5.56 0.00 36.40 2.66
4354 4466 1.017177 CCAACAGCCGCGCTAAACTA 61.017 55.000 5.56 0.00 36.40 2.24
4355 4467 0.793861 CAACAGCCGCGCTAAACTAA 59.206 50.000 5.56 0.00 36.40 2.24
4356 4468 0.794473 AACAGCCGCGCTAAACTAAC 59.206 50.000 5.56 0.00 36.40 2.34
4357 4469 1.343821 CAGCCGCGCTAAACTAACG 59.656 57.895 5.56 0.00 36.40 3.18
4361 4473 2.020969 GCGCTAAACTAACGCCGC 59.979 61.111 0.00 0.00 46.63 6.53
4362 4474 2.315356 CGCTAAACTAACGCCGCG 59.685 61.111 12.14 12.14 34.50 6.46
4363 4475 2.020969 GCTAAACTAACGCCGCGC 59.979 61.111 13.88 0.00 0.00 6.86
4364 4476 2.699212 CTAAACTAACGCCGCGCC 59.301 61.111 13.88 0.00 0.00 6.53
4365 4477 3.134141 CTAAACTAACGCCGCGCCG 62.134 63.158 13.88 8.36 0.00 6.46
4374 4486 4.174129 GCCGCGCCGCAAATTAGT 62.174 61.111 15.97 0.00 0.00 2.24
4375 4487 2.022762 CCGCGCCGCAAATTAGTC 59.977 61.111 10.75 0.00 0.00 2.59
4376 4488 2.461110 CCGCGCCGCAAATTAGTCT 61.461 57.895 10.75 0.00 0.00 3.24
4377 4489 1.296867 CGCGCCGCAAATTAGTCTG 60.297 57.895 10.75 0.00 0.00 3.51
4378 4490 1.794222 GCGCCGCAAATTAGTCTGT 59.206 52.632 3.15 0.00 0.00 3.41
4379 4491 0.168128 GCGCCGCAAATTAGTCTGTT 59.832 50.000 3.15 0.00 0.00 3.16
4380 4492 1.401018 GCGCCGCAAATTAGTCTGTTT 60.401 47.619 3.15 0.00 0.00 2.83
4381 4493 2.920647 GCGCCGCAAATTAGTCTGTTTT 60.921 45.455 3.15 0.00 0.00 2.43
4382 4494 3.668491 GCGCCGCAAATTAGTCTGTTTTA 60.668 43.478 3.15 0.00 0.00 1.52
4383 4495 4.088648 CGCCGCAAATTAGTCTGTTTTAG 58.911 43.478 0.00 0.00 0.00 1.85
4384 4496 3.851969 GCCGCAAATTAGTCTGTTTTAGC 59.148 43.478 0.00 0.00 0.00 3.09
4385 4497 4.088648 CCGCAAATTAGTCTGTTTTAGCG 58.911 43.478 0.00 0.00 40.95 4.26
4386 4498 3.538392 CGCAAATTAGTCTGTTTTAGCGC 59.462 43.478 0.00 0.00 34.98 5.92
4387 4499 3.538392 GCAAATTAGTCTGTTTTAGCGCG 59.462 43.478 0.00 0.00 0.00 6.86
4388 4500 3.385079 AATTAGTCTGTTTTAGCGCGC 57.615 42.857 26.66 26.66 0.00 6.86
4389 4501 0.711670 TTAGTCTGTTTTAGCGCGCG 59.288 50.000 28.44 28.44 0.00 6.86
4390 4502 1.680105 TAGTCTGTTTTAGCGCGCGC 61.680 55.000 45.10 45.10 42.33 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.927782 TGTGACCGCTGCACCACC 62.928 66.667 0.00 0.00 35.43 4.61
15 16 1.880796 CACGTGCGTCACCTTGTGA 60.881 57.895 0.82 0.00 40.50 3.58
44 45 3.332493 CTTGATGCTGCACGGTGGC 62.332 63.158 3.57 6.35 0.00 5.01
89 91 1.006102 CTTGGTCTTGACGTCCGCT 60.006 57.895 14.12 0.00 0.00 5.52
145 147 4.966787 GGGGTGAAGGTGCGGCAA 62.967 66.667 3.23 0.00 0.00 4.52
152 154 3.157680 CAGTTCCGGGGTGAAGGT 58.842 61.111 0.00 0.00 0.00 3.50
183 185 2.985847 GCTTGAACTTGCCGGGCT 60.986 61.111 21.46 0.00 0.00 5.19
209 211 2.817834 GCCGTCATAGCGTGGCAA 60.818 61.111 0.00 0.00 46.76 4.52
291 293 0.037975 CCAGTTTGCCATGACCTTGC 60.038 55.000 0.00 0.00 0.00 4.01
369 371 3.933886 AGCTCATCCCAAGAGGAGATTA 58.066 45.455 8.78 0.00 46.66 1.75
451 453 4.859798 CGGGAAGAGATACGATAGAATTGC 59.140 45.833 0.00 0.00 41.38 3.56
742 747 6.710597 ATGCTATGACTTGCTGAATTCAAT 57.289 33.333 9.88 0.81 0.00 2.57
743 748 7.812690 ATATGCTATGACTTGCTGAATTCAA 57.187 32.000 9.88 0.00 0.00 2.69
794 800 5.064441 AGCCAGATTTGAAATGCAGTAAC 57.936 39.130 0.00 0.00 0.00 2.50
874 880 4.540099 TGTGAAGGAAGGTTAGGATCCATT 59.460 41.667 15.82 0.00 35.62 3.16
908 914 3.353836 CCACGCACCGTTTCAGGG 61.354 66.667 0.00 0.00 38.32 4.45
942 948 0.254347 TGGGGAATGGGTAATGGGGA 60.254 55.000 0.00 0.00 0.00 4.81
944 950 2.179865 AGAATGGGGAATGGGTAATGGG 59.820 50.000 0.00 0.00 0.00 4.00
945 951 3.618120 AGAATGGGGAATGGGTAATGG 57.382 47.619 0.00 0.00 0.00 3.16
947 953 6.162241 AGAGTAAAGAATGGGGAATGGGTAAT 59.838 38.462 0.00 0.00 0.00 1.89
949 955 5.043762 AGAGTAAAGAATGGGGAATGGGTA 58.956 41.667 0.00 0.00 0.00 3.69
1071 1124 2.933287 AAGTGGTCGATGGCCCCA 60.933 61.111 0.00 0.00 0.00 4.96
1111 1164 4.451150 GGTGCTGCGGATGTCGGA 62.451 66.667 0.00 0.00 39.69 4.55
1180 1233 1.906105 TACACTGGGATTCGGGTGCC 61.906 60.000 0.00 0.00 33.53 5.01
1213 1267 5.585445 TCTCTGAGACAGTATTCGAGGTTAC 59.415 44.000 2.58 0.00 32.61 2.50
1224 1278 2.420058 TGCCGATCTCTGAGACAGTA 57.580 50.000 10.00 0.00 32.61 2.74
1231 1285 6.706270 GGTAATAGAAAAATGCCGATCTCTGA 59.294 38.462 0.00 0.00 0.00 3.27
1246 1300 2.306512 AGCAACACCCCGGTAATAGAAA 59.693 45.455 0.00 0.00 0.00 2.52
1248 1302 1.575419 AGCAACACCCCGGTAATAGA 58.425 50.000 0.00 0.00 0.00 1.98
1251 1305 0.696501 AGAAGCAACACCCCGGTAAT 59.303 50.000 0.00 0.00 0.00 1.89
1252 1306 0.475044 AAGAAGCAACACCCCGGTAA 59.525 50.000 0.00 0.00 0.00 2.85
1253 1307 0.035739 GAAGAAGCAACACCCCGGTA 59.964 55.000 0.00 0.00 0.00 4.02
1255 1309 0.323629 TAGAAGAAGCAACACCCCGG 59.676 55.000 0.00 0.00 0.00 5.73
1257 1311 3.421844 ACATTAGAAGAAGCAACACCCC 58.578 45.455 0.00 0.00 0.00 4.95
1258 1312 3.440522 GGACATTAGAAGAAGCAACACCC 59.559 47.826 0.00 0.00 0.00 4.61
1259 1313 3.440522 GGGACATTAGAAGAAGCAACACC 59.559 47.826 0.00 0.00 0.00 4.16
1272 1327 6.456501 CGGTAATAGAGAAAGGGGACATTAG 58.543 44.000 0.00 0.00 0.00 1.73
1273 1328 5.221581 GCGGTAATAGAGAAAGGGGACATTA 60.222 44.000 0.00 0.00 0.00 1.90
1274 1329 4.444449 GCGGTAATAGAGAAAGGGGACATT 60.444 45.833 0.00 0.00 0.00 2.71
1275 1330 3.071167 GCGGTAATAGAGAAAGGGGACAT 59.929 47.826 0.00 0.00 0.00 3.06
1276 1331 2.433239 GCGGTAATAGAGAAAGGGGACA 59.567 50.000 0.00 0.00 0.00 4.02
1277 1332 2.545322 CGCGGTAATAGAGAAAGGGGAC 60.545 54.545 0.00 0.00 0.00 4.46
1278 1333 1.684983 CGCGGTAATAGAGAAAGGGGA 59.315 52.381 0.00 0.00 0.00 4.81
1279 1334 1.270147 CCGCGGTAATAGAGAAAGGGG 60.270 57.143 19.50 0.00 0.00 4.79
1339 1394 3.257393 CCACAAGGAAGAATCTCACGAG 58.743 50.000 0.00 0.00 36.89 4.18
1380 1435 3.331478 AGACCTGATCAGAGCAAACAG 57.669 47.619 24.62 7.03 0.00 3.16
1381 1436 4.383444 CCATAGACCTGATCAGAGCAAACA 60.383 45.833 24.62 2.83 0.00 2.83
1496 1554 2.027745 TCACTTTAGGCTTCTCCTGCTG 60.028 50.000 0.00 0.00 46.98 4.41
1497 1555 2.235898 CTCACTTTAGGCTTCTCCTGCT 59.764 50.000 0.00 0.00 46.98 4.24
1498 1556 2.626840 CTCACTTTAGGCTTCTCCTGC 58.373 52.381 0.00 0.00 46.98 4.85
1499 1557 2.235898 AGCTCACTTTAGGCTTCTCCTG 59.764 50.000 0.00 0.00 46.98 3.86
1501 1559 2.419436 GGAGCTCACTTTAGGCTTCTCC 60.419 54.545 17.19 0.00 36.37 3.71
1502 1560 2.419436 GGGAGCTCACTTTAGGCTTCTC 60.419 54.545 17.19 0.00 36.37 2.87
1503 1561 1.557371 GGGAGCTCACTTTAGGCTTCT 59.443 52.381 17.19 0.00 36.37 2.85
1504 1562 1.557371 AGGGAGCTCACTTTAGGCTTC 59.443 52.381 14.34 0.00 36.37 3.86
1505 1563 1.662686 AGGGAGCTCACTTTAGGCTT 58.337 50.000 14.34 0.00 36.37 4.35
1529 1587 6.744537 GTGAGATAAGCACACAAAATGACATC 59.255 38.462 0.00 0.00 37.91 3.06
1571 1629 7.230747 TGGATGAAACCTGAAAACTAATCAGA 58.769 34.615 5.16 0.00 45.74 3.27
1586 1644 5.106594 GCAAACCAAATTGATGGATGAAACC 60.107 40.000 3.10 0.00 43.54 3.27
1759 1817 6.379988 GCATCCCTCCTATTTTCTTTAAACCA 59.620 38.462 0.00 0.00 0.00 3.67
1800 1858 9.075678 ACTAGTAGAGAACAAACTTGTAGCTTA 57.924 33.333 3.59 0.00 41.31 3.09
2085 2143 6.582672 GCTCAATTCTTTTAGCCTTGTAACAC 59.417 38.462 0.00 0.00 0.00 3.32
2130 2188 6.365247 CCGTTTCTAACCGATCCTGTATATTG 59.635 42.308 0.00 0.00 0.00 1.90
2137 2195 1.287425 GCCGTTTCTAACCGATCCTG 58.713 55.000 0.00 0.00 0.00 3.86
2406 2486 5.961272 AGTTTGTAAACACTTGGACCAAAG 58.039 37.500 8.59 6.58 41.30 2.77
2508 2593 8.044908 ACTCAACTTCCGTATACCATGTTATTT 58.955 33.333 0.00 0.00 0.00 1.40
2614 2699 8.964476 AATTATGAGAGAACGTATGGACAATT 57.036 30.769 0.00 0.00 0.00 2.32
2693 2778 9.614792 CCTCTGGCTTTTTATGTATAACTAAGT 57.385 33.333 0.00 0.00 0.00 2.24
3069 3154 5.121454 CACAAAGCCTCAGTTTAGAGCTAAG 59.879 44.000 0.00 0.00 34.26 2.18
3092 3177 4.278170 CCAAGACCAGTTAAGAATTGCACA 59.722 41.667 0.00 0.00 0.00 4.57
3137 3222 1.018226 CCTCAGAGGTTGCTGCTTCG 61.018 60.000 8.54 0.00 35.86 3.79
3148 3233 1.739562 GCTGTTCGTGCCTCAGAGG 60.740 63.158 12.81 12.81 38.80 3.69
3160 3245 0.953727 TGGCATGTCACTTGCTGTTC 59.046 50.000 14.82 0.00 40.03 3.18
3312 3397 2.520536 ATCCATAGCAGGGACGCCC 61.521 63.158 6.80 6.80 45.90 6.13
3395 3480 1.002069 TTCCTGGGATTGGAGCATGT 58.998 50.000 0.00 0.00 34.76 3.21
3429 3514 2.827921 GTGGGGCTTCATTTCACATTCT 59.172 45.455 0.00 0.00 0.00 2.40
3493 3579 3.332919 AGCAATTAGGCTATGAGCATCG 58.667 45.455 12.90 0.00 44.75 3.84
3551 3644 7.279313 GCAAGCATTTATCACTGAATCCAAAAT 59.721 33.333 0.00 0.00 0.00 1.82
3563 3658 6.428385 AAGTCTACAGCAAGCATTTATCAC 57.572 37.500 0.00 0.00 0.00 3.06
3566 3661 6.816640 TCGTAAAGTCTACAGCAAGCATTTAT 59.183 34.615 0.00 0.00 0.00 1.40
3584 3679 6.939551 TTCACGACTAAGGAAATCGTAAAG 57.060 37.500 0.00 0.00 46.76 1.85
3604 3699 9.157104 TCAAACTATATCGTACTTTTGCATTCA 57.843 29.630 0.00 0.00 0.00 2.57
3605 3700 9.982291 TTCAAACTATATCGTACTTTTGCATTC 57.018 29.630 0.00 0.00 0.00 2.67
3612 3707 7.315142 TCACCGTTCAAACTATATCGTACTTT 58.685 34.615 0.00 0.00 0.00 2.66
3618 3713 4.547587 GCGTTCACCGTTCAAACTATATCG 60.548 45.833 0.00 0.00 39.32 2.92
3758 3853 4.201990 CCTGCAAAACTGATATCCTTCAGC 60.202 45.833 0.00 0.00 45.75 4.26
3820 3915 5.972382 CCGTAAGTTCTACAGTAAGCATCTC 59.028 44.000 0.00 0.00 0.00 2.75
3859 3954 1.134340 ACTGGACCACACTTTTGCGTA 60.134 47.619 0.00 0.00 0.00 4.42
3862 3957 2.165437 TCAAACTGGACCACACTTTTGC 59.835 45.455 0.00 0.00 31.47 3.68
4084 4184 8.871629 TTCATAAACTGGATAAAAGGCTTGTA 57.128 30.769 0.00 0.00 0.00 2.41
4085 4185 7.775053 TTCATAAACTGGATAAAAGGCTTGT 57.225 32.000 0.00 0.00 0.00 3.16
4086 4186 9.657419 AATTTCATAAACTGGATAAAAGGCTTG 57.343 29.630 0.00 0.00 0.00 4.01
4198 4305 3.673484 CACCCACCCAGCAAAGCG 61.673 66.667 0.00 0.00 0.00 4.68
4199 4306 2.133641 AACACCCACCCAGCAAAGC 61.134 57.895 0.00 0.00 0.00 3.51
4329 4441 3.869272 CGCGGCTGTTGGAGATGC 61.869 66.667 0.00 0.00 0.00 3.91
4332 4444 2.443260 TTTAGCGCGGCTGTTGGAGA 62.443 55.000 8.83 0.00 40.10 3.71
4333 4445 2.032634 TTTAGCGCGGCTGTTGGAG 61.033 57.895 8.83 0.00 40.10 3.86
4334 4446 2.031314 TTTAGCGCGGCTGTTGGA 59.969 55.556 8.83 0.00 40.10 3.53
4335 4447 1.017177 TAGTTTAGCGCGGCTGTTGG 61.017 55.000 8.83 0.00 40.10 3.77
4336 4448 0.793861 TTAGTTTAGCGCGGCTGTTG 59.206 50.000 8.83 0.00 40.10 3.33
4337 4449 0.794473 GTTAGTTTAGCGCGGCTGTT 59.206 50.000 8.83 0.00 40.10 3.16
4338 4450 1.349259 CGTTAGTTTAGCGCGGCTGT 61.349 55.000 8.83 0.00 40.10 4.40
4339 4451 1.343821 CGTTAGTTTAGCGCGGCTG 59.656 57.895 8.83 0.00 40.10 4.85
4340 4452 3.776656 CGTTAGTTTAGCGCGGCT 58.223 55.556 8.83 8.38 43.41 5.52
4345 4457 2.315356 CGCGGCGTTAGTTTAGCG 59.685 61.111 15.36 0.00 41.56 4.26
4346 4458 2.020969 GCGCGGCGTTAGTTTAGC 59.979 61.111 24.46 0.00 0.00 3.09
4347 4459 2.699212 GGCGCGGCGTTAGTTTAG 59.301 61.111 24.46 0.00 0.00 1.85
4348 4460 3.180614 CGGCGCGGCGTTAGTTTA 61.181 61.111 41.95 0.00 0.00 2.01
4357 4469 4.174129 ACTAATTTGCGGCGCGGC 62.174 61.111 30.55 30.55 0.00 6.53
4358 4470 2.022762 GACTAATTTGCGGCGCGG 59.977 61.111 28.09 11.08 0.00 6.46
4359 4471 1.296867 CAGACTAATTTGCGGCGCG 60.297 57.895 28.09 14.11 0.00 6.86
4360 4472 0.168128 AACAGACTAATTTGCGGCGC 59.832 50.000 27.44 27.44 0.00 6.53
4361 4473 2.611974 AAACAGACTAATTTGCGGCG 57.388 45.000 0.51 0.51 0.00 6.46
4362 4474 3.851969 GCTAAAACAGACTAATTTGCGGC 59.148 43.478 0.00 0.00 0.00 6.53
4363 4475 4.088648 CGCTAAAACAGACTAATTTGCGG 58.911 43.478 11.93 0.00 33.82 5.69
4364 4476 3.538392 GCGCTAAAACAGACTAATTTGCG 59.462 43.478 0.00 14.06 37.02 4.85
4365 4477 3.538392 CGCGCTAAAACAGACTAATTTGC 59.462 43.478 5.56 0.00 0.00 3.68
4366 4478 3.538392 GCGCGCTAAAACAGACTAATTTG 59.462 43.478 26.67 0.00 0.00 2.32
4367 4479 3.723835 CGCGCGCTAAAACAGACTAATTT 60.724 43.478 30.48 0.00 0.00 1.82
4368 4480 2.222729 CGCGCGCTAAAACAGACTAATT 60.223 45.455 30.48 0.00 0.00 1.40
4369 4481 1.323534 CGCGCGCTAAAACAGACTAAT 59.676 47.619 30.48 0.00 0.00 1.73
4370 4482 0.711670 CGCGCGCTAAAACAGACTAA 59.288 50.000 30.48 0.00 0.00 2.24
4371 4483 1.680105 GCGCGCGCTAAAACAGACTA 61.680 55.000 44.38 0.00 38.26 2.59
4372 4484 3.011760 GCGCGCGCTAAAACAGACT 62.012 57.895 44.38 0.00 38.26 3.24
4373 4485 2.570838 GCGCGCGCTAAAACAGAC 60.571 61.111 44.38 14.45 38.26 3.51
4374 4486 4.128982 CGCGCGCGCTAAAACAGA 62.129 61.111 45.97 0.00 39.32 3.41


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

AutoCloner maintained by Alex Coulton.