Multiple sequence alignment - TraesCS4A01G177700

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 TraesCS4A01G177700 chr4A 100.000 2711 0 0 1 2711 449401047 449398337 0.000000e+00 5007.0
1 TraesCS4A01G177700 chr4A 77.703 148 21 10 2482 2618 37805060 37805206 2.240000e-11 80.5
2 TraesCS4A01G177700 chr4B 93.287 2458 114 15 270 2711 184300417 184302839 0.000000e+00 3578.0
3 TraesCS4A01G177700 chr4B 84.000 100 14 2 80 178 369047630 369047728 7.990000e-16 95.3
4 TraesCS4A01G177700 chr4B 86.538 52 6 1 77 128 27929176 27929226 3.770000e-04 56.5
5 TraesCS4A01G177700 chr4D 94.458 2039 96 7 1 2031 121473049 121475078 0.000000e+00 3123.0
6 TraesCS4A01G177700 chr4D 95.322 171 5 1 2036 2206 121475124 121475291 4.450000e-68 268.0
7 TraesCS4A01G177700 chr4D 87.500 72 9 0 86 157 346380775 346380704 1.730000e-12 84.2
8 TraesCS4A01G177700 chr7B 90.816 98 9 0 2523 2620 106804193 106804096 6.090000e-27 132.0
9 TraesCS4A01G177700 chr7B 100.000 30 0 0 99 128 162120896 162120867 3.770000e-04 56.5
10 TraesCS4A01G177700 chr3B 90.426 94 8 1 2524 2617 655635076 655634984 3.670000e-24 122.0
11 TraesCS4A01G177700 chr3B 87.234 94 12 0 2524 2617 118507362 118507269 1.030000e-19 108.0
12 TraesCS4A01G177700 chr7D 79.562 137 16 9 2486 2611 611253589 611253724 1.340000e-13 87.9
13 TraesCS4A01G177700 chr7D 100.000 30 0 0 99 128 197883751 197883722 3.770000e-04 56.5
14 TraesCS4A01G177700 chr2B 77.703 148 21 9 2482 2617 602996447 602996300 2.240000e-11 80.5
15 TraesCS4A01G177700 chr2D 77.551 147 22 9 2482 2617 512769338 512769192 8.050000e-11 78.7
16 TraesCS4A01G177700 chr2D 86.441 59 7 1 2469 2527 335122942 335122885 2.250000e-06 63.9
17 TraesCS4A01G177700 chr6D 77.941 136 19 9 2486 2610 355103991 355103856 1.040000e-09 75.0
18 TraesCS4A01G177700 chr5A 90.909 55 2 2 2473 2527 341688270 341688321 1.350000e-08 71.3
19 TraesCS4A01G177700 chr6B 95.238 42 2 0 2486 2527 133694882 133694841 1.740000e-07 67.6
20 TraesCS4A01G177700 chr3D 91.111 45 4 0 84 128 7224587 7224631 8.100000e-06 62.1
21 TraesCS4A01G177700 chr3A 82.857 70 11 1 86 154 593353504 593353435 8.100000e-06 62.1
22 TraesCS4A01G177700 chr6A 90.909 44 4 0 85 128 93892399 93892356 2.920000e-05 60.2


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 TraesCS4A01G177700 chr4A 449398337 449401047 2710 True 5007.0 5007 100.000 1 2711 1 chr4A.!!$R1 2710
1 TraesCS4A01G177700 chr4B 184300417 184302839 2422 False 3578.0 3578 93.287 270 2711 1 chr4B.!!$F2 2441
2 TraesCS4A01G177700 chr4D 121473049 121475291 2242 False 1695.5 3123 94.890 1 2206 2 chr4D.!!$F1 2205

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
962 968 0.178975 CTACGAGGGGAGGCTCTCAT 60.179 60.0 17.73 9.61 31.08 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2605 2669 0.114954 TGTAGTTGTACCCCCTCCGT 59.885 55.0 0.0 0.0 0.0 4.69 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 1.965414 TCAGACAGGCCTTATGGGAA 58.035 50.000 0.00 0.00 37.23 3.97
83 85 4.494515 GGGAAAGCCCGTCAAAGT 57.505 55.556 0.00 0.00 46.48 2.66
85 87 1.450025 GGGAAAGCCCGTCAAAGTAG 58.550 55.000 0.00 0.00 46.48 2.57
89 91 3.306571 GGAAAGCCCGTCAAAGTAGTACT 60.307 47.826 0.00 0.00 0.00 2.73
91 93 5.473039 GAAAGCCCGTCAAAGTAGTACTAA 58.527 41.667 3.61 0.00 0.00 2.24
95 97 4.082571 GCCCGTCAAAGTAGTACTAACTCA 60.083 45.833 3.61 0.00 37.15 3.41
97 99 5.392811 CCCGTCAAAGTAGTACTAACTCAGG 60.393 48.000 3.61 3.82 37.15 3.86
98 100 5.182760 CCGTCAAAGTAGTACTAACTCAGGT 59.817 44.000 3.61 0.00 37.15 4.00
104 106 8.746530 CAAAGTAGTACTAACTCAGGTCCATAA 58.253 37.037 3.61 0.00 37.15 1.90
114 116 4.710375 ACTCAGGTCCATAATAAGTGTCGT 59.290 41.667 0.00 0.00 0.00 4.34
125 127 8.932791 CCATAATAAGTGTCGTAGTTTTGAACT 58.067 33.333 0.00 0.00 45.40 3.01
132 134 2.725723 TCGTAGTTTTGAACTAACCGCG 59.274 45.455 0.00 0.00 44.95 6.46
143 145 1.600485 ACTAACCGCGGTTCAAAACAG 59.400 47.619 44.24 34.32 39.31 3.16
144 146 1.600485 CTAACCGCGGTTCAAAACAGT 59.400 47.619 44.24 22.14 39.31 3.55
149 151 1.002900 CGCGGTTCAAAACAGTGACAT 60.003 47.619 0.00 0.00 39.02 3.06
158 160 8.334632 GGTTCAAAACAGTGACATTTATTTTGG 58.665 33.333 13.15 0.00 37.53 3.28
162 164 9.258826 CAAAACAGTGACATTTATTTTGGATCA 57.741 29.630 0.00 0.00 34.77 2.92
168 170 7.454380 AGTGACATTTATTTTGGATCAAAGGGA 59.546 33.333 0.00 0.00 34.72 4.20
184 186 6.797707 TCAAAGGGAGTACTAGTTTAGAGGA 58.202 40.000 0.00 0.00 0.00 3.71
196 198 7.566569 ACTAGTTTAGAGGAGGAAATAAAGCC 58.433 38.462 0.00 0.00 0.00 4.35
271 273 2.301346 CAGACCCTGGAATAATGTGGC 58.699 52.381 0.00 0.00 0.00 5.01
302 304 2.403252 AGGGTCAATCGATTGTGTCC 57.597 50.000 31.49 28.13 38.84 4.02
351 353 6.346096 GGTTGGCATTAGACTGTCAGTATTA 58.654 40.000 5.21 0.00 31.32 0.98
357 359 7.863375 GGCATTAGACTGTCAGTATTACTGTAG 59.137 40.741 20.43 20.01 46.03 2.74
385 387 6.801862 GCGATCATGTTTATAATAAACTGGGC 59.198 38.462 0.00 0.00 0.00 5.36
432 434 8.741603 TCATATTCATGACATGTTGATCAACT 57.258 30.769 32.57 17.55 37.91 3.16
452 454 5.622346 ACTGGGAGTTTATGATCTTCTCC 57.378 43.478 6.37 6.37 42.53 3.71
504 506 1.250328 TGTCAAGCTGGGCAATCAAG 58.750 50.000 0.00 0.00 0.00 3.02
626 628 1.756538 ACTTTGCCCACAAGGAACAAG 59.243 47.619 0.00 0.00 36.43 3.16
719 721 2.498078 ACTCCAACTCAACCTAGCTAGC 59.502 50.000 15.74 6.62 0.00 3.42
803 805 1.267806 CAAACAACAGTAGCCAGCCTG 59.732 52.381 0.00 0.00 34.82 4.85
889 895 3.269178 GTGCTCATCTCCCTTTCTTCAG 58.731 50.000 0.00 0.00 0.00 3.02
932 938 2.776536 CCTCTCCAACTCCAATCATCCT 59.223 50.000 0.00 0.00 0.00 3.24
962 968 0.178975 CTACGAGGGGAGGCTCTCAT 60.179 60.000 17.73 9.61 31.08 2.90
963 969 0.261991 TACGAGGGGAGGCTCTCATT 59.738 55.000 17.73 3.18 31.08 2.57
986 992 4.529897 TGTGCAGATCTGGATAGCAAAAT 58.470 39.130 23.89 0.00 34.93 1.82
988 994 4.820716 GTGCAGATCTGGATAGCAAAATCT 59.179 41.667 23.89 0.00 34.93 2.40
1005 1011 6.346096 CAAAATCTGGAAGCAATCAATGGAT 58.654 36.000 0.00 0.00 34.43 3.41
1009 1015 5.205821 TCTGGAAGCAATCAATGGATCAAT 58.794 37.500 0.00 0.00 31.88 2.57
1023 1029 1.942657 GATCAATTAGCCAAGCGCAGA 59.057 47.619 11.47 0.00 41.38 4.26
1074 1080 2.883468 CGATCCGTCCTCGTCCTCG 61.883 68.421 0.00 0.00 38.55 4.63
1157 1163 1.888436 TACTCCTGCACCTTCTGCCG 61.888 60.000 0.00 0.00 46.51 5.69
1158 1164 4.704833 TCCTGCACCTTCTGCCGC 62.705 66.667 0.00 0.00 46.51 6.53
1304 1310 1.737029 CGACTCTACCAGTGCCATGTG 60.737 57.143 0.00 0.00 34.41 3.21
1391 1397 6.409704 TCATCAAGGAGAGGAATAACAACAG 58.590 40.000 0.00 0.00 33.45 3.16
1429 1435 3.119029 AGCAGTGAGAGATCAAGAAGCTC 60.119 47.826 0.00 0.00 0.00 4.09
1609 1615 9.369672 CTAGTAGTTCTAGTCTTAATCCCCATT 57.630 37.037 0.00 0.00 40.72 3.16
1755 1761 7.391554 TGAAATCGATGAATTCTTTTCCACTCT 59.608 33.333 7.05 0.00 0.00 3.24
1800 1809 5.242434 TCTAGCTCGTTAAATTTGCTTCCA 58.758 37.500 5.41 0.00 35.47 3.53
1885 1894 6.304208 GCTTTGTTCATTGTTTCTCTTCGATC 59.696 38.462 0.00 0.00 0.00 3.69
1976 1985 9.448438 TGTTGAAATGTATATGTGCTAGAGTTT 57.552 29.630 0.00 0.00 0.00 2.66
2031 2040 7.879677 TGTTCTGAAGTCTTGTATCATGTTGAT 59.120 33.333 0.00 0.00 40.72 2.57
2032 2041 7.838771 TCTGAAGTCTTGTATCATGTTGATG 57.161 36.000 0.30 0.00 37.70 3.07
2074 2124 4.021719 AGTGATCAGTGGCAGAAAATTTGG 60.022 41.667 1.14 0.00 0.00 3.28
2211 2264 4.833811 TGGCAACATCGATCCTCG 57.166 55.556 0.00 0.00 46.17 4.63
2225 2278 1.216710 CCTCGCCACTTCTCTCCAC 59.783 63.158 0.00 0.00 0.00 4.02
2234 2287 1.178276 CTTCTCTCCACTAGCACCGT 58.822 55.000 0.00 0.00 0.00 4.83
2277 2330 4.275443 GCCTTTGCCAAATGAAACAATGAA 59.725 37.500 0.00 0.00 0.00 2.57
2321 2374 9.209175 CCAACTCTATAGTGATTTATTGCCTAC 57.791 37.037 8.76 0.00 35.62 3.18
2347 2400 7.801716 TCGAATATAACCCAAATCAAAGAGG 57.198 36.000 0.00 0.00 0.00 3.69
2397 2450 3.838565 TGCCCCAAGAACTTAAATGACA 58.161 40.909 0.00 0.00 0.00 3.58
2463 2516 7.041508 GGAGCACCATCTTTGAGATACTAAATG 60.042 40.741 0.00 0.00 32.12 2.32
2488 2541 8.136165 TGTCTGAAGTAACTACTCTCTTTGTTC 58.864 37.037 0.00 0.00 34.99 3.18
2546 2610 9.817809 TGGACTAAAATGAGTGAATCTATACAC 57.182 33.333 0.00 0.00 37.30 2.90
2547 2611 9.262358 GGACTAAAATGAGTGAATCTATACACC 57.738 37.037 0.00 0.00 37.69 4.16
2555 2619 9.770097 ATGAGTGAATCTATACACCTAAACATG 57.230 33.333 0.00 0.00 37.69 3.21
2605 2669 7.584122 AGCTAGAACATCTTATACTTCGGAA 57.416 36.000 0.00 0.00 0.00 4.30
2679 2745 3.345808 GTGTGTGCGCCGACATGT 61.346 61.111 4.18 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 7.419057 CCATAAGGCCTGTCTGAATTAGAACTA 60.419 40.741 5.69 0.00 37.12 2.24
54 56 1.393603 GCTTTCCCATAAGGCCTGTC 58.606 55.000 5.69 0.00 34.51 3.51
55 57 0.033109 GGCTTTCCCATAAGGCCTGT 60.033 55.000 5.69 0.00 42.93 4.00
70 72 4.525874 AGTTAGTACTACTTTGACGGGCTT 59.474 41.667 0.91 0.00 31.21 4.35
75 77 6.251655 ACCTGAGTTAGTACTACTTTGACG 57.748 41.667 0.91 0.00 33.84 4.35
85 87 8.693625 ACACTTATTATGGACCTGAGTTAGTAC 58.306 37.037 0.00 0.00 0.00 2.73
89 91 6.379133 ACGACACTTATTATGGACCTGAGTTA 59.621 38.462 0.00 0.00 0.00 2.24
91 93 4.710375 ACGACACTTATTATGGACCTGAGT 59.290 41.667 0.00 0.00 0.00 3.41
95 97 6.786967 AACTACGACACTTATTATGGACCT 57.213 37.500 0.00 0.00 0.00 3.85
97 99 8.470040 TCAAAACTACGACACTTATTATGGAC 57.530 34.615 0.00 0.00 0.00 4.02
98 100 8.928733 GTTCAAAACTACGACACTTATTATGGA 58.071 33.333 0.00 0.00 0.00 3.41
104 106 7.115378 CGGTTAGTTCAAAACTACGACACTTAT 59.885 37.037 0.00 0.00 43.30 1.73
114 116 3.110447 ACCGCGGTTAGTTCAAAACTA 57.890 42.857 28.70 0.00 42.81 2.24
125 127 1.331138 CACTGTTTTGAACCGCGGTTA 59.669 47.619 41.27 25.90 38.60 2.85
132 134 8.334632 CCAAAATAAATGTCACTGTTTTGAACC 58.665 33.333 15.02 0.00 38.26 3.62
143 145 7.610865 TCCCTTTGATCCAAAATAAATGTCAC 58.389 34.615 0.00 0.00 32.75 3.67
144 146 7.454380 ACTCCCTTTGATCCAAAATAAATGTCA 59.546 33.333 0.00 0.00 32.75 3.58
149 151 9.681062 CTAGTACTCCCTTTGATCCAAAATAAA 57.319 33.333 0.00 0.00 32.75 1.40
158 160 7.560626 TCCTCTAAACTAGTACTCCCTTTGATC 59.439 40.741 0.00 0.00 0.00 2.92
162 164 6.010918 TCCTCCTCTAAACTAGTACTCCCTTT 60.011 42.308 0.00 0.00 0.00 3.11
174 176 6.644308 AGGCTTTATTTCCTCCTCTAAACT 57.356 37.500 0.00 0.00 0.00 2.66
194 196 9.822185 ATCAATTGGTCTTTTATATGAAAAGGC 57.178 29.630 5.42 10.97 40.17 4.35
214 216 4.836125 AGTTTTGACGAGCACATCAATT 57.164 36.364 0.00 0.00 34.87 2.32
271 273 2.489938 TTGACCCTTCCAAGATTCGG 57.510 50.000 0.00 0.00 0.00 4.30
302 304 4.201628 GCTTGCTAGTGACGACTAAACATG 60.202 45.833 0.00 0.00 34.14 3.21
351 353 2.680312 AACATGATCGCAGCTACAGT 57.320 45.000 0.00 0.00 0.00 3.55
357 359 7.535258 CCAGTTTATTATAAACATGATCGCAGC 59.465 37.037 24.20 0.00 32.81 5.25
432 434 5.163405 CGAAGGAGAAGATCATAAACTCCCA 60.163 44.000 0.00 0.00 45.53 4.37
452 454 4.576053 TGTCATTATTTGCTCCATCCGAAG 59.424 41.667 0.00 0.00 0.00 3.79
504 506 0.744771 GTGTCCCCTTCGAATCTGGC 60.745 60.000 0.00 0.00 0.00 4.85
536 538 2.407340 ATCTATCCAGGTGAGGGGAC 57.593 55.000 0.00 0.00 35.67 4.46
539 541 4.119556 TGACTATCTATCCAGGTGAGGG 57.880 50.000 0.00 0.00 0.00 4.30
719 721 7.121974 CACCTACAGTGTTATTTTCTGTCAG 57.878 40.000 0.00 0.00 41.93 3.51
803 805 4.627467 CCAGTACAAGATAGTGTGCAGTTC 59.373 45.833 0.00 0.00 36.66 3.01
962 968 3.632643 TGCTATCCAGATCTGCACAAA 57.367 42.857 17.76 0.16 0.00 2.83
963 969 3.632643 TTGCTATCCAGATCTGCACAA 57.367 42.857 17.76 12.36 32.80 3.33
986 992 4.239428 TGATCCATTGATTGCTTCCAGA 57.761 40.909 0.00 0.00 0.00 3.86
988 994 5.943349 AATTGATCCATTGATTGCTTCCA 57.057 34.783 0.00 0.00 0.00 3.53
1005 1011 1.372582 CTCTGCGCTTGGCTAATTGA 58.627 50.000 9.73 0.00 44.05 2.57
1009 1015 2.436646 GCCTCTGCGCTTGGCTAA 60.437 61.111 24.10 0.00 43.05 3.09
1018 1024 3.694058 AAGCTGGGATGCCTCTGCG 62.694 63.158 4.35 0.00 41.78 5.18
1051 1057 3.518998 CGAGGACGGATCGCTGGT 61.519 66.667 0.00 0.00 32.81 4.00
1074 1080 3.334054 AAGGCCTGCTCCTCCCAC 61.334 66.667 5.69 0.00 34.82 4.61
1249 1255 1.691196 TCAGCTTGTTCTTGTTGGGG 58.309 50.000 0.00 0.00 0.00 4.96
1391 1397 1.359475 GCTATGGAGACGACGACCC 59.641 63.158 0.00 0.00 0.00 4.46
1429 1435 2.427095 TGTCATCGTACTGGTGATCTGG 59.573 50.000 4.41 0.00 0.00 3.86
1609 1615 5.960811 ACAGATCTACTTCTCCTTGATCCAA 59.039 40.000 0.00 0.00 35.46 3.53
1826 1835 8.953368 AGAGACAGAAGCAATTTTTGATTTTT 57.047 26.923 0.00 0.00 39.73 1.94
1827 1836 8.953368 AAGAGACAGAAGCAATTTTTGATTTT 57.047 26.923 0.00 0.00 39.73 1.82
1828 1837 8.953368 AAAGAGACAGAAGCAATTTTTGATTT 57.047 26.923 0.00 0.00 39.73 2.17
1885 1894 2.791383 TGGCCAACAACGAAGAATTG 57.209 45.000 0.61 0.00 0.00 2.32
2074 2124 8.992835 AGATAAAGAAAAATGGCAATCACTTC 57.007 30.769 0.00 0.00 0.00 3.01
2169 2222 8.180267 CACCTCTTTTCTTGATGATGTACAATC 58.820 37.037 0.00 0.00 0.00 2.67
2170 2223 7.121759 CCACCTCTTTTCTTGATGATGTACAAT 59.878 37.037 0.00 0.00 0.00 2.71
2171 2224 6.430925 CCACCTCTTTTCTTGATGATGTACAA 59.569 38.462 0.00 0.00 0.00 2.41
2211 2264 0.898320 TGCTAGTGGAGAGAAGTGGC 59.102 55.000 0.00 0.00 0.00 5.01
2225 2278 6.132791 TCTACTTGATTAGAACGGTGCTAG 57.867 41.667 0.00 0.00 0.00 3.42
2234 2287 8.514594 CAAAGGCAAACATCTACTTGATTAGAA 58.485 33.333 0.00 0.00 31.78 2.10
2277 2330 1.035139 GGCGATTTTCATCCAGCCAT 58.965 50.000 0.00 0.00 43.65 4.40
2321 2374 8.345565 CCTCTTTGATTTGGGTTATATTCGAAG 58.654 37.037 3.35 0.00 0.00 3.79
2347 2400 7.332182 CACTTTACCTTATCTCTCCTTGACAAC 59.668 40.741 0.00 0.00 0.00 3.32
2463 2516 7.595875 GGAACAAAGAGAGTAGTTACTTCAGAC 59.404 40.741 0.00 0.00 36.50 3.51
2483 2536 9.015367 TCCAAAACATCTTATAATTCGGAACAA 57.985 29.630 0.00 0.00 0.00 2.83
2484 2537 8.568676 TCCAAAACATCTTATAATTCGGAACA 57.431 30.769 0.00 0.00 0.00 3.18
2586 2650 5.585390 TCCGTTCCGAAGTATAAGATGTTC 58.415 41.667 0.00 0.00 0.00 3.18
2587 2651 5.451520 CCTCCGTTCCGAAGTATAAGATGTT 60.452 44.000 0.00 0.00 0.00 2.71
2598 2662 1.683365 TACCCCCTCCGTTCCGAAG 60.683 63.158 0.00 0.00 0.00 3.79
2605 2669 0.114954 TGTAGTTGTACCCCCTCCGT 59.885 55.000 0.00 0.00 0.00 4.69
2613 2677 7.562135 TCTTGGGATTTAGATGTAGTTGTACC 58.438 38.462 0.00 0.00 0.00 3.34
2651 2715 1.234821 CGCACACACAAGGGTACAAT 58.765 50.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.