Multiple sequence alignment - TraesCS6B01G379300

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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 TraesCS6B01G379300 chr6B 100.000 3112 0 0 1 3112 653873547 653870436 0.000000e+00 5747.0
1 TraesCS6B01G379300 chr6B 88.626 1688 166 12 700 2376 653715843 653714171 0.000000e+00 2030.0
2 TraesCS6B01G379300 chr6B 88.340 1681 165 9 701 2376 653788972 653787318 0.000000e+00 1989.0
3 TraesCS6B01G379300 chr6B 89.051 1580 153 8 808 2376 653856640 653855070 0.000000e+00 1941.0
4 TraesCS6B01G379300 chr6B 89.220 1475 148 9 700 2170 653195014 653193547 0.000000e+00 1832.0
5 TraesCS6B01G379300 chr6B 89.120 1397 111 15 5 1395 653699932 653698571 0.000000e+00 1700.0
6 TraesCS6B01G379300 chr6B 84.471 586 78 9 2534 3112 653697624 653697045 1.620000e-157 566.0
7 TraesCS6B01G379300 chr6B 87.059 170 21 1 2370 2539 708939714 708939546 1.140000e-44 191.0
8 TraesCS6B01G379300 chr6B 89.610 77 4 2 2255 2328 655054671 655054746 9.190000e-16 95.3
9 TraesCS6B01G379300 chr6B 87.879 66 4 3 2373 2437 459754977 459755039 1.200000e-09 75.0
10 TraesCS6B01G379300 chr6D 95.162 3121 134 11 1 3112 433281575 433278463 0.000000e+00 4911.0
11 TraesCS6B01G379300 chr6D 93.462 2386 131 14 1 2376 433156231 433153861 0.000000e+00 3518.0
12 TraesCS6B01G379300 chr6D 93.536 2274 130 10 113 2376 432932317 432930051 0.000000e+00 3369.0
13 TraesCS6B01G379300 chr6D 89.622 1667 154 9 700 2361 433259321 433257669 0.000000e+00 2102.0
14 TraesCS6B01G379300 chr6D 90.355 1576 134 7 808 2376 432914545 432912981 0.000000e+00 2052.0
15 TraesCS6B01G379300 chr6D 87.629 582 68 4 2534 3112 433153866 433153286 0.000000e+00 673.0
16 TraesCS6B01G379300 chr6D 88.022 359 42 1 2542 2899 432930048 432929690 1.030000e-114 424.0
17 TraesCS6B01G379300 chr6D 86.774 310 28 6 2070 2376 433037324 433037025 1.790000e-87 333.0
18 TraesCS6B01G379300 chr6D 87.324 213 27 0 2534 2746 432912986 432912774 8.620000e-61 244.0
19 TraesCS6B01G379300 chr6D 89.655 58 4 1 586 641 432914759 432914702 4.300000e-09 73.1
20 TraesCS6B01G379300 chr6D 84.932 73 7 3 2366 2437 460272526 460272595 1.550000e-08 71.3
21 TraesCS6B01G379300 chr6A 93.930 3130 167 11 1 3112 579144047 579140923 0.000000e+00 4706.0
22 TraesCS6B01G379300 chr6A 89.270 1575 153 5 808 2376 579125017 579123453 0.000000e+00 1958.0
23 TraesCS6B01G379300 chr3D 83.889 360 54 4 2757 3112 605638285 605637926 1.070000e-89 340.0
24 TraesCS6B01G379300 chr5A 83.889 360 53 5 2757 3112 589001983 589002341 3.840000e-89 339.0
25 TraesCS6B01G379300 chr5A 90.164 61 3 2 2375 2435 315138522 315138579 3.330000e-10 76.8
26 TraesCS6B01G379300 chr2D 83.333 360 53 7 2758 3112 604075056 604074699 2.990000e-85 326.0
27 TraesCS6B01G379300 chr7D 83.237 346 54 4 2768 3110 479999365 479999709 6.480000e-82 315.0
28 TraesCS6B01G379300 chr7D 74.371 437 82 18 1 426 500745104 500745521 3.210000e-35 159.0
29 TraesCS6B01G379300 chr7D 97.917 48 0 1 2374 2421 612887618 612887664 7.150000e-12 82.4
30 TraesCS6B01G379300 chr7D 88.060 67 6 2 2371 2437 137568026 137567962 9.250000e-11 78.7
31 TraesCS6B01G379300 chr5D 82.123 358 60 4 2755 3109 51636523 51636879 1.400000e-78 303.0
32 TraesCS6B01G379300 chr1D 91.837 49 3 1 2373 2421 24143753 24143800 2.000000e-07 67.6


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 TraesCS6B01G379300 chr6B 653870436 653873547 3111 True 5747.0 5747 100.000000 1 3112 1 chr6B.!!$R5 3111
1 TraesCS6B01G379300 chr6B 653714171 653715843 1672 True 2030.0 2030 88.626000 700 2376 1 chr6B.!!$R2 1676
2 TraesCS6B01G379300 chr6B 653787318 653788972 1654 True 1989.0 1989 88.340000 701 2376 1 chr6B.!!$R3 1675
3 TraesCS6B01G379300 chr6B 653855070 653856640 1570 True 1941.0 1941 89.051000 808 2376 1 chr6B.!!$R4 1568
4 TraesCS6B01G379300 chr6B 653193547 653195014 1467 True 1832.0 1832 89.220000 700 2170 1 chr6B.!!$R1 1470
5 TraesCS6B01G379300 chr6B 653697045 653699932 2887 True 1133.0 1700 86.795500 5 3112 2 chr6B.!!$R7 3107
6 TraesCS6B01G379300 chr6D 433278463 433281575 3112 True 4911.0 4911 95.162000 1 3112 1 chr6D.!!$R3 3111
7 TraesCS6B01G379300 chr6D 433257669 433259321 1652 True 2102.0 2102 89.622000 700 2361 1 chr6D.!!$R2 1661
8 TraesCS6B01G379300 chr6D 433153286 433156231 2945 True 2095.5 3518 90.545500 1 3112 2 chr6D.!!$R6 3111
9 TraesCS6B01G379300 chr6D 432929690 432932317 2627 True 1896.5 3369 90.779000 113 2899 2 chr6D.!!$R5 2786
10 TraesCS6B01G379300 chr6D 432912774 432914759 1985 True 789.7 2052 89.111333 586 2746 3 chr6D.!!$R4 2160
11 TraesCS6B01G379300 chr6A 579140923 579144047 3124 True 4706.0 4706 93.930000 1 3112 1 chr6A.!!$R2 3111
12 TraesCS6B01G379300 chr6A 579123453 579125017 1564 True 1958.0 1958 89.270000 808 2376 1 chr6A.!!$R1 1568

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
880 919 0.037605 CCGCTACGTTGGAGACCTTT 60.038 55.000 0.0 0.0 0.00 3.11 F
1417 1463 1.002430 GTGCAGTCACTCCCATCAAGA 59.998 52.381 0.0 0.0 40.03 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1772 1821 1.136110 TCATAGCTTTCGATGGTCGCA 59.864 47.619 0.0 0.0 40.21 5.10 R
2989 3056 0.109226 CGGACGAACTTGAGGAGGAC 60.109 60.000 0.0 0.0 0.00 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
57 58 5.104259 AGGAAGAGAAAAGTGTTGTCTGT 57.896 39.130 0.00 0.00 0.00 3.41
168 169 2.043852 AACCCAACAACCCGCACA 60.044 55.556 0.00 0.00 0.00 4.57
201 202 1.891919 GTGACCGCACACACACCAT 60.892 57.895 5.56 0.00 44.51 3.55
209 210 0.531753 CACACACACCATGACCGTCA 60.532 55.000 3.10 3.10 0.00 4.35
260 270 5.305585 TGAAATTGTTAGTCGAAAGGAGCT 58.694 37.500 0.00 0.00 0.00 4.09
281 291 4.382320 GCGTGGCCGGGAAGTACA 62.382 66.667 2.18 0.00 33.68 2.90
291 301 3.267483 CCGGGAAGTACATTAGGTGTTG 58.733 50.000 0.00 0.00 42.29 3.33
317 327 4.430137 AATTCTTGCACTAGACGTACGA 57.570 40.909 24.41 0.00 0.00 3.43
320 330 4.430137 TCTTGCACTAGACGTACGATTT 57.570 40.909 24.41 9.12 0.00 2.17
324 334 2.805845 CACTAGACGTACGATTTGGGG 58.194 52.381 24.41 5.97 0.00 4.96
344 354 2.229302 GGCTCACGGAGTCCATATAGAC 59.771 54.545 10.49 0.00 41.61 2.59
385 395 9.801192 TGAGTATCAAGCATTGTTTGGACTCCA 62.801 40.741 26.77 19.14 45.97 3.86
490 505 2.125106 CCGTGTTGCCCTCCTAGC 60.125 66.667 0.00 0.00 0.00 3.42
543 558 4.502105 TTGGCATGCTACAAGGATTCTA 57.498 40.909 18.92 0.00 0.00 2.10
571 586 7.446106 TGTATTCTCTGTTGGTACCCATAAT 57.554 36.000 10.07 4.57 31.53 1.28
677 714 2.223044 GCATAGACGGCAGCAAACTTAC 60.223 50.000 0.00 0.00 0.00 2.34
880 919 0.037605 CCGCTACGTTGGAGACCTTT 60.038 55.000 0.00 0.00 0.00 3.11
952 993 7.329226 CCAATTTCATTCGTAGAAACAAAGCAT 59.671 33.333 0.00 0.00 45.90 3.79
954 995 9.906660 AATTTCATTCGTAGAAACAAAGCATAA 57.093 25.926 0.00 0.00 45.90 1.90
992 1033 1.376543 ACTCGCAAGCAATCCATCAG 58.623 50.000 0.00 0.00 37.18 2.90
1014 1060 5.646793 CAGATATACCATGGCCATCTCAAAG 59.353 44.000 17.61 2.97 0.00 2.77
1100 1146 1.061131 CAACGATGACTTGTCGATGGC 59.939 52.381 2.28 0.00 41.40 4.40
1151 1197 1.928503 CAACCGTGTGTACAAAGACGT 59.071 47.619 17.30 0.00 0.00 4.34
1155 1201 2.472488 CCGTGTGTACAAAGACGTTACC 59.528 50.000 17.30 0.00 0.00 2.85
1342 1388 1.134068 GGGTTCCTACCAGATTCAGGC 60.134 57.143 0.00 0.00 46.96 4.85
1417 1463 1.002430 GTGCAGTCACTCCCATCAAGA 59.998 52.381 0.00 0.00 40.03 3.02
1569 1618 1.524002 GCTGCTACAGAGGGCATCA 59.476 57.895 0.58 0.00 37.83 3.07
1771 1820 2.821969 GCAAGAGTGGAACCAATGATGT 59.178 45.455 0.00 0.00 37.80 3.06
1772 1821 3.256631 GCAAGAGTGGAACCAATGATGTT 59.743 43.478 0.00 0.00 37.80 2.71
1782 1831 1.268184 CCAATGATGTTGCGACCATCG 60.268 52.381 0.45 0.00 41.28 3.84
2033 2082 0.600255 CATGGGGCGAGAACGGATAC 60.600 60.000 0.00 0.00 40.15 2.24
2075 2124 2.401766 CGACAAGAGGGGCATGTGC 61.402 63.158 0.00 0.00 41.14 4.57
2117 2166 1.898863 ACCCCACTGCATAGAAGGAT 58.101 50.000 0.00 0.00 0.00 3.24
2400 2460 4.475747 TCCCTCCGTTCCCAAATATAAGTT 59.524 41.667 0.00 0.00 0.00 2.66
2403 2463 6.829811 CCCTCCGTTCCCAAATATAAGTTTTA 59.170 38.462 0.00 0.00 0.00 1.52
2544 2605 7.979786 TTTAGGAACAGAGGAAGTATCTGAT 57.020 36.000 9.78 0.00 45.80 2.90
2884 2950 3.725032 GACGGGGAGGGGGTTTCC 61.725 72.222 0.00 0.00 0.00 3.13
2928 2994 5.130643 GCAGATAGGTAGGGTTTTAGTCCTT 59.869 44.000 0.00 0.00 34.75 3.36
2989 3056 1.135333 GAGTAGTCTTTCGGGCTCTGG 59.865 57.143 0.00 0.00 0.00 3.86
3011 3078 1.270147 CCTCCTCAAGTTCGTCCGTTT 60.270 52.381 0.00 0.00 0.00 3.60
3056 3123 3.849911 CGTAGATTCCTGTCAGCTTTCA 58.150 45.455 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.396166 CCAACACAGACAACACTTTTCTCT 59.604 41.667 0.00 0.00 0.00 3.10
57 58 2.248280 AGCGACACATACAACCAACA 57.752 45.000 0.00 0.00 0.00 3.33
92 93 1.626654 CGCCCTGCAAAGTAGACACG 61.627 60.000 0.00 0.00 0.00 4.49
145 146 2.419739 GGGTTGTTGGGTTGTGCGT 61.420 57.895 0.00 0.00 0.00 5.24
168 169 1.270678 GGTCACCCTAAGAAGCGTGTT 60.271 52.381 0.00 0.00 33.91 3.32
201 202 2.447630 ACAATCCCTGTGACGGTCA 58.552 52.632 6.76 6.76 36.69 4.02
209 210 5.219739 AGTACCATATCTCACAATCCCTGT 58.780 41.667 0.00 0.00 39.56 4.00
226 227 8.525316 TCGACTAACAATTTCATAGAAGTACCA 58.475 33.333 0.00 0.00 0.00 3.25
260 270 4.697756 CTTCCCGGCCACGCAGAA 62.698 66.667 2.24 0.00 39.22 3.02
281 291 8.421002 AGTGCAAGAATTTTAACAACACCTAAT 58.579 29.630 0.00 0.00 0.00 1.73
291 301 6.946584 CGTACGTCTAGTGCAAGAATTTTAAC 59.053 38.462 7.22 0.00 35.00 2.01
317 327 1.299976 GACTCCGTGAGCCCCAAAT 59.700 57.895 1.36 0.00 32.04 2.32
320 330 2.523740 TATGGACTCCGTGAGCCCCA 62.524 60.000 13.73 13.73 39.02 4.96
324 334 2.229302 GGTCTATATGGACTCCGTGAGC 59.771 54.545 17.58 0.00 36.55 4.26
571 586 2.552809 GGTACCTACCCCGCAAGAAAAA 60.553 50.000 4.06 0.00 40.53 1.94
677 714 5.005779 GCGTGAGTACAGAGGACAAAATATG 59.994 44.000 0.00 0.00 0.00 1.78
743 781 2.028567 TGCACGGTGATGTTGACAGATA 60.029 45.455 13.29 0.00 0.00 1.98
952 993 5.849510 AGTACTAGTGTGCAATGTGTGTTA 58.150 37.500 5.39 0.00 0.00 2.41
954 995 4.307432 GAGTACTAGTGTGCAATGTGTGT 58.693 43.478 5.39 0.00 0.00 3.72
992 1033 4.946157 CCTTTGAGATGGCCATGGTATATC 59.054 45.833 26.56 14.81 0.00 1.63
1014 1060 2.100418 GAGAAGGCCAATGATCAAAGCC 59.900 50.000 20.70 20.70 44.20 4.35
1032 1078 0.615331 AGAAGCAAAGGCATCCGAGA 59.385 50.000 0.00 0.00 44.61 4.04
1078 1124 2.993220 CCATCGACAAGTCATCGTTGAA 59.007 45.455 0.00 0.00 40.21 2.69
1100 1146 1.377366 CCAGCTCTCATGCCTTGCAG 61.377 60.000 0.00 0.00 43.65 4.41
1151 1197 1.766494 TCGGTATGCCTTCTCGGTAA 58.234 50.000 0.00 0.00 34.25 2.85
1155 1201 2.797156 CTCAAATCGGTATGCCTTCTCG 59.203 50.000 0.00 0.00 0.00 4.04
1417 1463 1.533753 CACCACATTGGCCCTGGTT 60.534 57.895 0.00 0.00 42.67 3.67
1569 1618 5.535753 AGCTTGCCAGTTTTGAGTTTAAT 57.464 34.783 0.00 0.00 0.00 1.40
1771 1820 1.933181 CATAGCTTTCGATGGTCGCAA 59.067 47.619 0.00 0.00 40.21 4.85
1772 1821 1.136110 TCATAGCTTTCGATGGTCGCA 59.864 47.619 0.00 0.00 40.21 5.10
1782 1831 4.336713 GGTTGGAACATCCTCATAGCTTTC 59.663 45.833 0.00 0.00 44.36 2.62
1970 2019 3.894427 ACAACCAATACTTTGTGCCATCA 59.106 39.130 0.00 0.00 34.61 3.07
2033 2082 6.480320 CGGTAATGTCCTTCTCCATTCTTAAG 59.520 42.308 0.00 0.00 33.54 1.85
2529 2590 8.602472 ACAAGAACTAATCAGATACTTCCTCT 57.398 34.615 0.00 0.00 0.00 3.69
2796 2861 1.837538 GCGGAGATCGAGGAGAGACG 61.838 65.000 0.00 0.00 42.43 4.18
2802 2867 4.501285 ACCGGCGGAGATCGAGGA 62.501 66.667 35.78 0.00 42.43 3.71
2863 2928 4.585216 ACCCCCTCCCCGTCAACA 62.585 66.667 0.00 0.00 0.00 3.33
2948 3014 2.989840 CAAAGAAGAAGCGTCGTCATCT 59.010 45.455 16.65 6.45 34.97 2.90
2989 3056 0.109226 CGGACGAACTTGAGGAGGAC 60.109 60.000 0.00 0.00 0.00 3.85
3011 3078 2.698797 GGAGTTCCGTCTAATCCATCCA 59.301 50.000 0.00 0.00 0.00 3.41
3056 3123 3.148279 CTCTAACCTCGCCGCCCT 61.148 66.667 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.