Multiple sequence alignment - TraesCS7B01G373500

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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 TraesCS7B01G373500 chr7B 100.000 2556 0 0 1 2556 639269187 639266632 0.000000e+00 4721.0
1 TraesCS7B01G373500 chr7B 98.413 63 1 0 1157 1219 639268102 639268040 7.480000e-21 111.0
2 TraesCS7B01G373500 chr3A 97.446 1253 18 6 799 2047 670851354 670852596 0.000000e+00 2124.0
3 TraesCS7B01G373500 chr3A 93.214 840 28 10 1 812 670849104 670849942 0.000000e+00 1208.0
4 TraesCS7B01G373500 chr3A 97.250 509 13 1 2049 2556 670856243 670856751 0.000000e+00 861.0
5 TraesCS7B01G373500 chr3A 95.604 91 3 1 565 654 670854717 670854807 7.370000e-31 145.0
6 TraesCS7B01G373500 chr3A 98.361 61 1 0 1159 1219 670851642 670851702 9.670000e-20 108.0
7 TraesCS7B01G373500 chrUn 95.729 1241 26 7 814 2047 67700841 67699621 0.000000e+00 1973.0
8 TraesCS7B01G373500 chrUn 98.913 92 0 1 565 655 67697441 67697350 2.030000e-36 163.0
9 TraesCS7B01G373500 chrUn 98.592 71 1 0 1086 1156 67700497 67700427 2.670000e-25 126.0
10 TraesCS7B01G373500 chrUn 96.825 63 2 0 1157 1219 67700568 67700506 3.480000e-19 106.0
11 TraesCS7B01G373500 chrUn 97.917 48 1 0 2509 2556 67696488 67696441 1.630000e-12 84.2
12 TraesCS7B01G373500 chr5D 95.729 1241 26 7 814 2047 15677501 15676281 0.000000e+00 1973.0
13 TraesCS7B01G373500 chr5D 93.395 863 35 8 1157 2005 258644167 258645021 0.000000e+00 1258.0
14 TraesCS7B01G373500 chr5D 93.017 802 24 7 1 772 15724577 15723778 0.000000e+00 1142.0
15 TraesCS7B01G373500 chr5D 95.388 477 17 4 682 1156 258643765 258644238 0.000000e+00 754.0
16 TraesCS7B01G373500 chr5D 98.913 92 0 1 565 655 15674101 15674010 2.030000e-36 163.0
17 TraesCS7B01G373500 chr5D 98.592 71 1 0 1086 1156 15677157 15677087 2.670000e-25 126.0
18 TraesCS7B01G373500 chr5D 96.825 63 2 0 1157 1219 15677228 15677166 3.480000e-19 106.0
19 TraesCS7B01G373500 chr5D 97.917 48 1 0 2509 2556 15673148 15673101 1.630000e-12 84.2
20 TraesCS7B01G373500 chr4A 93.919 1184 32 17 1 1156 586499219 586498048 0.000000e+00 1751.0
21 TraesCS7B01G373500 chr4A 97.542 895 9 5 1157 2047 586498118 586497233 0.000000e+00 1519.0
22 TraesCS7B01G373500 chr4A 97.041 507 14 1 2051 2556 586493564 586493058 0.000000e+00 852.0
23 TraesCS7B01G373500 chr4A 95.604 91 3 1 565 654 586495095 586495005 7.370000e-31 145.0
24 TraesCS7B01G373500 chr5A 93.395 863 35 8 1157 2005 343454472 343455326 0.000000e+00 1258.0
25 TraesCS7B01G373500 chr5A 94.969 477 20 3 682 1156 343454069 343454543 0.000000e+00 745.0
26 TraesCS7B01G373500 chr5B 93.048 863 37 9 1157 2005 292736718 292737571 0.000000e+00 1240.0
27 TraesCS7B01G373500 chr5B 94.549 477 19 6 682 1156 292736318 292736789 0.000000e+00 730.0
28 TraesCS7B01G373500 chr5B 89.720 321 11 4 2239 2556 321543402 321543703 8.570000e-105 390.0
29 TraesCS7B01G373500 chr5B 93.548 93 4 2 170 262 321543315 321543405 1.230000e-28 137.0
30 TraesCS7B01G373500 chr7A 95.086 407 18 2 2151 2556 630044965 630045370 7.710000e-180 640.0
31 TraesCS7B01G373500 chr7A 98.113 106 1 1 2049 2153 630044575 630044680 1.560000e-42 183.0
32 TraesCS7B01G373500 chr1D 95.911 269 9 2 2049 2315 208426268 208426000 3.910000e-118 435.0
33 TraesCS7B01G373500 chr1D 94.286 210 11 1 2348 2556 208426009 208425800 1.140000e-83 320.0
34 TraesCS7B01G373500 chr1D 79.937 319 46 7 369 676 295962033 295962344 4.280000e-53 219.0
35 TraesCS7B01G373500 chr2A 95.131 267 11 2 2049 2314 197542185 197542450 1.090000e-113 420.0
36 TraesCS7B01G373500 chr2A 93.810 210 12 1 2348 2556 197542451 197542660 5.310000e-82 315.0
37 TraesCS7B01G373500 chr1A 80.734 327 38 11 369 676 368820095 368820415 5.500000e-57 231.0
38 TraesCS7B01G373500 chr3D 90.741 162 15 0 160 321 491180432 491180593 1.540000e-52 217.0
39 TraesCS7B01G373500 chr1B 79.937 319 42 11 369 676 397442351 397442658 5.540000e-52 215.0
40 TraesCS7B01G373500 chr2D 93.814 97 5 1 2430 2525 29646502 29646598 7.370000e-31 145.0


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 TraesCS7B01G373500 chr7B 639266632 639269187 2555 True 2416.00 4721 99.2065 1 2556 2 chr7B.!!$R1 2555
1 TraesCS7B01G373500 chr3A 670849104 670856751 7647 False 889.20 2124 96.3750 1 2556 5 chr3A.!!$F1 2555
2 TraesCS7B01G373500 chrUn 67696441 67700841 4400 True 490.44 1973 97.5952 565 2556 5 chrUn.!!$R1 1991
3 TraesCS7B01G373500 chr5D 15723778 15724577 799 True 1142.00 1142 93.0170 1 772 1 chr5D.!!$R1 771
4 TraesCS7B01G373500 chr5D 258643765 258645021 1256 False 1006.00 1258 94.3915 682 2005 2 chr5D.!!$F1 1323
5 TraesCS7B01G373500 chr5D 15673101 15677501 4400 True 490.44 1973 97.5952 565 2556 5 chr5D.!!$R2 1991
6 TraesCS7B01G373500 chr4A 586493058 586499219 6161 True 1066.75 1751 96.0265 1 2556 4 chr4A.!!$R1 2555
7 TraesCS7B01G373500 chr5A 343454069 343455326 1257 False 1001.50 1258 94.1820 682 2005 2 chr5A.!!$F1 1323
8 TraesCS7B01G373500 chr5B 292736318 292737571 1253 False 985.00 1240 93.7985 682 2005 2 chr5B.!!$F1 1323
9 TraesCS7B01G373500 chr7A 630044575 630045370 795 False 411.50 640 96.5995 2049 2556 2 chr7A.!!$F1 507

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
95 100 0.112412 ATCACGCAACCTCCCCTTTT 59.888 50.0 0.0 0.0 0.00 2.27 F
328 357 0.723981 GTCGATTTGCCAGACTCAGC 59.276 55.0 0.0 0.0 32.58 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1238 2770 1.076777 CAATGGCTCCGAACCCCAT 60.077 57.895 0.0 0.0 40.94 4.00 R
2289 7867 3.478780 GGAGGGTGTGTACCTGCA 58.521 61.111 0.0 0.0 46.66 4.41 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
95 100 0.112412 ATCACGCAACCTCCCCTTTT 59.888 50.000 0.00 0.00 0.00 2.27
164 193 3.760035 CACTACAGTCCGCCGCCT 61.760 66.667 0.00 0.00 0.00 5.52
328 357 0.723981 GTCGATTTGCCAGACTCAGC 59.276 55.000 0.00 0.00 32.58 4.26
331 360 1.673923 CGATTTGCCAGACTCAGCTCA 60.674 52.381 0.00 0.00 0.00 4.26
336 365 1.072806 TGCCAGACTCAGCTCAACATT 59.927 47.619 0.00 0.00 0.00 2.71
346 375 3.386867 CTCAACATTGCGGCCGCTC 62.387 63.158 45.79 23.37 42.51 5.03
692 723 2.426738 CGCTGGATTTGATAAAAGGGCA 59.573 45.455 0.00 0.00 0.00 5.36
746 780 9.797642 AATACATGATGAGCCTATTAAACATGA 57.202 29.630 0.00 0.00 37.74 3.07
817 2276 1.428448 TCGGACACTGATTTCAAGCG 58.572 50.000 0.00 0.00 0.00 4.68
960 2421 7.441157 TGTTACTTCTGTCAGTTGTAATGGAAG 59.559 37.037 16.94 0.00 36.17 3.46
1199 2731 7.454380 TCCACAAGAAAAATCCCATTTGAGTAT 59.546 33.333 0.00 0.00 31.77 2.12
1219 2751 9.713713 TGAGTATAAACTTGTATTTACTGTGCA 57.286 29.630 0.00 0.00 35.56 4.57
1221 2753 9.720769 AGTATAAACTTGTATTTACTGTGCAGT 57.279 29.630 9.90 9.90 37.86 4.40
1222 2754 9.755064 GTATAAACTTGTATTTACTGTGCAGTG 57.245 33.333 14.44 0.00 42.52 3.66
1238 2770 5.127031 TGTGCAGTGTGCTAGATACTTATCA 59.873 40.000 0.00 0.00 45.31 2.15
1617 3170 9.204570 AGTTATGCGGTTACTAAGCTATAAATG 57.795 33.333 0.00 0.00 0.00 2.32
1700 3254 6.662414 TTTTCTCCAATATACTTGTCTGCG 57.338 37.500 0.00 0.00 0.00 5.18
2220 7798 1.757699 AGGTGCGGAGGATAGTTCTTC 59.242 52.381 0.00 0.00 0.00 2.87
2289 7867 5.637810 CCGTATACTTGACTGTGTTGTTGAT 59.362 40.000 0.56 0.00 0.00 2.57
2341 7919 7.185671 TCCTGATATTTTCCTTCCCCTTTCTTA 59.814 37.037 0.00 0.00 0.00 2.10
2458 8036 3.267031 TGACTAGAGGATGACAGAGGACA 59.733 47.826 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 100 1.383248 GCAGCCTAGGGAAGGGAGA 60.383 63.158 11.72 0.00 46.65 3.71
150 155 4.753662 AGGAGGCGGCGGACTGTA 62.754 66.667 3.42 0.00 0.00 2.74
346 375 1.830477 CTCCTCTTCCTCACCTTGGAG 59.170 57.143 0.00 0.00 34.76 3.86
746 780 7.125792 AGTAGGATCCACGTGAAATAGAAAT 57.874 36.000 19.30 0.00 0.00 2.17
752 786 5.934402 ACTAAGTAGGATCCACGTGAAAT 57.066 39.130 19.30 10.24 0.00 2.17
791 825 1.742761 AATCAGTGTCCGATTGCCTG 58.257 50.000 0.00 0.00 31.90 4.85
817 2276 9.135843 CAAATATATGCAACATGATGAACCATC 57.864 33.333 7.22 0.00 40.88 3.51
960 2421 3.996363 GGCCAAAGTCCAAAACATGAATC 59.004 43.478 0.00 0.00 0.00 2.52
1199 2731 7.635423 CACACTGCACAGTAAATACAAGTTTA 58.365 34.615 2.38 0.00 40.20 2.01
1215 2747 5.592054 TGATAAGTATCTAGCACACTGCAC 58.408 41.667 0.00 0.00 38.50 4.57
1216 2748 5.852282 TGATAAGTATCTAGCACACTGCA 57.148 39.130 0.00 0.00 38.50 4.41
1217 2749 5.636965 CCATGATAAGTATCTAGCACACTGC 59.363 44.000 0.00 0.00 37.33 4.40
1218 2750 6.162079 CCCATGATAAGTATCTAGCACACTG 58.838 44.000 0.00 0.00 33.88 3.66
1219 2751 5.247110 CCCCATGATAAGTATCTAGCACACT 59.753 44.000 0.00 0.00 33.88 3.55
1220 2752 5.012148 ACCCCATGATAAGTATCTAGCACAC 59.988 44.000 0.00 0.00 33.88 3.82
1221 2753 5.155161 ACCCCATGATAAGTATCTAGCACA 58.845 41.667 0.00 0.00 33.88 4.57
1222 2754 5.746990 ACCCCATGATAAGTATCTAGCAC 57.253 43.478 0.00 0.00 33.88 4.40
1238 2770 1.076777 CAATGGCTCCGAACCCCAT 60.077 57.895 0.00 0.00 40.94 4.00
1596 3140 7.852971 AAACATTTATAGCTTAGTAACCGCA 57.147 32.000 0.00 0.00 0.00 5.69
1617 3170 6.039382 GTGATCCACAATCCCAACCTATAAAC 59.961 42.308 0.00 0.00 34.08 2.01
1700 3254 9.968870 AGAAATAAGATGTAAATCTCCTACGAC 57.031 33.333 0.00 0.00 0.00 4.34
2047 3607 6.313519 ACATGGATAGTTAGAACCACACAT 57.686 37.500 0.00 0.00 35.19 3.21
2289 7867 3.478780 GGAGGGTGTGTACCTGCA 58.521 61.111 0.00 0.00 46.66 4.41
2341 7919 2.225293 TGGTCTAGAAGTAGGGCACTGT 60.225 50.000 0.00 0.00 37.63 3.55
2458 8036 2.877168 GCTGCTGGATCAAAATCTCGAT 59.123 45.455 0.00 0.00 32.12 3.59


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

AutoCloner maintained by Alex Coulton.