Multiple sequence alignment - TraesCS4A01G391300

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 TraesCS4A01G391300 chr4A 100.000 3184 0 0 1 3184 668111372 668108189 0.000000e+00 5880.0
1 TraesCS4A01G391300 chr4A 82.578 2141 274 53 901 2962 668163006 668160886 0.000000e+00 1796.0
2 TraesCS4A01G391300 chr4A 80.702 1653 238 38 671 2264 668086332 668084702 0.000000e+00 1210.0
3 TraesCS4A01G391300 chr4A 82.505 1006 169 5 1021 2023 668149004 668148003 0.000000e+00 876.0
4 TraesCS4A01G391300 chr4A 88.696 690 65 10 2281 2959 668147646 668146959 0.000000e+00 830.0
5 TraesCS4A01G391300 chr4A 88.158 532 63 0 2428 2959 667860126 667859595 4.480000e-178 634.0
6 TraesCS4A01G391300 chr4A 92.453 212 16 0 2966 3177 668083875 668083664 1.440000e-78 303.0
7 TraesCS4A01G391300 chr4A 90.086 232 23 0 2953 3184 668146822 668146591 5.160000e-78 302.0
8 TraesCS4A01G391300 chr4A 83.333 90 15 0 117 206 668164010 668163921 2.040000e-12 84.2
9 TraesCS4A01G391300 chr7A 94.872 2691 80 16 318 2959 55429210 55426529 0.000000e+00 4152.0
10 TraesCS4A01G391300 chr7A 80.704 1648 241 36 671 2264 55385414 55383790 0.000000e+00 1210.0
11 TraesCS4A01G391300 chr7A 83.366 1010 158 7 1018 2021 55895532 55894527 0.000000e+00 926.0
12 TraesCS4A01G391300 chr7A 87.500 696 74 10 2275 2959 55882248 55881555 0.000000e+00 791.0
13 TraesCS4A01G391300 chr7A 97.414 232 6 0 2953 3184 55426392 55426161 2.300000e-106 396.0
14 TraesCS4A01G391300 chr7A 87.220 313 34 6 1 308 55429812 55429501 5.050000e-93 351.0
15 TraesCS4A01G391300 chr7A 93.243 222 13 2 2045 2266 55882516 55882297 3.060000e-85 326.0
16 TraesCS4A01G391300 chr7A 89.655 232 24 0 2953 3184 55893377 55893146 2.400000e-76 296.0
17 TraesCS4A01G391300 chr7A 89.224 232 25 0 2953 3184 55881418 55881187 1.120000e-74 291.0
18 TraesCS4A01G391300 chr7D 96.300 2027 60 7 946 2959 53485505 53483481 0.000000e+00 3314.0
19 TraesCS4A01G391300 chr7D 93.264 2019 90 15 315 2309 52694512 52696508 0.000000e+00 2933.0
20 TraesCS4A01G391300 chr7D 80.547 1645 239 43 671 2255 53427641 53426018 0.000000e+00 1190.0
21 TraesCS4A01G391300 chr7D 80.989 1415 226 27 867 2242 53510131 53508721 0.000000e+00 1083.0
22 TraesCS4A01G391300 chr7D 82.386 1232 179 20 1065 2264 52821413 52822638 0.000000e+00 1038.0
23 TraesCS4A01G391300 chr7D 82.368 1208 187 20 1065 2262 52829675 52830866 0.000000e+00 1027.0
24 TraesCS4A01G391300 chr7D 96.514 545 19 0 2415 2959 52696515 52697059 0.000000e+00 902.0
25 TraesCS4A01G391300 chr7D 82.820 1007 164 5 1021 2023 53498767 53497766 0.000000e+00 893.0
26 TraesCS4A01G391300 chr7D 88.362 696 68 10 2275 2959 53497431 53496738 0.000000e+00 824.0
27 TraesCS4A01G391300 chr7D 89.159 535 53 4 2428 2959 53508487 53507955 0.000000e+00 662.0
28 TraesCS4A01G391300 chr7D 87.732 538 64 2 2423 2959 52822779 52823315 7.500000e-176 627.0
29 TraesCS4A01G391300 chr7D 98.276 232 4 0 2953 3184 53483344 53483113 1.060000e-109 407.0
30 TraesCS4A01G391300 chr7D 97.797 227 5 0 2953 3179 52697196 52697422 2.980000e-105 392.0
31 TraesCS4A01G391300 chr7D 90.033 301 30 0 8 308 52693917 52694217 1.070000e-104 390.0
32 TraesCS4A01G391300 chr7D 93.694 222 12 2 2045 2266 53497687 53497468 6.580000e-87 331.0
33 TraesCS4A01G391300 chr7D 92.453 212 16 0 2966 3177 53425181 53424970 1.440000e-78 303.0
34 TraesCS4A01G391300 chr7D 90.749 227 21 0 2953 3179 53496601 53496375 1.440000e-78 303.0
35 TraesCS4A01G391300 chr7D 90.476 231 15 5 2042 2266 53433366 53433137 6.680000e-77 298.0
36 TraesCS4A01G391300 chr7D 91.469 211 18 0 1 211 53486477 53486267 1.120000e-74 291.0


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 TraesCS4A01G391300 chr4A 668108189 668111372 3183 True 5880.000000 5880 100.000000 1 3184 1 chr4A.!!$R2 3183
1 TraesCS4A01G391300 chr4A 668160886 668164010 3124 True 940.100000 1796 82.955500 117 2962 2 chr4A.!!$R5 2845
2 TraesCS4A01G391300 chr4A 668083664 668086332 2668 True 756.500000 1210 86.577500 671 3177 2 chr4A.!!$R3 2506
3 TraesCS4A01G391300 chr4A 668146591 668149004 2413 True 669.333333 876 87.095667 1021 3184 3 chr4A.!!$R4 2163
4 TraesCS4A01G391300 chr4A 667859595 667860126 531 True 634.000000 634 88.158000 2428 2959 1 chr4A.!!$R1 531
5 TraesCS4A01G391300 chr7A 55426161 55429812 3651 True 1633.000000 4152 93.168667 1 3184 3 chr7A.!!$R2 3183
6 TraesCS4A01G391300 chr7A 55383790 55385414 1624 True 1210.000000 1210 80.704000 671 2264 1 chr7A.!!$R1 1593
7 TraesCS4A01G391300 chr7A 55893146 55895532 2386 True 611.000000 926 86.510500 1018 3184 2 chr7A.!!$R4 2166
8 TraesCS4A01G391300 chr7A 55881187 55882516 1329 True 469.333333 791 89.989000 2045 3184 3 chr7A.!!$R3 1139
9 TraesCS4A01G391300 chr7D 53483113 53486477 3364 True 1337.333333 3314 95.348333 1 3184 3 chr7D.!!$R3 3183
10 TraesCS4A01G391300 chr7D 52693917 52697422 3505 False 1154.250000 2933 94.402000 8 3179 4 chr7D.!!$F2 3171
11 TraesCS4A01G391300 chr7D 52829675 52830866 1191 False 1027.000000 1027 82.368000 1065 2262 1 chr7D.!!$F1 1197
12 TraesCS4A01G391300 chr7D 53507955 53510131 2176 True 872.500000 1083 85.074000 867 2959 2 chr7D.!!$R5 2092
13 TraesCS4A01G391300 chr7D 52821413 52823315 1902 False 832.500000 1038 85.059000 1065 2959 2 chr7D.!!$F3 1894
14 TraesCS4A01G391300 chr7D 53424970 53427641 2671 True 746.500000 1190 86.500000 671 3177 2 chr7D.!!$R2 2506
15 TraesCS4A01G391300 chr7D 53496375 53498767 2392 True 587.750000 893 88.906250 1021 3179 4 chr7D.!!$R4 2158

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
88 89 0.171455 GATCCTAGTATCCGGCGCTG 59.829 60.0 9.96 9.96 0.00 5.18 F
358 934 1.286248 GTGTTGGTCCTATCCCCACT 58.714 55.0 0.00 0.00 0.00 4.00 F
1047 1843 2.317149 ATCCAGCCCAGCTAGAACGC 62.317 60.0 0.00 0.00 36.40 4.84 F
1398 2204 0.316204 ACTTCAGCAATGGCAGCAAC 59.684 50.0 0.00 0.00 44.61 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1324 2130 0.768221 ACCTCACCCAAGGCAAGAGA 60.768 55.000 0.00 0.00 40.34 3.10 R
1398 2204 1.785041 CGTCCAAACCACTGGTGCTG 61.785 60.000 0.00 2.63 35.34 4.41 R
1935 2741 2.057137 AACCTTGAGAGCAGTTGCAA 57.943 45.000 6.90 0.00 45.16 4.08 R
3141 4245 1.068753 CATCGCGAGCAGGAAGGAT 59.931 57.895 16.66 0.00 0.00 3.24 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
88 89 0.171455 GATCCTAGTATCCGGCGCTG 59.829 60.000 9.96 9.96 0.00 5.18
140 141 3.912907 CCTCCGCGGCCGTATTCT 61.913 66.667 28.70 0.00 0.00 2.40
144 145 4.891727 CGCGGCCGTATTCTGCCT 62.892 66.667 28.70 0.00 45.71 4.75
165 166 1.801332 GCGCCGTTCTACTCTCAGA 59.199 57.895 0.00 0.00 0.00 3.27
224 225 5.729510 TGTACAGTACAATGCAATAGAGCA 58.270 37.500 11.21 0.00 40.51 4.26
291 488 7.404671 AAAATAATCAATTTCCTGCGGTAGT 57.595 32.000 0.00 0.00 36.76 2.73
292 489 6.377327 AATAATCAATTTCCTGCGGTAGTG 57.623 37.500 0.00 0.00 0.00 2.74
302 499 2.673368 CCTGCGGTAGTGTGATCTTTTC 59.327 50.000 0.00 0.00 0.00 2.29
308 505 5.063060 GCGGTAGTGTGATCTTTTCGTTTAT 59.937 40.000 0.00 0.00 0.00 1.40
310 507 6.953743 CGGTAGTGTGATCTTTTCGTTTATTG 59.046 38.462 0.00 0.00 0.00 1.90
313 510 4.857037 GTGTGATCTTTTCGTTTATTGGGC 59.143 41.667 0.00 0.00 0.00 5.36
324 892 3.919804 CGTTTATTGGGCAAGATGTGTTG 59.080 43.478 0.00 0.00 0.00 3.33
327 895 6.624861 CGTTTATTGGGCAAGATGTGTTGTAT 60.625 38.462 0.00 0.00 0.00 2.29
358 934 1.286248 GTGTTGGTCCTATCCCCACT 58.714 55.000 0.00 0.00 0.00 4.00
398 975 7.753309 TTTAGCTTTATACAAGTGGAGCAAA 57.247 32.000 0.00 0.00 32.78 3.68
501 1112 7.675062 ACAAGTTGCATATGAAAACCCAAATA 58.325 30.769 6.97 0.00 0.00 1.40
502 1113 8.153550 ACAAGTTGCATATGAAAACCCAAATAA 58.846 29.630 6.97 0.00 0.00 1.40
503 1114 8.997323 CAAGTTGCATATGAAAACCCAAATAAA 58.003 29.630 6.97 0.00 0.00 1.40
504 1115 9.737844 AAGTTGCATATGAAAACCCAAATAAAT 57.262 25.926 6.97 0.00 0.00 1.40
579 1200 8.186821 GGTACTACTTTCGCTACAATTTCTAGA 58.813 37.037 0.00 0.00 0.00 2.43
624 1259 5.105957 ACATGTAGTCTGAAGTGAGTAGCAG 60.106 44.000 0.00 0.00 0.00 4.24
884 1590 5.655090 TCCTGTATGATTCGACTTGTAAGGA 59.345 40.000 0.00 0.00 0.00 3.36
937 1644 6.099269 AGGAATGGCTTCAGCATATTTTGAAT 59.901 34.615 0.30 0.00 44.36 2.57
975 1765 7.050970 TGTTATCTACTCGTATGCTGGATTT 57.949 36.000 0.00 0.00 0.00 2.17
976 1766 7.145985 TGTTATCTACTCGTATGCTGGATTTC 58.854 38.462 0.00 0.00 0.00 2.17
977 1767 7.014326 TGTTATCTACTCGTATGCTGGATTTCT 59.986 37.037 0.00 0.00 0.00 2.52
978 1768 5.854010 TCTACTCGTATGCTGGATTTCTT 57.146 39.130 0.00 0.00 0.00 2.52
979 1769 5.592054 TCTACTCGTATGCTGGATTTCTTG 58.408 41.667 0.00 0.00 0.00 3.02
1047 1843 2.317149 ATCCAGCCCAGCTAGAACGC 62.317 60.000 0.00 0.00 36.40 4.84
1324 2130 3.644335 GGACTTAGGGTACTGGACATCT 58.356 50.000 0.00 0.00 0.00 2.90
1398 2204 0.316204 ACTTCAGCAATGGCAGCAAC 59.684 50.000 0.00 0.00 44.61 4.17
1434 2240 3.830178 TGGACGTCTTAACTCTTGATCCA 59.170 43.478 16.46 0.00 0.00 3.41
1454 2260 5.013547 TCCATTTCATACGGTTTCCAACAT 58.986 37.500 0.00 0.00 0.00 2.71
1455 2261 5.101628 CCATTTCATACGGTTTCCAACATG 58.898 41.667 0.00 0.00 0.00 3.21
1542 2348 1.717032 ACCAGCTTGAGTACCTCACA 58.283 50.000 0.00 0.00 40.46 3.58
1935 2741 3.332385 AATGGCCCCGGTTACCGT 61.332 61.111 22.78 0.00 46.80 4.83
2064 2944 2.628178 TCATGTTGACGTTCTCCTCACT 59.372 45.455 0.00 0.00 0.00 3.41
2592 3552 9.927668 ATCAAATTATTTCAAAACAGGTCGATT 57.072 25.926 0.00 0.00 0.00 3.34
2757 3718 3.342377 TCATGAATGTGGCCGAAACTA 57.658 42.857 0.00 0.00 0.00 2.24
2768 3729 5.221342 TGTGGCCGAAACTAATGAATTTGTT 60.221 36.000 0.00 0.00 37.33 2.83
2936 3897 0.252012 CACCTCCCTCTCTGGACACT 60.252 60.000 0.00 0.00 38.35 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 110 1.660917 GGAGGAGAACGGATAGCGG 59.339 63.158 0.00 0.00 0.00 5.52
144 145 2.749044 AGAGTAGAACGGCGCGGA 60.749 61.111 22.76 0.00 0.00 5.54
165 166 1.078989 ACCTTACAGGGTCTGGTAGCT 59.921 52.381 0.00 0.00 40.58 3.32
201 202 5.580691 GTGCTCTATTGCATTGTACTGTACA 59.419 40.000 16.26 16.26 45.23 2.90
291 488 4.520874 TGCCCAATAAACGAAAAGATCACA 59.479 37.500 0.00 0.00 0.00 3.58
292 489 5.054390 TGCCCAATAAACGAAAAGATCAC 57.946 39.130 0.00 0.00 0.00 3.06
302 499 3.848272 ACACATCTTGCCCAATAAACG 57.152 42.857 0.00 0.00 0.00 3.60
308 505 3.257873 CCAATACAACACATCTTGCCCAA 59.742 43.478 0.00 0.00 0.00 4.12
310 507 2.166254 CCCAATACAACACATCTTGCCC 59.834 50.000 0.00 0.00 0.00 5.36
313 510 4.218200 TCTTGCCCAATACAACACATCTTG 59.782 41.667 0.00 0.00 0.00 3.02
324 892 3.258123 ACCAACACATTCTTGCCCAATAC 59.742 43.478 0.00 0.00 0.00 1.89
327 895 1.686052 GACCAACACATTCTTGCCCAA 59.314 47.619 0.00 0.00 0.00 4.12
398 975 6.769341 AGTTACAGACTTAATTGACCCGTTTT 59.231 34.615 0.00 0.00 33.92 2.43
463 1073 8.720562 CATATGCAACTTGTCGGATGAAATATA 58.279 33.333 0.00 0.00 0.00 0.86
477 1087 8.545229 TTATTTGGGTTTTCATATGCAACTTG 57.455 30.769 14.00 0.00 0.00 3.16
503 1114 8.603181 GCTTTTCAGTTTGTATGTGTTTTTCAT 58.397 29.630 0.00 0.00 0.00 2.57
504 1115 7.816995 AGCTTTTCAGTTTGTATGTGTTTTTCA 59.183 29.630 0.00 0.00 0.00 2.69
591 1212 7.656137 TCACTTCAGACTACATGTTTCTTTACC 59.344 37.037 2.30 0.00 0.00 2.85
624 1259 3.601435 GGAGTAGACCAAAAAGGAGAGC 58.399 50.000 0.00 0.00 41.22 4.09
754 1404 9.482627 AATAGAGCTATTACATAAACTCTGCAC 57.517 33.333 1.04 0.00 36.07 4.57
884 1590 6.270695 AGTCCAAACATCATTCAGGGAAAATT 59.729 34.615 0.00 0.00 0.00 1.82
1324 2130 0.768221 ACCTCACCCAAGGCAAGAGA 60.768 55.000 0.00 0.00 40.34 3.10
1398 2204 1.785041 CGTCCAAACCACTGGTGCTG 61.785 60.000 0.00 2.63 35.34 4.41
1454 2260 5.049474 CCGATTGATGTCAACTTGTTCTTCA 60.049 40.000 0.00 0.00 38.86 3.02
1455 2261 5.385617 CCGATTGATGTCAACTTGTTCTTC 58.614 41.667 0.00 0.00 38.86 2.87
1542 2348 2.950309 GGATGAAATGCATGAGTCAGCT 59.050 45.455 17.78 3.41 37.34 4.24
1935 2741 2.057137 AACCTTGAGAGCAGTTGCAA 57.943 45.000 6.90 0.00 45.16 4.08
2064 2944 4.151121 TGATGTCTGCCATTTCAAGGAAA 58.849 39.130 0.00 0.00 35.94 3.13
2576 3536 6.206438 TCATCAATGAATCGACCTGTTTTGAA 59.794 34.615 0.00 0.00 33.08 2.69
2592 3552 7.567458 TCTTCCTGTGTGAATATCATCAATGA 58.433 34.615 0.00 0.00 41.70 2.57
2768 3729 8.417106 GTCTGTGAAAGTATGATAATCTCCTGA 58.583 37.037 0.00 0.00 0.00 3.86
3141 4245 1.068753 CATCGCGAGCAGGAAGGAT 59.931 57.895 16.66 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.