Multiple sequence alignment - TraesCS4B01G372000

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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 TraesCS4B01G372000 chr4B 100.000 2549 0 0 1 2549 657234073 657231525 0.000000e+00 4708.0
1 TraesCS4B01G372000 chr4B 95.382 1992 74 8 567 2549 80653676 80651694 0.000000e+00 3153.0
2 TraesCS4B01G372000 chr4B 95.761 1958 77 5 569 2524 648881433 648879480 0.000000e+00 3151.0
3 TraesCS4B01G372000 chr4B 95.701 1954 68 6 569 2520 89561743 89563682 0.000000e+00 3129.0
4 TraesCS4B01G372000 chr4B 85.093 322 30 9 259 568 206876780 206877095 1.900000e-81 313.0
5 TraesCS4B01G372000 chr4B 84.665 313 29 9 262 568 119871397 119871098 6.900000e-76 294.0
6 TraesCS4B01G372000 chr4B 90.244 164 13 3 341 503 238589016 238589177 7.140000e-51 211.0
7 TraesCS4B01G372000 chr1B 95.723 1964 76 7 564 2524 639164489 639162531 0.000000e+00 3155.0
8 TraesCS4B01G372000 chr1B 81.443 582 55 28 32 568 136392993 136393566 6.520000e-116 427.0
9 TraesCS4B01G372000 chr1B 80.149 403 40 21 63 426 235849271 235848870 5.410000e-67 265.0
10 TraesCS4B01G372000 chr7B 95.626 1966 77 7 565 2524 129569436 129567474 0.000000e+00 3145.0
11 TraesCS4B01G372000 chr7B 94.538 1959 95 8 568 2524 81247810 81249758 0.000000e+00 3014.0
12 TraesCS4B01G372000 chr7B 95.732 492 18 2 2033 2524 52061407 52061895 0.000000e+00 789.0
13 TraesCS4B01G372000 chr7B 84.201 538 43 20 69 568 302119478 302118945 3.810000e-133 484.0
14 TraesCS4B01G372000 chr7B 82.083 240 23 14 35 255 96933488 96933726 1.200000e-43 187.0
15 TraesCS4B01G372000 chr2B 95.712 1959 75 8 568 2524 62450927 62452878 0.000000e+00 3144.0
16 TraesCS4B01G372000 chr2B 94.972 1949 79 5 565 2511 666075777 666073846 0.000000e+00 3038.0
17 TraesCS4B01G372000 chr6B 94.411 2004 87 13 560 2549 44370171 44368179 0.000000e+00 3057.0
18 TraesCS4B01G372000 chr3B 94.847 1960 86 11 567 2524 804661030 804662976 0.000000e+00 3046.0
19 TraesCS4B01G372000 chr5D 85.340 573 43 12 30 566 345704666 345704099 2.870000e-154 555.0
20 TraesCS4B01G372000 chr7D 84.247 584 35 23 30 566 113338661 113339234 1.350000e-142 516.0
21 TraesCS4B01G372000 chr7D 84.028 432 31 24 169 568 550298699 550298274 5.150000e-102 381.0
22 TraesCS4B01G372000 chr7D 86.513 304 20 15 267 568 617391933 617391649 5.290000e-82 315.0
23 TraesCS4B01G372000 chr7D 78.692 474 47 33 63 492 33413003 33412540 1.500000e-67 267.0
24 TraesCS4B01G372000 chr6D 83.197 613 52 22 1 568 129458641 129458035 4.860000e-142 514.0
25 TraesCS4B01G372000 chr6D 82.185 595 48 24 23 568 329347998 329348583 2.310000e-125 459.0
26 TraesCS4B01G372000 chr6D 81.250 464 31 25 157 568 342780362 342780821 8.800000e-85 324.0
27 TraesCS4B01G372000 chr6D 77.221 439 51 29 74 492 246914922 246915331 7.140000e-51 211.0
28 TraesCS4B01G372000 chr6D 79.217 332 36 22 166 492 246923564 246923867 1.550000e-47 200.0
29 TraesCS4B01G372000 chr4A 82.373 573 59 24 30 566 307197224 307197790 6.430000e-126 460.0
30 TraesCS4B01G372000 chr4A 81.915 470 40 19 118 548 271315671 271316134 3.120000e-94 355.0
31 TraesCS4B01G372000 chr4A 88.686 274 22 6 301 568 384011859 384011589 2.450000e-85 326.0
32 TraesCS4B01G372000 chr4A 79.505 283 27 18 1 255 664583355 664583634 3.370000e-39 172.0
33 TraesCS4B01G372000 chr3D 87.792 385 34 10 190 564 584390627 584391008 3.010000e-119 438.0
34 TraesCS4B01G372000 chr3D 80.899 623 47 32 1 565 212831036 212831644 2.340000e-115 425.0
35 TraesCS4B01G372000 chr3D 80.435 598 52 32 30 568 116307230 116306639 1.840000e-106 396.0
36 TraesCS4B01G372000 chr3D 97.297 37 1 0 1 37 602578713 602578677 2.120000e-06 63.9
37 TraesCS4B01G372000 chr2D 81.783 516 51 15 92 568 564351970 564352481 2.380000e-105 392.0
38 TraesCS4B01G372000 chr2D 82.808 349 31 20 166 492 97735616 97735957 4.150000e-73 285.0
39 TraesCS4B01G372000 chr3A 88.498 313 24 10 259 568 291507360 291507663 4.010000e-98 368.0
40 TraesCS4B01G372000 chr3A 79.953 429 41 20 1 395 664280560 664280143 8.980000e-70 274.0
41 TraesCS4B01G372000 chr7A 83.059 425 39 19 172 568 222419907 222419488 3.120000e-94 355.0
42 TraesCS4B01G372000 chr7A 91.200 125 10 1 48 172 222419999 222419876 4.360000e-38 169.0
43 TraesCS4B01G372000 chr1D 80.972 494 41 30 122 568 442861066 442860579 2.430000e-90 342.0
44 TraesCS4B01G372000 chr1D 82.985 335 24 19 259 568 374573487 374573813 3.230000e-69 272.0
45 TraesCS4B01G372000 chr1D 78.444 450 32 23 134 541 427223024 427222598 1.520000e-57 233.0
46 TraesCS4B01G372000 chr6A 81.963 438 37 24 159 568 266802601 266802178 1.460000e-87 333.0
47 TraesCS4B01G372000 chr4D 78.161 609 59 32 30 568 306454203 306453599 1.140000e-83 320.0
48 TraesCS4B01G372000 chr4D 97.500 40 1 0 134 173 504024175 504024214 4.550000e-08 69.4
49 TraesCS4B01G372000 chr1A 86.139 101 11 2 441 540 366044691 366044789 3.470000e-19 106.0


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 TraesCS4B01G372000 chr4B 657231525 657234073 2548 True 4708 4708 100.0000 1 2549 1 chr4B.!!$R4 2548
1 TraesCS4B01G372000 chr4B 80651694 80653676 1982 True 3153 3153 95.3820 567 2549 1 chr4B.!!$R1 1982
2 TraesCS4B01G372000 chr4B 648879480 648881433 1953 True 3151 3151 95.7610 569 2524 1 chr4B.!!$R3 1955
3 TraesCS4B01G372000 chr4B 89561743 89563682 1939 False 3129 3129 95.7010 569 2520 1 chr4B.!!$F1 1951
4 TraesCS4B01G372000 chr1B 639162531 639164489 1958 True 3155 3155 95.7230 564 2524 1 chr1B.!!$R2 1960
5 TraesCS4B01G372000 chr1B 136392993 136393566 573 False 427 427 81.4430 32 568 1 chr1B.!!$F1 536
6 TraesCS4B01G372000 chr7B 129567474 129569436 1962 True 3145 3145 95.6260 565 2524 1 chr7B.!!$R1 1959
7 TraesCS4B01G372000 chr7B 81247810 81249758 1948 False 3014 3014 94.5380 568 2524 1 chr7B.!!$F2 1956
8 TraesCS4B01G372000 chr7B 302118945 302119478 533 True 484 484 84.2010 69 568 1 chr7B.!!$R2 499
9 TraesCS4B01G372000 chr2B 62450927 62452878 1951 False 3144 3144 95.7120 568 2524 1 chr2B.!!$F1 1956
10 TraesCS4B01G372000 chr2B 666073846 666075777 1931 True 3038 3038 94.9720 565 2511 1 chr2B.!!$R1 1946
11 TraesCS4B01G372000 chr6B 44368179 44370171 1992 True 3057 3057 94.4110 560 2549 1 chr6B.!!$R1 1989
12 TraesCS4B01G372000 chr3B 804661030 804662976 1946 False 3046 3046 94.8470 567 2524 1 chr3B.!!$F1 1957
13 TraesCS4B01G372000 chr5D 345704099 345704666 567 True 555 555 85.3400 30 566 1 chr5D.!!$R1 536
14 TraesCS4B01G372000 chr7D 113338661 113339234 573 False 516 516 84.2470 30 566 1 chr7D.!!$F1 536
15 TraesCS4B01G372000 chr6D 129458035 129458641 606 True 514 514 83.1970 1 568 1 chr6D.!!$R1 567
16 TraesCS4B01G372000 chr6D 329347998 329348583 585 False 459 459 82.1850 23 568 1 chr6D.!!$F3 545
17 TraesCS4B01G372000 chr4A 307197224 307197790 566 False 460 460 82.3730 30 566 1 chr4A.!!$F2 536
18 TraesCS4B01G372000 chr3D 212831036 212831644 608 False 425 425 80.8990 1 565 1 chr3D.!!$F1 564
19 TraesCS4B01G372000 chr3D 116306639 116307230 591 True 396 396 80.4350 30 568 1 chr3D.!!$R1 538
20 TraesCS4B01G372000 chr2D 564351970 564352481 511 False 392 392 81.7830 92 568 1 chr2D.!!$F2 476
21 TraesCS4B01G372000 chr7A 222419488 222419999 511 True 262 355 87.1295 48 568 2 chr7A.!!$R1 520
22 TraesCS4B01G372000 chr4D 306453599 306454203 604 True 320 320 78.1610 30 568 1 chr4D.!!$R1 538

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
803 970 1.559682 GGACCCAACAGAGAGCCATTA 59.44 52.381 0.0 0.0 0.0 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 2159 1.265454 GGGTTCGAGTCCCCATCTGT 61.265 60.0 14.49 0.0 40.88 3.41 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
113 148 2.172293 ACTTGGCAAAATTTTGAGCCCA 59.828 40.909 30.40 24.19 46.45 5.36
117 152 1.863267 CAAAATTTTGAGCCCACGCA 58.137 45.000 23.72 0.00 40.55 5.24
188 234 2.289072 GCTAAGCGCTGGATCCTAATCA 60.289 50.000 12.58 0.00 32.57 2.57
203 249 4.039245 TCCTAATCAAGCGCTACTGCTAAT 59.961 41.667 12.05 0.00 46.60 1.73
207 253 4.600012 TCAAGCGCTACTGCTAATTTTC 57.400 40.909 12.05 0.00 46.60 2.29
208 254 3.062099 TCAAGCGCTACTGCTAATTTTCG 59.938 43.478 12.05 0.00 46.60 3.46
442 601 4.796038 TTTTTCTCGACGATAGGGTCTT 57.204 40.909 0.00 0.00 43.77 3.01
800 967 2.224159 GGGACCCAACAGAGAGCCA 61.224 63.158 5.33 0.00 0.00 4.75
803 970 1.559682 GGACCCAACAGAGAGCCATTA 59.440 52.381 0.00 0.00 0.00 1.90
845 1012 2.295253 GCTATATAAGCGGGCGACAT 57.705 50.000 0.00 0.00 42.53 3.06
1069 1241 1.002430 GTGTGGAGATGCCTGTCTTCA 59.998 52.381 0.00 0.00 37.63 3.02
1125 1297 2.550208 GGTTTCTCACACACCGAGGAAT 60.550 50.000 0.00 0.00 30.73 3.01
1149 1321 3.192844 AGAATCATCCGTTCTACGTGTGT 59.807 43.478 0.00 0.00 40.58 3.72
1152 1324 3.076621 TCATCCGTTCTACGTGTGTAGT 58.923 45.455 0.00 0.00 46.70 2.73
1182 1354 2.024414 GTAAGAATCGGGGCAATTGCT 58.976 47.619 28.42 8.90 41.70 3.91
1318 1492 3.693085 TCAAGAAGAGCATGAAGAATGGC 59.307 43.478 0.00 0.00 36.71 4.40
2051 2235 1.755380 GGTAACCGCTAGGACAGATGT 59.245 52.381 0.00 0.00 41.02 3.06
2166 2351 3.751175 CGCATGAGAGTGGTTTTCCTTTA 59.249 43.478 0.00 0.00 41.38 1.85
2168 2353 5.644644 GCATGAGAGTGGTTTTCCTTTATG 58.355 41.667 0.00 0.00 41.38 1.90
2273 2458 5.054477 GCACTTGGTTTAGTGTTAGAGTGA 58.946 41.667 0.00 0.00 45.76 3.41
2539 2741 2.288825 ACGGACTCATGACGAAACATGT 60.289 45.455 10.77 0.00 45.21 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 75 0.048117 ACCTCTCCCCCTCCTCTCTA 59.952 60.000 0.00 0.00 0.00 2.43
113 148 4.083484 GCTATTTTGAGTTAACCACTGCGT 60.083 41.667 0.88 0.00 35.01 5.24
117 152 7.387948 CACTACTGCTATTTTGAGTTAACCACT 59.612 37.037 0.88 0.00 39.07 4.00
188 234 6.622896 AAATTCGAAAATTAGCAGTAGCGCTT 60.623 34.615 18.68 0.00 43.56 4.68
437 596 0.035458 CACAGTGTGGGAGGAAGACC 59.965 60.000 15.86 0.00 0.00 3.85
527 694 7.528481 TGTGTACACACTTAAGTAACTGTTG 57.472 36.000 24.62 0.00 46.55 3.33
696 863 1.869132 GGCCGAGTCAAAACGTTAACT 59.131 47.619 0.00 5.89 0.00 2.24
699 866 0.393820 AGGGCCGAGTCAAAACGTTA 59.606 50.000 0.00 0.00 0.00 3.18
747 914 4.089923 GTGCAACGGTCTGAATAAAATTGC 59.910 41.667 0.00 0.00 41.17 3.56
800 967 1.867233 CGCAACGGCTCTATGCTTAAT 59.133 47.619 0.00 0.00 42.39 1.40
803 970 1.815421 CCGCAACGGCTCTATGCTT 60.815 57.895 0.00 0.00 41.17 3.91
970 1141 1.214589 CCGAACGGGATCTCAACGT 59.785 57.895 5.25 0.00 43.43 3.99
1069 1241 2.591753 CCGGCACCATGGACAGAT 59.408 61.111 21.47 0.00 0.00 2.90
1125 1297 9.472789 CTACACACGTAGAACGGATGATTCTGA 62.473 44.444 10.81 0.00 46.98 3.27
1149 1321 4.344102 CCGATTCTTACCCCATTCTCACTA 59.656 45.833 0.00 0.00 0.00 2.74
1152 1324 2.438021 CCCGATTCTTACCCCATTCTCA 59.562 50.000 0.00 0.00 0.00 3.27
1182 1354 0.616371 ATCCCGACCACGAAAATGGA 59.384 50.000 0.00 0.00 43.02 3.41
1387 1561 0.529833 GCTAGCTCTCTGTCAGTGCA 59.470 55.000 7.70 0.00 43.07 4.57
1975 2159 1.265454 GGGTTCGAGTCCCCATCTGT 61.265 60.000 14.49 0.00 40.88 3.41
2051 2235 3.009033 CCCTACCCATGTCAAACTCTTGA 59.991 47.826 0.00 0.00 39.30 3.02
2117 2302 5.355071 TGCAAACATTCATGGTCTCACTATC 59.645 40.000 0.00 0.00 0.00 2.08
2166 2351 4.503643 CCCTCCAAAATTTCAGTGCAACAT 60.504 41.667 0.00 0.00 41.43 2.71
2168 2353 3.181466 ACCCTCCAAAATTTCAGTGCAAC 60.181 43.478 0.00 0.00 0.00 4.17
2273 2458 6.616577 TCCCTTTAAATCCTAAACCAAGTGT 58.383 36.000 0.00 0.00 0.00 3.55
2514 2705 2.993899 GTTTCGTCATGAGTCCGTGAAT 59.006 45.455 0.00 0.00 39.78 2.57


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

AutoCloner maintained by Alex Coulton.