Multiple sequence alignment - TraesCS6B01G228700

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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 TraesCS6B01G228700 chr6B 100.000 1465 0 0 949 2413 363203630 363205094 0.000000e+00 2706.0
1 TraesCS6B01G228700 chr6B 100.000 645 0 0 1 645 363202682 363203326 0.000000e+00 1192.0
2 TraesCS6B01G228700 chr7A 94.422 1488 56 8 949 2413 707844426 707845909 0.000000e+00 2263.0
3 TraesCS6B01G228700 chr7A 93.548 1488 69 7 949 2413 650324524 650323041 0.000000e+00 2191.0
4 TraesCS6B01G228700 chr7A 93.347 1488 70 9 949 2413 650260708 650259227 0.000000e+00 2172.0
5 TraesCS6B01G228700 chr7A 91.935 1488 73 24 949 2413 615539003 615537540 0.000000e+00 2039.0
6 TraesCS6B01G228700 chr7A 93.694 333 21 0 270 602 650261427 650261095 1.290000e-137 499.0
7 TraesCS6B01G228700 chr7A 93.656 331 21 0 270 600 707843677 707844007 1.670000e-136 496.0
8 TraesCS6B01G228700 chr7A 92.937 269 19 0 1 269 622694855 622694587 2.250000e-105 392.0
9 TraesCS6B01G228700 chr7A 92.308 52 4 0 574 625 107669427 107669376 9.250000e-10 75.0
10 TraesCS6B01G228700 chr2A 94.173 1493 54 9 949 2413 600113398 600111911 0.000000e+00 2244.0
11 TraesCS6B01G228700 chr2A 94.086 1488 60 8 949 2413 23796220 23797702 0.000000e+00 2235.0
12 TraesCS6B01G228700 chr2A 94.106 1459 57 10 978 2413 571019198 571020650 0.000000e+00 2191.0
13 TraesCS6B01G228700 chr2A 94.309 369 20 1 270 637 23795588 23795956 4.500000e-157 564.0
14 TraesCS6B01G228700 chr2A 92.593 270 18 2 1 269 725038014 725037746 1.050000e-103 387.0
15 TraesCS6B01G228700 chr1A 93.750 1488 66 7 949 2413 380400848 380402331 0.000000e+00 2207.0
16 TraesCS6B01G228700 chr1A 93.616 1488 67 8 949 2413 531840015 531838533 0.000000e+00 2196.0
17 TraesCS6B01G228700 chr1A 94.482 1178 41 6 1259 2413 504203197 504204373 0.000000e+00 1794.0
18 TraesCS6B01G228700 chr1A 94.681 376 20 0 270 645 11026862 11026487 3.460000e-163 584.0
19 TraesCS6B01G228700 chr1B 93.683 1488 66 8 949 2413 658504096 658502614 0.000000e+00 2202.0
20 TraesCS6B01G228700 chr1B 93.503 354 22 1 270 623 235897031 235897383 2.130000e-145 525.0
21 TraesCS6B01G228700 chr1B 95.527 313 13 1 270 582 658504799 658504488 1.290000e-137 499.0
22 TraesCS6B01G228700 chr1B 97.770 269 6 0 1 269 235896734 235897002 4.700000e-127 464.0
23 TraesCS6B01G228700 chr1B 97.398 269 7 0 1 269 658505096 658504828 2.190000e-125 459.0
24 TraesCS6B01G228700 chr7B 92.717 1483 59 10 954 2413 544973060 544974516 0.000000e+00 2095.0
25 TraesCS6B01G228700 chr7B 93.617 376 24 0 270 645 544972344 544972719 1.620000e-156 562.0
26 TraesCS6B01G228700 chr5A 92.406 1488 69 12 949 2413 507565670 507564204 0.000000e+00 2082.0
27 TraesCS6B01G228700 chr5A 94.595 370 19 1 270 639 603018657 603019025 2.690000e-159 571.0
28 TraesCS6B01G228700 chr5A 92.717 357 25 1 270 626 507566262 507565907 4.600000e-142 514.0
29 TraesCS6B01G228700 chr3B 94.768 1338 44 7 1099 2413 59100218 59101552 0.000000e+00 2060.0
30 TraesCS6B01G228700 chr3B 98.141 269 5 0 1 269 59099251 59099519 1.010000e-128 470.0
31 TraesCS6B01G228700 chr3B 100.000 33 0 0 587 619 280583514 280583546 7.200000e-06 62.1
32 TraesCS6B01G228700 chr2B 92.708 1152 56 8 949 2077 811325 810179 0.000000e+00 1637.0
33 TraesCS6B01G228700 chr2B 96.654 269 9 0 1 269 812130 811862 4.730000e-122 448.0
34 TraesCS6B01G228700 chr4D 94.052 269 16 0 1 269 4184706 4184974 2.230000e-110 409.0
35 TraesCS6B01G228700 chrUn 93.680 269 17 0 1 269 24704468 24704736 1.040000e-108 403.0
36 TraesCS6B01G228700 chr5D 92.937 269 19 0 1 269 221497473 221497741 2.250000e-105 392.0


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 TraesCS6B01G228700 chr6B 363202682 363205094 2412 False 1949.000000 2706 100.0000 1 2413 2 chr6B.!!$F1 2412
1 TraesCS6B01G228700 chr7A 650323041 650324524 1483 True 2191.000000 2191 93.5480 949 2413 1 chr7A.!!$R4 1464
2 TraesCS6B01G228700 chr7A 615537540 615539003 1463 True 2039.000000 2039 91.9350 949 2413 1 chr7A.!!$R2 1464
3 TraesCS6B01G228700 chr7A 707843677 707845909 2232 False 1379.500000 2263 94.0390 270 2413 2 chr7A.!!$F1 2143
4 TraesCS6B01G228700 chr7A 650259227 650261427 2200 True 1335.500000 2172 93.5205 270 2413 2 chr7A.!!$R5 2143
5 TraesCS6B01G228700 chr2A 600111911 600113398 1487 True 2244.000000 2244 94.1730 949 2413 1 chr2A.!!$R1 1464
6 TraesCS6B01G228700 chr2A 571019198 571020650 1452 False 2191.000000 2191 94.1060 978 2413 1 chr2A.!!$F1 1435
7 TraesCS6B01G228700 chr2A 23795588 23797702 2114 False 1399.500000 2235 94.1975 270 2413 2 chr2A.!!$F2 2143
8 TraesCS6B01G228700 chr1A 380400848 380402331 1483 False 2207.000000 2207 93.7500 949 2413 1 chr1A.!!$F1 1464
9 TraesCS6B01G228700 chr1A 531838533 531840015 1482 True 2196.000000 2196 93.6160 949 2413 1 chr1A.!!$R2 1464
10 TraesCS6B01G228700 chr1A 504203197 504204373 1176 False 1794.000000 1794 94.4820 1259 2413 1 chr1A.!!$F2 1154
11 TraesCS6B01G228700 chr1B 658502614 658505096 2482 True 1053.333333 2202 95.5360 1 2413 3 chr1B.!!$R1 2412
12 TraesCS6B01G228700 chr1B 235896734 235897383 649 False 494.500000 525 95.6365 1 623 2 chr1B.!!$F1 622
13 TraesCS6B01G228700 chr7B 544972344 544974516 2172 False 1328.500000 2095 93.1670 270 2413 2 chr7B.!!$F1 2143
14 TraesCS6B01G228700 chr5A 507564204 507566262 2058 True 1298.000000 2082 92.5615 270 2413 2 chr5A.!!$R1 2143
15 TraesCS6B01G228700 chr3B 59099251 59101552 2301 False 1265.000000 2060 96.4545 1 2413 2 chr3B.!!$F2 2412
16 TraesCS6B01G228700 chr2B 810179 812130 1951 True 1042.500000 1637 94.6810 1 2077 2 chr2B.!!$R1 2076

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
490 520 0.483328 CCTAGATCTCCCTCCCCGAA 59.517 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 2466 1.327303 TCCCAAATTGTGTGGTGAGC 58.673 50.0 0.0 0.0 34.01 4.26 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
345 375 1.402896 CCCCTAAGCCGATCTGAGCA 61.403 60.000 0.00 0.00 0.00 4.26
378 408 6.463049 CCATACAGATCCAACGTCTCCTAAAT 60.463 42.308 0.00 0.00 0.00 1.40
436 466 1.550374 TCCCCTCCCTCTCCCTCTT 60.550 63.158 0.00 0.00 0.00 2.85
439 469 1.598856 CCCTCCCTCTCCCTCTTCCT 61.599 65.000 0.00 0.00 0.00 3.36
473 503 3.756783 CCTCCCTCTCCCCGACCT 61.757 72.222 0.00 0.00 0.00 3.85
490 520 0.483328 CCTAGATCTCCCTCCCCGAA 59.517 60.000 0.00 0.00 0.00 4.30
579 609 0.949105 GACCTGCAACGACCAACGAT 60.949 55.000 0.00 0.00 45.77 3.73
583 613 0.795698 TGCAACGACCAACGATGATG 59.204 50.000 0.00 0.00 45.29 3.07
619 650 2.770048 CTCCTTCCCCATCCCGCT 60.770 66.667 0.00 0.00 0.00 5.52
640 1143 1.248486 CGGCGAGGAGATCCATTCTA 58.752 55.000 0.00 0.00 38.89 2.10
1020 1766 2.366266 AGCACAAATCCAAACAGCACAT 59.634 40.909 0.00 0.00 0.00 3.21
1026 1772 5.221481 ACAAATCCAAACAGCACATCATTCA 60.221 36.000 0.00 0.00 0.00 2.57
1129 1875 4.758251 CAGCCATGGACGCCGTCA 62.758 66.667 20.08 5.71 33.68 4.35
1140 1886 2.737376 GCCGTCAACTCCGTGGTC 60.737 66.667 0.00 0.00 0.00 4.02
1144 1890 1.658673 GTCAACTCCGTGGTCGACT 59.341 57.895 16.46 0.00 39.71 4.18
1149 1895 1.977544 CTCCGTGGTCGACTCCCTT 60.978 63.158 16.46 0.00 39.71 3.95
1150 1896 1.935327 CTCCGTGGTCGACTCCCTTC 61.935 65.000 16.46 0.00 39.71 3.46
1151 1897 2.572284 CGTGGTCGACTCCCTTCC 59.428 66.667 16.46 0.00 39.71 3.46
1362 2109 1.005394 GGGTTCGTCGGCTTCTTCA 60.005 57.895 0.00 0.00 0.00 3.02
1483 2230 4.021102 AGTTAGACTTGGGTCATGTTGG 57.979 45.455 0.00 0.00 44.36 3.77
1490 2237 3.499737 GGTCATGTTGGCTCGCGG 61.500 66.667 6.13 0.00 0.00 6.46
1617 2365 7.660208 TGTCAATTTCTACCTTGTTAGGAGAAC 59.340 37.037 0.00 0.00 45.05 3.01
1706 2454 2.674754 GCAGGACGAATTGGGGGA 59.325 61.111 0.00 0.00 0.00 4.81
1718 2466 0.334676 TTGGGGGAATAGGCTGGTTG 59.665 55.000 0.00 0.00 0.00 3.77
1850 2620 3.564511 CAATGTTTGTCCATGGTTCGTC 58.435 45.455 12.58 2.06 0.00 4.20
1860 2630 2.550978 CATGGTTCGTCCTATGTGTCC 58.449 52.381 0.00 0.00 37.07 4.02
2121 2894 9.649167 GAAAATCCTGATTGAAAATGAAGATGT 57.351 29.630 0.00 0.00 0.00 3.06
2172 2945 4.041567 TGTGTTTCCTGAGCTCTTCCAATA 59.958 41.667 16.19 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
254 255 7.537596 TGTATCATTTGGGAATTTGTCAAGT 57.462 32.000 0.00 0.00 0.00 3.16
345 375 2.832838 TGGATCTGTATGGTGTGGACT 58.167 47.619 0.00 0.00 0.00 3.85
473 503 0.187851 GGTTCGGGGAGGGAGATCTA 59.812 60.000 0.00 0.00 0.00 1.98
490 520 2.360980 CGGAGAGGGAGGTCTGGT 59.639 66.667 0.00 0.00 0.00 4.00
619 650 2.369257 GAATGGATCTCCTCGCCGCA 62.369 60.000 0.00 0.00 36.82 5.69
972 1718 0.701659 TACGAGGAGGGGAGGAGGAT 60.702 60.000 0.00 0.00 0.00 3.24
1020 1766 0.608035 GGAAGCCAACGGGTGAATGA 60.608 55.000 0.00 0.00 36.17 2.57
1129 1875 2.273912 GGGAGTCGACCACGGAGTT 61.274 63.158 13.01 0.00 41.61 3.01
1144 1890 2.926242 AAACTCGCGGGGAAGGGA 60.926 61.111 12.42 0.00 0.00 4.20
1149 1895 4.257654 TTGGCAAACTCGCGGGGA 62.258 61.111 12.42 0.00 0.00 4.81
1150 1896 3.737172 CTTGGCAAACTCGCGGGG 61.737 66.667 12.42 4.49 0.00 5.73
1151 1897 3.737172 CCTTGGCAAACTCGCGGG 61.737 66.667 3.27 3.27 0.00 6.13
1362 2109 2.781757 TGGGGATGAAGATGAGCTTGAT 59.218 45.455 0.00 0.00 36.83 2.57
1483 2230 1.738099 AACAGATCACACCGCGAGC 60.738 57.895 8.23 0.00 0.00 5.03
1593 2341 7.974504 AGTTCTCCTAACAAGGTAGAAATTGA 58.025 34.615 0.00 0.00 31.76 2.57
1617 2365 3.384789 TGATTACCCTTGACTCATCCGAG 59.615 47.826 0.00 0.00 45.49 4.63
1718 2466 1.327303 TCCCAAATTGTGTGGTGAGC 58.673 50.000 0.00 0.00 34.01 4.26
1850 2620 7.935755 AGAATGAAGAATACATGGACACATAGG 59.064 37.037 0.00 0.00 34.99 2.57
1860 2630 9.241317 GGTGCATTAAAGAATGAAGAATACATG 57.759 33.333 1.88 0.00 44.59 3.21
2172 2945 3.885297 CCGGCATGGATTCTAAGAAATGT 59.115 43.478 0.00 0.00 42.00 2.71
2252 3030 4.940046 CCACATGAAACAGCTAGAACAGAT 59.060 41.667 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.