Multiple sequence alignment - TraesCS7B01G077400

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 TraesCS7B01G077400 chr7B 100.000 2357 0 0 1 2357 87119159 87121515 0.000000e+00 4353
1 TraesCS7B01G077400 chr1B 90.615 1577 130 11 178 1744 593051645 593053213 0.000000e+00 2076
2 TraesCS7B01G077400 chr7D 82.975 1768 249 32 3 1743 577855704 577853962 0.000000e+00 1550
3 TraesCS7B01G077400 chr7D 87.988 641 50 14 1743 2357 125882733 125883372 0.000000e+00 732
4 TraesCS7B01G077400 chr7D 90.361 332 31 1 1743 2073 125875614 125875945 3.600000e-118 435
5 TraesCS7B01G077400 chr7D 90.055 181 13 3 1567 1746 158993226 158993402 1.820000e-56 230
6 TraesCS7B01G077400 chr3A 88.651 1216 126 9 3 1210 595278535 595279746 0.000000e+00 1471
7 TraesCS7B01G077400 chr3A 79.601 1353 247 25 1 1338 712704146 712702808 0.000000e+00 942
8 TraesCS7B01G077400 chr3A 85.165 546 67 9 1197 1730 595281334 595281877 4.430000e-152 547
9 TraesCS7B01G077400 chr2A 81.479 1771 276 39 3 1743 650490741 650492489 0.000000e+00 1406
10 TraesCS7B01G077400 chr5B 80.658 1763 284 43 12 1744 17684772 17683037 0.000000e+00 1314
11 TraesCS7B01G077400 chr5B 85.849 212 24 6 1537 1743 511814245 511814455 1.100000e-53 220
12 TraesCS7B01G077400 chr6B 83.346 1297 194 13 3 1292 39894781 39896062 0.000000e+00 1179
13 TraesCS7B01G077400 chr6B 79.520 1333 253 16 4 1325 450591052 450592375 0.000000e+00 931
14 TraesCS7B01G077400 chr6B 78.907 787 156 9 557 1338 658638792 658638011 2.080000e-145 525
15 TraesCS7B01G077400 chr5A 78.915 1788 302 53 1 1746 455337663 455335909 0.000000e+00 1144
16 TraesCS7B01G077400 chr7A 79.569 1346 260 10 1 1338 582112546 582111208 0.000000e+00 948
17 TraesCS7B01G077400 chr7A 86.842 646 50 13 1743 2357 127366806 127367447 0.000000e+00 689
18 TraesCS7B01G077400 chr4B 77.083 1344 281 17 3 1332 623488470 623489800 0.000000e+00 750
19 TraesCS7B01G077400 chr6D 77.836 573 85 29 1200 1743 84476721 84476162 1.360000e-82 316
20 TraesCS7B01G077400 chr3D 82.353 255 42 2 1815 2066 446817284 446817538 3.940000e-53 219
21 TraesCS7B01G077400 chr3D 82.490 257 38 5 1815 2066 584095006 584095260 3.940000e-53 219
22 TraesCS7B01G077400 chr5D 81.961 255 37 7 1818 2066 40677680 40677429 8.540000e-50 207
23 TraesCS7B01G077400 chr5D 81.890 254 39 5 1818 2066 413460037 413459786 8.540000e-50 207
24 TraesCS7B01G077400 chr5D 81.890 254 39 5 1818 2066 545267011 545266760 8.540000e-50 207
25 TraesCS7B01G077400 chr4D 81.890 254 39 5 1818 2066 266113018 266112767 8.540000e-50 207


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 TraesCS7B01G077400 chr7B 87119159 87121515 2356 False 4353 4353 100.000 1 2357 1 chr7B.!!$F1 2356
1 TraesCS7B01G077400 chr1B 593051645 593053213 1568 False 2076 2076 90.615 178 1744 1 chr1B.!!$F1 1566
2 TraesCS7B01G077400 chr7D 577853962 577855704 1742 True 1550 1550 82.975 3 1743 1 chr7D.!!$R1 1740
3 TraesCS7B01G077400 chr7D 125882733 125883372 639 False 732 732 87.988 1743 2357 1 chr7D.!!$F2 614
4 TraesCS7B01G077400 chr3A 595278535 595281877 3342 False 1009 1471 86.908 3 1730 2 chr3A.!!$F1 1727
5 TraesCS7B01G077400 chr3A 712702808 712704146 1338 True 942 942 79.601 1 1338 1 chr3A.!!$R1 1337
6 TraesCS7B01G077400 chr2A 650490741 650492489 1748 False 1406 1406 81.479 3 1743 1 chr2A.!!$F1 1740
7 TraesCS7B01G077400 chr5B 17683037 17684772 1735 True 1314 1314 80.658 12 1744 1 chr5B.!!$R1 1732
8 TraesCS7B01G077400 chr6B 39894781 39896062 1281 False 1179 1179 83.346 3 1292 1 chr6B.!!$F1 1289
9 TraesCS7B01G077400 chr6B 450591052 450592375 1323 False 931 931 79.520 4 1325 1 chr6B.!!$F2 1321
10 TraesCS7B01G077400 chr6B 658638011 658638792 781 True 525 525 78.907 557 1338 1 chr6B.!!$R1 781
11 TraesCS7B01G077400 chr5A 455335909 455337663 1754 True 1144 1144 78.915 1 1746 1 chr5A.!!$R1 1745
12 TraesCS7B01G077400 chr7A 582111208 582112546 1338 True 948 948 79.569 1 1338 1 chr7A.!!$R1 1337
13 TraesCS7B01G077400 chr7A 127366806 127367447 641 False 689 689 86.842 1743 2357 1 chr7A.!!$F1 614
14 TraesCS7B01G077400 chr4B 623488470 623489800 1330 False 750 750 77.083 3 1332 1 chr4B.!!$F1 1329
15 TraesCS7B01G077400 chr6D 84476162 84476721 559 True 316 316 77.836 1200 1743 1 chr6D.!!$R1 543

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
230 235 0.470766 AGGAGCCAAACGTTACCACA 59.529 50.0 0.00 0.0 0.00 4.17 F
1136 1152 0.251354 CTAGCTGCTCTTTGCTGGGA 59.749 55.0 4.91 0.0 43.37 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 2969 0.543749 CCGCCCTTCCTTCTTCATCT 59.456 55.000 0.0 0.0 0.00 2.90 R
2036 3709 4.027991 CGATGACGACGAAAGCAAAATTTC 59.972 41.667 0.0 0.0 42.66 2.17 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
73 74 1.952296 GATTGGTAATGCAGCCTCCTG 59.048 52.381 0.00 0.00 42.13 3.86
206 210 0.595095 AGCGCTTTTTCTGGCAAGAG 59.405 50.000 2.64 0.00 32.79 2.85
214 218 0.986527 TTCTGGCAAGAGCATGAGGA 59.013 50.000 0.00 0.00 44.61 3.71
230 235 0.470766 AGGAGCCAAACGTTACCACA 59.529 50.000 0.00 0.00 0.00 4.17
257 262 6.018180 GGTTAAATGGTCCAGAATATGTCGAC 60.018 42.308 9.11 9.11 0.00 4.20
427 437 7.565029 CCATTAAAACTAGATTTGGGGATTCCT 59.435 37.037 8.15 0.00 36.20 3.36
442 452 3.650461 GGATTCCTCTATCTGGAAGGCTT 59.350 47.826 0.00 0.00 45.43 4.35
580 590 8.352942 AGTTTCCTATTCTTTTCAATGTGTGTC 58.647 33.333 0.00 0.00 0.00 3.67
597 607 8.668510 ATGTGTGTCATAATCAAGAGATTACC 57.331 34.615 0.46 0.00 46.43 2.85
615 625 2.995283 ACCGTGGCTAAATTTAGGGAC 58.005 47.619 23.37 9.44 0.00 4.46
616 626 1.937899 CCGTGGCTAAATTTAGGGACG 59.062 52.381 23.37 8.80 0.00 4.79
620 630 2.572556 TGGCTAAATTTAGGGACGGTGA 59.427 45.455 23.37 0.00 0.00 4.02
923 939 2.646175 GCAGACGTGGGTGGCTAGA 61.646 63.158 0.00 0.00 0.00 2.43
1042 1058 0.546122 TTTGGGCACGGATAGATGCT 59.454 50.000 0.00 0.00 41.74 3.79
1136 1152 0.251354 CTAGCTGCTCTTTGCTGGGA 59.749 55.000 4.91 0.00 43.37 4.37
1320 2938 3.879295 ACGCCTTAAACATGATGAGGATG 59.121 43.478 14.96 9.97 0.00 3.51
1339 2957 2.666190 GTGCAGCGCCAAGAGACA 60.666 61.111 2.29 0.00 0.00 3.41
1343 2961 1.446792 CAGCGCCAAGAGACACGAT 60.447 57.895 2.29 0.00 0.00 3.73
1347 2965 1.291184 CGCCAAGAGACACGATGCAA 61.291 55.000 0.00 0.00 0.00 4.08
1351 2969 1.532437 CAAGAGACACGATGCAAAGCA 59.468 47.619 0.00 0.00 44.86 3.91
1394 3024 1.961180 CTCGGGGCTGGGAGTACTTG 61.961 65.000 0.00 0.00 0.00 3.16
1415 3064 2.106938 CCGCGCTTCTGGCTCATA 59.893 61.111 5.56 0.00 39.13 2.15
1427 3076 3.943381 TCTGGCTCATATGTCTTTTGCTG 59.057 43.478 1.90 0.00 0.00 4.41
1458 3115 2.677836 TGCTGTGTGTTGAAGACTGTTC 59.322 45.455 0.00 0.00 0.00 3.18
1465 3122 2.429250 TGTTGAAGACTGTTCGGTCAGA 59.571 45.455 13.25 0.00 38.57 3.27
1513 3174 1.131638 TTGGGTATGGCCTAGCTGAG 58.868 55.000 3.32 0.00 37.43 3.35
1516 3177 1.277557 GGGTATGGCCTAGCTGAGATG 59.722 57.143 3.32 0.00 37.43 2.90
1533 3194 3.569491 AGATGGGCTTGTAATGAATGGG 58.431 45.455 0.00 0.00 0.00 4.00
1540 3201 4.342092 GGCTTGTAATGAATGGGTTGCTAT 59.658 41.667 0.00 0.00 0.00 2.97
1611 3274 4.467084 GGGCTGCCCGATGACGAA 62.467 66.667 24.16 0.00 42.66 3.85
1761 3425 2.031919 CACTGGCGCACCCTTGTA 59.968 61.111 10.83 0.00 33.59 2.41
1882 3555 4.671831 TCATTTAATGCACCTCCCAAAGA 58.328 39.130 0.00 0.00 0.00 2.52
1940 3613 9.890629 ATATTCTTATTTGTGACACTAGCTTCA 57.109 29.630 7.20 0.00 0.00 3.02
1982 3655 7.973048 ATACTATCTTGTGAACTCTGGGTAA 57.027 36.000 0.00 0.00 0.00 2.85
1990 3663 5.258051 TGTGAACTCTGGGTAACAAAACTT 58.742 37.500 0.00 0.00 39.74 2.66
2004 3677 7.812669 GGTAACAAAACTTCATTGGATACCTTG 59.187 37.037 12.43 0.00 39.16 3.61
2036 3709 2.824341 GGGGAGTACATACCATCTACCG 59.176 54.545 0.00 0.00 32.08 4.02
2082 3755 5.446340 CGTCCACCGTAACTTTAATAAAGGC 60.446 44.000 16.15 6.08 42.82 4.35
2201 3897 8.414778 TGAATGGTTTTTACAAGGTTCGTAAAT 58.585 29.630 0.00 0.00 38.32 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 85 5.352284 TGAATTAAGAAGGATGAGACGCTC 58.648 41.667 0.58 0.58 0.00 5.03
82 86 5.344743 TGAATTAAGAAGGATGAGACGCT 57.655 39.130 0.00 0.00 0.00 5.07
83 87 5.178438 GGATGAATTAAGAAGGATGAGACGC 59.822 44.000 0.00 0.00 0.00 5.19
159 163 6.237942 CGATGTTTATCCAGCTTAACAGTCAG 60.238 42.308 0.00 0.00 34.37 3.51
163 167 7.534085 TTACGATGTTTATCCAGCTTAACAG 57.466 36.000 0.00 0.00 34.37 3.16
206 210 1.130561 GTAACGTTTGGCTCCTCATGC 59.869 52.381 5.91 0.00 0.00 4.06
214 218 1.243902 CCATGTGGTAACGTTTGGCT 58.756 50.000 5.91 0.00 42.51 4.75
230 235 6.486657 CGACATATTCTGGACCATTTAACCAT 59.513 38.462 0.00 0.00 33.08 3.55
257 262 4.115199 CCAGGCCCCCTCTTTCGG 62.115 72.222 0.00 0.00 0.00 4.30
278 288 6.862194 ACATTTTGTTTGCGTAAATCTTTCG 58.138 32.000 0.99 0.00 0.00 3.46
427 437 6.158695 ACCTTCATAAAAGCCTTCCAGATAGA 59.841 38.462 0.00 0.00 0.00 1.98
442 452 6.958192 AGGTAGTACTCCTTGACCTTCATAAA 59.042 38.462 8.26 0.00 37.20 1.40
519 529 1.826024 CTCCTCCCCACAAGGATCG 59.174 63.158 0.00 0.00 42.01 3.69
580 590 5.300752 AGCCACGGTAATCTCTTGATTATG 58.699 41.667 2.44 2.17 44.16 1.90
597 607 1.937899 CCGTCCCTAAATTTAGCCACG 59.062 52.381 25.62 25.62 35.65 4.94
772 786 7.313731 AGGTTCCTCTCCAGGTAATCATATAA 58.686 38.462 0.00 0.00 41.28 0.98
923 939 2.624838 CAGAAAGGACACACATGCCTTT 59.375 45.455 12.47 12.47 46.30 3.11
929 945 7.450074 TCTATTGTTACAGAAAGGACACACAT 58.550 34.615 0.00 0.00 0.00 3.21
981 997 3.451178 ACATAACTCTAGCAACCGGACAT 59.549 43.478 9.46 0.00 0.00 3.06
1136 1152 5.913137 TTTATTTCGGCAATTCCACATCT 57.087 34.783 0.00 0.00 34.01 2.90
1304 2922 4.587891 TGCACACATCCTCATCATGTTTA 58.412 39.130 0.00 0.00 31.83 2.01
1320 2938 2.666190 TCTCTTGGCGCTGCACAC 60.666 61.111 7.64 0.00 0.00 3.82
1339 2957 2.703416 TCTTCATCTGCTTTGCATCGT 58.297 42.857 0.00 0.00 38.13 3.73
1343 2961 3.144657 TCCTTCTTCATCTGCTTTGCA 57.855 42.857 0.00 0.00 36.92 4.08
1347 2965 2.620108 GCCCTTCCTTCTTCATCTGCTT 60.620 50.000 0.00 0.00 0.00 3.91
1351 2969 0.543749 CCGCCCTTCCTTCTTCATCT 59.456 55.000 0.00 0.00 0.00 2.90
1415 3064 2.420022 GCATACGACCAGCAAAAGACAT 59.580 45.455 0.00 0.00 0.00 3.06
1427 3076 0.670546 ACACACAGCAGCATACGACC 60.671 55.000 0.00 0.00 0.00 4.79
1458 3115 1.133982 CAGAGACCTCACATCTGACCG 59.866 57.143 0.00 0.00 42.48 4.79
1465 3122 1.193323 CAGGAGCAGAGACCTCACAT 58.807 55.000 0.00 0.00 33.91 3.21
1513 3174 3.299503 ACCCATTCATTACAAGCCCATC 58.700 45.455 0.00 0.00 0.00 3.51
1516 3177 2.418609 GCAACCCATTCATTACAAGCCC 60.419 50.000 0.00 0.00 0.00 5.19
1552 3214 3.825014 ACGACACCTGAACTACTACACAT 59.175 43.478 0.00 0.00 0.00 3.21
1610 3273 0.893727 GGAAACCCACGGTGAGCATT 60.894 55.000 10.28 0.00 35.34 3.56
1611 3274 1.303317 GGAAACCCACGGTGAGCAT 60.303 57.895 10.28 0.00 35.34 3.79
1757 3420 0.822164 GGAAGGAGCGGCTACTACAA 59.178 55.000 16.59 0.00 0.00 2.41
1761 3425 2.764547 GGGGAAGGAGCGGCTACT 60.765 66.667 9.47 9.47 0.00 2.57
1790 3462 0.992695 GAAGGAGGGGTTGCTACCTT 59.007 55.000 17.03 5.98 44.38 3.50
1792 3464 0.914902 AGGAAGGAGGGGTTGCTACC 60.915 60.000 9.03 9.03 44.22 3.18
1930 3603 7.648142 TCCTAAAAACAAACATGAAGCTAGTG 58.352 34.615 0.00 0.00 0.00 2.74
1931 3604 7.817418 TCCTAAAAACAAACATGAAGCTAGT 57.183 32.000 0.00 0.00 0.00 2.57
1982 3655 5.539955 AGCAAGGTATCCAATGAAGTTTTGT 59.460 36.000 0.00 0.00 0.00 2.83
1990 3663 4.591321 AAAGGAGCAAGGTATCCAATGA 57.409 40.909 0.00 0.00 38.12 2.57
2036 3709 4.027991 CGATGACGACGAAAGCAAAATTTC 59.972 41.667 0.00 0.00 42.66 2.17
2169 3865 8.472007 AACCTTGTAAAAACCATTCATGACTA 57.528 30.769 0.00 0.00 0.00 2.59
2171 3867 6.362283 CGAACCTTGTAAAAACCATTCATGAC 59.638 38.462 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.