Multiple sequence alignment - TraesCS7D01G337000

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 TraesCS7D01G337000 chr7D 100.000 2591 0 0 1 2591 429712343 429709753 0.000000e+00 4785.0
1 TraesCS7D01G337000 chr7D 84.991 1106 88 45 944 2030 430097155 430096109 0.000000e+00 1051.0
2 TraesCS7D01G337000 chr7D 92.070 517 31 6 9 516 557359736 557360251 0.000000e+00 719.0
3 TraesCS7D01G337000 chr7D 89.362 141 11 2 2373 2510 430095432 430095293 9.530000e-40 174.0
4 TraesCS7D01G337000 chr7B 93.258 2047 92 23 528 2543 447220262 447218231 0.000000e+00 2974.0
5 TraesCS7D01G337000 chr7B 93.169 1947 57 24 524 2443 386553842 386555739 0.000000e+00 2789.0
6 TraesCS7D01G337000 chr7B 91.231 707 40 6 944 1646 447477961 447477273 0.000000e+00 942.0
7 TraesCS7D01G337000 chr7B 88.406 138 15 1 2373 2510 447476401 447476265 5.740000e-37 165.0
8 TraesCS7D01G337000 chr7B 84.483 174 15 8 2185 2356 447476719 447476556 7.420000e-36 161.0
9 TraesCS7D01G337000 chr7B 88.350 103 9 1 2032 2131 447476914 447476812 1.260000e-23 121.0
10 TraesCS7D01G337000 chr7A 85.615 1154 82 38 530 1631 502621389 502622510 0.000000e+00 1134.0
11 TraesCS7D01G337000 chr7A 82.959 1291 117 65 770 2024 502359885 502361108 0.000000e+00 1070.0
12 TraesCS7D01G337000 chr7A 89.333 150 11 3 2374 2520 502623454 502623601 1.580000e-42 183.0
13 TraesCS7D01G337000 chr7A 94.624 93 5 0 2253 2345 502381562 502381654 7.470000e-31 145.0
14 TraesCS7D01G337000 chr7A 92.079 101 8 0 2031 2131 502622880 502622980 2.690000e-30 143.0
15 TraesCS7D01G337000 chr7A 79.188 197 23 6 2159 2344 502623061 502623250 1.260000e-23 121.0
16 TraesCS7D01G337000 chr7A 89.362 94 9 1 2038 2131 502362146 502362238 1.630000e-22 117.0
17 TraesCS7D01G337000 chr7A 80.537 149 17 6 2373 2510 502381809 502381956 1.270000e-18 104.0
18 TraesCS7D01G337000 chr7A 87.805 82 9 1 2373 2454 665376629 665376709 7.630000e-16 95.3
19 TraesCS7D01G337000 chr6B 92.365 537 27 7 1 524 693806506 693805971 0.000000e+00 752.0
20 TraesCS7D01G337000 chr5D 92.586 526 28 4 9 524 408295460 408295984 0.000000e+00 745.0
21 TraesCS7D01G337000 chr5D 91.841 527 30 8 9 524 122627210 122626686 0.000000e+00 723.0
22 TraesCS7D01G337000 chr1B 92.176 524 34 6 9 526 659568685 659568163 0.000000e+00 734.0
23 TraesCS7D01G337000 chr1B 87.004 554 66 3 1041 1594 62527926 62528473 1.020000e-173 619.0
24 TraesCS7D01G337000 chr6D 92.030 527 31 5 9 526 120665545 120666069 0.000000e+00 730.0
25 TraesCS7D01G337000 chr2D 92.190 525 28 7 9 524 562351981 562351461 0.000000e+00 730.0
26 TraesCS7D01G337000 chr4D 91.165 532 27 9 1 526 370367469 370366952 0.000000e+00 704.0
27 TraesCS7D01G337000 chr1D 91.238 525 30 9 9 523 66415467 66415985 0.000000e+00 701.0
28 TraesCS7D01G337000 chr1D 85.191 601 79 5 1041 1636 42344580 42345175 2.200000e-170 608.0
29 TraesCS7D01G337000 chr1A 82.593 540 83 8 1059 1594 42279933 42279401 1.400000e-127 466.0


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 TraesCS7D01G337000 chr7D 429709753 429712343 2590 True 4785.00 4785 100.00000 1 2591 1 chr7D.!!$R1 2590
1 TraesCS7D01G337000 chr7D 557359736 557360251 515 False 719.00 719 92.07000 9 516 1 chr7D.!!$F1 507
2 TraesCS7D01G337000 chr7D 430095293 430097155 1862 True 612.50 1051 87.17650 944 2510 2 chr7D.!!$R2 1566
3 TraesCS7D01G337000 chr7B 447218231 447220262 2031 True 2974.00 2974 93.25800 528 2543 1 chr7B.!!$R1 2015
4 TraesCS7D01G337000 chr7B 386553842 386555739 1897 False 2789.00 2789 93.16900 524 2443 1 chr7B.!!$F1 1919
5 TraesCS7D01G337000 chr7B 447476265 447477961 1696 True 347.25 942 88.11750 944 2510 4 chr7B.!!$R2 1566
6 TraesCS7D01G337000 chr7A 502359885 502362238 2353 False 593.50 1070 86.16050 770 2131 2 chr7A.!!$F2 1361
7 TraesCS7D01G337000 chr7A 502621389 502623601 2212 False 395.25 1134 86.55375 530 2520 4 chr7A.!!$F4 1990
8 TraesCS7D01G337000 chr6B 693805971 693806506 535 True 752.00 752 92.36500 1 524 1 chr6B.!!$R1 523
9 TraesCS7D01G337000 chr5D 408295460 408295984 524 False 745.00 745 92.58600 9 524 1 chr5D.!!$F1 515
10 TraesCS7D01G337000 chr5D 122626686 122627210 524 True 723.00 723 91.84100 9 524 1 chr5D.!!$R1 515
11 TraesCS7D01G337000 chr1B 659568163 659568685 522 True 734.00 734 92.17600 9 526 1 chr1B.!!$R1 517
12 TraesCS7D01G337000 chr1B 62527926 62528473 547 False 619.00 619 87.00400 1041 1594 1 chr1B.!!$F1 553
13 TraesCS7D01G337000 chr6D 120665545 120666069 524 False 730.00 730 92.03000 9 526 1 chr6D.!!$F1 517
14 TraesCS7D01G337000 chr2D 562351461 562351981 520 True 730.00 730 92.19000 9 524 1 chr2D.!!$R1 515
15 TraesCS7D01G337000 chr4D 370366952 370367469 517 True 704.00 704 91.16500 1 526 1 chr4D.!!$R1 525
16 TraesCS7D01G337000 chr1D 66415467 66415985 518 False 701.00 701 91.23800 9 523 1 chr1D.!!$F2 514
17 TraesCS7D01G337000 chr1D 42344580 42345175 595 False 608.00 608 85.19100 1041 1636 1 chr1D.!!$F1 595
18 TraesCS7D01G337000 chr1A 42279401 42279933 532 True 466.00 466 82.59300 1059 1594 1 chr1A.!!$R1 535

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
158 159 0.335361 ATACCTCGGACCAGACCAGT 59.665 55.0 0.0 0.0 0.0 4.00 F
467 502 0.459489 GCCAAACCAGACAAACAGCA 59.541 50.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1422 1532 1.151450 CTGCACCTCCACCACCTTT 59.849 57.895 0.00 0.00 0.0 3.11 R
2430 4096 0.375803 ACACTTGGTTTTGACGCGAC 59.624 50.000 15.93 7.62 0.0 5.19 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
158 159 0.335361 ATACCTCGGACCAGACCAGT 59.665 55.000 0.00 0.00 0.00 4.00
164 165 1.878656 CGGACCAGACCAGTGAGGAC 61.879 65.000 0.00 0.00 41.22 3.85
433 458 2.483877 CTCAATTTTGACGTGGCTGCTA 59.516 45.455 0.00 0.00 32.90 3.49
464 499 2.010582 GCCGCCAAACCAGACAAACA 62.011 55.000 0.00 0.00 0.00 2.83
467 502 0.459489 GCCAAACCAGACAAACAGCA 59.541 50.000 0.00 0.00 0.00 4.41
545 580 3.389925 ACGTACAAACTTGATCCCGAA 57.610 42.857 0.00 0.00 0.00 4.30
551 586 2.100605 AACTTGATCCCGAAGCTGTC 57.899 50.000 0.00 0.00 0.00 3.51
563 598 4.470050 GCTGTCGTTTCGCTCGCG 62.470 66.667 0.00 0.00 41.35 5.87
594 629 3.787001 GTTGCGAGCCTAGGCCCT 61.787 66.667 30.42 13.32 43.17 5.19
924 987 3.864686 CTTTGCATCGCCGTCCCG 61.865 66.667 0.00 0.00 0.00 5.14
982 1071 1.301874 CCGCCGTGTTTACTTCCCA 60.302 57.895 0.00 0.00 0.00 4.37
1348 1458 3.615811 AGTGGGAGGCCCTGGAGA 61.616 66.667 0.00 0.00 45.70 3.71
1422 1532 4.077184 ATGAGCGCCGTCGGGAAA 62.077 61.111 14.38 0.00 35.95 3.13
1441 1551 2.357593 AAAGGTGGTGGAGGTGCAGG 62.358 60.000 0.00 0.00 0.00 4.85
1518 1628 4.069232 CTGCCGGTCTTCGCCAGA 62.069 66.667 1.90 0.00 45.87 3.86
1600 1718 2.772691 CCGCAGTAGTCCCGGTCTC 61.773 68.421 0.00 0.00 37.36 3.36
1601 1719 2.772691 CGCAGTAGTCCCGGTCTCC 61.773 68.421 0.00 0.00 0.00 3.71
1602 1720 2.424733 GCAGTAGTCCCGGTCTCCC 61.425 68.421 0.00 0.00 0.00 4.30
1662 1780 4.072131 TCTTTGAGCTTCGGTTAATTGCT 58.928 39.130 0.00 0.00 36.63 3.91
1754 1874 6.238374 GGGGATTATTGTTCACGAGTACAATG 60.238 42.308 21.78 0.00 43.03 2.82
1774 1894 3.460103 TGGACGAGTTACTGGTTTCAAC 58.540 45.455 0.88 0.00 0.00 3.18
1976 2122 6.203647 ACCAAAATAAGTTTCCTTTCGAACG 58.796 36.000 0.00 0.00 31.89 3.95
2118 3293 9.469807 AATGCTAAGTCTAACTATTCTGATTCG 57.530 33.333 0.00 0.00 0.00 3.34
2134 3340 9.770097 ATTCTGATTCGTATGATTGATTGTAGT 57.230 29.630 0.00 0.00 0.00 2.73
2430 4096 3.487202 CAACCGGTGTGCGATCCG 61.487 66.667 8.52 6.34 45.42 4.18
2443 4109 1.418755 GATCCGTCGCGTCAAAACC 59.581 57.895 5.77 0.00 0.00 3.27
2446 4112 1.083015 CCGTCGCGTCAAAACCAAG 60.083 57.895 5.77 0.00 0.00 3.61
2564 4233 2.994699 CCCCCAACATGGCGTAGA 59.005 61.111 0.00 0.00 35.79 2.59
2565 4234 1.451387 CCCCCAACATGGCGTAGAC 60.451 63.158 0.00 0.00 35.79 2.59
2566 4235 1.451387 CCCCAACATGGCGTAGACC 60.451 63.158 0.00 0.00 35.79 3.85
2567 4236 1.298340 CCCAACATGGCGTAGACCA 59.702 57.895 0.00 0.00 45.82 4.02
2568 4237 0.744414 CCCAACATGGCGTAGACCAG 60.744 60.000 0.00 0.00 44.71 4.00
2569 4238 0.036388 CCAACATGGCGTAGACCAGT 60.036 55.000 0.00 0.00 44.71 4.00
2570 4239 1.206132 CCAACATGGCGTAGACCAGTA 59.794 52.381 0.00 0.00 44.71 2.74
2571 4240 2.354303 CCAACATGGCGTAGACCAGTAA 60.354 50.000 0.00 0.00 44.71 2.24
2572 4241 3.331150 CAACATGGCGTAGACCAGTAAA 58.669 45.455 0.00 0.00 44.71 2.01
2573 4242 3.247006 ACATGGCGTAGACCAGTAAAG 57.753 47.619 0.00 0.00 44.71 1.85
2574 4243 1.933853 CATGGCGTAGACCAGTAAAGC 59.066 52.381 0.00 0.00 44.71 3.51
2575 4244 0.248289 TGGCGTAGACCAGTAAAGCC 59.752 55.000 0.00 0.00 43.05 4.35
2576 4245 0.248289 GGCGTAGACCAGTAAAGCCA 59.752 55.000 0.00 0.00 42.37 4.75
2577 4246 1.641577 GCGTAGACCAGTAAAGCCAG 58.358 55.000 0.00 0.00 0.00 4.85
2578 4247 1.203994 GCGTAGACCAGTAAAGCCAGA 59.796 52.381 0.00 0.00 0.00 3.86
2579 4248 2.353406 GCGTAGACCAGTAAAGCCAGAA 60.353 50.000 0.00 0.00 0.00 3.02
2580 4249 3.512680 CGTAGACCAGTAAAGCCAGAAG 58.487 50.000 0.00 0.00 0.00 2.85
2581 4250 3.192844 CGTAGACCAGTAAAGCCAGAAGA 59.807 47.826 0.00 0.00 0.00 2.87
2582 4251 4.321750 CGTAGACCAGTAAAGCCAGAAGAA 60.322 45.833 0.00 0.00 0.00 2.52
2583 4252 4.009370 AGACCAGTAAAGCCAGAAGAAC 57.991 45.455 0.00 0.00 0.00 3.01
2584 4253 3.391296 AGACCAGTAAAGCCAGAAGAACA 59.609 43.478 0.00 0.00 0.00 3.18
2585 4254 4.042187 AGACCAGTAAAGCCAGAAGAACAT 59.958 41.667 0.00 0.00 0.00 2.71
2586 4255 4.074970 ACCAGTAAAGCCAGAAGAACATG 58.925 43.478 0.00 0.00 0.00 3.21
2587 4256 3.441572 CCAGTAAAGCCAGAAGAACATGG 59.558 47.826 0.00 0.00 39.73 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 159 0.032540 CATCATCATCGCCGTCCTCA 59.967 55.000 0.00 0.00 0.00 3.86
164 165 0.712222 CGTCATCATCATCATCGCCG 59.288 55.000 0.00 0.00 0.00 6.46
518 553 4.031426 GGATCAAGTTTGTACGTAAGAGCG 59.969 45.833 0.00 0.00 43.62 5.03
545 580 3.106407 GCGAGCGAAACGACAGCT 61.106 61.111 0.00 0.00 44.80 4.24
594 629 0.108520 GAATCGTGCGTCCCACCTAA 60.109 55.000 0.00 0.00 41.53 2.69
709 767 3.576550 CTCGGATTTGGGAAAGGGAAAAA 59.423 43.478 0.00 0.00 0.00 1.94
924 987 0.671781 TTGCTTGCTTCTCTCTCGGC 60.672 55.000 0.00 0.00 0.00 5.54
970 1058 4.282449 TCTCTCAACGATGGGAAGTAAACA 59.718 41.667 0.00 0.00 35.04 2.83
975 1063 1.205893 GCTCTCTCAACGATGGGAAGT 59.794 52.381 0.00 0.00 35.04 3.01
982 1071 1.107114 ATGGTCGCTCTCTCAACGAT 58.893 50.000 0.00 0.00 38.22 3.73
1422 1532 1.151450 CTGCACCTCCACCACCTTT 59.849 57.895 0.00 0.00 0.00 3.11
1497 1607 4.742201 GCGAAGACCGGCAGCTCA 62.742 66.667 0.00 0.00 39.04 4.26
1597 1715 3.132139 CGAAGCTCGTCCGGGAGA 61.132 66.667 11.50 5.82 36.08 3.71
1600 1718 2.216750 TTAACCGAAGCTCGTCCGGG 62.217 60.000 17.18 0.00 46.83 5.73
1602 1720 1.197910 GATTAACCGAAGCTCGTCCG 58.802 55.000 0.00 0.00 38.40 4.79
1662 1780 8.985315 AAGATGATCTAAGAACAATGGCAATA 57.015 30.769 0.00 0.00 0.00 1.90
1754 1874 3.460103 TGTTGAAACCAGTAACTCGTCC 58.540 45.455 0.00 0.00 0.00 4.79
1976 2122 2.316119 CTTTACGAAAGGTGCAGCAC 57.684 50.000 17.97 17.97 34.85 4.40
2151 3357 7.553504 AATTTAGGGCAGTGTAGGAATTTTT 57.446 32.000 0.00 0.00 0.00 1.94
2152 3358 7.553504 AAATTTAGGGCAGTGTAGGAATTTT 57.446 32.000 0.00 0.00 0.00 1.82
2153 3359 7.454694 AGAAAATTTAGGGCAGTGTAGGAATTT 59.545 33.333 0.00 0.00 0.00 1.82
2154 3360 6.954102 AGAAAATTTAGGGCAGTGTAGGAATT 59.046 34.615 0.00 0.00 0.00 2.17
2155 3361 6.494059 AGAAAATTTAGGGCAGTGTAGGAAT 58.506 36.000 0.00 0.00 0.00 3.01
2156 3362 5.887754 AGAAAATTTAGGGCAGTGTAGGAA 58.112 37.500 0.00 0.00 0.00 3.36
2159 3365 5.476945 ACCAAGAAAATTTAGGGCAGTGTAG 59.523 40.000 0.00 0.00 0.00 2.74
2430 4096 0.375803 ACACTTGGTTTTGACGCGAC 59.624 50.000 15.93 7.62 0.00 5.19
2549 4218 0.744414 CTGGTCTACGCCATGTTGGG 60.744 60.000 0.00 0.00 38.19 4.12
2550 4219 0.036388 ACTGGTCTACGCCATGTTGG 60.036 55.000 0.00 0.00 41.55 3.77
2551 4220 2.665649 TACTGGTCTACGCCATGTTG 57.334 50.000 0.00 0.00 37.96 3.33
2552 4221 3.596214 CTTTACTGGTCTACGCCATGTT 58.404 45.455 0.00 0.00 37.96 2.71
2553 4222 2.677037 GCTTTACTGGTCTACGCCATGT 60.677 50.000 0.00 0.00 37.96 3.21
2554 4223 1.933853 GCTTTACTGGTCTACGCCATG 59.066 52.381 0.00 0.00 37.96 3.66
2555 4224 1.134491 GGCTTTACTGGTCTACGCCAT 60.134 52.381 0.00 0.00 37.96 4.40
2556 4225 0.248289 GGCTTTACTGGTCTACGCCA 59.752 55.000 0.00 0.00 36.16 5.69
2557 4226 0.248289 TGGCTTTACTGGTCTACGCC 59.752 55.000 0.00 0.00 36.64 5.68
2558 4227 1.203994 TCTGGCTTTACTGGTCTACGC 59.796 52.381 0.00 0.00 0.00 4.42
2559 4228 3.192844 TCTTCTGGCTTTACTGGTCTACG 59.807 47.826 0.00 0.00 0.00 3.51
2560 4229 4.803098 TCTTCTGGCTTTACTGGTCTAC 57.197 45.455 0.00 0.00 0.00 2.59
2561 4230 4.591498 TGTTCTTCTGGCTTTACTGGTCTA 59.409 41.667 0.00 0.00 0.00 2.59
2562 4231 3.391296 TGTTCTTCTGGCTTTACTGGTCT 59.609 43.478 0.00 0.00 0.00 3.85
2563 4232 3.740115 TGTTCTTCTGGCTTTACTGGTC 58.260 45.455 0.00 0.00 0.00 4.02
2564 4233 3.857157 TGTTCTTCTGGCTTTACTGGT 57.143 42.857 0.00 0.00 0.00 4.00
2565 4234 3.441572 CCATGTTCTTCTGGCTTTACTGG 59.558 47.826 0.00 0.00 0.00 4.00
2566 4235 4.691860 CCATGTTCTTCTGGCTTTACTG 57.308 45.455 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.