Multiple sequence alignment - TraesCS7A01G567300

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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 TraesCS7A01G567300 chr7A 100.000 2561 0 0 1 2561 736015002 736012442 0.000000e+00 4730.0
1 TraesCS7A01G567300 chr7A 89.981 539 54 0 943 1481 735902354 735902892 0.000000e+00 697.0
2 TraesCS7A01G567300 chr7A 83.457 538 86 3 943 1478 736060516 736059980 4.920000e-137 497.0
3 TraesCS7A01G567300 chr5D 93.818 1100 50 2 1480 2561 428470908 428472007 0.000000e+00 1639.0
4 TraesCS7A01G567300 chr5D 92.647 1088 71 7 1480 2560 464904271 464905356 0.000000e+00 1557.0
5 TraesCS7A01G567300 chr5D 92.528 1084 74 5 1483 2560 554754412 554753330 0.000000e+00 1546.0
6 TraesCS7A01G567300 chr5D 92.754 345 22 2 602 945 233739768 233739426 1.770000e-136 496.0
7 TraesCS7A01G567300 chr3D 93.578 1090 55 6 1485 2561 508062466 508063553 0.000000e+00 1611.0
8 TraesCS7A01G567300 chr3D 86.023 973 63 34 1 946 597190368 597189442 0.000000e+00 990.0
9 TraesCS7A01G567300 chr3D 90.528 644 32 11 302 944 571446719 571446104 0.000000e+00 824.0
10 TraesCS7A01G567300 chr3D 91.849 503 24 1 1 486 597186259 597185757 0.000000e+00 686.0
11 TraesCS7A01G567300 chr6B 93.486 1090 57 6 1483 2561 77802600 77801514 0.000000e+00 1607.0
12 TraesCS7A01G567300 chr6B 92.969 128 8 1 108 235 483536289 483536163 4.350000e-43 185.0
13 TraesCS7A01G567300 chr6B 90.678 118 9 2 1 116 483536424 483536307 3.410000e-34 156.0
14 TraesCS7A01G567300 chrUn 93.253 1082 70 2 1480 2561 88753410 88754488 0.000000e+00 1591.0
15 TraesCS7A01G567300 chrUn 89.739 614 35 11 336 946 100487242 100486654 0.000000e+00 760.0
16 TraesCS7A01G567300 chrUn 100.000 28 0 0 443 470 83023663 83023636 5.000000e-03 52.8
17 TraesCS7A01G567300 chr7D 92.969 1081 71 5 1483 2560 98404400 98403322 0.000000e+00 1570.0
18 TraesCS7A01G567300 chr7D 92.606 1082 69 7 1485 2560 554471365 554470289 0.000000e+00 1544.0
19 TraesCS7A01G567300 chr7D 92.150 535 42 0 941 1475 632096451 632096985 0.000000e+00 756.0
20 TraesCS7A01G567300 chr7D 85.347 505 37 8 1 488 204881432 204881916 2.960000e-134 488.0
21 TraesCS7A01G567300 chr7D 96.774 124 4 0 108 231 629133950 629133827 9.290000e-50 207.0
22 TraesCS7A01G567300 chr7D 93.333 90 6 0 6 95 629135536 629135447 1.600000e-27 134.0
23 TraesCS7A01G567300 chr7D 95.161 62 3 0 7 68 43116271 43116210 5.830000e-17 99.0
24 TraesCS7A01G567300 chr2D 92.528 1084 74 5 1483 2560 319689185 319688103 0.000000e+00 1546.0
25 TraesCS7A01G567300 chr2D 93.162 351 19 4 594 942 247393986 247394333 6.320000e-141 510.0
26 TraesCS7A01G567300 chr2D 95.570 316 9 4 630 944 501304335 501304024 3.800000e-138 501.0
27 TraesCS7A01G567300 chr1A 93.651 567 28 4 1 567 351994977 351994419 0.000000e+00 841.0
28 TraesCS7A01G567300 chr1A 88.191 398 29 13 553 945 351994474 351994090 2.320000e-125 459.0
29 TraesCS7A01G567300 chr1A 96.850 127 3 1 109 235 301158860 301158735 7.180000e-51 211.0
30 TraesCS7A01G567300 chr7B 91.497 541 46 0 941 1481 744248007 744248547 0.000000e+00 745.0
31 TraesCS7A01G567300 chr7B 91.497 541 46 0 941 1481 744295138 744294598 0.000000e+00 745.0
32 TraesCS7A01G567300 chr7B 90.459 545 46 5 941 1481 744007414 744006872 0.000000e+00 713.0
33 TraesCS7A01G567300 chr7B 85.393 534 74 3 950 1479 744207083 744207616 3.720000e-153 551.0
34 TraesCS7A01G567300 chr7B 83.835 532 82 3 952 1479 744176567 744177098 1.060000e-138 503.0
35 TraesCS7A01G567300 chr2B 90.424 543 50 2 941 1481 782185995 782185453 0.000000e+00 713.0
36 TraesCS7A01G567300 chr6D 93.557 357 17 5 594 947 40653992 40653639 6.280000e-146 527.0
37 TraesCS7A01G567300 chr1D 91.831 355 23 5 594 945 238057422 238057773 8.230000e-135 490.0
38 TraesCS7A01G567300 chr1D 95.312 128 5 1 108 235 237767500 237767374 4.320000e-48 202.0
39 TraesCS7A01G567300 chr1B 95.312 128 5 1 108 235 336786594 336786720 4.320000e-48 202.0
40 TraesCS7A01G567300 chr4A 96.774 62 2 0 7 68 650871562 650871623 1.250000e-18 104.0
41 TraesCS7A01G567300 chr3B 96.774 62 2 0 7 68 142726576 142726637 1.250000e-18 104.0


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 TraesCS7A01G567300 chr7A 736012442 736015002 2560 True 4730 4730 100.000 1 2561 1 chr7A.!!$R1 2560
1 TraesCS7A01G567300 chr7A 735902354 735902892 538 False 697 697 89.981 943 1481 1 chr7A.!!$F1 538
2 TraesCS7A01G567300 chr7A 736059980 736060516 536 True 497 497 83.457 943 1478 1 chr7A.!!$R2 535
3 TraesCS7A01G567300 chr5D 428470908 428472007 1099 False 1639 1639 93.818 1480 2561 1 chr5D.!!$F1 1081
4 TraesCS7A01G567300 chr5D 464904271 464905356 1085 False 1557 1557 92.647 1480 2560 1 chr5D.!!$F2 1080
5 TraesCS7A01G567300 chr5D 554753330 554754412 1082 True 1546 1546 92.528 1483 2560 1 chr5D.!!$R2 1077
6 TraesCS7A01G567300 chr3D 508062466 508063553 1087 False 1611 1611 93.578 1485 2561 1 chr3D.!!$F1 1076
7 TraesCS7A01G567300 chr3D 597185757 597190368 4611 True 838 990 88.936 1 946 2 chr3D.!!$R2 945
8 TraesCS7A01G567300 chr3D 571446104 571446719 615 True 824 824 90.528 302 944 1 chr3D.!!$R1 642
9 TraesCS7A01G567300 chr6B 77801514 77802600 1086 True 1607 1607 93.486 1483 2561 1 chr6B.!!$R1 1078
10 TraesCS7A01G567300 chrUn 88753410 88754488 1078 False 1591 1591 93.253 1480 2561 1 chrUn.!!$F1 1081
11 TraesCS7A01G567300 chrUn 100486654 100487242 588 True 760 760 89.739 336 946 1 chrUn.!!$R2 610
12 TraesCS7A01G567300 chr7D 98403322 98404400 1078 True 1570 1570 92.969 1483 2560 1 chr7D.!!$R2 1077
13 TraesCS7A01G567300 chr7D 554470289 554471365 1076 True 1544 1544 92.606 1485 2560 1 chr7D.!!$R3 1075
14 TraesCS7A01G567300 chr7D 632096451 632096985 534 False 756 756 92.150 941 1475 1 chr7D.!!$F2 534
15 TraesCS7A01G567300 chr2D 319688103 319689185 1082 True 1546 1546 92.528 1483 2560 1 chr2D.!!$R1 1077
16 TraesCS7A01G567300 chr1A 351994090 351994977 887 True 650 841 90.921 1 945 2 chr1A.!!$R2 944
17 TraesCS7A01G567300 chr7B 744248007 744248547 540 False 745 745 91.497 941 1481 1 chr7B.!!$F3 540
18 TraesCS7A01G567300 chr7B 744294598 744295138 540 True 745 745 91.497 941 1481 1 chr7B.!!$R2 540
19 TraesCS7A01G567300 chr7B 744006872 744007414 542 True 713 713 90.459 941 1481 1 chr7B.!!$R1 540
20 TraesCS7A01G567300 chr7B 744207083 744207616 533 False 551 551 85.393 950 1479 1 chr7B.!!$F2 529
21 TraesCS7A01G567300 chr7B 744176567 744177098 531 False 503 503 83.835 952 1479 1 chr7B.!!$F1 527
22 TraesCS7A01G567300 chr2B 782185453 782185995 542 True 713 713 90.424 941 1481 1 chr2B.!!$R1 540

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
821 842 0.101759 GGTGATACTGCCGACGCTAA 59.898 55.0 0.0 0.0 35.36 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 4478 0.909133 TCATGCCTGGTCAGCAGGTA 60.909 55.0 23.95 20.49 44.9 3.08 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
77 78 2.047179 GTCGGTGGAGAAGGTGCC 60.047 66.667 0.00 0.00 0.00 5.01
80 81 3.256960 GGTGGAGAAGGTGCCCCA 61.257 66.667 0.00 0.00 0.00 4.96
257 275 3.322466 CCCAGGGACAGCTCCGTT 61.322 66.667 0.00 0.00 37.46 4.44
263 281 2.355837 GACAGCTCCGTTGCGTCA 60.356 61.111 12.73 0.00 36.89 4.35
293 311 1.344438 TCGAACACCATGCTCTTGACT 59.656 47.619 0.00 0.00 0.00 3.41
393 411 2.750350 CACCGCTCCTCCTTGGTT 59.250 61.111 0.00 0.00 37.07 3.67
670 688 1.840737 CGGAACAGGGAGAGAGAAGA 58.159 55.000 0.00 0.00 0.00 2.87
719 737 4.468689 GAAAGCGACGGGGGAGGG 62.469 72.222 0.00 0.00 0.00 4.30
768 788 2.670789 GCATGCATAAACAAACCGCTGA 60.671 45.455 14.21 0.00 0.00 4.26
820 841 1.731433 GGGTGATACTGCCGACGCTA 61.731 60.000 0.00 0.00 35.36 4.26
821 842 0.101759 GGTGATACTGCCGACGCTAA 59.898 55.000 0.00 0.00 35.36 3.09
861 882 1.774300 AAAAAGCGATCCTGGGGGT 59.226 52.632 0.00 0.00 0.00 4.95
1061 2039 4.099170 GCTCACGCAGGCAGCAAG 62.099 66.667 1.96 0.00 46.13 4.01
1188 3484 1.887198 ACCGACGAGACTGTTCAAGAT 59.113 47.619 0.00 0.00 0.00 2.40
1248 3544 1.003580 GACATCCTTGACCTCTGCCAA 59.996 52.381 0.00 0.00 0.00 4.52
1421 3720 5.629020 GCGTTGCTTTAAACTTCATCAATCA 59.371 36.000 0.00 0.00 0.00 2.57
1528 3916 8.079203 TGCATACGGCCACTTTATTAATTATTG 58.921 33.333 2.24 0.00 43.89 1.90
1554 3942 8.709646 GTCACAAGACCTAACAAAGTAATACAG 58.290 37.037 0.00 0.00 38.89 2.74
1580 3968 1.547372 AGACTAAAGCCGCCGTCTAAA 59.453 47.619 0.00 0.00 35.15 1.85
1608 3997 0.744874 TGTCGCTACACCTATCCAGC 59.255 55.000 0.00 0.00 0.00 4.85
1613 4002 2.820197 CGCTACACCTATCCAGCTGATA 59.180 50.000 17.39 10.16 34.76 2.15
1622 4011 1.224592 CCAGCTGATAAAGGGGCGT 59.775 57.895 17.39 0.00 0.00 5.68
1659 4049 2.831685 TACCAAACAGACATCGCAGT 57.168 45.000 0.00 0.00 0.00 4.40
1778 4176 1.134280 CCACCGCTCCATCTTCAGAAT 60.134 52.381 0.00 0.00 0.00 2.40
1818 4216 0.741326 GCTCAGTCCAGCTATCGTCA 59.259 55.000 0.00 0.00 36.38 4.35
1926 4439 2.410322 CTGCCAAGTACCACCAGCCA 62.410 60.000 0.00 0.00 0.00 4.75
1965 4478 1.132643 GGAAGATCTGTCGTGCGTAGT 59.867 52.381 0.00 0.00 0.00 2.73
1972 4617 1.239296 TGTCGTGCGTAGTACCTGCT 61.239 55.000 0.00 0.00 41.02 4.24
2090 4803 2.124819 CTTCCAGCGCTGCTCCAT 60.125 61.111 31.96 0.00 36.40 3.41
2395 5132 2.107141 CTAGCTACACCGGCCAGC 59.893 66.667 13.21 13.21 35.49 4.85
2459 5223 1.874915 CGCCGTCGCCGATCTAAAA 60.875 57.895 0.00 0.00 35.63 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
268 286 0.741221 GAGCATGGTGTTCGACCTCC 60.741 60.000 0.00 0.00 46.32 4.30
283 301 1.134995 CGTCCTGCATAGTCAAGAGCA 60.135 52.381 0.00 0.00 35.43 4.26
316 334 2.125673 CGTCCGAGCCGTTTCCAT 60.126 61.111 0.00 0.00 0.00 3.41
655 673 2.359143 CCATCCTCTTCTCTCTCCCTGT 60.359 54.545 0.00 0.00 0.00 4.00
670 688 1.022903 ACCTTCTCTCTCCCCATCCT 58.977 55.000 0.00 0.00 0.00 3.24
719 737 2.124403 CTGCAGCCACATCTCCCC 60.124 66.667 0.00 0.00 0.00 4.81
768 788 2.430610 GGGAGGCATCTGAGAGCGT 61.431 63.158 0.00 0.59 0.00 5.07
821 842 1.213491 GCCGGTTTCGTGCAATTTTT 58.787 45.000 1.90 0.00 34.38 1.94
990 1929 1.271325 ACCATCGCCATTGTTGTCAGA 60.271 47.619 0.00 0.00 0.00 3.27
992 1931 0.880441 CACCATCGCCATTGTTGTCA 59.120 50.000 0.00 0.00 0.00 3.58
1061 2039 5.355596 CCAACATAGTCTTCACCTCATCTC 58.644 45.833 0.00 0.00 0.00 2.75
1165 3461 0.591659 TGAACAGTCTCGTCGGTGAG 59.408 55.000 0.00 0.00 37.33 3.51
1188 3484 3.506743 TTGAGCTGCCCCACCCAA 61.507 61.111 0.00 0.00 0.00 4.12
1248 3544 1.471119 CATGCTTCATGGCCTTGAGT 58.529 50.000 19.64 6.73 38.11 3.41
1407 3706 4.939255 AGGACCCATGATTGATGAAGTTT 58.061 39.130 0.00 0.00 33.31 2.66
1481 3869 3.473647 CCCAGATGCAGAGGCCGA 61.474 66.667 0.00 0.00 40.13 5.54
1528 3916 8.597662 TGTATTACTTTGTTAGGTCTTGTGAC 57.402 34.615 0.00 0.00 42.22 3.67
1540 3928 9.991906 TTAGTCTTACTGCTGTATTACTTTGTT 57.008 29.630 17.70 3.50 31.13 2.83
1554 3942 1.007580 GGCGGCTTTAGTCTTACTGC 58.992 55.000 0.00 0.00 0.00 4.40
1580 3968 1.937899 GGTGTAGCGACAGTTTGTTGT 59.062 47.619 0.00 0.00 35.82 3.32
1608 3997 3.368531 GGCTATCTACGCCCCTTTATCAG 60.369 52.174 0.00 0.00 41.73 2.90
1622 4011 3.078458 TGGTATTAGGCCCAGGCTATCTA 59.922 47.826 8.89 0.00 40.30 1.98
1659 4049 6.070767 CCTCAGGTCTTAGATGTTAGGTTTGA 60.071 42.308 0.00 0.00 0.00 2.69
1778 4176 3.191162 GCAAGGTTGATGCATCAGTACAA 59.809 43.478 27.25 11.51 43.29 2.41
1863 4261 4.664677 ACCGTGACGTGCTCAGCC 62.665 66.667 3.64 0.00 0.00 4.85
1926 4439 3.620488 TCCAAAGACTTCAAGCTGTGTT 58.380 40.909 0.00 0.00 0.00 3.32
1965 4478 0.909133 TCATGCCTGGTCAGCAGGTA 60.909 55.000 23.95 20.49 44.90 3.08
1972 4617 1.236616 CGCTTTGTCATGCCTGGTCA 61.237 55.000 0.00 0.00 0.00 4.02
2090 4803 4.801330 TCTCTCTTGGAAGCATCGTTTA 57.199 40.909 0.00 0.00 0.00 2.01
2134 4847 1.993391 TGGGGTTCCAGATCGGACC 60.993 63.158 5.89 9.82 46.36 4.46
2395 5132 1.077930 CACCCCTGGCAGATCTGTG 60.078 63.158 23.38 12.88 0.00 3.66
2459 5223 2.124570 GGCGGCATGTCATCTGGT 60.125 61.111 3.07 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.