Multiple sequence alignment - TraesCS3D01G463100

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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 TraesCS3D01G463100 chr3D 100.000 2732 0 0 370 3101 567220828 567218097 0.000000e+00 5046.0
1 TraesCS3D01G463100 chr3D 82.824 1112 135 33 1898 2995 567228774 567227705 0.000000e+00 944.0
2 TraesCS3D01G463100 chr3D 87.162 740 70 13 2373 3098 569541269 569541997 0.000000e+00 817.0
3 TraesCS3D01G463100 chr3D 83.562 584 67 15 983 1545 567302000 567301425 1.270000e-143 520.0
4 TraesCS3D01G463100 chr3D 79.777 539 62 20 957 1462 569129490 569128966 6.360000e-92 348.0
5 TraesCS3D01G463100 chr3D 82.203 354 43 7 981 1317 567137856 567138206 1.410000e-73 287.0
6 TraesCS3D01G463100 chr3D 84.791 263 33 5 985 1245 569676778 569676521 1.100000e-64 257.0
7 TraesCS3D01G463100 chr3D 85.845 219 18 4 2104 2319 569540871 569541079 1.450000e-53 220.0
8 TraesCS3D01G463100 chr3D 73.208 530 99 25 1046 1553 569644459 569643951 5.360000e-33 152.0
9 TraesCS3D01G463100 chr3D 78.636 220 25 17 2462 2673 565083994 565084199 3.250000e-25 126.0
10 TraesCS3D01G463100 chr3D 100.000 61 0 0 1 61 567221197 567221137 2.530000e-21 113.0
11 TraesCS3D01G463100 chr3A 89.891 2196 177 20 817 3003 700572076 700574235 0.000000e+00 2784.0
12 TraesCS3D01G463100 chr3A 92.352 1203 78 4 1899 3092 701860146 701861343 0.000000e+00 1700.0
13 TraesCS3D01G463100 chr3A 86.175 434 41 8 370 785 701859676 701860108 4.720000e-123 451.0
14 TraesCS3D01G463100 chr3A 87.681 276 17 10 555 817 700571774 700572045 3.890000e-79 305.0
15 TraesCS3D01G463100 chr3A 74.495 545 100 21 1048 1553 700631937 700631393 1.890000e-47 200.0
16 TraesCS3D01G463100 chr3A 75.419 358 67 12 1217 1553 702012851 702012494 1.490000e-33 154.0
17 TraesCS3D01G463100 chr3A 92.857 70 5 0 371 440 700571252 700571321 5.470000e-18 102.0
18 TraesCS3D01G463100 chrUn 89.872 1402 119 8 1442 2833 41106641 41105253 0.000000e+00 1781.0
19 TraesCS3D01G463100 chrUn 81.669 851 121 15 1344 2188 279458730 279457909 0.000000e+00 675.0
20 TraesCS3D01G463100 chrUn 92.112 393 31 0 983 1375 41107069 41106677 3.490000e-154 555.0
21 TraesCS3D01G463100 chrUn 81.579 380 53 9 957 1330 279459145 279458777 6.500000e-77 298.0
22 TraesCS3D01G463100 chrUn 92.090 177 14 0 2925 3101 41103199 41103023 1.850000e-62 250.0
23 TraesCS3D01G463100 chrUn 86.885 61 5 3 4 61 41108007 41107947 7.180000e-07 65.8
24 TraesCS3D01G463100 chr3B 89.061 1225 120 6 774 1996 755033864 755035076 0.000000e+00 1507.0
25 TraesCS3D01G463100 chr3B 87.193 734 74 17 2373 3096 756184747 756184024 0.000000e+00 817.0
26 TraesCS3D01G463100 chr3B 83.314 875 116 17 1502 2369 756186036 756185185 0.000000e+00 780.0
27 TraesCS3D01G463100 chr3B 91.651 527 38 2 2398 2923 755040105 755040626 0.000000e+00 725.0
28 TraesCS3D01G463100 chr3B 90.143 558 44 9 951 1507 756187558 756187011 0.000000e+00 715.0
29 TraesCS3D01G463100 chr3B 96.627 415 12 1 370 782 754991026 754991440 0.000000e+00 688.0
30 TraesCS3D01G463100 chr3B 81.395 860 125 15 1332 2185 754879912 754880742 0.000000e+00 669.0
31 TraesCS3D01G463100 chr3B 93.822 437 18 2 1979 2406 755037061 755037497 0.000000e+00 649.0
32 TraesCS3D01G463100 chr3B 83.289 377 48 8 957 1327 754879507 754879874 1.780000e-87 333.0
33 TraesCS3D01G463100 chr3B 73.424 587 106 21 994 1553 755246921 755246358 1.140000e-39 174.0
34 TraesCS3D01G463100 chr3B 92.063 63 3 2 1 61 754990874 754990936 1.530000e-13 87.9


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 TraesCS3D01G463100 chr3D 567218097 567221197 3100 True 2579.500000 5046 100.000000 1 3101 2 chr3D.!!$R6 3100
1 TraesCS3D01G463100 chr3D 567227705 567228774 1069 True 944.000000 944 82.824000 1898 2995 1 chr3D.!!$R1 1097
2 TraesCS3D01G463100 chr3D 567301425 567302000 575 True 520.000000 520 83.562000 983 1545 1 chr3D.!!$R2 562
3 TraesCS3D01G463100 chr3D 569540871 569541997 1126 False 518.500000 817 86.503500 2104 3098 2 chr3D.!!$F3 994
4 TraesCS3D01G463100 chr3D 569128966 569129490 524 True 348.000000 348 79.777000 957 1462 1 chr3D.!!$R3 505
5 TraesCS3D01G463100 chr3A 701859676 701861343 1667 False 1075.500000 1700 89.263500 370 3092 2 chr3A.!!$F2 2722
6 TraesCS3D01G463100 chr3A 700571252 700574235 2983 False 1063.666667 2784 90.143000 371 3003 3 chr3A.!!$F1 2632
7 TraesCS3D01G463100 chrUn 41103023 41108007 4984 True 662.950000 1781 90.239750 4 3101 4 chrUn.!!$R1 3097
8 TraesCS3D01G463100 chrUn 279457909 279459145 1236 True 486.500000 675 81.624000 957 2188 2 chrUn.!!$R2 1231
9 TraesCS3D01G463100 chr3B 755033864 755040626 6762 False 960.333333 1507 91.511333 774 2923 3 chr3B.!!$F3 2149
10 TraesCS3D01G463100 chr3B 756184024 756187558 3534 True 770.666667 817 86.883333 951 3096 3 chr3B.!!$R2 2145
11 TraesCS3D01G463100 chr3B 754879507 754880742 1235 False 501.000000 669 82.342000 957 2185 2 chr3B.!!$F1 1228
12 TraesCS3D01G463100 chr3B 754990874 754991440 566 False 387.950000 688 94.345000 1 782 2 chr3B.!!$F2 781

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
981 1494 0.179145 CCGCCTACTACCACAACTCG 60.179 60.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2857 11684 0.961019 TCAGCATGGAGGCACAAAAC 59.039 50.0 0.0 0.0 36.16 2.43 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
52 54 2.071540 GTGCTTCCGGTACCACTTTAC 58.928 52.381 13.54 0.00 0.00 2.01
55 57 3.770933 TGCTTCCGGTACCACTTTACTAT 59.229 43.478 13.54 0.00 0.00 2.12
612 960 0.895559 CTCCTGGGGTTGTTGCTTCC 60.896 60.000 0.00 0.00 0.00 3.46
649 1071 2.822764 TGTACACATAACACACACGCA 58.177 42.857 0.00 0.00 0.00 5.24
947 1413 0.802607 CTGCCGAAAGACCTACGCTC 60.803 60.000 0.00 0.00 0.00 5.03
948 1414 1.518792 GCCGAAAGACCTACGCTCC 60.519 63.158 0.00 0.00 0.00 4.70
949 1415 1.226603 CCGAAAGACCTACGCTCCG 60.227 63.158 0.00 0.00 0.00 4.63
981 1494 0.179145 CCGCCTACTACCACAACTCG 60.179 60.000 0.00 0.00 0.00 4.18
1317 1855 2.262774 CTTCCTGCGATGGCCTCCTT 62.263 60.000 3.32 0.00 38.85 3.36
1320 1858 1.402896 CCTGCGATGGCCTCCTTCTA 61.403 60.000 3.32 0.00 38.85 2.10
1468 2048 1.741770 CGGCTGCTACTGACCAACC 60.742 63.158 0.00 0.00 0.00 3.77
1473 2053 1.895798 CTGCTACTGACCAACCTCAGA 59.104 52.381 3.23 0.00 40.28 3.27
1561 3127 2.823747 GGGTGGTTGGAGATGGTAAAAC 59.176 50.000 0.00 0.00 0.00 2.43
1566 3132 2.396590 TGGAGATGGTAAAACCGCTC 57.603 50.000 9.19 9.19 42.58 5.03
1616 3186 4.966168 TGATAGCCTACATTGGTTCCTACA 59.034 41.667 0.00 0.00 0.00 2.74
1621 3191 4.323562 GCCTACATTGGTTCCTACAGAAGT 60.324 45.833 0.00 0.00 34.29 3.01
1659 3229 2.496111 GTATTTGACACCACCACCGAA 58.504 47.619 0.00 0.00 0.00 4.30
1763 3333 1.634960 TGCCATAATGATGCCATGGG 58.365 50.000 15.13 0.00 39.74 4.00
1773 3343 1.891150 GATGCCATGGGAATCATCACC 59.109 52.381 11.10 0.00 37.68 4.02
2157 5767 3.647113 AGCTGTCATATCCTCATGAGCTT 59.353 43.478 17.76 8.86 34.52 3.74
2158 5768 4.102838 AGCTGTCATATCCTCATGAGCTTT 59.897 41.667 17.76 6.38 34.52 3.51
2169 5779 5.604231 TCCTCATGAGCTTTACCATCTATGT 59.396 40.000 17.76 0.00 0.00 2.29
2218 5828 1.862827 CCTCTTTGCTTTGCTTTGCAC 59.137 47.619 0.00 0.00 38.71 4.57
2437 9222 5.460419 GTGATCTTAGTGCTCGATTGTTAGG 59.540 44.000 0.00 0.00 0.00 2.69
2506 9297 3.771577 ACCTTTTCACCTAGTGGTCTG 57.228 47.619 0.00 0.00 46.60 3.51
2507 9298 3.314693 ACCTTTTCACCTAGTGGTCTGA 58.685 45.455 0.00 0.00 46.60 3.27
2567 9358 4.024556 ACTTTGTTGAAGCTGACGATGAAG 60.025 41.667 0.00 0.00 39.04 3.02
2570 9361 2.391616 TGAAGCTGACGATGAAGCAT 57.608 45.000 0.00 0.00 42.06 3.79
2580 9373 4.398988 TGACGATGAAGCATAGGCAAAAAT 59.601 37.500 0.67 0.00 44.61 1.82
2640 9435 6.783708 AGAAGAGCTTGTAATACTAGCAGT 57.216 37.500 24.04 11.10 46.76 4.40
2641 9436 7.176589 AGAAGAGCTTGTAATACTAGCAGTT 57.823 36.000 24.04 17.35 46.76 3.16
2642 9437 8.294954 AGAAGAGCTTGTAATACTAGCAGTTA 57.705 34.615 24.04 0.00 46.76 2.24
2643 9438 8.919145 AGAAGAGCTTGTAATACTAGCAGTTAT 58.081 33.333 24.04 13.41 46.76 1.89
2721 9519 7.926674 TTTCTCTGTGAATCAATTGCATCTA 57.073 32.000 0.00 0.00 34.24 1.98
2840 11666 4.716784 AGAATGGACTGATACTGCAACCTA 59.283 41.667 0.00 0.00 0.00 3.08
2857 11684 7.925993 TGCAACCTAAAAATCTATGAATACCG 58.074 34.615 0.00 0.00 0.00 4.02
2883 11711 1.448540 CCTCCATGCTGACACCGTC 60.449 63.158 0.00 0.00 0.00 4.79
2933 11761 7.051623 TCTCTTACTGTTTTACTTTTCCTGCA 58.948 34.615 0.00 0.00 0.00 4.41
3044 11872 1.825622 GCTATTGTCAGGCCCAGGC 60.826 63.158 0.00 0.00 41.06 4.85
3077 11905 3.175438 TCATGTCTCAAGGAGGACAGA 57.825 47.619 0.00 0.00 44.13 3.41
3080 11908 2.964209 TGTCTCAAGGAGGACAGAACT 58.036 47.619 0.00 0.00 37.52 3.01
3088 11916 0.827368 GAGGACAGAACTAGGCCTGG 59.173 60.000 17.99 16.79 34.85 4.45
3098 11926 0.396435 CTAGGCCTGGTGTGTGACAA 59.604 55.000 17.99 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
460 470 2.052690 CGATGTCGGAGGGGTCACT 61.053 63.158 0.00 0.00 35.37 3.41
612 960 1.432514 ACAACTGTACATGCGCAGAG 58.567 50.000 18.32 13.98 36.62 3.35
649 1071 0.543174 GAGGGAGGGAGACAGTGTGT 60.543 60.000 0.00 0.00 0.00 3.72
1186 1701 1.921869 GAGAAAATGGGGAGGGCGGA 61.922 60.000 0.00 0.00 0.00 5.54
1225 1748 2.266055 GTGGTCCAAGGCGAGGAG 59.734 66.667 0.00 0.00 35.42 3.69
1392 1963 0.883833 TCCTGAAGTCCGACGGTAAC 59.116 55.000 14.79 5.63 0.00 2.50
1491 2077 1.421410 GCGTAAGGACATGACAGCCG 61.421 60.000 0.00 0.00 38.28 5.52
1498 2084 0.811616 GAGCCCAGCGTAAGGACATG 60.812 60.000 0.00 0.00 38.28 3.21
1561 3127 3.304257 CAGATATCTCGAACAAGAGCGG 58.696 50.000 1.03 0.00 38.12 5.52
1566 3132 3.181471 ACAGGGCAGATATCTCGAACAAG 60.181 47.826 1.03 0.00 0.00 3.16
1683 3253 1.138069 TCACTGTCGCCAAGAACAAGA 59.862 47.619 0.00 0.00 0.00 3.02
1773 3343 3.250762 CGTAATCCTGCAACACCCATATG 59.749 47.826 0.00 0.00 0.00 1.78
2011 5583 8.189709 TGTTTGAGCTGATATTCATATATCGC 57.810 34.615 0.00 0.00 43.70 4.58
2157 5767 7.446106 ACTTGGTCCAATACATAGATGGTAA 57.554 36.000 4.34 0.00 35.66 2.85
2158 5768 8.593679 CATACTTGGTCCAATACATAGATGGTA 58.406 37.037 4.34 0.38 35.66 3.25
2169 5779 5.070446 CAGTAGGCTCATACTTGGTCCAATA 59.930 44.000 4.34 0.81 33.68 1.90
2437 9222 7.710676 ACAGTGACATGAGGGATATAGATAC 57.289 40.000 0.00 0.00 0.00 2.24
2544 9335 3.466836 TCATCGTCAGCTTCAACAAAGT 58.533 40.909 0.00 0.00 37.31 2.66
2567 9358 8.971321 CAACAAGTGATATATTTTTGCCTATGC 58.029 33.333 0.00 0.00 38.26 3.14
2570 9361 8.682710 GGTCAACAAGTGATATATTTTTGCCTA 58.317 33.333 0.00 0.00 38.90 3.93
2580 9373 6.000840 TGTTTGCAGGTCAACAAGTGATATA 58.999 36.000 0.00 0.00 38.90 0.86
2648 9443 9.537192 CATTGACTATGATGCAACCATTTAATT 57.463 29.630 9.75 0.00 36.26 1.40
2684 9479 9.483062 GATTCACAGAGAAAAATGAATTACGAG 57.517 33.333 0.00 0.00 40.88 4.18
2822 9620 6.599638 AGATTTTTAGGTTGCAGTATCAGTCC 59.400 38.462 0.00 0.00 0.00 3.85
2840 11666 7.544217 GGCACAAAACGGTATTCATAGATTTTT 59.456 33.333 0.00 0.00 0.00 1.94
2857 11684 0.961019 TCAGCATGGAGGCACAAAAC 59.039 50.000 0.00 0.00 36.16 2.43
2933 11761 7.715657 TCAAGCACTGATACTCAAAATGTTTT 58.284 30.769 0.00 0.00 0.00 2.43
2949 11777 9.874215 CAGATTAAACATATACATCAAGCACTG 57.126 33.333 0.00 0.00 0.00 3.66
3044 11872 0.591170 GACATGAACACAACGTGGGG 59.409 55.000 0.00 0.00 37.94 4.96
3050 11878 3.499918 CCTCCTTGAGACATGAACACAAC 59.500 47.826 0.00 0.00 0.00 3.32
3077 11905 0.396811 GTCACACACCAGGCCTAGTT 59.603 55.000 3.98 0.00 0.00 2.24
3080 11908 0.107831 GTTGTCACACACCAGGCCTA 59.892 55.000 3.98 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.