Multiple sequence alignment - TraesCS7D01G133200

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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 TraesCS7D01G133200 chr7D 100.000 3101 0 0 1 3101 84406025 84409125 0.000000e+00 5727.0
1 TraesCS7D01G133200 chr7D 94.525 621 26 6 2484 3101 554837774 554838389 0.000000e+00 952.0
2 TraesCS7D01G133200 chr7D 92.436 661 39 11 2446 3101 626224360 626225014 0.000000e+00 933.0
3 TraesCS7D01G133200 chr7D 82.545 888 131 15 573 1444 590731905 590732784 0.000000e+00 760.0
4 TraesCS7D01G133200 chr7D 82.686 849 126 11 607 1444 590652009 590652847 0.000000e+00 734.0
5 TraesCS7D01G133200 chr7D 83.311 737 107 9 711 1444 590647666 590648389 0.000000e+00 665.0
6 TraesCS7D01G133200 chr7D 95.722 187 8 0 1447 1633 99965762 99965948 5.030000e-78 302.0
7 TraesCS7D01G133200 chr7B 90.734 1457 98 15 1 1444 33955542 33956974 0.000000e+00 1908.0
8 TraesCS7D01G133200 chr7B 94.332 1235 56 5 1 1229 34140144 34141370 0.000000e+00 1881.0
9 TraesCS7D01G133200 chr7B 86.524 1217 99 26 281 1444 34048125 34049329 0.000000e+00 1279.0
10 TraesCS7D01G133200 chr7B 82.746 852 123 13 605 1444 23318135 23317296 0.000000e+00 737.0
11 TraesCS7D01G133200 chr7B 82.130 845 109 22 605 1434 665534602 665535419 0.000000e+00 686.0
12 TraesCS7D01G133200 chr7B 93.527 448 13 5 2001 2438 34146741 34147182 0.000000e+00 652.0
13 TraesCS7D01G133200 chr7B 82.603 730 108 13 712 1437 23325675 23324961 7.300000e-176 627.0
14 TraesCS7D01G133200 chr7B 88.989 445 33 7 2001 2438 34049325 34049760 1.270000e-148 536.0
15 TraesCS7D01G133200 chr7B 89.973 369 14 2 2001 2369 33956970 33957315 3.650000e-124 455.0
16 TraesCS7D01G133200 chr7B 88.699 292 17 7 1 283 34047680 34047964 2.960000e-90 342.0
17 TraesCS7D01G133200 chr7A 90.040 1486 81 18 1 1444 85692990 85694450 0.000000e+00 1862.0
18 TraesCS7D01G133200 chr7A 82.857 420 47 20 1468 1877 675130682 675130278 1.370000e-93 353.0
19 TraesCS7D01G133200 chr7A 92.797 236 7 5 2001 2235 85694446 85694672 1.780000e-87 333.0
20 TraesCS7D01G133200 chr7A 82.933 375 41 19 1511 1874 675132121 675131759 1.790000e-82 316.0
21 TraesCS7D01G133200 chr7A 95.349 43 0 2 2192 2232 85694693 85694735 2.000000e-07 67.6
22 TraesCS7D01G133200 chr5D 97.741 664 15 0 2438 3101 254948074 254947411 0.000000e+00 1144.0
23 TraesCS7D01G133200 chr5D 93.844 666 35 6 2438 3101 238185723 238185062 0.000000e+00 998.0
24 TraesCS7D01G133200 chr5D 91.377 661 45 12 2446 3101 420971196 420971849 0.000000e+00 894.0
25 TraesCS7D01G133200 chr5D 94.444 558 28 3 1445 2000 404243974 404244530 0.000000e+00 856.0
26 TraesCS7D01G133200 chr5D 94.424 556 25 5 1445 1998 404241058 404241609 0.000000e+00 850.0
27 TraesCS7D01G133200 chr5D 93.967 547 31 2 1445 1990 404242530 404243075 0.000000e+00 826.0
28 TraesCS7D01G133200 chr3D 96.396 666 22 2 2437 3101 313296454 313297118 0.000000e+00 1096.0
29 TraesCS7D01G133200 chr4D 96.241 665 23 2 2438 3101 362483001 362483664 0.000000e+00 1088.0
30 TraesCS7D01G133200 chr4D 94.444 558 30 1 1445 2001 228781527 228780970 0.000000e+00 857.0
31 TraesCS7D01G133200 chr4D 91.697 554 34 1 1445 1998 228780054 228779513 0.000000e+00 758.0
32 TraesCS7D01G133200 chr2D 95.195 666 27 5 2438 3101 76573420 76574082 0.000000e+00 1048.0
33 TraesCS7D01G133200 chr2D 94.527 676 31 5 2428 3101 96778769 96779440 0.000000e+00 1038.0
34 TraesCS7D01G133200 chr2D 84.314 153 9 6 1847 1998 638457542 638457680 5.390000e-28 135.0
35 TraesCS7D01G133200 chr2D 85.185 135 6 5 1867 2001 638458079 638458199 3.250000e-25 126.0
36 TraesCS7D01G133200 chr6B 91.489 564 41 6 1445 2003 296847929 296847368 0.000000e+00 769.0
37 TraesCS7D01G133200 chr2A 90.857 525 31 3 1445 1964 289760993 289760481 0.000000e+00 688.0
38 TraesCS7D01G133200 chr6D 97.500 160 4 0 1445 1604 428425322 428425481 1.100000e-69 274.0
39 TraesCS7D01G133200 chr2B 93.956 182 8 3 1445 1625 654731064 654730885 3.940000e-69 272.0


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 TraesCS7D01G133200 chr7D 84406025 84409125 3100 False 5727.0 5727 100.000000 1 3101 1 chr7D.!!$F1 3100
1 TraesCS7D01G133200 chr7D 554837774 554838389 615 False 952.0 952 94.525000 2484 3101 1 chr7D.!!$F3 617
2 TraesCS7D01G133200 chr7D 626224360 626225014 654 False 933.0 933 92.436000 2446 3101 1 chr7D.!!$F5 655
3 TraesCS7D01G133200 chr7D 590731905 590732784 879 False 760.0 760 82.545000 573 1444 1 chr7D.!!$F4 871
4 TraesCS7D01G133200 chr7D 590647666 590652847 5181 False 699.5 734 82.998500 607 1444 2 chr7D.!!$F6 837
5 TraesCS7D01G133200 chr7B 34140144 34141370 1226 False 1881.0 1881 94.332000 1 1229 1 chr7B.!!$F1 1228
6 TraesCS7D01G133200 chr7B 33955542 33957315 1773 False 1181.5 1908 90.353500 1 2369 2 chr7B.!!$F4 2368
7 TraesCS7D01G133200 chr7B 23317296 23318135 839 True 737.0 737 82.746000 605 1444 1 chr7B.!!$R1 839
8 TraesCS7D01G133200 chr7B 34047680 34049760 2080 False 719.0 1279 88.070667 1 2438 3 chr7B.!!$F5 2437
9 TraesCS7D01G133200 chr7B 665534602 665535419 817 False 686.0 686 82.130000 605 1434 1 chr7B.!!$F3 829
10 TraesCS7D01G133200 chr7B 23324961 23325675 714 True 627.0 627 82.603000 712 1437 1 chr7B.!!$R2 725
11 TraesCS7D01G133200 chr7A 85692990 85694735 1745 False 754.2 1862 92.728667 1 2235 3 chr7A.!!$F1 2234
12 TraesCS7D01G133200 chr7A 675130278 675132121 1843 True 334.5 353 82.895000 1468 1877 2 chr7A.!!$R1 409
13 TraesCS7D01G133200 chr5D 254947411 254948074 663 True 1144.0 1144 97.741000 2438 3101 1 chr5D.!!$R2 663
14 TraesCS7D01G133200 chr5D 238185062 238185723 661 True 998.0 998 93.844000 2438 3101 1 chr5D.!!$R1 663
15 TraesCS7D01G133200 chr5D 420971196 420971849 653 False 894.0 894 91.377000 2446 3101 1 chr5D.!!$F1 655
16 TraesCS7D01G133200 chr5D 404241058 404244530 3472 False 844.0 856 94.278333 1445 2000 3 chr5D.!!$F2 555
17 TraesCS7D01G133200 chr3D 313296454 313297118 664 False 1096.0 1096 96.396000 2437 3101 1 chr3D.!!$F1 664
18 TraesCS7D01G133200 chr4D 362483001 362483664 663 False 1088.0 1088 96.241000 2438 3101 1 chr4D.!!$F1 663
19 TraesCS7D01G133200 chr4D 228779513 228781527 2014 True 807.5 857 93.070500 1445 2001 2 chr4D.!!$R1 556
20 TraesCS7D01G133200 chr2D 76573420 76574082 662 False 1048.0 1048 95.195000 2438 3101 1 chr2D.!!$F1 663
21 TraesCS7D01G133200 chr2D 96778769 96779440 671 False 1038.0 1038 94.527000 2428 3101 1 chr2D.!!$F2 673
22 TraesCS7D01G133200 chr6B 296847368 296847929 561 True 769.0 769 91.489000 1445 2003 1 chr6B.!!$R1 558
23 TraesCS7D01G133200 chr2A 289760481 289760993 512 True 688.0 688 90.857000 1445 1964 1 chr2A.!!$R1 519

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
232 248 6.862209 AGCACAGTTTACAAAATTCTTGTGA 58.138 32.000 13.08 5.53 34.11 3.58 F
1071 4867 1.768077 GCACCAGGCTCTATCCCCT 60.768 63.158 0.00 0.00 40.25 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 5200 0.320421 GCAGCTCCGTGGTGTTCTTA 60.320 55.0 6.7 0.0 45.23 2.1 R
2612 12368 0.902531 CCGTACTTCCCACCACATCT 59.097 55.0 0.0 0.0 0.00 2.9 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
232 248 6.862209 AGCACAGTTTACAAAATTCTTGTGA 58.138 32.000 13.08 5.53 34.11 3.58
1054 4850 2.036764 GACGGGAACATTGCTAGCGC 62.037 60.000 10.77 0.00 0.00 5.92
1071 4867 1.768077 GCACCAGGCTCTATCCCCT 60.768 63.158 0.00 0.00 40.25 4.79
1374 5170 2.572284 GCGTTCAGCGAGGTAGGT 59.428 61.111 0.00 0.00 44.77 3.08
1382 5178 2.753452 TCAGCGAGGTAGGTCTACAAAG 59.247 50.000 9.94 2.24 37.78 2.77
1404 5200 1.000896 CTTCTTCCCCAATGCCGGT 60.001 57.895 1.90 0.00 0.00 5.28
1434 5230 0.532573 CGGAGCTGCTGAAGAACCTA 59.467 55.000 7.01 0.00 0.00 3.08
1532 5328 2.704065 ACGAAGAGGAAGGTGAAGGAAA 59.296 45.455 0.00 0.00 0.00 3.13
1613 5426 3.119955 GGCGTGTATTTCTTTTCCCTGAC 60.120 47.826 0.00 0.00 0.00 3.51
1647 5461 2.662596 CCCAGGCGAGCTACACAA 59.337 61.111 0.00 0.00 0.00 3.33
1672 5488 1.490490 CTGGAGCAGGCTTTATACCCA 59.510 52.381 0.00 0.00 0.00 4.51
1679 5495 1.164041 GGCTTTATACCCACGCGCAT 61.164 55.000 5.73 0.00 0.00 4.73
1784 10008 4.498520 CGCAGTCGCCGTGATCCT 62.499 66.667 0.00 0.00 33.11 3.24
1794 10018 1.607801 CCGTGATCCTGAGTCCAGCA 61.608 60.000 0.00 0.00 39.07 4.41
1803 10027 3.226429 GAGTCCAGCACCTGACGCA 62.226 63.158 0.00 0.00 32.44 5.24
1877 10101 1.270571 TGGACACACACGCATACACAT 60.271 47.619 0.00 0.00 0.00 3.21
1900 11584 4.079958 TCTGGCCTATACACTAGTCAGACA 60.080 45.833 3.32 0.00 0.00 3.41
2000 11685 2.371841 TCGCCATGGCTTATTCCTACAT 59.628 45.455 33.07 0.00 39.32 2.29
2001 11686 2.485426 CGCCATGGCTTATTCCTACATG 59.515 50.000 33.07 9.99 38.82 3.21
2008 11693 3.498481 GGCTTATTCCTACATGGGCATCA 60.498 47.826 0.00 0.00 36.20 3.07
2114 11800 5.752472 AGCTCACTTGATGTTTAGATGATCG 59.248 40.000 0.00 0.00 0.00 3.69
2277 12029 9.920946 ACATATATCCTTGGATGTAAAGTTTGT 57.079 29.630 12.08 7.77 30.83 2.83
2284 12036 7.340743 TCCTTGGATGTAAAGTTTGTCTTTCAA 59.659 33.333 0.00 1.38 44.18 2.69
2362 12114 3.454812 ACCTCGCCCAAAGTCTATGTAAT 59.545 43.478 0.00 0.00 0.00 1.89
2369 12121 6.459923 GCCCAAAGTCTATGTAATCTCCTAG 58.540 44.000 0.00 0.00 0.00 3.02
2385 12137 6.531503 TCTCCTAGGTCATAAAGTCACAAG 57.468 41.667 9.08 0.00 0.00 3.16
2387 12139 6.497259 TCTCCTAGGTCATAAAGTCACAAGTT 59.503 38.462 9.08 0.00 0.00 2.66
2422 12175 3.695830 AATAAGGCGGACTTTGTCTCA 57.304 42.857 0.00 0.00 40.64 3.27
2425 12178 0.036010 AGGCGGACTTTGTCTCATGG 60.036 55.000 0.00 0.00 32.47 3.66
2519 12274 1.271127 TGATGAGCCCGATGGGTTGA 61.271 55.000 3.40 0.00 46.51 3.18
2612 12368 3.887716 GCACTAAACCTAGATCGGTAGGA 59.112 47.826 13.58 0.00 42.18 2.94
2636 12393 2.652530 GTGGGAAGTACGGCGTCA 59.347 61.111 19.21 3.80 0.00 4.35
2725 12482 2.903357 CCATAGTGGGCTGAGCGT 59.097 61.111 0.00 0.00 32.67 5.07
2832 12589 9.237846 GATCTCAACTTTTACTTTTGACCTTTG 57.762 33.333 0.00 0.00 0.00 2.77
3036 12793 2.288457 CCATGTCGACTGTGTGTTCTCT 60.288 50.000 17.92 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 53 7.894753 TGCCAAATCATTACCATTAGATCAA 57.105 32.000 0.00 0.00 0.00 2.57
232 248 6.059787 AGTGCAAGATAGAAGACTTGGAAT 57.940 37.500 0.00 0.00 43.54 3.01
282 464 0.820891 GGCCTCACTGGTATGCATGG 60.821 60.000 10.16 0.00 38.35 3.66
761 4529 3.605231 GCAACGTTGGTGTGTGTATGTAC 60.605 47.826 28.33 3.87 0.00 2.90
764 4532 1.658931 CGCAACGTTGGTGTGTGTATG 60.659 52.381 28.33 0.49 0.00 2.39
765 4533 0.584396 CGCAACGTTGGTGTGTGTAT 59.416 50.000 28.33 0.00 0.00 2.29
768 4536 2.788581 ACGCAACGTTGGTGTGTG 59.211 55.556 28.33 12.93 36.35 3.82
1054 4850 0.761802 GAAGGGGATAGAGCCTGGTG 59.238 60.000 0.00 0.00 0.00 4.17
1071 4867 1.527380 GCCGTGGTTGGTGAAGGAA 60.527 57.895 0.00 0.00 0.00 3.36
1126 4922 1.492176 GGTGGTGAGGATGATGACCAT 59.508 52.381 0.00 0.00 40.55 3.55
1279 5075 2.726351 GGAGCCTCCGGAACTCAGG 61.726 68.421 26.96 17.00 31.88 3.86
1314 5110 3.391965 TGTGAAGATGGCATGCAAAAAC 58.608 40.909 21.36 8.40 0.00 2.43
1368 5164 3.055747 AGAAGCAGCTTTGTAGACCTACC 60.056 47.826 9.62 0.00 35.26 3.18
1371 5167 3.558109 GGAAGAAGCAGCTTTGTAGACCT 60.558 47.826 9.62 0.00 0.00 3.85
1374 5170 2.290323 GGGGAAGAAGCAGCTTTGTAGA 60.290 50.000 9.62 0.00 0.00 2.59
1382 5178 1.514553 GCATTGGGGAAGAAGCAGC 59.485 57.895 0.00 0.00 0.00 5.25
1404 5200 0.320421 GCAGCTCCGTGGTGTTCTTA 60.320 55.000 6.70 0.00 45.23 2.10
1434 5230 1.685355 GGCAACAACAGCCCAAAGGT 61.685 55.000 0.00 0.00 46.50 3.50
1532 5328 0.468226 TGTGTCCTGCGTCCTTCTTT 59.532 50.000 0.00 0.00 0.00 2.52
1613 5426 0.602905 GGGGTGAACTGAGTTCGTGG 60.603 60.000 19.31 0.00 44.55 4.94
1647 5461 1.944177 TAAAGCCTGCTCCAGACTCT 58.056 50.000 0.00 0.00 32.44 3.24
1784 10008 3.051210 CGTCAGGTGCTGGACTCA 58.949 61.111 0.00 0.00 31.51 3.41
1794 10018 3.626924 GGGGTGACTGCGTCAGGT 61.627 66.667 10.88 0.00 43.57 4.00
1803 10027 0.639392 AGATGCTAGGAGGGGTGACT 59.361 55.000 0.00 0.00 0.00 3.41
1871 10095 5.702266 ACTAGTGTATAGGCCAGATGTGTA 58.298 41.667 5.01 0.00 0.00 2.90
1877 10101 4.079958 TGTCTGACTAGTGTATAGGCCAGA 60.080 45.833 5.01 0.92 0.00 3.86
1900 11584 1.837439 TCTGGGCATAATCCGACTTGT 59.163 47.619 0.00 0.00 0.00 3.16
1910 11594 1.638070 TGTTGGATGGTCTGGGCATAA 59.362 47.619 0.00 0.00 0.00 1.90
2000 11685 1.003003 TCGACAGAAATGTGATGCCCA 59.997 47.619 0.00 0.00 0.00 5.36
2001 11686 1.667724 CTCGACAGAAATGTGATGCCC 59.332 52.381 0.00 0.00 0.00 5.36
2008 11693 5.123186 TGAACACAAAACTCGACAGAAATGT 59.877 36.000 0.00 0.00 0.00 2.71
2065 11750 1.006102 GAGGAGTGGTGTCGGTGTG 60.006 63.158 0.00 0.00 0.00 3.82
2362 12114 6.017192 ACTTGTGACTTTATGACCTAGGAGA 58.983 40.000 17.98 0.64 0.00 3.71
2369 12121 8.871686 ATTCAAAAACTTGTGACTTTATGACC 57.128 30.769 0.00 0.00 0.00 4.02
2385 12137 7.947830 CCGCCTTATTTTCGTAAATTCAAAAAC 59.052 33.333 5.29 0.00 35.61 2.43
2387 12139 7.326547 GTCCGCCTTATTTTCGTAAATTCAAAA 59.673 33.333 5.29 0.00 35.61 2.44
2404 12157 2.354704 CCATGAGACAAAGTCCGCCTTA 60.355 50.000 0.00 0.00 32.18 2.69
2405 12158 1.611673 CCATGAGACAAAGTCCGCCTT 60.612 52.381 0.00 0.00 32.18 4.35
2408 12161 1.734465 CTTCCATGAGACAAAGTCCGC 59.266 52.381 0.00 0.00 32.18 5.54
2422 12175 4.366267 ACTCTACAACCATCTCCTTCCAT 58.634 43.478 0.00 0.00 0.00 3.41
2425 12178 4.027437 AGGACTCTACAACCATCTCCTTC 58.973 47.826 0.00 0.00 0.00 3.46
2612 12368 0.902531 CCGTACTTCCCACCACATCT 59.097 55.000 0.00 0.00 0.00 2.90
2694 12451 2.957902 CTATGGGTGACGGGCCCCTA 62.958 65.000 18.66 0.00 45.49 3.53
3036 12793 3.705934 TTGCCGCCCAGTGTGTTCA 62.706 57.895 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.