Multiple sequence alignment - TraesCS6B01G443900

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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 TraesCS6B01G443900 chr6B 100.000 3056 0 0 1 3056 706867694 706870749 0.000000e+00 5644.0
1 TraesCS6B01G443900 chr6B 83.156 1407 201 18 800 2199 706850603 706851980 0.000000e+00 1253.0
2 TraesCS6B01G443900 chr6B 84.274 248 27 2 1207 1454 706797445 706797680 6.590000e-57 231.0
3 TraesCS6B01G443900 chr6A 94.233 2896 146 10 167 3056 610124237 610127117 0.000000e+00 4403.0
4 TraesCS6B01G443900 chr6A 84.177 1403 190 15 800 2199 610066715 610068088 0.000000e+00 1332.0
5 TraesCS6B01G443900 chr6A 83.560 1326 188 17 887 2199 610063285 610064593 0.000000e+00 1214.0
6 TraesCS6B01G443900 chr6A 84.974 772 113 3 1429 2199 610087981 610088750 0.000000e+00 780.0
7 TraesCS6B01G443900 chr6A 87.298 433 44 7 2614 3045 35471051 35470629 4.580000e-133 484.0
8 TraesCS6B01G443900 chr6A 79.219 640 89 19 800 1433 610078646 610079247 3.670000e-109 405.0
9 TraesCS6B01G443900 chr6A 79.258 593 85 17 800 1390 610090845 610091401 2.220000e-101 379.0
10 TraesCS6B01G443900 chr5B 80.565 1487 244 32 965 2424 48146359 48147827 0.000000e+00 1103.0
11 TraesCS6B01G443900 chr5B 79.056 1504 231 47 965 2424 47128120 47126657 0.000000e+00 955.0
12 TraesCS6B01G443900 chr5B 81.302 722 107 23 1808 2508 46770902 46770188 7.400000e-156 560.0
13 TraesCS6B01G443900 chr5B 82.207 444 38 19 2614 3056 60588780 60589183 8.110000e-91 344.0
14 TraesCS6B01G443900 chr5B 88.000 175 19 2 2366 2539 48147886 48148059 3.990000e-49 206.0
15 TraesCS6B01G443900 chr5B 86.239 109 13 2 2427 2534 46630111 46630004 1.930000e-22 117.0
16 TraesCS6B01G443900 chr6D 86.355 1004 125 4 1207 2199 463531518 463532520 0.000000e+00 1085.0
17 TraesCS6B01G443900 chr5A 79.819 1546 226 46 1019 2534 36799303 36797814 0.000000e+00 1048.0
18 TraesCS6B01G443900 chr5A 78.765 1587 270 43 999 2549 36942966 36941411 0.000000e+00 1002.0
19 TraesCS6B01G443900 chr5A 80.702 627 97 20 1901 2508 36945739 36945118 1.660000e-127 466.0
20 TraesCS6B01G443900 chr5A 87.429 175 20 2 2366 2539 37400760 37400587 1.860000e-47 200.0
21 TraesCS6B01G443900 chr5A 86.331 139 17 2 2372 2508 37592677 37592539 1.900000e-32 150.0
22 TraesCS6B01G443900 chr5D 79.663 1544 230 43 1019 2534 45938810 45940297 0.000000e+00 1035.0
23 TraesCS6B01G443900 chr5D 83.092 692 100 8 1729 2406 46085511 46084823 5.600000e-172 614.0
24 TraesCS6B01G443900 chr5D 87.417 453 53 2 2606 3054 357879689 357880141 4.520000e-143 518.0
25 TraesCS6B01G443900 chr5D 84.798 421 56 3 2636 3055 184101453 184101866 1.690000e-112 416.0
26 TraesCS6B01G443900 chr5D 90.909 77 6 1 2366 2442 46274262 46274187 5.390000e-18 102.0
27 TraesCS6B01G443900 chr5D 89.655 58 5 1 2367 2424 46084810 46084754 4.230000e-09 73.1
28 TraesCS6B01G443900 chr2B 78.338 1468 245 39 966 2400 731710588 731712015 0.000000e+00 881.0
29 TraesCS6B01G443900 chr2B 87.919 447 48 4 2615 3056 29538589 29539034 3.490000e-144 521.0
30 TraesCS6B01G443900 chr2A 90.237 379 33 2 1 377 2768888 2769264 2.740000e-135 492.0
31 TraesCS6B01G443900 chr2A 89.362 376 34 5 1 375 597494786 597495156 4.610000e-128 468.0
32 TraesCS6B01G443900 chr2A 87.139 381 37 9 1 377 565490473 565490845 3.640000e-114 422.0
33 TraesCS6B01G443900 chr2A 86.979 384 37 9 1 377 3452389 3452766 1.310000e-113 420.0
34 TraesCS6B01G443900 chr2A 86.684 383 41 7 1 378 424558769 424558392 1.690000e-112 416.0
35 TraesCS6B01G443900 chr2A 85.542 332 45 3 467 796 597496408 597496738 8.110000e-91 344.0
36 TraesCS6B01G443900 chr2A 78.613 346 70 1 2614 2955 705288550 705288895 3.070000e-55 226.0
37 TraesCS6B01G443900 chr2A 80.682 264 34 6 537 800 2770520 2770766 4.020000e-44 189.0
38 TraesCS6B01G443900 chr7A 90.160 376 35 2 1 375 336207292 336207666 3.540000e-134 488.0
39 TraesCS6B01G443900 chr7A 83.438 320 48 5 472 788 336208924 336209241 2.980000e-75 292.0
40 TraesCS6B01G443900 chr7A 92.453 53 4 0 748 800 107872657 107872709 3.270000e-10 76.8
41 TraesCS6B01G443900 chr1A 87.067 433 45 7 2614 3045 45834999 45834577 2.130000e-131 479.0
42 TraesCS6B01G443900 chr1A 86.911 382 39 8 1 377 331791785 331792160 4.710000e-113 418.0
43 TraesCS6B01G443900 chr7B 89.153 378 38 3 1 377 285448597 285448222 4.610000e-128 468.0
44 TraesCS6B01G443900 chr4D 84.964 419 48 11 386 799 233196154 233195746 7.890000e-111 411.0
45 TraesCS6B01G443900 chr4A 83.632 446 59 7 2614 3055 165054596 165055031 1.020000e-109 407.0
46 TraesCS6B01G443900 chr1D 83.696 368 44 8 437 799 396104076 396103720 1.760000e-87 333.0
47 TraesCS6B01G443900 chr3A 86.184 304 31 7 2615 2917 354813826 354813533 4.920000e-83 318.0


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 TraesCS6B01G443900 chr6B 706867694 706870749 3055 False 5644.00 5644 100.0000 1 3056 1 chr6B.!!$F3 3055
1 TraesCS6B01G443900 chr6B 706850603 706851980 1377 False 1253.00 1253 83.1560 800 2199 1 chr6B.!!$F2 1399
2 TraesCS6B01G443900 chr6A 610124237 610127117 2880 False 4403.00 4403 94.2330 167 3056 1 chr6A.!!$F2 2889
3 TraesCS6B01G443900 chr6A 610063285 610068088 4803 False 1273.00 1332 83.8685 800 2199 2 chr6A.!!$F3 1399
4 TraesCS6B01G443900 chr6A 610087981 610091401 3420 False 579.50 780 82.1160 800 2199 2 chr6A.!!$F4 1399
5 TraesCS6B01G443900 chr6A 610078646 610079247 601 False 405.00 405 79.2190 800 1433 1 chr6A.!!$F1 633
6 TraesCS6B01G443900 chr5B 47126657 47128120 1463 True 955.00 955 79.0560 965 2424 1 chr5B.!!$R3 1459
7 TraesCS6B01G443900 chr5B 48146359 48148059 1700 False 654.50 1103 84.2825 965 2539 2 chr5B.!!$F2 1574
8 TraesCS6B01G443900 chr5B 46770188 46770902 714 True 560.00 560 81.3020 1808 2508 1 chr5B.!!$R2 700
9 TraesCS6B01G443900 chr6D 463531518 463532520 1002 False 1085.00 1085 86.3550 1207 2199 1 chr6D.!!$F1 992
10 TraesCS6B01G443900 chr5A 36797814 36799303 1489 True 1048.00 1048 79.8190 1019 2534 1 chr5A.!!$R1 1515
11 TraesCS6B01G443900 chr5A 36941411 36945739 4328 True 734.00 1002 79.7335 999 2549 2 chr5A.!!$R4 1550
12 TraesCS6B01G443900 chr5D 45938810 45940297 1487 False 1035.00 1035 79.6630 1019 2534 1 chr5D.!!$F1 1515
13 TraesCS6B01G443900 chr5D 46084754 46085511 757 True 343.55 614 86.3735 1729 2424 2 chr5D.!!$R2 695
14 TraesCS6B01G443900 chr2B 731710588 731712015 1427 False 881.00 881 78.3380 966 2400 1 chr2B.!!$F2 1434
15 TraesCS6B01G443900 chr2A 597494786 597496738 1952 False 406.00 468 87.4520 1 796 2 chr2A.!!$F5 795
16 TraesCS6B01G443900 chr2A 2768888 2770766 1878 False 340.50 492 85.4595 1 800 2 chr2A.!!$F4 799
17 TraesCS6B01G443900 chr7A 336207292 336209241 1949 False 390.00 488 86.7990 1 788 2 chr7A.!!$F2 787

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
852 2220 0.917333 TAACCTTCCCCCAATCCGCT 60.917 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2641 9206 0.385598 ACATGATATCGACGGACGCG 60.386 55.0 3.53 3.53 42.26 6.01 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
64 65 9.294030 GCATTGAATTGTCAAGTTATAGAAAGG 57.706 33.333 0.00 0.00 46.75 3.11
177 179 5.336213 GCCCAATTGCTCATAATGTAGATGG 60.336 44.000 0.00 0.00 0.00 3.51
178 180 6.005823 CCCAATTGCTCATAATGTAGATGGA 58.994 40.000 0.00 0.00 0.00 3.41
204 206 6.946009 ACCACATAGCCAAAGTACAAAGTTAT 59.054 34.615 0.00 0.00 0.00 1.89
302 304 4.808414 TGTCTTCCATCAAGTAGACTGG 57.192 45.455 0.00 0.00 38.23 4.00
333 335 9.378597 CACAAATCATGAAGCTATCTAATTTCG 57.621 33.333 0.00 0.00 0.00 3.46
351 353 1.198178 TCGGCAGTTAAACAAATCCGC 59.802 47.619 0.00 0.00 35.78 5.54
401 1726 3.861840 CTCATGTTACATTGGTCGGAGT 58.138 45.455 0.00 0.00 0.00 3.85
405 1730 2.028476 TGTTACATTGGTCGGAGTCAGG 60.028 50.000 0.00 0.00 0.00 3.86
426 1751 5.305386 CAGGGACTCATATAACTCATGTGGA 59.695 44.000 0.00 0.00 34.60 4.02
430 1755 6.652481 GGACTCATATAACTCATGTGGATTGG 59.348 42.308 0.00 0.00 0.00 3.16
431 1756 7.379059 ACTCATATAACTCATGTGGATTGGA 57.621 36.000 0.00 0.00 0.00 3.53
447 1772 2.347490 GACTGCCGTGGTGTCCAT 59.653 61.111 0.00 0.00 35.28 3.41
456 1781 2.124570 GGTGTCCATGCGAGCCAT 60.125 61.111 0.00 0.00 33.39 4.40
669 2034 1.589993 CAGCGCTCTGTGGTATCCG 60.590 63.158 7.13 0.00 35.61 4.18
728 2093 1.166531 ACAGGAAAGCCGACAACAGC 61.167 55.000 0.00 0.00 39.96 4.40
779 2144 1.831580 AGATGGCTGGAAAAGTGCTC 58.168 50.000 0.00 0.00 0.00 4.26
781 2146 1.888512 GATGGCTGGAAAAGTGCTCAA 59.111 47.619 0.00 0.00 0.00 3.02
852 2220 0.917333 TAACCTTCCCCCAATCCGCT 60.917 55.000 0.00 0.00 0.00 5.52
1004 2780 0.687757 CTCCCGACTCCCTCAATGGA 60.688 60.000 0.00 0.00 38.35 3.41
1005 2781 0.031111 TCCCGACTCCCTCAATGGAT 60.031 55.000 0.00 0.00 38.35 3.41
1148 2937 5.129485 TCCTCTATTCTCCACCATTCTTCAC 59.871 44.000 0.00 0.00 0.00 3.18
1151 2940 3.874383 TTCTCCACCATTCTTCACCAA 57.126 42.857 0.00 0.00 0.00 3.67
1179 2968 3.898123 ACGAATGGTGCATCCTCTACTAT 59.102 43.478 0.00 0.00 37.07 2.12
1214 3011 0.321996 GACGAGAGGAGCCAAGGTTT 59.678 55.000 0.00 0.00 0.00 3.27
1302 3100 1.692173 TAGATGCGGTTAGGGGGCAC 61.692 60.000 0.00 0.00 39.84 5.01
1305 3103 2.516225 GCGGTTAGGGGGCACATC 60.516 66.667 0.00 0.00 0.00 3.06
1491 3318 2.665000 CCGCCCTCTGAGCTTTCA 59.335 61.111 0.00 0.00 0.00 2.69
1681 3518 2.120232 CTATCGACGACATGCAACCTC 58.880 52.381 0.00 0.00 0.00 3.85
1755 3592 8.168058 TCCATGGTTGATCTTGATGATAATGAT 58.832 33.333 12.58 0.00 35.14 2.45
1998 7515 6.987386 AGGGTATCTACATCTCAAAAGATCG 58.013 40.000 0.00 0.00 40.38 3.69
2005 7522 7.036220 TCTACATCTCAAAAGATCGTTTCCTC 58.964 38.462 3.46 0.00 40.38 3.71
2074 7592 8.732746 AATTTAGTATGTCAACCTGGTATGAC 57.267 34.615 23.52 23.52 44.84 3.06
2099 7617 2.999355 CTGCTTGTCCTTCAGTTCTAGC 59.001 50.000 0.00 0.00 0.00 3.42
2361 8271 8.376270 AGTTACTCTTTTATCTGCTTACCTTGT 58.624 33.333 0.00 0.00 0.00 3.16
2365 8275 7.502561 ACTCTTTTATCTGCTTACCTTGTTTGT 59.497 33.333 0.00 0.00 0.00 2.83
2628 9193 1.186267 AGGGTACTAGCATAGCCCGC 61.186 60.000 5.27 0.00 43.44 6.13
2655 9220 2.330393 CACCGCGTCCGTCGATAT 59.670 61.111 4.92 0.00 42.86 1.63
2701 9266 9.550406 TGTTTACTACTTGCAGTTAGTGTTATT 57.450 29.630 16.00 0.00 0.00 1.40
2928 10151 2.549064 TGATCATCCTAATGTGGGCG 57.451 50.000 0.00 0.00 34.32 6.13
2969 10528 8.457261 GCTCATGATGAAGTGATAAAGAACTTT 58.543 33.333 0.00 5.18 36.77 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.923143 AATTCAATGCTGATATGGTGAATTATG 57.077 29.630 7.47 0.00 41.49 1.90
38 39 9.294030 CCTTTCTATAACTTGACAATTCAATGC 57.706 33.333 0.00 0.00 41.05 3.56
63 64 3.064931 GCTATCTACGTATTGGCAACCC 58.935 50.000 0.00 0.00 0.00 4.11
64 65 3.991367 AGCTATCTACGTATTGGCAACC 58.009 45.455 0.00 0.00 0.00 3.77
143 145 1.420891 AGCAATTGGGCACATTGGTTT 59.579 42.857 7.72 0.00 32.89 3.27
177 179 5.240844 ACTTTGTACTTTGGCTATGTGGTTC 59.759 40.000 0.00 0.00 0.00 3.62
178 180 5.137551 ACTTTGTACTTTGGCTATGTGGTT 58.862 37.500 0.00 0.00 0.00 3.67
204 206 1.895131 GGGCTTTCTCCATTCTTGCAA 59.105 47.619 0.00 0.00 0.00 4.08
302 304 1.547372 AGCTTCATGATTTGTGGTGCC 59.453 47.619 0.00 0.00 0.00 5.01
316 318 5.023533 ACTGCCGAAATTAGATAGCTTCA 57.976 39.130 0.00 0.00 0.00 3.02
333 335 2.715737 TGCGGATTTGTTTAACTGCC 57.284 45.000 0.00 0.00 34.25 4.85
351 353 7.727331 ATGTGTATTTGGTTTGGTGAATTTG 57.273 32.000 0.00 0.00 0.00 2.32
401 1726 5.305386 CCACATGAGTTATATGAGTCCCTGA 59.695 44.000 0.00 0.00 0.00 3.86
405 1730 6.652481 CCAATCCACATGAGTTATATGAGTCC 59.348 42.308 0.00 0.00 0.00 3.85
411 1736 6.000219 GCAGTCCAATCCACATGAGTTATAT 59.000 40.000 0.00 0.00 0.00 0.86
426 1751 1.302511 GACACCACGGCAGTCCAAT 60.303 57.895 0.00 0.00 0.00 3.16
430 1755 2.034879 CATGGACACCACGGCAGTC 61.035 63.158 0.00 1.65 35.80 3.51
431 1756 2.032528 CATGGACACCACGGCAGT 59.967 61.111 0.00 0.00 35.80 4.40
445 1770 2.890109 GCGGAGAATGGCTCGCATG 61.890 63.158 0.00 0.00 44.91 4.06
447 1772 4.838152 GGCGGAGAATGGCTCGCA 62.838 66.667 8.73 0.00 44.91 5.10
456 1781 3.136123 CTACGGTCGGGCGGAGAA 61.136 66.667 0.00 0.00 0.00 2.87
669 2034 1.372128 CTCGCTTGGGCTTTGTTGC 60.372 57.895 0.00 0.00 36.09 4.17
720 2085 1.078759 CCGTCGGATGAGCTGTTGTC 61.079 60.000 4.91 0.00 0.00 3.18
728 2093 4.307432 AGCAATATTAACCGTCGGATGAG 58.693 43.478 20.51 0.37 0.00 2.90
811 2176 1.003118 GGTTTTGATTTGGAAGGGGGC 59.997 52.381 0.00 0.00 0.00 5.80
852 2220 1.860676 CGACCTCAAAAAGTGACCGA 58.139 50.000 0.00 0.00 31.13 4.69
890 2258 2.445845 TATGGGAGGGGAGTGGCG 60.446 66.667 0.00 0.00 0.00 5.69
892 2260 1.770518 GGGTATGGGAGGGGAGTGG 60.771 68.421 0.00 0.00 0.00 4.00
1004 2780 2.224606 CTATTGAACCCTGCGATGCAT 58.775 47.619 0.00 0.00 38.13 3.96
1005 2781 1.065491 ACTATTGAACCCTGCGATGCA 60.065 47.619 0.00 0.00 36.92 3.96
1148 2937 0.167251 GCACCATTCGTAACCGTTGG 59.833 55.000 0.00 0.00 41.23 3.77
1151 2940 1.365699 GATGCACCATTCGTAACCGT 58.634 50.000 0.00 0.00 35.01 4.83
1214 3011 1.271054 GCTTGAGGAAGACAGAGGCAA 60.271 52.381 0.00 0.00 0.00 4.52
1302 3100 2.223340 GCTGAACACCGGCTTAATGATG 60.223 50.000 0.00 0.00 43.80 3.07
1305 3103 3.996825 GCTGAACACCGGCTTAATG 57.003 52.632 0.00 0.00 43.80 1.90
1468 3295 2.348998 CTCAGAGGGCGGCACTTT 59.651 61.111 6.05 0.00 0.00 2.66
1681 3518 4.746611 GTGAAGAAATGCCTTGAAAACAGG 59.253 41.667 0.00 0.00 34.08 4.00
1947 3969 2.353579 TGCGAGCACATCATTCATTCTG 59.646 45.455 0.00 0.00 0.00 3.02
2074 7592 3.007398 AGAACTGAAGGACAAGCAGTAGG 59.993 47.826 0.00 0.00 41.65 3.18
2099 7617 7.283807 TCTCCAAACCAACATGATAATGATCTG 59.716 37.037 0.00 0.00 32.79 2.90
2361 8271 7.048629 TCATTCTTCACATAAAGCCAACAAA 57.951 32.000 0.00 0.00 0.00 2.83
2365 8275 9.638239 GTTTTATCATTCTTCACATAAAGCCAA 57.362 29.630 0.00 0.00 0.00 4.52
2606 9171 2.290768 CGGGCTATGCTAGTACCCTCTA 60.291 54.545 3.93 0.00 38.50 2.43
2639 9204 1.512996 ATGATATCGACGGACGCGGT 61.513 55.000 12.47 0.00 42.26 5.68
2641 9206 0.385598 ACATGATATCGACGGACGCG 60.386 55.000 3.53 3.53 42.26 6.01
2645 9210 4.584327 ATGAACACATGATATCGACGGA 57.416 40.909 0.00 0.00 0.00 4.69
2655 9220 9.838975 GTAAACACAATTCATATGAACACATGA 57.161 29.630 20.19 0.00 36.80 3.07
2701 9266 9.687210 CGTACAATAACCTGCTATACAAGATAA 57.313 33.333 0.00 0.00 0.00 1.75
2770 9580 2.816689 CAACATGCATGGTGCCAATAG 58.183 47.619 30.48 6.69 44.23 1.73
2842 10065 2.442212 TCGTGCCACGACAAGAATAA 57.558 45.000 17.22 0.00 46.73 1.40
2920 10143 1.635817 AATCCTACAGGCGCCCACAT 61.636 55.000 26.15 8.87 34.44 3.21
2928 10151 3.070159 TCATGAGCACTAATCCTACAGGC 59.930 47.826 0.00 0.00 34.44 4.85
2969 10528 1.795768 CTAGAGGCAACAGTTCGCAA 58.204 50.000 9.14 0.00 41.41 4.85


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

AutoCloner maintained by Alex Coulton.