Multiple sequence alignment - TraesCS6D01G089600

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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 TraesCS6D01G089600 chr6D 100.000 3965 0 0 1 3965 55635861 55631897 0.000000e+00 7323.0
1 TraesCS6D01G089600 chr6D 94.929 848 33 3 1 841 383599591 383600435 0.000000e+00 1319.0
2 TraesCS6D01G089600 chr6D 89.691 1067 58 23 2915 3965 55407619 55406589 0.000000e+00 1314.0
3 TraesCS6D01G089600 chr6D 88.533 375 36 4 3591 3965 55317043 55316676 7.820000e-122 448.0
4 TraesCS6D01G089600 chr6D 84.444 450 58 8 2832 3274 55317969 55317525 2.190000e-117 433.0
5 TraesCS6D01G089600 chr6D 83.051 472 53 12 2832 3277 55110071 55109601 1.720000e-108 403.0
6 TraesCS6D01G089600 chr6D 94.470 217 11 1 2742 2958 55427466 55427251 2.280000e-87 333.0
7 TraesCS6D01G089600 chr6D 85.985 264 24 3 3279 3534 55109503 55109245 1.820000e-68 270.0
8 TraesCS6D01G089600 chr6D 92.199 141 11 0 2603 2743 55427842 55427702 2.420000e-47 200.0
9 TraesCS6D01G089600 chr6D 79.054 296 37 16 3000 3277 55427250 55426962 3.150000e-41 180.0
10 TraesCS6D01G089600 chr6D 83.125 160 17 6 3798 3949 46942432 46942589 1.920000e-28 137.0
11 TraesCS6D01G089600 chr6D 89.873 79 8 0 2529 2607 55432727 55432649 7.010000e-18 102.0
12 TraesCS6D01G089600 chr6B 92.654 3090 135 40 890 3965 125410912 125407901 0.000000e+00 4364.0
13 TraesCS6D01G089600 chr6B 85.398 452 56 6 2832 3277 125341163 125340716 1.000000e-125 460.0
14 TraesCS6D01G089600 chr6B 88.564 376 37 4 3591 3965 125340145 125339775 6.040000e-123 451.0
15 TraesCS6D01G089600 chr6B 85.446 426 50 8 2832 3250 125384114 125383694 2.190000e-117 433.0
16 TraesCS6D01G089600 chr6B 95.238 42 2 0 3924 3965 125339163 125339122 2.560000e-07 67.6
17 TraesCS6D01G089600 chr6A 91.585 2436 139 28 890 3278 69139652 69137236 0.000000e+00 3302.0
18 TraesCS6D01G089600 chr6A 90.274 1059 55 25 2920 3965 69136443 69135420 0.000000e+00 1341.0
19 TraesCS6D01G089600 chr1D 95.755 848 29 2 1 841 234905670 234906517 0.000000e+00 1360.0
20 TraesCS6D01G089600 chr1D 95.244 841 30 3 1 834 146641906 146641069 0.000000e+00 1323.0
21 TraesCS6D01G089600 chr1A 95.165 848 33 4 1 841 76767874 76767028 0.000000e+00 1332.0
22 TraesCS6D01G089600 chr7D 95.047 848 32 4 1 841 414295238 414294394 0.000000e+00 1325.0
23 TraesCS6D01G089600 chr2A 94.929 848 35 3 1 841 422559078 422559924 0.000000e+00 1321.0
24 TraesCS6D01G089600 chr3D 94.929 848 31 5 1 841 94759794 94760636 0.000000e+00 1317.0
25 TraesCS6D01G089600 chr5D 94.811 848 34 3 1 841 352236399 352237243 0.000000e+00 1314.0
26 TraesCS6D01G089600 chr5D 94.700 849 34 5 1 841 167754683 167755528 0.000000e+00 1308.0
27 TraesCS6D01G089600 chr5A 79.528 381 65 7 1082 1449 691824208 691824588 3.930000e-65 259.0


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 TraesCS6D01G089600 chr6D 55631897 55635861 3964 True 7323.000000 7323 100.000000 1 3965 1 chr6D.!!$R3 3964
1 TraesCS6D01G089600 chr6D 383599591 383600435 844 False 1319.000000 1319 94.929000 1 841 1 chr6D.!!$F2 840
2 TraesCS6D01G089600 chr6D 55406589 55407619 1030 True 1314.000000 1314 89.691000 2915 3965 1 chr6D.!!$R1 1050
3 TraesCS6D01G089600 chr6D 55316676 55317969 1293 True 440.500000 448 86.488500 2832 3965 2 chr6D.!!$R5 1133
4 TraesCS6D01G089600 chr6D 55109245 55110071 826 True 336.500000 403 84.518000 2832 3534 2 chr6D.!!$R4 702
5 TraesCS6D01G089600 chr6D 55426962 55427842 880 True 237.666667 333 88.574333 2603 3277 3 chr6D.!!$R6 674
6 TraesCS6D01G089600 chr6B 125407901 125410912 3011 True 4364.000000 4364 92.654000 890 3965 1 chr6B.!!$R2 3075
7 TraesCS6D01G089600 chr6B 125339122 125341163 2041 True 326.200000 460 89.733333 2832 3965 3 chr6B.!!$R3 1133
8 TraesCS6D01G089600 chr6A 69135420 69139652 4232 True 2321.500000 3302 90.929500 890 3965 2 chr6A.!!$R1 3075
9 TraesCS6D01G089600 chr1D 234905670 234906517 847 False 1360.000000 1360 95.755000 1 841 1 chr1D.!!$F1 840
10 TraesCS6D01G089600 chr1D 146641069 146641906 837 True 1323.000000 1323 95.244000 1 834 1 chr1D.!!$R1 833
11 TraesCS6D01G089600 chr1A 76767028 76767874 846 True 1332.000000 1332 95.165000 1 841 1 chr1A.!!$R1 840
12 TraesCS6D01G089600 chr7D 414294394 414295238 844 True 1325.000000 1325 95.047000 1 841 1 chr7D.!!$R1 840
13 TraesCS6D01G089600 chr2A 422559078 422559924 846 False 1321.000000 1321 94.929000 1 841 1 chr2A.!!$F1 840
14 TraesCS6D01G089600 chr3D 94759794 94760636 842 False 1317.000000 1317 94.929000 1 841 1 chr3D.!!$F1 840
15 TraesCS6D01G089600 chr5D 352236399 352237243 844 False 1314.000000 1314 94.811000 1 841 1 chr5D.!!$F2 840
16 TraesCS6D01G089600 chr5D 167754683 167755528 845 False 1308.000000 1308 94.700000 1 841 1 chr5D.!!$F1 840

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
716 726 1.390123 CTTACACGCCACACAATCGAG 59.610 52.381 0.00 0.00 0.00 4.04 F
1030 1041 0.800683 TCGATTCAGTTCGCGCGATT 60.801 50.000 35.21 22.08 38.97 3.34 F
1801 1839 0.871057 GAAGAGACCTGTGCACAAGC 59.129 55.000 21.98 12.63 42.57 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 2301 1.033746 CGGTCCTTGGCAGCATGAAT 61.034 55.000 0.0 0.0 39.69 2.57 R
2655 2696 1.355381 ACAGCATCATTTCCCACCAGA 59.645 47.619 0.0 0.0 0.00 3.86 R
3434 5027 0.521291 TTATGCGCACAAGAGGTTGC 59.479 50.000 14.9 0.0 37.14 4.17 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
242 248 2.112297 GGCAAACACGGGACTCCA 59.888 61.111 0.00 0.00 0.00 3.86
312 318 3.264666 CTCGAGCGGAGAAATCCAG 57.735 57.895 0.00 0.00 46.23 3.86
388 394 2.203337 TTCAAGCTGCGGGCACTT 60.203 55.556 0.00 0.00 44.79 3.16
519 525 3.253061 TGCGGATGGTGGGTTGGA 61.253 61.111 0.00 0.00 0.00 3.53
596 605 2.048597 CGTGCTAGACGGCAACCA 60.049 61.111 0.00 0.00 44.85 3.67
639 648 2.288025 AACCGTAGTCCCACCGCAT 61.288 57.895 0.00 0.00 0.00 4.73
703 713 2.183555 GGCGACCCCTCTTACACG 59.816 66.667 0.00 0.00 0.00 4.49
716 726 1.390123 CTTACACGCCACACAATCGAG 59.610 52.381 0.00 0.00 0.00 4.04
729 739 1.654105 CAATCGAGTTGTCCTACGTGC 59.346 52.381 0.00 0.00 33.01 5.34
841 851 2.161609 GTGTGGGCATTAGACTTTTCGG 59.838 50.000 0.00 0.00 0.00 4.30
842 852 2.039216 TGTGGGCATTAGACTTTTCGGA 59.961 45.455 0.00 0.00 0.00 4.55
843 853 3.078837 GTGGGCATTAGACTTTTCGGAA 58.921 45.455 0.00 0.00 0.00 4.30
844 854 3.504520 GTGGGCATTAGACTTTTCGGAAA 59.495 43.478 0.00 0.00 0.00 3.13
845 855 4.022676 GTGGGCATTAGACTTTTCGGAAAA 60.023 41.667 14.64 14.64 0.00 2.29
846 856 4.585162 TGGGCATTAGACTTTTCGGAAAAA 59.415 37.500 15.99 2.61 33.42 1.94
922 932 9.915629 AGTATATTCAAATTCGGATAGACTGAC 57.084 33.333 0.00 0.00 33.15 3.51
1002 1013 4.157120 CCCTAACCCCACGCCTCG 62.157 72.222 0.00 0.00 0.00 4.63
1030 1041 0.800683 TCGATTCAGTTCGCGCGATT 60.801 50.000 35.21 22.08 38.97 3.34
1508 1534 3.764160 CTTCATCCCCTGGCGCTCC 62.764 68.421 7.64 0.00 0.00 4.70
1556 1594 1.079750 GTGAGGGTGAGAAGACGGC 60.080 63.158 0.00 0.00 0.00 5.68
1557 1595 1.533033 TGAGGGTGAGAAGACGGCA 60.533 57.895 0.00 0.00 0.00 5.69
1615 1653 2.749441 GGCAGGAGAAGCACAGCC 60.749 66.667 0.00 0.00 34.71 4.85
1675 1713 4.820744 ATGCCGGCCATGGTGGTC 62.821 66.667 26.77 15.66 40.46 4.02
1801 1839 0.871057 GAAGAGACCTGTGCACAAGC 59.129 55.000 21.98 12.63 42.57 4.01
1839 1880 2.370189 AGGGAGAGACAAGAAACCTGTG 59.630 50.000 0.00 0.00 0.00 3.66
1864 1905 3.477210 AGGATAAGAAACCATCCGAGC 57.523 47.619 0.00 0.00 44.62 5.03
2032 2073 1.723870 GCAGGTAGCAATGCGGAAG 59.276 57.895 0.00 0.00 44.79 3.46
2136 2177 1.153745 GCTCTGTGAATCGGTCGCT 60.154 57.895 2.93 0.00 37.65 4.93
2194 2235 4.339530 CACGGATATCCTCTTCTGTTCAGA 59.660 45.833 19.61 0.00 28.98 3.27
2260 2301 6.091034 GCGATCTATTGACGTACTGAGAGATA 59.909 42.308 0.00 0.00 0.00 1.98
2325 2366 1.924552 GTTGGGGTTAATGGGGTAGGA 59.075 52.381 0.00 0.00 0.00 2.94
2628 2669 5.378230 AGCTCATCAATCTCAATAACCCA 57.622 39.130 0.00 0.00 0.00 4.51
2655 2696 2.430694 GGTTTTGTTTGTGGGAGAAGCT 59.569 45.455 0.00 0.00 0.00 3.74
2936 4375 1.268899 GCATGCTGCACTCCCATATTC 59.731 52.381 11.37 0.00 44.26 1.75
3063 4510 9.052759 GGAACTAGAAATTTCTGTGTTACTTCA 57.947 33.333 27.37 5.52 38.19 3.02
3101 4567 8.365399 TGTATATTCATTCGGCTCTTGTTTAG 57.635 34.615 0.00 0.00 0.00 1.85
3160 4630 3.565764 TGGAGCAAGAGGATTATGGTG 57.434 47.619 0.00 0.00 0.00 4.17
3244 4715 8.020861 ACGACGTGCTAGTAAAATTTATTTCA 57.979 30.769 0.00 0.00 0.00 2.69
3246 4717 9.144085 CGACGTGCTAGTAAAATTTATTTCATC 57.856 33.333 0.00 0.00 0.00 2.92
3265 4736 7.822161 TTCATCTTTCACAATCTTCTTTCCA 57.178 32.000 0.00 0.00 0.00 3.53
3266 4737 7.822161 TCATCTTTCACAATCTTCTTTCCAA 57.178 32.000 0.00 0.00 0.00 3.53
3267 4738 8.413309 TCATCTTTCACAATCTTCTTTCCAAT 57.587 30.769 0.00 0.00 0.00 3.16
3268 4739 8.301720 TCATCTTTCACAATCTTCTTTCCAATG 58.698 33.333 0.00 0.00 0.00 2.82
3269 4740 7.587037 TCTTTCACAATCTTCTTTCCAATGT 57.413 32.000 0.00 0.00 0.00 2.71
3419 5012 2.938451 TGAAGCTTGCAATCTGTATCCG 59.062 45.455 2.10 0.00 0.00 4.18
3434 5027 3.623960 TGTATCCGGTTCGCTTTATTTGG 59.376 43.478 0.00 0.00 0.00 3.28
3446 5039 3.989817 GCTTTATTTGGCAACCTCTTGTG 59.010 43.478 0.00 0.00 0.00 3.33
3473 5066 6.238211 GCATAATAAATTGTCTCGTGCTGAGT 60.238 38.462 6.46 0.00 45.46 3.41
3526 5217 0.750850 GGCGAGGCCTGATAACAGTA 59.249 55.000 12.00 0.00 46.69 2.74
3575 5266 2.022625 TGTGATTCCTCTCCCCTCATCT 60.023 50.000 0.00 0.00 0.00 2.90
3600 5374 4.388165 CAGTCTGTCAGCTTACATTGTGAG 59.612 45.833 0.23 4.29 0.00 3.51
3618 5392 5.410924 TGTGAGGTTATCAGATGTTTCTCG 58.589 41.667 0.00 0.00 39.07 4.04
3705 5480 1.275291 TCGGCTCCGTTCTTCAGATTT 59.725 47.619 8.28 0.00 40.74 2.17
3716 5491 7.588854 TCCGTTCTTCAGATTTATTACGTATCG 59.411 37.037 0.00 0.00 0.00 2.92
3813 5606 9.452517 AATATATAGCATAGGATGGGTACATGT 57.547 33.333 2.69 2.69 37.47 3.21
3814 5607 3.777106 AGCATAGGATGGGTACATGTG 57.223 47.619 9.11 0.00 37.47 3.21
3929 6375 8.043113 TGCAGATATAATGGTAAAGGCTATGAG 58.957 37.037 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 98 6.089417 GCATTTTTGTAGTTGTTAGTCATGCC 59.911 38.462 0.00 0.00 0.00 4.40
201 207 2.410469 GATGGCATTGCGCAGGTC 59.590 61.111 11.31 9.71 45.17 3.85
388 394 0.743701 GACCAGAGAGTCTACGCCGA 60.744 60.000 0.00 0.00 33.79 5.54
614 623 4.382320 GGACTACGGTTGCGCCCA 62.382 66.667 4.18 0.00 0.00 5.36
626 635 3.792736 GGGCATGCGGTGGGACTA 61.793 66.667 12.44 0.00 0.00 2.59
716 726 2.231820 GTGTGGCACGTAGGACAAC 58.768 57.895 13.77 0.00 0.00 3.32
729 739 1.667724 GATCTGGCTGATTTCGTGTGG 59.332 52.381 8.36 0.00 35.14 4.17
1002 1013 2.092838 CGAACTGAATCGAAAGACTGGC 59.907 50.000 0.00 0.00 46.97 4.85
1030 1041 1.448893 GGCGGCGAACTGAATACCA 60.449 57.895 12.98 0.00 0.00 3.25
1089 1100 0.035725 TGAGCAGCTCCTCCAACATG 60.036 55.000 20.16 0.00 0.00 3.21
1162 1173 2.731571 CGATCGGGGAGCCCTTCAA 61.732 63.158 7.38 0.00 42.67 2.69
1255 1278 1.138047 GCGTTGTCGTAGGTCCATCG 61.138 60.000 0.00 0.00 39.49 3.84
1257 1280 1.153901 CGCGTTGTCGTAGGTCCAT 60.154 57.895 0.00 0.00 39.49 3.41
1481 1504 1.452833 GGGGATGAAGCTGCTGGAC 60.453 63.158 1.35 0.00 0.00 4.02
1484 1507 1.453379 CCAGGGGATGAAGCTGCTG 60.453 63.158 1.35 0.00 0.00 4.41
1485 1508 3.004951 CCAGGGGATGAAGCTGCT 58.995 61.111 0.00 0.00 0.00 4.24
1486 1509 2.832201 GCCAGGGGATGAAGCTGC 60.832 66.667 0.00 0.00 0.00 5.25
1557 1595 3.037549 GTCATCCTTCCCAGACTCATCT 58.962 50.000 0.00 0.00 34.57 2.90
1615 1653 1.886313 CGCTACCATCTGCTGCTGG 60.886 63.158 11.50 11.50 38.55 4.85
1675 1713 2.887152 CCTCCTCCCTTTTCACAACAAG 59.113 50.000 0.00 0.00 0.00 3.16
1801 1839 2.500098 TCCCTGGTCTCGGTTTCTTATG 59.500 50.000 0.00 0.00 0.00 1.90
1839 1880 2.959030 GGATGGTTTCTTATCCTTGGGC 59.041 50.000 0.00 0.00 39.78 5.36
1887 1928 3.933722 CCTCCGCCATGATCCGCT 61.934 66.667 0.00 0.00 0.00 5.52
2028 2069 3.678529 GCAGATCAGACTCCTTCACTTCC 60.679 52.174 0.00 0.00 0.00 3.46
2032 2073 2.999355 GTTGCAGATCAGACTCCTTCAC 59.001 50.000 0.00 0.00 0.00 3.18
2061 2102 2.933260 GAGCCGGTCTTTCAGAGATTTC 59.067 50.000 1.90 0.00 36.61 2.17
2130 2171 1.801309 CTAGGAGGCTAGCAGCGACC 61.801 65.000 18.24 11.32 43.62 4.79
2194 2235 1.761784 CAGAGCCTCTTCCATAGCTGT 59.238 52.381 0.00 0.00 35.23 4.40
2260 2301 1.033746 CGGTCCTTGGCAGCATGAAT 61.034 55.000 0.00 0.00 39.69 2.57
2284 2325 3.623060 ACAAAGACGATGACATATGGTGC 59.377 43.478 7.80 0.00 0.00 5.01
2286 2327 4.635765 CCAACAAAGACGATGACATATGGT 59.364 41.667 7.80 0.00 0.00 3.55
2325 2366 3.506067 CCTTTGCGAGGTTAGTGGATTTT 59.494 43.478 0.00 0.00 40.95 1.82
2374 2415 1.901650 GCTGCCAGCGTGACACTAAC 61.902 60.000 0.00 0.00 0.00 2.34
2433 2474 2.543687 GAAGCCTGCGAGCGTGAGTA 62.544 60.000 0.00 0.00 38.01 2.59
2436 2477 3.921767 CTGAAGCCTGCGAGCGTGA 62.922 63.158 0.00 0.00 38.01 4.35
2439 2480 1.760268 GAATCTGAAGCCTGCGAGCG 61.760 60.000 0.00 0.00 38.01 5.03
2628 2669 3.891366 CTCCCACAAACAAAACCAGATCT 59.109 43.478 0.00 0.00 0.00 2.75
2655 2696 1.355381 ACAGCATCATTTCCCACCAGA 59.645 47.619 0.00 0.00 0.00 3.86
2688 2729 5.050023 GTCTGTCAGTTTCTGGCTAAACTTC 60.050 44.000 13.53 10.99 45.20 3.01
3088 4554 5.917541 TCTTAACAACTAAACAAGAGCCG 57.082 39.130 0.00 0.00 0.00 5.52
3137 4607 4.891756 CACCATAATCCTCTTGCTCCAAAT 59.108 41.667 0.00 0.00 0.00 2.32
3160 4630 4.023365 ACTCTGAGCTCAACTGAAATTTGC 60.023 41.667 18.85 0.00 0.00 3.68
3244 4715 8.186709 ACATTGGAAAGAAGATTGTGAAAGAT 57.813 30.769 0.00 0.00 0.00 2.40
3246 4717 8.139989 AGAACATTGGAAAGAAGATTGTGAAAG 58.860 33.333 0.00 0.00 0.00 2.62
3247 4718 8.010733 AGAACATTGGAAAGAAGATTGTGAAA 57.989 30.769 0.00 0.00 0.00 2.69
3248 4719 7.587037 AGAACATTGGAAAGAAGATTGTGAA 57.413 32.000 0.00 0.00 0.00 3.18
3251 4722 8.260114 ACAAAAGAACATTGGAAAGAAGATTGT 58.740 29.630 0.00 0.00 32.02 2.71
3252 4723 8.652810 ACAAAAGAACATTGGAAAGAAGATTG 57.347 30.769 0.00 0.00 32.02 2.67
3419 5012 2.029380 AGGTTGCCAAATAAAGCGAACC 60.029 45.455 0.00 0.00 38.93 3.62
3434 5027 0.521291 TTATGCGCACAAGAGGTTGC 59.479 50.000 14.90 0.00 37.14 4.17
3446 5039 3.659444 GCACGAGACAATTTATTATGCGC 59.341 43.478 0.00 0.00 0.00 6.09
3473 5066 8.752005 ATAGCAGAAAGTTAATTCAAGGCATA 57.248 30.769 0.00 0.00 0.00 3.14
3526 5217 2.183679 GTCAGGTGAGGGAAGACTGAT 58.816 52.381 0.00 0.00 39.97 2.90
3575 5266 4.751600 CACAATGTAAGCTGACAGACTGAA 59.248 41.667 10.38 0.00 31.51 3.02
3600 5374 6.969828 AACTTCGAGAAACATCTGATAACC 57.030 37.500 0.00 0.00 0.00 2.85
3705 5480 8.938906 TGCAATCTATGAGTACGATACGTAATA 58.061 33.333 0.00 1.09 43.95 0.98
3716 5491 5.446473 GCACACACTTGCAATCTATGAGTAC 60.446 44.000 0.00 0.00 42.49 2.73
3813 5606 9.958180 TTCTATCTTGATTTTACAACTGATCCA 57.042 29.630 0.00 0.00 0.00 3.41
3929 6375 9.903682 TCTTCAAAACATTCTGAAATTCTCATC 57.096 29.630 0.00 0.00 32.14 2.92


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

AutoCloner maintained by Alex Coulton.