Multiple sequence alignment - TraesCS7B01G367400

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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 TraesCS7B01G367400 chr7B 100.000 2807 0 0 1 2807 631404218 631407024 0.000000e+00 5184
1 TraesCS7B01G367400 chr7D 94.195 2808 96 28 1 2788 573191842 573194602 0.000000e+00 4220
2 TraesCS7B01G367400 chr7A 93.675 2672 120 28 1 2644 662966055 662968705 0.000000e+00 3952
3 TraesCS7B01G367400 chr7A 88.889 162 13 4 2642 2803 662968942 662969098 7.930000e-46 195
4 TraesCS7B01G367400 chrUn 100.000 410 0 0 2398 2807 294908612 294908203 0.000000e+00 758
5 TraesCS7B01G367400 chr6A 86.927 436 54 3 1042 1474 114459021 114458586 1.170000e-133 486
6 TraesCS7B01G367400 chr6D 86.468 436 56 3 1032 1464 94602348 94602783 2.530000e-130 475
7 TraesCS7B01G367400 chr6B 87.260 416 53 0 1032 1447 178273247 178272832 2.530000e-130 475
8 TraesCS7B01G367400 chr6B 85.195 385 57 0 1054 1438 687525398 687525014 2.030000e-106 396
9 TraesCS7B01G367400 chr2A 86.889 389 49 2 1051 1438 626589669 626589282 4.290000e-118 435
10 TraesCS7B01G367400 chr1D 84.559 408 59 4 1054 1459 393750473 393750068 4.360000e-108 401
11 TraesCS7B01G367400 chr1A 83.902 410 62 4 1048 1455 492046060 492046467 3.390000e-104 388


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 TraesCS7B01G367400 chr7B 631404218 631407024 2806 False 5184.0 5184 100.000 1 2807 1 chr7B.!!$F1 2806
1 TraesCS7B01G367400 chr7D 573191842 573194602 2760 False 4220.0 4220 94.195 1 2788 1 chr7D.!!$F1 2787
2 TraesCS7B01G367400 chr7A 662966055 662969098 3043 False 2073.5 3952 91.282 1 2803 2 chr7A.!!$F1 2802

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
845 868 0.03601 AGCTGAAGGACCGACCAATG 60.036 55.0 0.0 0.0 42.04 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2737 3027 0.602372 CCACCCGCAAACCAATTTGG 60.602 55.0 14.02 14.02 44.64 3.28 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
232 240 2.856988 GTCCCCTCACCCCCACAA 60.857 66.667 0.00 0.00 0.00 3.33
254 262 2.856988 TTTCCCACGGCTCCCCTT 60.857 61.111 0.00 0.00 0.00 3.95
263 271 4.760220 GCTCCCCTTCCCCCTCCA 62.760 72.222 0.00 0.00 0.00 3.86
270 282 4.585216 TTCCCCCTCCACCCGTGT 62.585 66.667 0.00 0.00 0.00 4.49
298 310 5.298777 GGCTATCTACCCACCTATATACACG 59.701 48.000 0.00 0.00 0.00 4.49
333 345 2.243774 TACTGCCCCTCCTCCCTCTG 62.244 65.000 0.00 0.00 0.00 3.35
671 692 4.388499 CGGGCCTGCACCGTACTT 62.388 66.667 0.84 0.00 46.03 2.24
684 705 2.561419 ACCGTACTTCAAGCTAGCTCAA 59.439 45.455 19.65 12.93 0.00 3.02
721 742 1.004277 TCCACTTCGATTCCCCCTTTG 59.996 52.381 0.00 0.00 0.00 2.77
764 785 1.741401 TGCGCCCTCGAGAAACATG 60.741 57.895 15.71 0.00 38.10 3.21
767 788 2.464459 GCCCTCGAGAAACATGGCG 61.464 63.158 15.71 0.00 0.00 5.69
781 802 0.175760 ATGGCGTGTACAGCTACAGG 59.824 55.000 14.28 5.19 40.36 4.00
834 857 0.252479 ACCATGAGCTGAGCTGAAGG 59.748 55.000 13.71 13.58 39.88 3.46
838 861 1.153667 GAGCTGAGCTGAAGGACCG 60.154 63.158 13.71 0.00 39.88 4.79
839 862 1.599606 GAGCTGAGCTGAAGGACCGA 61.600 60.000 13.71 0.00 39.88 4.69
840 863 1.446966 GCTGAGCTGAAGGACCGAC 60.447 63.158 0.00 0.00 0.00 4.79
841 864 1.216710 CTGAGCTGAAGGACCGACC 59.783 63.158 0.00 0.00 39.35 4.79
842 865 1.533033 TGAGCTGAAGGACCGACCA 60.533 57.895 0.00 0.00 42.04 4.02
843 866 1.118965 TGAGCTGAAGGACCGACCAA 61.119 55.000 0.00 0.00 42.04 3.67
844 867 0.250513 GAGCTGAAGGACCGACCAAT 59.749 55.000 0.00 0.00 42.04 3.16
845 868 0.036010 AGCTGAAGGACCGACCAATG 60.036 55.000 0.00 0.00 42.04 2.82
846 869 0.036388 GCTGAAGGACCGACCAATGA 60.036 55.000 0.00 0.00 42.04 2.57
847 870 1.610624 GCTGAAGGACCGACCAATGAA 60.611 52.381 0.00 0.00 42.04 2.57
848 871 2.076863 CTGAAGGACCGACCAATGAAC 58.923 52.381 0.00 0.00 42.04 3.18
849 872 1.271163 TGAAGGACCGACCAATGAACC 60.271 52.381 0.00 0.00 42.04 3.62
854 877 0.038166 ACCGACCAATGAACCATGCT 59.962 50.000 0.00 0.00 0.00 3.79
894 917 2.045242 CACTGGCTGGCTGCTGAT 60.045 61.111 16.14 0.00 42.39 2.90
929 952 2.297315 GCTTTTGGTTTTAGGCAGCTCT 59.703 45.455 0.00 0.00 0.00 4.09
935 958 2.494059 GTTTTAGGCAGCTCTGTGTGA 58.506 47.619 0.00 0.00 0.00 3.58
936 959 2.169832 TTTAGGCAGCTCTGTGTGAC 57.830 50.000 0.00 0.00 0.00 3.67
937 960 0.321671 TTAGGCAGCTCTGTGTGACC 59.678 55.000 0.00 0.00 0.00 4.02
938 961 1.877576 TAGGCAGCTCTGTGTGACCG 61.878 60.000 0.00 0.00 0.00 4.79
939 962 3.418068 GCAGCTCTGTGTGACCGC 61.418 66.667 0.00 0.00 0.00 5.68
940 963 3.108289 CAGCTCTGTGTGACCGCG 61.108 66.667 0.00 0.00 0.00 6.46
941 964 3.606662 AGCTCTGTGTGACCGCGT 61.607 61.111 4.92 0.00 0.00 6.01
942 965 3.406361 GCTCTGTGTGACCGCGTG 61.406 66.667 4.92 0.00 0.00 5.34
1203 1226 0.250338 AGTTCGGCAAGACCAAGGTC 60.250 55.000 11.29 11.29 44.86 3.85
1209 1232 1.071471 CAAGACCAAGGTCCACGCT 59.929 57.895 15.36 0.00 45.59 5.07
1210 1233 0.951040 CAAGACCAAGGTCCACGCTC 60.951 60.000 15.36 0.00 45.59 5.03
1212 1235 2.847234 ACCAAGGTCCACGCTCCA 60.847 61.111 0.00 0.00 0.00 3.86
2173 2199 2.681848 GCTAGAATGTGCACTGCTGATT 59.318 45.455 19.41 8.77 0.00 2.57
2192 2218 4.340097 TGATTGATTGATTCATGGCTCCAC 59.660 41.667 0.00 0.00 33.34 4.02
2194 2220 2.292267 GATTGATTCATGGCTCCACGT 58.708 47.619 0.00 0.00 0.00 4.49
2220 2246 4.385358 AATTTGTTGCGTTCTTCCTGTT 57.615 36.364 0.00 0.00 0.00 3.16
2330 2376 7.413438 GCGTCATCTGTATGTTTCATCTTTCTT 60.413 37.037 0.00 0.00 34.50 2.52
2331 2377 8.446273 CGTCATCTGTATGTTTCATCTTTCTTT 58.554 33.333 0.00 0.00 34.50 2.52
2373 2424 8.352752 TCGTATGCTTTCACTGTATATTTCTG 57.647 34.615 0.00 0.00 0.00 3.02
2448 2499 3.797184 GCTTCCAATTGGTTTGCACGTTA 60.797 43.478 23.76 0.00 36.34 3.18
2513 2564 2.823196 TTGCATAGAAAATCCGCACG 57.177 45.000 0.00 0.00 31.10 5.34
2719 3009 9.784531 ACTTGAGTCTAATTGGATGGTATAATG 57.215 33.333 0.00 0.00 0.00 1.90
2720 3010 8.621532 TTGAGTCTAATTGGATGGTATAATGC 57.378 34.615 0.00 0.00 0.00 3.56
2729 3019 6.413783 TGGATGGTATAATGCGAGAGTTAA 57.586 37.500 0.00 0.00 0.00 2.01
2794 3084 8.532186 AGATAAGAGACAGTTCTATCATGTGT 57.468 34.615 0.00 0.00 29.47 3.72
2795 3085 8.976353 AGATAAGAGACAGTTCTATCATGTGTT 58.024 33.333 0.00 0.00 29.47 3.32
2796 3086 8.939201 ATAAGAGACAGTTCTATCATGTGTTG 57.061 34.615 0.00 0.00 29.47 3.33
2798 3088 4.256920 AGACAGTTCTATCATGTGTTGCC 58.743 43.478 0.00 0.00 0.00 4.52
2799 3089 4.002982 GACAGTTCTATCATGTGTTGCCA 58.997 43.478 0.00 0.00 0.00 4.92
2801 3091 5.012239 ACAGTTCTATCATGTGTTGCCATT 58.988 37.500 0.00 0.00 0.00 3.16
2802 3092 6.179756 ACAGTTCTATCATGTGTTGCCATTA 58.820 36.000 0.00 0.00 0.00 1.90
2803 3093 6.658816 ACAGTTCTATCATGTGTTGCCATTAA 59.341 34.615 0.00 0.00 0.00 1.40
2804 3094 7.340232 ACAGTTCTATCATGTGTTGCCATTAAT 59.660 33.333 0.00 0.00 0.00 1.40
2805 3095 8.192774 CAGTTCTATCATGTGTTGCCATTAATT 58.807 33.333 0.00 0.00 0.00 1.40
2806 3096 9.407380 AGTTCTATCATGTGTTGCCATTAATTA 57.593 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
232 240 2.032681 GAGCCGTGGGAAAGCTGT 59.967 61.111 0.00 0.00 36.87 4.40
270 282 0.260816 AGGTGGGTAGATAGCCGTGA 59.739 55.000 3.79 0.00 46.56 4.35
272 284 2.994957 ATAGGTGGGTAGATAGCCGT 57.005 50.000 3.79 0.00 46.56 5.68
314 326 1.941820 AGAGGGAGGAGGGGCAGTA 60.942 63.158 0.00 0.00 0.00 2.74
319 331 2.445654 GAGCAGAGGGAGGAGGGG 60.446 72.222 0.00 0.00 0.00 4.79
388 400 3.816523 GGTAGAAGGAGAGATCGATCGTT 59.183 47.826 19.33 11.68 0.00 3.85
389 401 3.404899 GGTAGAAGGAGAGATCGATCGT 58.595 50.000 19.33 11.16 0.00 3.73
449 461 0.729116 CACATCTTACCTGGCAAGCG 59.271 55.000 1.54 0.00 0.00 4.68
461 473 2.834549 AGGAAGATCGACCACACATCTT 59.165 45.455 12.36 0.00 39.17 2.40
518 530 1.965930 CCGCACAACCAGCAGCTAA 60.966 57.895 0.00 0.00 0.00 3.09
671 692 1.066573 GCTGGTCTTGAGCTAGCTTGA 60.067 52.381 20.42 14.50 33.37 3.02
698 719 0.837272 GGGGGAATCGAAGTGGATCA 59.163 55.000 0.00 0.00 0.00 2.92
721 742 4.846168 AAATCTGACTCTAGGGTTTCCC 57.154 45.455 0.00 0.00 45.90 3.97
764 785 1.810030 GCCTGTAGCTGTACACGCC 60.810 63.158 11.98 1.80 36.00 5.68
781 802 0.179051 AGCTAAGCATCAGCCAGAGC 60.179 55.000 0.00 0.00 43.56 4.09
786 807 2.032204 CGAATCAAGCTAAGCATCAGCC 60.032 50.000 0.00 0.00 43.56 4.85
789 810 3.860641 TGACGAATCAAGCTAAGCATCA 58.139 40.909 0.00 0.00 0.00 3.07
834 857 0.451783 GCATGGTTCATTGGTCGGTC 59.548 55.000 0.00 0.00 0.00 4.79
838 861 0.179156 CGCAGCATGGTTCATTGGTC 60.179 55.000 0.00 0.00 35.86 4.02
839 862 0.608856 TCGCAGCATGGTTCATTGGT 60.609 50.000 0.00 0.00 35.86 3.67
840 863 0.527113 TTCGCAGCATGGTTCATTGG 59.473 50.000 0.00 0.00 35.86 3.16
841 864 1.200716 AGTTCGCAGCATGGTTCATTG 59.799 47.619 0.00 0.00 35.86 2.82
842 865 1.200716 CAGTTCGCAGCATGGTTCATT 59.799 47.619 0.00 0.00 35.86 2.57
843 866 0.806868 CAGTTCGCAGCATGGTTCAT 59.193 50.000 0.00 0.00 35.86 2.57
844 867 0.250252 TCAGTTCGCAGCATGGTTCA 60.250 50.000 0.00 0.00 35.86 3.18
845 868 1.089920 ATCAGTTCGCAGCATGGTTC 58.910 50.000 0.00 0.00 35.86 3.62
846 869 0.806868 CATCAGTTCGCAGCATGGTT 59.193 50.000 0.00 0.00 35.86 3.67
847 870 0.036105 TCATCAGTTCGCAGCATGGT 60.036 50.000 0.00 0.00 35.86 3.55
848 871 0.656259 CTCATCAGTTCGCAGCATGG 59.344 55.000 0.00 0.00 35.86 3.66
849 872 0.027716 GCTCATCAGTTCGCAGCATG 59.972 55.000 0.00 0.00 40.87 4.06
854 877 0.532115 TAGCTGCTCATCAGTTCGCA 59.468 50.000 4.91 0.00 44.66 5.10
919 942 1.877576 CGGTCACACAGAGCTGCCTA 61.878 60.000 0.00 0.00 42.56 3.93
929 952 0.667453 TTAGTACACGCGGTCACACA 59.333 50.000 12.47 0.00 0.00 3.72
935 958 2.568090 CCCGTTAGTACACGCGGT 59.432 61.111 12.47 8.38 42.36 5.68
936 959 2.882301 GCCCGTTAGTACACGCGG 60.882 66.667 12.47 12.91 43.40 6.46
937 960 3.242474 CGCCCGTTAGTACACGCG 61.242 66.667 3.53 3.53 38.93 6.01
938 961 2.882301 CCGCCCGTTAGTACACGC 60.882 66.667 0.00 0.00 38.93 5.34
939 962 2.882301 GCCGCCCGTTAGTACACG 60.882 66.667 0.00 0.00 40.02 4.49
940 963 2.510012 GGCCGCCCGTTAGTACAC 60.510 66.667 0.00 0.00 0.00 2.90
1092 1115 1.375013 GCGAAGGTACTGCCCGAAA 60.375 57.895 0.00 0.00 40.86 3.46
1209 1232 2.532715 AAGAAGGGGCAGCCTGGA 60.533 61.111 12.43 0.00 0.00 3.86
1210 1233 2.044551 GAAGAAGGGGCAGCCTGG 60.045 66.667 12.43 0.00 0.00 4.45
1212 1235 3.721706 CCGAAGAAGGGGCAGCCT 61.722 66.667 12.43 0.00 0.00 4.58
1513 1536 4.529219 CGGCGCTGCTACATGGGA 62.529 66.667 7.64 0.00 0.00 4.37
1670 1693 4.254709 TGTTGCCGCTGGAGCTGT 62.255 61.111 0.00 0.00 39.32 4.40
1722 1745 2.771763 CTATGGCCATCTCGTCGCCC 62.772 65.000 24.80 0.00 42.29 6.13
2173 2199 2.291365 CGTGGAGCCATGAATCAATCA 58.709 47.619 2.49 0.00 43.67 2.57
2192 2218 6.799925 AGGAAGAACGCAACAAATTAAATACG 59.200 34.615 0.00 0.00 0.00 3.06
2194 2220 7.653647 ACAGGAAGAACGCAACAAATTAAATA 58.346 30.769 0.00 0.00 0.00 1.40
2220 2246 5.402398 CACATCAGTAAGATCTGTTCGACA 58.598 41.667 0.00 0.00 33.72 4.35
2330 2376 8.243426 AGCATACGAGAAATCAAAGCAAATAAA 58.757 29.630 0.00 0.00 0.00 1.40
2331 2377 7.761409 AGCATACGAGAAATCAAAGCAAATAA 58.239 30.769 0.00 0.00 0.00 1.40
2332 2378 7.320443 AGCATACGAGAAATCAAAGCAAATA 57.680 32.000 0.00 0.00 0.00 1.40
2333 2379 6.199937 AGCATACGAGAAATCAAAGCAAAT 57.800 33.333 0.00 0.00 0.00 2.32
2339 2390 6.204688 ACAGTGAAAGCATACGAGAAATCAAA 59.795 34.615 0.00 0.00 0.00 2.69
2491 2542 3.483196 CGTGCGGATTTTCTATGCAAATG 59.517 43.478 0.00 0.00 37.30 2.32
2509 2560 0.727398 GACTTCAATGGTAGCCGTGC 59.273 55.000 0.00 0.00 0.00 5.34
2513 2564 2.819608 TGCAAAGACTTCAATGGTAGCC 59.180 45.455 0.00 0.00 0.00 3.93
2602 2653 8.635765 AGTTGTATCCAAACATCTAACATGTT 57.364 30.769 16.68 16.68 43.35 2.71
2603 2654 9.905713 ATAGTTGTATCCAAACATCTAACATGT 57.094 29.630 0.00 0.00 36.04 3.21
2625 2676 6.042437 TGTCAGATACAATGCATCCAGATAGT 59.958 38.462 0.00 0.00 34.29 2.12
2631 2682 5.072193 ACCTATGTCAGATACAATGCATCCA 59.928 40.000 0.00 0.00 42.70 3.41
2639 2690 9.747898 AAAATACCAAACCTATGTCAGATACAA 57.252 29.630 0.00 0.00 42.70 2.41
2694 2984 8.725148 GCATTATACCATCCAATTAGACTCAAG 58.275 37.037 0.00 0.00 0.00 3.02
2737 3027 0.602372 CCACCCGCAAACCAATTTGG 60.602 55.000 14.02 14.02 44.64 3.28
2741 3031 0.893727 GTCTCCACCCGCAAACCAAT 60.894 55.000 0.00 0.00 0.00 3.16
2742 3032 1.527380 GTCTCCACCCGCAAACCAA 60.527 57.895 0.00 0.00 0.00 3.67
2743 3033 2.112297 GTCTCCACCCGCAAACCA 59.888 61.111 0.00 0.00 0.00 3.67
2744 3034 2.671963 GGTCTCCACCCGCAAACC 60.672 66.667 0.00 0.00 36.54 3.27
2745 3035 3.047877 CGGTCTCCACCCGCAAAC 61.048 66.667 0.00 0.00 40.01 2.93
2751 3041 2.941480 TCTTAGATACGGTCTCCACCC 58.059 52.381 0.00 0.00 40.01 4.61
2752 3042 6.002704 TCTTATCTTAGATACGGTCTCCACC 58.997 44.000 0.81 0.00 38.42 4.61


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

AutoCloner maintained by Alex Coulton.