Multiple sequence alignment - TraesCS7B01G145400

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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 TraesCS7B01G145400 chr7B 100.000 3842 0 0 1 3842 188605311 188601470 0.000000e+00 7095.0
1 TraesCS7B01G145400 chr7D 95.477 3847 124 25 1 3816 213373536 213377363 0.000000e+00 6095.0
2 TraesCS7B01G145400 chr7D 96.970 33 1 0 3810 3842 231549226 231549194 5.360000e-04 56.5
3 TraesCS7B01G145400 chr7D 96.970 33 1 0 3810 3842 231598286 231598254 5.360000e-04 56.5
4 TraesCS7B01G145400 chr7A 96.770 2198 64 4 738 2931 224987317 224989511 0.000000e+00 3659.0
5 TraesCS7B01G145400 chr7A 91.022 724 44 8 1 707 224986597 224987316 0.000000e+00 957.0
6 TraesCS7B01G145400 chr7A 89.466 655 25 11 3162 3814 224989724 224990336 0.000000e+00 787.0
7 TraesCS7B01G145400 chr5B 80.407 786 146 4 1082 1860 449752506 449751722 3.310000e-165 592.0
8 TraesCS7B01G145400 chr5D 78.247 947 180 17 1082 2006 376664380 376663438 5.530000e-163 584.0
9 TraesCS7B01G145400 chr5D 96.970 33 1 0 3810 3842 6232863 6232831 5.360000e-04 56.5
10 TraesCS7B01G145400 chr5D 96.970 33 1 0 3810 3842 483804391 483804359 5.360000e-04 56.5
11 TraesCS7B01G145400 chr5A 79.771 786 151 3 1082 1860 477437375 477436591 7.210000e-157 564.0
12 TraesCS7B01G145400 chrUn 96.970 33 1 0 3810 3842 407032780 407032812 5.360000e-04 56.5
13 TraesCS7B01G145400 chr6D 96.970 33 1 0 3810 3842 210721969 210721937 5.360000e-04 56.5
14 TraesCS7B01G145400 chr1D 96.970 33 1 0 3810 3842 252846692 252846724 5.360000e-04 56.5
15 TraesCS7B01G145400 chr1D 96.970 33 1 0 3810 3842 254480365 254480397 5.360000e-04 56.5
16 TraesCS7B01G145400 chr1D 96.970 33 1 0 3810 3842 461628341 461628309 5.360000e-04 56.5


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 TraesCS7B01G145400 chr7B 188601470 188605311 3841 True 7095 7095 100.000000 1 3842 1 chr7B.!!$R1 3841
1 TraesCS7B01G145400 chr7D 213373536 213377363 3827 False 6095 6095 95.477000 1 3816 1 chr7D.!!$F1 3815
2 TraesCS7B01G145400 chr7A 224986597 224990336 3739 False 1801 3659 92.419333 1 3814 3 chr7A.!!$F1 3813
3 TraesCS7B01G145400 chr5B 449751722 449752506 784 True 592 592 80.407000 1082 1860 1 chr5B.!!$R1 778
4 TraesCS7B01G145400 chr5D 376663438 376664380 942 True 584 584 78.247000 1082 2006 1 chr5D.!!$R2 924
5 TraesCS7B01G145400 chr5A 477436591 477437375 784 True 564 564 79.771000 1082 1860 1 chr5A.!!$R1 778

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
326 342 0.801251 CCGTTTCTCGACGAGGTAGT 59.199 55.000 23.92 0.0 45.47 2.73 F
448 466 1.167781 TTCGTTGCTCCCCGTTTTCC 61.168 55.000 0.00 0.0 0.00 3.13 F
519 537 3.079960 TCGGCGTCTCTGTATTGATTC 57.920 47.619 6.85 0.0 0.00 2.52 F
717 735 3.444703 ACATGCTAGGATGTTCTCGTC 57.555 47.619 22.81 0.0 32.38 4.20 F
2554 2591 1.952296 ACCAGTCTTCTGCTGCAAAAG 59.048 47.619 9.40 9.4 40.09 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1632 1657 0.036010 AAGCAATCCACCACTCCTCG 60.036 55.0 0.0 0.0 0.00 4.63 R
2124 2161 0.875059 GTCTTCTTCGCTTTGGTGGG 59.125 55.0 0.0 0.0 0.00 4.61 R
2175 2212 5.200483 TCATTCCTTTGTGTTCCTTCAACT 58.800 37.5 0.0 0.0 35.79 3.16 R
2666 2706 1.081892 ACTCATGATCTGTTGCGTGC 58.918 50.0 0.0 0.0 0.00 5.34 R
3526 3641 0.034756 ATCTTAGCCACACGCACACA 59.965 50.0 0.0 0.0 41.38 3.72 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
280 296 4.548513 CTCCCCTCTCCTCCCCCG 62.549 77.778 0.00 0.00 0.00 5.73
326 342 0.801251 CCGTTTCTCGACGAGGTAGT 59.199 55.000 23.92 0.00 45.47 2.73
327 343 1.202009 CCGTTTCTCGACGAGGTAGTC 60.202 57.143 23.92 9.87 45.47 2.59
383 401 3.611025 TTTTGGTGGGATTGGTCTCTT 57.389 42.857 0.00 0.00 0.00 2.85
385 403 3.611025 TTGGTGGGATTGGTCTCTTTT 57.389 42.857 0.00 0.00 0.00 2.27
394 412 2.721425 TGGTCTCTTTTGTTCCCGTT 57.279 45.000 0.00 0.00 0.00 4.44
397 415 2.207590 GTCTCTTTTGTTCCCGTTCGT 58.792 47.619 0.00 0.00 0.00 3.85
448 466 1.167781 TTCGTTGCTCCCCGTTTTCC 61.168 55.000 0.00 0.00 0.00 3.13
519 537 3.079960 TCGGCGTCTCTGTATTGATTC 57.920 47.619 6.85 0.00 0.00 2.52
567 585 4.907269 TGCCCCTCACATAGATTGATCTTA 59.093 41.667 0.00 0.00 38.32 2.10
625 643 6.698008 TTGGCTTTGATAATGTAGTGATGG 57.302 37.500 0.00 0.00 0.00 3.51
669 687 7.177744 GGATGGTCTTGGTTCCTTACAAATTTA 59.822 37.037 0.00 0.00 0.00 1.40
670 688 7.899648 TGGTCTTGGTTCCTTACAAATTTAA 57.100 32.000 0.00 0.00 0.00 1.52
717 735 3.444703 ACATGCTAGGATGTTCTCGTC 57.555 47.619 22.81 0.00 32.38 4.20
734 752 4.388773 TCTCGTCACAGTGCACATTATTTC 59.611 41.667 21.04 2.26 0.00 2.17
756 775 8.469309 TTTCTTTGATCAGGTCAGAAGAAAAT 57.531 30.769 20.57 0.00 42.58 1.82
761 780 4.705110 TCAGGTCAGAAGAAAATCACCA 57.295 40.909 0.00 0.00 0.00 4.17
765 784 7.230747 TCAGGTCAGAAGAAAATCACCATTAA 58.769 34.615 0.00 0.00 0.00 1.40
846 865 5.447818 GCACTGTATGGTCACAATTCTAAGC 60.448 44.000 0.00 0.00 0.00 3.09
850 869 4.708726 ATGGTCACAATTCTAAGCTTGC 57.291 40.909 9.86 0.00 0.00 4.01
857 876 7.308589 GGTCACAATTCTAAGCTTGCTCTTTTA 60.309 37.037 9.86 0.00 0.00 1.52
861 880 5.613358 TTCTAAGCTTGCTCTTTTACAGC 57.387 39.130 9.86 0.00 37.40 4.40
891 910 7.108841 AGCATTGCATTTTCAGATATTGACT 57.891 32.000 11.91 0.00 34.94 3.41
907 926 8.746530 AGATATTGACTGCATCAGAATTTTTGT 58.253 29.630 0.29 0.00 38.99 2.83
953 972 6.403866 TGATGGTGCAAAGAAAATAAGTGT 57.596 33.333 0.00 0.00 0.00 3.55
984 1003 5.977635 TGAGTAGGGTGATGTTATTGAGTG 58.022 41.667 0.00 0.00 0.00 3.51
985 1004 4.770795 AGTAGGGTGATGTTATTGAGTGC 58.229 43.478 0.00 0.00 0.00 4.40
1011 1030 7.812191 CAGTAAGCACTAGAGATGATGGATAAC 59.188 40.741 0.00 0.00 32.21 1.89
1012 1031 6.992664 AAGCACTAGAGATGATGGATAACT 57.007 37.500 0.00 0.00 0.00 2.24
1098 1117 3.635836 TCTCTGAGAATGATGTCAGCGAT 59.364 43.478 4.57 0.00 44.48 4.58
1707 1732 6.990349 ACAGAAAACCTCACGATCTTAAGAAA 59.010 34.615 9.71 0.00 0.00 2.52
1891 1919 3.687212 CAGTATTGGCAACGGTGTATCAA 59.313 43.478 0.00 5.40 42.51 2.57
2088 2125 5.351233 AAAAACGTCATGATAAACGCTCA 57.649 34.783 0.00 0.00 42.47 4.26
2124 2161 8.837788 TGCCTAGTACTAAGGAAACTAAAAAC 57.162 34.615 17.59 2.52 42.68 2.43
2175 2212 3.136443 AGTGTTCTGTTGATGGGTCTGAA 59.864 43.478 0.00 0.00 0.00 3.02
2554 2591 1.952296 ACCAGTCTTCTGCTGCAAAAG 59.048 47.619 9.40 9.40 40.09 2.27
2853 2893 5.895534 TCTGGGAACGTAATGTAGGTAATCT 59.104 40.000 0.00 0.00 0.00 2.40
2968 3073 1.482954 TCATCTCTCTCTGTGGGCAG 58.517 55.000 0.00 0.00 43.87 4.85
3031 3142 9.569122 GAGGTTGGTTAGAGGCAATTATATTTA 57.431 33.333 0.00 0.00 0.00 1.40
3068 3179 2.092323 CCATACGTGTGAGAGGTGAGA 58.908 52.381 14.51 0.00 0.00 3.27
3130 3241 5.632347 GTCCAGCAAAGAAAGATTGTGATTG 59.368 40.000 0.00 0.00 0.00 2.67
3152 3263 3.064545 GCTCAGCTGAATTCGCAAGTAAT 59.935 43.478 18.85 1.09 39.48 1.89
3188 3299 5.983720 GCGAGAATTACTCCTGCTGTTATTA 59.016 40.000 0.00 0.00 42.18 0.98
3189 3300 6.647067 GCGAGAATTACTCCTGCTGTTATTAT 59.353 38.462 0.00 0.00 42.18 1.28
3190 3301 7.171678 GCGAGAATTACTCCTGCTGTTATTATT 59.828 37.037 0.00 0.00 42.18 1.40
3233 3344 2.291465 TGCATGTCTTGTTCTCAGTTGC 59.709 45.455 0.00 0.00 0.00 4.17
3266 3377 6.040209 TCTCTTTGTAACGGGTGCTTATTA 57.960 37.500 0.00 0.00 0.00 0.98
3354 3465 0.384309 CCATGACATGCTGATGTGGC 59.616 55.000 10.10 0.00 43.22 5.01
3465 3580 8.700439 TTAGCCTGTAAAAACTTGGTAGAATT 57.300 30.769 0.00 0.00 0.00 2.17
3468 3583 8.141909 AGCCTGTAAAAACTTGGTAGAATTTTC 58.858 33.333 0.00 0.00 31.46 2.29
3512 3627 3.733380 CGCGTCTGATGAAGAGAACTGAT 60.733 47.826 0.00 0.00 34.84 2.90
3520 3635 7.710044 TCTGATGAAGAGAACTGATATTTCTGC 59.290 37.037 0.00 0.00 33.30 4.26
3525 3640 8.509690 TGAAGAGAACTGATATTTCTGCTTTTG 58.490 33.333 0.00 0.00 33.30 2.44
3526 3641 7.992754 AGAGAACTGATATTTCTGCTTTTGT 57.007 32.000 0.00 0.00 33.30 2.83
3527 3642 7.814642 AGAGAACTGATATTTCTGCTTTTGTG 58.185 34.615 0.00 0.00 33.30 3.33
3529 3644 7.365741 AGAACTGATATTTCTGCTTTTGTGTG 58.634 34.615 0.00 0.00 31.88 3.82
3530 3645 6.639632 ACTGATATTTCTGCTTTTGTGTGT 57.360 33.333 0.00 0.00 0.00 3.72
3531 3646 6.441274 ACTGATATTTCTGCTTTTGTGTGTG 58.559 36.000 0.00 0.00 0.00 3.82
3532 3647 5.221880 TGATATTTCTGCTTTTGTGTGTGC 58.778 37.500 0.00 0.00 0.00 4.57
3533 3648 1.906757 TTTCTGCTTTTGTGTGTGCG 58.093 45.000 0.00 0.00 0.00 5.34
3601 3718 2.611751 TGTGTCGTCCTGAATGTTGTTG 59.388 45.455 0.00 0.00 0.00 3.33
3607 3724 6.127980 TGTCGTCCTGAATGTTGTTGTTTTTA 60.128 34.615 0.00 0.00 0.00 1.52
3640 3757 2.907695 TTTGCTGCTGGCTCACACCA 62.908 55.000 0.00 0.00 42.39 4.17
3698 3821 2.551938 GCTCTTTTTCTGCAGGGAGAGT 60.552 50.000 24.14 0.00 34.57 3.24
3702 3825 0.473694 TTTCTGCAGGGAGAGTGGGA 60.474 55.000 15.13 0.00 0.00 4.37
3706 3829 1.005215 CTGCAGGGAGAGTGGGAAAAT 59.995 52.381 5.57 0.00 0.00 1.82
3707 3830 1.428912 TGCAGGGAGAGTGGGAAAATT 59.571 47.619 0.00 0.00 0.00 1.82
3782 3905 1.464997 GGCATCGTGACTTTCAGTTCC 59.535 52.381 0.00 0.00 0.00 3.62
3816 3939 3.041211 TCTCTCAATGTCATACCCCCTG 58.959 50.000 0.00 0.00 0.00 4.45
3817 3940 1.490490 TCTCAATGTCATACCCCCTGC 59.510 52.381 0.00 0.00 0.00 4.85
3818 3941 0.180171 TCAATGTCATACCCCCTGCG 59.820 55.000 0.00 0.00 0.00 5.18
3819 3942 0.819259 CAATGTCATACCCCCTGCGG 60.819 60.000 0.00 0.00 0.00 5.69
3820 3943 0.986019 AATGTCATACCCCCTGCGGA 60.986 55.000 0.00 0.00 0.00 5.54
3821 3944 1.410850 ATGTCATACCCCCTGCGGAG 61.411 60.000 0.00 0.00 0.00 4.63
3822 3945 2.445845 TCATACCCCCTGCGGAGG 60.446 66.667 17.41 17.41 39.42 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
397 415 2.739292 GCAACAACTATCTATCGCCGA 58.261 47.619 0.00 0.00 0.00 5.54
403 421 3.819564 TCAGGCGCAACAACTATCTAT 57.180 42.857 10.83 0.00 0.00 1.98
519 537 1.964373 CCGAACTTCCAACCCCACG 60.964 63.158 0.00 0.00 0.00 4.94
592 610 6.769822 ACATTATCAAAGCCAATCGAGAAGAT 59.230 34.615 0.00 0.00 42.43 2.40
669 687 7.831193 ACTACAAGATTTCAGCAACTATGGATT 59.169 33.333 0.00 0.00 0.00 3.01
670 688 7.341805 ACTACAAGATTTCAGCAACTATGGAT 58.658 34.615 0.00 0.00 0.00 3.41
677 695 6.524586 GCATGTTACTACAAGATTTCAGCAAC 59.475 38.462 0.00 0.00 37.91 4.17
717 735 7.085746 TGATCAAAGAAATAATGTGCACTGTG 58.914 34.615 19.41 2.76 0.00 3.66
734 752 7.303998 GTGATTTTCTTCTGACCTGATCAAAG 58.696 38.462 0.00 0.00 36.69 2.77
846 865 4.092675 GCTAGTCAGCTGTAAAAGAGCAAG 59.907 45.833 14.67 0.00 44.93 4.01
861 880 5.556355 TCTGAAAATGCAATGCTAGTCAG 57.444 39.130 16.74 16.74 0.00 3.51
891 910 5.221402 TGCAACCTACAAAAATTCTGATGCA 60.221 36.000 0.00 0.00 36.65 3.96
907 926 7.722363 TCAATCGAAGTAATATCTGCAACCTA 58.278 34.615 0.00 0.00 0.00 3.08
953 972 1.429930 TCACCCTACTCAACTTGCCA 58.570 50.000 0.00 0.00 0.00 4.92
984 1003 4.038522 TCCATCATCTCTAGTGCTTACTGC 59.961 45.833 0.00 0.00 43.25 4.40
985 1004 5.781210 TCCATCATCTCTAGTGCTTACTG 57.219 43.478 0.00 0.00 0.00 2.74
1011 1030 3.046390 CTCCTTCGCGACAATAGCTAAG 58.954 50.000 9.15 0.00 37.21 2.18
1012 1031 2.798499 GCTCCTTCGCGACAATAGCTAA 60.798 50.000 9.15 0.00 0.00 3.09
1098 1117 1.007600 TCCTCAGCCTCAATCTCCTCA 59.992 52.381 0.00 0.00 0.00 3.86
1344 1369 2.093447 ACTGACAGGCTTCCCTTTATCG 60.093 50.000 7.51 0.00 40.33 2.92
1632 1657 0.036010 AAGCAATCCACCACTCCTCG 60.036 55.000 0.00 0.00 0.00 4.63
1707 1732 1.111277 GCACACCAACCTTCCAAACT 58.889 50.000 0.00 0.00 0.00 2.66
1891 1919 5.131142 CCCCTAGGTCAACAAGATGAGTATT 59.869 44.000 8.29 0.00 0.00 1.89
2088 2125 2.907042 AGTACTAGGCAGCCTTTGAGTT 59.093 45.455 22.26 0.00 34.61 3.01
2124 2161 0.875059 GTCTTCTTCGCTTTGGTGGG 59.125 55.000 0.00 0.00 0.00 4.61
2175 2212 5.200483 TCATTCCTTTGTGTTCCTTCAACT 58.800 37.500 0.00 0.00 35.79 3.16
2554 2591 8.732531 GTTATCCATAGATAGTGGTACTGAGTC 58.267 40.741 0.00 0.00 36.35 3.36
2666 2706 1.081892 ACTCATGATCTGTTGCGTGC 58.918 50.000 0.00 0.00 0.00 5.34
3107 3218 5.775686 CAATCACAATCTTTCTTTGCTGGA 58.224 37.500 0.00 0.00 0.00 3.86
3130 3241 0.801251 ACTTGCGAATTCAGCTGAGC 59.199 50.000 17.43 16.91 35.28 4.26
3152 3263 5.479306 AGTAATTCTCGCAACTAAGCTCAA 58.521 37.500 0.00 0.00 0.00 3.02
3188 3299 5.568620 AGACTTGTAAGACACTGGGAAAT 57.431 39.130 0.00 0.00 0.00 2.17
3189 3300 6.464222 CATAGACTTGTAAGACACTGGGAAA 58.536 40.000 0.00 0.00 0.00 3.13
3190 3301 5.568825 GCATAGACTTGTAAGACACTGGGAA 60.569 44.000 0.00 0.00 0.00 3.97
3233 3344 4.201628 CCGTTACAAAGAGAGCTGAAATCG 60.202 45.833 0.00 0.00 0.00 3.34
3266 3377 1.033746 CCGAGGGCTGCAATCAACAT 61.034 55.000 0.50 0.00 0.00 2.71
3286 3397 2.159653 CCTTTTTCTCAGCGATCAACCG 60.160 50.000 0.00 0.00 0.00 4.44
3287 3398 2.162408 CCCTTTTTCTCAGCGATCAACC 59.838 50.000 0.00 0.00 0.00 3.77
3354 3465 3.815962 TCTCTACTGTAGCAGGATTAGCG 59.184 47.826 9.98 0.00 35.51 4.26
3512 3627 3.066064 ACGCACACACAAAAGCAGAAATA 59.934 39.130 0.00 0.00 0.00 1.40
3520 3635 1.139226 GCCACACGCACACACAAAAG 61.139 55.000 0.00 0.00 37.47 2.27
3525 3640 0.878523 TCTTAGCCACACGCACACAC 60.879 55.000 0.00 0.00 41.38 3.82
3526 3641 0.034756 ATCTTAGCCACACGCACACA 59.965 50.000 0.00 0.00 41.38 3.72
3527 3642 0.443869 CATCTTAGCCACACGCACAC 59.556 55.000 0.00 0.00 41.38 3.82
3529 3644 1.438651 TTCATCTTAGCCACACGCAC 58.561 50.000 0.00 0.00 41.38 5.34
3530 3645 2.279741 GATTCATCTTAGCCACACGCA 58.720 47.619 0.00 0.00 41.38 5.24
3531 3646 1.258982 CGATTCATCTTAGCCACACGC 59.741 52.381 0.00 0.00 37.98 5.34
3532 3647 2.282555 CACGATTCATCTTAGCCACACG 59.717 50.000 0.00 0.00 0.00 4.49
3533 3648 3.521560 TCACGATTCATCTTAGCCACAC 58.478 45.455 0.00 0.00 0.00 3.82
3601 3718 7.168135 CAGCAAAATTCAGGACAGACTAAAAAC 59.832 37.037 0.00 0.00 0.00 2.43
3607 3724 2.555757 GCAGCAAAATTCAGGACAGACT 59.444 45.455 0.00 0.00 0.00 3.24
3640 3757 0.883833 GCAACAAGTACAGCCATGCT 59.116 50.000 0.00 0.00 40.77 3.79
3698 3821 3.695830 AGCTCGTACTCAATTTTCCCA 57.304 42.857 0.00 0.00 0.00 4.37
3755 3878 3.109547 GTCACGATGCCGCGACAA 61.110 61.111 8.23 0.00 44.56 3.18
3782 3905 1.376037 GAGAGACAAGGCCCAACCG 60.376 63.158 0.00 0.00 46.52 4.44


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

AutoCloner maintained by Alex Coulton.