Multiple sequence alignment - TraesCS7D01G429000

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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 TraesCS7D01G429000 chr7D 100.000 2817 0 0 1 2817 549124014 549121198 0.000000e+00 5203.0
1 TraesCS7D01G429000 chr7D 91.589 107 9 0 2534 2640 549121375 549121481 6.290000e-32 148.0
2 TraesCS7D01G429000 chr7A 92.388 2588 120 37 3 2539 634440010 634437449 0.000000e+00 3616.0
3 TraesCS7D01G429000 chr7A 89.922 129 7 3 2694 2816 634437334 634437206 8.080000e-36 161.0
4 TraesCS7D01G429000 chr7B 91.231 1129 57 15 1701 2817 592624792 592623694 0.000000e+00 1498.0
5 TraesCS7D01G429000 chr7B 95.766 496 16 3 524 1018 592625980 592625489 0.000000e+00 795.0
6 TraesCS7D01G429000 chr7B 84.595 766 47 33 1082 1801 592625468 592624728 0.000000e+00 695.0
7 TraesCS7D01G429000 chr7B 88.772 285 30 2 2023 2307 592676548 592676266 5.780000e-92 348.0
8 TraesCS7D01G429000 chr7B 91.753 97 8 0 448 544 592626099 592626003 4.890000e-28 135.0
9 TraesCS7D01G429000 chr5D 96.037 429 16 1 1 428 399326938 399327366 0.000000e+00 697.0
10 TraesCS7D01G429000 chr5D 95.082 427 20 1 1 427 439214822 439215247 0.000000e+00 671.0
11 TraesCS7D01G429000 chr5D 83.529 85 9 5 2595 2678 438373629 438373549 1.080000e-09 75.0
12 TraesCS7D01G429000 chr6B 95.561 428 19 0 1 428 695057925 695057498 0.000000e+00 686.0
13 TraesCS7D01G429000 chr4B 95.561 428 19 0 1 428 27479541 27479968 0.000000e+00 686.0
14 TraesCS7D01G429000 chr1A 95.561 428 19 0 1 428 493004948 493004521 0.000000e+00 686.0
15 TraesCS7D01G429000 chr3D 95.327 428 20 0 1 428 69661701 69661274 0.000000e+00 680.0
16 TraesCS7D01G429000 chr3D 89.855 69 6 1 2520 2588 26654112 26654179 1.390000e-13 87.9
17 TraesCS7D01G429000 chr2B 95.327 428 20 0 1 428 717930028 717930455 0.000000e+00 680.0
18 TraesCS7D01G429000 chr5A 95.093 428 21 0 1 428 671959614 671960041 0.000000e+00 675.0
19 TraesCS7D01G429000 chr6A 87.156 109 10 4 2534 2640 84900112 84900218 1.370000e-23 121.0
20 TraesCS7D01G429000 chr4D 88.462 104 6 3 2534 2637 313572319 313572416 1.370000e-23 121.0
21 TraesCS7D01G429000 chr6D 87.500 104 8 5 2537 2640 7460273 7460175 6.380000e-22 115.0
22 TraesCS7D01G429000 chr6D 86.792 106 7 3 2533 2637 7460174 7460273 8.250000e-21 111.0
23 TraesCS7D01G429000 chr6D 93.548 62 4 0 2527 2588 185368175 185368114 2.990000e-15 93.5
24 TraesCS7D01G429000 chr2D 93.333 60 3 1 2586 2644 267707113 267707172 1.390000e-13 87.9
25 TraesCS7D01G429000 chrUn 84.524 84 11 2 2504 2586 197752362 197752444 6.470000e-12 82.4
26 TraesCS7D01G429000 chr5B 90.000 60 4 2 2595 2654 312761860 312761803 3.010000e-10 76.8


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 TraesCS7D01G429000 chr7D 549121198 549124014 2816 True 5203.00 5203 100.00000 1 2817 1 chr7D.!!$R1 2816
1 TraesCS7D01G429000 chr7A 634437206 634440010 2804 True 1888.50 3616 91.15500 3 2816 2 chr7A.!!$R1 2813
2 TraesCS7D01G429000 chr7B 592623694 592626099 2405 True 780.75 1498 90.83625 448 2817 4 chr7B.!!$R2 2369

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
825 876 0.250727 TTCCTTGTGCTTCCCTTCCG 60.251 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2401 2565 1.339727 CCTTGTACTTGGTAGTGCCCC 60.34 57.143 0.0 0.0 36.29 5.8 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
35 36 3.699779 TGCTAGTTCATGAGCTACTCG 57.300 47.619 14.61 7.43 39.54 4.18
45 46 3.687572 TGAGCTACTCGATTACGTTCC 57.312 47.619 0.00 0.00 40.69 3.62
64 65 8.833231 ACGTTCCCTATTACAATGATCATAAG 57.167 34.615 9.04 7.55 0.00 1.73
80 81 5.975693 TCATAAGTGACATGGGAAAAACC 57.024 39.130 0.00 0.00 38.08 3.27
124 125 6.393171 TCATCTATAATGGATGAAGCGACTG 58.607 40.000 8.68 0.00 44.17 3.51
164 165 2.236146 TCAACGCATTCACCACCTCTAT 59.764 45.455 0.00 0.00 0.00 1.98
172 173 2.239400 TCACCACCTCTATGCTATCCG 58.761 52.381 0.00 0.00 0.00 4.18
200 201 5.412594 TCACTTCAATCTTACTGCATCCAAC 59.587 40.000 0.00 0.00 0.00 3.77
234 235 2.136298 TCAAACCAAACCTCACTGCA 57.864 45.000 0.00 0.00 0.00 4.41
244 245 1.884579 ACCTCACTGCAATTGCTTCTG 59.115 47.619 29.37 20.35 42.66 3.02
264 265 1.487482 CTGTGAACGAGTCGAAGCAA 58.513 50.000 21.50 0.65 0.00 3.91
265 266 1.858458 CTGTGAACGAGTCGAAGCAAA 59.142 47.619 21.50 8.01 0.00 3.68
273 274 2.003301 GAGTCGAAGCAAAGGTCCATC 58.997 52.381 0.00 0.00 0.00 3.51
363 364 4.268644 AGTGTGTCATTATCAAATCTCGCG 59.731 41.667 0.00 0.00 0.00 5.87
364 365 3.001228 TGTGTCATTATCAAATCTCGCGC 59.999 43.478 0.00 0.00 0.00 6.86
452 453 1.202806 TGCTCTCAGACACCCCAAAAG 60.203 52.381 0.00 0.00 0.00 2.27
483 484 2.193536 AAACAAAGCGCGCTTCCCT 61.194 52.632 42.82 27.36 34.84 4.20
574 620 2.202395 GCTGCTGGCCTTGGAAACA 61.202 57.895 3.32 0.00 34.39 2.83
825 876 0.250727 TTCCTTGTGCTTCCCTTCCG 60.251 55.000 0.00 0.00 0.00 4.30
835 886 1.895020 TTCCCTTCCGTGCTACGCAT 61.895 55.000 3.56 0.00 41.91 4.73
836 887 1.883084 CCCTTCCGTGCTACGCATC 60.883 63.158 3.56 0.00 41.91 3.91
837 888 1.141881 CCTTCCGTGCTACGCATCT 59.858 57.895 3.56 0.00 41.91 2.90
878 929 2.420129 CCTGGCAGGCGTCTATTTAAGT 60.420 50.000 22.68 0.00 0.00 2.24
888 939 3.195661 GTCTATTTAAGTCGCCCCACAG 58.804 50.000 0.00 0.00 0.00 3.66
891 942 2.757980 TTTAAGTCGCCCCACAGCCC 62.758 60.000 0.00 0.00 0.00 5.19
988 1040 0.614415 CTCCTCCTGACTCCTGCTGT 60.614 60.000 0.00 0.00 0.00 4.40
997 1049 1.153409 CTCCTGCTGTAGCTGCCAG 60.153 63.158 10.08 10.08 42.66 4.85
1068 1128 8.313292 CCCAACATCTCTTTTTATGATTTTCCA 58.687 33.333 0.00 0.00 0.00 3.53
1120 1180 6.738114 TGGTTGATGAACAGATCAAGAAAAC 58.262 36.000 0.00 0.00 41.85 2.43
1135 1195 6.779860 TCAAGAAAACCAATAGGAAGTAGCT 58.220 36.000 0.00 0.00 38.69 3.32
1216 1294 8.236586 TGGATTAGTTGATCATTCGTCAAAAAG 58.763 33.333 0.00 0.00 37.34 2.27
1217 1295 8.237267 GGATTAGTTGATCATTCGTCAAAAAGT 58.763 33.333 0.00 0.00 37.34 2.66
1228 1307 7.803189 TCATTCGTCAAAAAGTAAGATTGCTTC 59.197 33.333 0.00 0.00 35.56 3.86
1229 1308 5.675970 TCGTCAAAAAGTAAGATTGCTTCG 58.324 37.500 0.00 0.00 35.56 3.79
1429 1523 3.902150 GCTTCCTTTCAAAGCTACCAAC 58.098 45.455 0.00 0.00 44.53 3.77
1474 1584 5.710613 GAAAATCAGTTTCAACCGCAAAA 57.289 34.783 0.00 0.00 44.42 2.44
1536 1651 6.875972 ACTGAACTAGAATTCTATGGTGGT 57.124 37.500 15.47 7.02 0.00 4.16
1541 1656 6.472686 ACTAGAATTCTATGGTGGTCTCAC 57.527 41.667 15.47 0.00 42.91 3.51
1567 1682 1.457346 ATGCTTTGCTTCTTCTCCCG 58.543 50.000 0.00 0.00 0.00 5.14
1569 1684 0.321653 GCTTTGCTTCTTCTCCCGGA 60.322 55.000 0.73 0.00 0.00 5.14
1819 1970 0.948623 CCAACACCGTCGCTTGATGA 60.949 55.000 4.54 0.00 0.00 2.92
1820 1971 0.163788 CAACACCGTCGCTTGATGAC 59.836 55.000 0.00 0.00 0.00 3.06
2070 2233 7.042658 GCCGTCCATGTTAAATTTACACAAAAA 60.043 33.333 13.50 4.20 0.00 1.94
2116 2279 5.949354 ACAATGTTGTATTAAGGCCTGCTTA 59.051 36.000 5.69 0.00 40.16 3.09
2171 2334 1.758440 TTGCTTGAGACTGCTCGGGT 61.758 55.000 0.00 0.00 44.33 5.28
2203 2366 2.739292 GCACAGAGTCGTCAACAACTA 58.261 47.619 0.00 0.00 0.00 2.24
2388 2552 2.426023 GAGCCCGTGGAGTTGTGT 59.574 61.111 0.00 0.00 0.00 3.72
2390 2554 2.668550 GCCCGTGGAGTTGTGTCC 60.669 66.667 0.00 0.00 37.10 4.02
2432 2596 1.209621 AGTACAAGGTGGTGGTGTGT 58.790 50.000 0.00 0.00 0.00 3.72
2535 2714 4.521146 AGTGCAAATGTCTCCTTCCATAG 58.479 43.478 0.00 0.00 0.00 2.23
2564 2743 5.449314 CCCTCCGTCTCATAATATAAGAGCG 60.449 48.000 0.00 0.00 0.00 5.03
2578 2757 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
2579 2758 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
2580 2759 3.793559 AGAGCGTTTTTGACACTACACT 58.206 40.909 0.00 0.00 0.00 3.55
2581 2760 4.940463 AGAGCGTTTTTGACACTACACTA 58.060 39.130 0.00 0.00 0.00 2.74
2582 2761 5.353938 AGAGCGTTTTTGACACTACACTAA 58.646 37.500 0.00 0.00 0.00 2.24
2583 2762 5.989777 AGAGCGTTTTTGACACTACACTAAT 59.010 36.000 0.00 0.00 0.00 1.73
2584 2763 5.985781 AGCGTTTTTGACACTACACTAATG 58.014 37.500 0.00 0.00 0.00 1.90
2585 2764 5.526111 AGCGTTTTTGACACTACACTAATGT 59.474 36.000 0.00 0.00 43.30 2.71
2586 2765 6.702723 AGCGTTTTTGACACTACACTAATGTA 59.297 34.615 0.00 0.00 40.48 2.29
2587 2766 7.225145 AGCGTTTTTGACACTACACTAATGTAA 59.775 33.333 0.00 0.00 40.84 2.41
2588 2767 8.013378 GCGTTTTTGACACTACACTAATGTAAT 58.987 33.333 0.00 0.00 40.84 1.89
2627 2806 9.261180 TCAAAAACGCTCTTATATTATGAGAGG 57.739 33.333 20.84 15.07 41.74 3.69
2766 3007 6.100859 ACCATGATGTTCACTATGGAGAATCT 59.899 38.462 17.85 0.00 42.05 2.40
2781 3022 7.395190 TGGAGAATCTGGTTATCATGTTTTG 57.605 36.000 0.00 0.00 33.73 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 8.827177 TGATCATTGTAATAGGGAACGTAATC 57.173 34.615 0.00 0.00 30.48 1.75
80 81 7.993101 AGATGACTGTTATTTCATGTCATTGG 58.007 34.615 8.08 0.00 44.97 3.16
164 165 5.674525 AGATTGAAGTGAATTCGGATAGCA 58.325 37.500 0.04 0.00 41.14 3.49
172 173 7.148188 TGGATGCAGTAAGATTGAAGTGAATTC 60.148 37.037 0.00 0.00 38.50 2.17
200 201 5.811399 TGGTTTGAATCTTGCTAATACCG 57.189 39.130 0.00 0.00 0.00 4.02
234 235 2.221169 TCGTTCACAGCAGAAGCAATT 58.779 42.857 0.00 0.00 45.49 2.32
244 245 0.939577 TGCTTCGACTCGTTCACAGC 60.940 55.000 0.00 0.00 0.00 4.40
264 265 4.400567 GCTGCTAATGAAAAGATGGACCTT 59.599 41.667 0.00 0.00 0.00 3.50
265 266 3.950395 GCTGCTAATGAAAAGATGGACCT 59.050 43.478 0.00 0.00 0.00 3.85
315 316 3.983344 CAGCAACATTTGGAGCAGTTAAC 59.017 43.478 0.00 0.00 0.00 2.01
316 317 3.552684 GCAGCAACATTTGGAGCAGTTAA 60.553 43.478 0.00 0.00 0.00 2.01
452 453 3.483558 CGCTTTGTTTGAGAGCAACTTTC 59.516 43.478 0.00 0.00 36.22 2.62
483 484 3.706594 CTCTAGGCCCACAACTATGAGAA 59.293 47.826 0.00 0.00 0.00 2.87
574 620 3.069729 GGGGTCGCTGTACATAGATTCTT 59.930 47.826 0.00 0.00 0.00 2.52
589 635 1.197036 CTTTTCTTTTCGAGGGGTCGC 59.803 52.381 0.00 0.00 0.00 5.19
642 689 0.251922 TGCCGGAAGTAGTACACCCT 60.252 55.000 5.05 0.00 0.00 4.34
835 886 4.775253 GGAGGAGGAAGAAGAAGAAGAAGA 59.225 45.833 0.00 0.00 0.00 2.87
836 887 4.777366 AGGAGGAGGAAGAAGAAGAAGAAG 59.223 45.833 0.00 0.00 0.00 2.85
837 888 4.530161 CAGGAGGAGGAAGAAGAAGAAGAA 59.470 45.833 0.00 0.00 0.00 2.52
888 939 0.462789 CTGGCTTCAATGATTGGGGC 59.537 55.000 5.20 11.08 0.00 5.80
891 942 3.119245 CCTGTTCTGGCTTCAATGATTGG 60.119 47.826 5.20 0.00 0.00 3.16
997 1049 3.161450 TACCTCGGAGGCCATGGC 61.161 66.667 29.47 29.47 39.63 4.40
1068 1128 4.293494 TGAGAAGAGAGGAACCATGCTAT 58.707 43.478 0.00 0.00 0.00 2.97
1120 1180 4.965200 AGGCTAAGCTACTTCCTATTGG 57.035 45.455 0.00 0.00 0.00 3.16
1135 1195 4.414182 AGAAGTCTCTCCTAGCTAGGCTAA 59.586 45.833 31.76 18.73 40.82 3.09
1216 1294 5.896974 GCTTATTTCGACGAAGCAATCTTAC 59.103 40.000 10.61 0.00 44.05 2.34
1217 1295 5.810587 AGCTTATTTCGACGAAGCAATCTTA 59.189 36.000 20.99 0.00 46.46 2.10
1228 1307 9.358123 CAAACATTATCTTAGCTTATTTCGACG 57.642 33.333 0.00 0.00 0.00 5.12
1429 1523 5.696270 TCACAAGCAGGTAGATATAAATGCG 59.304 40.000 0.00 0.00 38.65 4.73
1474 1584 7.639113 TGTGAAGTTTGTTTTAGTCATTCCT 57.361 32.000 0.00 0.00 0.00 3.36
1536 1651 2.086869 GCAAAGCATTAGCAGGTGAGA 58.913 47.619 0.00 0.00 45.49 3.27
1541 1656 3.442977 AGAAGAAGCAAAGCATTAGCAGG 59.557 43.478 0.00 0.00 45.49 4.85
1567 1682 4.200283 CTCTCGACGCCTGCCTCC 62.200 72.222 0.00 0.00 0.00 4.30
1594 1709 0.252479 CCTTCTGCTGCTCCATGTCT 59.748 55.000 0.00 0.00 0.00 3.41
1819 1970 1.746615 GGCATCATCTGTGCGTGGT 60.747 57.895 0.00 0.00 43.40 4.16
1820 1971 2.816360 CGGCATCATCTGTGCGTGG 61.816 63.158 0.00 0.00 43.40 4.94
1950 2110 3.364023 GGTCGACGTGTTCATTTGTCTAG 59.636 47.826 9.92 0.00 0.00 2.43
1955 2115 1.595328 TGTGGTCGACGTGTTCATTTG 59.405 47.619 9.92 0.00 0.00 2.32
2171 2334 3.067106 GACTCTGTGCGATTTCTCCAAA 58.933 45.455 0.00 0.00 0.00 3.28
2203 2366 1.964223 CAGATACACGGTAGCAGGGAT 59.036 52.381 0.00 0.00 0.00 3.85
2331 2495 6.149474 AGTTCGACTGCAAATACAAGCTATTT 59.851 34.615 0.00 0.00 0.00 1.40
2335 2499 3.403038 AGTTCGACTGCAAATACAAGCT 58.597 40.909 0.00 0.00 0.00 3.74
2339 2503 3.644823 TCGAAGTTCGACTGCAAATACA 58.355 40.909 23.54 0.00 44.82 2.29
2376 2540 1.372997 CTCCGGACACAACTCCACG 60.373 63.158 0.00 0.00 0.00 4.94
2401 2565 1.339727 CCTTGTACTTGGTAGTGCCCC 60.340 57.143 0.00 0.00 36.29 5.80
2402 2566 1.350019 ACCTTGTACTTGGTAGTGCCC 59.650 52.381 8.28 0.00 36.29 5.36
2535 2714 7.828223 TCTTATATTATGAGACGGAGGGAGTAC 59.172 40.741 0.00 0.00 0.00 2.73
2584 2763 8.995906 GCGTTTTTGACACTACATTGATATTAC 58.004 33.333 0.00 0.00 0.00 1.89
2585 2764 8.941977 AGCGTTTTTGACACTACATTGATATTA 58.058 29.630 0.00 0.00 0.00 0.98
2586 2765 7.816640 AGCGTTTTTGACACTACATTGATATT 58.183 30.769 0.00 0.00 0.00 1.28
2587 2766 7.334421 AGAGCGTTTTTGACACTACATTGATAT 59.666 33.333 0.00 0.00 0.00 1.63
2588 2767 6.649141 AGAGCGTTTTTGACACTACATTGATA 59.351 34.615 0.00 0.00 0.00 2.15
2589 2768 5.470098 AGAGCGTTTTTGACACTACATTGAT 59.530 36.000 0.00 0.00 0.00 2.57
2590 2769 4.814234 AGAGCGTTTTTGACACTACATTGA 59.186 37.500 0.00 0.00 0.00 2.57
2591 2770 5.095691 AGAGCGTTTTTGACACTACATTG 57.904 39.130 0.00 0.00 0.00 2.82
2592 2771 5.751243 AAGAGCGTTTTTGACACTACATT 57.249 34.783 0.00 0.00 0.00 2.71
2593 2772 8.718102 ATATAAGAGCGTTTTTGACACTACAT 57.282 30.769 0.00 0.00 0.00 2.29
2626 2805 5.163237 TGCAAATTATGTAGTACTCCCTCCC 60.163 44.000 0.00 0.00 0.00 4.30
2627 2806 5.925509 TGCAAATTATGTAGTACTCCCTCC 58.074 41.667 0.00 0.00 0.00 4.30
2628 2807 7.217200 TGATGCAAATTATGTAGTACTCCCTC 58.783 38.462 0.00 0.00 0.00 4.30
2766 3007 4.944619 TGCCAACAAAACATGATAACCA 57.055 36.364 0.00 0.00 0.00 3.67
2781 3022 5.463061 CCATGATAATCGGATTTTTGCCAAC 59.537 40.000 8.76 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.