Multiple sequence alignment - TraesCS4B01G027000

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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 TraesCS4B01G027000 chr4B 100.000 3038 0 0 1 3038 20354048 20357085 0.000000e+00 5611.0
1 TraesCS4B01G027000 chr4B 91.336 554 39 5 2488 3038 20370016 20369469 0.000000e+00 749.0
2 TraesCS4B01G027000 chr4B 91.136 361 31 1 1987 2347 20370390 20370031 3.520000e-134 488.0
3 TraesCS4B01G027000 chr4D 92.187 1587 86 14 426 1987 10828588 10830161 0.000000e+00 2209.0
4 TraesCS4B01G027000 chr4D 91.997 1587 89 14 426 1987 10810819 10812392 0.000000e+00 2193.0
5 TraesCS4B01G027000 chr4D 96.689 1057 29 5 1984 3038 10812509 10813561 0.000000e+00 1753.0
6 TraesCS4B01G027000 chr4D 96.023 1056 35 6 1984 3038 10830278 10831327 0.000000e+00 1711.0
7 TraesCS4B01G027000 chr4D 92.543 523 32 4 2488 3007 10881502 10880984 0.000000e+00 743.0
8 TraesCS4B01G027000 chr4D 95.533 403 13 3 1 399 10810419 10810820 9.180000e-180 640.0
9 TraesCS4B01G027000 chr4D 92.201 359 25 3 1989 2347 10881872 10881517 3.500000e-139 505.0
10 TraesCS4B01G027000 chr4A 89.758 1738 133 20 267 1981 591674130 591675845 0.000000e+00 2182.0
11 TraesCS4B01G027000 chr4A 89.713 1740 130 22 267 1981 592928150 592926435 0.000000e+00 2176.0
12 TraesCS4B01G027000 chr4A 89.483 1740 132 23 267 1981 591416145 591417858 0.000000e+00 2152.0
13 TraesCS4B01G027000 chr4A 89.368 1740 136 22 267 1981 591346626 591348341 0.000000e+00 2143.0
14 TraesCS4B01G027000 chr4A 89.195 1740 138 25 267 1981 592336496 592334782 0.000000e+00 2126.0
15 TraesCS4B01G027000 chr4A 89.195 1740 137 24 267 1981 591292860 591294573 0.000000e+00 2124.0
16 TraesCS4B01G027000 chr4A 89.080 1740 142 22 267 1981 592362818 592361102 0.000000e+00 2117.0
17 TraesCS4B01G027000 chr4A 89.474 1691 128 23 267 1932 592310539 592308874 0.000000e+00 2091.0
18 TraesCS4B01G027000 chr4A 89.119 1691 135 23 267 1932 591285291 591283625 0.000000e+00 2058.0
19 TraesCS4B01G027000 chr4A 89.184 1128 81 19 267 1374 592638766 592637660 0.000000e+00 1369.0
20 TraesCS4B01G027000 chr4A 87.730 163 20 0 1987 2149 591694065 591693903 1.110000e-44 191.0
21 TraesCS4B01G027000 chr5B 96.364 110 4 0 2383 2492 383646690 383646799 6.690000e-42 182.0
22 TraesCS4B01G027000 chr7A 92.683 123 9 0 2383 2505 729073329 729073207 8.660000e-41 178.0
23 TraesCS4B01G027000 chr7B 91.473 129 9 2 2364 2492 528214892 528215018 3.110000e-40 176.0
24 TraesCS4B01G027000 chr3B 92.623 122 7 2 2383 2502 822718761 822718640 1.120000e-39 174.0
25 TraesCS4B01G027000 chr3B 94.545 110 6 0 2383 2492 351679531 351679422 1.450000e-38 171.0
26 TraesCS4B01G027000 chr1A 93.966 116 6 1 2380 2495 384334444 384334558 1.120000e-39 174.0
27 TraesCS4B01G027000 chr6B 94.545 110 6 0 2383 2492 421417693 421417584 1.450000e-38 171.0
28 TraesCS4B01G027000 chr3D 90.476 42 4 0 2549 2590 13157401 13157360 4.230000e-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 TraesCS4B01G027000 chr4B 20354048 20357085 3037 False 5611.000000 5611 100.000000 1 3038 1 chr4B.!!$F1 3037
1 TraesCS4B01G027000 chr4B 20369469 20370390 921 True 618.500000 749 91.236000 1987 3038 2 chr4B.!!$R1 1051
2 TraesCS4B01G027000 chr4D 10828588 10831327 2739 False 1960.000000 2209 94.105000 426 3038 2 chr4D.!!$F2 2612
3 TraesCS4B01G027000 chr4D 10810419 10813561 3142 False 1528.666667 2193 94.739667 1 3038 3 chr4D.!!$F1 3037
4 TraesCS4B01G027000 chr4D 10880984 10881872 888 True 624.000000 743 92.372000 1989 3007 2 chr4D.!!$R1 1018
5 TraesCS4B01G027000 chr4A 591674130 591675845 1715 False 2182.000000 2182 89.758000 267 1981 1 chr4A.!!$F4 1714
6 TraesCS4B01G027000 chr4A 592926435 592928150 1715 True 2176.000000 2176 89.713000 267 1981 1 chr4A.!!$R7 1714
7 TraesCS4B01G027000 chr4A 591416145 591417858 1713 False 2152.000000 2152 89.483000 267 1981 1 chr4A.!!$F3 1714
8 TraesCS4B01G027000 chr4A 591346626 591348341 1715 False 2143.000000 2143 89.368000 267 1981 1 chr4A.!!$F2 1714
9 TraesCS4B01G027000 chr4A 592334782 592336496 1714 True 2126.000000 2126 89.195000 267 1981 1 chr4A.!!$R4 1714
10 TraesCS4B01G027000 chr4A 591292860 591294573 1713 False 2124.000000 2124 89.195000 267 1981 1 chr4A.!!$F1 1714
11 TraesCS4B01G027000 chr4A 592361102 592362818 1716 True 2117.000000 2117 89.080000 267 1981 1 chr4A.!!$R5 1714
12 TraesCS4B01G027000 chr4A 592308874 592310539 1665 True 2091.000000 2091 89.474000 267 1932 1 chr4A.!!$R3 1665
13 TraesCS4B01G027000 chr4A 591283625 591285291 1666 True 2058.000000 2058 89.119000 267 1932 1 chr4A.!!$R1 1665
14 TraesCS4B01G027000 chr4A 592637660 592638766 1106 True 1369.000000 1369 89.184000 267 1374 1 chr4A.!!$R6 1107

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
220 225 0.400594 CGGGGTCTCAACCTTCCTTT 59.599 55.0 0.0 0.0 45.66 3.11 F
363 368 0.991920 TGAGGGAGGTAAGGGCTTTG 59.008 55.0 0.0 0.0 0.00 2.77 F
1479 1515 0.877213 CTGCATCATCGTCGGCATCA 60.877 55.0 0.0 0.0 35.45 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1031 1051 0.040425 GGTTGGTTTGCACACTAGCG 60.040 55.000 2.52 0.00 37.31 4.26 R
1722 1758 0.182061 GGACTCCCGGGAATAAACCC 59.818 60.000 26.68 8.33 45.92 4.11 R
2698 2876 2.649312 AGGAATCTTCACATGGGGTTGA 59.351 45.455 0.00 0.00 0.00 3.18 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
136 137 1.477295 GGAGGACTTACTAGTTGCGCT 59.523 52.381 9.73 0.00 33.84 5.92
142 143 0.524414 TTACTAGTTGCGCTCGAGCA 59.476 50.000 34.69 16.77 46.54 4.26
148 149 2.510012 TGCGCTCGAGCATTCCAG 60.510 61.111 34.69 19.33 42.92 3.86
149 150 3.934684 GCGCTCGAGCATTCCAGC 61.935 66.667 34.69 24.66 42.21 4.85
220 225 0.400594 CGGGGTCTCAACCTTCCTTT 59.599 55.000 0.00 0.00 45.66 3.11
363 368 0.991920 TGAGGGAGGTAAGGGCTTTG 59.008 55.000 0.00 0.00 0.00 2.77
416 423 2.163010 AGCCAAGCAATGTTCGAGATTG 59.837 45.455 12.62 12.62 34.47 2.67
461 468 4.512944 TGCGCAAGAATTTTAAATGCCAAA 59.487 33.333 8.16 0.00 43.02 3.28
484 491 4.946478 ACTACCTTGACTATGATCTGCC 57.054 45.455 0.00 0.00 0.00 4.85
552 559 7.149973 ACATCATGTTTTGTCTTTCATCCTTG 58.850 34.615 0.00 0.00 0.00 3.61
561 568 1.470098 CTTTCATCCTTGAAGCGTGGG 59.530 52.381 0.00 0.00 42.60 4.61
568 575 4.067972 TCCTTGAAGCGTGGGTATATTC 57.932 45.455 0.00 0.00 0.00 1.75
569 576 3.139077 CCTTGAAGCGTGGGTATATTCC 58.861 50.000 0.00 0.00 0.00 3.01
654 662 1.483415 GTTACATCCACGGGCTCCTAA 59.517 52.381 0.00 0.00 0.00 2.69
668 676 5.712917 CGGGCTCCTAAGAAGAGAATACTAT 59.287 44.000 0.00 0.00 32.86 2.12
766 777 7.415541 CCAATCACATCTTCCAACGTTATTGAT 60.416 37.037 0.00 0.00 28.80 2.57
833 847 6.159988 AGTTAGCGATCTAATCAATGCTACC 58.840 40.000 0.00 0.00 37.16 3.18
887 902 6.074356 CGAGTTTAATGAGTTTGGCCAAAAAG 60.074 38.462 31.92 6.57 31.33 2.27
894 914 2.039418 GTTTGGCCAAAAAGGGAGAGT 58.961 47.619 31.92 0.00 38.09 3.24
953 973 3.649277 CTCCGGGCCTCTCAACGTG 62.649 68.421 0.84 0.00 0.00 4.49
983 1003 8.444715 CGGGTCGATGTATATATAGAGCTAATC 58.555 40.741 16.93 4.62 32.88 1.75
1020 1040 1.552337 ACATCGCACCACAATCTCTCT 59.448 47.619 0.00 0.00 0.00 3.10
1025 1045 2.626840 GCACCACAATCTCTCTTCCTC 58.373 52.381 0.00 0.00 0.00 3.71
1027 1047 3.678529 GCACCACAATCTCTCTTCCTCTC 60.679 52.174 0.00 0.00 0.00 3.20
1028 1048 2.757868 ACCACAATCTCTCTTCCTCTCG 59.242 50.000 0.00 0.00 0.00 4.04
1029 1049 2.757868 CCACAATCTCTCTTCCTCTCGT 59.242 50.000 0.00 0.00 0.00 4.18
1030 1050 3.948473 CCACAATCTCTCTTCCTCTCGTA 59.052 47.826 0.00 0.00 0.00 3.43
1031 1051 4.201970 CCACAATCTCTCTTCCTCTCGTAC 60.202 50.000 0.00 0.00 0.00 3.67
1032 1052 3.623960 ACAATCTCTCTTCCTCTCGTACG 59.376 47.826 9.53 9.53 0.00 3.67
1033 1053 1.654317 TCTCTCTTCCTCTCGTACGC 58.346 55.000 11.24 0.00 0.00 4.42
1382 1418 2.343758 GTCGGCTTCACTCTGGCA 59.656 61.111 0.00 0.00 0.00 4.92
1409 1445 2.677875 CTGAAAGCCCAGGGTGCC 60.678 66.667 7.55 0.00 0.00 5.01
1479 1515 0.877213 CTGCATCATCGTCGGCATCA 60.877 55.000 0.00 0.00 35.45 3.07
1541 1577 3.207669 GGCGAGCTCAAGGCCATG 61.208 66.667 21.98 2.45 46.13 3.66
1563 1599 3.077556 AGATGGACGCCGCCTTCT 61.078 61.111 9.16 9.16 37.55 2.85
1608 1644 1.526225 GCCCCGATAAAGGACAGGC 60.526 63.158 0.00 0.00 0.00 4.85
1611 1647 1.227556 CCGATAAAGGACAGGCCCG 60.228 63.158 0.00 0.00 37.37 6.13
1714 1750 1.646189 GAGTCCGCCATCAAGAAGAC 58.354 55.000 0.00 0.00 0.00 3.01
1721 1757 1.134670 GCCATCAAGAAGACCTACGCT 60.135 52.381 0.00 0.00 0.00 5.07
1722 1758 2.544685 CCATCAAGAAGACCTACGCTG 58.455 52.381 0.00 0.00 0.00 5.18
1723 1759 2.544685 CATCAAGAAGACCTACGCTGG 58.455 52.381 0.00 0.00 0.00 4.85
1728 1764 2.532843 AGAAGACCTACGCTGGGTTTA 58.467 47.619 1.71 0.00 37.17 2.01
1770 1806 2.669569 GCACGCTCTTTGAGGCCA 60.670 61.111 5.01 0.00 0.00 5.36
1771 1807 2.970974 GCACGCTCTTTGAGGCCAC 61.971 63.158 5.01 0.00 0.00 5.01
1805 1850 4.101448 GTCTCCATGGCCGCCACT 62.101 66.667 16.16 0.98 35.80 4.00
1873 1929 2.554462 TCTGAGCTCACCGCATATACTC 59.446 50.000 13.74 0.00 42.61 2.59
1880 1936 2.291465 TCACCGCATATACTCCACGTAC 59.709 50.000 0.00 0.00 0.00 3.67
1996 2172 3.856521 CGATCGATGACCTGATAAGCATC 59.143 47.826 10.26 0.00 35.10 3.91
2053 2229 8.905702 CGTATATTAAATTCTTTGCCATTCAGC 58.094 33.333 0.00 0.00 0.00 4.26
2067 2243 2.561478 TTCAGCTTTCACCAGGTACC 57.439 50.000 2.73 2.73 0.00 3.34
2099 2275 3.657015 TTGTAACCAACCATGCATGTG 57.343 42.857 24.58 16.78 0.00 3.21
2232 2408 4.464069 AAACAAGCAGCAGTTGGTTTTA 57.536 36.364 0.00 0.00 44.75 1.52
2394 2570 6.951198 ACCTCATATCATAAGTACTCCCTCTG 59.049 42.308 0.00 0.00 0.00 3.35
2419 2595 9.793259 TGTTCACTTTTATAAGACCTTGAAGAT 57.207 29.630 0.00 0.00 35.30 2.40
2698 2876 4.559153 CAGCGGAAAATTTTCATCCACTT 58.441 39.130 27.53 7.20 38.92 3.16
2784 2964 4.220693 TGGCATGATATCTTATTCCCGG 57.779 45.455 3.98 0.00 0.00 5.73
2830 3010 1.115467 ATCCCGCGAATCAGAGAAGT 58.885 50.000 8.23 0.00 0.00 3.01
2997 3177 5.066505 GCCACATATTAAAGAGGAGGTGTTG 59.933 44.000 0.00 0.00 0.00 3.33
3029 3209 8.327941 TCTTAGCTTGATATCATATGCAAACC 57.672 34.615 20.41 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.572151 CGCGATCACGAAAATTTAAAACTTTAT 58.428 29.630 0.00 0.00 42.66 1.40
136 137 2.202797 GAGCGCTGGAATGCTCGA 60.203 61.111 18.48 0.00 47.00 4.04
142 143 1.745489 GGAAACCGAGCGCTGGAAT 60.745 57.895 26.07 16.32 0.00 3.01
162 167 0.321298 TGAGTTACCTGCTTTCCGGC 60.321 55.000 0.00 0.00 0.00 6.13
252 257 5.891551 ACCAAAACTGATTTTAGGTGTGTCT 59.108 36.000 0.00 0.00 37.59 3.41
256 261 4.202212 GCCACCAAAACTGATTTTAGGTGT 60.202 41.667 20.32 3.64 44.73 4.16
395 402 2.119801 ATCTCGAACATTGCTTGGCT 57.880 45.000 0.00 0.00 0.00 4.75
407 414 5.205821 TCAGGGTTAGGTATCAATCTCGAA 58.794 41.667 0.00 0.00 0.00 3.71
416 423 5.297029 GCAGAACAAATCAGGGTTAGGTATC 59.703 44.000 0.00 0.00 0.00 2.24
461 468 6.015010 GTGGCAGATCATAGTCAAGGTAGTAT 60.015 42.308 0.00 0.00 0.00 2.12
471 478 5.233988 GGTAGATTGTGGCAGATCATAGTC 58.766 45.833 11.91 0.00 0.00 2.59
552 559 2.609737 CCTCGGAATATACCCACGCTTC 60.610 54.545 0.00 0.00 0.00 3.86
561 568 5.337330 CCCTGTACCAATCCTCGGAATATAC 60.337 48.000 0.00 0.00 0.00 1.47
568 575 1.696097 CCCCCTGTACCAATCCTCGG 61.696 65.000 0.00 0.00 0.00 4.63
569 576 0.689745 TCCCCCTGTACCAATCCTCG 60.690 60.000 0.00 0.00 0.00 4.63
833 847 5.722263 TCTTCATGCCACAAACCAATAATG 58.278 37.500 0.00 0.00 0.00 1.90
887 902 1.423921 CCTCCTCTCCTCTACTCTCCC 59.576 61.905 0.00 0.00 0.00 4.30
894 914 2.788807 AGCAATCTCCTCCTCTCCTCTA 59.211 50.000 0.00 0.00 0.00 2.43
953 973 0.452987 TATATACATCGACCCGCCGC 59.547 55.000 0.00 0.00 0.00 6.53
954 974 3.811497 TCTATATATACATCGACCCGCCG 59.189 47.826 0.00 0.00 0.00 6.46
955 975 4.320348 GCTCTATATATACATCGACCCGCC 60.320 50.000 0.00 0.00 0.00 6.13
1020 1040 1.736126 CACACTAGCGTACGAGAGGAA 59.264 52.381 21.65 0.00 0.00 3.36
1025 1045 1.385743 GTTTGCACACTAGCGTACGAG 59.614 52.381 21.65 11.14 37.31 4.18
1027 1047 0.437295 GGTTTGCACACTAGCGTACG 59.563 55.000 11.84 11.84 37.31 3.67
1028 1048 1.504359 TGGTTTGCACACTAGCGTAC 58.496 50.000 2.52 0.00 37.31 3.67
1029 1049 1.868498 GTTGGTTTGCACACTAGCGTA 59.132 47.619 2.52 0.00 37.31 4.42
1030 1050 0.661020 GTTGGTTTGCACACTAGCGT 59.339 50.000 2.52 0.00 37.31 5.07
1031 1051 0.040425 GGTTGGTTTGCACACTAGCG 60.040 55.000 2.52 0.00 37.31 4.26
1032 1052 1.028905 TGGTTGGTTTGCACACTAGC 58.971 50.000 2.52 0.00 0.00 3.42
1033 1053 2.540769 CGTTGGTTGGTTTGCACACTAG 60.541 50.000 2.52 0.00 0.00 2.57
1257 1293 3.134458 CGAATATCTTGCCCTTGTCCTC 58.866 50.000 0.00 0.00 0.00 3.71
1258 1294 2.505819 ACGAATATCTTGCCCTTGTCCT 59.494 45.455 0.00 0.00 0.00 3.85
1389 1425 2.116125 ACCCTGGGCTTTCAGTGC 59.884 61.111 14.08 0.00 33.14 4.40
1393 1429 3.506743 TGGCACCCTGGGCTTTCA 61.507 61.111 14.08 3.52 0.00 2.69
1409 1445 2.375345 ATACTTGGCCTCCGGGGTG 61.375 63.158 3.32 0.00 37.43 4.61
1479 1515 4.778143 GCCGGCGTGGACCTTCAT 62.778 66.667 12.58 0.00 42.00 2.57
1704 1740 1.482593 CCCAGCGTAGGTCTTCTTGAT 59.517 52.381 0.00 0.00 33.74 2.57
1722 1758 0.182061 GGACTCCCGGGAATAAACCC 59.818 60.000 26.68 8.33 45.92 4.11
1723 1759 0.182061 GGGACTCCCGGGAATAAACC 59.818 60.000 26.68 20.86 32.13 3.27
1761 1797 2.436109 GCTCAGGGTGGCCTCAAA 59.564 61.111 3.32 0.00 0.00 2.69
1770 1806 2.982130 GATGGTGTCGCTCAGGGT 59.018 61.111 0.00 0.00 0.00 4.34
1771 1807 2.202797 CGATGGTGTCGCTCAGGG 60.203 66.667 0.00 0.00 44.33 4.45
1873 1929 2.993220 ACGCATATGCATATGTACGTGG 59.007 45.455 32.88 22.99 41.63 4.94
1880 1936 3.428534 ACACACGTACGCATATGCATATG 59.571 43.478 33.25 33.25 42.30 1.78
1947 2003 5.447144 GGTGCATGAAACAAAAACCAAGAAC 60.447 40.000 0.00 0.00 0.00 3.01
2036 2212 4.992951 GTGAAAGCTGAATGGCAAAGAATT 59.007 37.500 0.00 0.00 34.17 2.17
2043 2219 1.250328 CTGGTGAAAGCTGAATGGCA 58.750 50.000 0.00 0.00 35.07 4.92
2053 2229 1.071071 TGTTCCGGTACCTGGTGAAAG 59.929 52.381 18.40 0.00 0.00 2.62
2067 2243 5.008811 TGGTTGGTTACAATTTAGTGTTCCG 59.991 40.000 0.00 0.00 39.13 4.30
2301 2477 2.729882 ACGCAATCTTCGTTGACACTAC 59.270 45.455 0.00 0.00 36.72 2.73
2429 2605 6.993902 ACTCAAAATGGATTGTTTTGCAGATT 59.006 30.769 6.49 0.00 43.04 2.40
2581 2758 4.082190 GGAAGAAAACAAGGGTTATGGCTC 60.082 45.833 0.00 0.00 35.82 4.70
2698 2876 2.649312 AGGAATCTTCACATGGGGTTGA 59.351 45.455 0.00 0.00 0.00 3.18
3005 3185 7.175467 TGGGTTTGCATATGATATCAAGCTAAG 59.825 37.037 21.29 6.31 0.00 2.18


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

AutoCloner maintained by Alex Coulton.