Multiple sequence alignment - TraesCS4D01G052600

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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 TraesCS4D01G052600 chr4D 100.000 3340 0 0 1 3340 28880280 28883619 0.000000e+00 6168.0
1 TraesCS4D01G052600 chr4D 83.333 198 33 0 1512 1709 80836572 80836769 2.050000e-42 183.0
2 TraesCS4D01G052600 chr4A 92.359 3311 127 50 1 3267 574842991 574839763 0.000000e+00 4597.0
3 TraesCS4D01G052600 chr4B 92.209 2426 89 53 1 2390 41196222 41198583 0.000000e+00 3341.0
4 TraesCS4D01G052600 chr4B 90.098 919 68 10 2426 3333 41199269 41200175 0.000000e+00 1171.0
5 TraesCS4D01G052600 chr3D 97.794 136 3 0 2099 2234 569929255 569929390 5.570000e-58 235.0
6 TraesCS4D01G052600 chr3D 84.834 211 30 2 1511 1720 180470744 180470535 9.390000e-51 211.0
7 TraesCS4D01G052600 chr3D 82.741 197 34 0 1511 1707 546198932 546198736 3.420000e-40 176.0
8 TraesCS4D01G052600 chr3B 85.308 211 29 2 1511 1720 258721284 258721075 2.020000e-52 217.0
9 TraesCS4D01G052600 chr3B 83.249 197 33 0 1511 1707 722590912 722590716 7.360000e-42 182.0
10 TraesCS4D01G052600 chr3A 85.308 211 29 2 1511 1720 225894569 225894360 2.020000e-52 217.0
11 TraesCS4D01G052600 chr6D 78.736 174 25 11 1522 1689 142138974 142138807 4.560000e-19 106.0
12 TraesCS4D01G052600 chr1D 93.878 49 2 1 417 465 413357406 413357453 4.620000e-09 73.1


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 TraesCS4D01G052600 chr4D 28880280 28883619 3339 False 6168 6168 100.0000 1 3340 1 chr4D.!!$F1 3339
1 TraesCS4D01G052600 chr4A 574839763 574842991 3228 True 4597 4597 92.3590 1 3267 1 chr4A.!!$R1 3266
2 TraesCS4D01G052600 chr4B 41196222 41200175 3953 False 2256 3341 91.1535 1 3333 2 chr4B.!!$F1 3332

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
643 653 0.035056 CTGGGGTTGGCCAGTTAGAG 60.035 60.0 5.11 0.0 36.17 2.43 F
1815 1872 0.314302 CGATAGCCCTAGGAACACCG 59.686 60.0 11.48 4.4 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 2398 0.392706 TACAGATGTAGCATGCCCCG 59.607 55.0 15.66 0.0 0.00 5.73 R
2686 3420 0.635009 ATAGTGGAAGGTCCGAGGGA 59.365 55.0 0.00 0.0 40.17 4.20 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
236 238 8.798859 ACTCTCAAATCAACTGTTGCTATAAT 57.201 30.769 15.52 0.96 0.00 1.28
263 266 4.341502 CCACCGGTTGCCGCAAAG 62.342 66.667 2.97 5.15 46.86 2.77
271 274 1.165270 GTTGCCGCAAAGGTCATAGT 58.835 50.000 7.54 0.00 43.70 2.12
272 275 2.352388 GTTGCCGCAAAGGTCATAGTA 58.648 47.619 7.54 0.00 43.70 1.82
394 397 4.277174 TCCGTATGTTGTTTGTTGAGCAAT 59.723 37.500 0.00 0.00 36.89 3.56
415 421 0.038159 GTAACTGGCGAGACACTGCT 60.038 55.000 1.44 0.00 0.00 4.24
417 423 3.117171 CTGGCGAGACACTGCTGC 61.117 66.667 0.00 0.00 0.00 5.25
418 424 3.871248 CTGGCGAGACACTGCTGCA 62.871 63.158 0.88 0.88 0.00 4.41
419 425 3.418068 GGCGAGACACTGCTGCAC 61.418 66.667 0.00 0.00 0.00 4.57
420 426 2.662857 GCGAGACACTGCTGCACA 60.663 61.111 0.00 0.00 0.00 4.57
421 427 2.031516 GCGAGACACTGCTGCACAT 61.032 57.895 0.00 0.00 0.00 3.21
422 428 0.737367 GCGAGACACTGCTGCACATA 60.737 55.000 0.00 0.00 0.00 2.29
618 628 4.097437 ACCGATCAACAATAACGAGAGCTA 59.903 41.667 0.00 0.00 0.00 3.32
619 629 4.677378 CCGATCAACAATAACGAGAGCTAG 59.323 45.833 0.00 0.00 0.00 3.42
620 630 4.147306 CGATCAACAATAACGAGAGCTAGC 59.853 45.833 6.62 6.62 0.00 3.42
621 631 4.450082 TCAACAATAACGAGAGCTAGCA 57.550 40.909 18.83 0.00 0.00 3.49
640 650 2.438795 GCTGGGGTTGGCCAGTTA 59.561 61.111 5.11 0.00 36.53 2.24
641 651 1.678970 GCTGGGGTTGGCCAGTTAG 60.679 63.158 5.11 2.84 36.53 2.34
642 652 2.074967 CTGGGGTTGGCCAGTTAGA 58.925 57.895 5.11 0.00 36.17 2.10
643 653 0.035056 CTGGGGTTGGCCAGTTAGAG 60.035 60.000 5.11 0.00 36.17 2.43
792 807 4.855340 TCTTCTCTTCCCTTCTCTCTCTC 58.145 47.826 0.00 0.00 0.00 3.20
855 876 8.462143 TCTGCGTCTGAAATTAGTTTAGTTAG 57.538 34.615 0.00 0.00 0.00 2.34
856 877 8.086522 TCTGCGTCTGAAATTAGTTTAGTTAGT 58.913 33.333 0.00 0.00 0.00 2.24
895 918 2.611292 CTGTTTATGTGCAGCTAGCCTC 59.389 50.000 12.13 3.80 44.83 4.70
942 969 4.703093 AGATAGCTAGCTAAAGGGATCGAC 59.297 45.833 27.47 9.29 31.73 4.20
974 1001 2.533129 GCGATTTGCTGCTATTCTTTGC 59.467 45.455 0.00 0.00 41.73 3.68
994 1021 2.477825 CTGCTTGGTTGATCGATCGAT 58.522 47.619 29.76 29.76 37.59 3.59
1357 1392 6.500684 TCACTTGTGGAGCAATTTTATCTC 57.499 37.500 0.64 0.00 36.36 2.75
1412 1447 6.950619 ACCTTTCTTGCTTCCTAATTCATCTT 59.049 34.615 0.00 0.00 0.00 2.40
1465 1501 2.093711 TGAAGCACATCGCCTAAGCTTA 60.094 45.455 5.94 5.94 44.73 3.09
1466 1502 2.691409 AGCACATCGCCTAAGCTTAA 57.309 45.000 7.74 0.00 44.04 1.85
1468 1504 3.545703 AGCACATCGCCTAAGCTTAATT 58.454 40.909 7.74 0.00 44.04 1.40
1469 1505 4.703897 AGCACATCGCCTAAGCTTAATTA 58.296 39.130 7.74 0.00 44.04 1.40
1472 1508 6.073003 AGCACATCGCCTAAGCTTAATTAATC 60.073 38.462 7.74 0.00 44.04 1.75
1495 1546 3.165071 ACCCATGGAAAATGACCTGTTC 58.835 45.455 15.22 0.00 0.00 3.18
1496 1547 3.181418 ACCCATGGAAAATGACCTGTTCT 60.181 43.478 15.22 0.00 0.00 3.01
1497 1548 3.445096 CCCATGGAAAATGACCTGTTCTC 59.555 47.826 15.22 0.00 0.00 2.87
1498 1549 4.338879 CCATGGAAAATGACCTGTTCTCT 58.661 43.478 5.56 0.00 0.00 3.10
1499 1550 4.157289 CCATGGAAAATGACCTGTTCTCTG 59.843 45.833 5.56 0.00 0.00 3.35
1500 1551 4.437682 TGGAAAATGACCTGTTCTCTGT 57.562 40.909 0.00 0.00 0.00 3.41
1501 1552 4.389374 TGGAAAATGACCTGTTCTCTGTC 58.611 43.478 0.00 0.00 0.00 3.51
1506 1557 2.666317 TGACCTGTTCTCTGTCTGTGA 58.334 47.619 0.00 0.00 0.00 3.58
1815 1872 0.314302 CGATAGCCCTAGGAACACCG 59.686 60.000 11.48 4.40 0.00 4.94
1819 1876 4.832608 CCCTAGGAACACCGCCGC 62.833 72.222 11.48 0.00 0.00 6.53
1842 1899 1.517475 GAGAAGCCGAGACTTCCGC 60.517 63.158 8.57 0.54 45.95 5.54
1963 2020 6.652900 TCATACACGAATGAAGGTGAAATGAA 59.347 34.615 0.00 0.00 37.26 2.57
2005 2063 5.393896 GCAGGGTTCTAGTATACAGACGTTT 60.394 44.000 5.50 0.00 0.00 3.60
2008 2066 6.662663 AGGGTTCTAGTATACAGACGTTTTCT 59.337 38.462 5.50 0.00 33.33 2.52
2012 2070 9.570488 GTTCTAGTATACAGACGTTTTCTCATT 57.430 33.333 5.50 0.00 28.96 2.57
2318 2397 2.747855 CTTTGTGAGGAGGCCGGC 60.748 66.667 21.18 21.18 0.00 6.13
2319 2398 4.344865 TTTGTGAGGAGGCCGGCC 62.345 66.667 39.29 39.29 0.00 6.13
2405 2484 9.773328 AAATGCAAACGTATATATATGACATGC 57.227 29.630 17.16 19.70 0.00 4.06
2410 2489 9.693157 CAAACGTATATATATGACATGCACATG 57.307 33.333 17.16 9.06 44.15 3.21
2467 3196 1.066573 CCGTCCATGCAGAGTTCTTCT 60.067 52.381 0.00 0.00 36.25 2.85
2600 3334 7.938140 TTTAGGGTTTTAATCAGTCTCATGG 57.062 36.000 0.00 0.00 0.00 3.66
2601 3335 4.860022 AGGGTTTTAATCAGTCTCATGGG 58.140 43.478 0.00 0.00 0.00 4.00
2602 3336 4.540099 AGGGTTTTAATCAGTCTCATGGGA 59.460 41.667 0.00 0.00 0.00 4.37
2603 3337 5.194537 AGGGTTTTAATCAGTCTCATGGGAT 59.805 40.000 0.00 0.00 0.00 3.85
2742 3476 3.460825 AGTCCCATGGTGTATTGTACCT 58.539 45.455 11.73 0.00 39.01 3.08
2812 3546 9.322773 CTCTCTGCTTTTCATATATCAGAAACA 57.677 33.333 2.87 0.05 33.82 2.83
2851 3585 2.043252 ACTACCAGGGACTAGAAGCAGT 59.957 50.000 0.00 0.00 36.02 4.40
2889 3623 1.962100 TGCACAATCATGGCAGAACAA 59.038 42.857 0.00 0.00 31.75 2.83
2982 3719 4.761975 ACAGACAGTTAAAACGACTCCAA 58.238 39.130 0.00 0.00 0.00 3.53
2996 3733 2.823747 GACTCCAACAACATAAACCCCC 59.176 50.000 0.00 0.00 0.00 5.40
3021 3758 0.322008 GCACCACAAGCTAGGCTCTT 60.322 55.000 0.00 0.00 38.25 2.85
3116 3854 5.057149 ACTTTCGCTAAACTTGACACTCAT 58.943 37.500 0.00 0.00 0.00 2.90
3134 3872 0.529992 ATGGAGCCTTTAGTACGCGC 60.530 55.000 5.73 0.00 0.00 6.86
3135 3873 1.881709 GGAGCCTTTAGTACGCGCC 60.882 63.158 5.73 0.00 35.29 6.53
3185 3924 9.069082 GTATGCTAGGGTCGTATCTATGATTAT 57.931 37.037 0.00 0.00 0.00 1.28
3242 3981 2.961062 ACGGTATAGGCGTTTATGACCT 59.039 45.455 0.00 0.00 37.61 3.85
3247 3986 1.286248 AGGCGTTTATGACCTTCCCT 58.714 50.000 0.00 0.00 0.00 4.20
3267 4006 4.446167 CCCTTCTATGCCATGTGGTAATGA 60.446 45.833 0.35 0.00 37.57 2.57
3271 4010 7.201938 CCTTCTATGCCATGTGGTAATGATTTT 60.202 37.037 0.35 0.00 37.57 1.82
3333 4073 5.957798 AGATTGGTTTCACTTGCATGTATG 58.042 37.500 4.73 0.00 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 50 4.513442 TGCAGGTTGGATCACTGTTATAC 58.487 43.478 0.00 0.00 34.79 1.47
49 51 4.384098 CCTGCAGGTTGGATCACTGTTATA 60.384 45.833 25.53 0.00 34.79 0.98
50 52 3.614092 CTGCAGGTTGGATCACTGTTAT 58.386 45.455 5.57 0.00 34.79 1.89
51 53 2.290260 CCTGCAGGTTGGATCACTGTTA 60.290 50.000 25.53 0.00 34.79 2.41
52 54 1.546323 CCTGCAGGTTGGATCACTGTT 60.546 52.381 25.53 0.00 34.79 3.16
53 55 0.037303 CCTGCAGGTTGGATCACTGT 59.963 55.000 25.53 0.00 34.79 3.55
54 56 1.310933 GCCTGCAGGTTGGATCACTG 61.311 60.000 32.81 4.20 37.57 3.66
236 238 1.813786 GCAACCGGTGGCTTGTATTAA 59.186 47.619 27.39 0.00 0.00 1.40
263 266 7.270047 TGCCAACAACTTACTATACTATGACC 58.730 38.462 0.00 0.00 0.00 4.02
271 274 7.398829 TGGAGAAATGCCAACAACTTACTATA 58.601 34.615 0.00 0.00 31.13 1.31
272 275 6.245408 TGGAGAAATGCCAACAACTTACTAT 58.755 36.000 0.00 0.00 31.13 2.12
292 295 1.728425 CATGTGTGACGTGTCATGGAG 59.272 52.381 5.91 0.00 42.18 3.86
394 397 1.872237 GCAGTGTCTCGCCAGTTACAA 60.872 52.381 0.00 0.00 0.00 2.41
415 421 6.035975 CACAAGATCAACGAACTATATGTGCA 59.964 38.462 0.00 0.00 0.00 4.57
417 423 6.756542 TCCACAAGATCAACGAACTATATGTG 59.243 38.462 0.00 0.00 35.45 3.21
418 424 6.757010 GTCCACAAGATCAACGAACTATATGT 59.243 38.462 0.00 0.00 0.00 2.29
419 425 6.201044 GGTCCACAAGATCAACGAACTATATG 59.799 42.308 0.00 0.00 0.00 1.78
420 426 6.098409 AGGTCCACAAGATCAACGAACTATAT 59.902 38.462 0.00 0.00 0.00 0.86
421 427 5.421056 AGGTCCACAAGATCAACGAACTATA 59.579 40.000 0.00 0.00 0.00 1.31
422 428 4.223032 AGGTCCACAAGATCAACGAACTAT 59.777 41.667 0.00 0.00 0.00 2.12
640 650 5.738909 CAGTTTCTCTCTCTCTCTCTCTCT 58.261 45.833 0.00 0.00 0.00 3.10
641 651 4.333926 GCAGTTTCTCTCTCTCTCTCTCTC 59.666 50.000 0.00 0.00 0.00 3.20
642 652 4.265073 GCAGTTTCTCTCTCTCTCTCTCT 58.735 47.826 0.00 0.00 0.00 3.10
643 653 3.378427 GGCAGTTTCTCTCTCTCTCTCTC 59.622 52.174 0.00 0.00 0.00 3.20
721 732 3.282885 CAAGAGAAAGATAAGGGGTGGC 58.717 50.000 0.00 0.00 0.00 5.01
792 807 4.252073 CCACTGGAGAGAGATGAACAAAG 58.748 47.826 0.00 0.00 0.00 2.77
932 955 3.292460 CTCTAACCTCTGTCGATCCCTT 58.708 50.000 0.00 0.00 0.00 3.95
966 993 3.366679 CGATCAACCAAGCAGCAAAGAAT 60.367 43.478 0.00 0.00 0.00 2.40
969 996 1.536766 TCGATCAACCAAGCAGCAAAG 59.463 47.619 0.00 0.00 0.00 2.77
974 1001 1.926561 TCGATCGATCAACCAAGCAG 58.073 50.000 24.40 5.61 0.00 4.24
994 1021 1.607801 CCTCTGGTGCACATCCTCGA 61.608 60.000 20.43 4.19 0.00 4.04
1144 1172 1.064505 CCACACATGATCGGTTGATGC 59.935 52.381 0.00 0.00 34.09 3.91
1412 1447 0.179111 ATAGCTAGCTTGTGCGCGAA 60.179 50.000 24.88 0.00 45.42 4.70
1465 1501 7.182568 AGGTCATTTTCCATGGGTTGATTAATT 59.817 33.333 13.02 0.00 0.00 1.40
1466 1502 6.673537 AGGTCATTTTCCATGGGTTGATTAAT 59.326 34.615 13.02 0.00 0.00 1.40
1468 1504 5.421693 CAGGTCATTTTCCATGGGTTGATTA 59.578 40.000 13.02 0.00 0.00 1.75
1469 1505 4.223477 CAGGTCATTTTCCATGGGTTGATT 59.777 41.667 13.02 1.15 0.00 2.57
1472 1508 2.899256 ACAGGTCATTTTCCATGGGTTG 59.101 45.455 13.02 4.93 0.00 3.77
1495 1546 3.969287 TCCCTGAAATCACAGACAGAG 57.031 47.619 0.00 0.00 39.94 3.35
1496 1547 3.903714 TCTTCCCTGAAATCACAGACAGA 59.096 43.478 0.00 0.00 39.94 3.41
1497 1548 4.252073 CTCTTCCCTGAAATCACAGACAG 58.748 47.826 0.00 0.00 39.94 3.51
1498 1549 3.557898 GCTCTTCCCTGAAATCACAGACA 60.558 47.826 0.00 0.00 39.94 3.41
1499 1550 3.006247 GCTCTTCCCTGAAATCACAGAC 58.994 50.000 0.00 0.00 39.94 3.51
1500 1551 2.909006 AGCTCTTCCCTGAAATCACAGA 59.091 45.455 0.00 0.00 39.94 3.41
1501 1552 3.008330 CAGCTCTTCCCTGAAATCACAG 58.992 50.000 0.00 0.00 37.61 3.66
1506 1557 1.340795 CCTGCAGCTCTTCCCTGAAAT 60.341 52.381 8.66 0.00 32.03 2.17
1842 1899 2.253758 CGGCCATGGTATTCGCCTG 61.254 63.158 14.67 0.00 39.34 4.85
1942 1999 5.473162 TCATTCATTTCACCTTCATTCGTGT 59.527 36.000 0.00 0.00 0.00 4.49
2005 2063 9.371136 CAGACATACAAGCTAAACTAATGAGAA 57.629 33.333 0.00 0.00 0.00 2.87
2008 2066 7.847096 TCCAGACATACAAGCTAAACTAATGA 58.153 34.615 0.00 0.00 0.00 2.57
2012 2070 7.847096 TCATTCCAGACATACAAGCTAAACTA 58.153 34.615 0.00 0.00 0.00 2.24
2318 2397 1.598962 CAGATGTAGCATGCCCCGG 60.599 63.158 15.66 0.00 0.00 5.73
2319 2398 0.392706 TACAGATGTAGCATGCCCCG 59.607 55.000 15.66 0.00 0.00 5.73
2320 2399 2.175878 CTACAGATGTAGCATGCCCC 57.824 55.000 15.66 5.58 41.15 5.80
2405 2484 7.907563 TGTGCGTACATCAATAAATTACATGTG 59.092 33.333 9.11 0.00 0.00 3.21
2410 2489 7.097047 GCATGTGTGCGTACATCAATAAATTAC 60.097 37.037 10.21 0.00 42.28 1.89
2467 3196 3.300388 AGCCTCGTTCTCCATATCTCAA 58.700 45.455 0.00 0.00 0.00 3.02
2686 3420 0.635009 ATAGTGGAAGGTCCGAGGGA 59.365 55.000 0.00 0.00 40.17 4.20
2742 3476 6.692849 ATAATAATCTCTGATGGACTGGCA 57.307 37.500 0.00 0.00 0.00 4.92
2812 3546 7.148137 CCTGGTAGTTGTAACAAAAGACAAGTT 60.148 37.037 0.83 0.00 39.39 2.66
2866 3600 2.131776 TCTGCCATGATTGTGCATCA 57.868 45.000 0.00 0.00 46.41 3.07
2878 3612 2.836981 AGTCTAGCTCTTGTTCTGCCAT 59.163 45.455 0.00 0.00 0.00 4.40
2905 3642 3.057033 GCTGTTTTGTGATCTTGGCAGAT 60.057 43.478 0.00 0.00 43.03 2.90
2940 3677 3.633525 TGTAGGTTATCGACGGTTATGCT 59.366 43.478 0.00 0.00 0.00 3.79
2948 3685 4.352600 AACTGTCTGTAGGTTATCGACG 57.647 45.455 0.00 0.00 0.00 5.12
2996 3733 2.859273 CTAGCTTGTGGTGCTCCCGG 62.859 65.000 1.59 0.00 41.46 5.73
2997 3734 1.448540 CTAGCTTGTGGTGCTCCCG 60.449 63.158 1.59 0.00 41.46 5.14
3021 3758 4.248908 TGGACTGCCATTCCCTGA 57.751 55.556 0.00 0.00 39.92 3.86
3116 3854 1.153706 GCGCGTACTAAAGGCTCCA 60.154 57.895 8.43 0.00 36.82 3.86
3134 3872 2.027745 AGCACACACATCCTTCTAGTGG 60.028 50.000 0.00 0.00 37.58 4.00
3135 3873 3.325293 AGCACACACATCCTTCTAGTG 57.675 47.619 0.00 0.00 39.12 2.74
3213 3952 5.376854 AAACGCCTATACCGTAATATCGT 57.623 39.130 0.00 0.00 38.06 3.73
3221 3960 2.961062 AGGTCATAAACGCCTATACCGT 59.039 45.455 0.00 0.00 41.24 4.83
3242 3981 1.922447 ACCACATGGCATAGAAGGGAA 59.078 47.619 0.00 0.00 39.32 3.97
3247 3986 7.658525 AAAATCATTACCACATGGCATAGAA 57.341 32.000 0.00 0.00 39.32 2.10
3302 4041 1.997606 GTGAAACCAATCTACGGACGG 59.002 52.381 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.