Multiple sequence alignment - TraesCS2B01G225500

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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 TraesCS2B01G225500 chr2B 100.000 2450 0 0 1 2450 215847187 215849636 0.000000e+00 4525.0
1 TraesCS2B01G225500 chr2B 94.797 2095 89 13 1 2078 430232444 430230353 0.000000e+00 3247.0
2 TraesCS2B01G225500 chr2B 89.102 1147 94 17 1328 2450 465663749 465662610 0.000000e+00 1397.0
3 TraesCS2B01G225500 chr2B 88.542 384 30 2 2081 2450 430229851 430229468 1.030000e-123 453.0
4 TraesCS2B01G225500 chr7D 88.188 2489 227 40 1 2450 131689412 131691872 0.000000e+00 2905.0
5 TraesCS2B01G225500 chr4B 87.343 2473 248 48 1 2442 551060055 551062493 0.000000e+00 2772.0
6 TraesCS2B01G225500 chr4B 88.908 595 51 13 1549 2136 9634866 9635452 0.000000e+00 719.0
7 TraesCS2B01G225500 chr4B 92.063 63 5 0 2012 2074 9635274 9635212 3.360000e-14 89.8
8 TraesCS2B01G225500 chr4B 100.000 28 0 0 2012 2039 9635855 9635882 4.000000e-03 52.8
9 TraesCS2B01G225500 chr4D 86.872 2506 250 46 1 2450 470196620 470194138 0.000000e+00 2732.0
10 TraesCS2B01G225500 chrUn 89.698 2155 186 24 1 2136 10399191 10401328 0.000000e+00 2717.0
11 TraesCS2B01G225500 chr1D 91.544 1963 145 11 1 1958 446419326 446421272 0.000000e+00 2686.0
12 TraesCS2B01G225500 chr2D 89.383 2157 187 30 1 2135 619853649 619855785 0.000000e+00 2676.0
13 TraesCS2B01G225500 chr3D 91.165 1992 143 16 1 1979 310406112 310408083 0.000000e+00 2673.0
14 TraesCS2B01G225500 chr3D 87.302 63 8 0 2012 2074 310408466 310408528 3.380000e-09 73.1
15 TraesCS2B01G225500 chr6D 91.632 1948 129 22 1 1929 377212223 377214155 0.000000e+00 2663.0
16 TraesCS2B01G225500 chr5D 93.045 1783 114 7 1 1777 348341261 348343039 0.000000e+00 2597.0
17 TraesCS2B01G225500 chr5D 86.154 65 7 2 2012 2075 445781436 445781373 4.370000e-08 69.4
18 TraesCS2B01G225500 chr5D 85.938 64 7 2 2012 2074 445781651 445781713 1.570000e-07 67.6
19 TraesCS2B01G225500 chr6B 89.726 2005 147 25 487 2450 605817299 605819285 0.000000e+00 2507.0
20 TraesCS2B01G225500 chr6B 85.687 524 44 13 1930 2450 157835380 157835875 7.760000e-145 523.0
21 TraesCS2B01G225500 chr3B 90.702 1796 116 21 690 2450 809559034 809557255 0.000000e+00 2344.0
22 TraesCS2B01G225500 chr3B 88.298 376 28 4 2090 2450 732876148 732875774 1.040000e-118 436.0
23 TraesCS2B01G225500 chr1B 84.151 530 61 14 1939 2450 504245703 504245179 2.190000e-135 492.0
24 TraesCS2B01G225500 chr1B 89.677 310 27 5 2144 2450 540287906 540287599 8.210000e-105 390.0
25 TraesCS2B01G225500 chr5B 90.625 64 4 2 2012 2074 98047799 98047737 1.560000e-12 84.2


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 TraesCS2B01G225500 chr2B 215847187 215849636 2449 False 4525.00 4525 100.0000 1 2450 1 chr2B.!!$F1 2449
1 TraesCS2B01G225500 chr2B 430229468 430232444 2976 True 1850.00 3247 91.6695 1 2450 2 chr2B.!!$R2 2449
2 TraesCS2B01G225500 chr2B 465662610 465663749 1139 True 1397.00 1397 89.1020 1328 2450 1 chr2B.!!$R1 1122
3 TraesCS2B01G225500 chr7D 131689412 131691872 2460 False 2905.00 2905 88.1880 1 2450 1 chr7D.!!$F1 2449
4 TraesCS2B01G225500 chr4B 551060055 551062493 2438 False 2772.00 2772 87.3430 1 2442 1 chr4B.!!$F1 2441
5 TraesCS2B01G225500 chr4B 9634866 9635882 1016 False 385.90 719 94.4540 1549 2136 2 chr4B.!!$F2 587
6 TraesCS2B01G225500 chr4D 470194138 470196620 2482 True 2732.00 2732 86.8720 1 2450 1 chr4D.!!$R1 2449
7 TraesCS2B01G225500 chrUn 10399191 10401328 2137 False 2717.00 2717 89.6980 1 2136 1 chrUn.!!$F1 2135
8 TraesCS2B01G225500 chr1D 446419326 446421272 1946 False 2686.00 2686 91.5440 1 1958 1 chr1D.!!$F1 1957
9 TraesCS2B01G225500 chr2D 619853649 619855785 2136 False 2676.00 2676 89.3830 1 2135 1 chr2D.!!$F1 2134
10 TraesCS2B01G225500 chr3D 310406112 310408528 2416 False 1373.05 2673 89.2335 1 2074 2 chr3D.!!$F1 2073
11 TraesCS2B01G225500 chr6D 377212223 377214155 1932 False 2663.00 2663 91.6320 1 1929 1 chr6D.!!$F1 1928
12 TraesCS2B01G225500 chr5D 348341261 348343039 1778 False 2597.00 2597 93.0450 1 1777 1 chr5D.!!$F1 1776
13 TraesCS2B01G225500 chr6B 605817299 605819285 1986 False 2507.00 2507 89.7260 487 2450 1 chr6B.!!$F2 1963
14 TraesCS2B01G225500 chr3B 809557255 809559034 1779 True 2344.00 2344 90.7020 690 2450 1 chr3B.!!$R2 1760
15 TraesCS2B01G225500 chr1B 504245179 504245703 524 True 492.00 492 84.1510 1939 2450 1 chr1B.!!$R1 511

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
439 440 1.064906 CCAGACATTGTGCCAGATCCT 60.065 52.381 0.0 0.0 0.0 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2790 0.40404 CTTACCACCAAGGCCCTTCA 59.596 55.0 0.0 0.0 43.14 3.02 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
158 159 1.116308 TCAAATCGATGAGCCGGGTA 58.884 50.000 5.91 0.00 0.00 3.69
250 251 1.070134 TGTGAGAGGCCACACAAGTAC 59.930 52.381 21.84 4.06 42.72 2.73
398 399 3.967467 ATCCTTTCCTTGATGCCTCAT 57.033 42.857 0.00 0.00 0.00 2.90
439 440 1.064906 CCAGACATTGTGCCAGATCCT 60.065 52.381 0.00 0.00 0.00 3.24
593 594 2.884012 TGTGGAGAATGCAACGAAACAT 59.116 40.909 0.00 0.00 39.09 2.71
598 599 4.151258 AGAATGCAACGAAACATGACAG 57.849 40.909 0.00 0.00 0.00 3.51
615 619 2.924290 GACAGAACGTTAGGAGATGCAC 59.076 50.000 0.00 0.00 0.00 4.57
619 623 2.279582 ACGTTAGGAGATGCACGAAG 57.720 50.000 0.00 0.00 36.48 3.79
620 624 1.816835 ACGTTAGGAGATGCACGAAGA 59.183 47.619 0.00 0.00 36.48 2.87
621 625 2.230508 ACGTTAGGAGATGCACGAAGAA 59.769 45.455 0.00 0.00 36.48 2.52
630 634 5.091261 AGATGCACGAAGAAACCTAGAAT 57.909 39.130 0.00 0.00 0.00 2.40
638 642 6.147821 CACGAAGAAACCTAGAATCAACATGT 59.852 38.462 0.00 0.00 0.00 3.21
670 674 1.340795 ACACGTGTAGGGAGGACTAGG 60.341 57.143 21.98 0.00 0.00 3.02
699 703 4.096003 CCGTGGCCGTGGAGGAAT 62.096 66.667 7.28 0.00 45.00 3.01
724 728 3.023116 CTTGGAGGGGGCCATGGA 61.023 66.667 18.40 0.00 37.86 3.41
847 853 2.306219 GTTGATAGGGGAAGGCCTATCC 59.694 54.545 20.01 20.01 42.26 2.59
949 985 7.596494 CCTCTTTACATGTCAATGTGTTCATT 58.404 34.615 0.00 0.00 46.66 2.57
982 1019 9.297037 ACTTAACATCTTTAATTGTTGTAGGCT 57.703 29.630 0.00 0.00 36.75 4.58
1146 1183 2.796500 GGTGTCCACCGACCAAAAA 58.204 52.632 0.00 0.00 42.29 1.94
1211 1248 1.212616 GCTTATGATCGTGCGCTTCT 58.787 50.000 9.73 0.00 0.00 2.85
1319 1356 1.115467 CAGTCACCGCCTCCTCTATT 58.885 55.000 0.00 0.00 0.00 1.73
1417 1455 0.949105 GCGGCTGTTCGAAGAAAGGA 60.949 55.000 0.00 0.00 45.90 3.36
1447 1485 0.038159 CTTGGAGGAAGAGCGTCGTT 60.038 55.000 0.00 0.00 32.82 3.85
1471 1509 1.519719 GAGAGGATGGAGCGCAAGT 59.480 57.895 11.47 0.00 41.68 3.16
1536 1574 1.834263 GAGGAGAGGGCAAGAAAGCTA 59.166 52.381 0.00 0.00 34.17 3.32
1578 1616 1.137872 GAGAAGGATGAGGCACGTGAT 59.862 52.381 22.23 6.57 0.00 3.06
1997 2064 1.874739 CGGTAAAACCAGAGGCGTTGA 60.875 52.381 0.00 0.00 38.47 3.18
2002 2069 0.180406 AACCAGAGGCGTTGACAGTT 59.820 50.000 0.00 0.00 0.00 3.16
2040 2230 3.851128 GCCTCTGGCGGTAGGGTC 61.851 72.222 12.00 0.00 39.62 4.46
2044 2234 4.162690 CTGGCGGTAGGGTCCTGC 62.163 72.222 0.00 0.00 0.00 4.85
2046 2236 3.712907 GGCGGTAGGGTCCTGCAA 61.713 66.667 7.38 0.00 0.00 4.08
2074 2264 1.152118 AGTGCCTGTGGTGGTAGGA 60.152 57.895 0.00 0.00 36.11 2.94
2100 2790 5.934043 GGTAAACCTACTGTGACGGTAAAAT 59.066 40.000 5.69 0.00 0.00 1.82
2113 2803 2.536066 GGTAAAATGAAGGGCCTTGGT 58.464 47.619 26.47 9.01 0.00 3.67
2122 2812 2.359011 GGCCTTGGTGGTAAGGGG 59.641 66.667 0.00 0.00 45.91 4.79
2165 2872 0.323629 CTTACCGCCAAGGGTCTTCA 59.676 55.000 0.00 0.00 46.96 3.02
2180 2887 4.062991 GGTCTTCATTTTACCGTCACAGT 58.937 43.478 0.00 0.00 0.00 3.55
2224 3231 1.686115 GGCACTAACGGTAGGGTCCTA 60.686 57.143 12.22 0.00 32.79 2.94
2300 3322 1.838077 CCTACCCCCTTCTGTCGAATT 59.162 52.381 0.00 0.00 0.00 2.17
2381 3404 8.311650 ACATAACTCAACTCAACATAGTTCAC 57.688 34.615 0.00 0.00 37.61 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 159 0.974383 CTACCGTCCCTTGTTGTCCT 59.026 55.000 0.00 0.00 0.00 3.85
250 251 1.952102 AATGCGAGCAAGGCCAATGG 61.952 55.000 5.01 0.00 0.00 3.16
398 399 1.399714 CCGTGATACTCAGGCCACTA 58.600 55.000 5.01 0.00 31.43 2.74
593 594 2.560981 TGCATCTCCTAACGTTCTGTCA 59.439 45.455 2.82 0.00 0.00 3.58
598 599 2.273370 TCGTGCATCTCCTAACGTTC 57.727 50.000 2.82 0.00 37.32 3.95
615 619 6.537566 CACATGTTGATTCTAGGTTTCTTCG 58.462 40.000 0.00 0.00 0.00 3.79
619 623 5.182001 AGTGCACATGTTGATTCTAGGTTTC 59.818 40.000 21.04 0.00 0.00 2.78
620 624 5.072741 AGTGCACATGTTGATTCTAGGTTT 58.927 37.500 21.04 0.00 0.00 3.27
621 625 4.655963 AGTGCACATGTTGATTCTAGGTT 58.344 39.130 21.04 0.00 0.00 3.50
630 634 4.035091 GTGTTTGACTAGTGCACATGTTGA 59.965 41.667 21.04 6.95 0.00 3.18
638 642 2.303163 ACACGTGTTTGACTAGTGCA 57.697 45.000 17.22 0.00 36.38 4.57
699 703 1.306997 CCCCCTCCAAGGCTAGTCA 60.307 63.158 0.00 0.00 32.73 3.41
720 724 2.277008 AGTCCTTCCTCCATGTCCAT 57.723 50.000 0.00 0.00 0.00 3.41
724 728 1.008938 AGGCTAGTCCTTCCTCCATGT 59.991 52.381 0.00 0.00 44.75 3.21
847 853 0.948623 TCCGGATTGAGCAACACGTG 60.949 55.000 15.48 15.48 0.00 4.49
982 1019 0.331278 ATGGAACCGGATGAAGCCAA 59.669 50.000 9.46 0.00 0.00 4.52
1146 1183 2.290323 CCTTCCTTCCGTCCATGACTTT 60.290 50.000 0.00 0.00 0.00 2.66
1211 1248 2.093869 GGTTGGTCATAGGCGTGAGTTA 60.094 50.000 0.00 0.00 0.00 2.24
1319 1356 5.650703 TGATCTATCCACGTGAAGTACTTGA 59.349 40.000 19.30 0.39 30.55 3.02
1417 1455 1.573108 TCCTCCAAGCCTCTTCGAAT 58.427 50.000 0.00 0.00 0.00 3.34
1447 1485 1.988293 CGCTCCATCCTCTCCTTCTA 58.012 55.000 0.00 0.00 0.00 2.10
1471 1509 1.453379 CCCTCTCCTCCTCGCGTTA 60.453 63.158 5.77 0.00 0.00 3.18
2040 2230 2.436646 CTGGCGGTAGGTTGCAGG 60.437 66.667 0.00 0.00 0.00 4.85
2044 2234 2.746277 GGCACTGGCGGTAGGTTG 60.746 66.667 0.00 0.00 42.47 3.77
2085 2775 3.408634 CCCTTCATTTTACCGTCACAGT 58.591 45.455 0.00 0.00 0.00 3.55
2100 2790 0.404040 CTTACCACCAAGGCCCTTCA 59.596 55.000 0.00 0.00 43.14 3.02
2122 2812 3.468063 CCTATGGCGGTAGGGTCC 58.532 66.667 7.65 0.00 38.05 4.46
2159 2866 5.347907 CCTACTGTGACGGTAAAATGAAGAC 59.652 44.000 5.69 0.00 0.00 3.01
2160 2867 5.011329 ACCTACTGTGACGGTAAAATGAAGA 59.989 40.000 5.69 0.00 0.00 2.87
2165 2872 5.173664 GCTAACCTACTGTGACGGTAAAAT 58.826 41.667 5.69 0.00 0.00 1.82
2211 3218 4.772678 GGTGTAGGACCCTACCGT 57.227 61.111 20.17 0.00 46.01 4.83
2224 3231 2.683933 CCTCTGGCGGTAGGGTGT 60.684 66.667 0.00 0.00 0.00 4.16
2381 3404 8.212317 TGAACATGTGTTATTCATGGATGTAG 57.788 34.615 0.00 0.00 44.57 2.74


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

AutoCloner maintained by Alex Coulton.