Multiple sequence alignment - TraesCS2B01G326000

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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 TraesCS2B01G326000 chr2B 100.000 2465 0 0 1 2465 465677004 465679468 0.000000e+00 4553.0
1 TraesCS2B01G326000 chr2B 95.197 1520 68 5 948 2465 44266196 44267712 0.000000e+00 2398.0
2 TraesCS2B01G326000 chr2B 97.569 946 21 2 1 945 384548123 384549067 0.000000e+00 1618.0
3 TraesCS2B01G326000 chr2B 97.371 951 20 5 1 949 456128604 456129551 0.000000e+00 1613.0
4 TraesCS2B01G326000 chr4B 87.525 1523 153 16 946 2465 11589845 11588357 0.000000e+00 1725.0
5 TraesCS2B01G326000 chr4B 97.360 947 23 2 1 945 277289240 277288294 0.000000e+00 1609.0
6 TraesCS2B01G326000 chr1B 97.886 946 19 1 1 945 53000285 52999340 0.000000e+00 1635.0
7 TraesCS2B01G326000 chr1B 97.466 947 20 4 1 945 487891958 487892902 0.000000e+00 1613.0
8 TraesCS2B01G326000 chr1B 90.476 63 6 0 2403 2465 92340903 92340965 1.570000e-12 84.2
9 TraesCS2B01G326000 chr6B 97.463 946 21 3 1 945 507639413 507640356 0.000000e+00 1611.0
10 TraesCS2B01G326000 chr6B 84.350 1016 153 5 946 1957 539720899 539719886 0.000000e+00 990.0
11 TraesCS2B01G326000 chr6B 78.445 566 113 8 1151 1711 65020990 65020429 6.480000e-96 361.0
12 TraesCS2B01G326000 chr7B 96.979 960 25 4 1 959 90816733 90815777 0.000000e+00 1609.0
13 TraesCS2B01G326000 chr7B 97.170 954 24 3 1 953 92326865 92325914 0.000000e+00 1609.0
14 TraesCS2B01G326000 chr7B 92.738 840 55 6 946 1781 586062793 586061956 0.000000e+00 1208.0
15 TraesCS2B01G326000 chr7B 89.420 690 71 2 1777 2465 586060390 586059702 0.000000e+00 869.0
16 TraesCS2B01G326000 chr5B 97.458 944 22 2 3 945 331585315 331586257 0.000000e+00 1609.0
17 TraesCS2B01G326000 chr5B 78.495 186 38 2 1147 1331 19556030 19556214 1.200000e-23 121.0
18 TraesCS2B01G326000 chr4D 84.286 70 8 3 2397 2465 506393355 506393288 5.690000e-07 65.8


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 TraesCS2B01G326000 chr2B 465677004 465679468 2464 False 4553.0 4553 100.000 1 2465 1 chr2B.!!$F4 2464
1 TraesCS2B01G326000 chr2B 44266196 44267712 1516 False 2398.0 2398 95.197 948 2465 1 chr2B.!!$F1 1517
2 TraesCS2B01G326000 chr2B 384548123 384549067 944 False 1618.0 1618 97.569 1 945 1 chr2B.!!$F2 944
3 TraesCS2B01G326000 chr2B 456128604 456129551 947 False 1613.0 1613 97.371 1 949 1 chr2B.!!$F3 948
4 TraesCS2B01G326000 chr4B 11588357 11589845 1488 True 1725.0 1725 87.525 946 2465 1 chr4B.!!$R1 1519
5 TraesCS2B01G326000 chr4B 277288294 277289240 946 True 1609.0 1609 97.360 1 945 1 chr4B.!!$R2 944
6 TraesCS2B01G326000 chr1B 52999340 53000285 945 True 1635.0 1635 97.886 1 945 1 chr1B.!!$R1 944
7 TraesCS2B01G326000 chr1B 487891958 487892902 944 False 1613.0 1613 97.466 1 945 1 chr1B.!!$F2 944
8 TraesCS2B01G326000 chr6B 507639413 507640356 943 False 1611.0 1611 97.463 1 945 1 chr6B.!!$F1 944
9 TraesCS2B01G326000 chr6B 539719886 539720899 1013 True 990.0 990 84.350 946 1957 1 chr6B.!!$R2 1011
10 TraesCS2B01G326000 chr6B 65020429 65020990 561 True 361.0 361 78.445 1151 1711 1 chr6B.!!$R1 560
11 TraesCS2B01G326000 chr7B 90815777 90816733 956 True 1609.0 1609 96.979 1 959 1 chr7B.!!$R1 958
12 TraesCS2B01G326000 chr7B 92325914 92326865 951 True 1609.0 1609 97.170 1 953 1 chr7B.!!$R2 952
13 TraesCS2B01G326000 chr7B 586059702 586062793 3091 True 1038.5 1208 91.079 946 2465 2 chr7B.!!$R3 1519
14 TraesCS2B01G326000 chr5B 331585315 331586257 942 False 1609.0 1609 97.458 3 945 1 chr5B.!!$F2 942

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
992 1009 0.393537 GTGCTGGGAGGGAATGTGAG 60.394 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 3965 1.011968 GCAGCGATCGTTGTGGTGTA 61.012 55.0 28.8 0.0 33.83 2.9 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
70 72 5.760743 TGTTTGTTGAGACCGATGAATTGTA 59.239 36.000 0.00 0.00 0.00 2.41
75 77 4.755411 TGAGACCGATGAATTGTAGGTTC 58.245 43.478 0.00 0.00 35.00 3.62
85 87 4.883585 TGAATTGTAGGTTCATGATCCAGC 59.116 41.667 22.09 14.86 31.07 4.85
679 683 7.297229 TGCTTTGTTTTTACTTTGCCTTTAC 57.703 32.000 0.00 0.00 0.00 2.01
897 903 8.488651 AAATACTTACGCTACTTTACTGCATT 57.511 30.769 0.00 0.00 0.00 3.56
987 1004 2.003548 GGAGGTGCTGGGAGGGAAT 61.004 63.158 0.00 0.00 0.00 3.01
988 1005 1.225704 GAGGTGCTGGGAGGGAATG 59.774 63.158 0.00 0.00 0.00 2.67
989 1006 1.542375 AGGTGCTGGGAGGGAATGT 60.542 57.895 0.00 0.00 0.00 2.71
990 1007 1.379044 GGTGCTGGGAGGGAATGTG 60.379 63.158 0.00 0.00 0.00 3.21
991 1008 1.685224 GTGCTGGGAGGGAATGTGA 59.315 57.895 0.00 0.00 0.00 3.58
992 1009 0.393537 GTGCTGGGAGGGAATGTGAG 60.394 60.000 0.00 0.00 0.00 3.51
993 1010 1.225704 GCTGGGAGGGAATGTGAGG 59.774 63.158 0.00 0.00 0.00 3.86
994 1011 1.918253 CTGGGAGGGAATGTGAGGG 59.082 63.158 0.00 0.00 0.00 4.30
995 1012 0.916358 CTGGGAGGGAATGTGAGGGT 60.916 60.000 0.00 0.00 0.00 4.34
996 1013 0.419865 TGGGAGGGAATGTGAGGGTA 59.580 55.000 0.00 0.00 0.00 3.69
1004 1021 2.505819 GGAATGTGAGGGTAGTCATGGT 59.494 50.000 0.00 0.00 0.00 3.55
1019 1036 0.417841 ATGGTGGTGGAGGGAGTAGT 59.582 55.000 0.00 0.00 0.00 2.73
1090 1107 2.100197 AGGTTCGAATCTCATCCGTGA 58.900 47.619 4.73 0.00 0.00 4.35
1452 1469 3.051341 AGGACATAGGGAACACCATAGGA 60.051 47.826 0.00 0.00 43.89 2.94
1539 1556 3.393609 TCAGGATGCAGATTGATAAGCCT 59.606 43.478 0.00 0.00 34.76 4.58
1564 1581 5.338632 TGATGAGGGGTTTTACTCTAGACA 58.661 41.667 0.00 0.00 34.84 3.41
1616 1634 1.028868 GGAAGGCAGACATGGTGAGC 61.029 60.000 0.00 0.00 0.00 4.26
1665 1683 2.232941 TGTCGGTTGGAGTATGAGTTCC 59.767 50.000 0.00 0.00 0.00 3.62
1730 1748 7.361286 GGAGACAAAGATTGTACCATCAAACTC 60.361 40.741 9.43 9.24 45.52 3.01
1771 1789 3.703001 ATTTGGTCGATGGTTGAGAGT 57.297 42.857 0.00 0.00 0.00 3.24
1786 3375 1.555075 GAGAGTGGATGTAGGCCAACA 59.445 52.381 5.01 0.00 37.12 3.33
1796 3385 0.345502 TAGGCCAACATAGAGGGGGT 59.654 55.000 5.01 0.00 0.00 4.95
1844 3433 1.829849 GGGAGAGGTTTAAGCGGTACT 59.170 52.381 0.00 0.00 0.00 2.73
1970 3559 2.293598 ATGGGAAGAGTGGGAAGGAT 57.706 50.000 0.00 0.00 0.00 3.24
2046 3635 1.986378 CGAGGAAACTAGTGCTTGACG 59.014 52.381 0.00 0.00 44.43 4.35
2076 3665 1.218047 GTGGTACATGCTGGCTCGA 59.782 57.895 0.00 0.00 44.52 4.04
2095 3684 3.117851 TCGAGAAGCCAGATAGAGAAGGA 60.118 47.826 0.00 0.00 0.00 3.36
2138 3727 3.394836 GAGGCTTCGCAGGAGGGT 61.395 66.667 0.00 0.00 0.00 4.34
2299 3888 2.378038 CTCAGGAGAGAAGAGGGACAG 58.622 57.143 0.00 0.00 44.98 3.51
2340 3929 3.191888 AGCTCAGTAAGAAGGGAAGGA 57.808 47.619 0.00 0.00 0.00 3.36
2361 3950 3.746792 TTCAGGAGATGAGTCAGGAGA 57.253 47.619 0.00 0.00 39.68 3.71
2372 3961 3.582647 TGAGTCAGGAGAATAACTTGGCA 59.417 43.478 0.00 0.00 0.00 4.92
2376 3965 3.074412 CAGGAGAATAACTTGGCAACGT 58.926 45.455 0.00 0.00 42.51 3.99
2382 3971 2.616634 TAACTTGGCAACGTACACCA 57.383 45.000 0.00 0.00 42.51 4.17
2402 3991 2.541346 CACAACGATCGCTGCTAATGAT 59.459 45.455 17.98 0.00 0.00 2.45
2450 4039 1.153249 CCGCCGGGAGCTATGAAAA 60.153 57.895 2.18 0.00 40.39 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 72 5.579753 AGATAATGCTGGATCATGAACCT 57.420 39.130 21.34 4.93 0.00 3.50
75 77 7.933215 TTTCCATAGATAATGCTGGATCATG 57.067 36.000 0.00 0.00 37.61 3.07
753 759 1.545841 GGGTTGTCAATCCCTTCACC 58.454 55.000 3.15 0.00 40.48 4.02
897 903 1.530891 TCCCCGAAGAGGAGAGGATA 58.469 55.000 0.00 0.00 45.00 2.59
987 1004 1.275666 CCACCATGACTACCCTCACA 58.724 55.000 0.00 0.00 0.00 3.58
988 1005 1.066143 CACCACCATGACTACCCTCAC 60.066 57.143 0.00 0.00 0.00 3.51
989 1006 1.275666 CACCACCATGACTACCCTCA 58.724 55.000 0.00 0.00 0.00 3.86
990 1007 0.541863 CCACCACCATGACTACCCTC 59.458 60.000 0.00 0.00 0.00 4.30
991 1008 0.118346 TCCACCACCATGACTACCCT 59.882 55.000 0.00 0.00 0.00 4.34
992 1009 0.541863 CTCCACCACCATGACTACCC 59.458 60.000 0.00 0.00 0.00 3.69
993 1010 0.541863 CCTCCACCACCATGACTACC 59.458 60.000 0.00 0.00 0.00 3.18
994 1011 0.541863 CCCTCCACCACCATGACTAC 59.458 60.000 0.00 0.00 0.00 2.73
995 1012 0.415830 TCCCTCCACCACCATGACTA 59.584 55.000 0.00 0.00 0.00 2.59
996 1013 0.911525 CTCCCTCCACCACCATGACT 60.912 60.000 0.00 0.00 0.00 3.41
1004 1021 1.000019 CCGACTACTCCCTCCACCA 60.000 63.158 0.00 0.00 0.00 4.17
1019 1036 1.923395 AACCCCTTCATCAGCCCGA 60.923 57.895 0.00 0.00 0.00 5.14
1090 1107 1.900545 GCCGACTCCTTGCCCTTACT 61.901 60.000 0.00 0.00 0.00 2.24
1092 1109 1.612442 AGCCGACTCCTTGCCCTTA 60.612 57.895 0.00 0.00 0.00 2.69
1113 1130 0.184933 TTACCTTGCCAACAGCCTGT 59.815 50.000 0.00 0.00 42.71 4.00
1452 1469 4.342378 CCAGTATCTGCCTACACATACACT 59.658 45.833 0.00 0.00 31.96 3.55
1462 1479 3.234353 CATCTGGTCCAGTATCTGCCTA 58.766 50.000 18.65 0.00 32.61 3.93
1539 1556 6.271391 TGTCTAGAGTAAAACCCCTCATCAAA 59.729 38.462 0.00 0.00 0.00 2.69
1616 1634 1.039785 TCTCCTCCTCGCCATCACTG 61.040 60.000 0.00 0.00 0.00 3.66
1665 1683 4.096382 ACAAGTATAGCAAAAATCCGGCAG 59.904 41.667 0.00 0.00 0.00 4.85
1730 1748 0.322906 GGGCCTGTTCTCCCTTCTTG 60.323 60.000 0.84 0.00 39.46 3.02
1771 1789 2.705658 CCTCTATGTTGGCCTACATCCA 59.294 50.000 31.88 19.77 39.39 3.41
1786 3375 2.657459 CTCTCCTCCATACCCCCTCTAT 59.343 54.545 0.00 0.00 0.00 1.98
1796 3385 2.043664 CCTCCATAGCCTCTCCTCCATA 59.956 54.545 0.00 0.00 0.00 2.74
1844 3433 8.437360 TCGATCTACTAAAACCATAGTTACGA 57.563 34.615 0.00 0.00 37.34 3.43
1970 3559 3.958147 TGATCGGGCTAGTAACTTCATCA 59.042 43.478 0.00 0.00 0.00 3.07
2046 3635 2.472695 TGTACCACCATTGCACTCTC 57.527 50.000 0.00 0.00 0.00 3.20
2076 3665 3.987745 TGTCCTTCTCTATCTGGCTTCT 58.012 45.455 0.00 0.00 0.00 2.85
2095 3684 5.301045 CCATGAACATCAGATTTGGCTATGT 59.699 40.000 0.00 0.00 32.32 2.29
2138 3727 2.642254 CCGCCGAGTACCTTCCACA 61.642 63.158 0.00 0.00 0.00 4.17
2184 3773 1.143073 ACCTCCTGGAAGTTTGTCACC 59.857 52.381 0.00 0.00 37.04 4.02
2299 3888 8.778358 TGAGCTTTTCTTCTTCTTCATTAGTTC 58.222 33.333 0.00 0.00 0.00 3.01
2340 3929 4.262891 TCTCCTGACTCATCTCCTGAAT 57.737 45.455 0.00 0.00 32.14 2.57
2361 3950 3.251487 GTGGTGTACGTTGCCAAGTTATT 59.749 43.478 0.00 0.00 33.66 1.40
2372 3961 1.411394 CGATCGTTGTGGTGTACGTT 58.589 50.000 7.03 0.00 38.79 3.99
2376 3965 1.011968 GCAGCGATCGTTGTGGTGTA 61.012 55.000 28.80 0.00 33.83 2.90
2382 3971 2.293677 TCATTAGCAGCGATCGTTGT 57.706 45.000 28.80 19.07 0.00 3.32
2402 3991 2.842462 AGCCCGGCCGATGTGATA 60.842 61.111 30.73 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.