Multiple sequence alignment - TraesCS2B01G489200

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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 TraesCS2B01G489200 chr2B 100.000 2213 0 0 1 2213 686782473 686784685 0.000000e+00 4087
1 TraesCS2B01G489200 chr2B 95.745 564 21 3 1652 2213 287036988 287037550 0.000000e+00 905
2 TraesCS2B01G489200 chr3A 93.584 1652 96 7 5 1651 664911323 664912969 0.000000e+00 2455
3 TraesCS2B01G489200 chr4A 93.778 1575 90 7 6 1576 552223069 552221499 0.000000e+00 2359
4 TraesCS2B01G489200 chr4A 93.688 1521 89 6 1 1517 465121947 465123464 0.000000e+00 2270
5 TraesCS2B01G489200 chr4D 94.114 1529 85 4 52 1576 45248080 45249607 0.000000e+00 2320
6 TraesCS2B01G489200 chr1B 94.207 1519 84 4 1 1517 27643370 27644886 0.000000e+00 2314
7 TraesCS2B01G489200 chr1B 95.915 563 19 4 1652 2213 362200169 362200728 0.000000e+00 909
8 TraesCS2B01G489200 chr1B 95.893 560 17 4 1654 2213 404976807 404977360 0.000000e+00 902
9 TraesCS2B01G489200 chr1B 90.370 135 13 0 1527 1661 552388467 552388333 6.280000e-41 178
10 TraesCS2B01G489200 chr1B 91.200 125 11 0 1527 1651 335427640 335427764 1.050000e-38 171
11 TraesCS2B01G489200 chr6B 93.939 1518 88 4 1 1517 177081549 177080035 0.000000e+00 2290
12 TraesCS2B01G489200 chr6B 92.449 1576 106 7 5 1576 483464131 483465697 0.000000e+00 2239
13 TraesCS2B01G489200 chr6B 89.222 167 14 4 1487 1651 656484101 656483937 2.880000e-49 206
14 TraesCS2B01G489200 chr6B 94.656 131 7 0 1527 1657 270899347 270899477 1.040000e-48 204
15 TraesCS2B01G489200 chr6B 89.706 136 11 3 1527 1662 68105298 68105430 1.050000e-38 171
16 TraesCS2B01G489200 chr2A 92.609 1583 106 9 1 1576 591092067 591093645 0.000000e+00 2265
17 TraesCS2B01G489200 chr2A 89.222 167 13 4 1487 1651 487633180 487633343 1.040000e-48 204
18 TraesCS2B01G489200 chr2A 90.385 156 9 6 1527 1678 397875137 397875290 1.340000e-47 200
19 TraesCS2B01G489200 chr2A 89.103 156 11 6 1527 1678 399423110 399422957 2.900000e-44 189
20 TraesCS2B01G489200 chr4B 93.210 1517 99 4 1 1516 569527591 569529104 0.000000e+00 2228
21 TraesCS2B01G489200 chr3B 96.092 563 17 4 1652 2213 105343181 105342623 0.000000e+00 913
22 TraesCS2B01G489200 chr3B 95.907 562 15 6 1652 2213 457950380 457949827 0.000000e+00 904
23 TraesCS2B01G489200 chr5B 95.622 571 15 6 1652 2213 224034647 224035216 0.000000e+00 907
24 TraesCS2B01G489200 chr7D 95.730 562 23 1 1652 2213 442645205 442645765 0.000000e+00 904
25 TraesCS2B01G489200 chr7B 95.907 562 16 6 1652 2213 403289951 403290505 0.000000e+00 904
26 TraesCS2B01G489200 chr7B 95.907 562 16 6 1652 2213 403317907 403318461 0.000000e+00 904
27 TraesCS2B01G489200 chr7B 90.370 135 11 2 1527 1660 615404088 615403955 2.260000e-40 176
28 TraesCS2B01G489200 chr1A 88.623 167 15 2 1488 1651 145813442 145813277 1.340000e-47 200
29 TraesCS2B01G489200 chr7A 92.701 137 8 2 1527 1662 254945612 254945477 1.730000e-46 196
30 TraesCS2B01G489200 chr7A 91.111 135 10 2 1527 1661 114450237 114450105 4.850000e-42 182
31 TraesCS2B01G489200 chr6A 88.095 168 16 3 1487 1651 604929380 604929546 1.730000e-46 196


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 TraesCS2B01G489200 chr2B 686782473 686784685 2212 False 4087 4087 100.000 1 2213 1 chr2B.!!$F2 2212
1 TraesCS2B01G489200 chr2B 287036988 287037550 562 False 905 905 95.745 1652 2213 1 chr2B.!!$F1 561
2 TraesCS2B01G489200 chr3A 664911323 664912969 1646 False 2455 2455 93.584 5 1651 1 chr3A.!!$F1 1646
3 TraesCS2B01G489200 chr4A 552221499 552223069 1570 True 2359 2359 93.778 6 1576 1 chr4A.!!$R1 1570
4 TraesCS2B01G489200 chr4A 465121947 465123464 1517 False 2270 2270 93.688 1 1517 1 chr4A.!!$F1 1516
5 TraesCS2B01G489200 chr4D 45248080 45249607 1527 False 2320 2320 94.114 52 1576 1 chr4D.!!$F1 1524
6 TraesCS2B01G489200 chr1B 27643370 27644886 1516 False 2314 2314 94.207 1 1517 1 chr1B.!!$F1 1516
7 TraesCS2B01G489200 chr1B 362200169 362200728 559 False 909 909 95.915 1652 2213 1 chr1B.!!$F3 561
8 TraesCS2B01G489200 chr1B 404976807 404977360 553 False 902 902 95.893 1654 2213 1 chr1B.!!$F4 559
9 TraesCS2B01G489200 chr6B 177080035 177081549 1514 True 2290 2290 93.939 1 1517 1 chr6B.!!$R1 1516
10 TraesCS2B01G489200 chr6B 483464131 483465697 1566 False 2239 2239 92.449 5 1576 1 chr6B.!!$F3 1571
11 TraesCS2B01G489200 chr2A 591092067 591093645 1578 False 2265 2265 92.609 1 1576 1 chr2A.!!$F3 1575
12 TraesCS2B01G489200 chr4B 569527591 569529104 1513 False 2228 2228 93.210 1 1516 1 chr4B.!!$F1 1515
13 TraesCS2B01G489200 chr3B 105342623 105343181 558 True 913 913 96.092 1652 2213 1 chr3B.!!$R1 561
14 TraesCS2B01G489200 chr3B 457949827 457950380 553 True 904 904 95.907 1652 2213 1 chr3B.!!$R2 561
15 TraesCS2B01G489200 chr5B 224034647 224035216 569 False 907 907 95.622 1652 2213 1 chr5B.!!$F1 561
16 TraesCS2B01G489200 chr7D 442645205 442645765 560 False 904 904 95.730 1652 2213 1 chr7D.!!$F1 561
17 TraesCS2B01G489200 chr7B 403289951 403290505 554 False 904 904 95.907 1652 2213 1 chr7B.!!$F1 561
18 TraesCS2B01G489200 chr7B 403317907 403318461 554 False 904 904 95.907 1652 2213 1 chr7B.!!$F2 561

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
442 446 1.006102 CTCCGTCCAAGTTGAGCGT 60.006 57.895 3.87 0.0 0.0 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 1622 0.108089 TAGCAGCGCGGGTAAAATGA 60.108 50.0 16.97 0.0 0.0 2.57 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
57 60 1.379044 GTGCCCCTAGCTTGCATGT 60.379 57.895 0.00 0.00 44.23 3.21
312 316 1.213537 CACAGGGATTTGGCAAGCG 59.786 57.895 0.00 0.00 0.00 4.68
356 360 4.495679 GCGATTTGCTCCGACATGATTTTA 60.496 41.667 0.00 0.00 41.73 1.52
396 400 4.937620 GCTCAACAAGATGAACCATACAGA 59.062 41.667 0.00 0.00 0.00 3.41
402 406 2.695666 AGATGAACCATACAGACGAGGG 59.304 50.000 0.00 0.00 0.00 4.30
442 446 1.006102 CTCCGTCCAAGTTGAGCGT 60.006 57.895 3.87 0.00 0.00 5.07
695 699 3.509442 TCAAGGTTTTGCAGGATCCAAT 58.491 40.909 15.82 0.00 34.21 3.16
714 718 1.254975 TGTGTCGCTAAGGCTGGCTA 61.255 55.000 3.41 0.00 36.09 3.93
763 767 6.967767 GGATACGAATCATATCTCTTGTACCG 59.032 42.308 0.00 0.00 33.41 4.02
816 820 4.459330 GCTCTGATTTCTTGGGCTAGATT 58.541 43.478 0.00 0.00 0.00 2.40
935 940 5.585820 TGATTCATGTGCATGTGCTAAAT 57.414 34.783 11.38 4.40 42.66 1.40
1056 1061 1.529244 GGTGGGCAGTGTGCTCTTT 60.529 57.895 0.00 0.00 46.08 2.52
1066 1071 4.237724 CAGTGTGCTCTTTAATGACTCGA 58.762 43.478 0.00 0.00 0.00 4.04
1101 1106 4.388499 AAGACCGGCGACCGCATT 62.388 61.111 9.30 0.00 46.86 3.56
1171 1176 2.680352 ACCTCGATGCCACGGTCT 60.680 61.111 0.00 0.00 0.00 3.85
1174 1179 2.678580 TCGATGCCACGGTCTGGA 60.679 61.111 0.00 0.00 43.95 3.86
1185 1192 1.003573 GGTCTGGAGGGAGGTCCAT 59.996 63.158 0.00 0.00 45.87 3.41
1223 1230 5.998981 CCGAGTCTTGGTAGATACATCTAGT 59.001 44.000 0.00 0.00 39.87 2.57
1225 1232 6.706716 CGAGTCTTGGTAGATACATCTAGTGA 59.293 42.308 0.00 0.00 39.87 3.41
1261 1268 0.323629 TTGGTGGAACGCTAGGGAAG 59.676 55.000 14.59 0.00 38.12 3.46
1264 1272 0.391263 GTGGAACGCTAGGGAAGGTG 60.391 60.000 14.59 0.00 35.02 4.00
1375 1383 5.507985 GCTGCAAGTGTTAAAGATGGTTCTT 60.508 40.000 0.00 0.00 39.24 2.52
1479 1488 5.030820 AGTTAGTAGTAGCATGGGGAAACT 58.969 41.667 0.00 0.00 0.00 2.66
1532 1541 1.327764 GCGCAGGTGTGAAATAGTAGC 59.672 52.381 0.30 0.00 0.00 3.58
1534 1543 2.348666 CGCAGGTGTGAAATAGTAGCAC 59.651 50.000 0.00 0.00 0.00 4.40
1587 1599 2.486918 TGTAGCGCGATACTAGTAGCA 58.513 47.619 31.61 10.11 0.00 3.49
1610 1622 1.452651 TACCCGCGCTGCTAGTAGT 60.453 57.895 5.56 0.00 0.00 2.73
1619 1631 3.245519 GCGCTGCTAGTAGTCATTTTACC 59.754 47.826 9.73 0.00 0.00 2.85
1622 1634 3.788937 TGCTAGTAGTCATTTTACCCGC 58.211 45.455 0.00 0.00 0.00 6.13
1669 1681 2.936498 GTGGCAATACATGAGCGTAAGT 59.064 45.455 0.00 0.00 41.68 2.24
1781 1795 5.259632 GCTAATCAATGGGCTATGGAGATT 58.740 41.667 9.94 9.94 0.00 2.40
1937 1951 2.417787 GCATTTTGAGGAAGCCCATCAC 60.418 50.000 0.00 0.00 33.88 3.06
2041 2055 6.660521 TGAAGATCATGGTGCTATTTTGAAGT 59.339 34.615 0.00 0.00 0.00 3.01
2098 2112 8.296000 CCCTTCTCTCTTTTTCTCTCATTTTTC 58.704 37.037 0.00 0.00 0.00 2.29
2181 2207 1.550976 GGAGTCTCATCCCGACTTGTT 59.449 52.381 1.47 0.00 41.53 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 60 3.193056 CCACCATGCACATACAACATCAA 59.807 43.478 0.00 0.00 0.00 2.57
136 140 5.446860 TCATCTCCTAACTACGTCCATCTT 58.553 41.667 0.00 0.00 0.00 2.40
146 150 5.835819 ACTTGCTAGCATCATCTCCTAACTA 59.164 40.000 20.13 0.00 0.00 2.24
201 205 7.482169 TCATAACATCACTTCTCCTAACTGT 57.518 36.000 0.00 0.00 0.00 3.55
297 301 0.831711 AAACCGCTTGCCAAATCCCT 60.832 50.000 0.00 0.00 0.00 4.20
356 360 3.156293 TGAGCTGCCAAAATACACACAT 58.844 40.909 0.00 0.00 0.00 3.21
402 406 3.196207 TTGCTGTGCCTGGGAGGTC 62.196 63.158 0.00 0.00 37.80 3.85
414 418 1.407656 TTGGACGGAGGAGTTGCTGT 61.408 55.000 0.00 0.00 0.00 4.40
536 540 3.717842 GGTGCTACCTGTTTGTGGA 57.282 52.632 0.00 0.00 34.73 4.02
695 699 1.254975 TAGCCAGCCTTAGCGACACA 61.255 55.000 0.00 0.00 46.67 3.72
763 767 4.024048 AGTTGTTCCATGAAACGATCACAC 60.024 41.667 0.00 0.00 41.93 3.82
793 797 2.171448 TCTAGCCCAAGAAATCAGAGCC 59.829 50.000 0.00 0.00 0.00 4.70
901 906 5.706833 TGCACATGAATCAATAGTGACAACT 59.293 36.000 14.89 0.00 40.67 3.16
958 963 2.386661 AGTTAGCGTCCACATCCAAG 57.613 50.000 0.00 0.00 0.00 3.61
1056 1061 1.471119 AGTCCGCCTTCGAGTCATTA 58.529 50.000 0.00 0.00 38.10 1.90
1099 1104 3.117625 ACCTGGATGATCATCTGTGCAAT 60.118 43.478 29.85 11.36 37.92 3.56
1101 1106 1.841919 ACCTGGATGATCATCTGTGCA 59.158 47.619 29.85 19.81 37.92 4.57
1171 1176 1.690633 GCAGATGGACCTCCCTCCA 60.691 63.158 0.00 0.00 44.72 3.86
1174 1179 2.039624 ACGCAGATGGACCTCCCT 59.960 61.111 0.00 0.00 35.38 4.20
1185 1192 1.467734 GACTCGGAGTTTAGACGCAGA 59.532 52.381 12.67 0.00 0.00 4.26
1223 1230 4.773149 ACCAACCTAAACAAACCACTTTCA 59.227 37.500 0.00 0.00 0.00 2.69
1225 1232 4.081365 CCACCAACCTAAACAAACCACTTT 60.081 41.667 0.00 0.00 0.00 2.66
1264 1272 3.763897 ACAACTATCATTGAAAGGTGGGC 59.236 43.478 0.00 0.00 32.06 5.36
1375 1383 6.016693 TCCAATGAAAAATAAGCTCACGTCAA 60.017 34.615 0.00 0.00 0.00 3.18
1380 1388 5.569059 CACGTCCAATGAAAAATAAGCTCAC 59.431 40.000 0.00 0.00 0.00 3.51
1469 1478 1.628846 AGCGAGTTGTAGTTTCCCCAT 59.371 47.619 0.00 0.00 0.00 4.00
1479 1488 8.915057 ATCCTAAATACTAGTAGCGAGTTGTA 57.085 34.615 8.85 0.00 0.00 2.41
1566 1578 2.874086 TGCTACTAGTATCGCGCTACAA 59.126 45.455 20.91 4.08 0.00 2.41
1573 1585 0.950116 ACCCGTGCTACTAGTATCGC 59.050 55.000 2.33 5.13 0.00 4.58
1574 1586 2.481952 GGTACCCGTGCTACTAGTATCG 59.518 54.545 2.33 8.79 0.00 2.92
1600 1612 3.802685 GCGGGTAAAATGACTACTAGCAG 59.197 47.826 0.00 0.00 0.00 4.24
1610 1622 0.108089 TAGCAGCGCGGGTAAAATGA 60.108 50.000 16.97 0.00 0.00 2.57
1619 1631 2.907897 AAAGGCTACTAGCAGCGCGG 62.908 60.000 8.83 2.11 44.75 6.46
1622 1634 1.291132 GGAAAAGGCTACTAGCAGCG 58.709 55.000 8.87 0.00 44.75 5.18
1669 1681 3.071457 CACCCATAGTGCTATGTCCATGA 59.929 47.826 15.52 0.00 40.90 3.07
1872 1886 2.158534 AGTTGGATGCACACCCACTTAA 60.159 45.455 11.14 0.00 30.80 1.85
1937 1951 9.778741 TTATAGAACTTGGCTTGTATATTCCAG 57.221 33.333 0.00 0.00 0.00 3.86
2041 2055 8.212312 TGTTACTATCCTTTTTCCACACTTGTA 58.788 33.333 0.00 0.00 0.00 2.41
2098 2112 2.967599 GGCCAAAGAAGCCCAAATAG 57.032 50.000 0.00 0.00 45.16 1.73
2181 2207 3.940335 TGATGGAGACTATGATTCCCCA 58.060 45.455 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.