Multiple sequence alignment - TraesCS1A01G266400

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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 TraesCS1A01G266400 chr1A 100.000 2584 0 0 1 2584 461966787 461964204 0.000000e+00 4772
1 TraesCS1A01G266400 chr1A 96.679 1054 32 3 2 1054 35564001 35562950 0.000000e+00 1749
2 TraesCS1A01G266400 chr2D 94.926 2089 70 14 2 2056 469107932 469105846 0.000000e+00 3238
3 TraesCS1A01G266400 chr2D 91.215 1696 110 22 2 1692 631749570 631747909 0.000000e+00 2270
4 TraesCS1A01G266400 chr2D 93.633 534 34 0 2051 2584 344390040 344390573 0.000000e+00 798
5 TraesCS1A01G266400 chr2D 92.833 293 20 1 1763 2054 617438833 617438541 8.550000e-115 424
6 TraesCS1A01G266400 chr7B 93.566 2067 108 18 2 2054 551484717 551482662 0.000000e+00 3057
7 TraesCS1A01G266400 chr3B 92.754 2084 97 24 2 2053 597426788 597428849 0.000000e+00 2963
8 TraesCS1A01G266400 chr3B 92.033 1343 92 12 359 1692 8505221 8506557 0.000000e+00 1873
9 TraesCS1A01G266400 chr4D 95.868 1694 64 6 2 1692 459191345 459193035 0.000000e+00 2736
10 TraesCS1A01G266400 chrUn 94.803 1674 48 15 416 2052 96553413 96555084 0.000000e+00 2573
11 TraesCS1A01G266400 chrUn 93.881 523 27 5 2 520 96553078 96553599 0.000000e+00 784
12 TraesCS1A01G266400 chr1B 91.774 1702 124 11 2 1692 127026367 127024671 0.000000e+00 2353
13 TraesCS1A01G266400 chr1B 92.884 801 41 11 1264 2052 470720338 470721134 0.000000e+00 1149
14 TraesCS1A01G266400 chr1B 91.185 329 21 5 1734 2055 127024686 127024359 8.490000e-120 440
15 TraesCS1A01G266400 chr7A 88.524 1612 119 34 495 2052 48781641 48783240 0.000000e+00 1892
16 TraesCS1A01G266400 chr7A 94.216 536 31 0 2049 2584 53984855 53984320 0.000000e+00 819
17 TraesCS1A01G266400 chr7A 93.657 536 34 0 2049 2584 290204221 290204756 0.000000e+00 802
18 TraesCS1A01G266400 chr2B 93.180 1085 70 4 610 1692 677292471 677293553 0.000000e+00 1591
19 TraesCS1A01G266400 chr7D 92.011 701 27 10 1381 2052 69948231 69948931 0.000000e+00 957
20 TraesCS1A01G266400 chr7D 93.820 534 33 0 2051 2584 185897798 185898331 0.000000e+00 804
21 TraesCS1A01G266400 chr3A 94.216 536 31 0 2049 2584 259353476 259354011 0.000000e+00 819
22 TraesCS1A01G266400 chr3A 93.843 536 33 0 2049 2584 132376254 132375719 0.000000e+00 808
23 TraesCS1A01G266400 chr5A 94.030 536 32 0 2049 2584 291197952 291197417 0.000000e+00 813
24 TraesCS1A01G266400 chr5A 89.813 589 51 8 2 586 570488398 570488981 0.000000e+00 747
25 TraesCS1A01G266400 chr3D 93.680 538 33 1 2048 2584 213025760 213025223 0.000000e+00 804
26 TraesCS1A01G266400 chr4A 93.470 536 35 0 2049 2584 161955456 161954921 0.000000e+00 797
27 TraesCS1A01G266400 chr6B 94.059 303 17 1 1759 2060 658405685 658405383 2.340000e-125 459


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 TraesCS1A01G266400 chr1A 461964204 461966787 2583 True 4772.0 4772 100.0000 1 2584 1 chr1A.!!$R2 2583
1 TraesCS1A01G266400 chr1A 35562950 35564001 1051 True 1749.0 1749 96.6790 2 1054 1 chr1A.!!$R1 1052
2 TraesCS1A01G266400 chr2D 469105846 469107932 2086 True 3238.0 3238 94.9260 2 2056 1 chr2D.!!$R1 2054
3 TraesCS1A01G266400 chr2D 631747909 631749570 1661 True 2270.0 2270 91.2150 2 1692 1 chr2D.!!$R3 1690
4 TraesCS1A01G266400 chr2D 344390040 344390573 533 False 798.0 798 93.6330 2051 2584 1 chr2D.!!$F1 533
5 TraesCS1A01G266400 chr7B 551482662 551484717 2055 True 3057.0 3057 93.5660 2 2054 1 chr7B.!!$R1 2052
6 TraesCS1A01G266400 chr3B 597426788 597428849 2061 False 2963.0 2963 92.7540 2 2053 1 chr3B.!!$F2 2051
7 TraesCS1A01G266400 chr3B 8505221 8506557 1336 False 1873.0 1873 92.0330 359 1692 1 chr3B.!!$F1 1333
8 TraesCS1A01G266400 chr4D 459191345 459193035 1690 False 2736.0 2736 95.8680 2 1692 1 chr4D.!!$F1 1690
9 TraesCS1A01G266400 chrUn 96553078 96555084 2006 False 1678.5 2573 94.3420 2 2052 2 chrUn.!!$F1 2050
10 TraesCS1A01G266400 chr1B 127024359 127026367 2008 True 1396.5 2353 91.4795 2 2055 2 chr1B.!!$R1 2053
11 TraesCS1A01G266400 chr1B 470720338 470721134 796 False 1149.0 1149 92.8840 1264 2052 1 chr1B.!!$F1 788
12 TraesCS1A01G266400 chr7A 48781641 48783240 1599 False 1892.0 1892 88.5240 495 2052 1 chr7A.!!$F1 1557
13 TraesCS1A01G266400 chr7A 53984320 53984855 535 True 819.0 819 94.2160 2049 2584 1 chr7A.!!$R1 535
14 TraesCS1A01G266400 chr7A 290204221 290204756 535 False 802.0 802 93.6570 2049 2584 1 chr7A.!!$F2 535
15 TraesCS1A01G266400 chr2B 677292471 677293553 1082 False 1591.0 1591 93.1800 610 1692 1 chr2B.!!$F1 1082
16 TraesCS1A01G266400 chr7D 69948231 69948931 700 False 957.0 957 92.0110 1381 2052 1 chr7D.!!$F1 671
17 TraesCS1A01G266400 chr7D 185897798 185898331 533 False 804.0 804 93.8200 2051 2584 1 chr7D.!!$F2 533
18 TraesCS1A01G266400 chr3A 259353476 259354011 535 False 819.0 819 94.2160 2049 2584 1 chr3A.!!$F1 535
19 TraesCS1A01G266400 chr3A 132375719 132376254 535 True 808.0 808 93.8430 2049 2584 1 chr3A.!!$R1 535
20 TraesCS1A01G266400 chr5A 291197417 291197952 535 True 813.0 813 94.0300 2049 2584 1 chr5A.!!$R1 535
21 TraesCS1A01G266400 chr5A 570488398 570488981 583 False 747.0 747 89.8130 2 586 1 chr5A.!!$F1 584
22 TraesCS1A01G266400 chr3D 213025223 213025760 537 True 804.0 804 93.6800 2048 2584 1 chr3D.!!$R1 536
23 TraesCS1A01G266400 chr4A 161954921 161955456 535 True 797.0 797 93.4700 2049 2584 1 chr4A.!!$R1 535


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
693 859 0.320374 CGCTACAAGTGGGAACTCCA 59.68 55.0 0.0 0.0 44.79 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1820 2.236489 AAGCAACCCAATGGCACTAT 57.764 45.0 0.0 0.0 33.59 2.12 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
26 27 2.235650 CTGTTGGATCTCTCAAGAGGCA 59.764 50.000 7.17 0.00 42.30 4.75
92 93 6.100004 CAGTCCAAGTCGACATTGTTATAGT 58.900 40.000 19.50 5.20 35.07 2.12
194 195 3.244976 CAATTCGAACATCAAGGCAACC 58.755 45.455 0.00 0.00 37.17 3.77
296 297 0.808125 AATTTATGAGTGCGCCGCAA 59.192 45.000 15.84 0.00 41.47 4.85
343 344 8.984891 CAACTACCTTTGCATTTATTTGATGA 57.015 30.769 0.00 0.00 0.00 2.92
527 683 6.186957 TGGGCAGATTGTGACTTTTATATGT 58.813 36.000 0.00 0.00 32.83 2.29
693 859 0.320374 CGCTACAAGTGGGAACTCCA 59.680 55.000 0.00 0.00 44.79 3.86
746 913 2.094182 CGTGACCAACACTATGCTAGGT 60.094 50.000 0.00 0.00 46.24 3.08
858 1025 4.774124 AGCAATTCAAGCTAGCTATCACA 58.226 39.130 19.70 0.83 41.32 3.58
861 1028 5.334724 GCAATTCAAGCTAGCTATCACATCC 60.335 44.000 19.70 0.00 0.00 3.51
976 1143 1.814394 CTTGCACAATTAGGCTCAGCA 59.186 47.619 0.00 0.00 0.00 4.41
994 1161 3.254166 CAGCAAAGAACACTATGCAGGTT 59.746 43.478 0.00 0.00 41.18 3.50
1426 1600 8.200120 TGATGATGATATACCCGATGATCTTTC 58.800 37.037 0.00 0.00 0.00 2.62
1427 1601 7.480760 TGATGATATACCCGATGATCTTTCA 57.519 36.000 0.00 0.00 36.00 2.69
1548 1725 7.773224 TGAAACTCTCTGAAACCAACAAATCTA 59.227 33.333 0.00 0.00 0.00 1.98
1605 1782 9.268268 TCTAAATTCGATATGGTTGTATGGTTC 57.732 33.333 0.00 0.00 0.00 3.62
1635 1820 5.159273 TGTGAACTTGACATGTATGGCTA 57.841 39.130 0.00 0.00 36.54 3.93
1659 1845 0.606130 GCCATTGGGTTGCTTTTGGG 60.606 55.000 4.53 0.00 36.17 4.12
1889 2235 5.945466 ATGCTGCCGAATTTTTGAATTTT 57.055 30.435 0.00 0.00 0.00 1.82
1981 2328 1.764134 ACCTACCAAACACAGGAACGA 59.236 47.619 0.00 0.00 33.44 3.85
1985 2332 4.998672 CCTACCAAACACAGGAACGAAATA 59.001 41.667 0.00 0.00 0.00 1.40
2058 2405 1.764134 ACCAAACACACCCTTACTCGA 59.236 47.619 0.00 0.00 0.00 4.04
2060 2407 3.181448 ACCAAACACACCCTTACTCGATT 60.181 43.478 0.00 0.00 0.00 3.34
2130 2477 5.500234 TCCATATCTGAACCCAAGAAAGTG 58.500 41.667 0.00 0.00 0.00 3.16
2170 2517 5.378230 ACCTGAATGGATTCAAGCTATGA 57.622 39.130 3.74 0.00 45.26 2.15
2187 2534 5.532406 AGCTATGAAAGAACAGCTTCAACAA 59.468 36.000 0.00 0.00 41.50 2.83
2296 2643 6.594788 ACAAACAAGATGAGCATGGTAAAT 57.405 33.333 0.00 0.00 0.00 1.40
2385 2732 1.352352 ACATTTGCTCCAGTGGCTAGT 59.648 47.619 3.51 0.00 0.00 2.57
2467 2814 4.225942 AGATGGATGTGAAGAGTGCCTTTA 59.774 41.667 0.00 0.00 34.68 1.85
2505 2852 5.237127 TGAAGAAGAAGTGTATGTTGCACAG 59.763 40.000 0.00 0.00 39.17 3.66
2528 2875 2.490903 CACCTGGCTTTCAAGATCCAAG 59.509 50.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.907486 TGAGAGATCCAACAGCCCTG 59.093 55.000 0.00 0.0 0.00 4.45
92 93 7.807433 GTGCATAATTATGAAGAACACAACACA 59.193 33.333 26.22 9.0 35.75 3.72
194 195 6.306987 ACCAAGGCCCTATTATCACTTAATG 58.693 40.000 0.00 0.0 32.66 1.90
527 683 8.659925 AATCAGCACAAACACATGATTTAAAA 57.340 26.923 0.00 0.0 37.31 1.52
693 859 4.772100 CCATACAATGACCCCACTTTTTCT 59.228 41.667 0.00 0.0 0.00 2.52
726 893 3.611766 ACCTAGCATAGTGTTGGTCAC 57.388 47.619 0.00 0.0 46.46 3.67
755 922 3.806949 TCCCTTTAGCAACAAGGTCAT 57.193 42.857 7.57 0.0 39.50 3.06
858 1025 6.127054 TGAGATGGTTTCTAACTTGATCGGAT 60.127 38.462 0.00 0.0 33.74 4.18
861 1028 6.813649 TCTTGAGATGGTTTCTAACTTGATCG 59.186 38.462 0.00 0.0 33.74 3.69
976 1143 5.954335 GCAATAACCTGCATAGTGTTCTTT 58.046 37.500 0.00 0.0 42.17 2.52
994 1161 9.964354 ATAATATAAGAAGCTCACCATGCAATA 57.036 29.630 0.00 0.0 0.00 1.90
1426 1600 7.912056 TCTTTCAAATTGGAGACTACATCTG 57.088 36.000 0.00 0.0 38.00 2.90
1427 1601 9.525826 AATTCTTTCAAATTGGAGACTACATCT 57.474 29.630 0.00 0.0 41.91 2.90
1548 1725 5.487488 TCTTCACATACCTACTCACCCAAAT 59.513 40.000 0.00 0.0 0.00 2.32
1635 1820 2.236489 AAGCAACCCAATGGCACTAT 57.764 45.000 0.00 0.0 33.59 2.12
1659 1845 5.763204 CCATACAGGTTCACATACCCAATAC 59.237 44.000 0.00 0.0 39.08 1.89
2058 2405 6.633500 TTTGCTAGTTGTGTTGCTCTTAAT 57.367 33.333 0.00 0.0 0.00 1.40
2060 2407 6.633500 AATTTGCTAGTTGTGTTGCTCTTA 57.367 33.333 0.00 0.0 0.00 2.10
2170 2517 5.521372 GCTCAAATTGTTGAAGCTGTTCTTT 59.479 36.000 0.00 0.0 43.18 2.52
2187 2534 5.263599 TCCCATACATTGTTCAGCTCAAAT 58.736 37.500 0.00 0.0 0.00 2.32
2296 2643 2.612212 GACGAGCCTTGTTTCTGACAAA 59.388 45.455 0.00 0.0 46.99 2.83
2385 2732 3.192001 GCAGAATGTGAATGGCTTCAAGA 59.808 43.478 0.00 0.0 42.85 3.02
2467 2814 4.774124 TCTTCTTCAATCTCGCCATTGAT 58.226 39.130 9.00 0.0 41.42 2.57
2476 2823 7.095060 TGCAACATACACTTCTTCTTCAATCTC 60.095 37.037 0.00 0.0 0.00 2.75
2518 2865 5.938710 CCATATCAGGATGTCTTGGATCTTG 59.061 44.000 0.00 0.0 37.40 3.02
2528 2875 6.058183 AGCTTGTAAACCATATCAGGATGTC 58.942 40.000 0.00 0.0 37.40 3.06



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

AutoCloner maintained by Alex Coulton.