Multiple sequence alignment - TraesCS2A01G347100

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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 TraesCS2A01G347100 chr2A 100.000 2472 0 0 1 2472 585249962 585252433 0.000000e+00 4566
1 TraesCS2A01G347100 chr2A 97.308 743 19 1 1 743 214831412 214830671 0.000000e+00 1260
2 TraesCS2A01G347100 chr6B 88.876 1744 159 19 743 2472 422931367 422933089 0.000000e+00 2113
3 TraesCS2A01G347100 chr4B 85.755 1748 219 22 739 2472 135090700 135088969 0.000000e+00 1821
4 TraesCS2A01G347100 chr1A 83.371 1750 248 25 739 2472 245434561 245432839 0.000000e+00 1580
5 TraesCS2A01G347100 chr1A 96.909 744 20 3 1 743 462299947 462299206 0.000000e+00 1243
6 TraesCS2A01G347100 chr1A 96.774 744 22 2 1 744 585420457 585421198 0.000000e+00 1240
7 TraesCS2A01G347100 chr7A 97.039 743 22 0 1 743 139992392 139993134 0.000000e+00 1251
8 TraesCS2A01G347100 chr7A 96.774 744 22 2 1 744 259592827 259592086 0.000000e+00 1240
9 TraesCS2A01G347100 chr6A 96.904 743 21 2 1 743 518742468 518743208 0.000000e+00 1243
10 TraesCS2A01G347100 chr6A 96.770 743 21 2 1 743 431170857 431171596 0.000000e+00 1236
11 TraesCS2A01G347100 chr5A 96.904 743 20 2 1 743 313957982 313957243 0.000000e+00 1242
12 TraesCS2A01G347100 chr5A 96.774 744 22 2 1 743 613607594 613608336 0.000000e+00 1240
13 TraesCS2A01G347100 chr6D 84.837 1042 138 13 1440 2471 472057995 472056964 0.000000e+00 1031
14 TraesCS2A01G347100 chr7B 75.850 1764 364 47 739 2470 15610285 15612018 0.000000e+00 841
15 TraesCS2A01G347100 chr2B 75.723 1763 367 48 739 2470 91563670 91561938 0.000000e+00 828
16 TraesCS2A01G347100 chr1B 79.045 1236 236 17 739 1962 555861417 555862641 0.000000e+00 826
17 TraesCS2A01G347100 chr3B 75.595 1766 363 55 739 2470 48963380 48961649 0.000000e+00 811
18 TraesCS2A01G347100 chr5B 75.411 1765 365 60 739 2470 45232398 45230670 0.000000e+00 791
19 TraesCS2A01G347100 chr5B 75.213 1763 374 51 739 2470 45269252 45267522 0.000000e+00 776
20 TraesCS2A01G347100 chr3A 78.706 742 137 13 1738 2470 467891155 467891884 2.220000e-130 475


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 TraesCS2A01G347100 chr2A 585249962 585252433 2471 False 4566 4566 100.000 1 2472 1 chr2A.!!$F1 2471
1 TraesCS2A01G347100 chr2A 214830671 214831412 741 True 1260 1260 97.308 1 743 1 chr2A.!!$R1 742
2 TraesCS2A01G347100 chr6B 422931367 422933089 1722 False 2113 2113 88.876 743 2472 1 chr6B.!!$F1 1729
3 TraesCS2A01G347100 chr4B 135088969 135090700 1731 True 1821 1821 85.755 739 2472 1 chr4B.!!$R1 1733
4 TraesCS2A01G347100 chr1A 245432839 245434561 1722 True 1580 1580 83.371 739 2472 1 chr1A.!!$R1 1733
5 TraesCS2A01G347100 chr1A 462299206 462299947 741 True 1243 1243 96.909 1 743 1 chr1A.!!$R2 742
6 TraesCS2A01G347100 chr1A 585420457 585421198 741 False 1240 1240 96.774 1 744 1 chr1A.!!$F1 743
7 TraesCS2A01G347100 chr7A 139992392 139993134 742 False 1251 1251 97.039 1 743 1 chr7A.!!$F1 742
8 TraesCS2A01G347100 chr7A 259592086 259592827 741 True 1240 1240 96.774 1 744 1 chr7A.!!$R1 743
9 TraesCS2A01G347100 chr6A 518742468 518743208 740 False 1243 1243 96.904 1 743 1 chr6A.!!$F2 742
10 TraesCS2A01G347100 chr6A 431170857 431171596 739 False 1236 1236 96.770 1 743 1 chr6A.!!$F1 742
11 TraesCS2A01G347100 chr5A 313957243 313957982 739 True 1242 1242 96.904 1 743 1 chr5A.!!$R1 742
12 TraesCS2A01G347100 chr5A 613607594 613608336 742 False 1240 1240 96.774 1 743 1 chr5A.!!$F1 742
13 TraesCS2A01G347100 chr6D 472056964 472057995 1031 True 1031 1031 84.837 1440 2471 1 chr6D.!!$R1 1031
14 TraesCS2A01G347100 chr7B 15610285 15612018 1733 False 841 841 75.850 739 2470 1 chr7B.!!$F1 1731
15 TraesCS2A01G347100 chr2B 91561938 91563670 1732 True 828 828 75.723 739 2470 1 chr2B.!!$R1 1731
16 TraesCS2A01G347100 chr1B 555861417 555862641 1224 False 826 826 79.045 739 1962 1 chr1B.!!$F1 1223
17 TraesCS2A01G347100 chr3B 48961649 48963380 1731 True 811 811 75.595 739 2470 1 chr3B.!!$R1 1731
18 TraesCS2A01G347100 chr5B 45230670 45232398 1728 True 791 791 75.411 739 2470 1 chr5B.!!$R1 1731
19 TraesCS2A01G347100 chr5B 45267522 45269252 1730 True 776 776 75.213 739 2470 1 chr5B.!!$R2 1731
20 TraesCS2A01G347100 chr3A 467891155 467891884 729 False 475 475 78.706 1738 2470 1 chr3A.!!$F1 732

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
981 986 1.476891 TGTCGGGCTATTGTGAGTCTC 59.523 52.381 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2397 2426 0.551396 CATACCCTTCTTCCCCACCC 59.449 60.0 0.0 0.0 0.0 4.61 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
53 54 1.687612 CCAGTGACAGAAGGGGCAT 59.312 57.895 0.00 0.00 0.00 4.40
72 73 4.513692 GGCATCAAGGCACGTATTGTATTA 59.486 41.667 0.00 0.00 43.51 0.98
96 99 3.387699 TGCCATCGAGGATAACAAGATGA 59.612 43.478 0.00 0.00 40.62 2.92
98 101 4.564041 CCATCGAGGATAACAAGATGAGG 58.436 47.826 0.00 0.00 40.62 3.86
576 581 2.554344 GGATTGACAACCCCTAAGTGCA 60.554 50.000 0.00 0.00 0.00 4.57
683 688 4.388378 ACTGAGGGAAATACTTACGCTC 57.612 45.455 0.00 0.00 41.65 5.03
760 765 4.085357 AGCACACCTAATCAGAACACAA 57.915 40.909 0.00 0.00 0.00 3.33
834 839 7.095565 GGCAGACAGTTAGAAGAGTTCTTTAAC 60.096 40.741 13.27 13.27 41.14 2.01
886 891 6.591935 TCGGCTAGATTGATTGGTCTTAATT 58.408 36.000 0.00 0.00 0.00 1.40
912 917 4.001618 TGTCATGAGATTTCGTTCACCA 57.998 40.909 0.00 0.00 0.00 4.17
940 945 1.979855 TGACAAGGCTTGCTTTGCTA 58.020 45.000 26.45 3.18 0.00 3.49
951 956 5.574443 GGCTTGCTTTGCTAAAACTATGAAG 59.426 40.000 0.00 0.00 0.00 3.02
970 975 5.553123 TGAAGATTAAAAGTTGTCGGGCTA 58.447 37.500 0.00 0.00 0.00 3.93
981 986 1.476891 TGTCGGGCTATTGTGAGTCTC 59.523 52.381 0.00 0.00 0.00 3.36
992 997 6.426937 GCTATTGTGAGTCTCAAAAAGTGGTA 59.573 38.462 9.55 0.00 25.67 3.25
1035 1040 4.279922 GGTGTACTTAACATTGCTTGGGTT 59.720 41.667 0.00 0.00 41.10 4.11
1192 1197 3.772387 AGAGATGCTGAAGATATCCCGA 58.228 45.455 0.00 0.00 0.00 5.14
1225 1230 1.139520 GTGCTAGGCGGCCATTTTG 59.860 57.895 23.09 7.05 0.00 2.44
1228 1233 1.133945 TGCTAGGCGGCCATTTTGATA 60.134 47.619 23.09 1.51 0.00 2.15
1253 1261 7.913674 ATTTCTTCTATTCAGTGGACAAGAC 57.086 36.000 0.00 0.00 0.00 3.01
1301 1310 3.387050 GGAATTACCGTGTCCTAGGATGT 59.613 47.826 16.27 12.36 0.00 3.06
1311 1320 1.364678 TCCTAGGATGTTGACAGGGGA 59.635 52.381 7.62 0.00 0.00 4.81
1333 1342 2.774809 GTCTCTCCTAAAAGGGCCAGAT 59.225 50.000 6.18 0.00 35.59 2.90
1339 1349 5.431731 TCTCCTAAAAGGGCCAGATTCATTA 59.568 40.000 6.18 0.00 35.59 1.90
1384 1395 1.377856 GGCTCCTCCTCCACTTTGC 60.378 63.158 0.00 0.00 0.00 3.68
1394 1405 2.222027 CTCCACTTTGCGGAACTTCTT 58.778 47.619 0.00 0.00 30.33 2.52
1453 1464 7.685849 TTGCCTACTATAGTGGAAACCTTAT 57.314 36.000 17.19 0.00 0.00 1.73
1472 1485 7.793036 ACCTTATAAGAGAATGGTAGGTTGAC 58.207 38.462 14.28 0.00 30.93 3.18
1477 1490 6.884280 AAGAGAATGGTAGGTTGACAAAAG 57.116 37.500 0.00 0.00 0.00 2.27
1541 1555 7.384660 GTGAGGAGATTAGCAATGATCTACTTG 59.615 40.741 0.04 0.00 42.32 3.16
1648 1664 7.921304 TGGTGAATTATATGCAGATCATACCT 58.079 34.615 0.00 0.00 40.22 3.08
1663 1679 9.303116 CAGATCATACCTAGTACTCTGGTTAAT 57.697 37.037 20.93 13.73 35.48 1.40
1694 1711 7.403312 TTTACATCATATTTGGAGGTTGTGG 57.597 36.000 0.00 0.00 31.07 4.17
1783 1802 9.286170 GTACTCTGTACAATCTCCTGATACATA 57.714 37.037 0.00 0.00 31.70 2.29
1797 1817 6.335311 TCCTGATACATATGGGGAGGAAAATT 59.665 38.462 7.80 0.00 0.00 1.82
1840 1860 0.108585 GTGGTGGAAGAAGTGCAGGA 59.891 55.000 0.00 0.00 0.00 3.86
1846 1867 1.279271 GGAAGAAGTGCAGGAAGGCTA 59.721 52.381 0.00 0.00 34.04 3.93
1863 1884 3.764972 AGGCTAAGTCAGAGGACAACTAC 59.235 47.826 0.00 0.00 46.80 2.73
1882 1903 8.682710 ACAACTACTGTTAACATTGAACACATT 58.317 29.630 20.90 0.62 32.99 2.71
1965 1987 6.886459 CCCTAACTCCAATTCTTTTGAGATCA 59.114 38.462 0.00 0.00 30.93 2.92
1970 1992 7.533426 ACTCCAATTCTTTTGAGATCATTTCG 58.467 34.615 0.00 0.00 30.93 3.46
2031 2053 9.180678 GTGTTGATATTCCTAACAACAACTTTG 57.819 33.333 11.99 0.00 46.04 2.77
2201 2227 7.662258 AGAGATGGTGAGATTGATGATGATTTC 59.338 37.037 0.00 0.00 0.00 2.17
2289 2318 9.011095 ACTAGAAGTTAGAAAAATAAAGTGGGC 57.989 33.333 0.00 0.00 0.00 5.36
2305 2334 1.376609 GGGCTTTGATGCAGGTACGG 61.377 60.000 0.00 0.00 34.04 4.02
2352 2381 4.889409 AGCAAAACTCACTCTCCAAAATGA 59.111 37.500 0.00 0.00 0.00 2.57
2356 2385 7.483307 CAAAACTCACTCTCCAAAATGAAAGA 58.517 34.615 0.00 0.00 0.00 2.52
2392 2421 4.017126 GTCTCTTTTGGAATTGTAGGGGG 58.983 47.826 0.00 0.00 0.00 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 5.008217 GGCAATAATACAATACGTGCCTTGA 59.992 40.000 12.45 0.51 45.26 3.02
72 73 4.422073 TCTTGTTATCCTCGATGGCAAT 57.578 40.909 0.00 0.00 35.26 3.56
126 130 5.866159 AGCAAGATGACATGATGTAGAGA 57.134 39.130 0.00 0.00 0.00 3.10
302 306 4.744570 AGCAATTGACAGAATTGAGCATG 58.255 39.130 10.34 0.00 39.36 4.06
576 581 5.410355 AACAATAGCTCAATGCAACCAAT 57.590 34.783 0.00 0.00 45.94 3.16
683 688 1.948145 GAGAGGATGATGCAGCAAAGG 59.052 52.381 9.54 0.00 0.00 3.11
760 765 9.295825 TGTGATCACAATAAACTTGTTCCTATT 57.704 29.630 26.02 0.00 38.56 1.73
787 792 0.034089 GTAGCCTGCCCCTCAACAAT 60.034 55.000 0.00 0.00 0.00 2.71
822 827 6.017440 TGTTAATGCAAGCGTTAAAGAACTCT 60.017 34.615 18.06 0.00 38.59 3.24
834 839 5.029650 TCTAGTTTGTGTTAATGCAAGCG 57.970 39.130 0.00 0.00 32.37 4.68
886 891 6.293407 GGTGAACGAAATCTCATGACAAAAGA 60.293 38.462 0.00 0.00 0.00 2.52
912 917 2.242043 CAAGCCTTGTCAACATCCCTT 58.758 47.619 0.00 0.00 0.00 3.95
940 945 9.893305 CCGACAACTTTTAATCTTCATAGTTTT 57.107 29.630 0.00 0.00 0.00 2.43
951 956 6.027749 CACAATAGCCCGACAACTTTTAATC 58.972 40.000 0.00 0.00 0.00 1.75
964 969 2.672961 TTGAGACTCACAATAGCCCG 57.327 50.000 4.15 0.00 0.00 6.13
970 975 6.998074 TCATACCACTTTTTGAGACTCACAAT 59.002 34.615 4.15 0.00 0.00 2.71
981 986 7.483307 CACCCATAGATTCATACCACTTTTTG 58.517 38.462 0.00 0.00 0.00 2.44
992 997 2.158415 CCCTTGGCACCCATAGATTCAT 60.158 50.000 0.00 0.00 31.53 2.57
1071 1076 7.281040 AGACCCAACATATGCAATATTTCTG 57.719 36.000 1.58 0.00 37.44 3.02
1126 1131 4.487019 GACTCAGGTCTGTTAACAGTAGC 58.513 47.826 29.83 24.38 44.12 3.58
1192 1197 2.687566 CACCCCCTCGGCCTTAGT 60.688 66.667 0.00 0.00 33.26 2.24
1215 1220 9.185192 GAATAGAAGAAATTATCAAAATGGCCG 57.815 33.333 0.00 0.00 0.00 6.13
1228 1233 8.160106 AGTCTTGTCCACTGAATAGAAGAAATT 58.840 33.333 0.00 0.00 0.00 1.82
1279 1288 3.387050 ACATCCTAGGACACGGTAATTCC 59.613 47.826 15.42 0.00 0.00 3.01
1287 1296 2.417379 CCTGTCAACATCCTAGGACACG 60.417 54.545 15.42 8.41 35.51 4.49
1301 1310 3.383162 GGAGAGACTCCCCTGTCAA 57.617 57.895 6.54 0.00 44.36 3.18
1311 1320 2.192263 CTGGCCCTTTTAGGAGAGACT 58.808 52.381 0.00 0.00 37.67 3.24
1333 1342 7.172875 CCCATCAGTTTGCACATTTTTAATGAA 59.827 33.333 6.42 0.00 0.00 2.57
1339 1349 3.140623 GCCCATCAGTTTGCACATTTTT 58.859 40.909 0.00 0.00 0.00 1.94
1365 1375 2.069776 CAAAGTGGAGGAGGAGCCA 58.930 57.895 0.00 0.00 40.02 4.75
1384 1395 0.875059 GGTGGAGCAAAGAAGTTCCG 59.125 55.000 0.00 0.00 41.31 4.30
1394 1405 1.962807 CAACTGAATTGGGTGGAGCAA 59.037 47.619 0.00 0.00 34.34 3.91
1453 1464 6.940298 CCTTTTGTCAACCTACCATTCTCTTA 59.060 38.462 0.00 0.00 0.00 2.10
1461 1472 2.738587 TGCCTTTTGTCAACCTACCA 57.261 45.000 0.00 0.00 0.00 3.25
1472 1485 1.969923 TCATTGTCCCCTTGCCTTTTG 59.030 47.619 0.00 0.00 0.00 2.44
1477 1490 1.923356 TTCTTCATTGTCCCCTTGCC 58.077 50.000 0.00 0.00 0.00 4.52
1632 1648 7.559533 CCAGAGTACTAGGTATGATCTGCATAT 59.440 40.741 0.00 0.00 41.29 1.78
1667 1683 9.304731 CACAACCTCCAAATATGATGTAAATTG 57.695 33.333 0.00 0.00 0.00 2.32
1670 1686 6.951198 ACCACAACCTCCAAATATGATGTAAA 59.049 34.615 0.00 0.00 0.00 2.01
1682 1699 1.282653 TGTCCCACCACAACCTCCAA 61.283 55.000 0.00 0.00 0.00 3.53
1702 1719 3.772025 AGGAGATAACTCAGTGACAAGGG 59.228 47.826 2.13 0.00 44.22 3.95
1783 1802 4.078932 ACATCCAAATTTTCCTCCCCAT 57.921 40.909 0.00 0.00 0.00 4.00
1797 1817 4.141801 CGGTGGAGTAGGAATAACATCCAA 60.142 45.833 0.00 0.00 42.27 3.53
1840 1860 3.243724 AGTTGTCCTCTGACTTAGCCTT 58.756 45.455 0.00 0.00 42.28 4.35
1846 1867 6.097839 TGTTAACAGTAGTTGTCCTCTGACTT 59.902 38.462 3.59 0.00 42.28 3.01
1863 1884 6.738114 ACTCCAATGTGTTCAATGTTAACAG 58.262 36.000 14.65 1.35 37.51 3.16
1985 2007 8.038944 TCAACACCCATCATTAAAGTAGTAGAC 58.961 37.037 0.00 0.00 0.00 2.59
2031 2053 2.684881 CCCTAATCACATCAACCACAGC 59.315 50.000 0.00 0.00 0.00 4.40
2083 2105 8.491950 GTTGTTTCTCTACATTCTCAGTCTTTC 58.508 37.037 0.00 0.00 0.00 2.62
2132 2155 6.544928 GGAGATTTATCCCCAACAACATTT 57.455 37.500 0.00 0.00 32.79 2.32
2201 2227 9.137459 TCCTTCCTTCTAGATCTTACAATAGTG 57.863 37.037 0.00 0.00 0.00 2.74
2272 2301 7.096551 GCATCAAAGCCCACTTTATTTTTCTA 58.903 34.615 0.00 0.00 44.41 2.10
2289 2318 0.676466 TGGCCGTACCTGCATCAAAG 60.676 55.000 0.00 0.00 40.22 2.77
2305 2334 0.817654 GGTTTACCAAGAGGCATGGC 59.182 55.000 12.14 12.14 41.89 4.40
2365 2394 8.272173 CCCCTACAATTCCAAAAGAGACTAATA 58.728 37.037 0.00 0.00 0.00 0.98
2393 2422 4.426313 CTTCTTCCCCACCCCCGC 62.426 72.222 0.00 0.00 0.00 6.13
2394 2423 3.728373 CCTTCTTCCCCACCCCCG 61.728 72.222 0.00 0.00 0.00 5.73
2395 2424 2.793484 TACCCTTCTTCCCCACCCCC 62.793 65.000 0.00 0.00 0.00 5.40
2396 2425 0.626574 ATACCCTTCTTCCCCACCCC 60.627 60.000 0.00 0.00 0.00 4.95
2397 2426 0.551396 CATACCCTTCTTCCCCACCC 59.449 60.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.