Multiple sequence alignment - TraesCS2A01G194200

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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 TraesCS2A01G194200 chr2A 100.000 3312 0 0 1 3312 162290446 162293757 0.000000e+00 6117
1 TraesCS2A01G194200 chr2D 95.012 3268 118 25 70 3312 138756870 138753623 0.000000e+00 5090
2 TraesCS2A01G194200 chr2D 90.000 210 14 3 1 207 138756994 138756789 7.050000e-67 265
3 TraesCS2A01G194200 chr2B 94.387 2530 92 24 12 2520 197213395 197210895 0.000000e+00 3840
4 TraesCS2A01G194200 chr2B 96.163 808 29 2 2506 3312 197210878 197210072 0.000000e+00 1319


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 TraesCS2A01G194200 chr2A 162290446 162293757 3311 False 6117.0 6117 100.000 1 3312 1 chr2A.!!$F1 3311
1 TraesCS2A01G194200 chr2D 138753623 138756994 3371 True 2677.5 5090 92.506 1 3312 2 chr2D.!!$R1 3311
2 TraesCS2A01G194200 chr2B 197210072 197213395 3323 True 2579.5 3840 95.275 12 3312 2 chr2B.!!$R1 3300

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
959 1028 0.837272 GTATACTGCCCTCCCTTGCA 59.163 55.0 0.0 0.0 35.86 4.08 F
1259 1329 0.328258 ACCAGTTTCCTTGATCCGGG 59.672 55.0 0.0 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 1886 4.142093 ACATTTATCAACCATGCAGCCTTC 60.142 41.667 0.0 0.0 0.00 3.46 R
3047 3169 2.112190 GAGAGGGTTCGGAGGAAGATT 58.888 52.381 0.0 0.0 31.49 2.40 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
109 111 0.896940 CTGGTGCAAGATTGGCCACT 60.897 55.000 3.88 0.00 0.00 4.00
156 160 7.919690 TGCTATTTTGTACATAGTGCAAGATC 58.080 34.615 7.14 0.00 39.08 2.75
157 161 7.065894 GCTATTTTGTACATAGTGCAAGATCG 58.934 38.462 7.14 3.89 39.08 3.69
158 162 7.042725 GCTATTTTGTACATAGTGCAAGATCGA 60.043 37.037 7.14 0.00 39.08 3.59
159 163 7.792374 ATTTTGTACATAGTGCAAGATCGAT 57.208 32.000 0.00 0.00 39.08 3.59
182 242 3.766591 TGGCCACCACTTACAAATTATGG 59.233 43.478 0.00 0.00 36.46 2.74
232 292 5.709966 AGAATTCGCCACAATCTTAAAACC 58.290 37.500 0.00 0.00 0.00 3.27
239 299 4.083003 GCCACAATCTTAAAACCACATCGA 60.083 41.667 0.00 0.00 0.00 3.59
243 303 7.273381 CCACAATCTTAAAACCACATCGAAATC 59.727 37.037 0.00 0.00 0.00 2.17
265 325 8.523915 AATCCTATAATTGAACTCACATGCAA 57.476 30.769 0.00 0.00 0.00 4.08
452 512 6.717413 TCAATAACAACCACACGAACTAAAC 58.283 36.000 0.00 0.00 0.00 2.01
487 550 1.743252 GCTGCTTCCAACCTCTCGG 60.743 63.158 0.00 0.00 0.00 4.63
519 582 2.047844 CTCAGCTCACCACCACCG 60.048 66.667 0.00 0.00 0.00 4.94
671 734 2.223340 GCGCATGAGGGTCTTGTTTATG 60.223 50.000 0.30 0.00 0.00 1.90
752 815 2.357881 GACGGACGGTTTGACCCC 60.358 66.667 0.00 0.00 33.75 4.95
775 838 5.258622 CGGAGATAACATTTCTTTGCTTCG 58.741 41.667 0.00 0.00 0.00 3.79
777 840 6.481984 GGAGATAACATTTCTTTGCTTCGAG 58.518 40.000 0.00 0.00 0.00 4.04
782 845 3.499918 ACATTTCTTTGCTTCGAGACAGG 59.500 43.478 0.00 0.00 0.00 4.00
809 877 7.623999 ACTAGGTGATGATAAGGTGATTGAT 57.376 36.000 0.00 0.00 0.00 2.57
845 913 4.688879 CGTACTTTGTCAACAATAGAGGCA 59.311 41.667 0.00 0.00 35.55 4.75
847 915 5.695851 ACTTTGTCAACAATAGAGGCAAG 57.304 39.130 0.00 0.00 35.55 4.01
959 1028 0.837272 GTATACTGCCCTCCCTTGCA 59.163 55.000 0.00 0.00 35.86 4.08
1043 1113 2.202756 GCCGATGGAGACCGACAC 60.203 66.667 0.00 0.00 0.00 3.67
1136 1206 2.575461 GGCCATGTTCTTGCCTGC 59.425 61.111 0.00 0.00 42.01 4.85
1182 1252 2.017782 TCTAGCTGCCTCAACTACGAG 58.982 52.381 0.00 0.00 0.00 4.18
1221 1291 4.486503 CAGCCTCAGCCTCAGCCC 62.487 72.222 0.00 0.00 41.25 5.19
1259 1329 0.328258 ACCAGTTTCCTTGATCCGGG 59.672 55.000 0.00 0.00 0.00 5.73
1260 1330 1.032114 CCAGTTTCCTTGATCCGGGC 61.032 60.000 0.00 0.00 0.00 6.13
1290 1360 0.765510 AGAGCTTTGAGTTCCCGGTT 59.234 50.000 0.00 0.00 0.00 4.44
1309 1379 0.991355 TATGGACCCCTTCCCGCATT 60.991 55.000 0.00 0.00 45.17 3.56
1349 1419 2.201022 CCGACATCCCCTACCTCGG 61.201 68.421 0.00 0.00 38.12 4.63
1400 1470 4.332637 CAACTGTGCACCAGCCGC 62.333 66.667 15.69 0.00 45.68 6.53
1416 1486 2.866028 GCAGGTGAAGAAGCAGCG 59.134 61.111 0.00 0.00 40.96 5.18
1427 1497 5.178996 GTGAAGAAGCAGCGAATGATCATAT 59.821 40.000 9.04 0.00 0.00 1.78
1498 1568 7.173735 GCTTTCAGAAATTTCAATGGATTGGTT 59.826 33.333 19.99 0.00 38.30 3.67
1705 1775 1.569479 GCAACACCAAGTCGAGCTCC 61.569 60.000 8.47 0.00 0.00 4.70
1844 1919 5.517770 GCTGCATGGTTGATAAATGTTTCTC 59.482 40.000 0.00 0.00 0.00 2.87
1862 1937 8.698973 TGTTTCTCAATTCTAATGGGTGTAAA 57.301 30.769 0.00 0.00 0.00 2.01
2047 2122 5.430089 AGGTCTAACTTGGATTAATCTGGCT 59.570 40.000 14.95 0.22 0.00 4.75
2154 2229 7.202016 TCAACATCTACATTTCCTTGTCAAC 57.798 36.000 0.00 0.00 0.00 3.18
2629 2737 4.431416 TGACTTCATAACAACACTGGGT 57.569 40.909 0.00 0.00 0.00 4.51
2671 2787 0.492730 TACCAGGGTCCCAGTTACCA 59.507 55.000 11.55 0.00 38.87 3.25
2809 2927 2.344592 ACCATAACCTCCAGAACACCA 58.655 47.619 0.00 0.00 0.00 4.17
2905 3026 6.757010 GTGACGATGATCCACTTACATTAACT 59.243 38.462 0.00 0.00 0.00 2.24
2913 3034 9.739276 TGATCCACTTACATTAACTTCTGAAAT 57.261 29.630 0.00 0.00 0.00 2.17
2938 3060 7.290110 TGTTCATTCTGTTTCTGTCTAGAGA 57.710 36.000 0.00 0.00 33.70 3.10
2985 3107 8.091449 ACAACTAATTCTCCTCTTCAGTTACTG 58.909 37.037 5.94 5.94 0.00 2.74
3047 3169 2.428925 CCTTAGGAGCGCCCCGTAA 61.429 63.158 2.29 8.02 34.66 3.18
3086 3208 1.153745 GCACGCATCGTTCTCCTCT 60.154 57.895 0.00 0.00 38.32 3.69
3099 3221 1.544691 TCTCCTCTTCCTCGGAAAACG 59.455 52.381 0.00 0.00 46.11 3.60
3146 3268 2.812619 CCCCGGAAGCATCCTCTCC 61.813 68.421 0.73 0.00 44.17 3.71
3208 3330 4.845580 CTGCAGAAGCCCCGCGAT 62.846 66.667 8.42 0.00 41.13 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 137 7.792374 ATCGATCTTGCACTATGTACAAAAT 57.208 32.000 0.00 0.00 0.00 1.82
156 160 1.529226 TTGTAAGTGGTGGCCAATCG 58.471 50.000 7.24 0.00 34.18 3.34
157 161 4.535526 AATTTGTAAGTGGTGGCCAATC 57.464 40.909 7.24 3.15 34.18 2.67
158 162 5.104982 CCATAATTTGTAAGTGGTGGCCAAT 60.105 40.000 7.24 0.00 34.18 3.16
159 163 4.221703 CCATAATTTGTAAGTGGTGGCCAA 59.778 41.667 7.24 0.00 34.18 4.52
182 242 6.944234 ATGTAAAGAAAATAGCAGTAGCCC 57.056 37.500 0.00 0.00 43.56 5.19
209 269 5.242838 TGGTTTTAAGATTGTGGCGAATTCT 59.757 36.000 3.52 0.00 0.00 2.40
215 275 3.634568 TGTGGTTTTAAGATTGTGGCG 57.365 42.857 0.00 0.00 0.00 5.69
232 292 9.045223 TGAGTTCAATTATAGGATTTCGATGTG 57.955 33.333 0.00 0.00 0.00 3.21
239 299 8.523915 TGCATGTGAGTTCAATTATAGGATTT 57.476 30.769 0.00 0.00 0.00 2.17
243 303 9.590451 AAAATTGCATGTGAGTTCAATTATAGG 57.410 29.630 7.01 0.00 37.94 2.57
265 325 9.649167 CAGAATTTCTGCCTTCATTCTTAAAAT 57.351 29.630 13.20 0.00 37.72 1.82
452 512 2.878935 GCAGCCAGGATCATTATGGGAG 60.879 54.545 0.00 0.00 34.52 4.30
487 550 0.322008 CTGAGGGGTTGAGGTTGAGC 60.322 60.000 0.00 0.00 0.00 4.26
671 734 3.902150 TCTTGATCTTGATATCGACGGC 58.098 45.455 0.00 0.00 0.00 5.68
730 793 3.101428 CAAACCGTCCGTCCGTCG 61.101 66.667 0.00 0.00 39.52 5.12
752 815 5.063438 TCGAAGCAAAGAAATGTTATCTCCG 59.937 40.000 0.00 0.00 0.00 4.63
753 816 6.313905 TCTCGAAGCAAAGAAATGTTATCTCC 59.686 38.462 0.00 0.00 0.00 3.71
775 838 2.497675 TCATCACCTAGTTGCCTGTCTC 59.502 50.000 0.00 0.00 0.00 3.36
777 840 3.550437 ATCATCACCTAGTTGCCTGTC 57.450 47.619 0.00 0.00 0.00 3.51
782 845 5.023533 TCACCTTATCATCACCTAGTTGC 57.976 43.478 0.00 0.00 0.00 4.17
788 851 6.666678 ACAATCAATCACCTTATCATCACCT 58.333 36.000 0.00 0.00 0.00 4.00
809 877 4.382291 ACAAAGTACGGAAGCATGTACAA 58.618 39.130 0.00 0.00 42.62 2.41
959 1028 0.678048 GGAAGGCTCAACCGCTCAAT 60.678 55.000 0.00 0.00 46.52 2.57
1043 1113 1.874019 CCGAGGAACTGCGACATCG 60.874 63.158 0.00 0.00 41.55 3.84
1136 1206 2.273179 TTGGAGTCGGTGTCGAGGG 61.273 63.158 0.00 0.00 46.91 4.30
1221 1291 4.988598 ACGCTGGAACTGTGGCCG 62.989 66.667 0.00 0.00 42.13 6.13
1227 1297 0.532862 AACTGGTGACGCTGGAACTG 60.533 55.000 0.00 0.00 0.00 3.16
1309 1379 1.681780 GCAATGGGACTGGAATTCGGA 60.682 52.381 0.00 0.00 0.00 4.55
1400 1470 1.129998 CATTCGCTGCTTCTTCACCTG 59.870 52.381 0.00 0.00 0.00 4.00
1416 1486 9.764363 TTGTTAGTCACAGGTATATGATCATTC 57.236 33.333 14.65 5.21 36.48 2.67
1427 1497 5.145564 ACTTCCTCTTGTTAGTCACAGGTA 58.854 41.667 0.00 0.00 36.48 3.08
1691 1761 1.001406 CTTCTTGGAGCTCGACTTGGT 59.999 52.381 7.83 0.00 0.00 3.67
1705 1775 1.805869 CTCTGGTGCCTGTCTTCTTG 58.194 55.000 0.00 0.00 0.00 3.02
1816 1886 4.142093 ACATTTATCAACCATGCAGCCTTC 60.142 41.667 0.00 0.00 0.00 3.46
1821 1891 6.623486 TGAGAAACATTTATCAACCATGCAG 58.377 36.000 0.00 0.00 35.67 4.41
2047 2122 4.681074 TGTACTGATGTCAACCTGTCAA 57.319 40.909 0.00 0.00 0.00 3.18
2154 2229 6.443934 TGGTTATGACAAATATTTGGTCGG 57.556 37.500 27.43 6.98 42.34 4.79
2193 2269 7.381948 TCAACAACTGCACATAAATGTTTGATC 59.618 33.333 10.63 0.00 39.39 2.92
2421 2497 9.308318 GCCAAGAAAAGTATGAAGTAAAACAAA 57.692 29.630 0.00 0.00 0.00 2.83
2736 2854 5.613964 ACGAAGTTTGTGCAAATTTAACG 57.386 34.783 5.59 8.25 37.78 3.18
2905 3026 8.469200 ACAGAAACAGAATGAACAATTTCAGAA 58.531 29.630 0.00 0.00 45.07 3.02
2913 3034 7.726216 TCTCTAGACAGAAACAGAATGAACAA 58.274 34.615 0.00 0.00 39.69 2.83
2926 3048 9.616156 CAGTAACTAGGTAATCTCTAGACAGAA 57.384 37.037 5.29 0.00 38.02 3.02
2938 3060 6.862469 TGTTAGTGGCAGTAACTAGGTAAT 57.138 37.500 33.42 0.00 35.55 1.89
2985 3107 4.083003 AGCGCTAGAGAGTATGAATAGTGC 60.083 45.833 8.99 7.74 45.69 4.40
3047 3169 2.112190 GAGAGGGTTCGGAGGAAGATT 58.888 52.381 0.00 0.00 31.49 2.40
3086 3208 2.280254 TGCGCGTTTTCCGAGGAA 60.280 55.556 8.43 0.00 39.56 3.36
3142 3264 3.381983 ATGTCGTGCGGCAGGAGA 61.382 61.111 24.06 23.00 31.29 3.71
3146 3268 3.049674 AACCATGTCGTGCGGCAG 61.050 61.111 1.18 0.00 31.29 4.85


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

AutoCloner maintained by Alex Coulton.