Multiple sequence alignment - TraesCS7A01G252100

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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 TraesCS7A01G252100 chr7A 100.000 3449 0 0 1 3449 236620958 236624406 0.000000e+00 6370
1 TraesCS7A01G252100 chr7D 93.437 3078 109 28 437 3449 222146662 222149711 0.000000e+00 4479
2 TraesCS7A01G252100 chr7D 95.538 381 15 2 1 380 222145671 222146050 2.940000e-170 608
3 TraesCS7A01G252100 chr7B 93.626 2824 96 24 697 3449 174568006 174565196 0.000000e+00 4141
4 TraesCS7A01G252100 chr4B 77.215 316 62 9 387 700 651805344 651805651 3.540000e-40 176
5 TraesCS7A01G252100 chr4B 76.699 309 63 8 387 693 386207526 386207827 2.750000e-36 163
6 TraesCS7A01G252100 chr3B 76.948 308 60 10 387 691 420422697 420422996 7.660000e-37 165
7 TraesCS7A01G252100 chr2A 77.320 291 57 8 405 693 745772648 745772365 2.750000e-36 163
8 TraesCS7A01G252100 chr5B 76.471 306 62 9 387 690 583119789 583120086 1.280000e-34 158
9 TraesCS7A01G252100 chr1B 76.527 311 58 13 387 692 13553905 13554205 4.610000e-34 156
10 TraesCS7A01G252100 chr1B 76.897 290 58 8 405 692 327730191 327729909 4.610000e-34 156
11 TraesCS7A01G252100 chr6A 76.125 289 59 8 405 691 438583128 438582848 3.590000e-30 143


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 TraesCS7A01G252100 chr7A 236620958 236624406 3448 False 6370.0 6370 100.0000 1 3449 1 chr7A.!!$F1 3448
1 TraesCS7A01G252100 chr7D 222145671 222149711 4040 False 2543.5 4479 94.4875 1 3449 2 chr7D.!!$F1 3448
2 TraesCS7A01G252100 chr7B 174565196 174568006 2810 True 4141.0 4141 93.6260 697 3449 1 chr7B.!!$R1 2752

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
890 1450 0.034059 CTCGTCCTCTGTTGGCTGTT 59.966 55.0 0.0 0.0 0.0 3.16 F
891 1451 0.249868 TCGTCCTCTGTTGGCTGTTG 60.250 55.0 0.0 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 2454 0.036010 CATCGAAGCCAAGTCCCACT 60.036 55.000 0.0 0.0 0.0 4.00 R
2720 3333 1.211457 AGCTCCTGGATTGAAGCGAAT 59.789 47.619 0.0 0.0 0.0 3.34 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
121 123 5.972107 ATCAAATTGACCAACTCCTTCTG 57.028 39.130 0.00 0.00 0.00 3.02
122 124 5.047566 TCAAATTGACCAACTCCTTCTGA 57.952 39.130 0.00 0.00 0.00 3.27
134 136 5.337578 ACTCCTTCTGACTAGCTCATTTC 57.662 43.478 0.00 0.00 0.00 2.17
136 138 4.357325 TCCTTCTGACTAGCTCATTTCCT 58.643 43.478 0.00 0.00 0.00 3.36
150 152 3.511146 TCATTTCCTCCAATTCCTGCAAC 59.489 43.478 0.00 0.00 0.00 4.17
156 158 2.629617 CTCCAATTCCTGCAACTTTGGT 59.370 45.455 13.81 0.00 38.36 3.67
210 212 0.608130 TGAGGACGAGATTGTGTGGG 59.392 55.000 0.00 0.00 0.00 4.61
211 213 0.608640 GAGGACGAGATTGTGTGGGT 59.391 55.000 0.00 0.00 0.00 4.51
269 271 1.675483 TGTGCAACGTGAGCAAGAAAT 59.325 42.857 16.34 0.00 44.64 2.17
307 309 8.970859 TTAATTCAAATGTTGGTTCACCATTT 57.029 26.923 0.00 0.00 46.97 2.32
316 318 1.611491 GGTTCACCATTTCGGCTTTGA 59.389 47.619 0.00 0.00 39.03 2.69
333 335 4.736759 GCTTTGAGGCATGATCAAGGAATG 60.737 45.833 20.35 0.00 37.91 2.67
341 343 3.726557 TGATCAAGGAATGGCTTCAGT 57.273 42.857 0.00 0.00 32.70 3.41
362 364 0.172578 CGTAAGCATCGACACCTCCA 59.827 55.000 0.00 0.00 0.00 3.86
391 411 1.331756 CAAATCCGAATTGGCCTCTCG 59.668 52.381 3.32 9.52 37.80 4.04
400 420 0.608640 TTGGCCTCTCGGACTCTTTC 59.391 55.000 3.32 0.00 39.94 2.62
401 421 0.541998 TGGCCTCTCGGACTCTTTCA 60.542 55.000 3.32 0.00 39.94 2.69
422 442 1.198094 TCCCAACAGGAAGGCGATGA 61.198 55.000 0.00 0.00 43.78 2.92
424 444 1.361668 CCAACAGGAAGGCGATGACG 61.362 60.000 0.00 0.00 42.93 4.35
432 452 4.891566 GGCGATGACGTCTCTTGT 57.108 55.556 17.92 0.00 41.20 3.16
461 1018 3.108376 ACCTCTTGGACCATCTAGAACC 58.892 50.000 0.00 0.00 37.04 3.62
462 1019 3.246167 ACCTCTTGGACCATCTAGAACCT 60.246 47.826 0.00 0.00 37.04 3.50
496 1053 3.340034 TGTCTTCCGTCACAAAAGTGTT 58.660 40.909 0.00 0.00 35.07 3.32
504 1061 3.374058 CGTCACAAAAGTGTTCCACTCTT 59.626 43.478 0.00 0.00 44.62 2.85
582 1139 2.095059 AGAAGTTGCGTTTGATCATGCC 60.095 45.455 11.24 0.00 0.00 4.40
683 1240 4.808558 CAAATCTTTTGCCTCGGATTCAA 58.191 39.130 0.00 0.00 0.00 2.69
684 1241 5.229423 CAAATCTTTTGCCTCGGATTCAAA 58.771 37.500 0.00 2.08 0.00 2.69
685 1242 5.467035 AATCTTTTGCCTCGGATTCAAAA 57.533 34.783 13.31 13.31 37.36 2.44
686 1243 4.927978 TCTTTTGCCTCGGATTCAAAAA 57.072 36.364 14.28 4.48 38.65 1.94
724 1281 1.862201 GGTCATCGAAACAACACACGA 59.138 47.619 0.00 0.00 39.01 4.35
728 1285 4.433304 GTCATCGAAACAACACACGAAAAG 59.567 41.667 0.00 0.00 38.22 2.27
732 1289 5.450171 TCGAAACAACACACGAAAAGAAAA 58.550 33.333 0.00 0.00 0.00 2.29
733 1290 5.913514 TCGAAACAACACACGAAAAGAAAAA 59.086 32.000 0.00 0.00 0.00 1.94
885 1445 1.957562 ACGTCTCGTCCTCTGTTGG 59.042 57.895 0.00 0.00 33.69 3.77
886 1446 1.444553 CGTCTCGTCCTCTGTTGGC 60.445 63.158 0.00 0.00 0.00 4.52
887 1447 1.867919 CGTCTCGTCCTCTGTTGGCT 61.868 60.000 0.00 0.00 0.00 4.75
888 1448 0.389166 GTCTCGTCCTCTGTTGGCTG 60.389 60.000 0.00 0.00 0.00 4.85
889 1449 0.827925 TCTCGTCCTCTGTTGGCTGT 60.828 55.000 0.00 0.00 0.00 4.40
890 1450 0.034059 CTCGTCCTCTGTTGGCTGTT 59.966 55.000 0.00 0.00 0.00 3.16
891 1451 0.249868 TCGTCCTCTGTTGGCTGTTG 60.250 55.000 0.00 0.00 0.00 3.33
892 1452 1.845809 CGTCCTCTGTTGGCTGTTGC 61.846 60.000 0.00 0.00 38.76 4.17
893 1453 0.536006 GTCCTCTGTTGGCTGTTGCT 60.536 55.000 0.00 0.00 39.59 3.91
894 1454 0.535780 TCCTCTGTTGGCTGTTGCTG 60.536 55.000 0.00 0.00 39.59 4.41
895 1455 0.820891 CCTCTGTTGGCTGTTGCTGT 60.821 55.000 0.00 0.00 39.59 4.40
971 1532 4.361971 TCGCCGTCTCCCTCACCT 62.362 66.667 0.00 0.00 0.00 4.00
1078 1645 0.621082 CTTCTCCTTCCCCAACCCTC 59.379 60.000 0.00 0.00 0.00 4.30
1089 1656 0.978146 CCAACCCTCTCCTCCACGAT 60.978 60.000 0.00 0.00 0.00 3.73
1105 1672 0.810031 CGATGCCTCCAACCCTTACG 60.810 60.000 0.00 0.00 0.00 3.18
1338 1905 2.200092 GAGATCCCCGCTCCCTCT 59.800 66.667 0.00 0.00 0.00 3.69
1351 1918 2.416432 CCCTCTCCTCGGGTCGTTC 61.416 68.421 0.00 0.00 36.91 3.95
1669 2236 1.506718 CCAATGTCTGCTGCTGCTG 59.493 57.895 17.00 15.94 40.48 4.41
1671 2238 2.341101 AATGTCTGCTGCTGCTGCC 61.341 57.895 25.44 12.89 40.48 4.85
1683 2250 2.745492 GCTGCCGCTGCTTCTTCT 60.745 61.111 14.47 0.00 38.71 2.85
1684 2251 2.331132 GCTGCCGCTGCTTCTTCTT 61.331 57.895 14.47 0.00 38.71 2.52
1685 2252 1.792941 CTGCCGCTGCTTCTTCTTC 59.207 57.895 0.70 0.00 38.71 2.87
1794 2361 0.828762 TTGCTGGCCTTGCACTCATT 60.829 50.000 20.55 0.00 40.40 2.57
1828 2395 0.250513 GGAGAATGCTCGGTCAGGTT 59.749 55.000 0.00 0.00 42.25 3.50
1887 2454 2.842496 AGCTCTTCCAATGTCCATCAGA 59.158 45.455 0.00 0.00 0.00 3.27
1944 2511 4.307432 CTGATTGTGTTGTCCTAGACGTT 58.693 43.478 0.00 0.00 34.95 3.99
2014 2581 3.181488 TGTTGGCGATGCTATTCAAATGG 60.181 43.478 0.00 0.00 0.00 3.16
2266 2833 4.957296 TCACCAGGTTTTCTCTGAGTTAC 58.043 43.478 4.32 1.89 34.36 2.50
2268 2835 4.511826 CACCAGGTTTTCTCTGAGTTACAC 59.488 45.833 4.32 0.00 34.36 2.90
2453 3020 4.318332 TGCTGTTTGAAGTCATGACCTAG 58.682 43.478 22.21 10.73 0.00 3.02
2639 3235 6.737720 TCATATCTGAGTGAGCAATACCTT 57.262 37.500 0.00 0.00 0.00 3.50
2715 3328 1.697982 AGTGCGGGGTAAAGAACTCTT 59.302 47.619 0.00 0.00 37.91 2.85
2720 3333 2.882137 CGGGGTAAAGAACTCTTGCAAA 59.118 45.455 0.00 0.00 36.12 3.68
2780 3394 4.139859 TGGAAGTTCACGACCAGTTAAA 57.860 40.909 5.01 0.00 0.00 1.52
2888 3502 6.423776 TCATCAACTGATAGGTGCATATGA 57.576 37.500 6.97 0.00 31.59 2.15
2938 3553 4.986034 CCATTGTACGACAGTAAGTGTTCA 59.014 41.667 0.00 0.00 40.56 3.18
3001 3617 6.920210 GTGCCAGAATCTATTTTTAGCCATTC 59.080 38.462 0.00 0.00 0.00 2.67
3003 3619 6.145535 CCAGAATCTATTTTTAGCCATTCGC 58.854 40.000 0.00 0.00 37.98 4.70
3018 3634 3.421888 CCATTCGCAACTTCGTTTTTCTG 59.578 43.478 0.00 0.00 0.00 3.02
3022 3638 3.617706 TCGCAACTTCGTTTTTCTGTACA 59.382 39.130 0.00 0.00 0.00 2.90
3243 3861 4.278310 AGGTTGCCTTGTTCAGTAAACTT 58.722 39.130 0.00 0.00 38.76 2.66
3256 3874 3.428870 CAGTAAACTTGTCTACAGCGTGG 59.571 47.826 0.00 0.00 0.00 4.94
3291 3919 6.709846 AGCATATACAATTGAGCTCTCCTTTC 59.290 38.462 16.19 0.00 0.00 2.62
3378 4006 4.590222 CCAATTATTTAGCTGGGCAGGAAT 59.410 41.667 0.00 0.00 0.00 3.01
3386 4014 1.615384 GCTGGGCAGGAATCTTTCTGT 60.615 52.381 0.40 0.00 33.81 3.41
3416 4052 2.785562 TGGTGGGGTCAACTTTATTCG 58.214 47.619 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 75 2.953466 TATCCAAGAACCGTCCTTCG 57.047 50.000 0.00 0.00 39.52 3.79
121 123 4.819088 GGAATTGGAGGAAATGAGCTAGTC 59.181 45.833 0.00 0.00 0.00 2.59
122 124 4.476479 AGGAATTGGAGGAAATGAGCTAGT 59.524 41.667 0.00 0.00 0.00 2.57
134 136 2.028748 CCAAAGTTGCAGGAATTGGAGG 60.029 50.000 14.10 0.00 42.46 4.30
136 138 2.627699 GACCAAAGTTGCAGGAATTGGA 59.372 45.455 21.91 0.00 42.46 3.53
156 158 4.023980 AGATGGAAGTCGTGAATGGTAGA 58.976 43.478 0.00 0.00 0.00 2.59
210 212 0.105964 TGCCCACTGACAGTGTGTAC 59.894 55.000 29.09 17.46 44.50 2.90
211 213 0.833949 TTGCCCACTGACAGTGTGTA 59.166 50.000 29.09 18.13 44.50 2.90
250 252 2.046313 CATTTCTTGCTCACGTTGCAC 58.954 47.619 11.90 0.00 40.40 4.57
269 271 7.961351 ACATTTGAATTAAAGGTGGTCAATCA 58.039 30.769 0.00 0.00 41.31 2.57
307 309 0.252761 TGATCATGCCTCAAAGCCGA 59.747 50.000 0.00 0.00 0.00 5.54
316 318 1.217183 AGCCATTCCTTGATCATGCCT 59.783 47.619 0.00 0.00 0.00 4.75
333 335 1.324736 CGATGCTTACGAACTGAAGCC 59.675 52.381 4.31 0.00 46.12 4.35
341 343 1.135199 GGAGGTGTCGATGCTTACGAA 60.135 52.381 0.00 0.00 41.31 3.85
362 364 2.428171 CAATTCGGATTTGGTGCCAGAT 59.572 45.455 5.01 0.00 0.00 2.90
391 411 3.084786 CCTGTTGGGAATGAAAGAGTCC 58.915 50.000 0.00 0.00 38.18 3.85
422 442 4.463186 AGAGGTAAGCAATACAAGAGACGT 59.537 41.667 0.00 0.00 36.14 4.34
424 444 5.582665 CCAAGAGGTAAGCAATACAAGAGAC 59.417 44.000 2.63 0.00 36.14 3.36
432 452 4.721776 AGATGGTCCAAGAGGTAAGCAATA 59.278 41.667 0.00 0.00 35.89 1.90
496 1053 4.021229 TGGCTAGAATTACGAAGAGTGGA 58.979 43.478 0.00 0.00 0.00 4.02
501 1058 5.401531 AGTGTTGGCTAGAATTACGAAGA 57.598 39.130 0.00 0.00 0.00 2.87
504 1061 6.036735 GCATTTAGTGTTGGCTAGAATTACGA 59.963 38.462 0.00 0.00 0.00 3.43
539 1096 1.078426 CCCCTGCGGTAGACCAAAG 60.078 63.158 0.00 0.00 35.14 2.77
582 1139 7.387948 CCATATTACAAAAGGATTACTCTCCCG 59.612 40.741 0.00 0.00 35.79 5.14
664 1221 5.467035 TTTTTGAATCCGAGGCAAAAGAT 57.533 34.783 0.00 0.00 41.02 2.40
732 1289 8.849168 TCTTCTTGTGTTGTGTTGATATGATTT 58.151 29.630 0.00 0.00 0.00 2.17
733 1290 8.394971 TCTTCTTGTGTTGTGTTGATATGATT 57.605 30.769 0.00 0.00 0.00 2.57
822 1379 7.574607 GGCTATACCTACAAATAATGCCCTAT 58.425 38.462 0.00 0.00 34.51 2.57
885 1445 1.363807 GGGACCAAACAGCAACAGC 59.636 57.895 0.00 0.00 0.00 4.40
886 1446 1.654220 CGGGACCAAACAGCAACAG 59.346 57.895 0.00 0.00 0.00 3.16
887 1447 2.485795 GCGGGACCAAACAGCAACA 61.486 57.895 0.00 0.00 0.00 3.33
888 1448 2.335011 GCGGGACCAAACAGCAAC 59.665 61.111 0.00 0.00 0.00 4.17
889 1449 3.283684 CGCGGGACCAAACAGCAA 61.284 61.111 0.00 0.00 0.00 3.91
890 1450 3.545124 ATCGCGGGACCAAACAGCA 62.545 57.895 6.13 0.00 0.00 4.41
891 1451 2.746277 ATCGCGGGACCAAACAGC 60.746 61.111 6.13 0.00 0.00 4.40
892 1452 3.039202 GCATCGCGGGACCAAACAG 62.039 63.158 6.13 0.00 0.00 3.16
893 1453 3.053291 GCATCGCGGGACCAAACA 61.053 61.111 6.13 0.00 0.00 2.83
894 1454 1.933115 AATGCATCGCGGGACCAAAC 61.933 55.000 6.13 0.00 0.00 2.93
895 1455 1.677300 AATGCATCGCGGGACCAAA 60.677 52.632 6.13 0.00 0.00 3.28
1022 1589 4.175489 CGATGTGCTGCAGCTGGC 62.175 66.667 36.61 25.92 42.66 4.85
1078 1645 1.617018 TTGGAGGCATCGTGGAGGAG 61.617 60.000 0.00 0.00 0.00 3.69
1146 1713 3.866582 GGGGCAGGGGAGTCGATG 61.867 72.222 0.00 0.00 0.00 3.84
1338 1905 3.744719 CAGCGAACGACCCGAGGA 61.745 66.667 0.00 0.00 0.00 3.71
1669 2236 1.569479 AACGAAGAAGAAGCAGCGGC 61.569 55.000 0.00 0.00 41.61 6.53
1671 2238 0.861837 ACAACGAAGAAGAAGCAGCG 59.138 50.000 0.00 0.00 0.00 5.18
1683 2250 0.958091 CCAATGCCTCCAACAACGAA 59.042 50.000 0.00 0.00 0.00 3.85
1684 2251 0.109532 TCCAATGCCTCCAACAACGA 59.890 50.000 0.00 0.00 0.00 3.85
1685 2252 0.523072 CTCCAATGCCTCCAACAACG 59.477 55.000 0.00 0.00 0.00 4.10
1779 2346 1.820519 GAATCAATGAGTGCAAGGCCA 59.179 47.619 5.01 0.00 0.00 5.36
1794 2361 2.159179 TCTCCTCCACCGATGAATCA 57.841 50.000 0.00 0.00 0.00 2.57
1887 2454 0.036010 CATCGAAGCCAAGTCCCACT 60.036 55.000 0.00 0.00 0.00 4.00
1944 2511 3.826157 CCAGTCCAAAATAGTTCCTTGCA 59.174 43.478 0.00 0.00 0.00 4.08
2014 2581 3.507233 TCTCCATGTGCAAAATCCTGAAC 59.493 43.478 0.00 0.00 0.00 3.18
2266 2833 6.315144 TCACCATTACCAACATCTATTTCGTG 59.685 38.462 0.00 0.00 0.00 4.35
2268 2835 6.918892 TCACCATTACCAACATCTATTTCG 57.081 37.500 0.00 0.00 0.00 3.46
2453 3020 1.555967 AGTCTGGAACAGCCTCTCTC 58.444 55.000 0.00 0.00 43.12 3.20
2639 3235 5.128827 AGCCTCGGAAGACAATATGAAGTTA 59.871 40.000 0.00 0.00 35.39 2.24
2715 3328 2.094597 CCTGGATTGAAGCGAATTTGCA 60.095 45.455 19.82 0.00 37.31 4.08
2720 3333 1.211457 AGCTCCTGGATTGAAGCGAAT 59.789 47.619 0.00 0.00 0.00 3.34
2770 3384 4.521256 TGTGGCATTAACCTTTAACTGGTC 59.479 41.667 0.00 0.00 36.69 4.02
2780 3394 3.495331 TGTCAACATGTGGCATTAACCT 58.505 40.909 0.00 0.00 36.75 3.50
2888 3502 4.639310 GCAGGACAGAACAATCTTCATGAT 59.361 41.667 0.00 0.00 36.89 2.45
3018 3634 2.838386 TACTGCTCGTCGGAATGTAC 57.162 50.000 0.00 0.00 0.00 2.90
3022 3638 4.000988 ACAAAATTACTGCTCGTCGGAAT 58.999 39.130 0.00 0.00 0.00 3.01
3171 3789 2.495669 ACCCCATAAAAGCCAATTGACG 59.504 45.455 7.12 0.00 0.00 4.35
3213 3831 2.793278 ACAAGGCAACCTTAAAAGCG 57.207 45.000 0.00 0.00 42.67 4.68
3243 3861 5.847111 ATAGATTAACCACGCTGTAGACA 57.153 39.130 0.00 0.00 0.00 3.41
3281 3909 2.937519 CAAATAGGGGGAAAGGAGAGC 58.062 52.381 0.00 0.00 0.00 4.09
3291 3919 3.450817 CCAACCTAAAAGCAAATAGGGGG 59.549 47.826 11.84 9.26 42.51 5.40
3416 4052 3.276857 TGCTCATCCAAGAAGCTTGATC 58.723 45.455 2.10 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.