Multiple sequence alignment - TraesCS1B01G219800

Loading Multiple Alignment...

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 TraesCS1B01G219800 chr1B 100.000 2789 0 0 1 2789 396969811 396972599 0.000000e+00 5151.0
1 TraesCS1B01G219800 chr1D 93.831 2788 113 20 1 2762 295440535 295443289 0.000000e+00 4141.0
2 TraesCS1B01G219800 chr1A 94.902 1628 60 8 744 2355 368745654 368747274 0.000000e+00 2525.0
3 TraesCS1B01G219800 chr1A 91.444 748 42 8 2 744 368744336 368745066 0.000000e+00 1007.0
4 TraesCS1B01G219800 chr1A 91.045 201 13 3 2562 2762 368747384 368747579 1.650000e-67 267.0
5 TraesCS1B01G219800 chr6D 92.000 100 7 1 2354 2453 200398812 200398714 3.750000e-29 139.0
6 TraesCS1B01G219800 chr5B 90.654 107 7 3 2348 2453 689895818 689895714 3.750000e-29 139.0
7 TraesCS1B01G219800 chr6A 91.000 100 8 1 2354 2453 596589447 596589349 1.740000e-27 134.0
8 TraesCS1B01G219800 chr6A 96.875 32 1 0 2528 2559 106716585 106716554 1.000000e-03 54.7
9 TraesCS1B01G219800 chr7B 88.991 109 9 3 2349 2456 237489415 237489309 6.270000e-27 132.0
10 TraesCS1B01G219800 chr7B 90.099 101 9 1 2356 2456 134634217 134634118 2.250000e-26 130.0
11 TraesCS1B01G219800 chr4B 90.909 99 8 1 2355 2453 539496809 539496712 6.270000e-27 132.0
12 TraesCS1B01G219800 chr6B 90.099 101 9 1 2355 2455 488851335 488851434 2.250000e-26 130.0
13 TraesCS1B01G219800 chr7D 88.182 110 9 4 2349 2456 258225686 258225579 8.110000e-26 128.0
14 TraesCS1B01G219800 chr2D 95.000 40 2 0 2522 2561 7074402 7074441 2.320000e-06 63.9
15 TraesCS1B01G219800 chr5A 100.000 30 0 0 2531 2560 46587565 46587536 3.880000e-04 56.5
16 TraesCS1B01G219800 chrUn 100.000 28 0 0 2522 2549 43095524 43095551 5.000000e-03 52.8
17 TraesCS1B01G219800 chrUn 100.000 28 0 0 2522 2549 43259034 43259007 5.000000e-03 52.8
18 TraesCS1B01G219800 chrUn 100.000 28 0 0 2522 2549 262842380 262842407 5.000000e-03 52.8
19 TraesCS1B01G219800 chrUn 100.000 28 0 0 2522 2549 293234347 293234374 5.000000e-03 52.8


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 TraesCS1B01G219800 chr1B 396969811 396972599 2788 False 5151.000000 5151 100.000000 1 2789 1 chr1B.!!$F1 2788
1 TraesCS1B01G219800 chr1D 295440535 295443289 2754 False 4141.000000 4141 93.831000 1 2762 1 chr1D.!!$F1 2761
2 TraesCS1B01G219800 chr1A 368744336 368747579 3243 False 1266.333333 2525 92.463667 2 2762 3 chr1A.!!$F1 2760

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
991 1606 0.921256 CCTTCCAGATCCCACCCCTT 60.921 60.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2815 1.339929 GCACGGGGTGAACTGAATTTT 59.66 47.619 0.0 0.0 35.23 1.82 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
72 73 4.260907 GCATGTTCAATAGCGTGACATCAT 60.261 41.667 0.00 0.00 0.00 2.45
88 89 9.463443 CGTGACATCATTTGTATGTAAGAGATA 57.537 33.333 0.00 0.00 39.18 1.98
130 131 3.913163 AGGTGGATGAAAGAGAAAGAGGT 59.087 43.478 0.00 0.00 0.00 3.85
137 138 8.217799 TGGATGAAAGAGAAAGAGGTTTTCTTA 58.782 33.333 3.90 0.00 45.41 2.10
241 253 8.256356 ACACATAGTCAAGGCTAAAGATAGAT 57.744 34.615 0.00 0.00 0.00 1.98
275 287 5.287752 ACATATCGTTGTATGTGTTGTCGAC 59.712 40.000 9.11 9.11 42.20 4.20
284 296 1.519676 TGTTGTCGACGGTGGTGTG 60.520 57.895 11.62 0.00 0.00 3.82
325 337 5.306160 TGGTAGTACAAACTTGCCTAAGAGT 59.694 40.000 2.06 0.00 37.15 3.24
374 386 4.332543 GCCAATCGTCATCATAACTGTCAA 59.667 41.667 0.00 0.00 0.00 3.18
453 466 6.158695 TCATTATCCTTTATATCTGGCCTCCC 59.841 42.308 3.32 0.00 0.00 4.30
562 576 3.539604 GATGACACAGAGATTGGGGAAG 58.460 50.000 0.00 0.00 33.14 3.46
591 605 4.428615 TCATTGTCGAATGAGTCACGTA 57.571 40.909 0.00 0.00 42.56 3.57
592 606 4.163552 TCATTGTCGAATGAGTCACGTAC 58.836 43.478 0.00 0.00 42.56 3.67
717 736 6.568869 TCAGACATTTCCAAAACGTGAAATT 58.431 32.000 8.42 2.69 38.73 1.82
766 1377 3.127895 TGCATTTCCCTTTACGATTTCCG 59.872 43.478 0.00 0.00 45.44 4.30
986 1601 2.514824 GCGCCTTCCAGATCCCAC 60.515 66.667 0.00 0.00 0.00 4.61
987 1602 2.190578 CGCCTTCCAGATCCCACC 59.809 66.667 0.00 0.00 0.00 4.61
988 1603 2.597903 GCCTTCCAGATCCCACCC 59.402 66.667 0.00 0.00 0.00 4.61
989 1604 3.061905 GCCTTCCAGATCCCACCCC 62.062 68.421 0.00 0.00 0.00 4.95
990 1605 1.308216 CCTTCCAGATCCCACCCCT 60.308 63.158 0.00 0.00 0.00 4.79
991 1606 0.921256 CCTTCCAGATCCCACCCCTT 60.921 60.000 0.00 0.00 0.00 3.95
1422 2037 4.458829 TCCGTCGCCCATCCCTCT 62.459 66.667 0.00 0.00 0.00 3.69
1978 2594 4.676986 GCCGGGGAAATAATGAAAACTGAC 60.677 45.833 2.18 0.00 0.00 3.51
2048 2666 4.223144 TGCTATGCTCTTATCACTGGGTA 58.777 43.478 0.00 0.00 0.00 3.69
2093 2712 5.767816 ACTGGGTTCTTTTGTTGTGATAC 57.232 39.130 0.00 0.00 0.00 2.24
2111 2730 7.512130 TGTGATACCTAAGAGACCGACTATTA 58.488 38.462 0.00 0.00 32.10 0.98
2145 2764 8.631695 GTTTTCATAAGCTATCGTTAGATCTCG 58.368 37.037 0.00 0.00 38.26 4.04
2191 2812 5.653769 TCTCTTGATTTGAATCCATTCCCAC 59.346 40.000 1.56 0.00 35.97 4.61
2194 2815 4.414677 TGATTTGAATCCATTCCCACACA 58.585 39.130 1.56 0.00 35.97 3.72
2228 2849 0.320596 CCGTGCAAATGCCCATGTTT 60.321 50.000 2.46 0.00 41.18 2.83
2329 2951 3.314635 AGACTGATCGATGGTACCGTTAC 59.685 47.826 8.35 0.00 0.00 2.50
2368 2996 5.516059 TGTATGATATACTCCCTCCGTCT 57.484 43.478 0.00 0.00 0.00 4.18
2382 3010 4.562757 CCCTCCGTCTCAAAATAAGTGTCA 60.563 45.833 0.00 0.00 0.00 3.58
2387 3015 6.147164 TCCGTCTCAAAATAAGTGTCATCAAC 59.853 38.462 0.00 0.00 0.00 3.18
2392 3020 9.219603 TCTCAAAATAAGTGTCATCAACCTTAG 57.780 33.333 0.00 0.00 29.73 2.18
2443 3071 5.897377 ATTGAGGAACTTATTTTGGGACG 57.103 39.130 0.00 0.00 41.55 4.79
2448 3076 3.307904 GGAACTTATTTTGGGACGGAGGA 60.308 47.826 0.00 0.00 0.00 3.71
2455 3083 2.019807 TTGGGACGGAGGAAGTAGTT 57.980 50.000 0.00 0.00 0.00 2.24
2507 3135 9.629649 TGGGATAATATGTCCTTAATACTTCCT 57.370 33.333 7.20 0.00 36.00 3.36
2513 3141 5.934402 TGTCCTTAATACTTCCTCTGTCC 57.066 43.478 0.00 0.00 0.00 4.02
2514 3142 5.590818 TGTCCTTAATACTTCCTCTGTCCT 58.409 41.667 0.00 0.00 0.00 3.85
2515 3143 5.422331 TGTCCTTAATACTTCCTCTGTCCTG 59.578 44.000 0.00 0.00 0.00 3.86
2516 3144 5.657302 GTCCTTAATACTTCCTCTGTCCTGA 59.343 44.000 0.00 0.00 0.00 3.86
2517 3145 6.154706 GTCCTTAATACTTCCTCTGTCCTGAA 59.845 42.308 0.00 0.00 0.00 3.02
2518 3146 6.903534 TCCTTAATACTTCCTCTGTCCTGAAT 59.096 38.462 0.00 0.00 0.00 2.57
2519 3147 7.403231 TCCTTAATACTTCCTCTGTCCTGAATT 59.597 37.037 0.00 0.00 0.00 2.17
2520 3148 8.705594 CCTTAATACTTCCTCTGTCCTGAATTA 58.294 37.037 0.00 0.00 0.00 1.40
2598 3276 1.349067 ACCTGTGAAGTACTCCCACC 58.651 55.000 19.47 7.77 0.00 4.61
2607 3285 2.652590 AGTACTCCCACCGTATCTGAC 58.347 52.381 0.00 0.00 0.00 3.51
2718 3396 8.322906 TGACTTTCATTTCGTGATAATTCAGT 57.677 30.769 0.00 0.00 36.54 3.41
2722 3400 6.844696 TCATTTCGTGATAATTCAGTAGGC 57.155 37.500 0.00 0.00 30.85 3.93
2767 3445 4.838904 GAAGTATTCAGGGTAAGTGGGT 57.161 45.455 0.00 0.00 46.62 4.51
2768 3446 5.945144 GAAGTATTCAGGGTAAGTGGGTA 57.055 43.478 0.00 0.00 46.62 3.69
2769 3447 6.303903 GAAGTATTCAGGGTAAGTGGGTAA 57.696 41.667 0.00 0.00 46.62 2.85
2770 3448 5.688814 AGTATTCAGGGTAAGTGGGTAAC 57.311 43.478 0.00 0.00 0.00 2.50
2771 3449 5.347978 AGTATTCAGGGTAAGTGGGTAACT 58.652 41.667 0.00 0.00 42.60 2.24
2772 3450 6.505754 AGTATTCAGGGTAAGTGGGTAACTA 58.494 40.000 0.00 0.00 38.56 2.24
2781 3459 1.109609 GTGGGTAACTACTCCCTCCG 58.890 60.000 0.00 0.00 46.07 4.63
2782 3460 0.706433 TGGGTAACTACTCCCTCCGT 59.294 55.000 0.00 0.00 43.74 4.69
2783 3461 1.077663 TGGGTAACTACTCCCTCCGTT 59.922 52.381 0.00 0.00 43.74 4.44
2784 3462 1.753649 GGGTAACTACTCCCTCCGTTC 59.246 57.143 0.00 0.00 40.48 3.95
2785 3463 1.753649 GGTAACTACTCCCTCCGTTCC 59.246 57.143 0.00 0.00 0.00 3.62
2786 3464 2.622714 GGTAACTACTCCCTCCGTTCCT 60.623 54.545 0.00 0.00 0.00 3.36
2787 3465 3.372025 GGTAACTACTCCCTCCGTTCCTA 60.372 52.174 0.00 0.00 0.00 2.94
2788 3466 3.463048 AACTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 6.279123 TGAGATTGCAGCAAAACAATTGTAA 58.721 32.000 12.97 0.00 36.65 2.41
13 14 5.840715 TGAGATTGCAGCAAAACAATTGTA 58.159 33.333 12.97 0.00 36.65 2.41
88 89 7.056635 CCACCTCATCTAAATTTCTATGTGGT 58.943 38.462 21.92 21.92 43.43 4.16
89 90 7.282585 TCCACCTCATCTAAATTTCTATGTGG 58.717 38.462 21.08 21.08 39.68 4.17
137 138 9.429359 GATGTCCATCGATTGTCTTCTATTATT 57.571 33.333 0.00 0.00 0.00 1.40
143 144 5.350504 AAGATGTCCATCGATTGTCTTCT 57.649 39.130 0.00 0.81 42.48 2.85
275 287 1.667236 ATCATGCATACACACCACCG 58.333 50.000 0.00 0.00 0.00 4.94
284 296 9.869757 TGTACTACCAATACATATCATGCATAC 57.130 33.333 0.00 0.00 0.00 2.39
374 386 8.806177 TGTCGTATTTATTTAGCGTCACATAT 57.194 30.769 0.00 0.00 0.00 1.78
382 394 8.003508 TGCTAGAATGTCGTATTTATTTAGCG 57.996 34.615 0.00 0.00 34.16 4.26
395 407 7.142021 AGTATGACAACTATGCTAGAATGTCG 58.858 38.462 17.48 0.00 42.93 4.35
479 492 4.334443 GCACAACTTTCATATGTAGTGCG 58.666 43.478 12.00 9.73 41.13 5.34
501 514 0.784778 GAAGTTCTCTTCGTGCCACG 59.215 55.000 11.80 11.80 44.19 4.94
591 605 1.879575 TTGGCTGCCTCCATACTAGT 58.120 50.000 21.03 0.00 35.77 2.57
592 606 4.223700 TCATATTGGCTGCCTCCATACTAG 59.776 45.833 21.03 7.65 35.77 2.57
661 678 9.357652 CCAATTTTGGTCTAAAATACATCAGTG 57.642 33.333 7.27 1.43 45.74 3.66
717 736 2.733218 CGTCTGCGTTTCTGCCGA 60.733 61.111 0.00 0.00 0.00 5.54
766 1377 2.203480 TGGCCCAGGAAAGTGTGC 60.203 61.111 0.00 0.00 0.00 4.57
879 1490 1.712977 CCGCTGATCTTCTTGCTGCC 61.713 60.000 0.00 0.00 0.00 4.85
971 1586 2.597903 GGGTGGGATCTGGAAGGC 59.402 66.667 0.00 0.00 0.00 4.35
975 1590 1.307866 GGAAGGGGTGGGATCTGGA 60.308 63.158 0.00 0.00 0.00 3.86
986 1601 3.809013 CCATGGGGACGGAAGGGG 61.809 72.222 2.85 0.00 35.59 4.79
987 1602 4.506255 GCCATGGGGACGGAAGGG 62.506 72.222 15.13 0.00 35.59 3.95
988 1603 4.506255 GGCCATGGGGACGGAAGG 62.506 72.222 15.13 0.00 35.59 3.46
1115 1730 4.489771 GATGGAGGGTGTGGGCGG 62.490 72.222 0.00 0.00 0.00 6.13
1131 1746 4.796231 GAGAAGAAGCGCGCGGGA 62.796 66.667 33.06 0.00 0.00 5.14
1416 2031 1.939082 CGGAGGAGGAGGAAGAGGGA 61.939 65.000 0.00 0.00 0.00 4.20
1422 2037 0.179015 CGATCTCGGAGGAGGAGGAA 60.179 60.000 4.96 0.00 40.85 3.36
1978 2594 6.609237 ATCGTGTTGAATGGATTATCACAG 57.391 37.500 0.00 0.00 0.00 3.66
2048 2666 7.815068 CAGTAACTGCACTAGAAAATCTACAGT 59.185 37.037 0.00 4.29 36.19 3.55
2093 2712 8.827677 CCAAAATTTAATAGTCGGTCTCTTAGG 58.172 37.037 0.00 0.00 0.00 2.69
2111 2730 9.705290 AACGATAGCTTATGAAAACCAAAATTT 57.295 25.926 0.00 0.00 42.67 1.82
2134 2753 3.822996 ACTGAACACACGAGATCTAACG 58.177 45.455 0.00 0.00 0.00 3.18
2145 2764 6.729187 AGAAAAGCTAATGAACTGAACACAC 58.271 36.000 0.00 0.00 0.00 3.82
2191 2812 2.360801 ACGGGGTGAACTGAATTTTGTG 59.639 45.455 0.00 0.00 0.00 3.33
2194 2815 1.339929 GCACGGGGTGAACTGAATTTT 59.660 47.619 0.00 0.00 35.23 1.82
2228 2849 6.627287 CGGAAGTTCATGATAGTAAGGACACA 60.627 42.308 5.01 0.00 0.00 3.72
2359 2987 3.933332 GACACTTATTTTGAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2368 2996 8.918202 ACTAAGGTTGATGACACTTATTTTGA 57.082 30.769 0.00 0.00 0.00 2.69
2382 3010 6.313744 GTGCAAAGTTGTACTAAGGTTGAT 57.686 37.500 5.17 0.00 40.10 2.57
2421 3049 4.705023 CCGTCCCAAAATAAGTTCCTCAAT 59.295 41.667 0.00 0.00 0.00 2.57
2428 3056 4.202535 ACTTCCTCCGTCCCAAAATAAGTT 60.203 41.667 0.00 0.00 0.00 2.66
2438 3066 1.553706 TCAACTACTTCCTCCGTCCC 58.446 55.000 0.00 0.00 0.00 4.46
2441 3069 2.322658 TGGTTCAACTACTTCCTCCGT 58.677 47.619 0.00 0.00 0.00 4.69
2481 3109 9.629649 AGGAAGTATTAAGGACATATTATCCCA 57.370 33.333 0.00 0.00 36.86 4.37
2494 3122 6.546428 TTCAGGACAGAGGAAGTATTAAGG 57.454 41.667 0.00 0.00 0.00 2.69
2504 3132 4.651503 GGACAGATAATTCAGGACAGAGGA 59.348 45.833 0.00 0.00 0.00 3.71
2507 3135 5.272402 TCAGGACAGATAATTCAGGACAGA 58.728 41.667 0.00 0.00 0.00 3.41
2508 3136 5.604758 TCAGGACAGATAATTCAGGACAG 57.395 43.478 0.00 0.00 0.00 3.51
2509 3137 6.566079 ATTCAGGACAGATAATTCAGGACA 57.434 37.500 0.00 0.00 0.00 4.02
2510 3138 8.207545 AGTAATTCAGGACAGATAATTCAGGAC 58.792 37.037 0.00 0.00 0.00 3.85
2511 3139 8.324191 AGTAATTCAGGACAGATAATTCAGGA 57.676 34.615 0.00 0.00 0.00 3.86
2512 3140 8.834465 CAAGTAATTCAGGACAGATAATTCAGG 58.166 37.037 0.00 0.00 0.00 3.86
2513 3141 9.388506 ACAAGTAATTCAGGACAGATAATTCAG 57.611 33.333 0.00 0.00 0.00 3.02
2514 3142 9.383519 GACAAGTAATTCAGGACAGATAATTCA 57.616 33.333 0.00 0.00 0.00 2.57
2515 3143 9.606631 AGACAAGTAATTCAGGACAGATAATTC 57.393 33.333 0.00 0.00 0.00 2.17
2516 3144 9.965902 AAGACAAGTAATTCAGGACAGATAATT 57.034 29.630 0.00 0.00 0.00 1.40
2519 3147 9.475620 TCTAAGACAAGTAATTCAGGACAGATA 57.524 33.333 0.00 0.00 0.00 1.98
2520 3148 8.367660 TCTAAGACAAGTAATTCAGGACAGAT 57.632 34.615 0.00 0.00 0.00 2.90
2558 3186 8.424918 ACAGGTAAGGATGAGAACTATTACATG 58.575 37.037 6.13 6.13 39.48 3.21
2598 3276 6.729187 TCTGTAATGTCATCAGTCAGATACG 58.271 40.000 2.42 0.00 34.43 3.06
2607 3285 6.510536 TGTATGCTCTCTGTAATGTCATCAG 58.489 40.000 0.00 0.00 0.00 2.90
2722 3400 6.265196 TCAGGTAGGCATTGGCAAAATATAAG 59.735 38.462 13.20 0.00 43.71 1.73
2764 3442 1.753649 GAACGGAGGGAGTAGTTACCC 59.246 57.143 0.00 0.00 45.88 3.69
2765 3443 1.753649 GGAACGGAGGGAGTAGTTACC 59.246 57.143 0.00 0.00 0.00 2.85
2766 3444 2.732763 AGGAACGGAGGGAGTAGTTAC 58.267 52.381 0.00 0.00 0.00 2.50
2767 3445 4.591321 TTAGGAACGGAGGGAGTAGTTA 57.409 45.455 0.00 0.00 0.00 2.24
2768 3446 3.463048 TTAGGAACGGAGGGAGTAGTT 57.537 47.619 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.