Multiple sequence alignment - TraesCS6A01G106700

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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 TraesCS6A01G106700 chr6A 100.000 3157 0 0 1 3157 74541296 74544452 0.000000e+00 5830
1 TraesCS6A01G106700 chr6A 95.909 1271 52 0 1303 2573 602833708 602834978 0.000000e+00 2060
2 TraesCS6A01G106700 chr7B 96.799 2093 66 1 485 2576 459588683 459586591 0.000000e+00 3493
3 TraesCS6A01G106700 chr7B 93.602 719 38 7 1 717 458098012 458097300 0.000000e+00 1066
4 TraesCS6A01G106700 chr7B 92.697 178 10 2 2 178 579524374 579524549 1.450000e-63 254
5 TraesCS6A01G106700 chr4D 96.568 1661 49 3 916 2575 451883451 451881798 0.000000e+00 2745
6 TraesCS6A01G106700 chr2B 96.454 1664 56 2 913 2573 638286678 638288341 0.000000e+00 2743
7 TraesCS6A01G106700 chr2B 96.527 979 34 0 1595 2573 39141195 39142173 0.000000e+00 1620
8 TraesCS6A01G106700 chr2B 95.356 689 28 2 912 1599 39117544 39118229 0.000000e+00 1092
9 TraesCS6A01G106700 chr2B 77.835 388 52 18 220 577 710279168 710279551 3.190000e-50 209
10 TraesCS6A01G106700 chr2B 85.714 140 18 2 1154 1292 34080966 34080828 2.540000e-31 147
11 TraesCS6A01G106700 chr2D 95.678 1666 59 6 913 2573 344567689 344569346 0.000000e+00 2665
12 TraesCS6A01G106700 chr2D 79.775 267 43 10 2586 2841 626336955 626336689 1.930000e-42 183
13 TraesCS6A01G106700 chr5B 95.610 1663 69 3 914 2573 547904887 547906548 0.000000e+00 2663
14 TraesCS6A01G106700 chr5B 94.019 719 39 4 1 717 325085816 325085100 0.000000e+00 1086
15 TraesCS6A01G106700 chr5B 93.602 719 40 5 1 717 455364211 455364925 0.000000e+00 1068
16 TraesCS6A01G106700 chr3B 95.373 1664 74 2 913 2573 629799281 629800944 0.000000e+00 2643
17 TraesCS6A01G106700 chr3B 93.872 718 37 5 2 717 603633500 603634212 0.000000e+00 1075
18 TraesCS6A01G106700 chr3B 89.509 591 47 7 2580 3157 764578452 764579040 0.000000e+00 734
19 TraesCS6A01G106700 chr1B 95.261 1667 76 2 913 2576 109348891 109347225 0.000000e+00 2638
20 TraesCS6A01G106700 chr3D 86.677 1291 159 9 1289 2573 549726280 549724997 0.000000e+00 1419
21 TraesCS6A01G106700 chr6B 94.437 719 34 6 1 717 100950040 100950754 0.000000e+00 1101
22 TraesCS6A01G106700 chr6B 93.602 719 40 4 1 717 513641300 513640586 0.000000e+00 1068
23 TraesCS6A01G106700 chr7A 93.463 719 42 4 1 717 220538324 220537609 0.000000e+00 1062
24 TraesCS6A01G106700 chr7A 90.051 593 40 10 2580 3157 45917102 45916514 0.000000e+00 750
25 TraesCS6A01G106700 chr4B 93.324 719 40 6 1 717 642684162 642683450 0.000000e+00 1055
26 TraesCS6A01G106700 chr5A 87.692 650 53 7 179 804 375557264 375556618 0.000000e+00 732


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 TraesCS6A01G106700 chr6A 74541296 74544452 3156 False 5830 5830 100.000 1 3157 1 chr6A.!!$F1 3156
1 TraesCS6A01G106700 chr6A 602833708 602834978 1270 False 2060 2060 95.909 1303 2573 1 chr6A.!!$F2 1270
2 TraesCS6A01G106700 chr7B 459586591 459588683 2092 True 3493 3493 96.799 485 2576 1 chr7B.!!$R2 2091
3 TraesCS6A01G106700 chr7B 458097300 458098012 712 True 1066 1066 93.602 1 717 1 chr7B.!!$R1 716
4 TraesCS6A01G106700 chr4D 451881798 451883451 1653 True 2745 2745 96.568 916 2575 1 chr4D.!!$R1 1659
5 TraesCS6A01G106700 chr2B 638286678 638288341 1663 False 2743 2743 96.454 913 2573 1 chr2B.!!$F3 1660
6 TraesCS6A01G106700 chr2B 39141195 39142173 978 False 1620 1620 96.527 1595 2573 1 chr2B.!!$F2 978
7 TraesCS6A01G106700 chr2B 39117544 39118229 685 False 1092 1092 95.356 912 1599 1 chr2B.!!$F1 687
8 TraesCS6A01G106700 chr2D 344567689 344569346 1657 False 2665 2665 95.678 913 2573 1 chr2D.!!$F1 1660
9 TraesCS6A01G106700 chr5B 547904887 547906548 1661 False 2663 2663 95.610 914 2573 1 chr5B.!!$F2 1659
10 TraesCS6A01G106700 chr5B 325085100 325085816 716 True 1086 1086 94.019 1 717 1 chr5B.!!$R1 716
11 TraesCS6A01G106700 chr5B 455364211 455364925 714 False 1068 1068 93.602 1 717 1 chr5B.!!$F1 716
12 TraesCS6A01G106700 chr3B 629799281 629800944 1663 False 2643 2643 95.373 913 2573 1 chr3B.!!$F2 1660
13 TraesCS6A01G106700 chr3B 603633500 603634212 712 False 1075 1075 93.872 2 717 1 chr3B.!!$F1 715
14 TraesCS6A01G106700 chr3B 764578452 764579040 588 False 734 734 89.509 2580 3157 1 chr3B.!!$F3 577
15 TraesCS6A01G106700 chr1B 109347225 109348891 1666 True 2638 2638 95.261 913 2576 1 chr1B.!!$R1 1663
16 TraesCS6A01G106700 chr3D 549724997 549726280 1283 True 1419 1419 86.677 1289 2573 1 chr3D.!!$R1 1284
17 TraesCS6A01G106700 chr6B 100950040 100950754 714 False 1101 1101 94.437 1 717 1 chr6B.!!$F1 716
18 TraesCS6A01G106700 chr6B 513640586 513641300 714 True 1068 1068 93.602 1 717 1 chr6B.!!$R1 716
19 TraesCS6A01G106700 chr7A 220537609 220538324 715 True 1062 1062 93.463 1 717 1 chr7A.!!$R2 716
20 TraesCS6A01G106700 chr7A 45916514 45917102 588 True 750 750 90.051 2580 3157 1 chr7A.!!$R1 577
21 TraesCS6A01G106700 chr4B 642683450 642684162 712 True 1055 1055 93.324 1 717 1 chr4B.!!$R1 716
22 TraesCS6A01G106700 chr5A 375556618 375557264 646 True 732 732 87.692 179 804 1 chr5A.!!$R1 625

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
396 421 0.109226 ACTCGAAGAAGTAGCGCCAC 60.109 55.0 2.29 0.0 34.09 5.01 F
1968 2006 0.107410 TGCTGACCACGGTGAACTTT 60.107 50.0 10.28 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2032 2070 0.034089 GCCTTTAGTGATGGTGGCCT 60.034 55.0 3.32 0.0 34.81 5.19 R
2893 2940 2.843401 TGGCTTCTGTAAAGCGGTAA 57.157 45.0 3.89 0.0 43.89 2.85 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
54 55 6.294508 CCGGTCAAAATCTTACCACTCAATTT 60.295 38.462 0.00 0.00 32.55 1.82
168 170 1.032794 TCTCGCATAGCCACTACTGG 58.967 55.000 0.00 0.00 41.13 4.00
204 206 2.089980 GGAAGTCTTCATGCATGTGCT 58.910 47.619 25.43 15.64 42.66 4.40
218 220 3.441572 GCATGTGCTCCTTGTTCAATACT 59.558 43.478 0.00 0.00 38.21 2.12
287 289 1.862602 GACACCAAATCCCGCCACAC 61.863 60.000 0.00 0.00 0.00 3.82
319 322 2.196595 CTAACCTCATCACCCCAGGAA 58.803 52.381 0.00 0.00 0.00 3.36
326 329 0.991920 ATCACCCCAGGAAACGACAT 59.008 50.000 0.00 0.00 0.00 3.06
369 394 2.223340 CGGCTATGTTCAAATGGACTGC 60.223 50.000 0.00 0.00 0.00 4.40
396 421 0.109226 ACTCGAAGAAGTAGCGCCAC 60.109 55.000 2.29 0.00 34.09 5.01
652 678 2.024941 ACCATCCATTCCCAAGGAGTTC 60.025 50.000 0.00 0.00 37.34 3.01
653 679 2.659428 CATCCATTCCCAAGGAGTTCC 58.341 52.381 0.00 0.00 37.34 3.62
711 741 6.478673 GGGTTTTTATTCACAGAAACAAGTGG 59.521 38.462 0.00 0.00 36.43 4.00
1051 1081 0.255890 AGCCAATGATACCAGCGGTT 59.744 50.000 5.57 0.00 37.09 4.44
1082 1112 7.841282 TTACCCATGGTAATTCTGAAAAACA 57.159 32.000 11.73 0.00 42.44 2.83
1083 1113 6.096673 ACCCATGGTAATTCTGAAAAACAC 57.903 37.500 11.73 0.00 32.11 3.32
1390 1423 8.144478 TGTTTATGTTATCCTCTATCTGCTGTC 58.856 37.037 0.00 0.00 0.00 3.51
1465 1498 2.863740 CGGAAGCACAATAAGCGATACA 59.136 45.455 0.00 0.00 37.01 2.29
1474 1507 9.273016 AGCACAATAAGCGATACAAGTATATTT 57.727 29.630 0.00 0.00 37.01 1.40
1650 1683 2.814805 ACATAGGTGAGCCTTGCAAT 57.185 45.000 0.00 0.00 44.18 3.56
1968 2006 0.107410 TGCTGACCACGGTGAACTTT 60.107 50.000 10.28 0.00 0.00 2.66
2007 2045 2.111043 CAACCACCGTCACAGCCT 59.889 61.111 0.00 0.00 0.00 4.58
2026 2064 2.424956 CCTGCTTTATCAAGGGAGTTGC 59.575 50.000 0.00 0.00 35.94 4.17
2032 2070 5.741673 GCTTTATCAAGGGAGTTGCCAAAAA 60.742 40.000 0.00 0.00 38.95 1.94
2068 2106 1.293498 GCTGGAGCGACTTCTTCCA 59.707 57.895 0.00 0.00 0.00 3.53
2576 2618 3.454375 CGCAACGGGTCATCTAGTAATT 58.546 45.455 0.00 0.00 0.00 1.40
2577 2619 3.489785 CGCAACGGGTCATCTAGTAATTC 59.510 47.826 0.00 0.00 0.00 2.17
2578 2620 4.694339 GCAACGGGTCATCTAGTAATTCT 58.306 43.478 0.00 0.00 0.00 2.40
2645 2687 4.319766 GGACTGAACTATGTTTGTGTGCAG 60.320 45.833 0.00 0.00 41.74 4.41
2653 2695 1.202867 TGTTTGTGTGCAGCATAGGGA 60.203 47.619 0.00 0.00 0.00 4.20
2690 2732 5.738619 TGCAAGAGTGTGGAGTTATAAGA 57.261 39.130 0.00 0.00 0.00 2.10
2726 2770 9.741647 GTTAGTATAGTACAAATGACCACCTAC 57.258 37.037 0.00 0.00 0.00 3.18
2735 2779 2.465860 TGACCACCTACGAAATGGTG 57.534 50.000 9.52 10.68 46.86 4.17
2839 2885 2.172082 CCATCCAGGACACATCAGACAT 59.828 50.000 0.00 0.00 41.22 3.06
2879 2926 4.099266 GGAAAGGTATGGCATGCAATACAA 59.901 41.667 35.21 9.50 35.17 2.41
2906 2953 9.997482 AAAACATATTGTATTACCGCTTTACAG 57.003 29.630 0.00 0.00 0.00 2.74
2917 2964 2.032178 CCGCTTTACAGAAGCCAATAGC 59.968 50.000 5.29 0.00 40.02 2.97
2974 3021 6.770785 ACTTCAGCCAGATAAAAAGTTACACA 59.229 34.615 0.00 0.00 0.00 3.72
3014 3061 5.065914 AGGCGCATGTAAAAGATGATGTAT 58.934 37.500 10.83 0.00 0.00 2.29
3054 3101 8.293114 ACGAAAAACAAATCAACCACATATTC 57.707 30.769 0.00 0.00 0.00 1.75
3062 3109 7.768582 ACAAATCAACCACATATTCGTGATAGA 59.231 33.333 0.00 0.00 39.34 1.98
3142 3199 2.823196 TCGAGTGCCAATATTTTGCG 57.177 45.000 3.08 0.00 0.00 4.85
3144 3201 1.467204 CGAGTGCCAATATTTTGCGCA 60.467 47.619 5.66 5.66 36.97 6.09
3151 3208 3.799917 GCCAATATTTTGCGCATAGGCTT 60.800 43.478 12.75 0.00 38.10 4.35
3153 3210 3.923017 ATATTTTGCGCATAGGCTTCC 57.077 42.857 12.75 0.00 38.10 3.46
3155 3212 1.252175 TTTTGCGCATAGGCTTCCAA 58.748 45.000 12.75 0.00 38.10 3.53
3156 3213 1.473258 TTTGCGCATAGGCTTCCAAT 58.527 45.000 12.75 0.00 38.10 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 138 0.976641 TGCGAGATGGTCTTGGAACT 59.023 50.000 0.00 0.00 0.00 3.01
137 139 2.029838 ATGCGAGATGGTCTTGGAAC 57.970 50.000 0.00 0.00 31.79 3.62
287 289 3.887621 TGAGGTTAGGGTTTCTCATCG 57.112 47.619 0.00 0.00 32.10 3.84
319 322 4.790123 GCTCTAGCGTAGATTCATGTCGTT 60.790 45.833 0.00 0.00 33.66 3.85
369 394 4.143514 CGCTACTTCTTCGAGTTTGTCTTG 60.144 45.833 0.00 0.00 0.00 3.02
396 421 4.873129 CGACACTCGGGCGGATGG 62.873 72.222 0.00 0.00 36.00 3.51
404 429 1.734477 CTTGCAGGTCGACACTCGG 60.734 63.158 18.91 1.86 40.88 4.63
537 563 3.556423 GCAAACTCTCCCCTCGAAACTTA 60.556 47.826 0.00 0.00 0.00 2.24
711 741 1.001378 ACGCTTGTTTCTGCAACATCC 60.001 47.619 0.00 0.00 45.17 3.51
836 866 5.123186 TGAAAGTTTCTCACGCAAAGAAAGA 59.877 36.000 16.33 0.00 41.94 2.52
1167 1199 6.579666 ACATACTTGATCAACTTGCATGTT 57.420 33.333 11.92 11.92 0.00 2.71
1390 1423 4.396166 AGGAGATCATTGTAAAAGGTTGCG 59.604 41.667 0.00 0.00 0.00 4.85
1465 1498 6.570378 GCTTTGCATGGGCGATAAATATACTT 60.570 38.462 0.00 0.00 45.35 2.24
1474 1507 0.740149 CTTGCTTTGCATGGGCGATA 59.260 50.000 0.00 0.00 45.35 2.92
1650 1683 6.183360 GGCGACTAAACTCATCTAAGTAGTGA 60.183 42.308 0.00 0.00 0.00 3.41
1968 2006 4.202451 TGTTCCATCTCCAGTTGTGATTGA 60.202 41.667 0.00 0.00 0.00 2.57
2007 2045 2.224992 TGGCAACTCCCTTGATAAAGCA 60.225 45.455 0.00 0.00 37.61 3.91
2026 2064 1.341080 AGTGATGGTGGCCTTTTTGG 58.659 50.000 3.32 0.00 39.35 3.28
2032 2070 0.034089 GCCTTTAGTGATGGTGGCCT 60.034 55.000 3.32 0.00 34.81 5.19
2068 2106 0.611200 TTCGTTCATGTGGGTCCGAT 59.389 50.000 0.00 0.00 0.00 4.18
2594 2636 6.053005 AGGATTCACGTTGTCTTGACTTTAA 58.947 36.000 2.35 0.00 0.00 1.52
2598 2640 3.753294 AGGATTCACGTTGTCTTGACT 57.247 42.857 2.35 0.00 0.00 3.41
2645 2687 4.660789 ACAATTTGATGCTTCCCTATGC 57.339 40.909 2.79 0.00 0.00 3.14
2653 2695 5.235616 CACTCTTGCAAACAATTTGATGCTT 59.764 36.000 22.65 0.40 43.26 3.91
2706 2750 6.534475 TTCGTAGGTGGTCATTTGTACTAT 57.466 37.500 0.00 0.00 0.00 2.12
2760 2804 7.759489 TGTTTGTAGTGCTTAGAAATTCCAT 57.241 32.000 0.00 0.00 28.61 3.41
2801 2847 6.258507 CCTGGATGGTTTGTTTCTTCTTTTTG 59.741 38.462 0.00 0.00 0.00 2.44
2802 2848 6.156083 TCCTGGATGGTTTGTTTCTTCTTTTT 59.844 34.615 0.00 0.00 37.07 1.94
2810 2856 2.955660 TGTGTCCTGGATGGTTTGTTTC 59.044 45.455 0.00 0.00 37.07 2.78
2839 2885 5.536916 ACCTTTCCACCATGTCGAAAAATTA 59.463 36.000 0.00 0.00 0.00 1.40
2893 2940 2.843401 TGGCTTCTGTAAAGCGGTAA 57.157 45.000 3.89 0.00 43.89 2.85
2950 2997 7.202016 TGTGTAACTTTTTATCTGGCTGAAG 57.798 36.000 0.00 0.00 38.04 3.02
2991 3038 3.282021 ACATCATCTTTTACATGCGCCT 58.718 40.909 4.18 0.00 0.00 5.52
3014 3061 9.941664 TTTGTTTTTCGTTCCGTAATAATACAA 57.058 25.926 0.00 0.00 32.02 2.41
3025 3072 4.027214 GTGGTTGATTTGTTTTTCGTTCCG 60.027 41.667 0.00 0.00 0.00 4.30
3030 3077 7.114247 ACGAATATGTGGTTGATTTGTTTTTCG 59.886 33.333 0.00 0.00 36.67 3.46
3043 3090 8.255206 TGTAGTTTCTATCACGAATATGTGGTT 58.745 33.333 0.00 0.00 40.31 3.67
3054 3101 7.539712 AAACATCCATGTAGTTTCTATCACG 57.460 36.000 0.00 0.00 40.80 4.35
3106 3163 7.027161 GGCACTCGATATTGTGTTACAAAATT 58.973 34.615 6.04 0.00 41.96 1.82


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

AutoCloner maintained by Alex Coulton.