Multiple sequence alignment - TraesCS3B01G157300

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 TraesCS3B01G157300 chr3B 100.000 4274 0 0 1 4274 151117295 151113022 0.000000e+00 7893.0
1 TraesCS3B01G157300 chr3B 95.321 2800 112 12 1 2786 154423205 154420411 0.000000e+00 4427.0
2 TraesCS3B01G157300 chr3B 94.147 1401 72 5 1 1392 204205770 204207169 0.000000e+00 2124.0
3 TraesCS3B01G157300 chr5B 95.448 2790 113 12 1 2784 75080944 75083725 0.000000e+00 4436.0
4 TraesCS3B01G157300 chr5B 95.098 2795 119 14 1 2784 67028543 67025756 0.000000e+00 4386.0
5 TraesCS3B01G157300 chr2B 95.235 2791 120 12 1 2786 480005988 480008770 0.000000e+00 4405.0
6 TraesCS3B01G157300 chr2B 96.777 993 31 1 3281 4273 339517174 339518165 0.000000e+00 1655.0
7 TraesCS3B01G157300 chr2B 96.680 994 32 1 3280 4273 192408572 192409564 0.000000e+00 1652.0
8 TraesCS3B01G157300 chr2B 96.768 990 32 0 3280 4269 339525313 339526302 0.000000e+00 1652.0
9 TraesCS3B01G157300 chr2B 96.386 996 34 2 3280 4273 330496585 330495590 0.000000e+00 1639.0
10 TraesCS3B01G157300 chr7B 94.635 2796 123 12 1 2788 671265821 671263045 0.000000e+00 4307.0
11 TraesCS3B01G157300 chr7B 96.771 991 32 0 3281 4271 466968822 466967832 0.000000e+00 1653.0
12 TraesCS3B01G157300 chr1B 94.330 2804 125 15 1 2787 630555005 630552219 0.000000e+00 4266.0
13 TraesCS3B01G157300 chr1B 96.976 992 28 2 3283 4273 398215920 398214930 0.000000e+00 1664.0
14 TraesCS3B01G157300 chr1B 96.386 996 32 4 3281 4273 489795553 489796547 0.000000e+00 1637.0
15 TraesCS3B01G157300 chr1B 87.912 91 9 2 2706 2795 200989356 200989445 5.840000e-19 106.0
16 TraesCS3B01G157300 chr4B 93.786 2800 132 18 1 2788 561750576 561747807 0.000000e+00 4169.0
17 TraesCS3B01G157300 chr4B 96.667 990 32 1 3281 4269 344559067 344560056 0.000000e+00 1644.0
18 TraesCS3B01G157300 chr6B 95.041 2299 96 10 1 2284 678840589 678842884 0.000000e+00 3598.0
19 TraesCS3B01G157300 chr6B 95.273 2073 79 10 224 2284 678821581 678823646 0.000000e+00 3267.0
20 TraesCS3B01G157300 chr6B 96.378 994 36 0 3280 4273 524910079 524909086 0.000000e+00 1637.0
21 TraesCS3B01G157300 chr3D 93.034 445 29 2 2786 3229 100501663 100501220 0.000000e+00 649.0
22 TraesCS3B01G157300 chr3D 92.308 65 5 0 3219 3283 100501159 100501095 4.550000e-15 93.5
23 TraesCS3B01G157300 chr3A 91.192 193 16 1 3035 3226 555393901 555394093 1.180000e-65 261.0
24 TraesCS3B01G157300 chr3A 83.217 143 13 5 3079 3220 555482837 555482969 2.090000e-23 121.0


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 TraesCS3B01G157300 chr3B 151113022 151117295 4273 True 7893.00 7893 100.000 1 4274 1 chr3B.!!$R1 4273
1 TraesCS3B01G157300 chr3B 154420411 154423205 2794 True 4427.00 4427 95.321 1 2786 1 chr3B.!!$R2 2785
2 TraesCS3B01G157300 chr3B 204205770 204207169 1399 False 2124.00 2124 94.147 1 1392 1 chr3B.!!$F1 1391
3 TraesCS3B01G157300 chr5B 75080944 75083725 2781 False 4436.00 4436 95.448 1 2784 1 chr5B.!!$F1 2783
4 TraesCS3B01G157300 chr5B 67025756 67028543 2787 True 4386.00 4386 95.098 1 2784 1 chr5B.!!$R1 2783
5 TraesCS3B01G157300 chr2B 480005988 480008770 2782 False 4405.00 4405 95.235 1 2786 1 chr2B.!!$F4 2785
6 TraesCS3B01G157300 chr2B 339517174 339518165 991 False 1655.00 1655 96.777 3281 4273 1 chr2B.!!$F2 992
7 TraesCS3B01G157300 chr2B 192408572 192409564 992 False 1652.00 1652 96.680 3280 4273 1 chr2B.!!$F1 993
8 TraesCS3B01G157300 chr2B 339525313 339526302 989 False 1652.00 1652 96.768 3280 4269 1 chr2B.!!$F3 989
9 TraesCS3B01G157300 chr2B 330495590 330496585 995 True 1639.00 1639 96.386 3280 4273 1 chr2B.!!$R1 993
10 TraesCS3B01G157300 chr7B 671263045 671265821 2776 True 4307.00 4307 94.635 1 2788 1 chr7B.!!$R2 2787
11 TraesCS3B01G157300 chr7B 466967832 466968822 990 True 1653.00 1653 96.771 3281 4271 1 chr7B.!!$R1 990
12 TraesCS3B01G157300 chr1B 630552219 630555005 2786 True 4266.00 4266 94.330 1 2787 1 chr1B.!!$R2 2786
13 TraesCS3B01G157300 chr1B 398214930 398215920 990 True 1664.00 1664 96.976 3283 4273 1 chr1B.!!$R1 990
14 TraesCS3B01G157300 chr1B 489795553 489796547 994 False 1637.00 1637 96.386 3281 4273 1 chr1B.!!$F2 992
15 TraesCS3B01G157300 chr4B 561747807 561750576 2769 True 4169.00 4169 93.786 1 2788 1 chr4B.!!$R1 2787
16 TraesCS3B01G157300 chr4B 344559067 344560056 989 False 1644.00 1644 96.667 3281 4269 1 chr4B.!!$F1 988
17 TraesCS3B01G157300 chr6B 678840589 678842884 2295 False 3598.00 3598 95.041 1 2284 1 chr6B.!!$F2 2283
18 TraesCS3B01G157300 chr6B 678821581 678823646 2065 False 3267.00 3267 95.273 224 2284 1 chr6B.!!$F1 2060
19 TraesCS3B01G157300 chr6B 524909086 524910079 993 True 1637.00 1637 96.378 3280 4273 1 chr6B.!!$R1 993
20 TraesCS3B01G157300 chr3D 100501095 100501663 568 True 371.25 649 92.671 2786 3283 2 chr3D.!!$R1 497

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
188 189 0.446222 CGCCTTAATGGTTCCACACG 59.554 55.0 0.00 0.0 38.35 4.49 F
1376 1418 1.251527 CCGGCTAGTGTCACCTGAGT 61.252 60.0 0.00 0.0 0.00 3.41 F
3049 3102 0.100503 GAAACAAAGCACCGCAGTGT 59.899 50.0 1.33 0.0 46.35 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 1979 0.687757 ATCTTCCACTCCGGCTGCTA 60.688 55.0 0.0 0.0 33.14 3.49 R
3271 3396 0.594602 GGGGCGTCACAAAGGTTTAC 59.405 55.0 0.0 0.0 0.00 2.01 R
4006 4136 2.762535 ACACACCCAGATAAGTTCCG 57.237 50.0 0.0 0.0 0.00 4.30 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
80 81 2.508928 CCGTGGACCTGTGTTGGT 59.491 61.111 0.00 0.00 44.10 3.67
97 98 0.605319 GGTTTGAGTCCATGTCCGCA 60.605 55.000 0.00 0.00 0.00 5.69
119 120 3.934684 GCCGCTGCTCGCATTCTC 61.935 66.667 0.00 0.00 39.08 2.87
139 140 4.738998 CACCCATCGCCCAAGCCA 62.739 66.667 0.00 0.00 34.57 4.75
141 142 4.431131 CCCATCGCCCAAGCCAGT 62.431 66.667 0.00 0.00 34.57 4.00
167 168 3.009473 AGGAGCAAACTCAATAGCCTTGA 59.991 43.478 0.00 0.00 45.42 3.02
188 189 0.446222 CGCCTTAATGGTTCCACACG 59.554 55.000 0.00 0.00 38.35 4.49
263 264 2.515926 GCTCCTCGCTGATGTATCAA 57.484 50.000 0.00 0.00 36.18 2.57
483 484 1.748244 CGTGCAGGAATCCATCACCAT 60.748 52.381 15.00 0.00 0.00 3.55
930 971 3.713764 CCATAGACCACAAATCCTCCTCT 59.286 47.826 0.00 0.00 0.00 3.69
1006 1047 5.130145 CACCCAGAGACCAATAGAAAGATCT 59.870 44.000 0.00 0.00 39.82 2.75
1040 1082 1.458398 TGCCCGTGTGTATCAATTGG 58.542 50.000 5.42 0.00 0.00 3.16
1128 1170 7.893236 CGTCTAATCTATTCGAGTGTTTTTGTG 59.107 37.037 0.00 0.00 0.00 3.33
1307 1349 3.365265 GGCACAAGGGCTTCACCG 61.365 66.667 0.00 0.00 40.62 4.94
1321 1363 2.158959 CACCGTCCGCAAGATCGAC 61.159 63.158 0.00 0.00 43.02 4.20
1376 1418 1.251527 CCGGCTAGTGTCACCTGAGT 61.252 60.000 0.00 0.00 0.00 3.41
1501 1543 3.090532 GGCCCTCCCGTTCCAGAT 61.091 66.667 0.00 0.00 0.00 2.90
1712 1754 2.550606 GAGATGATCTTCTCCTACGCGT 59.449 50.000 22.26 19.17 36.87 6.01
1719 1761 1.812686 TTCTCCTACGCGTTGCACCT 61.813 55.000 20.78 0.00 0.00 4.00
1892 1934 3.755628 GGCTGCACGAGGACGGTA 61.756 66.667 0.50 0.00 44.46 4.02
2083 2126 2.607750 GGGGCACAGAGGAGTCCA 60.608 66.667 12.86 0.00 0.00 4.02
2125 2168 2.874648 AAGAAGATGATGGCGGCGCA 62.875 55.000 34.36 19.88 0.00 6.09
2467 2515 1.530323 GTTTATGTGGGCGGTGAAGT 58.470 50.000 0.00 0.00 0.00 3.01
2503 2551 3.307904 GGAGGGGAGACGAAAAATAACCA 60.308 47.826 0.00 0.00 0.00 3.67
2549 2598 2.753452 TGCCTTGTACGTTTGGTTTTGA 59.247 40.909 0.00 0.00 0.00 2.69
2573 2622 8.000127 TGATATTTGAAGATTGATCACCATCCA 59.000 33.333 0.00 0.00 0.00 3.41
2722 2774 4.026357 GGGAGGTGGGAGGGAGGT 62.026 72.222 0.00 0.00 0.00 3.85
2725 2777 4.400251 AGGTGGGAGGGAGGTCGG 62.400 72.222 0.00 0.00 0.00 4.79
2751 2804 6.887626 AAAACTAGAGAAAAATAACCGGCA 57.112 33.333 0.00 0.00 0.00 5.69
2800 2853 8.568617 AGGAGTAGAGATACCCATTAAACAAT 57.431 34.615 0.00 0.00 0.00 2.71
2802 2855 9.930693 GGAGTAGAGATACCCATTAAACAATAG 57.069 37.037 0.00 0.00 0.00 1.73
2846 2899 9.664332 AAATGCCACATCTCATATCTATTCTAC 57.336 33.333 0.00 0.00 0.00 2.59
2904 2957 2.837291 GCTTGTGTTGCCACCCCA 60.837 61.111 0.00 0.00 41.09 4.96
2907 2960 0.540365 CTTGTGTTGCCACCCCATCT 60.540 55.000 0.00 0.00 41.09 2.90
2926 2979 7.124147 CCCCATCTATTTTTCAGTACAATGGTT 59.876 37.037 0.00 0.00 31.30 3.67
2936 2989 6.968263 TCAGTACAATGGTTGGAAATTTCA 57.032 33.333 19.49 3.64 34.12 2.69
2938 2991 8.642935 TCAGTACAATGGTTGGAAATTTCATA 57.357 30.769 19.49 5.48 34.12 2.15
3049 3102 0.100503 GAAACAAAGCACCGCAGTGT 59.899 50.000 1.33 0.00 46.35 3.55
3065 3118 4.323602 CGCAGTGTAATGTGTGTACTGTAG 59.676 45.833 0.00 0.00 40.52 2.74
3079 3132 9.719279 GTGTGTACTGTAGTTATAAGATCAGTC 57.281 37.037 15.11 10.26 37.35 3.51
3109 3162 2.700897 TGGATTCTAACCTGCTAGGAGC 59.299 50.000 5.59 0.00 42.82 4.70
3115 3168 4.611367 TCTAACCTGCTAGGAGCTTTAGT 58.389 43.478 20.66 7.29 42.97 2.24
3117 3170 3.618690 ACCTGCTAGGAGCTTTAGTTG 57.381 47.619 5.59 0.00 42.97 3.16
3129 3182 6.039047 AGGAGCTTTAGTTGCAACATCATATG 59.961 38.462 30.11 14.12 0.00 1.78
3174 3227 9.143155 TCTATAGACATTGTACAATCAGCCTTA 57.857 33.333 18.25 6.25 0.00 2.69
3177 3230 7.145932 AGACATTGTACAATCAGCCTTAAAC 57.854 36.000 18.25 1.76 0.00 2.01
3185 3238 5.324409 ACAATCAGCCTTAAACAATCTCCA 58.676 37.500 0.00 0.00 0.00 3.86
3199 3252 4.159135 ACAATCTCCATTGGCACTGAAATC 59.841 41.667 6.39 0.00 43.47 2.17
3215 3268 3.059257 TGAAATCGGAAACACACACATCG 60.059 43.478 0.00 0.00 0.00 3.84
3233 3358 6.073222 ACACATCGACTTGTTGATTTTCCTAC 60.073 38.462 1.00 0.00 0.00 3.18
3675 3805 1.335132 GGATCCTGGGCTCCAACGTA 61.335 60.000 3.84 0.00 30.80 3.57
4006 4136 2.100631 CGATCACCGGGTTGTCTGC 61.101 63.158 6.32 0.00 33.91 4.26
4217 4347 1.067846 CCTCGGAAGATCAACACGTCA 60.068 52.381 0.00 0.00 40.84 4.35
4256 4386 4.057428 GAGAGGTCAGCACGCCGT 62.057 66.667 0.00 0.00 0.00 5.68
4273 4403 2.479837 CCGTTCTAAATCCTATGCGCA 58.520 47.619 14.96 14.96 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 1.890876 CGGACATGGACTCAAACCAA 58.109 50.000 0.00 0.00 40.93 3.67
80 81 0.396435 ACTGCGGACATGGACTCAAA 59.604 50.000 0.00 0.00 0.00 2.69
119 120 4.820744 CTTGGGCGATGGGTGGGG 62.821 72.222 0.00 0.00 0.00 4.96
139 140 4.938226 GCTATTGAGTTTGCTCCTAACACT 59.062 41.667 0.00 0.00 40.95 3.55
141 142 4.019321 AGGCTATTGAGTTTGCTCCTAACA 60.019 41.667 0.00 0.00 40.95 2.41
167 168 0.402504 TGTGGAACCATTAAGGCGGT 59.597 50.000 0.00 0.00 43.14 5.68
188 189 3.375642 TGATGCTTGATTCGATCTCGTC 58.624 45.455 0.00 0.00 40.80 4.20
263 264 2.754658 CCTCCCCGCACTCTACGT 60.755 66.667 0.00 0.00 0.00 3.57
483 484 3.285484 GGACGGAACTACTGATCCTACA 58.715 50.000 0.00 0.00 33.52 2.74
753 781 7.790861 TGACTTCTTTTCGAAAAAGACAAAC 57.209 32.000 22.67 11.97 36.14 2.93
953 994 2.572229 TAGGGGTGCAGGGTAATACA 57.428 50.000 0.00 0.00 0.00 2.29
1106 1148 7.295201 GCACACAAAAACACTCGAATAGATTA 58.705 34.615 0.00 0.00 0.00 1.75
1128 1170 1.328374 ACCAGAAAAACACGTACGCAC 59.672 47.619 16.72 0.00 0.00 5.34
1176 1218 1.760875 GACATCCAGCCCCCGACTA 60.761 63.158 0.00 0.00 0.00 2.59
1307 1349 3.255379 GGCGTCGATCTTGCGGAC 61.255 66.667 0.00 0.00 0.00 4.79
1501 1543 2.195567 GGAGCCACAAAGCAGTGCA 61.196 57.895 19.20 0.00 38.18 4.57
1587 1629 1.522668 CATCGCCTCAAAGGACACAA 58.477 50.000 0.00 0.00 37.67 3.33
1622 1664 2.178521 CAGGTCGTCGTCTTCCGG 59.821 66.667 0.00 0.00 37.11 5.14
1719 1761 2.933878 GAATATGGTGCGCCCGTCCA 62.934 60.000 15.15 9.11 35.15 4.02
1891 1933 1.591703 CTGGCAGGAGCAGACGTTA 59.408 57.895 6.61 0.00 44.61 3.18
1892 1934 2.345244 CTGGCAGGAGCAGACGTT 59.655 61.111 6.61 0.00 44.61 3.99
1937 1979 0.687757 ATCTTCCACTCCGGCTGCTA 60.688 55.000 0.00 0.00 33.14 3.49
2083 2126 4.476846 TCTCTCTGATCTCCTTGACTAGGT 59.523 45.833 2.75 0.00 45.03 3.08
2100 2143 2.364970 CCGCCATCATCTTCTTCTCTCT 59.635 50.000 0.00 0.00 0.00 3.10
2125 2168 1.687612 CCTGCCCTCATGTGTCCTT 59.312 57.895 0.00 0.00 0.00 3.36
2172 2215 2.503061 CCATCACTGCCCTCCTCG 59.497 66.667 0.00 0.00 0.00 4.63
2315 2358 2.202703 GTACGGCGTGCGAGGATT 60.203 61.111 24.86 0.00 0.00 3.01
2467 2515 1.460255 CCTCCCACCTGCCTTTTCA 59.540 57.895 0.00 0.00 0.00 2.69
2549 2598 8.951614 ATGGATGGTGATCAATCTTCAAATAT 57.048 30.769 0.00 0.00 0.00 1.28
2733 2785 5.416271 AGTCTGCCGGTTATTTTTCTCTA 57.584 39.130 1.90 0.00 0.00 2.43
2736 2789 6.093633 GTGAATAGTCTGCCGGTTATTTTTCT 59.906 38.462 1.90 0.00 0.00 2.52
2751 2804 2.906389 TGGAGCAGTTGGTGAATAGTCT 59.094 45.455 0.00 0.00 0.00 3.24
2800 2853 8.082852 GGCATTTTAGTCACGATTATCTCTCTA 58.917 37.037 0.00 0.00 0.00 2.43
2802 2855 6.701841 TGGCATTTTAGTCACGATTATCTCTC 59.298 38.462 0.00 0.00 0.00 3.20
2804 2857 6.257849 TGTGGCATTTTAGTCACGATTATCTC 59.742 38.462 0.00 0.00 46.75 2.75
2812 2865 3.684305 TGAGATGTGGCATTTTAGTCACG 59.316 43.478 0.00 0.00 46.75 4.35
2903 2956 8.739039 TCCAACCATTGTACTGAAAAATAGATG 58.261 33.333 0.00 0.00 0.00 2.90
2904 2957 8.877864 TCCAACCATTGTACTGAAAAATAGAT 57.122 30.769 0.00 0.00 0.00 1.98
2999 3052 8.070034 TCCAAGATATTTAGTTCGTTGTCCTA 57.930 34.615 0.00 0.00 0.00 2.94
3073 3126 9.178758 GGTTAGAATCCAATTTTAGTGACTGAT 57.821 33.333 0.00 0.00 0.00 2.90
3079 3132 7.396540 AGCAGGTTAGAATCCAATTTTAGTG 57.603 36.000 0.00 0.00 0.00 2.74
3109 3162 9.454585 CATTACCATATGATGTTGCAACTAAAG 57.545 33.333 28.61 12.57 0.00 1.85
3117 3170 9.579768 TGTTTTTACATTACCATATGATGTTGC 57.420 29.630 12.28 2.83 38.43 4.17
3152 3205 7.880713 TGTTTAAGGCTGATTGTACAATGTCTA 59.119 33.333 25.42 8.25 0.00 2.59
3153 3206 6.714810 TGTTTAAGGCTGATTGTACAATGTCT 59.285 34.615 25.42 15.49 0.00 3.41
3174 3227 3.499338 TCAGTGCCAATGGAGATTGTTT 58.501 40.909 2.05 0.00 37.82 2.83
3177 3230 4.679662 GATTTCAGTGCCAATGGAGATTG 58.320 43.478 2.05 0.00 39.04 2.67
3185 3238 2.890311 TGTTTCCGATTTCAGTGCCAAT 59.110 40.909 0.00 0.00 0.00 3.16
3199 3252 1.497991 AGTCGATGTGTGTGTTTCCG 58.502 50.000 0.00 0.00 0.00 4.30
3215 3268 7.648142 TGTCAATGTAGGAAAATCAACAAGTC 58.352 34.615 0.00 0.00 0.00 3.01
3264 3389 4.268522 CGTCACAAAGGTTTACGAAACAG 58.731 43.478 10.99 3.17 43.15 3.16
3265 3390 3.485546 GCGTCACAAAGGTTTACGAAACA 60.486 43.478 10.99 0.00 43.15 2.83
3271 3396 0.594602 GGGGCGTCACAAAGGTTTAC 59.405 55.000 0.00 0.00 0.00 2.01
3647 3777 2.446848 CCCAGGATCCAGACGCCAT 61.447 63.158 15.82 0.00 0.00 4.40
4006 4136 2.762535 ACACACCCAGATAAGTTCCG 57.237 50.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.