Multiple sequence alignment - TraesCS7B01G185200

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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 TraesCS7B01G185200 chr7B 100.000 4384 0 0 1 4384 300326995 300331378 0.000000e+00 8096.0
1 TraesCS7B01G185200 chr7B 96.341 4400 142 9 1 4384 132452508 132448112 0.000000e+00 7215.0
2 TraesCS7B01G185200 chr7B 95.570 3025 129 5 79 3101 344957770 344960791 0.000000e+00 4839.0
3 TraesCS7B01G185200 chr7B 94.381 1317 47 7 3088 4384 344964123 344965432 0.000000e+00 1997.0
4 TraesCS7B01G185200 chr7B 96.386 83 2 1 1 83 344948694 344948775 7.650000e-28 135.0
5 TraesCS7B01G185200 chr5B 91.938 3374 217 22 399 3738 269528748 269525396 0.000000e+00 4673.0
6 TraesCS7B01G185200 chr5B 93.231 650 42 1 3733 4382 269495446 269494799 0.000000e+00 955.0
7 TraesCS7B01G185200 chr5B 88.166 676 72 5 672 1341 347127021 347127694 0.000000e+00 798.0
8 TraesCS7B01G185200 chr5B 83.032 554 74 8 748 1294 289570947 289571487 6.590000e-133 484.0
9 TraesCS7B01G185200 chr5B 82.585 557 76 8 748 1297 118648314 118647772 5.130000e-129 472.0
10 TraesCS7B01G185200 chr5B 84.746 354 46 7 941 1293 51015645 51015991 9.020000e-92 348.0
11 TraesCS7B01G185200 chr5B 86.159 289 27 8 1339 1619 347127753 347128036 2.560000e-77 300.0
12 TraesCS7B01G185200 chr5B 97.959 49 1 0 239 287 269528801 269528753 7.810000e-13 86.1
13 TraesCS7B01G185200 chr3B 97.538 2640 56 6 1407 4044 661422053 661419421 0.000000e+00 4506.0
14 TraesCS7B01G185200 chr3B 86.996 1092 90 15 2133 3220 387731385 387730342 0.000000e+00 1182.0
15 TraesCS7B01G185200 chr3B 86.055 1090 92 30 3321 4359 387730328 387729248 0.000000e+00 1116.0
16 TraesCS7B01G185200 chr3B 86.491 607 48 16 324 928 397326929 397326355 1.720000e-178 636.0
17 TraesCS7B01G185200 chr3B 89.888 445 40 4 3827 4270 414212607 414212167 6.360000e-158 568.0
18 TraesCS7B01G185200 chr3B 84.175 297 39 6 134 424 428199660 428199954 9.280000e-72 281.0
19 TraesCS7B01G185200 chr3B 79.641 167 27 6 80 241 728796178 728796342 3.580000e-21 113.0
20 TraesCS7B01G185200 chr5D 94.742 2092 95 9 394 2480 235200460 235202541 0.000000e+00 3240.0
21 TraesCS7B01G185200 chr5D 92.415 1292 67 7 2471 3738 235209931 235211215 0.000000e+00 1814.0
22 TraesCS7B01G185200 chr5D 93.538 650 37 2 3733 4382 235250129 235250773 0.000000e+00 963.0
23 TraesCS7B01G185200 chr5D 94.421 233 11 2 1 233 235199438 235199668 1.500000e-94 357.0
24 TraesCS7B01G185200 chr5D 100.000 52 0 0 236 287 235200409 235200460 3.610000e-16 97.1
25 TraesCS7B01G185200 chr5D 97.222 36 1 0 2090 2125 104696775 104696740 1.320000e-05 62.1
26 TraesCS7B01G185200 chr5D 94.872 39 2 0 2087 2125 123562606 123562644 1.320000e-05 62.1
27 TraesCS7B01G185200 chr5A 96.151 1481 51 3 394 1873 607812920 607814395 0.000000e+00 2414.0
28 TraesCS7B01G185200 chr5A 94.771 1090 35 2 3313 4382 607831996 607833083 0.000000e+00 1677.0
29 TraesCS7B01G185200 chr5A 95.833 288 10 2 1 287 607812634 607812920 8.590000e-127 464.0
30 TraesCS7B01G185200 chr5A 95.257 253 8 2 1969 2221 607827833 607828081 8.830000e-107 398.0
31 TraesCS7B01G185200 chr5A 94.872 39 2 0 2087 2125 219532093 219532131 1.320000e-05 62.1
32 TraesCS7B01G185200 chr7A 85.941 1764 165 26 2127 3859 354012254 354013965 0.000000e+00 1807.0
33 TraesCS7B01G185200 chr7A 88.189 254 26 3 676 928 38082812 38082562 2.560000e-77 300.0
34 TraesCS7B01G185200 chr4B 87.224 1088 97 17 2139 3220 233233971 233232920 0.000000e+00 1201.0
35 TraesCS7B01G185200 chr4B 87.786 655 49 17 3730 4359 233232375 233231727 0.000000e+00 737.0
36 TraesCS7B01G185200 chr4B 87.351 419 36 13 3324 3730 233232903 233232490 8.590000e-127 464.0
37 TraesCS7B01G185200 chr1B 87.222 1080 100 16 2139 3214 163775012 163776057 0.000000e+00 1195.0
38 TraesCS7B01G185200 chr1B 87.062 657 50 19 3730 4359 163776609 163777257 0.000000e+00 710.0
39 TraesCS7B01G185200 chr1B 86.557 424 41 14 3321 3732 163776077 163776496 1.860000e-123 453.0
40 TraesCS7B01G185200 chr4D 87.763 809 62 12 2133 2934 144436799 144437577 0.000000e+00 911.0
41 TraesCS7B01G185200 chr2A 86.700 812 73 15 2127 2934 396394732 396395512 0.000000e+00 869.0
42 TraesCS7B01G185200 chr2A 85.135 814 76 15 2136 2934 137521207 137520424 0.000000e+00 791.0
43 TraesCS7B01G185200 chr2A 90.187 214 15 6 462 670 381735590 381735378 1.550000e-69 274.0
44 TraesCS7B01G185200 chr2A 83.172 309 28 11 4072 4359 216517905 216518210 1.210000e-65 261.0
45 TraesCS7B01G185200 chr1D 87.690 593 60 9 2136 2723 214082974 214082390 0.000000e+00 678.0
46 TraesCS7B01G185200 chr2D 88.565 446 44 6 3827 4270 225136385 225135945 6.450000e-148 534.0
47 TraesCS7B01G185200 chr6A 84.419 430 53 11 134 551 230690969 230691396 1.130000e-110 411.0
48 TraesCS7B01G185200 chr6A 91.038 212 15 4 462 670 197864494 197864284 2.580000e-72 283.0
49 TraesCS7B01G185200 chr4A 86.667 375 43 6 134 503 181378146 181377774 4.080000e-110 409.0
50 TraesCS7B01G185200 chr4A 84.691 405 46 10 1655 2047 715763719 715763319 1.480000e-104 390.0
51 TraesCS7B01G185200 chr4A 90.625 64 5 1 178 241 44785187 44785249 2.810000e-12 84.2
52 TraesCS7B01G185200 chr2B 84.536 291 42 2 1051 1341 410264709 410264996 7.180000e-73 285.0
53 TraesCS7B01G185200 chr6B 85.849 212 25 4 724 935 154508824 154508618 2.050000e-53 220.0
54 TraesCS7B01G185200 chr6B 97.183 71 2 0 1813 1883 539536042 539536112 2.140000e-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 TraesCS7B01G185200 chr7B 300326995 300331378 4383 False 8096.000000 8096 100.000000 1 4384 1 chr7B.!!$F1 4383
1 TraesCS7B01G185200 chr7B 132448112 132452508 4396 True 7215.000000 7215 96.341000 1 4384 1 chr7B.!!$R1 4383
2 TraesCS7B01G185200 chr7B 344957770 344965432 7662 False 3418.000000 4839 94.975500 79 4384 2 chr7B.!!$F3 4305
3 TraesCS7B01G185200 chr5B 269525396 269528801 3405 True 2379.550000 4673 94.948500 239 3738 2 chr5B.!!$R3 3499
4 TraesCS7B01G185200 chr5B 269494799 269495446 647 True 955.000000 955 93.231000 3733 4382 1 chr5B.!!$R2 649
5 TraesCS7B01G185200 chr5B 347127021 347128036 1015 False 549.000000 798 87.162500 672 1619 2 chr5B.!!$F3 947
6 TraesCS7B01G185200 chr5B 289570947 289571487 540 False 484.000000 484 83.032000 748 1294 1 chr5B.!!$F2 546
7 TraesCS7B01G185200 chr5B 118647772 118648314 542 True 472.000000 472 82.585000 748 1297 1 chr5B.!!$R1 549
8 TraesCS7B01G185200 chr3B 661419421 661422053 2632 True 4506.000000 4506 97.538000 1407 4044 1 chr3B.!!$R3 2637
9 TraesCS7B01G185200 chr3B 387729248 387731385 2137 True 1149.000000 1182 86.525500 2133 4359 2 chr3B.!!$R4 2226
10 TraesCS7B01G185200 chr3B 397326355 397326929 574 True 636.000000 636 86.491000 324 928 1 chr3B.!!$R1 604
11 TraesCS7B01G185200 chr5D 235209931 235211215 1284 False 1814.000000 1814 92.415000 2471 3738 1 chr5D.!!$F2 1267
12 TraesCS7B01G185200 chr5D 235199438 235202541 3103 False 1231.366667 3240 96.387667 1 2480 3 chr5D.!!$F4 2479
13 TraesCS7B01G185200 chr5D 235250129 235250773 644 False 963.000000 963 93.538000 3733 4382 1 chr5D.!!$F3 649
14 TraesCS7B01G185200 chr5A 607812634 607814395 1761 False 1439.000000 2414 95.992000 1 1873 2 chr5A.!!$F2 1872
15 TraesCS7B01G185200 chr5A 607827833 607833083 5250 False 1037.500000 1677 95.014000 1969 4382 2 chr5A.!!$F3 2413
16 TraesCS7B01G185200 chr7A 354012254 354013965 1711 False 1807.000000 1807 85.941000 2127 3859 1 chr7A.!!$F1 1732
17 TraesCS7B01G185200 chr4B 233231727 233233971 2244 True 800.666667 1201 87.453667 2139 4359 3 chr4B.!!$R1 2220
18 TraesCS7B01G185200 chr1B 163775012 163777257 2245 False 786.000000 1195 86.947000 2139 4359 3 chr1B.!!$F1 2220
19 TraesCS7B01G185200 chr4D 144436799 144437577 778 False 911.000000 911 87.763000 2133 2934 1 chr4D.!!$F1 801
20 TraesCS7B01G185200 chr2A 396394732 396395512 780 False 869.000000 869 86.700000 2127 2934 1 chr2A.!!$F2 807
21 TraesCS7B01G185200 chr2A 137520424 137521207 783 True 791.000000 791 85.135000 2136 2934 1 chr2A.!!$R1 798
22 TraesCS7B01G185200 chr1D 214082390 214082974 584 True 678.000000 678 87.690000 2136 2723 1 chr1D.!!$R1 587

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
711 1451 0.834687 AAGGAACGTCCCAGCCACTA 60.835 55.0 0.0 0.0 37.19 2.74 F
2177 3012 0.178767 CATGCTCTGTTCCGATGGGA 59.821 55.0 0.0 0.0 41.83 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2446 4110 0.390124 AACCGTAGAACAGGCGTCAA 59.610 50.000 0.00 0.0 0.00 3.18 R
4018 10601 1.340991 TGGCAGGCCCAAAGATTCTAC 60.341 52.381 8.02 0.0 41.82 2.59 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
297 1036 3.845259 GCTCGGCCGGTGTATGGA 61.845 66.667 27.83 1.15 0.00 3.41
299 1038 1.812686 GCTCGGCCGGTGTATGGATA 61.813 60.000 27.83 0.00 0.00 2.59
396 1135 2.604139 CTACCTCCAGATCCCCTCTTC 58.396 57.143 0.00 0.00 29.16 2.87
527 1266 3.386078 GTCTCTTCCATGCTGGTCTATCA 59.614 47.826 2.68 0.00 39.03 2.15
541 1280 4.192317 GGTCTATCAATTCCTTGACGCTT 58.808 43.478 0.00 0.00 43.92 4.68
655 1395 1.532868 CTTGCTCCTCTCGTGTTTTGG 59.467 52.381 0.00 0.00 0.00 3.28
711 1451 0.834687 AAGGAACGTCCCAGCCACTA 60.835 55.000 0.00 0.00 37.19 2.74
960 1712 1.980765 TGATCTCTGCCTGTTTCCTGT 59.019 47.619 0.00 0.00 0.00 4.00
966 1718 0.981183 TGCCTGTTTCCTGTACCGAT 59.019 50.000 0.00 0.00 0.00 4.18
987 1739 6.128172 CCGATAGAGCTTTGTGTTCATCTTTT 60.128 38.462 0.00 0.00 39.76 2.27
1030 1787 1.302431 CACCACATCGGACTTGGCA 60.302 57.895 6.62 0.00 38.63 4.92
1091 1848 8.764287 CGGCAAAATAACTTCTCTTTTCAAAAT 58.236 29.630 0.00 0.00 0.00 1.82
1150 1908 4.272748 AGGAAGTCAGCAAAAGTCGTTTAC 59.727 41.667 0.00 0.00 0.00 2.01
1243 2001 7.290857 TCTGAAATTAGTTGTCGCATAGAAC 57.709 36.000 0.00 0.00 0.00 3.01
1385 2206 6.923508 GCACTTACTTTTTGTGAGCCTATTTT 59.076 34.615 0.00 0.00 35.91 1.82
1437 2261 6.406692 AGTTAGACACTGTGCTTCTTCTTA 57.593 37.500 7.90 0.00 32.83 2.10
2177 3012 0.178767 CATGCTCTGTTCCGATGGGA 59.821 55.000 0.00 0.00 41.83 4.37
2187 3022 2.801631 CCGATGGGACTCCTCTGCC 61.802 68.421 0.00 0.00 34.06 4.85
2223 3058 5.367945 TGGTTGAGGTTTGTACTTCTCTT 57.632 39.130 0.00 0.00 31.99 2.85
2224 3059 6.488769 TGGTTGAGGTTTGTACTTCTCTTA 57.511 37.500 0.00 0.00 31.99 2.10
2298 3133 1.254313 GTTTGCCTTTGTTTCGTTCGC 59.746 47.619 0.00 0.00 0.00 4.70
2428 3804 0.318107 GAAATGCGTGTGTGCTGCTT 60.318 50.000 0.00 0.00 35.36 3.91
2446 4110 3.004210 TGCTTGATAAAATGCGTGTGTGT 59.996 39.130 0.00 0.00 0.00 3.72
2622 4561 1.007734 GTCGTTGTGCTCTGACCGA 60.008 57.895 0.00 0.00 0.00 4.69
2668 4660 5.123502 GGTTGTACGATCTCTTCTGTCACTA 59.876 44.000 0.00 0.00 0.00 2.74
2832 4916 2.897846 TCGGGCGTTGTGTGTTGG 60.898 61.111 0.00 0.00 0.00 3.77
2893 4978 2.884012 CAGGGTGTGTATGCTTGTTTCA 59.116 45.455 0.00 0.00 0.00 2.69
3072 5686 1.078759 CCGAGGTGCAGCTACTTTCG 61.079 60.000 20.22 17.21 0.00 3.46
3133 9218 4.097741 CCACTTGATTGGTTTTGTCTCACA 59.902 41.667 0.00 0.00 0.00 3.58
3466 9907 6.485313 CACAACAGTCTATTGAGGTTGGTTAA 59.515 38.462 18.79 0.00 40.26 2.01
3883 10465 9.758651 GTTTCTGTTATTCTTATGTTTTGGGTT 57.241 29.630 0.00 0.00 0.00 4.11
4018 10601 3.315470 CAGAATGATGCTGGATGTCCTTG 59.685 47.826 0.00 0.00 39.69 3.61
4118 10707 1.378531 TTGTTCAGATATGCACGCCC 58.621 50.000 0.00 0.00 0.00 6.13
4136 10725 3.561725 CGCCCTTTTGTCATCTAGAATCC 59.438 47.826 0.00 0.00 0.00 3.01
4147 10736 7.568349 TGTCATCTAGAATCCTTGCATTTAGT 58.432 34.615 0.00 0.00 0.00 2.24
4329 10936 5.275067 TGCAAGTTACTTGGCAAAGAAAT 57.725 34.783 24.13 0.00 41.31 2.17
4332 10939 6.597280 TGCAAGTTACTTGGCAAAGAAATTTT 59.403 30.769 24.13 0.00 41.31 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 142 3.157949 GCCTAGAGCTCGGGCCTT 61.158 66.667 30.51 8.95 39.96 4.35
297 1036 2.189521 CAAACTCCCGGCCGCTAT 59.810 61.111 22.85 0.73 0.00 2.97
337 1076 1.370587 GGCTCGTCAGCTAGACTCGT 61.371 60.000 12.45 0.00 46.03 4.18
359 1098 2.041216 GGTAGGAGGACAAACCAACCAT 59.959 50.000 0.00 0.00 42.04 3.55
396 1135 1.715785 GGGAGAGGAGGAGAATGAGG 58.284 60.000 0.00 0.00 0.00 3.86
527 1266 4.278170 TCATGAACAAAGCGTCAAGGAATT 59.722 37.500 0.00 0.00 0.00 2.17
541 1280 5.282055 AGAACAGAGTCAGTCATGAACAA 57.718 39.130 0.00 0.00 37.14 2.83
655 1395 3.056322 ACCATACACCTCGGTCAAACTAC 60.056 47.826 0.00 0.00 0.00 2.73
711 1451 7.891498 ATTTCACAAAACAAAGTAGGGTACT 57.109 32.000 0.00 0.00 41.73 2.73
960 1712 4.794278 TGAACACAAAGCTCTATCGGTA 57.206 40.909 0.00 0.00 0.00 4.02
966 1718 7.283127 ACAGAAAAAGATGAACACAAAGCTCTA 59.717 33.333 0.00 0.00 0.00 2.43
987 1739 6.031964 ACTCCTTCCATAGATCCTACAGAA 57.968 41.667 0.00 0.00 0.00 3.02
1091 1848 7.667219 TGTGATAGATAGATCATGTGCTGAGTA 59.333 37.037 0.00 0.00 38.11 2.59
1095 1852 6.689554 AGTGTGATAGATAGATCATGTGCTG 58.310 40.000 0.00 0.00 38.11 4.41
1150 1908 6.600822 ACACCATGGATTCTTACTCATTCAAG 59.399 38.462 21.47 0.00 0.00 3.02
1243 2001 2.820197 GAGCCTAGTTTCCCAAACCAAG 59.180 50.000 0.00 0.00 42.34 3.61
1356 2175 4.440112 GGCTCACAAAAAGTAAGTGCAGTT 60.440 41.667 12.28 12.28 33.44 3.16
1385 2206 8.055181 ACCATTCAGCCTCTTATTATTTTGAGA 58.945 33.333 0.00 0.00 0.00 3.27
1485 2314 6.656902 AGAGGCATATGAATTCTCTCAACAA 58.343 36.000 6.97 0.00 29.81 2.83
1558 2388 5.411361 TGCTTGAAGTTATATTGCGTGAGTT 59.589 36.000 0.00 0.00 0.00 3.01
2154 2989 1.274703 ATCGGAACAGAGCATGGGGT 61.275 55.000 0.00 0.00 0.00 4.95
2190 3025 2.594303 TCAACCAGCGGCAACCAG 60.594 61.111 1.45 0.00 0.00 4.00
2223 3058 0.927537 CGGCGAAGAACATGCGAATA 59.072 50.000 0.00 0.00 0.00 1.75
2224 3059 1.715585 CGGCGAAGAACATGCGAAT 59.284 52.632 0.00 0.00 0.00 3.34
2298 3133 2.108344 AAACCGTACCAAACTGCGCG 62.108 55.000 0.00 0.00 0.00 6.86
2428 3804 4.532276 GTCAACACACACGCATTTTATCA 58.468 39.130 0.00 0.00 0.00 2.15
2446 4110 0.390124 AACCGTAGAACAGGCGTCAA 59.610 50.000 0.00 0.00 0.00 3.18
2632 4614 3.852286 TCGTACAACCTGCGAAATACAT 58.148 40.909 0.00 0.00 33.62 2.29
2668 4660 5.738909 AGAAACCTTGATGAGTCGAATGAT 58.261 37.500 0.00 0.00 0.00 2.45
2832 4916 6.129769 CGAAATATAAGTAGCACGAGAACGAC 60.130 42.308 0.00 0.00 42.66 4.34
2893 4978 4.765339 GCCTCCAAAACAGGTATAACAACT 59.235 41.667 0.00 0.00 32.98 3.16
3072 5686 3.450904 TGGGTATATAGCATGAGGGGTC 58.549 50.000 13.65 0.00 0.00 4.46
3133 9218 2.345244 CCAGAGCTCGCCTTGTGT 59.655 61.111 8.37 0.00 0.00 3.72
3737 10317 5.645624 TCGAAATTCTGTGAAGCAACAAAA 58.354 33.333 0.00 0.00 0.00 2.44
3925 10507 9.823098 GATGCTATTAATTTGCAGAGTATGAAG 57.177 33.333 16.92 0.00 40.18 3.02
4018 10601 1.340991 TGGCAGGCCCAAAGATTCTAC 60.341 52.381 8.02 0.00 41.82 2.59
4118 10707 6.748333 TGCAAGGATTCTAGATGACAAAAG 57.252 37.500 0.00 0.00 0.00 2.27
4199 10788 9.383519 GTGAGAAATAATCTGTCCAATCTACAA 57.616 33.333 0.00 0.00 38.96 2.41
4332 10939 5.744171 ACATGTATCCACTATGCAGACAAA 58.256 37.500 0.00 0.00 33.37 2.83


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

AutoCloner maintained by Alex Coulton.