Multiple sequence alignment - TraesCS3D01G227000

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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 TraesCS3D01G227000 chr3D 100.000 4201 0 0 1 4201 308580590 308584790 0.000000e+00 7758.0
1 TraesCS3D01G227000 chr7A 96.764 3894 116 6 4 3888 120878022 120874130 0.000000e+00 6484.0
2 TraesCS3D01G227000 chr7A 96.417 1200 40 2 1 1197 60244582 60245781 0.000000e+00 1975.0
3 TraesCS3D01G227000 chr7A 96.745 891 23 4 2836 3723 1838457 1837570 0.000000e+00 1480.0
4 TraesCS3D01G227000 chr7A 97.637 804 18 1 3086 3888 60245776 60246579 0.000000e+00 1378.0
5 TraesCS3D01G227000 chr7A 96.007 551 21 1 1023 1572 1838995 1838445 0.000000e+00 894.0
6 TraesCS3D01G227000 chr7B 94.985 3789 174 8 114 3888 247418239 247414453 0.000000e+00 5930.0
7 TraesCS3D01G227000 chr7B 97.222 36 1 0 4092 4127 240322223 240322188 1.260000e-05 62.1
8 TraesCS3D01G227000 chr2B 94.077 2769 153 6 1 2764 343519859 343517097 0.000000e+00 4194.0
9 TraesCS3D01G227000 chr2B 89.114 542 35 10 2754 3295 344017673 344018190 0.000000e+00 652.0
10 TraesCS3D01G227000 chr2B 96.990 299 6 1 1736 2031 60148192 60147894 2.260000e-137 499.0
11 TraesCS3D01G227000 chr2B 92.271 207 15 1 2550 2756 188267592 188267387 4.110000e-75 292.0
12 TraesCS3D01G227000 chr2B 90.821 207 18 1 2550 2756 188028820 188028615 4.140000e-70 276.0
13 TraesCS3D01G227000 chr2B 89.952 209 18 2 2262 2468 568040157 568039950 2.490000e-67 267.0
14 TraesCS3D01G227000 chr6D 95.627 1578 60 5 1 1572 458962518 458960944 0.000000e+00 2523.0
15 TraesCS3D01G227000 chr6D 97.224 1369 32 4 2836 4201 458960956 458959591 0.000000e+00 2313.0
16 TraesCS3D01G227000 chr6D 96.042 1137 39 4 1633 2764 57918086 57916951 0.000000e+00 1845.0
17 TraesCS3D01G227000 chr6D 94.336 1183 45 4 2129 3289 318035056 318033874 0.000000e+00 1794.0
18 TraesCS3D01G227000 chr6D 90.274 987 53 23 1329 2304 456330880 456331834 0.000000e+00 1251.0
19 TraesCS3D01G227000 chr6D 88.928 849 50 14 1422 2260 456330859 456330045 0.000000e+00 1007.0
20 TraesCS3D01G227000 chr4D 93.029 1578 99 8 1 1572 285092887 285091315 0.000000e+00 2294.0
21 TraesCS3D01G227000 chr4D 95.398 1369 56 5 2836 4201 285091327 285089963 0.000000e+00 2172.0
22 TraesCS3D01G227000 chr4A 92.030 1443 97 8 1957 3387 281065837 281064401 0.000000e+00 2012.0
23 TraesCS3D01G227000 chr1A 96.509 1203 41 1 1 1202 112006454 112007656 0.000000e+00 1988.0
24 TraesCS3D01G227000 chr1A 93.750 48 2 1 2648 2694 541894418 541894371 2.100000e-08 71.3
25 TraesCS3D01G227000 chrUn 96.497 1199 40 1 1 1197 86476507 86475309 0.000000e+00 1980.0
26 TraesCS3D01G227000 chrUn 96.420 1201 39 2 1 1197 206762829 206764029 0.000000e+00 1977.0
27 TraesCS3D01G227000 chrUn 97.886 804 16 1 3086 3888 86475314 86474511 0.000000e+00 1389.0
28 TraesCS3D01G227000 chr3A 96.566 961 27 5 2836 3794 51899845 51898889 0.000000e+00 1587.0
29 TraesCS3D01G227000 chr3A 96.588 469 16 0 3733 4201 624952638 624953106 0.000000e+00 778.0
30 TraesCS3D01G227000 chr3A 95.592 431 18 1 1143 1572 51900263 51899833 0.000000e+00 689.0
31 TraesCS3D01G227000 chr4B 97.509 803 20 0 3086 3888 209274888 209275690 0.000000e+00 1373.0
32 TraesCS3D01G227000 chr4B 88.889 297 23 2 2860 3156 177063345 177063059 1.440000e-94 357.0
33 TraesCS3D01G227000 chr6B 88.426 985 66 23 1329 2304 693826288 693827233 0.000000e+00 1144.0
34 TraesCS3D01G227000 chr6B 86.526 950 61 23 1419 2357 693826282 693825389 0.000000e+00 983.0
35 TraesCS3D01G227000 chr6B 89.121 239 22 4 1169 1405 322176545 322176781 1.140000e-75 294.0
36 TraesCS3D01G227000 chr3B 91.697 831 50 12 883 1711 550329272 550328459 0.000000e+00 1134.0
37 TraesCS3D01G227000 chr6A 92.147 573 35 4 1740 2304 602987156 602987726 0.000000e+00 800.0
38 TraesCS3D01G227000 chr6A 92.446 556 31 6 1334 1879 602986860 602986306 0.000000e+00 784.0
39 TraesCS3D01G227000 chr1D 95.094 265 13 0 2357 2621 409922089 409922353 6.500000e-113 418.0
40 TraesCS3D01G227000 chr1D 96.296 135 4 1 4068 4201 318564584 318564718 1.970000e-53 220.0
41 TraesCS3D01G227000 chr2D 92.308 221 17 0 2262 2482 483175427 483175207 8.770000e-82 315.0
42 TraesCS3D01G227000 chr5D 95.181 83 4 0 3857 3939 362083533 362083615 9.480000e-27 132.0
43 TraesCS3D01G227000 chr5B 97.222 36 1 0 4092 4127 127818655 127818620 1.260000e-05 62.1
44 TraesCS3D01G227000 chr1B 97.222 36 1 0 4092 4127 517085769 517085804 1.260000e-05 62.1
45 TraesCS3D01G227000 chr1B 97.222 36 1 0 4092 4127 638738867 638738832 1.260000e-05 62.1


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 TraesCS3D01G227000 chr3D 308580590 308584790 4200 False 7758.0 7758 100.0000 1 4201 1 chr3D.!!$F1 4200
1 TraesCS3D01G227000 chr7A 120874130 120878022 3892 True 6484.0 6484 96.7640 4 3888 1 chr7A.!!$R1 3884
2 TraesCS3D01G227000 chr7A 60244582 60246579 1997 False 1676.5 1975 97.0270 1 3888 2 chr7A.!!$F1 3887
3 TraesCS3D01G227000 chr7A 1837570 1838995 1425 True 1187.0 1480 96.3760 1023 3723 2 chr7A.!!$R2 2700
4 TraesCS3D01G227000 chr7B 247414453 247418239 3786 True 5930.0 5930 94.9850 114 3888 1 chr7B.!!$R2 3774
5 TraesCS3D01G227000 chr2B 343517097 343519859 2762 True 4194.0 4194 94.0770 1 2764 1 chr2B.!!$R4 2763
6 TraesCS3D01G227000 chr2B 344017673 344018190 517 False 652.0 652 89.1140 2754 3295 1 chr2B.!!$F1 541
7 TraesCS3D01G227000 chr6D 458959591 458962518 2927 True 2418.0 2523 96.4255 1 4201 2 chr6D.!!$R4 4200
8 TraesCS3D01G227000 chr6D 57916951 57918086 1135 True 1845.0 1845 96.0420 1633 2764 1 chr6D.!!$R1 1131
9 TraesCS3D01G227000 chr6D 318033874 318035056 1182 True 1794.0 1794 94.3360 2129 3289 1 chr6D.!!$R2 1160
10 TraesCS3D01G227000 chr6D 456330880 456331834 954 False 1251.0 1251 90.2740 1329 2304 1 chr6D.!!$F1 975
11 TraesCS3D01G227000 chr6D 456330045 456330859 814 True 1007.0 1007 88.9280 1422 2260 1 chr6D.!!$R3 838
12 TraesCS3D01G227000 chr4D 285089963 285092887 2924 True 2233.0 2294 94.2135 1 4201 2 chr4D.!!$R1 4200
13 TraesCS3D01G227000 chr4A 281064401 281065837 1436 True 2012.0 2012 92.0300 1957 3387 1 chr4A.!!$R1 1430
14 TraesCS3D01G227000 chr1A 112006454 112007656 1202 False 1988.0 1988 96.5090 1 1202 1 chr1A.!!$F1 1201
15 TraesCS3D01G227000 chrUn 206762829 206764029 1200 False 1977.0 1977 96.4200 1 1197 1 chrUn.!!$F1 1196
16 TraesCS3D01G227000 chrUn 86474511 86476507 1996 True 1684.5 1980 97.1915 1 3888 2 chrUn.!!$R1 3887
17 TraesCS3D01G227000 chr3A 51898889 51900263 1374 True 1138.0 1587 96.0790 1143 3794 2 chr3A.!!$R1 2651
18 TraesCS3D01G227000 chr4B 209274888 209275690 802 False 1373.0 1373 97.5090 3086 3888 1 chr4B.!!$F1 802
19 TraesCS3D01G227000 chr6B 693826288 693827233 945 False 1144.0 1144 88.4260 1329 2304 1 chr6B.!!$F2 975
20 TraesCS3D01G227000 chr6B 693825389 693826282 893 True 983.0 983 86.5260 1419 2357 1 chr6B.!!$R1 938
21 TraesCS3D01G227000 chr3B 550328459 550329272 813 True 1134.0 1134 91.6970 883 1711 1 chr3B.!!$R1 828
22 TraesCS3D01G227000 chr6A 602987156 602987726 570 False 800.0 800 92.1470 1740 2304 1 chr6A.!!$F1 564
23 TraesCS3D01G227000 chr6A 602986306 602986860 554 True 784.0 784 92.4460 1334 1879 1 chr6A.!!$R1 545

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
185 186 0.108329 GGTACAGCCGCTAAGCTCAA 60.108 55.000 0.0 0.00 42.61 3.02 F
1339 1359 1.739929 CATGTGCAGGCCGACGTTA 60.740 57.895 0.0 0.00 0.00 3.18 F
2456 2506 2.516906 TGAAATCTGCCATGTTCAGCA 58.483 42.857 7.2 1.44 37.46 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 1994 0.393537 CCTGATGAGTCACTTGCCCC 60.394 60.0 0.0 0.0 0.00 5.80 R
2880 2958 1.557099 AGAAGGGCATGTACTCGACA 58.443 50.0 0.0 0.0 43.97 4.35 R
4090 4170 0.539438 AAGGCTTTCGGCATTCACCA 60.539 50.0 0.0 0.0 41.32 4.17 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
36 37 2.614057 GCCTGATACCGACTTTCATTGG 59.386 50.000 0.00 0.00 0.00 3.16
185 186 0.108329 GGTACAGCCGCTAAGCTCAA 60.108 55.000 0.00 0.00 42.61 3.02
306 310 2.234143 TCTGATCATAGAGGAGCCGTG 58.766 52.381 0.00 0.00 0.00 4.94
327 331 5.351465 CGTGTGAAGCTAAGGTTTCATGTAT 59.649 40.000 0.00 0.00 42.75 2.29
328 332 6.533723 CGTGTGAAGCTAAGGTTTCATGTATA 59.466 38.462 0.00 0.00 42.75 1.47
335 339 8.863872 AGCTAAGGTTTCATGTATAGTTTTGT 57.136 30.769 0.00 0.00 0.00 2.83
530 536 2.091665 CCAGAGGGGGAATTAGTTGCAT 60.092 50.000 0.00 0.00 0.00 3.96
573 579 8.356000 TCCGGTATCAAATATGGTTTCTTTTT 57.644 30.769 0.00 0.00 0.00 1.94
687 697 4.341235 CACGATTCTCCCAGTGTAGGAATA 59.659 45.833 0.00 0.00 31.49 1.75
714 724 7.036220 CACTAGTTATCTTGACCTTGATTCGT 58.964 38.462 0.00 0.00 0.00 3.85
749 759 8.757982 TTTTCCTTACTATACTCCAGTACGAT 57.242 34.615 0.00 0.00 32.72 3.73
783 794 1.870402 TGTGTACTCAACGGTGCATTG 59.130 47.619 0.00 0.00 34.67 2.82
968 979 7.147724 ACCAAATCATAGGATCTAACACGAGAA 60.148 37.037 0.00 0.00 31.88 2.87
1156 1173 2.936202 CAAGATGATTTCCCCGGATGT 58.064 47.619 0.73 0.00 0.00 3.06
1291 1310 5.717654 TGGTTGGTAATTAGGGTTTGATTCC 59.282 40.000 0.00 0.00 0.00 3.01
1292 1311 5.717654 GGTTGGTAATTAGGGTTTGATTCCA 59.282 40.000 0.00 0.00 0.00 3.53
1339 1359 1.739929 CATGTGCAGGCCGACGTTA 60.740 57.895 0.00 0.00 0.00 3.18
1473 1496 2.590092 GGCAATGTACGCCTCCCT 59.410 61.111 3.25 0.00 46.56 4.20
1572 1595 6.765989 TGGTAGATGTTAGTGATATTGTTGGC 59.234 38.462 0.00 0.00 0.00 4.52
1675 1698 2.559231 TGTCGTGCATGGTCACTTACTA 59.441 45.455 5.98 0.00 34.92 1.82
1948 1994 2.593346 AGGATCTTGCAGCTTACTCG 57.407 50.000 0.00 0.00 0.00 4.18
2089 2136 5.824904 TCTCTAAAAGATGCTTCAATGGC 57.175 39.130 2.07 0.00 0.00 4.40
2295 2345 4.202151 TGTCCTCTGATTATCGATGTGGTG 60.202 45.833 8.54 0.00 0.00 4.17
2297 2347 4.405680 TCCTCTGATTATCGATGTGGTGTT 59.594 41.667 8.54 0.00 0.00 3.32
2334 2384 5.009631 AGTTGCATTCAATACAGGCAGTTA 58.990 37.500 0.00 0.00 35.68 2.24
2456 2506 2.516906 TGAAATCTGCCATGTTCAGCA 58.483 42.857 7.20 1.44 37.46 4.41
2533 2583 7.770433 AGATTTCGAATCATGTGTTCTTGGATA 59.230 33.333 0.00 0.51 0.00 2.59
2536 2586 6.639563 TCGAATCATGTGTTCTTGGATAGAA 58.360 36.000 10.37 0.00 40.57 2.10
2630 2680 4.329392 GTTGAAACGGAAAAGGGATCCTA 58.671 43.478 12.58 0.00 34.66 2.94
2873 2951 4.365514 TGCAGGGTAAAGTGATCAAGAA 57.634 40.909 0.00 0.00 0.00 2.52
2880 2958 5.998363 GGGTAAAGTGATCAAGAACAAGAGT 59.002 40.000 0.00 0.00 0.00 3.24
2976 3054 3.253921 TCAAATTCGACCTCTACGTCACA 59.746 43.478 0.00 0.00 32.74 3.58
3032 3110 9.331282 ACCAAATCTTATATAACTTGAGAGTGC 57.669 33.333 8.03 0.00 35.91 4.40
3103 3181 2.202878 GCCTCGGTGCGCTATTCA 60.203 61.111 9.73 0.00 0.00 2.57
3205 3283 3.084039 CTGGCTCCTTGACTGCAATAAA 58.916 45.455 0.00 0.00 32.68 1.40
3253 3332 4.394729 GGAATCTAGAGACCGAGACTGAT 58.605 47.826 0.00 0.00 0.00 2.90
3512 3592 0.667487 CATCGCTACCCGCATACTGG 60.667 60.000 0.00 0.00 39.08 4.00
3624 3704 2.439409 CAACCCTCATGATGCACTTCA 58.561 47.619 0.00 0.00 0.00 3.02
3683 3763 2.271944 AACCCTTTTCTTAGCGCTGT 57.728 45.000 22.90 2.18 0.00 4.40
3870 3950 2.948979 CTGTTTTGTCAGTAGGTTGGCA 59.051 45.455 0.00 0.00 0.00 4.92
4090 4170 6.126038 TGAGAGAGATGAGGAACCTAACCTAT 60.126 42.308 0.00 0.00 37.93 2.57
4097 4177 5.036916 TGAGGAACCTAACCTATGGTGAAT 58.963 41.667 0.00 0.00 37.93 2.57
4153 4233 2.935955 CGGGCGTATTGAATCCGC 59.064 61.111 6.58 6.58 46.28 5.54
4193 4273 0.864659 TGATCGATTAGGGAGGGGGA 59.135 55.000 0.00 0.00 0.00 4.81
4194 4274 1.268066 GATCGATTAGGGAGGGGGAC 58.732 60.000 0.00 0.00 0.00 4.46
4195 4275 0.542232 ATCGATTAGGGAGGGGGACG 60.542 60.000 0.00 0.00 0.00 4.79
4196 4276 2.868986 CGATTAGGGAGGGGGACGC 61.869 68.421 0.00 0.00 43.76 5.19
4198 4278 2.967063 GATTAGGGAGGGGGACGCCT 62.967 65.000 7.74 7.74 44.92 5.52
4199 4279 2.967063 ATTAGGGAGGGGGACGCCTC 62.967 65.000 22.97 22.97 44.92 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 5.471456 CCATTCTCTATGTTTCATGGCCTAC 59.529 44.000 3.32 0.00 31.99 3.18
185 186 9.965824 CTAGTAACAACACTTGGAAATGAAAAT 57.034 29.630 0.00 0.00 34.12 1.82
306 310 8.494016 AACTATACATGAAACCTTAGCTTCAC 57.506 34.615 0.00 0.00 34.52 3.18
327 331 5.249852 AGCTCCCACCACTATTACAAAACTA 59.750 40.000 0.00 0.00 0.00 2.24
328 332 4.042934 AGCTCCCACCACTATTACAAAACT 59.957 41.667 0.00 0.00 0.00 2.66
335 339 2.827755 TCACAGCTCCCACCACTATTA 58.172 47.619 0.00 0.00 0.00 0.98
479 485 3.420893 TCACATTCGGCCAAAGAAGAAT 58.579 40.909 2.24 0.00 34.06 2.40
530 536 5.994887 CCGGAATATTCGGTTTGATAACA 57.005 39.130 18.48 0.00 42.33 2.41
687 697 7.545965 CGAATCAAGGTCAAGATAACTAGTGTT 59.454 37.037 0.00 0.00 39.98 3.32
749 759 7.384115 CGTTGAGTACACAGATTCTTTTCCTAA 59.616 37.037 0.00 0.00 0.00 2.69
992 1003 9.563748 GAGGGATTAGCTTATATAGATAGACGT 57.436 37.037 0.00 0.00 0.00 4.34
1228 1245 2.501223 TAGACAAGCGGACAAGGGCG 62.501 60.000 0.00 0.00 0.00 6.13
1229 1246 0.741221 CTAGACAAGCGGACAAGGGC 60.741 60.000 0.00 0.00 0.00 5.19
1291 1310 3.830192 GCAAGCGCCCCCTCATTG 61.830 66.667 2.29 0.50 0.00 2.82
1292 1311 3.590466 AAGCAAGCGCCCCCTCATT 62.590 57.895 2.29 0.00 39.83 2.57
1339 1359 2.715749 TGTTCTTGATGATCCGCCAT 57.284 45.000 0.00 0.00 0.00 4.40
1572 1595 2.522638 GGGAACGCACGCCTATTCG 61.523 63.158 0.00 0.00 0.00 3.34
1948 1994 0.393537 CCTGATGAGTCACTTGCCCC 60.394 60.000 0.00 0.00 0.00 5.80
2081 2128 3.309296 TGGTTAAAACAGGGCCATTGAA 58.691 40.909 6.18 0.00 0.00 2.69
2089 2136 3.142951 TGACACGATGGTTAAAACAGGG 58.857 45.455 0.00 0.00 0.00 4.45
2334 2384 6.210385 TGGTTGGCTAATCAATTGTACAACAT 59.790 34.615 11.22 0.00 38.83 2.71
2533 2583 6.875076 GTACAGGGACACATGTACTATTTCT 58.125 40.000 13.45 0.00 45.33 2.52
2630 2680 3.430374 CCCACGAGAAGAAACCGACATAT 60.430 47.826 0.00 0.00 0.00 1.78
2873 2951 2.352814 GGCATGTACTCGACACTCTTGT 60.353 50.000 0.00 0.00 42.17 3.16
2880 2958 1.557099 AGAAGGGCATGTACTCGACA 58.443 50.000 0.00 0.00 43.97 4.35
2976 3054 7.072562 ACCTGAAGATGGAGATATTACTGACT 58.927 38.462 0.00 0.00 0.00 3.41
3205 3283 6.097915 TGTTCTTACTGTAGCTAGCACTTT 57.902 37.500 18.83 0.00 0.00 2.66
3253 3332 7.255520 CGAATAGAAGTAGCCTAGCCTTTTCTA 60.256 40.741 8.76 8.76 0.00 2.10
3512 3592 9.508567 GTGGAATTCAATAGATTTAAGCAACTC 57.491 33.333 7.93 0.00 0.00 3.01
3594 3674 3.469859 TCATGAGGGTTGGGGATTTAGA 58.530 45.455 0.00 0.00 0.00 2.10
3624 3704 6.073222 GGTACGATAAGCGGAATGAATCAAAT 60.073 38.462 0.00 0.00 46.49 2.32
3837 3917 6.769512 ACTGACAAAACAGGATTTCTAGCTA 58.230 36.000 0.00 0.00 41.59 3.32
3870 3950 5.399152 GGGCTTTCCTTTATCCTCCTTGTAT 60.399 44.000 0.00 0.00 0.00 2.29
4090 4170 0.539438 AAGGCTTTCGGCATTCACCA 60.539 50.000 0.00 0.00 41.32 4.17
4097 4177 0.958382 AATGCGTAAGGCTTTCGGCA 60.958 50.000 24.32 21.40 44.05 5.69
4153 4233 3.067461 CAGAAGTGAAGAGATAGGGGTCG 59.933 52.174 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.