Multiple sequence alignment - TraesCS1D01G316500

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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 TraesCS1D01G316500 chr1D 100.000 2528 0 0 1 2528 411718541 411721068 0.000000e+00 4669.0
1 TraesCS1D01G316500 chr1D 89.428 1485 112 19 957 2403 411744507 411745984 0.000000e+00 1831.0
2 TraesCS1D01G316500 chr1D 94.000 1100 63 2 957 2055 411695031 411696128 0.000000e+00 1663.0
3 TraesCS1D01G316500 chr1D 96.127 852 11 4 1 838 411694051 411694894 0.000000e+00 1371.0
4 TraesCS1D01G316500 chr1D 93.857 879 53 1 957 1834 411701351 411702229 0.000000e+00 1323.0
5 TraesCS1D01G316500 chr1D 95.074 609 30 0 1899 2507 411702224 411702832 0.000000e+00 959.0
6 TraesCS1D01G316500 chr1D 93.902 410 25 0 2119 2528 411696130 411696539 9.930000e-174 619.0
7 TraesCS1D01G316500 chr1D 92.233 412 19 5 440 838 411743959 411744370 2.820000e-159 571.0
8 TraesCS1D01G316500 chr1D 91.667 408 19 5 440 838 411700813 411701214 3.680000e-153 551.0
9 TraesCS1D01G316500 chr1D 96.154 104 4 0 834 937 411694943 411695046 1.200000e-38 171.0
10 TraesCS1D01G316500 chr1D 93.269 104 7 0 834 937 411701263 411701366 1.210000e-33 154.0
11 TraesCS1D01G316500 chr1B 88.050 1615 143 21 957 2528 555065947 555067554 0.000000e+00 1868.0
12 TraesCS1D01G316500 chr1B 87.809 1616 146 17 957 2528 555060587 555062195 0.000000e+00 1845.0
13 TraesCS1D01G316500 chr1B 87.809 1616 144 19 957 2528 555012665 555014271 0.000000e+00 1844.0
14 TraesCS1D01G316500 chr1B 87.633 1601 138 25 973 2528 555071312 555072897 0.000000e+00 1805.0
15 TraesCS1D01G316500 chr1B 87.073 1609 160 18 957 2528 555057281 555058878 0.000000e+00 1775.0
16 TraesCS1D01G316500 chr1B 87.933 1500 130 23 957 2412 555018019 555019511 0.000000e+00 1720.0
17 TraesCS1D01G316500 chr1B 86.785 1574 160 20 991 2528 555004090 555005651 0.000000e+00 1711.0
18 TraesCS1D01G316500 chr1B 88.005 1484 131 21 973 2412 555076655 555078135 0.000000e+00 1711.0
19 TraesCS1D01G316500 chr1B 86.051 1441 137 21 957 2362 555032235 555033646 0.000000e+00 1489.0
20 TraesCS1D01G316500 chr1B 85.507 897 96 13 1664 2528 555008020 555008914 0.000000e+00 905.0
21 TraesCS1D01G316500 chr1B 84.821 560 59 11 1829 2362 555091505 555092064 7.960000e-150 540.0
22 TraesCS1D01G316500 chr1B 100.000 56 0 0 390 445 563574296 563574241 1.240000e-18 104.0
23 TraesCS1D01G316500 chrUn 93.484 1105 66 2 957 2055 11274638 11273534 0.000000e+00 1637.0
24 TraesCS1D01G316500 chrUn 90.754 411 26 6 440 838 346709947 346710357 2.860000e-149 538.0
25 TraesCS1D01G316500 chrUn 90.754 411 26 6 440 838 373706540 373706130 2.860000e-149 538.0
26 TraesCS1D01G316500 chrUn 90.754 411 26 6 440 838 373708406 373707996 2.860000e-149 538.0
27 TraesCS1D01G316500 chrUn 87.719 456 54 2 2074 2528 423066678 423066224 4.790000e-147 531.0
28 TraesCS1D01G316500 chrUn 88.647 414 31 8 440 838 435163656 435164068 8.130000e-135 490.0
29 TraesCS1D01G316500 chrUn 96.040 101 4 0 837 937 11274723 11274623 5.590000e-37 165.0
30 TraesCS1D01G316500 chrUn 94.059 101 6 0 837 937 435213676 435213576 1.210000e-33 154.0
31 TraesCS1D01G316500 chrUn 98.246 57 1 0 392 448 231394402 231394346 1.600000e-17 100.0
32 TraesCS1D01G316500 chrUn 90.789 76 2 5 391 463 43412782 43412709 2.070000e-16 97.1
33 TraesCS1D01G316500 chr1A 85.112 1424 168 14 1128 2528 508205748 508207150 0.000000e+00 1415.0
34 TraesCS1D01G316500 chr1A 83.521 1068 118 24 1509 2528 508333290 508334347 0.000000e+00 944.0
35 TraesCS1D01G316500 chr1A 90.754 411 26 6 440 838 508332215 508332625 2.860000e-149 538.0
36 TraesCS1D01G316500 chr1A 87.719 456 54 2 2074 2528 508284619 508285073 4.790000e-147 531.0
37 TraesCS1D01G316500 chr1A 90.268 411 28 6 440 838 508273283 508273693 6.190000e-146 527.0
38 TraesCS1D01G316500 chr1A 93.269 104 7 0 834 937 508278262 508278365 1.210000e-33 154.0
39 TraesCS1D01G316500 chr1A 93.269 104 7 0 834 937 508283569 508283672 1.210000e-33 154.0
40 TraesCS1D01G316500 chr1A 93.269 104 7 0 834 937 508305588 508305691 1.210000e-33 154.0
41 TraesCS1D01G316500 chr1A 93.269 104 7 0 834 937 508310472 508310575 1.210000e-33 154.0
42 TraesCS1D01G316500 chr1A 93.269 104 7 0 834 937 508315691 508315794 1.210000e-33 154.0
43 TraesCS1D01G316500 chr7D 91.935 248 12 2 1 241 359150883 359151129 8.660000e-90 340.0
44 TraesCS1D01G316500 chr7D 86.449 214 20 3 228 441 359151207 359151411 2.530000e-55 226.0
45 TraesCS1D01G316500 chr2D 91.532 248 13 4 1 241 451462117 451461871 4.030000e-88 335.0
46 TraesCS1D01G316500 chr2D 86.752 234 23 4 2 228 120986821 120986589 1.160000e-63 254.0
47 TraesCS1D01G316500 chr2D 83.028 218 15 8 228 444 451461793 451461597 7.190000e-41 178.0
48 TraesCS1D01G316500 chr2D 100.000 55 0 0 391 445 607998618 607998672 4.450000e-18 102.0
49 TraesCS1D01G316500 chr6A 92.308 234 11 1 2 228 539722162 539722395 2.430000e-85 326.0
50 TraesCS1D01G316500 chr2B 91.949 236 10 3 1 228 75343808 75344042 3.140000e-84 322.0
51 TraesCS1D01G316500 chr2B 85.915 213 18 4 224 435 75344116 75344317 1.520000e-52 217.0
52 TraesCS1D01G316500 chr2B 98.246 57 1 0 389 445 108995381 108995437 1.600000e-17 100.0
53 TraesCS1D01G316500 chr6B 90.086 232 14 5 5 228 205348224 205347994 2.460000e-75 292.0
54 TraesCS1D01G316500 chr7A 88.785 214 17 6 19 228 42010598 42010388 3.230000e-64 255.0
55 TraesCS1D01G316500 chr5A 82.955 176 17 11 4 175 535485661 535485827 2.030000e-31 147.0
56 TraesCS1D01G316500 chr5A 95.161 62 2 1 389 450 502170759 502170819 2.070000e-16 97.1
57 TraesCS1D01G316500 chr3D 95.312 64 1 2 385 448 560802166 560802105 1.600000e-17 100.0
58 TraesCS1D01G316500 chr3A 95.312 64 2 1 391 453 733615187 733615124 1.600000e-17 100.0


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 TraesCS1D01G316500 chr1D 411718541 411721068 2527 False 4669.00 4669 100.00000 1 2528 1 chr1D.!!$F1 2527
1 TraesCS1D01G316500 chr1D 411743959 411745984 2025 False 1201.00 1831 90.83050 440 2403 2 chr1D.!!$F4 1963
2 TraesCS1D01G316500 chr1D 411694051 411696539 2488 False 956.00 1663 95.04575 1 2528 4 chr1D.!!$F2 2527
3 TraesCS1D01G316500 chr1D 411700813 411702832 2019 False 746.75 1323 93.46675 440 2507 4 chr1D.!!$F3 2067
4 TraesCS1D01G316500 chr1B 555057281 555078135 20854 False 1800.80 1868 87.71400 957 2528 5 chr1B.!!$F4 1571
5 TraesCS1D01G316500 chr1B 555004090 555019511 15421 False 1545.00 1844 87.00850 957 2528 4 chr1B.!!$F3 1571
6 TraesCS1D01G316500 chr1B 555032235 555033646 1411 False 1489.00 1489 86.05100 957 2362 1 chr1B.!!$F1 1405
7 TraesCS1D01G316500 chr1B 555091505 555092064 559 False 540.00 540 84.82100 1829 2362 1 chr1B.!!$F2 533
8 TraesCS1D01G316500 chrUn 11273534 11274723 1189 True 901.00 1637 94.76200 837 2055 2 chrUn.!!$R5 1218
9 TraesCS1D01G316500 chrUn 373706130 373708406 2276 True 538.00 538 90.75400 440 838 2 chrUn.!!$R6 398
10 TraesCS1D01G316500 chr1A 508205748 508207150 1402 False 1415.00 1415 85.11200 1128 2528 1 chr1A.!!$F1 1400
11 TraesCS1D01G316500 chr1A 508332215 508334347 2132 False 741.00 944 87.13750 440 2528 2 chr1A.!!$F8 2088
12 TraesCS1D01G316500 chr1A 508283569 508285073 1504 False 342.50 531 90.49400 834 2528 2 chr1A.!!$F7 1694
13 TraesCS1D01G316500 chr7D 359150883 359151411 528 False 283.00 340 89.19200 1 441 2 chr7D.!!$F1 440
14 TraesCS1D01G316500 chr2D 451461597 451462117 520 True 256.50 335 87.28000 1 444 2 chr2D.!!$R2 443
15 TraesCS1D01G316500 chr2B 75343808 75344317 509 False 269.50 322 88.93200 1 435 2 chr2B.!!$F2 434

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
835 1009 0.736325 ACGCGCTTACACCTGATGAC 60.736 55.0 5.73 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 25688 1.004679 TCACTTGCGAGCATCAGCA 60.005 52.632 0.0 0.0 45.49 4.41 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
381 481 0.981183 ATCTACTCCCACCGCAAACA 59.019 50.000 0.00 0.00 0.00 2.83
481 587 8.506168 AATTTGTGTACTCTTGAGAAAAGACA 57.494 30.769 4.49 2.38 0.00 3.41
745 865 2.730604 GTGCACGCACCAACATGC 60.731 61.111 11.13 0.00 40.79 4.06
835 1009 0.736325 ACGCGCTTACACCTGATGAC 60.736 55.000 5.73 0.00 0.00 3.06
916 1090 8.764524 TCAAATTTCTCTCTAGTGCTAACTTC 57.235 34.615 0.00 0.00 37.88 3.01
918 1092 9.862371 CAAATTTCTCTCTAGTGCTAACTTCTA 57.138 33.333 0.00 0.00 37.88 2.10
920 1094 6.687081 TTCTCTCTAGTGCTAACTTCTAGC 57.313 41.667 0.00 0.00 37.88 3.42
921 1095 5.996644 TCTCTCTAGTGCTAACTTCTAGCT 58.003 41.667 5.44 0.00 40.95 3.32
922 1096 6.053005 TCTCTCTAGTGCTAACTTCTAGCTC 58.947 44.000 0.00 2.12 40.95 4.09
924 1098 3.878103 TCTAGTGCTAACTTCTAGCTCCG 59.122 47.826 0.00 0.00 40.95 4.63
925 1099 2.724454 AGTGCTAACTTCTAGCTCCGA 58.276 47.619 0.00 0.00 40.95 4.55
928 1102 3.316868 GTGCTAACTTCTAGCTCCGATCT 59.683 47.826 0.00 0.00 40.95 2.75
929 1103 3.954904 TGCTAACTTCTAGCTCCGATCTT 59.045 43.478 0.00 0.00 40.95 2.40
931 1105 4.979815 GCTAACTTCTAGCTCCGATCTTTC 59.020 45.833 0.00 0.00 37.56 2.62
932 1106 4.394439 AACTTCTAGCTCCGATCTTTCC 57.606 45.455 0.00 0.00 0.00 3.13
933 1107 3.366396 ACTTCTAGCTCCGATCTTTCCA 58.634 45.455 0.00 0.00 0.00 3.53
934 1108 3.383185 ACTTCTAGCTCCGATCTTTCCAG 59.617 47.826 0.00 0.00 0.00 3.86
935 1109 3.019799 TCTAGCTCCGATCTTTCCAGT 57.980 47.619 0.00 0.00 0.00 4.00
936 1110 3.366396 TCTAGCTCCGATCTTTCCAGTT 58.634 45.455 0.00 0.00 0.00 3.16
937 1111 3.769844 TCTAGCTCCGATCTTTCCAGTTT 59.230 43.478 0.00 0.00 0.00 2.66
938 1112 3.425162 AGCTCCGATCTTTCCAGTTTT 57.575 42.857 0.00 0.00 0.00 2.43
939 1113 3.756117 AGCTCCGATCTTTCCAGTTTTT 58.244 40.909 0.00 0.00 0.00 1.94
1122 14139 1.880027 CTGCAAACCAACTACACCCTC 59.120 52.381 0.00 0.00 0.00 4.30
1472 19843 1.281287 AGCTGGCATTGATCAGTCTGT 59.719 47.619 0.00 0.00 33.81 3.41
1534 19905 3.302870 CGTGTTGTTCTTTTAGTGACCGG 60.303 47.826 0.00 0.00 0.00 5.28
1540 19911 3.872511 TCTTTTAGTGACCGGCGATTA 57.127 42.857 9.30 0.00 0.00 1.75
1679 20067 9.801873 CAAACCGAACTATAATCATGGAAAAAT 57.198 29.630 0.00 0.00 0.00 1.82
1693 20082 3.964031 TGGAAAAATGTAAAGGGCAGTGT 59.036 39.130 0.00 0.00 0.00 3.55
1702 20091 2.032681 GGGCAGTGTGAGGTGTCC 59.967 66.667 0.00 0.00 0.00 4.02
1733 20122 0.511221 CAAATTTCGGTCGACTGCGT 59.489 50.000 19.89 4.92 38.98 5.24
1782 20171 2.086869 CCGTCTGATTTGGTTGCTCAT 58.913 47.619 0.00 0.00 0.00 2.90
1821 20211 2.434884 CGCAGTCTCGCCCAACAT 60.435 61.111 0.00 0.00 0.00 2.71
1982 25735 5.066505 CACACTAGTTCCAGCAAAAACTCTT 59.933 40.000 0.00 0.00 37.02 2.85
2253 26061 4.849329 CGGTGCCGTCGTAGCTCC 62.849 72.222 1.93 4.96 39.87 4.70
2260 26068 2.703798 CGTCGTAGCTCCCGGGAAA 61.704 63.158 26.68 10.42 0.00 3.13
2293 26139 1.871039 GTCGTTGAGGTTTTGCAGCTA 59.129 47.619 0.00 0.00 31.44 3.32
2432 26413 4.020543 ACCAACTAGTTCCAGCAAAAACA 58.979 39.130 4.77 0.00 0.00 2.83
2440 26421 0.033228 CCAGCAAAAACAATGGCCGA 59.967 50.000 0.00 0.00 0.00 5.54
2519 26500 4.812091 TCCGTCGTTTTTCTTTCAAGATGA 59.188 37.500 0.00 0.00 34.49 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
782 902 4.589374 AGGTATGGTAGGTCTAAGATGCAC 59.411 45.833 0.00 0.00 0.00 4.57
835 1009 3.002656 GCACGATGGAATGTGATGTAAGG 59.997 47.826 0.00 0.00 38.36 2.69
914 1088 3.366396 ACTGGAAAGATCGGAGCTAGAA 58.634 45.455 0.00 0.00 0.00 2.10
915 1089 3.019799 ACTGGAAAGATCGGAGCTAGA 57.980 47.619 0.00 0.00 0.00 2.43
916 1090 3.810310 AACTGGAAAGATCGGAGCTAG 57.190 47.619 0.00 0.00 0.00 3.42
918 1092 3.425162 AAAACTGGAAAGATCGGAGCT 57.575 42.857 0.00 0.00 0.00 4.09
952 1126 3.810386 GCTAACTGGAAAGATCGGATTCC 59.190 47.826 16.51 16.51 44.38 3.01
954 1128 4.762289 AGCTAACTGGAAAGATCGGATT 57.238 40.909 0.00 0.00 0.00 3.01
955 1129 4.262249 GCTAGCTAACTGGAAAGATCGGAT 60.262 45.833 7.70 0.00 0.00 4.18
966 8622 3.120477 CGATCGACTAGCTAGCTAACTGG 60.120 52.174 24.20 15.20 0.00 4.00
1100 14117 1.477923 GGGTGTAGTTGGTTTGCAGGA 60.478 52.381 0.00 0.00 0.00 3.86
1122 14139 1.187087 ACCTAGTTCTCGAAGCCCAG 58.813 55.000 0.00 0.00 0.00 4.45
1472 19843 4.382320 GACCTAACCGCGCCACCA 62.382 66.667 0.00 0.00 0.00 4.17
1483 19854 0.392461 GCGACAATGGCCAGACCTAA 60.392 55.000 13.05 0.00 40.22 2.69
1653 20026 9.801873 ATTTTTCCATGATTATAGTTCGGTTTG 57.198 29.630 0.00 0.00 0.00 2.93
1679 20067 1.136828 ACCTCACACTGCCCTTTACA 58.863 50.000 0.00 0.00 0.00 2.41
1733 20122 4.733815 GCAGCTTGCATCTAACGACTAGTA 60.734 45.833 0.00 0.00 44.26 1.82
1759 20148 1.883021 CAACCAAATCAGACGGCCC 59.117 57.895 0.00 0.00 0.00 5.80
1782 20171 1.229529 GGTGTGGGGAGGAAGGAGA 60.230 63.158 0.00 0.00 0.00 3.71
1854 20249 1.074775 GGAGGTGTGATGTTGCCCA 59.925 57.895 0.00 0.00 0.00 5.36
1935 25688 1.004679 TCACTTGCGAGCATCAGCA 60.005 52.632 0.00 0.00 45.49 4.41
1982 25735 1.603456 TGCAAATGCTGGAACGAGAA 58.397 45.000 6.97 0.00 42.66 2.87
2208 26006 2.672996 AATGGCCGCGTGCTTCTT 60.673 55.556 17.07 7.46 40.92 2.52
2253 26061 1.288752 GTGCAACCATGTTTCCCGG 59.711 57.895 0.00 0.00 0.00 5.73
2260 26068 1.525077 AACGACCGTGCAACCATGT 60.525 52.632 0.00 0.00 0.00 3.21
2293 26139 3.591789 TGCTAGAATAGGGCAGGAGAAT 58.408 45.455 0.00 0.00 39.70 2.40
2432 26413 2.346766 TGATGCTACATTCGGCCATT 57.653 45.000 2.24 0.00 0.00 3.16
2440 26421 2.423373 GGGGACACCATGATGCTACATT 60.423 50.000 0.00 0.00 39.85 2.71


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

AutoCloner maintained by Alex Coulton.