Multiple sequence alignment - TraesCS7A01G068100

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 TraesCS7A01G068100 chr7A 100.000 2494 0 0 1 2494 34142033 34139540 0.000000e+00 4606
1 TraesCS7A01G068100 chr7A 92.593 540 34 3 1798 2335 183798425 183798960 0.000000e+00 771
2 TraesCS7A01G068100 chr7A 92.568 444 24 2 662 1097 183771427 183771869 1.630000e-176 628
3 TraesCS7A01G068100 chr7B 91.204 2524 152 21 1 2494 19118301 19120784 0.000000e+00 3367
4 TraesCS7A01G068100 chr2B 98.934 1688 18 0 807 2494 250726009 250724322 0.000000e+00 3018
5 TraesCS7A01G068100 chr2B 89.072 851 73 11 1341 2187 480915575 480914741 0.000000e+00 1038
6 TraesCS7A01G068100 chr2B 99.134 231 2 0 1 231 250726234 250726004 1.380000e-112 416
7 TraesCS7A01G068100 chr5B 92.620 1084 62 10 1419 2494 535470306 535471379 0.000000e+00 1543
8 TraesCS7A01G068100 chr5B 89.307 851 72 12 1341 2187 547646744 547645909 0.000000e+00 1050
9 TraesCS7A01G068100 chr5B 88.364 550 32 6 1 520 535466446 535466993 1.260000e-177 632
10 TraesCS7A01G068100 chr5B 93.264 386 24 2 560 944 535466992 535467376 3.600000e-158 568
11 TraesCS7A01G068100 chr5B 96.096 333 13 0 935 1267 535469971 535470303 6.070000e-151 544
12 TraesCS7A01G068100 chr7D 86.051 1147 100 24 1 1100 56645809 56644676 0.000000e+00 1177
13 TraesCS7A01G068100 chr7D 85.963 1147 101 24 1 1100 416257739 416256606 0.000000e+00 1171
14 TraesCS7A01G068100 chr7D 87.643 963 76 20 1097 2038 56644735 56643795 0.000000e+00 1079
15 TraesCS7A01G068100 chr7D 87.565 957 76 20 1097 2032 573962536 573963470 0.000000e+00 1068
16 TraesCS7A01G068100 chr7D 88.402 845 67 16 281 1100 573961757 573962595 0.000000e+00 989
17 TraesCS7A01G068100 chr3D 85.789 1147 102 30 1 1100 610338195 610339327 0.000000e+00 1158
18 TraesCS7A01G068100 chr6A 90.588 850 64 8 1341 2187 593685792 593686628 0.000000e+00 1112
19 TraesCS7A01G068100 chr6A 77.480 373 56 17 493 844 431760424 431760059 5.440000e-47 198
20 TraesCS7A01G068100 chr6A 83.333 120 12 4 282 400 36489937 36490049 1.220000e-18 104
21 TraesCS7A01G068100 chr4D 90.120 668 51 9 1341 2004 334178507 334179163 0.000000e+00 854
22 TraesCS7A01G068100 chr4D 92.453 212 15 1 889 1100 334178155 334178365 4.030000e-78 302
23 TraesCS7A01G068100 chr4D 91.429 210 17 1 1097 1305 334178306 334178515 1.130000e-73 287
24 TraesCS7A01G068100 chr4D 97.744 133 3 0 2055 2187 334179167 334179299 1.930000e-56 230
25 TraesCS7A01G068100 chr3B 94.074 270 11 3 1918 2187 401009008 401009272 2.990000e-109 405
26 TraesCS7A01G068100 chr1D 78.244 501 70 22 1097 1578 478816210 478816690 4.060000e-73 285
27 TraesCS7A01G068100 chr1D 86.531 245 31 2 1097 1340 141712930 141713173 4.090000e-68 268
28 TraesCS7A01G068100 chr4A 87.347 245 29 2 1097 1340 419971433 419971676 1.890000e-71 279
29 TraesCS7A01G068100 chr4A 89.401 217 21 2 1124 1339 46437494 46437279 3.160000e-69 272
30 TraesCS7A01G068100 chr1B 78.063 506 66 26 1097 1578 666823220 666823704 6.790000e-71 278
31 TraesCS7A01G068100 chr6B 90.000 210 20 1 1097 1305 51419975 51419766 1.140000e-68 270
32 TraesCS7A01G068100 chr2D 85.714 245 33 2 1097 1340 305942564 305942321 8.850000e-65 257
33 TraesCS7A01G068100 chr5A 78.075 374 52 20 493 844 492996863 492996498 2.510000e-50 209


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 TraesCS7A01G068100 chr7A 34139540 34142033 2493 True 4606.00 4606 100.0000 1 2494 1 chr7A.!!$R1 2493
1 TraesCS7A01G068100 chr7A 183798425 183798960 535 False 771.00 771 92.5930 1798 2335 1 chr7A.!!$F2 537
2 TraesCS7A01G068100 chr7B 19118301 19120784 2483 False 3367.00 3367 91.2040 1 2494 1 chr7B.!!$F1 2493
3 TraesCS7A01G068100 chr2B 250724322 250726234 1912 True 1717.00 3018 99.0340 1 2494 2 chr2B.!!$R2 2493
4 TraesCS7A01G068100 chr2B 480914741 480915575 834 True 1038.00 1038 89.0720 1341 2187 1 chr2B.!!$R1 846
5 TraesCS7A01G068100 chr5B 547645909 547646744 835 True 1050.00 1050 89.3070 1341 2187 1 chr5B.!!$R1 846
6 TraesCS7A01G068100 chr5B 535466446 535471379 4933 False 821.75 1543 92.5860 1 2494 4 chr5B.!!$F1 2493
7 TraesCS7A01G068100 chr7D 416256606 416257739 1133 True 1171.00 1171 85.9630 1 1100 1 chr7D.!!$R1 1099
8 TraesCS7A01G068100 chr7D 56643795 56645809 2014 True 1128.00 1177 86.8470 1 2038 2 chr7D.!!$R2 2037
9 TraesCS7A01G068100 chr7D 573961757 573963470 1713 False 1028.50 1068 87.9835 281 2032 2 chr7D.!!$F1 1751
10 TraesCS7A01G068100 chr3D 610338195 610339327 1132 False 1158.00 1158 85.7890 1 1100 1 chr3D.!!$F1 1099
11 TraesCS7A01G068100 chr6A 593685792 593686628 836 False 1112.00 1112 90.5880 1341 2187 1 chr6A.!!$F2 846
12 TraesCS7A01G068100 chr4D 334178155 334179299 1144 False 418.25 854 92.9365 889 2187 4 chr4D.!!$F1 1298

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
646 694 0.177141 TTCAATCGGTCGATCCCACC 59.823 55.0 6.32 0.0 33.08 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 4374 0.809241 GACATGGAGAAGCTCAGCCG 60.809 60.0 0.0 0.0 31.08 5.52 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
25 26 3.224884 ACACACAAAAACAAGAACCGG 57.775 42.857 0.00 0.00 0.00 5.28
225 229 6.497259 ACCCGATGTCAAACAGATATAGGTAT 59.503 38.462 0.00 0.00 38.42 2.73
226 230 7.016268 ACCCGATGTCAAACAGATATAGGTATT 59.984 37.037 0.00 0.00 38.42 1.89
228 232 9.923143 CCGATGTCAAACAGATATAGGTATTTA 57.077 33.333 0.00 0.00 36.38 1.40
384 417 1.748122 CCTCCATGGACTGCTGCAC 60.748 63.158 11.44 0.00 38.35 4.57
460 497 2.752238 CCCTCTCGAGCACCGACT 60.752 66.667 7.81 0.00 43.23 4.18
485 522 4.383173 GTTGTCGTTCCCCTTCTTCTTAA 58.617 43.478 0.00 0.00 0.00 1.85
533 570 2.666098 CCACCCCGTCCCGATCTTT 61.666 63.158 0.00 0.00 0.00 2.52
619 664 4.395542 GCTTCTTCACAGCATCAATTCTCT 59.604 41.667 0.00 0.00 37.22 3.10
638 686 2.672874 TCTTTGCTGATTCAATCGGTCG 59.327 45.455 8.06 0.00 37.96 4.79
646 694 0.177141 TTCAATCGGTCGATCCCACC 59.823 55.000 6.32 0.00 33.08 4.61
696 745 2.285368 TCAGATCCGCCCTGGGTT 60.285 61.111 15.56 0.00 38.76 4.11
723 772 2.104622 TCCATGGCACGATCATACATGT 59.895 45.455 6.96 2.69 37.74 3.21
735 784 5.640732 GATCATACATGTTGTTGTGTTCCC 58.359 41.667 2.30 0.00 0.00 3.97
748 797 1.205417 GTGTTCCCGGATTCCGTCTTA 59.795 52.381 22.83 3.37 46.80 2.10
750 799 1.117150 TTCCCGGATTCCGTCTTAGG 58.883 55.000 22.83 16.10 46.80 2.69
1131 3798 3.385755 GGTTGATATGGCATTTTCCTGCT 59.614 43.478 4.78 0.00 41.95 4.24
1307 3974 4.702131 GGTGAGGCTAATTGTCAAATCTGT 59.298 41.667 0.00 0.00 0.00 3.41
1814 4510 0.535102 CGGCCTTGACTGTGAACCTT 60.535 55.000 0.00 0.00 0.00 3.50
1949 4650 1.406539 CAGGCCAAAGGTCATGCATAC 59.593 52.381 5.01 0.00 0.00 2.39
1951 4652 2.102578 GGCCAAAGGTCATGCATACTT 58.897 47.619 0.00 1.50 0.00 2.24
2410 5116 1.630878 GTTGGGATTCAGAGGAGGTGT 59.369 52.381 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.863454 CTCTGATCATGCGGCTGTAAC 59.137 52.381 0.00 0.00 0.00 2.50
225 229 2.822255 GCCCGCATCGCCTGTAAA 60.822 61.111 0.00 0.00 0.00 2.01
226 230 3.613877 TTGCCCGCATCGCCTGTAA 62.614 57.895 0.00 0.00 0.00 2.41
384 417 1.756538 GAAGCTCTCTCTCCCTGGAAG 59.243 57.143 0.00 0.00 0.00 3.46
435 472 2.756283 CTCGAGAGGGCCGGAAGT 60.756 66.667 6.58 0.00 0.00 3.01
460 497 1.117142 AGAAGGGGAACGACAACGGA 61.117 55.000 0.00 0.00 44.46 4.69
619 664 2.694213 TCGACCGATTGAATCAGCAAA 58.306 42.857 5.95 0.00 0.00 3.68
625 673 2.135933 GTGGGATCGACCGATTGAATC 58.864 52.381 6.36 0.00 40.11 2.52
646 694 0.916358 AAGGTCCCATCCTCACCCTG 60.916 60.000 0.00 0.00 36.74 4.45
653 701 0.625849 AATTGCGAAGGTCCCATCCT 59.374 50.000 0.00 0.00 39.84 3.24
696 745 1.552792 TGATCGTGCCATGGACACTAA 59.447 47.619 26.29 18.59 35.84 2.24
723 772 1.611519 GGAATCCGGGAACACAACAA 58.388 50.000 0.00 0.00 0.00 2.83
748 797 6.381994 AGCAAATCATACACAAATCATTCCCT 59.618 34.615 0.00 0.00 0.00 4.20
750 799 9.403110 GATAGCAAATCATACACAAATCATTCC 57.597 33.333 0.00 0.00 0.00 3.01
1131 3798 2.707257 TGCTCCCATGATAGCAGAATGA 59.293 45.455 15.43 0.00 43.56 2.57
1307 3974 0.473755 TGGTGCTGAAGCTTTCCTGA 59.526 50.000 0.00 0.00 42.66 3.86
1590 4277 7.121759 GTCTGCATATAACCCTGCATCATTTAT 59.878 37.037 0.00 0.00 46.48 1.40
1682 4372 3.397613 ATGGAGAAGCTCAGCCGCC 62.398 63.158 0.00 0.00 31.08 6.13
1683 4373 2.178890 CATGGAGAAGCTCAGCCGC 61.179 63.158 0.00 0.00 31.08 6.53
1684 4374 0.809241 GACATGGAGAAGCTCAGCCG 60.809 60.000 0.00 0.00 31.08 5.52
1814 4510 4.047059 GGAGACCGTCGCAACCGA 62.047 66.667 4.58 0.00 42.01 4.69
1949 4650 3.806316 AGCGATTCAAAACGTACCAAG 57.194 42.857 0.00 0.00 0.00 3.61
1951 4652 4.496360 TGATAGCGATTCAAAACGTACCA 58.504 39.130 0.00 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.