Multiple sequence alignment - TraesCS4A01G494100

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 TraesCS4A01G494100 chr4A 100.000 5129 0 0 1 5129 742272007 742266879 0.000000e+00 9472.0
1 TraesCS4A01G494100 chr4A 97.231 4189 109 6 1 4187 739830999 739835182 0.000000e+00 7086.0
2 TraesCS4A01G494100 chr4A 96.909 4109 113 11 78 4182 740063533 740059435 0.000000e+00 6872.0
3 TraesCS4A01G494100 chr4A 95.449 4109 155 10 78 4183 733929360 733925281 0.000000e+00 6523.0
4 TraesCS4A01G494100 chr4A 95.118 2253 108 1 1935 4187 740868120 740865870 0.000000e+00 3550.0
5 TraesCS4A01G494100 chr4A 94.491 2251 122 1 1935 4185 739808218 739810466 0.000000e+00 3469.0
6 TraesCS4A01G494100 chr4A 90.601 1032 93 2 340 1371 739806203 739807230 0.000000e+00 1365.0
7 TraesCS4A01G494100 chr4A 97.297 518 12 1 4190 4705 739835228 739835745 0.000000e+00 878.0
8 TraesCS4A01G494100 chr4A 92.123 584 38 3 4190 4771 739810514 739811091 0.000000e+00 817.0
9 TraesCS4A01G494100 chr4A 91.552 580 40 4 4194 4770 733925227 733924654 0.000000e+00 791.0
10 TraesCS4A01G494100 chr4A 91.096 584 43 4 4190 4771 740865824 740865248 0.000000e+00 782.0
11 TraesCS4A01G494100 chr4A 87.709 358 16 2 4773 5129 739835831 739836161 4.810000e-105 392.0
12 TraesCS4A01G494100 chr4A 91.288 264 20 1 4869 5129 740864821 740864558 1.760000e-94 357.0
13 TraesCS4A01G494100 chr4A 91.304 161 13 1 4773 4932 739811154 739811314 8.650000e-53 219.0
14 TraesCS4A01G494100 chr4A 89.759 166 15 2 4773 4937 733924594 733924430 1.450000e-50 211.0
15 TraesCS4A01G494100 chr4A 96.364 55 2 0 1 55 733929413 733929359 1.970000e-14 91.6
16 TraesCS4A01G494100 chr4A 94.545 55 2 1 1 55 740063585 740063532 3.290000e-12 84.2
17 TraesCS4A01G494100 chr7D 93.455 2628 146 15 1935 4550 3440478 3443091 0.000000e+00 3877.0
18 TraesCS4A01G494100 chr7D 93.025 2294 151 6 1894 4187 3699324 3701608 0.000000e+00 3341.0
19 TraesCS4A01G494100 chr7D 90.365 1287 70 20 1727 2985 3583121 3584381 0.000000e+00 1640.0
20 TraesCS4A01G494100 chr7D 89.409 1218 106 17 300 1505 3731313 3730107 0.000000e+00 1513.0
21 TraesCS4A01G494100 chr7D 91.168 1019 83 4 340 1356 3697390 3698403 0.000000e+00 1376.0
22 TraesCS4A01G494100 chr7D 92.414 580 31 5 4194 4770 3593562 3594131 0.000000e+00 815.0
23 TraesCS4A01G494100 chr7D 88.188 618 50 11 1123 1729 3582468 3583073 0.000000e+00 715.0
24 TraesCS4A01G494100 chr7D 86.565 588 39 10 4194 4771 2431931 2432488 3.390000e-171 612.0
25 TraesCS4A01G494100 chr7D 93.680 269 16 1 4859 5127 3594515 3594782 8.000000e-108 401.0
26 TraesCS4A01G494100 chr7D 92.683 164 11 1 4775 4937 3443468 3443631 8.590000e-58 235.0
27 TraesCS4A01G494100 chr7D 91.515 165 10 2 4773 4937 2432550 2432710 1.860000e-54 224.0
28 TraesCS4A01G494100 chr7A 91.206 2297 195 7 1893 4187 3582923 3585214 0.000000e+00 3116.0
29 TraesCS4A01G494100 chr7A 90.000 2300 189 25 1919 4187 3381207 3383496 0.000000e+00 2935.0
30 TraesCS4A01G494100 chr7A 89.318 1217 108 17 300 1505 2554257 2553052 0.000000e+00 1507.0
31 TraesCS4A01G494100 chr7A 90.891 1032 90 2 340 1371 3004360 3003333 0.000000e+00 1382.0
32 TraesCS4A01G494100 chr7A 89.128 1113 101 9 273 1378 3379537 3380636 0.000000e+00 1367.0
33 TraesCS4A01G494100 chr7A 92.479 585 35 3 4190 4771 3000079 2999501 0.000000e+00 828.0
34 TraesCS4A01G494100 chr7A 91.952 584 38 4 4190 4771 2550481 2549905 0.000000e+00 809.0
35 TraesCS4A01G494100 chr7A 91.610 584 34 4 4190 4771 3383542 3384112 0.000000e+00 793.0
36 TraesCS4A01G494100 chr7A 88.472 373 27 5 4773 5129 2847710 2847338 2.190000e-118 436.0
37 TraesCS4A01G494100 chr7A 85.680 419 26 15 4353 4770 2848154 2847769 1.330000e-110 411.0
38 TraesCS4A01G494100 chr7A 92.727 165 11 1 4773 4937 2549842 2549679 2.390000e-58 237.0
39 TraesCS4A01G494100 chr7A 90.909 165 15 0 4773 4937 3384176 3384340 6.680000e-54 222.0
40 TraesCS4A01G494100 chr7A 87.603 121 14 1 4791 4911 3585640 3585759 6.920000e-29 139.0
41 TraesCS4A01G494100 chr7A 88.172 93 11 0 4933 5025 3785891 3785983 1.510000e-20 111.0
42 TraesCS4A01G494100 chr7A 91.781 73 5 1 1611 1683 3582095 3582166 3.270000e-17 100.0
43 TraesCS4A01G494100 chr7A 93.750 64 4 0 1616 1679 3003193 3003130 4.230000e-16 97.1


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 TraesCS4A01G494100 chr4A 742266879 742272007 5128 True 9472.000000 9472 100.000000 1 5129 1 chr4A.!!$R1 5128
1 TraesCS4A01G494100 chr4A 740059435 740063585 4150 True 3478.100000 6872 95.727000 1 4182 2 chr4A.!!$R3 4181
2 TraesCS4A01G494100 chr4A 739830999 739836161 5162 False 2785.333333 7086 94.079000 1 5129 3 chr4A.!!$F2 5128
3 TraesCS4A01G494100 chr4A 733924430 733929413 4983 True 1904.150000 6523 93.281000 1 4937 4 chr4A.!!$R2 4936
4 TraesCS4A01G494100 chr4A 740864558 740868120 3562 True 1563.000000 3550 92.500667 1935 5129 3 chr4A.!!$R4 3194
5 TraesCS4A01G494100 chr4A 739806203 739811314 5111 False 1467.500000 3469 92.129750 340 4932 4 chr4A.!!$F1 4592
6 TraesCS4A01G494100 chr7D 3697390 3701608 4218 False 2358.500000 3341 92.096500 340 4187 2 chr7D.!!$F5 3847
7 TraesCS4A01G494100 chr7D 3440478 3443631 3153 False 2056.000000 3877 93.069000 1935 4937 2 chr7D.!!$F2 3002
8 TraesCS4A01G494100 chr7D 3730107 3731313 1206 True 1513.000000 1513 89.409000 300 1505 1 chr7D.!!$R1 1205
9 TraesCS4A01G494100 chr7D 3582468 3584381 1913 False 1177.500000 1640 89.276500 1123 2985 2 chr7D.!!$F3 1862
10 TraesCS4A01G494100 chr7D 3593562 3594782 1220 False 608.000000 815 93.047000 4194 5127 2 chr7D.!!$F4 933
11 TraesCS4A01G494100 chr7D 2431931 2432710 779 False 418.000000 612 89.040000 4194 4937 2 chr7D.!!$F1 743
12 TraesCS4A01G494100 chr7A 3379537 3384340 4803 False 1329.250000 2935 90.411750 273 4937 4 chr7A.!!$F2 4664
13 TraesCS4A01G494100 chr7A 3582095 3585759 3664 False 1118.333333 3116 90.196667 1611 4911 3 chr7A.!!$F3 3300
14 TraesCS4A01G494100 chr7A 2549679 2554257 4578 True 851.000000 1507 91.332333 300 4937 3 chr7A.!!$R1 4637
15 TraesCS4A01G494100 chr7A 2999501 3004360 4859 True 769.033333 1382 92.373333 340 4771 3 chr7A.!!$R3 4431
16 TraesCS4A01G494100 chr7A 2847338 2848154 816 True 423.500000 436 87.076000 4353 5129 2 chr7A.!!$R2 776

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
438 457 0.179134 AGTACACTCTGATTCGCGGC 60.179 55.000 6.13 0.0 0.00 6.53 F
439 458 1.226575 TACACTCTGATTCGCGGCG 60.227 57.895 17.70 17.7 0.00 6.46 F
2300 3221 1.315690 AATCTGCATTCAGCCGATGG 58.684 50.000 0.00 0.0 45.02 3.51 F
2475 3401 2.966050 TGCAACCCAACAAGAAACAAC 58.034 42.857 0.00 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2300 3221 1.153509 GCATTGGCATCACTTGGGC 60.154 57.895 0.0 0.0 40.72 5.36 R
2475 3401 5.295431 TGCAAACTTTACTCCAATGATCG 57.705 39.130 0.0 0.0 0.00 3.69 R
3566 4501 0.615331 TCTTGGAGGAGTGGTCATGC 59.385 55.000 0.0 0.0 0.00 4.06 R
4450 5450 0.396974 AACTCCAGCACTTTGGGCAA 60.397 50.000 0.0 0.0 38.81 4.52 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
83 84 5.620206 TGATATTAGGTGGGTTGTATGCAG 58.380 41.667 0.00 0.00 0.00 4.41
105 106 4.460382 AGAAAATGCAGTCATCGGTGAAAT 59.540 37.500 0.00 0.00 35.80 2.17
136 138 8.793592 GTTTGTATAGTTTCTTTGATTGGAGGT 58.206 33.333 0.00 0.00 0.00 3.85
277 280 1.402968 CAACAACTGCTGAGCACTGTT 59.597 47.619 19.17 19.17 38.92 3.16
303 306 3.506810 GCACTTGCAAGTTACAACAACA 58.493 40.909 29.23 0.00 41.59 3.33
323 326 4.868268 ACAGGAGGCAGATTGTAGTAGTA 58.132 43.478 0.00 0.00 0.00 1.82
396 406 3.645212 CCATGAGATCTCTCCTAGGCAAA 59.355 47.826 22.95 0.00 42.20 3.68
437 456 1.828832 GAGTACACTCTGATTCGCGG 58.171 55.000 6.13 0.00 39.81 6.46
438 457 0.179134 AGTACACTCTGATTCGCGGC 60.179 55.000 6.13 0.00 0.00 6.53
439 458 1.226575 TACACTCTGATTCGCGGCG 60.227 57.895 17.70 17.70 0.00 6.46
440 459 1.929806 TACACTCTGATTCGCGGCGT 61.930 55.000 22.90 3.24 0.00 5.68
632 669 1.383456 CCTCAGGACTCTCTCAGCGG 61.383 65.000 0.00 0.00 0.00 5.52
909 946 3.582647 TGAAGGTGGACATGAAGAAGCTA 59.417 43.478 0.00 0.00 0.00 3.32
946 983 5.163478 GCCAAACATGATAAAGGCTCTCATT 60.163 40.000 0.00 0.00 39.02 2.57
1605 1874 3.800506 AGTTACACAAGGAAGTTTCGTCG 59.199 43.478 0.00 0.00 0.00 5.12
1920 2803 7.831691 TTTCCTCAATGGTATGAACTTCAAA 57.168 32.000 0.00 0.00 37.07 2.69
1964 2847 8.527810 TCTCACTTGTATTTTGTTTCCTGTTTT 58.472 29.630 0.00 0.00 0.00 2.43
1965 2848 9.150348 CTCACTTGTATTTTGTTTCCTGTTTTT 57.850 29.630 0.00 0.00 0.00 1.94
2046 2929 3.665745 AGAAATTGGTTGCCACATGAC 57.334 42.857 0.00 0.00 30.78 3.06
2300 3221 1.315690 AATCTGCATTCAGCCGATGG 58.684 50.000 0.00 0.00 45.02 3.51
2475 3401 2.966050 TGCAACCCAACAAGAAACAAC 58.034 42.857 0.00 0.00 0.00 3.32
2864 3798 7.426743 GTCAAGCGAAGAGAATTTTATTACTGC 59.573 37.037 0.00 0.00 0.00 4.40
3187 4121 4.897509 TCAAAGATTGAGAAGCTCCAGA 57.102 40.909 0.00 0.00 34.08 3.86
3826 4767 3.432326 GCTTACCGACAGGGAGATCATTT 60.432 47.826 0.00 0.00 43.47 2.32
3906 4847 1.072965 AGGCTGAGCTTTGCAGTTACT 59.927 47.619 3.72 2.80 35.81 2.24
3912 4853 2.485814 GAGCTTTGCAGTTACTGGAAGG 59.514 50.000 20.73 20.73 42.27 3.46
3947 4888 3.495629 GCACTGGAGAGGATTGATATGCA 60.496 47.826 0.00 0.00 0.00 3.96
4164 5106 8.899427 ATATGTCACATTATCTTCCAGTTGAG 57.101 34.615 0.00 0.00 0.00 3.02
4187 5129 5.523916 AGCAACAAATCATCTGGTACGTATC 59.476 40.000 0.00 0.00 0.00 2.24
4188 5130 5.293324 GCAACAAATCATCTGGTACGTATCA 59.707 40.000 8.52 8.52 0.00 2.15
4192 5177 3.554259 TCATCTGGTACGTATCATCGC 57.446 47.619 9.38 0.00 0.00 4.58
4448 5448 1.834263 GGTGTATGGAGGTCTCTTGCT 59.166 52.381 0.00 0.00 0.00 3.91
4449 5449 2.159028 GGTGTATGGAGGTCTCTTGCTC 60.159 54.545 0.00 0.00 0.00 4.26
4450 5450 2.763448 GTGTATGGAGGTCTCTTGCTCT 59.237 50.000 0.00 0.00 0.00 4.09
4451 5451 3.196685 GTGTATGGAGGTCTCTTGCTCTT 59.803 47.826 0.00 0.00 0.00 2.85
4452 5452 3.196469 TGTATGGAGGTCTCTTGCTCTTG 59.804 47.826 0.00 0.00 0.00 3.02
4453 5453 0.322975 TGGAGGTCTCTTGCTCTTGC 59.677 55.000 0.00 0.00 40.20 4.01
4551 5687 1.172812 ACCAAGAACTCCCGCTTTGC 61.173 55.000 0.00 0.00 0.00 3.68
4771 5963 9.878599 CAATACTACCAGTAACAGTTTTTGAAG 57.121 33.333 0.00 0.00 33.89 3.02
4809 6069 6.053650 TCACAGAAATGGATGCTAATCTGAG 58.946 40.000 16.25 10.76 38.10 3.35
4872 6402 1.807573 GGCCGACAGAGCGAAAGAG 60.808 63.158 0.00 0.00 0.00 2.85
4947 6480 4.577693 CACTGCATGCATACCAGTTCTTAT 59.422 41.667 22.97 4.93 37.70 1.73
4974 6508 3.121944 CCTCTTCGAATGTCAGTTTGTCG 59.878 47.826 0.00 0.00 0.00 4.35
5022 6556 0.249868 TGAACTTGTCAGGAGGCACG 60.250 55.000 0.00 0.00 0.00 5.34
5024 6558 2.044806 AACTTGTCAGGAGGCACGCT 62.045 55.000 0.00 0.00 0.00 5.07
5056 6598 3.909430 AGCATGACATCAAGCAACTTTG 58.091 40.909 11.31 0.00 42.43 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 6.746900 GCATACAACCCACCTAATATCATGGA 60.747 42.308 0.00 0.00 33.80 3.41
83 84 3.829886 TTCACCGATGACTGCATTTTC 57.170 42.857 0.00 0.00 34.11 2.29
303 306 6.195700 TCTTTACTACTACAATCTGCCTCCT 58.804 40.000 0.00 0.00 0.00 3.69
323 326 7.127032 ACTCCATCTTCCTTATCTGTGATCTTT 59.873 37.037 0.00 0.00 0.00 2.52
396 406 2.044946 GCAAGGAGACCGCCCAAT 60.045 61.111 0.00 0.00 0.00 3.16
946 983 3.253921 CCAATCAATGACACAACAGCTCA 59.746 43.478 0.00 0.00 0.00 4.26
1587 1855 2.589798 TCGACGAAACTTCCTTGTGT 57.410 45.000 0.00 0.00 0.00 3.72
1724 2117 8.545472 TCCAATTTTAGTATGTTACCTGCTACT 58.455 33.333 0.00 0.00 0.00 2.57
1798 2242 7.054491 ACCTATGTCCAAATTGCCATATTTC 57.946 36.000 4.74 0.00 0.00 2.17
1904 2787 7.669722 TCCTTAGCTTTTTGAAGTTCATACCAT 59.330 33.333 6.36 0.00 0.00 3.55
1917 2800 7.592903 GTGAGAAGAAACATCCTTAGCTTTTTG 59.407 37.037 0.00 0.00 0.00 2.44
1920 2803 6.538263 AGTGAGAAGAAACATCCTTAGCTTT 58.462 36.000 0.00 0.00 0.00 3.51
2300 3221 1.153509 GCATTGGCATCACTTGGGC 60.154 57.895 0.00 0.00 40.72 5.36
2475 3401 5.295431 TGCAAACTTTACTCCAATGATCG 57.705 39.130 0.00 0.00 0.00 3.69
2864 3798 2.305928 TCAACCAATGTCCACCAACAG 58.694 47.619 0.00 0.00 31.50 3.16
3117 4051 3.125316 GGAGGCTCAAATACTTCAACACG 59.875 47.826 17.69 0.00 0.00 4.49
3187 4121 8.380742 TCCCTTATGTCAAGAGTTTCTAGATT 57.619 34.615 0.00 0.00 0.00 2.40
3566 4501 0.615331 TCTTGGAGGAGTGGTCATGC 59.385 55.000 0.00 0.00 0.00 4.06
3762 4703 5.079998 TGTCCACTATGTCCCTATCATCT 57.920 43.478 0.00 0.00 0.00 2.90
3826 4767 1.077005 CTTGAATCCCCCAGGTGGAAA 59.923 52.381 0.00 0.00 37.39 3.13
3906 4847 0.918983 CTGGCATTACCTCCCTTCCA 59.081 55.000 0.00 0.00 40.22 3.53
3912 4853 0.749454 CCAGTGCTGGCATTACCTCC 60.749 60.000 5.19 0.00 44.73 4.30
3947 4888 3.312736 TCCCTTCAAAGGCTTCAAACT 57.687 42.857 0.00 0.00 45.10 2.66
4156 5098 4.482386 CAGATGATTTGTTGCTCAACTGG 58.518 43.478 13.16 0.00 41.67 4.00
4164 5106 5.293324 TGATACGTACCAGATGATTTGTTGC 59.707 40.000 0.00 0.00 0.00 4.17
4187 5129 2.869801 TCTGTTTATTTAGCCCGCGATG 59.130 45.455 8.23 0.00 0.00 3.84
4188 5130 2.870411 GTCTGTTTATTTAGCCCGCGAT 59.130 45.455 8.23 0.00 0.00 4.58
4192 5177 3.006940 TGCAGTCTGTTTATTTAGCCCG 58.993 45.455 0.93 0.00 0.00 6.13
4448 5448 0.538057 CTCCAGCACTTTGGGCAAGA 60.538 55.000 0.00 0.00 38.81 3.02
4449 5449 0.825010 ACTCCAGCACTTTGGGCAAG 60.825 55.000 0.00 0.00 38.81 4.01
4450 5450 0.396974 AACTCCAGCACTTTGGGCAA 60.397 50.000 0.00 0.00 38.81 4.52
4451 5451 0.396974 AAACTCCAGCACTTTGGGCA 60.397 50.000 0.00 0.00 38.81 5.36
4452 5452 0.752658 AAAACTCCAGCACTTTGGGC 59.247 50.000 0.00 0.00 38.81 5.36
4453 5453 2.558359 CCTAAAACTCCAGCACTTTGGG 59.442 50.000 0.00 0.00 38.81 4.12
4551 5687 4.466567 TGCTAAGACAATCAAACACGTG 57.533 40.909 15.48 15.48 0.00 4.49
4708 5866 9.869844 CATTCGAGAATTCCTATGATAAAACAC 57.130 33.333 0.65 0.00 0.00 3.32
4709 5867 8.559536 GCATTCGAGAATTCCTATGATAAAACA 58.440 33.333 0.65 0.00 0.00 2.83
4710 5868 8.559536 TGCATTCGAGAATTCCTATGATAAAAC 58.440 33.333 0.65 0.00 0.00 2.43
4711 5869 8.675705 TGCATTCGAGAATTCCTATGATAAAA 57.324 30.769 0.65 0.00 0.00 1.52
4712 5870 8.853077 ATGCATTCGAGAATTCCTATGATAAA 57.147 30.769 0.65 0.00 0.00 1.40
4771 5963 9.330063 TCCATTTCTGTGATAAATGACTATGTC 57.670 33.333 9.50 0.00 43.79 3.06
4809 6069 1.246737 CCCTGCTCCTGCTTTGTTCC 61.247 60.000 0.00 0.00 40.48 3.62
4872 6402 6.910972 CAGATCATATTGACACTTTGCATCAC 59.089 38.462 0.00 0.00 0.00 3.06
4947 6480 4.336889 ACTGACATTCGAAGAGGTGAAA 57.663 40.909 3.35 0.00 38.43 2.69
4974 6508 0.373024 GCTCAAGCATCGACAAGCTC 59.627 55.000 9.00 0.00 40.90 4.09
5022 6556 0.249363 TCATGCTCGAGATCTGCAGC 60.249 55.000 18.75 13.51 40.18 5.25
5024 6558 0.819582 TGTCATGCTCGAGATCTGCA 59.180 50.000 18.75 7.82 41.13 4.41
5056 6598 6.021468 GCACGCATGATAAAACTAAATCACAC 60.021 38.462 0.00 0.00 35.06 3.82
5076 6618 2.743636 TAGGCTAGATATTGGCACGC 57.256 50.000 0.00 0.00 34.44 5.34


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

AutoCloner maintained by Alex Coulton.