Multiple sequence alignment - TraesCS1D01G041000

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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 TraesCS1D01G041000 chr1D 100.000 2198 0 0 1 2198 19929763 19927566 0.000000e+00 4060.0
1 TraesCS1D01G041000 chr1D 91.799 1134 79 11 867 1990 457052206 457051077 0.000000e+00 1567.0
2 TraesCS1D01G041000 chr1D 84.848 198 22 3 1996 2193 20940468 20940657 2.230000e-45 193.0
3 TraesCS1D01G041000 chr1D 82.160 213 17 8 1 195 20835796 20836005 1.750000e-36 163.0
4 TraesCS1D01G041000 chr7D 93.027 1133 63 12 861 1990 262098 260979 0.000000e+00 1640.0
5 TraesCS1D01G041000 chr7D 93.629 1083 64 4 913 1990 185759417 185760499 0.000000e+00 1613.0
6 TraesCS1D01G041000 chr7D 92.857 1106 67 10 895 1990 144158603 144159706 0.000000e+00 1594.0
7 TraesCS1D01G041000 chr7D 87.821 156 16 3 564 717 603679997 603680151 1.730000e-41 180.0
8 TraesCS1D01G041000 chr2D 92.586 1133 70 8 861 1990 171444148 171443027 0.000000e+00 1615.0
9 TraesCS1D01G041000 chr2D 93.530 1082 66 4 915 1993 461081609 461080529 0.000000e+00 1607.0
10 TraesCS1D01G041000 chr2D 79.412 170 31 4 562 728 644659426 644659594 1.380000e-22 117.0
11 TraesCS1D01G041000 chr3D 93.242 1095 71 3 899 1990 120627218 120626124 0.000000e+00 1609.0
12 TraesCS1D01G041000 chr3D 92.679 1120 74 6 874 1989 535577074 535578189 0.000000e+00 1607.0
13 TraesCS1D01G041000 chr3D 76.129 155 37 0 562 716 19163824 19163978 5.030000e-12 82.4
14 TraesCS1D01G041000 chr5D 92.368 1140 70 7 861 1991 511131687 511130556 0.000000e+00 1607.0
15 TraesCS1D01G041000 chr5D 77.876 226 39 8 496 714 260841257 260841478 1.770000e-26 130.0
16 TraesCS1D01G041000 chr1B 91.002 878 58 8 1 862 32070142 32069270 0.000000e+00 1164.0
17 TraesCS1D01G041000 chr1B 90.459 566 41 9 1 553 32142326 32141761 0.000000e+00 734.0
18 TraesCS1D01G041000 chr1B 90.982 499 34 8 66 553 32092636 32092138 0.000000e+00 662.0
19 TraesCS1D01G041000 chr1B 88.166 507 40 7 1 495 31965129 31964631 8.740000e-164 586.0
20 TraesCS1D01G041000 chr1B 87.887 355 33 3 53 398 32190441 32190088 2.030000e-110 409.0
21 TraesCS1D01G041000 chr1B 90.127 314 21 4 550 862 32141103 32140799 1.220000e-107 399.0
22 TraesCS1D01G041000 chr1B 89.338 272 27 2 127 398 32092104 32091835 7.520000e-90 340.0
23 TraesCS1D01G041000 chr1B 95.238 210 8 2 1990 2198 32140813 32140605 4.520000e-87 331.0
24 TraesCS1D01G041000 chr1B 93.684 95 2 2 721 815 31964629 31964539 2.940000e-29 139.0
25 TraesCS1D01G041000 chr1B 84.028 144 16 6 721 862 32189527 32189389 4.920000e-27 132.0
26 TraesCS1D01G041000 chr1B 86.066 122 13 2 2081 2198 32089856 32089735 6.370000e-26 128.0
27 TraesCS1D01G041000 chr1B 86.066 122 13 2 2081 2198 32188994 32188873 6.370000e-26 128.0
28 TraesCS1D01G041000 chr1B 83.969 131 17 3 721 850 32091271 32091144 2.960000e-24 122.0
29 TraesCS1D01G041000 chr1B 77.348 181 35 5 538 714 342295107 342294929 3.860000e-18 102.0
30 TraesCS1D01G041000 chr1B 80.392 153 10 11 4 137 34210021 34209870 4.990000e-17 99.0
31 TraesCS1D01G041000 chr1B 96.552 58 0 2 1 56 32119725 32119668 6.460000e-16 95.3
32 TraesCS1D01G041000 chr1A 95.475 221 8 1 642 862 21344676 21344458 3.470000e-93 351.0
33 TraesCS1D01G041000 chr1A 81.446 415 47 13 1 397 22364364 22364766 1.640000e-81 313.0
34 TraesCS1D01G041000 chr1A 93.780 209 3 1 1990 2198 21344472 21344274 2.740000e-79 305.0
35 TraesCS1D01G041000 chr1A 87.192 203 19 2 1996 2198 22363499 22363694 7.900000e-55 224.0
36 TraesCS1D01G041000 chr1A 82.105 190 23 6 2012 2197 22364960 22365142 3.780000e-33 152.0
37 TraesCS1D01G041000 chr4D 84.848 198 22 3 1996 2193 73325905 73326094 2.230000e-45 193.0
38 TraesCS1D01G041000 chr4D 83.663 202 22 2 1996 2193 73226178 73226372 1.730000e-41 180.0
39 TraesCS1D01G041000 chr2B 84.277 159 18 6 560 715 55893837 55893683 4.890000e-32 148.0


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 TraesCS1D01G041000 chr1D 19927566 19929763 2197 True 4060.000000 4060 100.000000 1 2198 1 chr1D.!!$R1 2197
1 TraesCS1D01G041000 chr1D 457051077 457052206 1129 True 1567.000000 1567 91.799000 867 1990 1 chr1D.!!$R2 1123
2 TraesCS1D01G041000 chr7D 260979 262098 1119 True 1640.000000 1640 93.027000 861 1990 1 chr7D.!!$R1 1129
3 TraesCS1D01G041000 chr7D 185759417 185760499 1082 False 1613.000000 1613 93.629000 913 1990 1 chr7D.!!$F2 1077
4 TraesCS1D01G041000 chr7D 144158603 144159706 1103 False 1594.000000 1594 92.857000 895 1990 1 chr7D.!!$F1 1095
5 TraesCS1D01G041000 chr2D 171443027 171444148 1121 True 1615.000000 1615 92.586000 861 1990 1 chr2D.!!$R1 1129
6 TraesCS1D01G041000 chr2D 461080529 461081609 1080 True 1607.000000 1607 93.530000 915 1993 1 chr2D.!!$R2 1078
7 TraesCS1D01G041000 chr3D 120626124 120627218 1094 True 1609.000000 1609 93.242000 899 1990 1 chr3D.!!$R1 1091
8 TraesCS1D01G041000 chr3D 535577074 535578189 1115 False 1607.000000 1607 92.679000 874 1989 1 chr3D.!!$F2 1115
9 TraesCS1D01G041000 chr5D 511130556 511131687 1131 True 1607.000000 1607 92.368000 861 1991 1 chr5D.!!$R1 1130
10 TraesCS1D01G041000 chr1B 32069270 32070142 872 True 1164.000000 1164 91.002000 1 862 1 chr1B.!!$R1 861
11 TraesCS1D01G041000 chr1B 32140605 32142326 1721 True 488.000000 734 91.941333 1 2198 3 chr1B.!!$R7 2197
12 TraesCS1D01G041000 chr1B 31964539 31965129 590 True 362.500000 586 90.925000 1 815 2 chr1B.!!$R5 814
13 TraesCS1D01G041000 chr1B 32089735 32092636 2901 True 313.000000 662 87.588750 66 2198 4 chr1B.!!$R6 2132
14 TraesCS1D01G041000 chr1B 32188873 32190441 1568 True 223.000000 409 85.993667 53 2198 3 chr1B.!!$R8 2145
15 TraesCS1D01G041000 chr1A 22363499 22365142 1643 False 229.666667 313 83.581000 1 2198 3 chr1A.!!$F1 2197

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
533 2338 0.031917 TTGCCCCCGGTCTCTACATA 60.032 55.0 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 4581 0.040058 ATGATGAAGGGGTGCAAGCA 59.96 50.0 0.0 0.0 34.77 3.91 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
95 964 3.054802 CAGAAGCTCCCAATACAAGAGGT 60.055 47.826 0.00 0.00 39.92 3.85
147 1031 2.372172 CCCATTCCATACAGGGGACTAC 59.628 54.545 0.00 0.00 41.49 2.73
179 1063 6.656693 AGCATAATACAAGACAAAGAGCAAGT 59.343 34.615 0.00 0.00 0.00 3.16
225 1109 7.921041 ATCTGATAGGAATGAGAGTTACCAA 57.079 36.000 0.00 0.00 28.27 3.67
299 1642 4.153475 GCAGCACCGTATAGTTCAGAAAAA 59.847 41.667 0.00 0.00 0.00 1.94
350 1693 0.247460 CCACGCTGAGATGAACAGGA 59.753 55.000 0.00 0.00 36.09 3.86
374 1717 4.036852 GCTTGGTTCTTGCTTTGTCTTAGT 59.963 41.667 0.00 0.00 0.00 2.24
437 2242 2.102252 CCTTCCAGGTCTGAGTCTATGC 59.898 54.545 0.00 0.00 0.00 3.14
463 2268 6.123651 ACAATTCACTTACAAGGTTGTGGTA 58.876 36.000 5.59 0.00 42.31 3.25
495 2300 1.959508 GCAACCTATGGGATTGTGGCA 60.960 52.381 0.25 0.00 36.25 4.92
524 2329 4.760220 AGGAGGATTGCCCCCGGT 62.760 66.667 0.00 0.00 34.66 5.28
533 2338 0.031917 TTGCCCCCGGTCTCTACATA 60.032 55.000 0.00 0.00 0.00 2.29
540 2346 4.041691 CCCCCGGTCTCTACATAAAATGAT 59.958 45.833 0.00 0.00 0.00 2.45
547 2353 6.016860 GGTCTCTACATAAAATGATGCATGCA 60.017 38.462 25.04 25.04 0.00 3.96
548 2354 7.420002 GTCTCTACATAAAATGATGCATGCAA 58.580 34.615 26.68 9.94 0.00 4.08
637 3105 3.486383 CCACAACCGGCATAAATAGGAT 58.514 45.455 0.00 0.00 0.00 3.24
673 3141 5.250774 ACACCTATCCTATTGTTGAACCACT 59.749 40.000 0.00 0.00 0.00 4.00
700 3168 1.335145 CCGGATGTAGGTATCCCGTT 58.665 55.000 0.00 0.00 43.02 4.44
893 3372 4.109675 CCCAACCCTAGCCACCCG 62.110 72.222 0.00 0.00 0.00 5.28
932 3430 2.408203 CCCTCCTCCTCCCTAGCCT 61.408 68.421 0.00 0.00 0.00 4.58
1034 3532 0.548031 CCTCATTTGCCCTGCCTCTA 59.452 55.000 0.00 0.00 0.00 2.43
1209 3716 2.598985 ATCTAGCGCCTCCCCTCG 60.599 66.667 2.29 0.00 0.00 4.63
1221 3728 2.995574 CCCTCGTCCCCTGTTCGT 60.996 66.667 0.00 0.00 0.00 3.85
1264 3771 1.896660 GCGCTTCCTTGGGTTGTCA 60.897 57.895 0.00 0.00 0.00 3.58
1306 3813 1.112113 GGTGGCGGAGATCTAGTTCA 58.888 55.000 0.00 0.00 0.00 3.18
1458 3968 1.199097 CTAACTTTGTTTGGCGGCGAT 59.801 47.619 12.98 0.00 0.00 4.58
1627 4386 0.733566 GGTCGTCGTTTGGCGTCATA 60.734 55.000 0.00 0.00 42.13 2.15
1820 4581 1.777272 GAGGTCTGGATATTTGGCCCT 59.223 52.381 0.00 0.00 0.00 5.19
1862 4623 1.618837 GGATTGGAGTAGCGGCAGATA 59.381 52.381 1.45 0.00 0.00 1.98
1944 4705 3.963665 TCAATAAAATAGCCGCATGCAC 58.036 40.909 19.57 9.19 44.83 4.57
2179 6150 3.610242 CGAACGCTCATGATATAAGAGGC 59.390 47.826 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
225 1109 6.360370 TCCTACATAGTCAGTTTCTGCTTT 57.640 37.500 0.00 0.00 0.00 3.51
299 1642 7.975616 GTGGTTCTATTATGCATCAACACAAAT 59.024 33.333 0.19 0.00 0.00 2.32
310 1653 5.356751 GTGGTTGATGTGGTTCTATTATGCA 59.643 40.000 0.00 0.00 0.00 3.96
350 1693 2.659428 AGACAAAGCAAGAACCAAGCT 58.341 42.857 0.00 0.00 41.03 3.74
374 1717 0.889994 TCTGGTTTTCGCTACCGCTA 59.110 50.000 0.00 0.00 38.55 4.26
437 2242 6.262273 ACCACAACCTTGTAAGTGAATTGTAG 59.738 38.462 0.00 0.00 39.91 2.74
495 2300 4.158579 GGCAATCCTCCTTTTCGAGAAAAT 59.841 41.667 10.90 0.00 39.29 1.82
524 2329 7.420002 GTTGCATGCATCATTTTATGTAGAGA 58.580 34.615 23.37 0.00 0.00 3.10
533 2338 7.633193 AAAATATGGTTGCATGCATCATTTT 57.367 28.000 29.45 25.04 0.00 1.82
540 2346 7.823310 ACTTTGATTAAAATATGGTTGCATGCA 59.177 29.630 18.46 18.46 0.00 3.96
607 3075 3.677002 CCGGTTGTGGCAATGTTTT 57.323 47.368 0.00 0.00 0.00 2.43
621 3089 6.213600 AGTCATCTAATCCTATTTATGCCGGT 59.786 38.462 1.90 0.00 0.00 5.28
633 3101 8.851876 AGGATAGGTGTATAGTCATCTAATCCT 58.148 37.037 0.00 0.00 36.05 3.24
700 3168 1.254026 CACTGTTGGGAGACGGTAGA 58.746 55.000 0.00 0.00 37.03 2.59
893 3372 1.231928 GAGGAGGGAGGAGGAGGAC 59.768 68.421 0.00 0.00 0.00 3.85
932 3430 1.162951 AAGGGAAGAGGAGGAGGGGA 61.163 60.000 0.00 0.00 0.00 4.81
1014 3512 1.000396 GAGGCAGGGCAAATGAGGT 60.000 57.895 0.00 0.00 0.00 3.85
1019 3517 0.392998 CACGTAGAGGCAGGGCAAAT 60.393 55.000 0.00 0.00 0.00 2.32
1020 3518 1.003839 CACGTAGAGGCAGGGCAAA 60.004 57.895 0.00 0.00 0.00 3.68
1034 3532 2.284405 ATCCGGAGTTCCCCACGT 60.284 61.111 11.34 0.00 0.00 4.49
1209 3716 2.737376 GCACGACGAACAGGGGAC 60.737 66.667 0.00 0.00 0.00 4.46
1245 3752 2.597510 ACAACCCAAGGAAGCGCC 60.598 61.111 2.29 0.00 0.00 6.53
1264 3771 0.900647 AGCGCCTCCTGTACAGAACT 60.901 55.000 24.68 8.64 0.00 3.01
1306 3813 2.584608 CCGACCAGGATTTCGCCT 59.415 61.111 0.00 0.00 45.00 5.52
1468 3978 2.358737 CAAGAAGGGAACGGCGCT 60.359 61.111 6.90 0.00 42.29 5.92
1781 4542 3.706594 CCTCTCACCTAAGCCTAACATCA 59.293 47.826 0.00 0.00 0.00 3.07
1820 4581 0.040058 ATGATGAAGGGGTGCAAGCA 59.960 50.000 0.00 0.00 34.77 3.91
1944 4705 1.000521 TGCCTTTGCATCTGGGAGG 60.001 57.895 0.00 0.00 44.23 4.30
1962 4723 1.203622 AGAAAAGGAGGATGACCCCCT 60.204 52.381 0.00 0.00 37.24 4.79
2005 4766 4.992951 AGTCTTGTACCAAACCGTATGAAC 59.007 41.667 0.00 0.00 0.00 3.18
2079 4840 6.015856 TGCAAGATTCCTGCTCTATCTACTAC 60.016 42.308 8.62 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.