Multiple sequence alignment - TraesCS1B01G163700

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 TraesCS1B01G163700 chr1B 100.000 2286 0 0 1 2286 286026393 286024108 0 4222
1 TraesCS1B01G163700 chr1B 94.052 1530 88 3 757 2286 286167347 286168873 0 2318
2 TraesCS1B01G163700 chr4D 95.556 1530 67 1 757 2286 483697116 483698644 0 2447
3 TraesCS1B01G163700 chr4D 94.892 1527 75 3 760 2286 135005461 135003938 0 2385
4 TraesCS1B01G163700 chr4D 93.975 1527 90 2 760 2286 241142485 241140961 0 2309
5 TraesCS1B01G163700 chr7A 93.660 1530 97 0 757 2286 571648192 571649721 0 2289
6 TraesCS1B01G163700 chr7A 95.669 762 33 0 1 762 563531540 563530779 0 1225
7 TraesCS1B01G163700 chr5D 93.652 1528 95 2 757 2284 79866012 79867537 0 2283
8 TraesCS1B01G163700 chr5D 92.997 1528 102 5 760 2286 197839138 197837615 0 2224
9 TraesCS1B01G163700 chr6B 94.418 1272 63 4 757 2028 53079772 53081035 0 1949
10 TraesCS1B01G163700 chr3A 96.060 1142 45 0 757 1898 191856306 191857447 0 1860
11 TraesCS1B01G163700 chr7D 95.932 762 31 0 1 762 579015519 579016280 0 1236
12 TraesCS1B01G163700 chr7D 95.445 461 21 0 1826 2286 48839271 48839731 0 736
13 TraesCS1B01G163700 chr2D 95.932 762 31 0 1 762 642937742 642938503 0 1236
14 TraesCS1B01G163700 chr1A 95.801 762 32 0 1 762 238155189 238154428 0 1230
15 TraesCS1B01G163700 chr1A 95.669 762 33 0 1 762 238109804 238109043 0 1225
16 TraesCS1B01G163700 chrUn 95.669 762 33 0 1 762 237257889 237257128 0 1225
17 TraesCS1B01G163700 chrUn 95.669 762 33 0 1 762 448234611 448235372 0 1225
18 TraesCS1B01G163700 chrUn 95.669 762 33 0 1 762 449238583 449237822 0 1225
19 TraesCS1B01G163700 chr5A 95.669 762 33 0 1 762 16577979 16577218 0 1225
20 TraesCS1B01G163700 chr1D 95.342 730 34 0 1557 2286 185763590 185764319 0 1160


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 TraesCS1B01G163700 chr1B 286024108 286026393 2285 True 4222 4222 100.000 1 2286 1 chr1B.!!$R1 2285
1 TraesCS1B01G163700 chr1B 286167347 286168873 1526 False 2318 2318 94.052 757 2286 1 chr1B.!!$F1 1529
2 TraesCS1B01G163700 chr4D 483697116 483698644 1528 False 2447 2447 95.556 757 2286 1 chr4D.!!$F1 1529
3 TraesCS1B01G163700 chr4D 135003938 135005461 1523 True 2385 2385 94.892 760 2286 1 chr4D.!!$R1 1526
4 TraesCS1B01G163700 chr4D 241140961 241142485 1524 True 2309 2309 93.975 760 2286 1 chr4D.!!$R2 1526
5 TraesCS1B01G163700 chr7A 571648192 571649721 1529 False 2289 2289 93.660 757 2286 1 chr7A.!!$F1 1529
6 TraesCS1B01G163700 chr7A 563530779 563531540 761 True 1225 1225 95.669 1 762 1 chr7A.!!$R1 761
7 TraesCS1B01G163700 chr5D 79866012 79867537 1525 False 2283 2283 93.652 757 2284 1 chr5D.!!$F1 1527
8 TraesCS1B01G163700 chr5D 197837615 197839138 1523 True 2224 2224 92.997 760 2286 1 chr5D.!!$R1 1526
9 TraesCS1B01G163700 chr6B 53079772 53081035 1263 False 1949 1949 94.418 757 2028 1 chr6B.!!$F1 1271
10 TraesCS1B01G163700 chr3A 191856306 191857447 1141 False 1860 1860 96.060 757 1898 1 chr3A.!!$F1 1141
11 TraesCS1B01G163700 chr7D 579015519 579016280 761 False 1236 1236 95.932 1 762 1 chr7D.!!$F2 761
12 TraesCS1B01G163700 chr2D 642937742 642938503 761 False 1236 1236 95.932 1 762 1 chr2D.!!$F1 761
13 TraesCS1B01G163700 chr1A 238154428 238155189 761 True 1230 1230 95.801 1 762 1 chr1A.!!$R2 761
14 TraesCS1B01G163700 chr1A 238109043 238109804 761 True 1225 1225 95.669 1 762 1 chr1A.!!$R1 761
15 TraesCS1B01G163700 chrUn 237257128 237257889 761 True 1225 1225 95.669 1 762 1 chrUn.!!$R1 761
16 TraesCS1B01G163700 chrUn 448234611 448235372 761 False 1225 1225 95.669 1 762 1 chrUn.!!$F1 761
17 TraesCS1B01G163700 chrUn 449237822 449238583 761 True 1225 1225 95.669 1 762 1 chrUn.!!$R2 761
18 TraesCS1B01G163700 chr5A 16577218 16577979 761 True 1225 1225 95.669 1 762 1 chr5A.!!$R1 761
19 TraesCS1B01G163700 chr1D 185763590 185764319 729 False 1160 1160 95.342 1557 2286 1 chr1D.!!$F1 729

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
152 153 0.32336 CCGGGATTTTGCCCTTCTCA 60.323 55.0 0.0 0.0 46.44 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 1995 0.183492 ATTGCCCATACCGACAGCAT 59.817 50.0 0.0 0.0 32.67 3.79 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 6.672266 TTCCAGTGGATCACTATAGAATCC 57.328 41.667 14.00 21.97 43.43 3.01
44 45 2.043115 TCCTCTAGAAGCAGGTTCTCCA 59.957 50.000 18.24 5.67 42.26 3.86
103 104 6.323996 AGAATGGACTTCTCCGTCATGTAATA 59.676 38.462 0.00 0.00 40.26 0.98
132 133 2.122769 TCACGGTCCTGTTCCCCA 60.123 61.111 0.00 0.00 0.00 4.96
152 153 0.323360 CCGGGATTTTGCCCTTCTCA 60.323 55.000 0.00 0.00 46.44 3.27
159 160 5.196695 GGATTTTGCCCTTCTCAACTAGAT 58.803 41.667 0.00 0.00 33.05 1.98
187 188 5.950549 GGAGATATTCATTCCATTCAGGCAT 59.049 40.000 0.00 0.00 37.29 4.40
188 189 7.037080 AGGAGATATTCATTCCATTCAGGCATA 60.037 37.037 0.00 0.00 37.29 3.14
327 328 1.153539 TTGGTTTGGATGGGGTCTCA 58.846 50.000 0.00 0.00 0.00 3.27
385 386 5.224135 AGACTTTCTCGCTCAGTAAAGAAC 58.776 41.667 0.00 0.00 33.98 3.01
391 392 4.517832 TCTCGCTCAGTAAAGAACAGTACA 59.482 41.667 0.00 0.00 0.00 2.90
399 400 2.649331 AAGAACAGTACACGCGCTAT 57.351 45.000 5.73 0.00 0.00 2.97
408 409 1.876714 CACGCGCTATGGCTTACGT 60.877 57.895 5.73 7.61 39.42 3.57
485 486 0.995024 ATGGCTGAGTGGCTTAAGGT 59.005 50.000 4.29 0.00 42.34 3.50
546 547 2.092375 GGGTTCGAATCCCATTTCCTCT 60.092 50.000 17.16 0.00 44.05 3.69
552 553 1.002069 ATCCCATTTCCTCTGGCACA 58.998 50.000 0.00 0.00 32.08 4.57
597 598 5.524971 TTACGTGAGAGAAAGAACCTCAA 57.475 39.130 0.00 0.00 38.49 3.02
648 649 1.746220 CTGCTTAGTGACTAGGAGCGT 59.254 52.381 5.87 0.00 36.17 5.07
703 704 1.000506 CGAAGAAGACCTTCCCGAACA 59.999 52.381 13.28 0.00 46.65 3.18
742 743 2.498726 GGCTCTCGGCTCTTGAGG 59.501 66.667 0.00 0.00 41.46 3.86
783 784 1.748493 AGAGCAAAACAAGCAACGGAA 59.252 42.857 0.00 0.00 0.00 4.30
992 994 2.439507 AGAGCAAGAGAACAAAGTGGGA 59.560 45.455 0.00 0.00 0.00 4.37
996 998 4.038402 AGCAAGAGAACAAAGTGGGATTTG 59.962 41.667 0.00 0.00 44.14 2.32
1022 1025 5.184864 TGATGTCGGAATTTGCACCTATTTT 59.815 36.000 0.00 0.00 0.00 1.82
1079 1082 1.766496 TCCACTCGGTGTTCCTTTTCT 59.234 47.619 3.82 0.00 0.00 2.52
1100 1103 8.506168 TTTCTATTTGCTTCCAATAGTTCGAT 57.494 30.769 0.00 0.00 0.00 3.59
1147 1150 0.620410 ATGTGGTTCCGATCCCTCCA 60.620 55.000 0.00 0.00 0.00 3.86
1175 1180 4.142337 TGCCAGAAGTCGTTTCGATATACA 60.142 41.667 0.00 0.00 40.86 2.29
1241 1246 3.958147 GTCACCTTTTCTTTTCCTTGGGA 59.042 43.478 0.00 0.00 0.00 4.37
1279 1284 4.643784 AGATTGATCTGTTTGGATCTTGGC 59.356 41.667 0.00 0.00 41.72 4.52
1322 1327 8.818622 TTGATTTTGATGATTGGATCTCTCTT 57.181 30.769 0.00 0.00 0.00 2.85
1330 1336 4.885907 TGATTGGATCTCTCTTTGAATGGC 59.114 41.667 0.00 0.00 0.00 4.40
1333 1339 4.863548 TGGATCTCTCTTTGAATGGCAAT 58.136 39.130 0.00 0.00 36.15 3.56
1398 1405 2.850568 GGGGGAAGGACATAGGAAAGAA 59.149 50.000 0.00 0.00 0.00 2.52
1504 1513 1.065199 CCAGAAGCAAGGAGTATGCCA 60.065 52.381 0.00 0.00 44.91 4.92
1716 1725 1.742268 GAGGAGTCAAGGATTTGCTGC 59.258 52.381 0.00 0.00 34.21 5.25
1798 1807 5.287674 TGAATGGAAGATGCCTCTAGAAG 57.712 43.478 0.00 0.00 0.00 2.85
1808 1817 4.986054 TGCCTCTAGAAGTTTTGGGTTA 57.014 40.909 0.00 0.00 0.00 2.85
1856 1865 4.102681 GCTAGCTCCCTTTCCCTTATTACA 59.897 45.833 7.70 0.00 0.00 2.41
1913 1922 7.787623 AGGGCTTGACTTACTTAACTTACTA 57.212 36.000 0.00 0.00 0.00 1.82
1914 1923 7.838884 AGGGCTTGACTTACTTAACTTACTAG 58.161 38.462 0.00 0.00 0.00 2.57
2031 2040 6.842163 TCTTAAGTTCTTTGATTGATTCCGC 58.158 36.000 1.63 0.00 0.00 5.54
2065 2074 5.180810 ACCAAAGTTCCTCTAATTCCTCC 57.819 43.478 0.00 0.00 0.00 4.30
2150 2159 4.324331 GGTACCTAGCAACCTTCATTCCTT 60.324 45.833 4.06 0.00 32.72 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.430332 CCTGGAGAACCTGCTTCTAGAG 59.570 54.545 0.00 0.00 39.53 2.43
44 45 1.112113 CACGTCCTACCATAGTGCCT 58.888 55.000 0.00 0.00 0.00 4.75
103 104 3.256136 CAGGACCGTGACTCTTCTAAACT 59.744 47.826 0.00 0.00 0.00 2.66
138 139 5.819991 TCATCTAGTTGAGAAGGGCAAAAT 58.180 37.500 0.00 0.00 37.85 1.82
152 153 9.163894 TGGAATGAATATCTCCTTCATCTAGTT 57.836 33.333 0.00 0.00 41.33 2.24
159 160 7.229308 CCTGAATGGAATGAATATCTCCTTCA 58.771 38.462 0.00 0.00 38.35 3.02
187 188 2.762459 ACGCCGCCCTTCCTCATA 60.762 61.111 0.00 0.00 0.00 2.15
188 189 4.162690 GACGCCGCCCTTCCTCAT 62.163 66.667 0.00 0.00 0.00 2.90
208 209 3.262915 CCAAGAGAGAAGACAGGGTCAAT 59.737 47.826 0.00 0.00 34.60 2.57
327 328 1.613630 ATCTCCCCAGCGTCCAAGT 60.614 57.895 0.00 0.00 0.00 3.16
361 362 5.455056 TCTTTACTGAGCGAGAAAGTCTT 57.545 39.130 0.00 0.00 32.05 3.01
364 365 4.945246 TGTTCTTTACTGAGCGAGAAAGT 58.055 39.130 0.00 0.00 32.05 2.66
385 386 0.806102 AAGCCATAGCGCGTGTACTG 60.806 55.000 8.43 0.00 46.67 2.74
391 392 0.317603 CTACGTAAGCCATAGCGCGT 60.318 55.000 8.43 8.13 46.67 6.01
399 400 2.098607 CGAAGATCCACTACGTAAGCCA 59.901 50.000 0.00 0.00 45.62 4.75
408 409 0.539986 GGTTGCCCGAAGATCCACTA 59.460 55.000 0.00 0.00 0.00 2.74
485 486 7.851387 TGTATGTCGATTTAGCAAACCAATA 57.149 32.000 0.00 0.00 0.00 1.90
546 547 0.320374 CCCGTTCTACTTCTGTGCCA 59.680 55.000 0.00 0.00 0.00 4.92
552 553 3.015312 GCCCGCCCGTTCTACTTCT 62.015 63.158 0.00 0.00 0.00 2.85
597 598 0.462047 GACGGCGGACTCCATCAATT 60.462 55.000 13.24 0.00 0.00 2.32
648 649 3.244911 CCAAGAACAAGAAAGGGGAGCTA 60.245 47.826 0.00 0.00 0.00 3.32
652 653 2.424234 CCACCAAGAACAAGAAAGGGGA 60.424 50.000 0.00 0.00 0.00 4.81
742 743 2.125350 CTGCGGTGGAGGAGCTTC 60.125 66.667 0.00 0.00 0.00 3.86
755 756 2.918131 GCTTGTTTTGCTCTAACCTGCG 60.918 50.000 0.00 0.00 0.00 5.18
783 784 1.002366 CTTTCGCGCTAGTTGCTCAT 58.998 50.000 5.56 0.00 40.11 2.90
858 859 3.888930 CCCCTTGCTCTTCACACTAAAAA 59.111 43.478 0.00 0.00 0.00 1.94
867 868 1.252904 GCAATGCCCCTTGCTCTTCA 61.253 55.000 0.00 0.00 46.32 3.02
966 968 3.389329 ACTTTGTTCTCTTGCTCTCCTCA 59.611 43.478 0.00 0.00 0.00 3.86
976 978 4.342092 CACCAAATCCCACTTTGTTCTCTT 59.658 41.667 0.00 0.00 34.90 2.85
992 994 3.257873 TGCAAATTCCGACATCACCAAAT 59.742 39.130 0.00 0.00 0.00 2.32
996 998 1.135402 GGTGCAAATTCCGACATCACC 60.135 52.381 0.00 0.00 36.20 4.02
1040 1043 7.042051 CGAGTGGAATCAAAGAAACTAGTGAAA 60.042 37.037 0.00 0.00 0.00 2.69
1042 1045 5.926542 CGAGTGGAATCAAAGAAACTAGTGA 59.073 40.000 0.00 0.00 0.00 3.41
1044 1047 5.221661 ACCGAGTGGAATCAAAGAAACTAGT 60.222 40.000 0.00 0.00 39.21 2.57
1079 1082 9.424319 GATAGATCGAACTATTGGAAGCAAATA 57.576 33.333 15.46 0.00 33.85 1.40
1100 1103 6.235231 AGGCCGACAATTTTTCTAGATAGA 57.765 37.500 0.00 0.00 0.00 1.98
1147 1150 2.417719 GAAACGACTTCTGGCATCACT 58.582 47.619 0.00 0.00 0.00 3.41
1241 1246 7.181125 ACAGATCAATCTTGTTAGGAGGTACTT 59.819 37.037 0.00 0.00 34.20 2.24
1279 1284 5.556006 ATCAATAAAAAGGCCATCATGGG 57.444 39.130 5.62 0.00 38.19 4.00
1322 1327 0.544833 AGCACCCCATTGCCATTCAA 60.545 50.000 0.00 0.00 44.14 2.69
1330 1336 1.439353 CGATCCGAAGCACCCCATTG 61.439 60.000 0.00 0.00 0.00 2.82
1333 1339 3.781307 CCGATCCGAAGCACCCCA 61.781 66.667 0.00 0.00 0.00 4.96
1428 1435 3.062234 CGCCGTTTTTCTTCTCTACCATC 59.938 47.826 0.00 0.00 0.00 3.51
1504 1513 0.248743 TGTTCTCGTCGAAACACGCT 60.249 50.000 14.73 0.00 39.74 5.07
1624 1633 8.466617 TCTGACTAAGACTATAGAATGTTCCC 57.533 38.462 6.78 0.00 0.00 3.97
1716 1725 3.997021 CCCTTTCTATGATCCGGAATTCG 59.003 47.826 9.01 0.00 38.88 3.34
1856 1865 6.426646 AGAATAGCGGAGAGAAATGGTAAT 57.573 37.500 0.00 0.00 0.00 1.89
1986 1995 0.183492 ATTGCCCATACCGACAGCAT 59.817 50.000 0.00 0.00 32.67 3.79
2031 2040 1.078426 CTTTGGTAGCACTCGGGGG 60.078 63.158 0.00 0.00 0.00 5.40
2065 2074 0.954452 GGCAAGGGAAATATCTGGCG 59.046 55.000 0.00 0.00 0.00 5.69
2121 2130 1.610554 GGTTGCTAGGTACCGCTCCA 61.611 60.000 6.18 0.00 0.00 3.86
2150 2159 1.336755 GCAAAGGCAAGACGGAAAAGA 59.663 47.619 0.00 0.00 40.72 2.52


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

AutoCloner maintained by Alex Coulton.