Multiple sequence alignment - TraesCS2B01G025700

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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 TraesCS2B01G025700 chr2B 100.000 2615 0 0 1 2615 11838592 11835978 0.000000e+00 4830
1 TraesCS2B01G025700 chr2D 93.155 2688 83 28 2 2615 9078754 9081414 0.000000e+00 3851
2 TraesCS2B01G025700 chr2A 93.486 2057 89 23 572 2615 8542912 8544936 0.000000e+00 3014
3 TraesCS2B01G025700 chr2A 84.817 382 34 10 10 379 8542131 8542500 1.910000e-96 363
4 TraesCS2B01G025700 chr2A 86.705 173 12 5 313 476 8542500 8542670 5.750000e-42 182
5 TraesCS2B01G025700 chr5D 87.500 192 24 0 1204 1395 322577507 322577698 3.390000e-54 222
6 TraesCS2B01G025700 chr5B 87.500 192 24 0 1204 1395 374191437 374191628 3.390000e-54 222
7 TraesCS2B01G025700 chr4A 85.417 144 17 3 1229 1370 582840662 582840521 2.100000e-31 147
8 TraesCS2B01G025700 chr4D 85.315 143 17 3 1229 1369 18464582 18464722 7.540000e-31 145
9 TraesCS2B01G025700 chr4B 84.722 144 18 3 1229 1370 30362610 30362751 9.760000e-30 141


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 TraesCS2B01G025700 chr2B 11835978 11838592 2614 True 4830.000000 4830 100.000 1 2615 1 chr2B.!!$R1 2614
1 TraesCS2B01G025700 chr2D 9078754 9081414 2660 False 3851.000000 3851 93.155 2 2615 1 chr2D.!!$F1 2613
2 TraesCS2B01G025700 chr2A 8542131 8544936 2805 False 1186.333333 3014 88.336 10 2615 3 chr2A.!!$F1 2605

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
392 470 0.252558 TTACCTCTCCTGACCCCACC 60.253 60.0 0.0 0.0 0.0 4.61 F
970 1215 0.808755 CCACCAAGAACCGCCATTAC 59.191 55.0 0.0 0.0 0.0 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1443 1697 1.575447 CCCCCTCCCCTTTCTCCTTG 61.575 65.0 0.00 0.00 0.00 3.61 R
1951 2207 2.961526 TGCACTAGCTAGCTGTTACC 57.038 50.0 27.68 11.67 42.74 2.85 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
24 25 2.582052 GGAATGGTTTGTCAGTGTCCA 58.418 47.619 0.00 0.00 0.00 4.02
34 35 4.619227 AGTGTCCAACGTGGCGGG 62.619 66.667 0.00 0.00 37.47 6.13
51 52 3.148279 GCGTCCCTCCTCCGTCAT 61.148 66.667 0.00 0.00 0.00 3.06
141 142 2.260869 CGGTGTTGGAGTTGCCCTG 61.261 63.158 0.00 0.00 34.97 4.45
161 162 2.629137 TGACATACAACGGGTGTAGTGT 59.371 45.455 12.02 14.44 45.88 3.55
205 216 6.812998 TCATTACCTAGCACTGTATGGTTAC 58.187 40.000 0.00 0.00 40.36 2.50
392 470 0.252558 TTACCTCTCCTGACCCCACC 60.253 60.000 0.00 0.00 0.00 4.61
487 595 2.061028 GCAGCCTGCAATTGTACAAAC 58.939 47.619 12.82 6.06 44.26 2.93
566 687 6.864165 GCCTGCAATGTACTTACTCTAGATAC 59.136 42.308 0.00 0.00 0.00 2.24
589 825 9.692749 ATACACGTACTTGTCCATATCTTAATG 57.307 33.333 8.46 0.00 0.00 1.90
640 878 2.685387 GATGCCGGCCTACAGTCTCG 62.685 65.000 26.77 0.00 0.00 4.04
724 969 2.103771 TGGACATGGATGCTTAGCTCTC 59.896 50.000 5.60 2.31 0.00 3.20
796 1041 5.179045 TCCGCATTAACACTAGCTAGTAC 57.821 43.478 25.63 8.72 34.13 2.73
814 1059 1.321074 ACTGCCGGCCACTACTAGAC 61.321 60.000 26.77 0.00 0.00 2.59
829 1074 2.245287 ACTAGACCAGGGACCTTCTAGG 59.755 54.545 22.13 10.25 37.61 3.02
850 1095 1.278985 TGTCCATCCACTGATCCACAC 59.721 52.381 0.00 0.00 0.00 3.82
861 1106 5.047306 CCACTGATCCACACTAGTTTACTGA 60.047 44.000 0.00 0.00 0.00 3.41
878 1123 4.853924 ACTGATTGGTTTGGTTTGCTAG 57.146 40.909 0.00 0.00 0.00 3.42
967 1212 1.863155 ATCCCACCAAGAACCGCCAT 61.863 55.000 0.00 0.00 0.00 4.40
970 1215 0.808755 CCACCAAGAACCGCCATTAC 59.191 55.000 0.00 0.00 0.00 1.89
1065 1310 1.226974 CGCCGAGATGTACCACCAG 60.227 63.158 0.00 0.00 0.00 4.00
1660 1914 7.325579 CGGCGGAGTACTAATTCTAATTACTTC 59.674 40.741 0.00 0.00 0.00 3.01
1700 1956 1.092348 GCAGCTGCATGACAGATTGA 58.908 50.000 33.36 0.00 44.43 2.57
1701 1957 1.202154 GCAGCTGCATGACAGATTGAC 60.202 52.381 33.36 0.00 44.43 3.18
1702 1958 2.081462 CAGCTGCATGACAGATTGACA 58.919 47.619 17.76 0.00 44.43 3.58
1703 1959 2.096013 CAGCTGCATGACAGATTGACAG 59.904 50.000 17.76 4.50 44.43 3.51
1704 1960 2.290134 AGCTGCATGACAGATTGACAGT 60.290 45.455 17.76 0.00 44.43 3.55
1705 1961 4.420639 AGCTGCATGACAGATTGACAGTG 61.421 47.826 17.76 0.00 44.43 3.66
1706 1962 3.405823 TGCATGACAGATTGACAGTGA 57.594 42.857 0.00 0.00 0.00 3.41
1707 1963 3.946606 TGCATGACAGATTGACAGTGAT 58.053 40.909 0.00 0.00 0.00 3.06
1708 1964 4.329392 TGCATGACAGATTGACAGTGATT 58.671 39.130 0.00 0.00 0.00 2.57
1709 1965 4.155280 TGCATGACAGATTGACAGTGATTG 59.845 41.667 0.00 0.00 0.00 2.67
1727 1983 6.864685 AGTGATTGATATGCAAACTTTGTGTG 59.135 34.615 3.48 0.00 40.48 3.82
1774 2030 7.628769 TCTTGCAAATCTTATGTTCATGCTA 57.371 32.000 0.00 0.00 33.66 3.49
1849 2105 3.063485 GTTCTCTTGGAGCTGTTCTGTC 58.937 50.000 0.00 0.00 0.00 3.51
1883 2139 7.119846 GTGCTACATGGGAATATCATCCTTAAC 59.880 40.741 0.00 0.00 39.57 2.01
1946 2202 4.829064 TTCAGGTGAAATTCTTGAACCG 57.171 40.909 0.00 0.00 35.99 4.44
1951 2207 3.058224 GGTGAAATTCTTGAACCGTCCTG 60.058 47.826 0.00 0.00 0.00 3.86
2005 2261 9.494479 GTACTCAATTTGTTCACATCACATATG 57.506 33.333 0.00 0.00 0.00 1.78
2084 2345 4.695606 TGATAGGTTTCCCTGAGTTAGGT 58.304 43.478 0.00 0.00 45.80 3.08
2109 2371 9.651718 GTTTTATACTTCATGCAGTATACAAGC 57.348 33.333 20.50 15.85 40.46 4.01
2110 2372 9.613428 TTTTATACTTCATGCAGTATACAAGCT 57.387 29.630 20.50 2.12 40.46 3.74
2112 2374 9.914131 TTATACTTCATGCAGTATACAAGCTAG 57.086 33.333 20.50 11.65 40.46 3.42
2197 2459 4.687948 CGGATGGCACTATATTTCAGTCAG 59.312 45.833 0.00 0.00 0.00 3.51
2348 2641 9.712305 ACATTAATGCAAGAGATATACCTGTAC 57.288 33.333 15.48 0.00 0.00 2.90
2349 2642 9.935241 CATTAATGCAAGAGATATACCTGTACT 57.065 33.333 1.74 0.00 0.00 2.73
2411 2704 5.122519 TGTGAGCAGAGTTGTCAAAACATA 58.877 37.500 0.00 0.00 34.73 2.29
2516 2817 9.722056 CCTTTGAAACATTGACTATAAGTATGC 57.278 33.333 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.179004 ACTGACAAACCATTCCGCCA 60.179 50.000 0.00 0.00 0.00 5.69
34 35 1.826921 TATGACGGAGGAGGGACGC 60.827 63.158 0.00 0.00 0.00 5.19
40 41 1.344763 GGGGAATGTATGACGGAGGAG 59.655 57.143 0.00 0.00 0.00 3.69
41 42 1.343580 TGGGGAATGTATGACGGAGGA 60.344 52.381 0.00 0.00 0.00 3.71
42 43 1.128200 TGGGGAATGTATGACGGAGG 58.872 55.000 0.00 0.00 0.00 4.30
47 48 5.476945 AGAAACAAAGTGGGGAATGTATGAC 59.523 40.000 0.00 0.00 0.00 3.06
51 52 4.148838 CCAGAAACAAAGTGGGGAATGTA 58.851 43.478 0.00 0.00 0.00 2.29
141 142 3.308438 ACACTACACCCGTTGTATGTC 57.692 47.619 0.00 0.00 40.06 3.06
205 216 6.599244 AGAATGGTCAGGTATTTGTACACATG 59.401 38.462 4.73 0.00 0.00 3.21
392 470 4.555511 GCTCTCAAAACTGTTTACTGGCAG 60.556 45.833 14.16 14.16 38.58 4.85
528 641 0.534873 TGCAGGCGTACTAGATTGCA 59.465 50.000 0.00 0.33 39.03 4.08
529 642 1.651987 TTGCAGGCGTACTAGATTGC 58.348 50.000 0.00 0.00 0.00 3.56
530 643 3.198068 ACATTGCAGGCGTACTAGATTG 58.802 45.455 0.00 0.00 0.00 2.67
531 644 3.543680 ACATTGCAGGCGTACTAGATT 57.456 42.857 0.00 0.00 0.00 2.40
533 646 3.021695 AGTACATTGCAGGCGTACTAGA 58.978 45.455 18.10 0.00 43.01 2.43
534 647 3.438297 AGTACATTGCAGGCGTACTAG 57.562 47.619 18.10 0.00 43.01 2.57
541 662 5.263968 TCTAGAGTAAGTACATTGCAGGC 57.736 43.478 0.00 0.00 0.00 4.85
566 687 6.701841 AGCATTAAGATATGGACAAGTACGTG 59.298 38.462 7.29 7.29 0.00 4.49
589 825 2.747855 CTTCGGGCCCACTTGAGC 60.748 66.667 24.92 0.00 0.00 4.26
741 986 8.305317 TCTTACTTCTACTTTTACTGCTCCTTC 58.695 37.037 0.00 0.00 0.00 3.46
796 1041 1.437986 GTCTAGTAGTGGCCGGCAG 59.562 63.158 30.85 15.41 0.00 4.85
829 1074 1.278985 TGTGGATCAGTGGATGGACAC 59.721 52.381 0.00 0.00 41.63 3.67
850 1095 6.640907 GCAAACCAAACCAATCAGTAAACTAG 59.359 38.462 0.00 0.00 0.00 2.57
861 1106 5.200368 CTTCACTAGCAAACCAAACCAAT 57.800 39.130 0.00 0.00 0.00 3.16
878 1123 5.864474 TCTCTCAAATAGTTCGAAGCTTCAC 59.136 40.000 25.47 16.75 0.00 3.18
967 1212 2.912295 GGTGGGTAGTAGGGTTTGGTAA 59.088 50.000 0.00 0.00 0.00 2.85
970 1215 0.251073 CGGTGGGTAGTAGGGTTTGG 59.749 60.000 0.00 0.00 0.00 3.28
997 1242 2.588596 CGCGGCTGGATGCATGTA 60.589 61.111 2.46 0.00 45.15 2.29
998 1243 4.783621 ACGCGGCTGGATGCATGT 62.784 61.111 12.47 0.00 45.15 3.21
1080 1331 3.791586 GTCCCCTCCTCCTGCAGC 61.792 72.222 8.66 0.00 0.00 5.25
1081 1332 3.086600 GGTCCCCTCCTCCTGCAG 61.087 72.222 6.78 6.78 0.00 4.41
1082 1333 4.741239 GGGTCCCCTCCTCCTGCA 62.741 72.222 0.00 0.00 0.00 4.41
1224 1475 4.555709 TTGCTGTGCCGGTCCGTT 62.556 61.111 11.06 0.00 0.00 4.44
1443 1697 1.575447 CCCCCTCCCCTTTCTCCTTG 61.575 65.000 0.00 0.00 0.00 3.61
1593 1847 1.879575 AGTCCAATCCTTCCATCGGA 58.120 50.000 0.00 0.00 34.52 4.55
1660 1914 9.163899 AGCTGCATATATACAAGAAATCATCTG 57.836 33.333 1.02 0.00 38.79 2.90
1663 1917 7.759465 GCAGCTGCATATATACAAGAAATCAT 58.241 34.615 33.36 0.00 41.59 2.45
1695 1951 7.478322 AGTTTGCATATCAATCACTGTCAATC 58.522 34.615 0.00 0.00 34.12 2.67
1700 1956 6.864685 CACAAAGTTTGCATATCAATCACTGT 59.135 34.615 15.59 0.00 34.12 3.55
1701 1957 6.864685 ACACAAAGTTTGCATATCAATCACTG 59.135 34.615 15.59 4.28 34.12 3.66
1702 1958 6.864685 CACACAAAGTTTGCATATCAATCACT 59.135 34.615 15.59 0.00 34.12 3.41
1703 1959 6.400303 GCACACAAAGTTTGCATATCAATCAC 60.400 38.462 15.59 0.00 38.84 3.06
1704 1960 5.634439 GCACACAAAGTTTGCATATCAATCA 59.366 36.000 15.59 0.00 38.84 2.57
1705 1961 5.634439 TGCACACAAAGTTTGCATATCAATC 59.366 36.000 15.59 0.00 42.99 2.67
1706 1962 5.539979 TGCACACAAAGTTTGCATATCAAT 58.460 33.333 15.59 0.00 42.99 2.57
1707 1963 4.941657 TGCACACAAAGTTTGCATATCAA 58.058 34.783 15.59 0.00 42.99 2.57
1708 1964 4.581077 TGCACACAAAGTTTGCATATCA 57.419 36.364 15.59 5.03 42.99 2.15
1709 1965 5.610124 CGTTTGCACACAAAGTTTGCATATC 60.610 40.000 15.59 2.58 46.26 1.63
1727 1983 5.296813 ACTCAATTAATCTCACCGTTTGC 57.703 39.130 0.00 0.00 0.00 3.68
1849 2105 3.071874 TCCCATGTAGCACTGGAAAAG 57.928 47.619 0.00 0.00 34.24 2.27
1883 2139 4.093408 CCGATCAAAACTGTATGTGACCTG 59.907 45.833 0.00 0.00 0.00 4.00
1946 2202 3.025262 ACTAGCTAGCTGTTACCAGGAC 58.975 50.000 27.68 0.00 39.22 3.85
1951 2207 2.961526 TGCACTAGCTAGCTGTTACC 57.038 50.000 27.68 11.67 42.74 2.85
2005 2261 7.872163 TGCATTTGTCATGATTCTTGTAAAC 57.128 32.000 0.00 0.00 0.00 2.01
2084 2345 9.613428 AGCTTGTATACTGCATGAAGTATAAAA 57.387 29.630 28.15 26.84 43.72 1.52
2109 2371 6.183361 ACCTGAAACCTGCTTATACATCCTAG 60.183 42.308 0.00 0.00 0.00 3.02
2110 2372 5.665812 ACCTGAAACCTGCTTATACATCCTA 59.334 40.000 0.00 0.00 0.00 2.94
2111 2373 4.475016 ACCTGAAACCTGCTTATACATCCT 59.525 41.667 0.00 0.00 0.00 3.24
2112 2374 4.781934 ACCTGAAACCTGCTTATACATCC 58.218 43.478 0.00 0.00 0.00 3.51
2213 2475 4.191544 CTCAAACTCAAGGTGACACTGAA 58.808 43.478 5.39 0.00 0.00 3.02
2214 2476 3.197766 ACTCAAACTCAAGGTGACACTGA 59.802 43.478 5.39 1.46 0.00 3.41
2215 2477 3.535561 ACTCAAACTCAAGGTGACACTG 58.464 45.455 5.39 0.00 0.00 3.66
2216 2478 3.914426 ACTCAAACTCAAGGTGACACT 57.086 42.857 5.39 0.00 0.00 3.55
2263 2525 7.039993 TGACTTGTATGTGACTAGCTTTCAGTA 60.040 37.037 0.00 0.00 34.59 2.74
2275 2537 3.728845 ACCTGTGTGACTTGTATGTGAC 58.271 45.455 0.00 0.00 0.00 3.67
2348 2641 8.828688 TTCTAATCATTCTCAGATACATGCAG 57.171 34.615 0.00 0.00 0.00 4.41
2349 2642 9.617523 TTTTCTAATCATTCTCAGATACATGCA 57.382 29.630 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.