Multiple sequence alignment - TraesCS4B01G241400

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 TraesCS4B01G241400 chr4B 100.000 2450 0 0 1 2450 500079262 500081711 0.000000e+00 4525
1 TraesCS4B01G241400 chr4B 90.458 1530 133 8 3 1528 500052957 500054477 0.000000e+00 2004
2 TraesCS4B01G241400 chr4D 91.895 2480 158 25 1 2444 403199881 403202353 0.000000e+00 3426
3 TraesCS4B01G241400 chr4D 90.566 1537 127 9 2 1528 403182290 403183818 0.000000e+00 2019
4 TraesCS4B01G241400 chr4A 94.790 1670 75 9 1 1666 60880102 60881763 0.000000e+00 2591
5 TraesCS4B01G241400 chr4A 91.099 1528 123 8 2 1525 60730630 60732148 0.000000e+00 2056
6 TraesCS4B01G241400 chr4A 82.833 233 22 11 2235 2450 60882665 60882896 2.490000e-45 193
7 TraesCS4B01G241400 chr4A 81.250 224 20 10 1661 1884 60882467 60882668 7.010000e-36 161
8 TraesCS4B01G241400 chr2D 87.121 1452 166 11 5 1442 645838270 645839714 0.000000e+00 1626
9 TraesCS4B01G241400 chr2D 81.323 257 39 9 1638 1892 539412792 539413041 1.490000e-47 200
10 TraesCS4B01G241400 chr2A 86.944 1440 170 13 5 1436 771538750 771540179 0.000000e+00 1602
11 TraesCS4B01G241400 chr2B 87.600 250 28 1 1192 1438 789673367 789673616 1.110000e-73 287
12 TraesCS4B01G241400 chr5A 83.012 259 34 4 1638 1895 559739180 559738931 2.450000e-55 226
13 TraesCS4B01G241400 chr5A 72.920 613 124 37 751 1349 309312108 309311524 9.010000e-40 174
14 TraesCS4B01G241400 chr5B 81.579 266 37 6 1633 1895 539929188 539928932 2.470000e-50 209
15 TraesCS4B01G241400 chr5B 73.254 587 119 34 784 1355 255681946 255681383 1.940000e-41 180
16 TraesCS4B01G241400 chr5D 82.143 252 32 6 1647 1895 443498423 443498182 1.150000e-48 204
17 TraesCS4B01G241400 chr6B 79.725 291 46 7 1597 1880 192354087 192353803 5.340000e-47 198
18 TraesCS4B01G241400 chr6D 79.038 291 48 7 1597 1880 105823588 105823304 1.160000e-43 187


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 TraesCS4B01G241400 chr4B 500079262 500081711 2449 False 4525.000000 4525 100.000 1 2450 1 chr4B.!!$F2 2449
1 TraesCS4B01G241400 chr4B 500052957 500054477 1520 False 2004.000000 2004 90.458 3 1528 1 chr4B.!!$F1 1525
2 TraesCS4B01G241400 chr4D 403199881 403202353 2472 False 3426.000000 3426 91.895 1 2444 1 chr4D.!!$F2 2443
3 TraesCS4B01G241400 chr4D 403182290 403183818 1528 False 2019.000000 2019 90.566 2 1528 1 chr4D.!!$F1 1526
4 TraesCS4B01G241400 chr4A 60730630 60732148 1518 False 2056.000000 2056 91.099 2 1525 1 chr4A.!!$F1 1523
5 TraesCS4B01G241400 chr4A 60880102 60882896 2794 False 981.666667 2591 86.291 1 2450 3 chr4A.!!$F2 2449
6 TraesCS4B01G241400 chr2D 645838270 645839714 1444 False 1626.000000 1626 87.121 5 1442 1 chr2D.!!$F2 1437
7 TraesCS4B01G241400 chr2A 771538750 771540179 1429 False 1602.000000 1602 86.944 5 1436 1 chr2A.!!$F1 1431

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
469 470 0.178068 ATATCTGCCGTGTCGCCTTT 59.822 50.0 0.0 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2339 3109 0.033504 TCGTTCTCCTCAAGGCACAC 59.966 55.0 0.0 0.0 34.44 3.82 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
106 107 4.034258 CTGCCAACCTGCACGCTG 62.034 66.667 0.00 0.00 36.04 5.18
460 461 2.325761 GCGTTCGATAATATCTGCCGT 58.674 47.619 0.00 0.00 0.00 5.68
469 470 0.178068 ATATCTGCCGTGTCGCCTTT 59.822 50.000 0.00 0.00 0.00 3.11
777 796 0.389817 CTGTCGAGGTTCATGGCGAA 60.390 55.000 0.00 0.00 34.29 4.70
1041 1064 2.202623 ACGAAGTCGATGCGGCTC 60.203 61.111 7.87 0.00 42.48 4.70
1356 1388 1.213013 GGAAGAGTTCGAGCTCGCA 59.787 57.895 30.97 19.02 40.26 5.10
1450 1482 4.681781 CGGTGAAGGCTAGAGTGAATTGAT 60.682 45.833 0.00 0.00 0.00 2.57
1454 1486 6.818644 GTGAAGGCTAGAGTGAATTGATTACA 59.181 38.462 0.00 0.00 0.00 2.41
1539 1576 6.599244 TGAAAGATGGATTCCAGAATACACAC 59.401 38.462 11.78 5.67 43.80 3.82
1540 1577 5.698741 AGATGGATTCCAGAATACACACA 57.301 39.130 11.78 0.00 43.80 3.72
1541 1578 6.065976 AGATGGATTCCAGAATACACACAA 57.934 37.500 11.78 0.00 43.80 3.33
1542 1579 6.666678 AGATGGATTCCAGAATACACACAAT 58.333 36.000 11.78 0.00 43.80 2.71
1544 1581 6.513806 TGGATTCCAGAATACACACAATTG 57.486 37.500 3.24 3.24 36.75 2.32
1545 1582 6.009589 TGGATTCCAGAATACACACAATTGT 58.990 36.000 4.92 4.92 36.75 2.71
1546 1583 6.150976 TGGATTCCAGAATACACACAATTGTC 59.849 38.462 8.48 0.00 36.75 3.18
1559 1596 6.379988 ACACACAATTGTCCTTTTTCTTAGGT 59.620 34.615 8.48 0.00 31.66 3.08
1561 1598 6.183360 ACACAATTGTCCTTTTTCTTAGGTGG 60.183 38.462 8.48 0.00 34.29 4.61
1581 1619 1.310904 GTGGTTTTTCTACGCCCACA 58.689 50.000 0.00 0.00 43.96 4.17
1607 1645 2.485677 CACCTGATGCACCCATGAC 58.514 57.895 0.00 0.00 0.00 3.06
1618 1656 2.717390 CACCCATGACCGGAAACATAA 58.283 47.619 9.46 0.00 0.00 1.90
1619 1657 2.422127 CACCCATGACCGGAAACATAAC 59.578 50.000 9.46 0.00 0.00 1.89
1620 1658 2.040545 ACCCATGACCGGAAACATAACA 59.959 45.455 9.46 0.00 0.00 2.41
1624 1662 5.160641 CCATGACCGGAAACATAACAAAAG 58.839 41.667 9.46 0.00 0.00 2.27
1631 1669 6.320418 ACCGGAAACATAACAAAAGAAACTCT 59.680 34.615 9.46 0.00 0.00 3.24
1666 2418 4.951715 AGCTTGATGGCTTTGAATATGACA 59.048 37.500 0.00 0.00 39.86 3.58
1689 2441 7.047271 ACAAAATGTTTCAGGTGCTTGTAAAT 58.953 30.769 0.00 0.00 0.00 1.40
1704 2456 6.096695 GCTTGTAAATTTTCGAGGCCAAATA 58.903 36.000 5.01 0.00 0.00 1.40
1734 2486 6.128418 CCGAGGAGCTCTCTAAAAAGAAAAAG 60.128 42.308 14.64 0.00 40.30 2.27
1735 2487 6.647067 CGAGGAGCTCTCTAAAAAGAAAAAGA 59.353 38.462 14.64 0.00 40.30 2.52
1736 2488 7.171678 CGAGGAGCTCTCTAAAAAGAAAAAGAA 59.828 37.037 14.64 0.00 40.30 2.52
1737 2489 8.753497 AGGAGCTCTCTAAAAAGAAAAAGAAA 57.247 30.769 14.64 0.00 0.00 2.52
1738 2490 9.190317 AGGAGCTCTCTAAAAAGAAAAAGAAAA 57.810 29.630 14.64 0.00 0.00 2.29
1739 2491 9.803315 GGAGCTCTCTAAAAAGAAAAAGAAAAA 57.197 29.630 14.64 0.00 0.00 1.94
1781 2533 7.495279 TGCACTTTCAAGCAGAATTTGTATTTT 59.505 29.630 0.00 0.00 35.83 1.82
1783 2535 8.819974 CACTTTCAAGCAGAATTTGTATTTTGT 58.180 29.630 0.00 0.00 35.83 2.83
1788 2540 9.809096 TCAAGCAGAATTTGTATTTTGTTTACA 57.191 25.926 0.00 0.00 30.87 2.41
1854 2607 6.806739 GCACCTAAAACAGTTGTTCATAATCC 59.193 38.462 0.00 0.00 37.25 3.01
1869 2622 7.341512 TGTTCATAATCCATGCCATGAAGTTTA 59.658 33.333 6.18 0.00 37.90 2.01
1910 2676 5.748670 TGTTGTGGGTACTATAAGCTTGA 57.251 39.130 9.86 0.00 0.00 3.02
1916 2682 6.041637 TGTGGGTACTATAAGCTTGATGTAGG 59.958 42.308 9.86 0.00 0.00 3.18
1964 2730 6.148976 GTAGGTATCCTTTGAACTGTTGTTCC 59.851 42.308 0.00 0.00 42.08 3.62
1989 2755 1.604147 GAACCCGGCTTCCATTTGGG 61.604 60.000 0.00 0.00 45.70 4.12
2008 2774 1.413077 GGAGAGAAAGACGTATGGGGG 59.587 57.143 0.00 0.00 0.00 5.40
2013 2779 2.238898 AGAAAGACGTATGGGGGAAAGG 59.761 50.000 0.00 0.00 0.00 3.11
2032 2798 6.912591 GGAAAGGCTAAATATTCAATGACACG 59.087 38.462 0.00 0.00 0.00 4.49
2034 2800 6.604735 AGGCTAAATATTCAATGACACGTC 57.395 37.500 0.00 0.00 0.00 4.34
2037 2803 7.653713 AGGCTAAATATTCAATGACACGTCTAG 59.346 37.037 0.00 0.00 0.00 2.43
2156 2925 8.128322 ACACATGTTAAAATATGCCCAAACTA 57.872 30.769 0.00 0.00 31.53 2.24
2158 2927 8.250332 CACATGTTAAAATATGCCCAAACTAGT 58.750 33.333 0.00 0.00 31.53 2.57
2259 3029 4.105858 ACCACTAAAGGAAAGCCTAAACCT 59.894 41.667 0.00 0.00 46.28 3.50
2272 3042 2.955660 CCTAAACCTTGGAGCAACAACA 59.044 45.455 0.00 0.00 0.00 3.33
2300 3070 4.407621 TCCTAAAGTTGAGAGTTGGACACA 59.592 41.667 0.00 0.00 0.00 3.72
2301 3071 5.071788 TCCTAAAGTTGAGAGTTGGACACAT 59.928 40.000 0.00 0.00 0.00 3.21
2307 3077 4.422073 TGAGAGTTGGACACATGTCTTT 57.578 40.909 11.63 0.00 44.20 2.52
2339 3109 4.695455 TCTTCATCTAACCAAGAAAAGCCG 59.305 41.667 0.00 0.00 37.89 5.52
2340 3110 4.015872 TCATCTAACCAAGAAAAGCCGT 57.984 40.909 0.00 0.00 37.89 5.68
2356 3126 0.951040 CCGTGTGCCTTGAGGAGAAC 60.951 60.000 0.06 0.00 37.39 3.01
2389 3176 3.815401 CCTCACAAAAGGAATGTCGAAGT 59.185 43.478 0.00 0.00 38.87 3.01
2394 3181 6.934645 TCACAAAAGGAATGTCGAAGTAGAAT 59.065 34.615 0.00 0.00 0.00 2.40
2444 3231 4.142227 GCTAACCCGACTTCAGATAGAACA 60.142 45.833 0.00 0.00 31.61 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 2.431683 GTGCAGGTTGGCAGGAGA 59.568 61.111 0.00 0.00 45.96 3.71
178 179 1.138266 GGGTAGTTATCGAAGCTGGCA 59.862 52.381 0.00 0.00 0.00 4.92
413 414 2.932234 CGAGCGTGTCCTGGAGGTT 61.932 63.158 0.00 0.00 36.34 3.50
460 461 2.816012 TCGTGGTCAAAGGCGACA 59.184 55.556 0.00 0.00 37.66 4.35
506 507 4.400961 GACTTCTGGGCCAGCGCT 62.401 66.667 29.02 2.64 34.44 5.92
512 522 2.185608 GCTCTCGACTTCTGGGCC 59.814 66.667 0.00 0.00 0.00 5.80
589 608 2.345991 GCGTACTGGAACCTGCCA 59.654 61.111 0.00 0.00 36.30 4.92
777 796 2.037367 TGTAGCTCTCGCCCTGGT 59.963 61.111 0.00 0.00 36.60 4.00
1027 1050 1.437986 GGTAGAGCCGCATCGACTT 59.562 57.895 0.00 0.00 0.00 3.01
1356 1388 4.508128 CGGTATGCGCCGTCCACT 62.508 66.667 4.18 0.00 46.11 4.00
1450 1482 7.070571 ACAAAATTTCCCTCCATCTTGTTGTAA 59.929 33.333 0.00 0.00 0.00 2.41
1454 1486 6.499106 AACAAAATTTCCCTCCATCTTGTT 57.501 33.333 0.00 0.00 32.46 2.83
1539 1576 5.304357 ACCCACCTAAGAAAAAGGACAATTG 59.696 40.000 3.24 3.24 37.57 2.32
1540 1577 5.304357 CACCCACCTAAGAAAAAGGACAATT 59.696 40.000 0.00 0.00 37.57 2.32
1541 1578 4.832823 CACCCACCTAAGAAAAAGGACAAT 59.167 41.667 0.00 0.00 37.57 2.71
1542 1579 4.211920 CACCCACCTAAGAAAAAGGACAA 58.788 43.478 0.00 0.00 37.57 3.18
1544 1581 3.154710 CCACCCACCTAAGAAAAAGGAC 58.845 50.000 0.00 0.00 37.57 3.85
1545 1582 2.787035 ACCACCCACCTAAGAAAAAGGA 59.213 45.455 0.00 0.00 37.57 3.36
1546 1583 3.238788 ACCACCCACCTAAGAAAAAGG 57.761 47.619 0.00 0.00 40.20 3.11
1559 1596 0.537828 GGGCGTAGAAAAACCACCCA 60.538 55.000 0.00 0.00 34.03 4.51
1561 1598 0.594602 GTGGGCGTAGAAAAACCACC 59.405 55.000 0.00 0.00 44.40 4.61
1607 1645 6.735130 AGAGTTTCTTTTGTTATGTTTCCGG 58.265 36.000 0.00 0.00 0.00 5.14
1619 1657 9.339492 GCTTCAGATCATTTAGAGTTTCTTTTG 57.661 33.333 0.00 0.00 0.00 2.44
1620 1658 9.294614 AGCTTCAGATCATTTAGAGTTTCTTTT 57.705 29.630 0.00 0.00 0.00 2.27
1624 1662 8.261492 TCAAGCTTCAGATCATTTAGAGTTTC 57.739 34.615 0.00 0.00 0.00 2.78
1631 1669 5.443283 AGCCATCAAGCTTCAGATCATTTA 58.557 37.500 0.00 0.00 41.41 1.40
1644 1688 5.252969 TGTCATATTCAAAGCCATCAAGC 57.747 39.130 0.00 0.00 0.00 4.01
1659 2411 6.594788 AGCACCTGAAACATTTTGTCATAT 57.405 33.333 0.00 0.00 0.00 1.78
1666 2418 8.504812 AAATTTACAAGCACCTGAAACATTTT 57.495 26.923 0.00 0.00 0.00 1.82
1689 2441 3.127895 CGGATGTTATTTGGCCTCGAAAA 59.872 43.478 3.32 0.00 0.00 2.29
1704 2456 2.738587 TAGAGAGCTCCTCGGATGTT 57.261 50.000 10.93 0.00 46.49 2.71
1747 2499 6.264744 ATTCTGCTTGAAAGTGCATATATGCT 59.735 34.615 32.00 16.51 44.94 3.79
1750 2502 8.472413 ACAAATTCTGCTTGAAAGTGCATATAT 58.528 29.630 0.00 0.00 38.29 0.86
1786 2538 9.811995 CCAAATAACATCAAATGATCTTCATGT 57.188 29.630 0.00 0.00 37.15 3.21
1787 2539 8.761497 GCCAAATAACATCAAATGATCTTCATG 58.239 33.333 0.00 0.00 37.15 3.07
1788 2540 7.929785 GGCCAAATAACATCAAATGATCTTCAT 59.070 33.333 0.00 0.00 39.09 2.57
1789 2541 7.093421 TGGCCAAATAACATCAAATGATCTTCA 60.093 33.333 0.61 0.00 31.21 3.02
1841 2594 5.518848 TCATGGCATGGATTATGAACAAC 57.481 39.130 26.15 0.00 39.21 3.32
1900 2666 6.978674 AGTAGTGCCTACATCAAGCTTATA 57.021 37.500 0.00 0.00 39.22 0.98
1903 2669 4.559862 AAGTAGTGCCTACATCAAGCTT 57.440 40.909 12.89 0.00 39.22 3.74
1933 2699 6.958192 ACAGTTCAAAGGATACCTACCTAAGA 59.042 38.462 0.00 0.00 36.67 2.10
1934 2700 7.184067 ACAGTTCAAAGGATACCTACCTAAG 57.816 40.000 0.00 0.00 36.67 2.18
1936 2702 6.499350 ACAACAGTTCAAAGGATACCTACCTA 59.501 38.462 0.00 0.00 36.67 3.08
1937 2703 5.309806 ACAACAGTTCAAAGGATACCTACCT 59.690 40.000 0.00 0.00 39.69 3.08
1938 2704 5.557866 ACAACAGTTCAAAGGATACCTACC 58.442 41.667 0.00 0.00 31.13 3.18
1939 2705 6.148976 GGAACAACAGTTCAAAGGATACCTAC 59.851 42.308 10.16 0.00 42.66 3.18
1943 2709 4.514066 ACGGAACAACAGTTCAAAGGATAC 59.486 41.667 10.16 0.00 42.66 2.24
1948 2714 4.573201 TCCTAACGGAACAACAGTTCAAAG 59.427 41.667 10.16 4.12 42.66 2.77
1964 2730 1.449070 GGAAGCCGGGTTCCTAACG 60.449 63.158 44.01 0.64 42.57 3.18
1989 2755 2.385803 TCCCCCATACGTCTTTCTCTC 58.614 52.381 0.00 0.00 0.00 3.20
1997 2763 1.125633 TAGCCTTTCCCCCATACGTC 58.874 55.000 0.00 0.00 0.00 4.34
1998 2764 1.587066 TTAGCCTTTCCCCCATACGT 58.413 50.000 0.00 0.00 0.00 3.57
2008 2774 7.472543 ACGTGTCATTGAATATTTAGCCTTTC 58.527 34.615 0.00 0.00 0.00 2.62
2013 2779 8.575565 TCTAGACGTGTCATTGAATATTTAGC 57.424 34.615 0.00 0.00 0.00 3.09
2079 2847 6.805713 AGTAACTAATTTGCACTGCACTTTT 58.194 32.000 2.26 0.67 38.71 2.27
2080 2848 6.391227 AGTAACTAATTTGCACTGCACTTT 57.609 33.333 2.26 3.18 38.71 2.66
2125 2893 6.205853 GGGCATATTTTAACATGTGTCGGATA 59.794 38.462 0.00 0.00 0.00 2.59
2129 2897 5.242069 TGGGCATATTTTAACATGTGTCG 57.758 39.130 0.00 0.00 0.00 4.35
2136 2904 7.768807 ACACTAGTTTGGGCATATTTTAACA 57.231 32.000 0.00 0.00 0.00 2.41
2139 2907 8.865420 TTGTACACTAGTTTGGGCATATTTTA 57.135 30.769 0.00 0.00 0.00 1.52
2156 2925 8.639761 AGACTGTGTTAGAACTATTTGTACACT 58.360 33.333 0.00 0.00 0.00 3.55
2211 2981 9.853555 GTATTGGTGTTGAAATGACATATTTGA 57.146 29.630 0.00 0.00 0.00 2.69
2212 2982 9.086336 GGTATTGGTGTTGAAATGACATATTTG 57.914 33.333 0.00 0.00 0.00 2.32
2213 2983 8.811017 TGGTATTGGTGTTGAAATGACATATTT 58.189 29.630 0.00 0.00 0.00 1.40
2214 2984 8.250332 GTGGTATTGGTGTTGAAATGACATATT 58.750 33.333 0.00 0.00 0.00 1.28
2259 3029 1.273048 GGATGCATGTTGTTGCTCCAA 59.727 47.619 2.46 0.00 43.18 3.53
2272 3042 4.946157 CCAACTCTCAACTTTAGGATGCAT 59.054 41.667 0.00 0.00 0.00 3.96
2276 3046 5.071788 TGTGTCCAACTCTCAACTTTAGGAT 59.928 40.000 0.00 0.00 0.00 3.24
2277 3047 4.407621 TGTGTCCAACTCTCAACTTTAGGA 59.592 41.667 0.00 0.00 0.00 2.94
2300 3070 7.106439 AGATGAAGATCGACACTAAAGACAT 57.894 36.000 0.00 0.00 33.34 3.06
2301 3071 6.516739 AGATGAAGATCGACACTAAAGACA 57.483 37.500 0.00 0.00 33.34 3.41
2307 3077 6.602009 TCTTGGTTAGATGAAGATCGACACTA 59.398 38.462 0.00 0.00 33.34 2.74
2339 3109 0.033504 TCGTTCTCCTCAAGGCACAC 59.966 55.000 0.00 0.00 34.44 3.82
2340 3110 0.318441 CTCGTTCTCCTCAAGGCACA 59.682 55.000 0.00 0.00 34.44 4.57
2389 3176 4.141937 CCATTCGTGGTTCTCCTCATTCTA 60.142 45.833 0.00 0.00 34.23 2.10
2394 3181 0.613260 CCCATTCGTGGTTCTCCTCA 59.387 55.000 0.00 0.00 34.23 3.86


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

AutoCloner maintained by Alex Coulton.