Multiple sequence alignment - TraesCS4A01G311900

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 TraesCS4A01G311900 chr4A 100.000 2699 0 0 1 2699 603503251 603505949 0.000000e+00 4985
1 TraesCS4A01G311900 chr4A 88.920 361 28 8 3 353 610249540 610249898 4.130000e-118 435
2 TraesCS4A01G311900 chr4A 88.031 259 21 6 293 548 610245239 610245490 5.650000e-77 298
3 TraesCS4A01G311900 chr4A 84.753 223 17 5 1 207 189219 189440 9.790000e-50 207
4 TraesCS4A01G311900 chr4D 92.256 1627 95 18 1039 2650 1254477 1252867 0.000000e+00 2278
5 TraesCS4A01G311900 chr4D 88.856 682 56 10 1 673 1255162 1254492 0.000000e+00 821
6 TraesCS4A01G311900 chr4D 83.607 183 10 3 99 268 459017 459192 1.290000e-33 154
7 TraesCS4A01G311900 chr4B 90.440 1590 92 26 911 2479 583302 584852 0.000000e+00 2039
8 TraesCS4A01G311900 chr4B 89.313 262 25 2 22 280 1266848 1267109 2.590000e-85 326
9 TraesCS4A01G311900 chr4B 89.655 203 17 3 2500 2699 584845 585046 3.450000e-64 255
10 TraesCS4A01G311900 chr4B 85.135 222 17 5 1 207 229868 230088 2.100000e-51 213
11 TraesCS4A01G311900 chr1D 90.447 649 38 13 271 908 445582939 445582304 0.000000e+00 833
12 TraesCS4A01G311900 chr1D 79.770 435 54 19 1062 1481 348714332 348713917 4.400000e-73 285
13 TraesCS4A01G311900 chr5B 88.829 555 49 8 1 548 705008107 705007559 0.000000e+00 669


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 TraesCS4A01G311900 chr4A 603503251 603505949 2698 False 4985.0 4985 100.0000 1 2699 1 chr4A.!!$F2 2698
1 TraesCS4A01G311900 chr4D 1252867 1255162 2295 True 1549.5 2278 90.5560 1 2650 2 chr4D.!!$R1 2649
2 TraesCS4A01G311900 chr4B 583302 585046 1744 False 1147.0 2039 90.0475 911 2699 2 chr4B.!!$F3 1788
3 TraesCS4A01G311900 chr1D 445582304 445582939 635 True 833.0 833 90.4470 271 908 1 chr1D.!!$R2 637
4 TraesCS4A01G311900 chr5B 705007559 705008107 548 True 669.0 669 88.8290 1 548 1 chr5B.!!$R1 547

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
638 658 1.153469 TCACTGTTGTCGTGCTGCA 60.153 52.632 0.0 0.0 32.54 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2621 2673 0.981183 TGTATCACCGGCTGTCCTTT 59.019 50.0 0.0 0.0 0.0 3.11 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
27 28 9.403110 GCATACTTCCAGATGCAAAATTTATAG 57.597 33.333 0.00 0.00 46.29 1.31
301 303 7.445707 TGCACCAGTTAAGTGTTTCATAATGTA 59.554 33.333 9.42 0.00 37.56 2.29
431 436 5.961396 ACTAGAAAACTCTAGAGCGTGAA 57.039 39.130 19.97 0.76 41.56 3.18
533 546 9.132521 CAAATCTTCAATTTATGTCCTTCACAC 57.867 33.333 0.00 0.00 38.04 3.82
550 570 8.768397 TCCTTCACACTCTATTATTGGTTATGT 58.232 33.333 0.00 0.00 0.00 2.29
557 577 9.436957 CACTCTATTATTGGTTATGTATGGTCC 57.563 37.037 0.00 0.00 0.00 4.46
577 597 5.699001 GGTCCACCCATTTTGTAATGTTTTC 59.301 40.000 0.00 0.00 39.62 2.29
583 603 5.123661 CCCATTTTGTAATGTTTTCCCATGC 59.876 40.000 0.00 0.00 39.62 4.06
614 634 8.677300 ACATATATTGAAGACGAAGCAAACATT 58.323 29.630 0.00 0.00 0.00 2.71
620 640 1.336755 GACGAAGCAAACATTGGTGGT 59.663 47.619 0.00 0.00 41.89 4.16
624 644 2.071778 AGCAAACATTGGTGGTCACT 57.928 45.000 0.93 0.00 40.37 3.41
627 647 2.159114 GCAAACATTGGTGGTCACTGTT 60.159 45.455 0.93 1.92 46.67 3.16
629 649 2.435372 ACATTGGTGGTCACTGTTGT 57.565 45.000 0.93 0.54 36.06 3.32
634 654 1.641677 GTGGTCACTGTTGTCGTGC 59.358 57.895 0.00 0.00 32.54 5.34
637 657 1.276844 GTCACTGTTGTCGTGCTGC 59.723 57.895 0.00 0.00 32.54 5.25
638 658 1.153469 TCACTGTTGTCGTGCTGCA 60.153 52.632 0.00 0.00 32.54 4.41
657 677 2.224079 GCACACAATCTTCACGACACAT 59.776 45.455 0.00 0.00 0.00 3.21
751 771 1.278238 AATTCTTCGCCGCTAGTTCG 58.722 50.000 0.00 0.00 0.00 3.95
766 786 3.897141 AGTTCGGGAGGAGAAGATTTC 57.103 47.619 0.00 0.00 0.00 2.17
814 834 5.825593 TGAGGGAATCAGTAGAACAACTT 57.174 39.130 0.00 0.00 32.77 2.66
908 928 6.147985 CGAGGACTGATCTTACGATAATCAGA 59.852 42.308 20.37 2.13 46.01 3.27
909 929 7.209471 AGGACTGATCTTACGATAATCAGAC 57.791 40.000 20.37 16.07 46.01 3.51
949 969 5.116180 TGATCATAATTGACGTGGAGGTTC 58.884 41.667 0.00 0.00 33.85 3.62
952 972 5.916267 ATCATAATTGACGTGGAGGTTCCAG 60.916 44.000 0.00 0.00 40.24 3.86
975 995 3.270877 GGTGCCTCCAATTAGTACTGTG 58.729 50.000 5.39 0.83 35.97 3.66
999 1019 6.920758 TGCAACAAACATTATTTGGTGAGTAC 59.079 34.615 18.98 4.28 46.88 2.73
1000 1020 6.920758 GCAACAAACATTATTTGGTGAGTACA 59.079 34.615 18.98 0.00 46.88 2.90
1171 1203 8.723942 ATAAACCATCTCTTATCAGTGAACAC 57.276 34.615 0.00 0.00 0.00 3.32
1188 1224 1.272203 ACACCTCACCACACAAAACCA 60.272 47.619 0.00 0.00 0.00 3.67
1201 1237 4.635765 ACACAAAACCAATCGATCGATCAT 59.364 37.500 29.48 13.61 33.08 2.45
1230 1266 1.614051 CCACAACAGCAGGATGGCTAA 60.614 52.381 0.00 0.00 43.68 3.09
1432 1468 2.602267 TGGACGACGGTGATGGGT 60.602 61.111 0.00 0.00 0.00 4.51
1620 1658 1.475392 CGATCGAGACCTCCACCTAGT 60.475 57.143 10.26 0.00 0.00 2.57
1645 1683 2.739292 GACAATCACCATGCATGCATC 58.261 47.619 30.07 13.06 33.90 3.91
1646 1684 2.100087 GACAATCACCATGCATGCATCA 59.900 45.455 30.07 14.51 33.90 3.07
1780 1826 5.803118 GTGTTATGCACGTTAATTAGACCC 58.197 41.667 0.00 0.00 38.45 4.46
1822 1868 5.175859 TCTTCCAACTTCATGTAATCCGAC 58.824 41.667 0.00 0.00 0.00 4.79
1863 1909 7.086376 AGTTTCACATGTATCTGCAATGAAAC 58.914 34.615 20.99 20.99 45.93 2.78
1941 1988 7.181125 ACTCAAGTGACCTATCCTTGATACTTT 59.819 37.037 0.00 0.00 39.42 2.66
1942 1989 7.918076 TCAAGTGACCTATCCTTGATACTTTT 58.082 34.615 0.00 0.00 37.29 2.27
1948 1995 7.619698 TGACCTATCCTTGATACTTTTCTCTCA 59.380 37.037 0.00 0.00 0.00 3.27
1984 2031 7.864108 TTTGCTGTAATGTGCAGATTATAGT 57.136 32.000 28.88 6.28 40.46 2.12
2044 2091 1.618343 TCGAGCCAGACTTGATTCACA 59.382 47.619 0.00 0.00 33.54 3.58
2057 2104 8.872845 AGACTTGATTCACAAAACAAATGTTTC 58.127 29.630 11.61 0.00 46.47 2.78
2095 2143 7.716799 TTTCACTGGATGTGCCTATAAAAAT 57.283 32.000 0.00 0.00 45.81 1.82
2105 2155 6.559810 TGTGCCTATAAAAATTCGACCAATG 58.440 36.000 0.00 0.00 0.00 2.82
2209 2259 3.770040 CCATCGTCCGGGAGTGCA 61.770 66.667 0.00 0.00 0.00 4.57
2242 2292 3.877508 GTGGATTACTCACCCATAAGCAC 59.122 47.826 0.00 0.00 31.94 4.40
2285 2335 9.491675 AATCATGTCTTCTCTGCTTATATTGAG 57.508 33.333 0.00 0.00 0.00 3.02
2291 2341 8.846211 GTCTTCTCTGCTTATATTGAGAGTACT 58.154 37.037 0.00 0.00 36.98 2.73
2292 2342 8.845227 TCTTCTCTGCTTATATTGAGAGTACTG 58.155 37.037 0.00 0.00 36.98 2.74
2304 2354 5.086104 TGAGAGTACTGCCTTTACCATTC 57.914 43.478 0.00 0.00 0.00 2.67
2308 2358 4.526970 AGTACTGCCTTTACCATTCCATG 58.473 43.478 0.00 0.00 0.00 3.66
2313 2363 4.155709 TGCCTTTACCATTCCATGAAACA 58.844 39.130 0.00 0.00 0.00 2.83
2376 2426 4.288626 ACATGGTAGACCTAAGAAAGCCAA 59.711 41.667 0.00 0.00 36.82 4.52
2378 2428 4.648651 TGGTAGACCTAAGAAAGCCAAAC 58.351 43.478 0.00 0.00 36.82 2.93
2487 2539 9.847706 ACGCAAAATATAAATCATGTGTTACAA 57.152 25.926 0.00 0.00 0.00 2.41
2598 2650 7.733402 ATAGATGCATGTTTTTGTTTTTGCT 57.267 28.000 2.46 0.00 0.00 3.91
2604 2656 7.088905 TGCATGTTTTTGTTTTTGCTGAAAAT 58.911 26.923 0.00 0.00 39.29 1.82
2621 2673 6.040842 GCTGAAAATGCCCCAGATCTATTAAA 59.959 38.462 0.00 0.00 0.00 1.52
2630 2682 5.532779 CCCCAGATCTATTAAAAAGGACAGC 59.467 44.000 0.00 0.00 0.00 4.40
2652 2704 2.200373 GTGATACAAAGCACCCCACT 57.800 50.000 0.00 0.00 35.96 4.00
2653 2705 2.514803 GTGATACAAAGCACCCCACTT 58.485 47.619 0.00 0.00 35.96 3.16
2654 2706 2.228822 GTGATACAAAGCACCCCACTTG 59.771 50.000 0.00 0.00 35.96 3.16
2665 2717 3.319122 GCACCCCACTTGGATATGAAATC 59.681 47.826 0.00 0.00 37.39 2.17
2674 2726 8.458843 CCACTTGGATATGAAATCGTAGTTTTT 58.541 33.333 0.00 0.00 37.39 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
221 223 3.275617 TGATGCCTGCCTACGTTTATT 57.724 42.857 0.00 0.00 0.00 1.40
228 230 7.693969 AATTAATATCTTGATGCCTGCCTAC 57.306 36.000 0.00 0.00 0.00 3.18
431 436 3.873805 GCTTGCCGCTTTTCTTCTT 57.126 47.368 0.00 0.00 35.14 2.52
533 546 9.436957 GTGGACCATACATAACCAATAATAGAG 57.563 37.037 0.00 0.00 32.32 2.43
557 577 5.615289 TGGGAAAACATTACAAAATGGGTG 58.385 37.500 3.41 0.00 45.72 4.61
577 597 6.263516 CTTCAATATATGTGAAGGCATGGG 57.736 41.667 19.48 4.51 45.44 4.00
614 634 0.461163 CACGACAACAGTGACCACCA 60.461 55.000 0.00 0.00 41.83 4.17
620 640 1.153469 TGCAGCACGACAACAGTGA 60.153 52.632 0.00 0.00 41.83 3.41
624 644 3.097672 GTGTGCAGCACGACAACA 58.902 55.556 20.67 0.00 38.45 3.33
634 654 1.866601 TGTCGTGAAGATTGTGTGCAG 59.133 47.619 0.00 0.00 0.00 4.41
637 657 4.923281 TCTATGTGTCGTGAAGATTGTGTG 59.077 41.667 0.00 0.00 0.00 3.82
638 658 5.048013 TCTCTATGTGTCGTGAAGATTGTGT 60.048 40.000 0.00 0.00 0.00 3.72
657 677 5.630121 GTCTCTTCCTCTCCATGATCTCTA 58.370 45.833 0.00 0.00 0.00 2.43
693 713 0.042131 ATCCCGTTGTCCCCTACAGA 59.958 55.000 0.00 0.00 39.87 3.41
694 714 0.178068 CATCCCGTTGTCCCCTACAG 59.822 60.000 0.00 0.00 39.87 2.74
748 768 2.176889 ACGAAATCTTCTCCTCCCGAA 58.823 47.619 0.00 0.00 0.00 4.30
751 771 4.072839 ACAAAACGAAATCTTCTCCTCCC 58.927 43.478 0.00 0.00 0.00 4.30
766 786 8.655970 AGAAAATTGAAAGGAAAGAACAAAACG 58.344 29.630 0.00 0.00 0.00 3.60
819 839 2.105134 TGTTCTCCCGGCAGTTAAGAAA 59.895 45.455 0.00 0.00 0.00 2.52
832 852 1.202604 TCGTGTCCAAGTTGTTCTCCC 60.203 52.381 1.45 0.00 0.00 4.30
934 954 1.056660 ACTGGAACCTCCACGTCAAT 58.943 50.000 0.00 0.00 42.67 2.57
937 957 1.004918 CCACTGGAACCTCCACGTC 60.005 63.158 0.00 0.00 42.67 4.34
971 991 5.752472 TCACCAAATAATGTTTGTTGCACAG 59.248 36.000 1.99 0.00 0.00 3.66
975 995 6.920758 TGTACTCACCAAATAATGTTTGTTGC 59.079 34.615 1.99 0.00 0.00 4.17
1003 1023 9.114952 TGAAATATGCGTGAACCAAGAAATATA 57.885 29.630 0.00 0.00 0.00 0.86
1171 1203 2.287547 CGATTGGTTTTGTGTGGTGAGG 60.288 50.000 0.00 0.00 0.00 3.86
1188 1224 4.302455 GTTGTGGAGATGATCGATCGATT 58.698 43.478 29.89 16.61 36.04 3.34
1201 1237 0.254462 TGCTGTTGTGGTTGTGGAGA 59.746 50.000 0.00 0.00 0.00 3.71
1230 1266 3.941188 CGGTGGAGCTGGTGGTGT 61.941 66.667 0.00 0.00 0.00 4.16
1328 1364 3.744719 CGGCACCGAGAGTTCCGA 61.745 66.667 2.01 0.00 42.43 4.55
1353 1389 3.645660 TCATTGGCTGCCCGGTCA 61.646 61.111 17.53 0.00 0.00 4.02
1432 1468 2.048033 ACGCACCCGAATACGCAA 60.048 55.556 0.00 0.00 38.29 4.85
1620 1658 2.106074 GCATGGTGATTGTCGGCGA 61.106 57.895 4.99 4.99 0.00 5.54
1645 1683 8.645110 TCCATATAGCATATCACTGGTATCATG 58.355 37.037 0.00 0.00 39.72 3.07
1646 1684 8.788238 TCCATATAGCATATCACTGGTATCAT 57.212 34.615 0.00 0.00 39.72 2.45
1668 1711 6.708502 TGTCTTGTTTTTAGTCGATCAATCCA 59.291 34.615 0.00 0.00 0.00 3.41
1822 1868 1.176527 AACTCGCAACCCATCATTGG 58.823 50.000 0.00 0.00 43.23 3.16
1836 1882 4.926860 TTGCAGATACATGTGAAACTCG 57.073 40.909 9.11 0.00 38.04 4.18
1984 2031 4.457257 TGCAATATGGAATTCAACACGTCA 59.543 37.500 7.93 0.00 0.00 4.35
2095 2143 1.270571 TGCTAGTGCACATTGGTCGAA 60.271 47.619 21.04 0.00 45.31 3.71
2166 2216 7.404671 AAATTGTCACAGACAGGTTTAAGTT 57.595 32.000 0.00 0.00 43.69 2.66
2209 2259 1.480954 AGTAATCCACTCGTTCCGCAT 59.519 47.619 0.00 0.00 28.33 4.73
2226 2276 3.580895 TGACTTGTGCTTATGGGTGAGTA 59.419 43.478 0.00 0.00 0.00 2.59
2232 2282 5.389859 TTTTCATGACTTGTGCTTATGGG 57.610 39.130 0.00 0.00 0.00 4.00
2242 2292 8.517878 AGACATGATTTACCTTTTCATGACTTG 58.482 33.333 16.55 0.00 44.55 3.16
2285 2335 4.216411 TGGAATGGTAAAGGCAGTACTC 57.784 45.455 0.00 0.00 0.00 2.59
2291 2341 4.155709 TGTTTCATGGAATGGTAAAGGCA 58.844 39.130 0.00 0.00 46.73 4.75
2292 2342 4.799564 TGTTTCATGGAATGGTAAAGGC 57.200 40.909 0.00 0.00 46.73 4.35
2304 2354 7.693120 CACACATGTTTTCTTTTTGTTTCATGG 59.307 33.333 0.00 0.00 36.68 3.66
2308 2358 7.127917 ACCACACATGTTTTCTTTTTGTTTC 57.872 32.000 0.00 0.00 0.00 2.78
2313 2363 6.592220 GGTTGTACCACACATGTTTTCTTTTT 59.408 34.615 0.00 0.00 38.42 1.94
2354 2404 4.487714 TGGCTTTCTTAGGTCTACCATG 57.512 45.455 1.26 0.00 38.89 3.66
2376 2426 7.944729 ATATCCATTTGTAGAACAGCTTGTT 57.055 32.000 1.82 1.82 44.37 2.83
2378 2428 8.892723 TGTTATATCCATTTGTAGAACAGCTTG 58.107 33.333 0.00 0.00 30.94 4.01
2487 2539 9.829507 TGGTTGAATGATTTACAAAAACTCATT 57.170 25.926 3.79 3.79 36.55 2.57
2511 2563 6.039047 ACTGTAAGCAGCTATTGATCATTTGG 59.961 38.462 0.00 0.00 46.30 3.28
2598 2650 7.969690 TTTTAATAGATCTGGGGCATTTTCA 57.030 32.000 5.18 0.00 0.00 2.69
2604 2656 5.044476 TGTCCTTTTTAATAGATCTGGGGCA 60.044 40.000 5.18 0.00 0.00 5.36
2621 2673 0.981183 TGTATCACCGGCTGTCCTTT 59.019 50.000 0.00 0.00 0.00 3.11
2674 2726 4.757657 TCAGGTTTAAAGCACGCATCTAAA 59.242 37.500 18.91 0.00 0.00 1.85
2675 2727 4.320023 TCAGGTTTAAAGCACGCATCTAA 58.680 39.130 18.91 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.