Multiple sequence alignment - TraesCS7D01G553400

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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 TraesCS7D01G553400 chr7D 100.000 3122 0 0 1 3122 636852661 636849540 0.000000e+00 5766.0
1 TraesCS7D01G553400 chr7D 80.724 1105 194 12 1018 2113 636779011 636777917 0.000000e+00 843.0
2 TraesCS7D01G553400 chr7D 79.552 1115 193 20 1015 2117 636820709 636819618 0.000000e+00 763.0
3 TraesCS7D01G553400 chr7B 93.174 2930 120 22 237 3122 739390423 739393316 0.000000e+00 4229.0
4 TraesCS7D01G553400 chr7B 81.174 579 96 10 1534 2102 739413864 739414439 1.320000e-123 453.0
5 TraesCS7D01G553400 chr7B 80.829 579 98 10 1534 2102 739417562 739418137 2.860000e-120 442.0
6 TraesCS7D01G553400 chr7B 85.250 400 49 8 2637 3029 739394167 739394563 1.350000e-108 403.0
7 TraesCS7D01G553400 chr7A 96.918 1882 54 2 808 2686 729275262 729277142 0.000000e+00 3151.0
8 TraesCS7D01G553400 chr7A 94.159 719 30 3 2405 3122 729307140 729307847 0.000000e+00 1085.0
9 TraesCS7D01G553400 chr7A 79.692 1103 183 18 1009 2103 729331360 729332429 0.000000e+00 758.0
10 TraesCS7D01G553400 chr7A 85.377 677 70 18 2469 3122 729277413 729278083 0.000000e+00 675.0
11 TraesCS7D01G553400 chr7A 92.778 180 11 1 605 782 729274745 729274924 3.090000e-65 259.0
12 TraesCS7D01G553400 chr7A 78.487 423 41 26 82 465 729273137 729273548 6.730000e-57 231.0
13 TraesCS7D01G553400 chr5B 80.078 1029 165 21 977 1980 63359728 63360741 0.000000e+00 728.0
14 TraesCS7D01G553400 chr5A 80.020 1021 159 27 977 1974 46570157 46571155 0.000000e+00 713.0
15 TraesCS7D01G553400 chr5D 80.680 559 84 12 974 1518 58234422 58234970 2.240000e-111 412.0
16 TraesCS7D01G553400 chr4B 89.000 200 14 3 409 601 116469570 116469768 1.120000e-59 241.0
17 TraesCS7D01G553400 chr4B 81.967 183 19 11 237 407 116469181 116469361 3.250000e-30 143.0
18 TraesCS7D01G553400 chr4B 78.571 140 15 9 280 407 418376494 418376630 9.280000e-11 78.7
19 TraesCS7D01G553400 chr2A 75.962 520 90 23 992 1504 773189002 773189493 5.210000e-58 235.0
20 TraesCS7D01G553400 chr6B 88.442 199 15 3 410 601 301530400 301530203 1.870000e-57 233.0
21 TraesCS7D01G553400 chr1A 75.154 487 113 8 1023 1505 16379778 16379296 4.050000e-54 222.0
22 TraesCS7D01G553400 chr1A 100.000 28 0 0 1288 1315 548526200 548526227 6.000000e-03 52.8


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 TraesCS7D01G553400 chr7D 636849540 636852661 3121 True 5766.0 5766 100.0000 1 3122 1 chr7D.!!$R3 3121
1 TraesCS7D01G553400 chr7D 636777917 636779011 1094 True 843.0 843 80.7240 1018 2113 1 chr7D.!!$R1 1095
2 TraesCS7D01G553400 chr7D 636819618 636820709 1091 True 763.0 763 79.5520 1015 2117 1 chr7D.!!$R2 1102
3 TraesCS7D01G553400 chr7B 739390423 739394563 4140 False 2316.0 4229 89.2120 237 3122 2 chr7B.!!$F1 2885
4 TraesCS7D01G553400 chr7B 739413864 739418137 4273 False 447.5 453 81.0015 1534 2102 2 chr7B.!!$F2 568
5 TraesCS7D01G553400 chr7A 729307140 729307847 707 False 1085.0 1085 94.1590 2405 3122 1 chr7A.!!$F1 717
6 TraesCS7D01G553400 chr7A 729273137 729278083 4946 False 1079.0 3151 88.3900 82 3122 4 chr7A.!!$F3 3040
7 TraesCS7D01G553400 chr7A 729331360 729332429 1069 False 758.0 758 79.6920 1009 2103 1 chr7A.!!$F2 1094
8 TraesCS7D01G553400 chr5B 63359728 63360741 1013 False 728.0 728 80.0780 977 1980 1 chr5B.!!$F1 1003
9 TraesCS7D01G553400 chr5A 46570157 46571155 998 False 713.0 713 80.0200 977 1974 1 chr5A.!!$F1 997
10 TraesCS7D01G553400 chr5D 58234422 58234970 548 False 412.0 412 80.6800 974 1518 1 chr5D.!!$F1 544

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
49 50 0.036010 CCCAGGTGGCAGAGTAAGTG 60.036 60.0 0.0 0.0 0.00 3.16 F
50 51 0.687354 CCAGGTGGCAGAGTAAGTGT 59.313 55.0 0.0 0.0 0.00 3.55 F
590 1739 0.753111 GGAGCATTCCCCATGTCCAC 60.753 60.0 0.0 0.0 37.53 4.02 F
594 1743 0.810648 CATTCCCCATGTCCACGTTG 59.189 55.0 0.0 0.0 0.00 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1506 2981 0.171231 CGTCAGGATCTTCGCTGTCA 59.829 55.000 0.00 0.0 0.00 3.58 R
1858 4171 0.473694 ATCCGGCTGGGTATCCATCA 60.474 55.000 12.87 0.0 43.11 3.07 R
1904 4223 1.180456 TGCACCCATTTGAGCACCAG 61.180 55.000 0.00 0.0 31.05 4.00 R
2512 4838 4.366267 AGAATAGGTGGGTTCAGAGTGAT 58.634 43.478 0.00 0.0 0.00 3.06 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
32 33 7.790823 AAATGATTTGTTTGCATATAAGCCC 57.209 32.000 0.00 0.00 0.00 5.19
35 36 4.734398 TTTGTTTGCATATAAGCCCAGG 57.266 40.909 0.00 0.00 0.00 4.45
36 37 3.380471 TGTTTGCATATAAGCCCAGGT 57.620 42.857 0.00 0.00 0.00 4.00
37 38 3.023119 TGTTTGCATATAAGCCCAGGTG 58.977 45.455 0.00 0.00 0.00 4.00
48 49 2.377136 CCCAGGTGGCAGAGTAAGT 58.623 57.895 0.00 0.00 0.00 2.24
49 50 0.036010 CCCAGGTGGCAGAGTAAGTG 60.036 60.000 0.00 0.00 0.00 3.16
50 51 0.687354 CCAGGTGGCAGAGTAAGTGT 59.313 55.000 0.00 0.00 0.00 3.55
51 52 1.072331 CCAGGTGGCAGAGTAAGTGTT 59.928 52.381 0.00 0.00 0.00 3.32
52 53 2.487265 CCAGGTGGCAGAGTAAGTGTTT 60.487 50.000 0.00 0.00 0.00 2.83
53 54 3.214328 CAGGTGGCAGAGTAAGTGTTTT 58.786 45.455 0.00 0.00 0.00 2.43
54 55 3.632145 CAGGTGGCAGAGTAAGTGTTTTT 59.368 43.478 0.00 0.00 0.00 1.94
154 155 2.757099 GGCCGACGAGTTCCCCTA 60.757 66.667 0.00 0.00 0.00 3.53
199 204 2.116383 CGCAGGATTCGAGGTACCT 58.884 57.895 16.26 16.26 0.00 3.08
202 207 1.776662 CAGGATTCGAGGTACCTCCA 58.223 55.000 31.78 20.27 39.77 3.86
208 213 3.468140 GAGGTACCTCCACCGCCC 61.468 72.222 28.87 3.88 43.84 6.13
233 238 3.041940 GGGTTCGCAGGACGTGTG 61.042 66.667 0.00 2.27 44.19 3.82
376 423 2.184579 GGAGTCGTACCTGCAGCC 59.815 66.667 8.66 0.00 0.00 4.85
400 447 3.151710 CCGATCCCCACGCAGGTA 61.152 66.667 0.00 0.00 34.66 3.08
402 449 1.445942 CGATCCCCACGCAGGTAAT 59.554 57.895 0.00 0.00 34.66 1.89
406 453 1.117150 TCCCCACGCAGGTAATACTC 58.883 55.000 0.00 0.00 34.66 2.59
407 454 1.120530 CCCCACGCAGGTAATACTCT 58.879 55.000 0.00 0.00 34.66 3.24
408 455 1.202533 CCCCACGCAGGTAATACTCTG 60.203 57.143 5.05 5.05 34.66 3.35
450 505 3.111853 TCTGCATAGTAGCCAAATCCG 57.888 47.619 0.00 0.00 0.00 4.18
525 1663 5.760253 ACATATGAGCTTAACCTGTATGTGC 59.240 40.000 10.38 0.00 32.04 4.57
549 1698 4.223923 ACTCTAGTGCAGAAACATTAGCCT 59.776 41.667 0.00 0.00 31.77 4.58
550 1699 5.422331 ACTCTAGTGCAGAAACATTAGCCTA 59.578 40.000 0.00 0.00 31.77 3.93
553 1702 3.691609 AGTGCAGAAACATTAGCCTAAGC 59.308 43.478 0.00 0.00 40.32 3.09
590 1739 0.753111 GGAGCATTCCCCATGTCCAC 60.753 60.000 0.00 0.00 37.53 4.02
594 1743 0.810648 CATTCCCCATGTCCACGTTG 59.189 55.000 0.00 0.00 0.00 4.10
708 1858 1.604604 TCTACCAAACAAGCAGGTGC 58.395 50.000 0.00 0.00 42.49 5.01
764 1916 8.571336 ACACTTGAATTCTCAGTTTTTATCAGG 58.429 33.333 7.05 0.00 31.69 3.86
791 1959 8.257306 GGCATGGAAGTGAATTTAGGATTTAAA 58.743 33.333 0.00 0.00 0.00 1.52
796 1964 9.586435 GGAAGTGAATTTAGGATTTAAATGTGG 57.414 33.333 5.17 0.00 0.00 4.17
797 1965 9.087424 GAAGTGAATTTAGGATTTAAATGTGGC 57.913 33.333 5.17 0.00 0.00 5.01
798 1966 8.366359 AGTGAATTTAGGATTTAAATGTGGCT 57.634 30.769 5.17 0.00 0.00 4.75
799 1967 8.253113 AGTGAATTTAGGATTTAAATGTGGCTG 58.747 33.333 5.17 0.00 0.00 4.85
800 1968 7.010460 GTGAATTTAGGATTTAAATGTGGCTGC 59.990 37.037 5.17 0.00 0.00 5.25
801 1969 6.796785 ATTTAGGATTTAAATGTGGCTGCT 57.203 33.333 5.17 0.00 0.00 4.24
982 2457 3.449018 CAGCTAGCTACCTCTGAAGGAAA 59.551 47.826 18.86 0.00 46.67 3.13
1437 2912 3.750373 AACCGCCGCAGTGTTCTGT 62.750 57.895 0.00 0.00 43.05 3.41
1506 2981 2.740452 GTTGTCTTCGTCTTCTCCGTT 58.260 47.619 0.00 0.00 0.00 4.44
1728 4041 1.962807 CATGGGCTGACTTGGTTCAAA 59.037 47.619 0.00 0.00 0.00 2.69
1852 4165 3.184382 TGTGGTCAAGGGAGATGACTA 57.816 47.619 6.62 0.00 45.13 2.59
1858 4171 3.135530 GTCAAGGGAGATGACTAATGCCT 59.864 47.826 0.00 0.00 43.03 4.75
1892 4205 2.017049 CCGGATCATCAACTTGGGAAC 58.983 52.381 0.00 0.00 0.00 3.62
1904 4223 5.820947 TCAACTTGGGAACTTTGTCTCTAAC 59.179 40.000 0.00 0.00 0.00 2.34
2150 4476 6.716934 AGCACTAGAGTTATTTAGCAGCTA 57.283 37.500 0.00 0.00 32.93 3.32
2154 4480 9.477484 GCACTAGAGTTATTTAGCAGCTAAATA 57.523 33.333 31.35 31.35 42.57 1.40
2274 4600 2.636647 TCATGTCACAGTGGCAGAAA 57.363 45.000 14.42 0.00 34.38 2.52
2362 4688 2.228822 GTGGAGTTGGCCTTGTATGTTG 59.771 50.000 3.32 0.00 0.00 3.33
2511 4837 7.147863 ACCATGCTTTCTCAAATATGCACAATA 60.148 33.333 0.00 0.00 33.16 1.90
2512 4838 7.707464 CCATGCTTTCTCAAATATGCACAATAA 59.293 33.333 0.00 0.00 33.16 1.40
2667 5005 3.440522 GGACACACCTTTAGGAATTCAGC 59.559 47.826 7.93 0.00 38.94 4.26
2767 5606 1.442688 GTTTGCTGCCAGTTAGCGC 60.443 57.895 0.00 0.00 44.01 5.92
2915 5771 1.979155 GCCTTGGGGTCTTTCCTGC 60.979 63.158 0.00 0.00 36.25 4.85
3036 5892 3.196254 GTGCAATCCAGGAATGGACAATT 59.804 43.478 21.30 0.00 41.33 2.32
3062 5918 3.068590 ACAAGTTGTGCTGCAGCTTAATT 59.931 39.130 36.61 24.23 44.98 1.40
3064 5920 1.723003 GTTGTGCTGCAGCTTAATTGC 59.277 47.619 36.61 17.41 42.66 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.323985 GGGCTTATATGCAAACAAATCATTTTA 57.676 29.630 12.22 0.00 34.04 1.52
12 13 5.163416 ACCTGGGCTTATATGCAAACAAATC 60.163 40.000 12.22 0.00 34.04 2.17
13 14 4.716287 ACCTGGGCTTATATGCAAACAAAT 59.284 37.500 12.22 0.00 34.04 2.32
14 15 4.081752 CACCTGGGCTTATATGCAAACAAA 60.082 41.667 12.22 0.00 34.04 2.83
15 16 3.446873 CACCTGGGCTTATATGCAAACAA 59.553 43.478 12.22 0.00 34.04 2.83
16 17 3.023119 CACCTGGGCTTATATGCAAACA 58.977 45.455 12.22 7.16 34.04 2.83
17 18 2.362077 CCACCTGGGCTTATATGCAAAC 59.638 50.000 12.22 3.31 34.04 2.93
18 19 2.665165 CCACCTGGGCTTATATGCAAA 58.335 47.619 12.22 0.00 34.04 3.68
19 20 2.363306 CCACCTGGGCTTATATGCAA 57.637 50.000 12.22 0.01 34.04 4.08
32 33 2.550830 AACACTTACTCTGCCACCTG 57.449 50.000 0.00 0.00 0.00 4.00
65 66 3.066814 CTTTGGCTGGGGCTCTGC 61.067 66.667 7.84 7.84 38.73 4.26
66 67 3.066814 GCTTTGGCTGGGGCTCTG 61.067 66.667 0.00 0.00 38.73 3.35
67 68 4.372999 GGCTTTGGCTGGGGCTCT 62.373 66.667 0.00 0.00 38.73 4.09
75 76 1.250840 GGAATGGAACGGCTTTGGCT 61.251 55.000 0.00 0.00 38.73 4.75
76 77 1.215382 GGAATGGAACGGCTTTGGC 59.785 57.895 0.00 0.00 37.82 4.52
78 79 1.154035 GCGGAATGGAACGGCTTTG 60.154 57.895 0.00 0.00 0.00 2.77
79 80 3.274067 GCGGAATGGAACGGCTTT 58.726 55.556 0.00 0.00 0.00 3.51
145 146 1.310373 CGGAGGAGGTAGGGGAACT 59.690 63.158 0.00 0.00 0.00 3.01
150 151 4.159108 AGGGCGGAGGAGGTAGGG 62.159 72.222 0.00 0.00 0.00 3.53
175 176 3.074369 TCGAATCCTGCGGCCTCA 61.074 61.111 0.00 0.00 0.00 3.86
176 177 2.279784 CTCGAATCCTGCGGCCTC 60.280 66.667 0.00 0.00 0.00 4.70
178 179 2.792947 TACCTCGAATCCTGCGGCC 61.793 63.158 0.00 0.00 0.00 6.13
182 187 0.389757 GGAGGTACCTCGAATCCTGC 59.610 60.000 31.00 14.08 43.59 4.85
184 189 1.688627 GGTGGAGGTACCTCGAATCCT 60.689 57.143 31.00 0.30 43.59 3.24
187 192 1.673808 GCGGTGGAGGTACCTCGAAT 61.674 60.000 31.00 2.74 43.59 3.34
365 412 4.840005 GGAGGCGGCTGCAGGTAC 62.840 72.222 25.60 4.20 45.35 3.34
386 433 1.692519 GAGTATTACCTGCGTGGGGAT 59.307 52.381 0.62 0.00 41.11 3.85
399 446 9.314321 GCAAGATTTGTTACTAGCAGAGTATTA 57.686 33.333 0.00 0.00 40.43 0.98
400 447 7.824289 TGCAAGATTTGTTACTAGCAGAGTATT 59.176 33.333 0.00 0.00 40.43 1.89
402 449 6.697395 TGCAAGATTTGTTACTAGCAGAGTA 58.303 36.000 0.00 0.00 39.81 2.59
406 453 8.025445 AGATTTTGCAAGATTTGTTACTAGCAG 58.975 33.333 3.69 0.00 31.87 4.24
407 454 7.809331 CAGATTTTGCAAGATTTGTTACTAGCA 59.191 33.333 11.19 0.00 0.00 3.49
408 455 8.166367 CAGATTTTGCAAGATTTGTTACTAGC 57.834 34.615 11.19 0.00 0.00 3.42
450 505 2.360165 CAGTATGAAGCAAGGGATTGCC 59.640 50.000 9.22 0.00 44.18 4.52
499 557 7.633621 CACATACAGGTTAAGCTCATATGTTG 58.366 38.462 25.05 19.45 31.18 3.33
549 1698 4.022416 CCCATTTGTGTAGTGCAAAGCTTA 60.022 41.667 0.00 0.00 38.91 3.09
550 1699 3.243839 CCCATTTGTGTAGTGCAAAGCTT 60.244 43.478 0.00 0.00 38.91 3.74
553 1702 3.612479 GCTCCCATTTGTGTAGTGCAAAG 60.612 47.826 0.00 0.00 38.91 2.77
554 1703 2.295909 GCTCCCATTTGTGTAGTGCAAA 59.704 45.455 0.00 0.00 39.69 3.68
555 1704 1.885887 GCTCCCATTTGTGTAGTGCAA 59.114 47.619 0.00 0.00 0.00 4.08
557 1706 1.533625 TGCTCCCATTTGTGTAGTGC 58.466 50.000 0.00 0.00 0.00 4.40
558 1707 3.129287 GGAATGCTCCCATTTGTGTAGTG 59.871 47.826 0.00 0.00 41.60 2.74
764 1916 3.631250 TCCTAAATTCACTTCCATGCCC 58.369 45.455 0.00 0.00 0.00 5.36
791 1959 0.536260 GTCTCTCTCAGCAGCCACAT 59.464 55.000 0.00 0.00 0.00 3.21
794 1962 2.346541 CGGTCTCTCTCAGCAGCCA 61.347 63.158 0.00 0.00 0.00 4.75
795 1963 1.391157 ATCGGTCTCTCTCAGCAGCC 61.391 60.000 0.00 0.00 0.00 4.85
796 1964 1.001815 GTATCGGTCTCTCTCAGCAGC 60.002 57.143 0.00 0.00 0.00 5.25
797 1965 1.262950 CGTATCGGTCTCTCTCAGCAG 59.737 57.143 0.00 0.00 0.00 4.24
798 1966 1.300481 CGTATCGGTCTCTCTCAGCA 58.700 55.000 0.00 0.00 0.00 4.41
799 1967 0.589223 CCGTATCGGTCTCTCTCAGC 59.411 60.000 0.00 0.00 42.73 4.26
1506 2981 0.171231 CGTCAGGATCTTCGCTGTCA 59.829 55.000 0.00 0.00 0.00 3.58
1852 4165 1.202976 GCTGGGTATCCATCAGGCATT 60.203 52.381 0.00 0.00 43.11 3.56
1858 4171 0.473694 ATCCGGCTGGGTATCCATCA 60.474 55.000 12.87 0.00 43.11 3.07
1892 4205 3.995199 TGAGCACCAGTTAGAGACAAAG 58.005 45.455 0.00 0.00 0.00 2.77
1904 4223 1.180456 TGCACCCATTTGAGCACCAG 61.180 55.000 0.00 0.00 31.05 4.00
2480 4806 6.038603 GCATATTTGAGAAAGCATGGTGACTA 59.961 38.462 0.00 0.00 0.00 2.59
2511 4837 4.785376 AGAATAGGTGGGTTCAGAGTGATT 59.215 41.667 0.00 0.00 0.00 2.57
2512 4838 4.366267 AGAATAGGTGGGTTCAGAGTGAT 58.634 43.478 0.00 0.00 0.00 3.06
2767 5606 0.250901 ACCAGCTAAAGCCACCACAG 60.251 55.000 0.00 0.00 43.38 3.66
2915 5771 8.592105 AATGAAATGACAGTTGGTGTATTTTG 57.408 30.769 0.00 0.00 40.56 2.44
2967 5823 3.092301 TGACTAGTGAGTGTCCAGATGG 58.908 50.000 0.00 0.00 35.45 3.51
3036 5892 3.411446 AGCTGCAGCACAACTTGTATAA 58.589 40.909 38.24 0.00 45.16 0.98
3062 5918 4.623002 TGTTCAGATACGTAAACACTGCA 58.377 39.130 0.00 0.00 0.00 4.41
3064 5920 4.684242 TGCTGTTCAGATACGTAAACACTG 59.316 41.667 0.00 7.61 0.00 3.66


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

AutoCloner maintained by Alex Coulton.