Multiple sequence alignment - TraesCS7D01G329200

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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 TraesCS7D01G329200 chr7D 100.000 3309 0 0 1 3309 420743946 420740638 0.000000e+00 6111.0
1 TraesCS7D01G329200 chr7D 81.992 261 45 2 1275 1534 33754878 33755137 1.550000e-53 220.0
2 TraesCS7D01G329200 chr7D 80.843 261 48 2 1275 1534 34011510 34011251 1.560000e-48 204.0
3 TraesCS7D01G329200 chr7D 80.843 261 48 2 1275 1534 34445253 34445512 1.560000e-48 204.0
4 TraesCS7D01G329200 chr7D 81.046 153 27 2 1027 1178 34011747 34011596 1.610000e-23 121.0
5 TraesCS7D01G329200 chr7D 81.379 145 27 0 1027 1171 34444996 34445140 5.800000e-23 119.0
6 TraesCS7D01G329200 chr7D 80.690 145 28 0 1027 1171 33754651 33754795 2.700000e-21 113.0
7 TraesCS7D01G329200 chr7D 80.690 145 28 0 1027 1171 34077143 34076999 2.700000e-21 113.0
8 TraesCS7D01G329200 chr7D 87.356 87 5 2 2255 2335 484370718 484370804 9.780000e-16 95.3
9 TraesCS7D01G329200 chr7D 90.164 61 3 3 3153 3212 119168362 119168420 3.540000e-10 76.8
10 TraesCS7D01G329200 chr7B 91.930 3259 156 46 1 3177 436788924 436785691 0.000000e+00 4462.0
11 TraesCS7D01G329200 chr7B 95.620 137 6 0 3173 3309 436785371 436785235 1.550000e-53 220.0
12 TraesCS7D01G329200 chr7B 90.164 61 3 3 3153 3212 80592686 80592744 3.540000e-10 76.8
13 TraesCS7D01G329200 chr7A 90.804 3121 146 63 1 3039 512327599 512330660 0.000000e+00 4043.0
14 TraesCS7D01G329200 chr7A 81.609 261 46 2 1275 1534 34519325 34519066 7.190000e-52 215.0
15 TraesCS7D01G329200 chr7A 96.078 51 2 0 3156 3206 419767012 419767062 2.120000e-12 84.2
16 TraesCS7D01G329200 chr4A 83.077 260 42 2 1275 1533 691324121 691324379 5.520000e-58 235.0
17 TraesCS7D01G329200 chr4A 82.283 254 45 0 1275 1528 691247028 691247281 1.550000e-53 220.0
18 TraesCS7D01G329200 chr4A 81.176 255 46 2 1275 1528 691150892 691151145 1.560000e-48 204.0
19 TraesCS7D01G329200 chr4A 82.759 145 25 0 1027 1171 691150665 691150809 2.680000e-26 130.0
20 TraesCS7D01G329200 chr4A 80.132 151 30 0 1027 1177 690886942 690886792 2.700000e-21 113.0
21 TraesCS7D01G329200 chr4A 80.690 145 28 0 1027 1171 691166529 691166673 2.700000e-21 113.0
22 TraesCS7D01G329200 chr2D 94.828 58 2 1 3159 3216 620203429 620203373 4.550000e-14 89.8
23 TraesCS7D01G329200 chr2B 94.828 58 2 1 3159 3216 759892439 759892383 4.550000e-14 89.8
24 TraesCS7D01G329200 chr2B 90.323 62 6 0 3159 3220 583065008 583064947 7.610000e-12 82.4
25 TraesCS7D01G329200 chr1A 92.857 56 4 0 3159 3214 104947019 104946964 7.610000e-12 82.4
26 TraesCS7D01G329200 chr2A 88.710 62 7 0 3159 3220 638309343 638309404 3.540000e-10 76.8


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 TraesCS7D01G329200 chr7D 420740638 420743946 3308 True 6111 6111 100.000 1 3309 1 chr7D.!!$R2 3308
1 TraesCS7D01G329200 chr7B 436785235 436788924 3689 True 2341 4462 93.775 1 3309 2 chr7B.!!$R1 3308
2 TraesCS7D01G329200 chr7A 512327599 512330660 3061 False 4043 4043 90.804 1 3039 1 chr7A.!!$F2 3038

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
755 771 0.770499 TCACTTCCCTTGCACCATCA 59.23 50.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2652 2773 0.040958 CAGAGCGCAAAAGACACCAC 60.041 55.0 11.47 0.0 0.0 4.16 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
28 29 3.634397 TTCCCATAGCCAAGACAAGAG 57.366 47.619 0.00 0.00 0.00 2.85
30 31 1.293924 CCATAGCCAAGACAAGAGCG 58.706 55.000 0.00 0.00 0.00 5.03
38 40 2.413765 CCAAGACAAGAGCGCAAGATTG 60.414 50.000 11.47 11.13 43.02 2.67
365 377 8.899427 AAGATCACACAGGAATGATACATTAG 57.101 34.615 0.00 0.00 35.67 1.73
472 484 7.722363 TCTTTTCATTTAGTCCTTCCAAAACC 58.278 34.615 0.00 0.00 0.00 3.27
517 529 3.603158 TTACTACATGTGCATGGACGT 57.397 42.857 13.03 9.78 42.91 4.34
522 534 2.778299 ACATGTGCATGGACGTTAGTT 58.222 42.857 9.66 0.00 42.91 2.24
619 635 1.259840 AAACCCATCCATGCACAGCC 61.260 55.000 0.00 0.00 0.00 4.85
725 741 2.557452 GCCCCTTCCCATATAACCCATG 60.557 54.545 0.00 0.00 0.00 3.66
755 771 0.770499 TCACTTCCCTTGCACCATCA 59.230 50.000 0.00 0.00 0.00 3.07
764 780 2.092538 CCTTGCACCATCATCTTCCTCT 60.093 50.000 0.00 0.00 0.00 3.69
786 802 3.906998 TGTTTCTCTTGCTTCTCTCTCG 58.093 45.455 0.00 0.00 0.00 4.04
787 803 2.645730 TTCTCTTGCTTCTCTCTCGC 57.354 50.000 0.00 0.00 0.00 5.03
788 804 1.832883 TCTCTTGCTTCTCTCTCGCT 58.167 50.000 0.00 0.00 0.00 4.93
789 805 1.742831 TCTCTTGCTTCTCTCTCGCTC 59.257 52.381 0.00 0.00 0.00 5.03
790 806 1.745087 CTCTTGCTTCTCTCTCGCTCT 59.255 52.381 0.00 0.00 0.00 4.09
791 807 1.742831 TCTTGCTTCTCTCTCGCTCTC 59.257 52.381 0.00 0.00 0.00 3.20
806 822 2.287308 CGCTCTCTCTATCCTTCGTTGG 60.287 54.545 0.00 0.00 0.00 3.77
832 871 1.615392 GCACAAAAGGCAACAGGAGAT 59.385 47.619 0.00 0.00 41.41 2.75
862 901 4.953579 AGGTTTGTGCTCTTCCTTTTGTTA 59.046 37.500 0.00 0.00 0.00 2.41
864 903 6.775629 AGGTTTGTGCTCTTCCTTTTGTTATA 59.224 34.615 0.00 0.00 0.00 0.98
866 905 8.736244 GGTTTGTGCTCTTCCTTTTGTTATATA 58.264 33.333 0.00 0.00 0.00 0.86
896 936 4.316645 CTCTATGCATGATGAGGAAGGTG 58.683 47.826 10.16 0.00 0.00 4.00
897 937 2.359981 ATGCATGATGAGGAAGGTGG 57.640 50.000 0.00 0.00 0.00 4.61
925 991 4.282703 AGCTTCTGATTTGGTTTTGCTGAT 59.717 37.500 0.00 0.00 0.00 2.90
929 995 4.344679 TCTGATTTGGTTTTGCTGATTGGT 59.655 37.500 0.00 0.00 0.00 3.67
938 1004 1.317613 TGCTGATTGGTTCCACACAC 58.682 50.000 0.00 0.00 0.00 3.82
939 1005 1.317613 GCTGATTGGTTCCACACACA 58.682 50.000 0.00 0.00 0.00 3.72
940 1006 1.888512 GCTGATTGGTTCCACACACAT 59.111 47.619 0.00 0.00 0.00 3.21
941 1007 2.352030 GCTGATTGGTTCCACACACATG 60.352 50.000 0.00 0.00 0.00 3.21
943 1009 2.238521 GATTGGTTCCACACACATGGT 58.761 47.619 0.00 0.00 40.95 3.55
1214 1291 2.047061 TCCCGTATTCAGGCAGCTAAT 58.953 47.619 0.00 0.00 0.00 1.73
1215 1292 2.438021 TCCCGTATTCAGGCAGCTAATT 59.562 45.455 0.00 0.00 0.00 1.40
1216 1293 2.549754 CCCGTATTCAGGCAGCTAATTG 59.450 50.000 0.00 0.00 0.00 2.32
1217 1294 3.466836 CCGTATTCAGGCAGCTAATTGA 58.533 45.455 0.00 0.00 0.00 2.57
1218 1295 4.067896 CCGTATTCAGGCAGCTAATTGAT 58.932 43.478 0.00 0.00 0.00 2.57
1220 1297 5.700832 CCGTATTCAGGCAGCTAATTGATAA 59.299 40.000 0.00 0.00 0.00 1.75
1222 1299 7.072030 CGTATTCAGGCAGCTAATTGATAAAC 58.928 38.462 0.00 0.00 0.00 2.01
1231 1324 8.405531 GGCAGCTAATTGATAAACATTAACTCA 58.594 33.333 0.00 0.00 0.00 3.41
1393 1491 3.562232 ACGGCGGGGTTCTGGAAA 61.562 61.111 13.24 0.00 0.00 3.13
1577 1675 2.512885 GCAAAGCATTCATCAGACACG 58.487 47.619 0.00 0.00 0.00 4.49
1603 1701 2.789409 AAGCAAGTCCCACAGATACC 57.211 50.000 0.00 0.00 0.00 2.73
1604 1702 0.537188 AGCAAGTCCCACAGATACCG 59.463 55.000 0.00 0.00 0.00 4.02
1769 1871 1.004277 CTTTCCCGGTTCCATCTTCCA 59.996 52.381 0.00 0.00 0.00 3.53
2188 2305 3.637998 GCATCAATGGCACCTTATCAG 57.362 47.619 0.00 0.00 0.00 2.90
2236 2353 2.033757 CTTGGAGGCAGCAGCACT 59.966 61.111 2.65 0.00 44.61 4.40
2239 2356 2.033141 GGAGGCAGCAGCACTTCA 59.967 61.111 2.65 0.00 44.61 3.02
2342 2459 1.753470 CCTAGCTAGCTGCCATGCT 59.247 57.895 27.68 14.21 46.11 3.79
2343 2460 0.972134 CCTAGCTAGCTGCCATGCTA 59.028 55.000 27.68 14.78 43.74 3.49
2652 2773 6.064846 AGAAAAATCTAGCAATGCATACGG 57.935 37.500 8.35 0.00 0.00 4.02
2653 2774 5.590259 AGAAAAATCTAGCAATGCATACGGT 59.410 36.000 8.35 2.49 0.00 4.83
2654 2775 4.818534 AAATCTAGCAATGCATACGGTG 57.181 40.909 8.35 0.00 0.00 4.94
2655 2776 2.238942 TCTAGCAATGCATACGGTGG 57.761 50.000 8.35 2.27 0.00 4.61
2816 2941 3.403038 GGCTGTTATATGCCCTGTACTG 58.597 50.000 0.00 0.00 43.11 2.74
3099 3233 9.248279 CATGATGCATGTAAGGTAGGCCTTTTT 62.248 40.741 12.58 5.90 42.88 1.94
3147 3281 4.142381 GGCAATTGTATGTTGAGAGAACCC 60.142 45.833 7.40 0.00 0.00 4.11
3149 3283 4.553330 ATTGTATGTTGAGAGAACCCGT 57.447 40.909 0.00 0.00 0.00 5.28
3153 3287 4.768448 TGTATGTTGAGAGAACCCGTAAGA 59.232 41.667 0.00 0.00 43.02 2.10
3249 3707 7.929785 GGGTGCTCATGAATGATTTGATTTATT 59.070 33.333 0.00 0.00 36.02 1.40
3300 3758 5.324409 TGAATGGTATCAAGCTGAGGTTTT 58.676 37.500 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.654683 GCGCTCTTGTCTTGGCTATG 59.345 55.000 0.00 0.00 0.00 2.23
14 15 0.034756 TTGCGCTCTTGTCTTGGCTA 59.965 50.000 9.73 0.00 0.00 3.93
15 16 1.227943 TTGCGCTCTTGTCTTGGCT 60.228 52.632 9.73 0.00 0.00 4.75
28 29 2.035066 AGATTAATGCCCAATCTTGCGC 59.965 45.455 0.00 0.00 39.20 6.09
30 31 5.693555 GCTTTAGATTAATGCCCAATCTTGC 59.306 40.000 9.11 8.29 41.72 4.01
38 40 2.605580 GCTGCGCTTTAGATTAATGCCC 60.606 50.000 9.73 0.00 35.97 5.36
57 59 2.018542 TCGCCTTACTTTATTGCGCT 57.981 45.000 9.73 0.00 44.50 5.92
145 152 1.764571 CGTGGGAGTCAGGGGAACAA 61.765 60.000 0.00 0.00 0.00 2.83
365 377 1.347707 TGGTGTCTCCATCTGGAACAC 59.652 52.381 22.72 22.72 44.91 3.32
441 453 4.344978 AGGACTAAATGAAAAGAAGGGGC 58.655 43.478 0.00 0.00 0.00 5.80
472 484 3.136123 CAGGCATGTCTTGGGGCG 61.136 66.667 0.00 0.00 0.00 6.13
517 529 7.785028 ACCATACTGATAGGATCACAGAACTAA 59.215 37.037 12.79 0.00 35.06 2.24
522 534 5.705400 TGACCATACTGATAGGATCACAGA 58.295 41.667 12.79 0.00 35.06 3.41
711 727 3.091545 GGATGTGCATGGGTTATATGGG 58.908 50.000 0.00 0.00 0.00 4.00
725 741 1.280421 AGGGAAGTGAAGAGGATGTGC 59.720 52.381 0.00 0.00 0.00 4.57
755 771 5.240013 AGCAAGAGAAACAAGAGGAAGAT 57.760 39.130 0.00 0.00 0.00 2.40
764 780 4.302455 CGAGAGAGAAGCAAGAGAAACAA 58.698 43.478 0.00 0.00 0.00 2.83
786 802 2.691011 ACCAACGAAGGATAGAGAGAGC 59.309 50.000 4.96 0.00 0.00 4.09
787 803 4.993029 AACCAACGAAGGATAGAGAGAG 57.007 45.455 4.96 0.00 0.00 3.20
788 804 4.081642 CCAAACCAACGAAGGATAGAGAGA 60.082 45.833 4.96 0.00 0.00 3.10
789 805 4.184629 CCAAACCAACGAAGGATAGAGAG 58.815 47.826 4.96 0.00 0.00 3.20
790 806 3.055385 CCCAAACCAACGAAGGATAGAGA 60.055 47.826 4.96 0.00 0.00 3.10
791 807 3.270877 CCCAAACCAACGAAGGATAGAG 58.729 50.000 4.96 0.00 0.00 2.43
806 822 1.013596 GTTGCCTTTTGTGCCCAAAC 58.986 50.000 0.00 0.00 40.19 2.93
824 863 4.342092 CACAAACCTTGGAAAATCTCCTGT 59.658 41.667 0.00 0.00 45.64 4.00
832 871 3.132111 GGAAGAGCACAAACCTTGGAAAA 59.868 43.478 0.00 0.00 34.12 2.29
866 905 8.384693 TCCTCATCATGCATAGAGGTAATAAT 57.615 34.615 27.67 2.10 46.09 1.28
896 936 3.078891 ACCAAATCAGAAGCTCCTTCC 57.921 47.619 1.60 0.00 40.98 3.46
897 937 5.225642 CAAAACCAAATCAGAAGCTCCTTC 58.774 41.667 0.00 0.00 40.45 3.46
925 991 1.397672 CACCATGTGTGTGGAACCAA 58.602 50.000 0.00 0.00 42.02 3.67
938 1004 4.843220 AGAAGAAGAAGCAAACACCATG 57.157 40.909 0.00 0.00 0.00 3.66
939 1005 5.136105 AGAAGAAGAAGAAGCAAACACCAT 58.864 37.500 0.00 0.00 0.00 3.55
940 1006 4.526970 AGAAGAAGAAGAAGCAAACACCA 58.473 39.130 0.00 0.00 0.00 4.17
941 1007 4.576463 TGAGAAGAAGAAGAAGCAAACACC 59.424 41.667 0.00 0.00 0.00 4.16
943 1009 5.674525 TCTGAGAAGAAGAAGAAGCAAACA 58.325 37.500 0.00 0.00 0.00 2.83
944 1010 6.400940 CGATCTGAGAAGAAGAAGAAGCAAAC 60.401 42.308 0.00 0.00 0.00 2.93
946 1012 5.047731 TCGATCTGAGAAGAAGAAGAAGCAA 60.048 40.000 0.00 0.00 0.00 3.91
947 1013 4.460731 TCGATCTGAGAAGAAGAAGAAGCA 59.539 41.667 0.00 0.00 0.00 3.91
948 1014 4.992688 TCGATCTGAGAAGAAGAAGAAGC 58.007 43.478 0.00 0.00 0.00 3.86
949 1015 7.031226 AGATCGATCTGAGAAGAAGAAGAAG 57.969 40.000 26.78 0.00 35.42 2.85
950 1016 7.403312 AAGATCGATCTGAGAAGAAGAAGAA 57.597 36.000 27.93 0.00 37.19 2.52
951 1017 7.228507 CCTAAGATCGATCTGAGAAGAAGAAGA 59.771 40.741 33.23 6.28 37.56 2.87
1193 1270 1.717032 TAGCTGCCTGAATACGGGAT 58.283 50.000 0.00 0.00 44.87 3.85
1194 1271 1.491668 TTAGCTGCCTGAATACGGGA 58.508 50.000 0.00 0.00 44.87 5.14
1214 1291 7.962373 CAGCACGATTGAGTTAATGTTTATCAA 59.038 33.333 0.00 0.00 34.64 2.57
1215 1292 7.333174 TCAGCACGATTGAGTTAATGTTTATCA 59.667 33.333 0.00 0.00 0.00 2.15
1216 1293 7.636359 GTCAGCACGATTGAGTTAATGTTTATC 59.364 37.037 0.00 0.00 0.00 1.75
1217 1294 7.119116 TGTCAGCACGATTGAGTTAATGTTTAT 59.881 33.333 0.00 0.00 0.00 1.40
1218 1295 6.425417 TGTCAGCACGATTGAGTTAATGTTTA 59.575 34.615 0.00 0.00 0.00 2.01
1220 1297 4.754618 TGTCAGCACGATTGAGTTAATGTT 59.245 37.500 0.00 0.00 0.00 2.71
1222 1299 4.926860 TGTCAGCACGATTGAGTTAATG 57.073 40.909 0.00 0.00 0.00 1.90
1231 1324 4.875536 TGCATATAGTTTGTCAGCACGATT 59.124 37.500 0.00 0.00 0.00 3.34
1577 1675 2.291741 CTGTGGGACTTGCTTTCAGTTC 59.708 50.000 0.00 0.00 0.00 3.01
1603 1701 2.076863 CTGGTAAGAAAAGACAGCCCG 58.923 52.381 0.00 0.00 0.00 6.13
1604 1702 3.141767 ACTGGTAAGAAAAGACAGCCC 57.858 47.619 0.00 0.00 32.60 5.19
1700 1802 2.511600 CATCTCCGCCGGGTTCAC 60.512 66.667 1.90 0.00 33.83 3.18
2167 2284 2.295349 CTGATAAGGTGCCATTGATGCC 59.705 50.000 0.00 0.00 0.00 4.40
2179 2296 1.211212 TGATGCTGCTGCTGATAAGGT 59.789 47.619 17.00 0.00 40.48 3.50
2206 2323 0.252479 CTCCAAGCTGCTCCATGAGT 59.748 55.000 1.00 0.00 31.39 3.41
2342 2459 9.746457 AGCTGATCAGATCAACAGTACTATATA 57.254 33.333 27.04 0.00 39.11 0.86
2343 2460 8.648698 AGCTGATCAGATCAACAGTACTATAT 57.351 34.615 27.04 0.00 39.11 0.86
2457 2574 6.422776 AACTCGAAGCCACATATACAAAAG 57.577 37.500 0.00 0.00 0.00 2.27
2652 2773 0.040958 CAGAGCGCAAAAGACACCAC 60.041 55.000 11.47 0.00 0.00 4.16
2653 2774 0.463654 ACAGAGCGCAAAAGACACCA 60.464 50.000 11.47 0.00 0.00 4.17
2654 2775 0.663153 AACAGAGCGCAAAAGACACC 59.337 50.000 11.47 0.00 0.00 4.16
2655 2776 1.064060 ACAACAGAGCGCAAAAGACAC 59.936 47.619 11.47 0.00 0.00 3.67
2824 2949 6.234177 ACTCTGAAGTTATGAAAGGGAACAG 58.766 40.000 0.00 0.00 28.74 3.16
3090 3224 2.762327 CACTATGCATGGAAAAAGGCCT 59.238 45.455 17.90 0.00 0.00 5.19
3099 3233 4.103627 ACTCATCATTCCACTATGCATGGA 59.896 41.667 17.90 10.46 44.74 3.41
3147 3281 6.602179 TCTCTCAACATGCATTTTTCTTACG 58.398 36.000 0.00 0.00 0.00 3.18
3153 3287 8.800332 ACTCTAATTCTCTCAACATGCATTTTT 58.200 29.630 0.00 0.00 0.00 1.94
3208 3666 4.907269 TGAGCACCCTTGAATCCTATATCA 59.093 41.667 0.00 0.00 0.00 2.15
3220 3678 4.158949 TCAAATCATTCATGAGCACCCTTG 59.841 41.667 0.00 0.00 40.64 3.61
3222 3680 3.972133 TCAAATCATTCATGAGCACCCT 58.028 40.909 0.00 0.00 40.64 4.34
3249 3707 8.814931 ACCAATCCATTGATGTTTTTGATCTAA 58.185 29.630 0.56 0.00 40.14 2.10
3257 3715 7.175293 CCATTCAAACCAATCCATTGATGTTTT 59.825 33.333 0.56 0.00 40.14 2.43


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

AutoCloner maintained by Alex Coulton.