Multiple sequence alignment - TraesCS3D01G044000

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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 TraesCS3D01G044000 chr3D 100.000 3028 0 0 1 3028 16886678 16889705 0.000000e+00 5592.0
1 TraesCS3D01G044000 chr3D 90.164 122 12 0 1287 1408 480149369 480149490 3.120000e-35 159.0
2 TraesCS3D01G044000 chr3A 91.347 3074 118 60 1 2996 19897134 19894131 0.000000e+00 4067.0
3 TraesCS3D01G044000 chr3A 90.833 120 11 0 1287 1406 623223457 623223576 8.690000e-36 161.0
4 TraesCS3D01G044000 chr3B 91.553 2356 72 58 725 3028 24261296 24263576 0.000000e+00 3131.0
5 TraesCS3D01G044000 chr3B 92.224 643 20 12 1 622 24260296 24260929 0.000000e+00 883.0
6 TraesCS3D01G044000 chr3B 91.228 114 10 0 1293 1406 640667601 640667714 4.040000e-34 156.0
7 TraesCS3D01G044000 chr3B 96.296 27 1 0 645 671 24260947 24260973 9.100000e-01 45.4
8 TraesCS3D01G044000 chr2D 94.697 132 2 2 2767 2898 85707786 85707660 1.840000e-47 200.0
9 TraesCS3D01G044000 chr2D 96.000 100 4 0 2889 2988 85707604 85707505 2.420000e-36 163.0
10 TraesCS3D01G044000 chr7D 82.292 96 12 5 1312 1403 265004811 265004717 9.000000e-11 78.7
11 TraesCS3D01G044000 chr7B 82.292 96 12 5 1312 1403 245211839 245211745 9.000000e-11 78.7
12 TraesCS3D01G044000 chr7A 81.250 96 13 5 1312 1403 289160994 289160900 4.190000e-09 73.1
13 TraesCS3D01G044000 chr5D 77.692 130 21 7 1304 1431 436971850 436971973 4.190000e-09 73.1


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 TraesCS3D01G044000 chr3D 16886678 16889705 3027 False 5592.000000 5592 100.000000 1 3028 1 chr3D.!!$F1 3027
1 TraesCS3D01G044000 chr3A 19894131 19897134 3003 True 4067.000000 4067 91.347000 1 2996 1 chr3A.!!$R1 2995
2 TraesCS3D01G044000 chr3B 24260296 24263576 3280 False 1353.133333 3131 93.357667 1 3028 3 chr3B.!!$F2 3027

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
944 1282 0.035458 GGACTACTGTGCTTGCCTGT 59.965 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 2466 0.250553 TGGTTCGGTTACAAGGCAGG 60.251 55.0 0.0 0.0 0.0 4.85 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
62 63 6.406065 GGTCCCTCTGTTATCTCTTTCTACAC 60.406 46.154 0.00 0.00 0.00 2.90
78 79 0.178068 ACACTACACATCGATGGGGC 59.822 55.000 30.17 0.00 34.87 5.80
80 81 1.300931 CTACACATCGATGGGGCCG 60.301 63.158 30.17 14.56 34.87 6.13
82 83 3.860605 CACATCGATGGGGCCGGA 61.861 66.667 28.09 0.00 0.00 5.14
164 173 5.182950 CCACTTATTGTATTGTGTTGCCTCA 59.817 40.000 0.00 0.00 0.00 3.86
566 616 2.437359 AAGCATGAGTCGCCCTGC 60.437 61.111 0.00 0.00 34.85 4.85
577 627 3.009115 GCCCTGCCCAGTCCAGTA 61.009 66.667 0.00 0.00 0.00 2.74
608 658 4.934623 CGCGTAGTACGTGCATAAAATA 57.065 40.909 21.96 0.00 45.29 1.40
609 659 4.915253 CGCGTAGTACGTGCATAAAATAG 58.085 43.478 21.96 0.00 45.29 1.73
610 660 4.438797 CGCGTAGTACGTGCATAAAATAGT 59.561 41.667 21.96 0.00 45.29 2.12
611 661 5.606726 CGCGTAGTACGTGCATAAAATAGTG 60.607 44.000 21.96 0.00 45.29 2.74
612 662 5.653657 CGTAGTACGTGCATAAAATAGTGC 58.346 41.667 14.62 0.00 36.74 4.40
613 663 5.230516 CGTAGTACGTGCATAAAATAGTGCA 59.769 40.000 14.62 0.00 39.81 4.57
718 775 0.618968 ACCACCACTGATCCCCTCTC 60.619 60.000 0.00 0.00 0.00 3.20
723 780 1.949449 ACTGATCCCCTCTCCCCCT 60.949 63.158 0.00 0.00 0.00 4.79
767 1094 7.849322 TCTCTCTCTATCTCTTCTAGCAGTA 57.151 40.000 0.00 0.00 0.00 2.74
838 1167 8.397957 AGTGCATGGGGGATATAAATAATGTTA 58.602 33.333 0.00 0.00 0.00 2.41
839 1168 8.686334 GTGCATGGGGGATATAAATAATGTTAG 58.314 37.037 0.00 0.00 0.00 2.34
840 1169 7.838696 TGCATGGGGGATATAAATAATGTTAGG 59.161 37.037 0.00 0.00 0.00 2.69
841 1170 8.058847 GCATGGGGGATATAAATAATGTTAGGA 58.941 37.037 0.00 0.00 0.00 2.94
900 1238 9.817365 GTATGTATTCAAATCATACATGCAGAC 57.183 33.333 13.47 3.12 44.23 3.51
941 1279 0.391793 GGAGGACTACTGTGCTTGCC 60.392 60.000 0.00 0.00 44.95 4.52
944 1282 0.035458 GGACTACTGTGCTTGCCTGT 59.965 55.000 0.00 0.00 0.00 4.00
945 1283 1.151668 GACTACTGTGCTTGCCTGTG 58.848 55.000 0.00 0.00 0.00 3.66
946 1284 0.886490 ACTACTGTGCTTGCCTGTGC 60.886 55.000 0.00 0.00 38.26 4.57
947 1285 1.904852 CTACTGTGCTTGCCTGTGCG 61.905 60.000 0.00 0.00 41.78 5.34
948 1286 2.658679 TACTGTGCTTGCCTGTGCGT 62.659 55.000 0.00 0.00 41.78 5.24
983 1321 5.104900 CCAGGTGTTATATATACTGCCCCTC 60.105 48.000 0.00 0.00 0.00 4.30
1064 1408 0.107606 TCCTCTCTCTTCTCCGTCCG 60.108 60.000 0.00 0.00 0.00 4.79
1109 1460 2.210961 TCCTCTAGTACGAGCATGACG 58.789 52.381 0.00 3.83 0.00 4.35
1229 1583 3.213402 GGCTCCGACTCCTCCTCG 61.213 72.222 0.00 0.00 0.00 4.63
1232 1586 1.078356 CTCCGACTCCTCCTCGTCA 60.078 63.158 0.00 0.00 0.00 4.35
1637 1991 3.883744 CTCCCACGGCTGCGTCTTT 62.884 63.158 0.00 0.00 0.00 2.52
1802 2156 0.760945 CCAGCTTCCCGAGATACCCT 60.761 60.000 0.00 0.00 0.00 4.34
1923 2277 0.241749 CGTACACTGTTGCTCCGGTA 59.758 55.000 0.00 0.00 0.00 4.02
2082 2444 0.464452 TTAGCTTCCGGGCTAGCTTC 59.536 55.000 24.69 6.61 45.03 3.86
2101 2463 3.497031 GAGTGTTAAGCCGGCCGC 61.497 66.667 26.15 16.01 37.98 6.53
2138 2503 0.033920 AACCAACTCCCGTACGTTCC 59.966 55.000 15.21 0.00 0.00 3.62
2167 2532 0.513385 CCGAGATCGATCGATGACGT 59.487 55.000 33.86 15.77 45.56 4.34
2206 2571 2.986534 ATCCATTCACCCATCCATCC 57.013 50.000 0.00 0.00 0.00 3.51
2207 2572 1.606026 TCCATTCACCCATCCATCCA 58.394 50.000 0.00 0.00 0.00 3.41
2211 2576 3.501568 CCATTCACCCATCCATCCATCAT 60.502 47.826 0.00 0.00 0.00 2.45
2213 2578 1.706866 TCACCCATCCATCCATCATCC 59.293 52.381 0.00 0.00 0.00 3.51
2214 2579 1.078955 ACCCATCCATCCATCATCCC 58.921 55.000 0.00 0.00 0.00 3.85
2272 2643 7.871973 CCCATTTTCTTGTTGATGTGTTAATCA 59.128 33.333 0.00 0.00 34.75 2.57
2287 2658 7.585286 GTGTTAATCACAATTAGTACGTCCA 57.415 36.000 0.00 0.00 45.51 4.02
2303 2674 1.008424 CCATCCATCGACGAGGACG 60.008 63.158 11.71 6.75 45.75 4.79
2324 2695 4.338118 ACGTGTGTTTGATTTGTCAAGGAT 59.662 37.500 0.00 0.00 0.00 3.24
2330 2701 5.106197 TGTTTGATTTGTCAAGGATGATCCG 60.106 40.000 5.71 0.00 42.75 4.18
2557 2943 8.017418 TGTTTGCCCCCTTTTAATTATATCTG 57.983 34.615 0.00 0.00 0.00 2.90
2670 3058 7.125053 ACTTCCTCTAGAATTAACCCAAGAGAG 59.875 40.741 0.00 0.00 33.82 3.20
2671 3059 6.742756 TCCTCTAGAATTAACCCAAGAGAGA 58.257 40.000 0.00 2.97 33.82 3.10
2704 3101 0.319211 TTGCAGTCGACAGTTACCCG 60.319 55.000 19.50 0.00 0.00 5.28
2715 3112 3.828451 GACAGTTACCCGTATAGGCCATA 59.172 47.826 5.01 0.00 39.21 2.74
2718 3115 5.012239 CAGTTACCCGTATAGGCCATACTA 58.988 45.833 5.01 0.00 37.89 1.82
2719 3116 5.012893 AGTTACCCGTATAGGCCATACTAC 58.987 45.833 5.01 0.00 37.89 2.73
2720 3117 2.812658 ACCCGTATAGGCCATACTACC 58.187 52.381 5.01 0.00 37.89 3.18
2721 3118 2.110543 ACCCGTATAGGCCATACTACCA 59.889 50.000 5.01 0.00 37.89 3.25
2722 3119 2.758979 CCCGTATAGGCCATACTACCAG 59.241 54.545 5.01 0.00 37.89 4.00
2723 3120 2.165845 CCGTATAGGCCATACTACCAGC 59.834 54.545 5.01 0.00 37.89 4.85
2724 3121 3.090037 CGTATAGGCCATACTACCAGCT 58.910 50.000 5.01 0.00 37.89 4.24
2725 3122 4.267536 CGTATAGGCCATACTACCAGCTA 58.732 47.826 5.01 0.00 37.89 3.32
2727 3124 2.777459 AGGCCATACTACCAGCTACT 57.223 50.000 5.01 0.00 0.00 2.57
2728 3125 2.320781 AGGCCATACTACCAGCTACTG 58.679 52.381 5.01 0.00 0.00 2.74
2731 3128 3.256136 GGCCATACTACCAGCTACTGTAG 59.744 52.174 10.48 10.48 0.00 2.74
2732 3129 3.890147 GCCATACTACCAGCTACTGTAGT 59.110 47.826 20.25 20.25 34.90 2.73
2835 3233 2.960170 GAGCGAGTACGTGTGGGT 59.040 61.111 0.00 0.00 41.98 4.51
2836 3234 1.443872 GAGCGAGTACGTGTGGGTG 60.444 63.158 0.00 0.00 41.98 4.61
2837 3235 2.138656 GAGCGAGTACGTGTGGGTGT 62.139 60.000 0.00 0.00 41.98 4.16
2932 3344 2.793946 GTGCGTGCATGGGTGATC 59.206 61.111 8.27 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 1.300931 CGGCCCCATCGATGTGTAG 60.301 63.158 23.27 8.40 0.00 2.74
78 79 3.469008 TCTTGTGTATTATGGCTCCGG 57.531 47.619 0.00 0.00 0.00 5.14
125 134 6.323739 ACAATAAGTGGATGGTTCTTTGTTGT 59.676 34.615 0.00 0.00 31.14 3.32
164 173 2.203153 GCGGTGTTGTGTGGAGGT 60.203 61.111 0.00 0.00 0.00 3.85
449 489 6.038356 CCGATCAAAGCATTTTTATTCAGCT 58.962 36.000 0.00 0.00 35.03 4.24
450 490 5.232838 CCCGATCAAAGCATTTTTATTCAGC 59.767 40.000 0.00 0.00 35.03 4.26
451 491 6.332630 ACCCGATCAAAGCATTTTTATTCAG 58.667 36.000 0.00 0.00 35.03 3.02
452 492 6.279513 ACCCGATCAAAGCATTTTTATTCA 57.720 33.333 0.00 0.00 35.03 2.57
566 616 0.898320 CTGGACTGTACTGGACTGGG 59.102 60.000 4.66 0.00 0.00 4.45
577 627 1.676635 TACTACGCGCCTGGACTGT 60.677 57.895 5.73 0.00 0.00 3.55
718 775 0.040351 TGTGTGAGAGAGAGAGGGGG 59.960 60.000 0.00 0.00 0.00 5.40
723 780 2.666272 AGGTGTGTGTGAGAGAGAGA 57.334 50.000 0.00 0.00 0.00 3.10
838 1167 1.655114 GCTCCTCCCTCCTCTCTCCT 61.655 65.000 0.00 0.00 0.00 3.69
839 1168 1.152546 GCTCCTCCCTCCTCTCTCC 60.153 68.421 0.00 0.00 0.00 3.71
840 1169 1.152546 GGCTCCTCCCTCCTCTCTC 60.153 68.421 0.00 0.00 0.00 3.20
841 1170 3.024217 GGCTCCTCCCTCCTCTCT 58.976 66.667 0.00 0.00 0.00 3.10
900 1238 5.366768 TCCCAGTGGATATAGGTGAAAGAAG 59.633 44.000 11.95 0.00 35.03 2.85
983 1321 3.569210 TGGCTGTGTCAGGTGGGG 61.569 66.667 0.00 0.00 31.21 4.96
1064 1408 1.846007 TTGAGCAGAGAGGAGGAGAC 58.154 55.000 0.00 0.00 0.00 3.36
1159 1513 2.115052 TGTCCATGGTGGTGTGGC 59.885 61.111 12.58 0.00 39.03 5.01
1229 1583 0.892755 TGGTCGTGGTGGTAGATGAC 59.107 55.000 0.00 0.00 0.00 3.06
1232 1586 1.601419 CCGTGGTCGTGGTGGTAGAT 61.601 60.000 0.00 0.00 35.01 1.98
2082 2444 2.818274 GGCCGGCTTAACACTCCG 60.818 66.667 28.56 0.00 42.58 4.63
2101 2463 2.045340 CGGTTACAAGGCAGGGGG 60.045 66.667 0.00 0.00 0.00 5.40
2104 2466 0.250553 TGGTTCGGTTACAAGGCAGG 60.251 55.000 0.00 0.00 0.00 4.85
2105 2467 1.265905 GTTGGTTCGGTTACAAGGCAG 59.734 52.381 0.00 0.00 0.00 4.85
2106 2468 1.134037 AGTTGGTTCGGTTACAAGGCA 60.134 47.619 0.00 0.00 0.00 4.75
2138 2503 4.509600 TCGATCGATCTCGGATCATATCAG 59.490 45.833 22.43 2.68 39.13 2.90
2167 2532 7.831691 TGGATTTGACCAAGAATTTACAAGA 57.168 32.000 0.00 0.00 36.96 3.02
2206 2571 2.885266 CAAATGGCAGAGAGGGATGATG 59.115 50.000 0.00 0.00 0.00 3.07
2207 2572 2.752154 GCAAATGGCAGAGAGGGATGAT 60.752 50.000 0.00 0.00 43.97 2.45
2272 2643 4.340097 TCGATGGATGGACGTACTAATTGT 59.660 41.667 0.00 0.00 0.00 2.71
2284 2655 1.444917 CGTCCTCGTCGATGGATGGA 61.445 60.000 18.05 7.70 36.12 3.41
2285 2656 1.008424 CGTCCTCGTCGATGGATGG 60.008 63.158 18.05 5.45 36.12 3.51
2286 2657 4.616592 CGTCCTCGTCGATGGATG 57.383 61.111 14.02 14.26 34.58 3.51
2303 2674 5.830912 TCATCCTTGACAAATCAAACACAC 58.169 37.500 0.00 0.00 44.28 3.82
2372 2758 3.011818 TGTCATGCATGTGAACATCCTC 58.988 45.455 25.43 6.08 33.61 3.71
2704 3101 5.125739 CAGTAGCTGGTAGTATGGCCTATAC 59.874 48.000 3.32 10.54 41.64 1.47
2724 3121 5.650703 TGTGTGATTGCTAGCTACTACAGTA 59.349 40.000 17.23 6.80 0.00 2.74
2725 3122 4.462834 TGTGTGATTGCTAGCTACTACAGT 59.537 41.667 17.23 0.00 0.00 3.55
2727 3124 4.219725 TGTGTGTGATTGCTAGCTACTACA 59.780 41.667 17.23 13.72 0.00 2.74
2728 3125 4.744570 TGTGTGTGATTGCTAGCTACTAC 58.255 43.478 17.23 11.35 0.00 2.73
2731 3128 3.935203 ACATGTGTGTGATTGCTAGCTAC 59.065 43.478 17.23 10.19 37.14 3.58
2732 3129 4.206477 ACATGTGTGTGATTGCTAGCTA 57.794 40.909 17.23 9.14 37.14 3.32
3002 3414 2.180159 TTGGCCTGGAGCGAAGTACC 62.180 60.000 3.32 0.00 45.17 3.34


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

AutoCloner maintained by Alex Coulton.