Multiple sequence alignment - TraesCS3D01G016800

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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 TraesCS3D01G016800 chr3D 100.000 3228 0 0 1 3228 5814779 5811552 0.000000e+00 5962.0
1 TraesCS3D01G016800 chr7D 91.988 2571 131 25 726 3228 42195566 42193003 0.000000e+00 3537.0
2 TraesCS3D01G016800 chr7D 83.333 738 73 20 1 700 42196291 42195566 1.260000e-178 636.0
3 TraesCS3D01G016800 chr3A 91.025 1493 82 18 1470 2932 15432050 15433520 0.000000e+00 1967.0
4 TraesCS3D01G016800 chr3A 86.788 1211 121 28 296 1475 15430555 15431757 0.000000e+00 1314.0
5 TraesCS3D01G016800 chr3A 90.235 850 55 4 2405 3228 12173731 12172884 0.000000e+00 1085.0
6 TraesCS3D01G016800 chr3A 88.220 747 66 13 743 1475 12175370 12174632 0.000000e+00 872.0
7 TraesCS3D01G016800 chr3A 91.980 399 20 2 1969 2355 12174144 12173746 1.690000e-152 549.0
8 TraesCS3D01G016800 chr3A 92.466 292 18 2 2 293 15430231 15430518 6.440000e-112 414.0
9 TraesCS3D01G016800 chr3A 90.444 293 24 2 1 293 12176397 12176109 1.820000e-102 383.0
10 TraesCS3D01G016800 chr3A 86.038 265 17 7 2983 3228 15433843 15434106 1.910000e-67 267.0
11 TraesCS3D01G016800 chr3A 92.655 177 11 2 574 750 12175873 12175699 1.490000e-63 254.0
12 TraesCS3D01G016800 chrUn 91.169 1223 80 10 1 1202 35513695 35514910 0.000000e+00 1635.0
13 TraesCS3D01G016800 chrUn 91.591 1106 69 9 1414 2496 36296313 36295209 0.000000e+00 1506.0
14 TraesCS3D01G016800 chrUn 91.768 826 36 7 2429 3228 35840246 35839427 0.000000e+00 1120.0
15 TraesCS3D01G016800 chrUn 90.235 850 55 4 2405 3228 32298618 32297771 0.000000e+00 1085.0
16 TraesCS3D01G016800 chrUn 90.152 853 56 4 2402 3228 267483830 267484680 0.000000e+00 1085.0
17 TraesCS3D01G016800 chrUn 90.841 797 63 6 1470 2256 36477680 36478476 0.000000e+00 1059.0
18 TraesCS3D01G016800 chrUn 90.176 794 60 9 597 1375 36297106 36296316 0.000000e+00 1018.0
19 TraesCS3D01G016800 chrUn 92.933 566 35 2 1824 2387 368221869 368221307 0.000000e+00 819.0
20 TraesCS3D01G016800 chrUn 87.645 688 63 13 802 1475 32300198 32299519 0.000000e+00 780.0
21 TraesCS3D01G016800 chrUn 88.788 553 42 18 429 969 36476637 36477181 0.000000e+00 660.0
22 TraesCS3D01G016800 chrUn 84.408 667 57 16 2597 3228 419490487 419489833 2.130000e-171 612.0
23 TraesCS3D01G016800 chrUn 91.980 399 20 2 1969 2355 32299031 32298633 1.690000e-152 549.0
24 TraesCS3D01G016800 chrUn 92.172 396 19 2 1969 2352 267483420 267483815 1.690000e-152 549.0
25 TraesCS3D01G016800 chrUn 85.768 534 54 12 956 1475 267482407 267482932 2.190000e-151 545.0
26 TraesCS3D01G016800 chrUn 92.128 343 23 2 1 343 36299240 36298902 6.260000e-132 481.0
27 TraesCS3D01G016800 chrUn 81.122 196 28 6 1040 1229 40584656 40584464 7.220000e-32 148.0
28 TraesCS3D01G016800 chrUn 100.000 32 0 0 122 153 36298801 36298770 3.480000e-05 60.2
29 TraesCS3D01G016800 chr3B 93.364 1085 54 4 1414 2481 11928125 11929208 0.000000e+00 1589.0
30 TraesCS3D01G016800 chr3B 90.759 790 68 4 1470 2256 11958358 11957571 0.000000e+00 1050.0
31 TraesCS3D01G016800 chr3B 89.924 794 62 9 597 1375 11927332 11928122 0.000000e+00 1007.0
32 TraesCS3D01G016800 chr3B 81.524 958 101 30 2311 3228 11957440 11956519 0.000000e+00 719.0
33 TraesCS3D01G016800 chr3B 88.727 550 42 18 432 969 11959419 11958878 0.000000e+00 654.0
34 TraesCS3D01G016800 chr3B 91.618 346 22 3 1 343 11925309 11925650 3.770000e-129 472.0
35 TraesCS3D01G016800 chr3B 78.663 389 33 25 2860 3228 11929215 11929573 2.520000e-51 213.0
36 TraesCS3D01G016800 chr3B 100.000 32 0 0 122 153 11925749 11925780 3.480000e-05 60.2
37 TraesCS3D01G016800 chr7B 85.321 763 103 5 1483 2242 40287313 40286557 0.000000e+00 780.0
38 TraesCS3D01G016800 chr7B 83.421 760 110 13 1480 2234 608301252 608300504 0.000000e+00 691.0
39 TraesCS3D01G016800 chr7B 79.268 164 21 10 2794 2954 608299969 608299816 5.700000e-18 102.0
40 TraesCS3D01G016800 chr7A 84.868 760 100 8 1482 2232 90481088 90480335 0.000000e+00 752.0
41 TraesCS3D01G016800 chr7A 86.458 96 8 4 2742 2835 90479655 90479563 2.050000e-17 100.0
42 TraesCS3D01G016800 chr6B 83.974 156 25 0 12 167 426024245 426024400 2.010000e-32 150.0
43 TraesCS3D01G016800 chr5D 88.542 96 7 3 2861 2955 493686739 493686831 2.630000e-21 113.0
44 TraesCS3D01G016800 chr5B 87.209 86 9 2 2872 2955 340571140 340571225 2.650000e-16 97.1


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 TraesCS3D01G016800 chr3D 5811552 5814779 3227 True 5962.000000 5962 100.000000 1 3228 1 chr3D.!!$R1 3227
1 TraesCS3D01G016800 chr7D 42193003 42196291 3288 True 2086.500000 3537 87.660500 1 3228 2 chr7D.!!$R1 3227
2 TraesCS3D01G016800 chr3A 15430231 15434106 3875 False 990.500000 1967 89.079250 2 3228 4 chr3A.!!$F1 3226
3 TraesCS3D01G016800 chr3A 12172884 12176397 3513 True 628.600000 1085 90.706800 1 3228 5 chr3A.!!$R1 3227
4 TraesCS3D01G016800 chrUn 35513695 35514910 1215 False 1635.000000 1635 91.169000 1 1202 1 chrUn.!!$F1 1201
5 TraesCS3D01G016800 chrUn 35839427 35840246 819 True 1120.000000 1120 91.768000 2429 3228 1 chrUn.!!$R1 799
6 TraesCS3D01G016800 chrUn 36476637 36478476 1839 False 859.500000 1059 89.814500 429 2256 2 chrUn.!!$F2 1827
7 TraesCS3D01G016800 chrUn 368221307 368221869 562 True 819.000000 819 92.933000 1824 2387 1 chrUn.!!$R3 563
8 TraesCS3D01G016800 chrUn 32297771 32300198 2427 True 804.666667 1085 89.953333 802 3228 3 chrUn.!!$R5 2426
9 TraesCS3D01G016800 chrUn 36295209 36299240 4031 True 766.300000 1506 93.473750 1 2496 4 chrUn.!!$R6 2495
10 TraesCS3D01G016800 chrUn 267482407 267484680 2273 False 726.333333 1085 89.364000 956 3228 3 chrUn.!!$F3 2272
11 TraesCS3D01G016800 chrUn 419489833 419490487 654 True 612.000000 612 84.408000 2597 3228 1 chrUn.!!$R4 631
12 TraesCS3D01G016800 chr3B 11956519 11959419 2900 True 807.666667 1050 87.003333 432 3228 3 chr3B.!!$R1 2796
13 TraesCS3D01G016800 chr3B 11925309 11929573 4264 False 668.240000 1589 90.713800 1 3228 5 chr3B.!!$F1 3227
14 TraesCS3D01G016800 chr7B 40286557 40287313 756 True 780.000000 780 85.321000 1483 2242 1 chr7B.!!$R1 759
15 TraesCS3D01G016800 chr7B 608299816 608301252 1436 True 396.500000 691 81.344500 1480 2954 2 chr7B.!!$R2 1474
16 TraesCS3D01G016800 chr7A 90479563 90481088 1525 True 426.000000 752 85.663000 1482 2835 2 chr7A.!!$R1 1353

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
442 521 1.135603 CGCATTCACAAGACCACCATG 60.136 52.381 0.00 0.0 0.0 3.66 F
602 2310 1.518325 TTGTCAGGCCACGTTACATG 58.482 50.000 5.01 0.0 0.0 3.21 F
983 3053 1.975660 TCCCCACTAAAACACACAGC 58.024 50.000 0.00 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1255 3327 1.145119 AGAGGGTGTTGGGGTTCTTTC 59.855 52.381 0.00 0.00 0.0 2.62 R
1801 4406 2.183555 CTCCAAGACCGGCCGTAC 59.816 66.667 26.12 17.28 0.0 3.67 R
2965 6263 3.297134 ACACACAACTTGACCCATCTT 57.703 42.857 0.00 0.00 0.0 2.40 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
163 164 6.373005 TGACAAGATCACCTCCTAAATGAA 57.627 37.500 0.00 0.00 29.99 2.57
173 174 6.100279 TCACCTCCTAAATGAATCTGCTATGT 59.900 38.462 0.00 0.00 0.00 2.29
180 181 4.550076 ATGAATCTGCTATGTCTAGGGC 57.450 45.455 0.00 0.00 0.00 5.19
187 188 4.141135 TCTGCTATGTCTAGGGCTCTACTT 60.141 45.833 0.00 0.00 0.00 2.24
222 226 6.283544 AGTAAGGCTTAGTCTAGTTTGGTC 57.716 41.667 7.33 0.00 0.00 4.02
231 235 9.872721 GCTTAGTCTAGTTTGGTCTAATTTAGT 57.127 33.333 3.45 0.00 0.00 2.24
256 260 9.353999 GTTTAACAGAATGATGGATTTTGGTAC 57.646 33.333 0.00 0.00 39.69 3.34
257 261 8.877864 TTAACAGAATGATGGATTTTGGTACT 57.122 30.769 0.00 0.00 39.69 2.73
259 263 8.511604 AACAGAATGATGGATTTTGGTACTAG 57.488 34.615 0.00 0.00 39.69 2.57
260 264 6.543831 ACAGAATGATGGATTTTGGTACTAGC 59.456 38.462 0.00 0.00 39.69 3.42
281 285 3.674281 GCATGCATCAATTCGTTCAACAA 59.326 39.130 14.21 0.00 0.00 2.83
305 346 4.483311 GGACGAGTACTTGTTAGTTCCAG 58.517 47.826 17.01 0.00 35.78 3.86
336 377 9.975218 ATTAGTACATGGAAGAGGTATTTTGTT 57.025 29.630 0.00 0.00 0.00 2.83
350 427 6.437162 AGGTATTTTGTTGCTGTTGGATGTAT 59.563 34.615 0.00 0.00 0.00 2.29
442 521 1.135603 CGCATTCACAAGACCACCATG 60.136 52.381 0.00 0.00 0.00 3.66
477 556 3.628646 AATCTCGCTGCCACCACCC 62.629 63.158 0.00 0.00 0.00 4.61
508 587 6.160664 TGACCGAATTCGACTAAATTGTTC 57.839 37.500 28.76 9.75 43.02 3.18
510 589 6.090358 TGACCGAATTCGACTAAATTGTTCTC 59.910 38.462 28.76 4.95 43.02 2.87
552 631 6.150307 TGTGTGGTTTGGTGAATGATATGTAC 59.850 38.462 0.00 0.00 0.00 2.90
602 2310 1.518325 TTGTCAGGCCACGTTACATG 58.482 50.000 5.01 0.00 0.00 3.21
691 2400 2.251818 CCATCATACCCTCTCATCCGT 58.748 52.381 0.00 0.00 0.00 4.69
875 2943 6.890979 ATTATTGGCAGCTATCTTTCCTTC 57.109 37.500 0.00 0.00 0.00 3.46
983 3053 1.975660 TCCCCACTAAAACACACAGC 58.024 50.000 0.00 0.00 0.00 4.40
1226 3296 2.029020 CCGTGTTCAAGGTGATCTCTCA 60.029 50.000 0.00 0.00 0.00 3.27
1244 3314 2.938451 CTCATCTTGCACCAAAGCGATA 59.062 45.455 0.00 0.00 37.31 2.92
1286 3363 4.383552 CCCAACACCCTCTTTCTATCTCTG 60.384 50.000 0.00 0.00 0.00 3.35
1331 3409 8.210946 AGATTCGGGAAGATCACACATTTATTA 58.789 33.333 0.00 0.00 0.00 0.98
1453 3751 3.279434 GCGGAGACCAAACATTATCCTT 58.721 45.455 0.00 0.00 0.00 3.36
1579 4175 2.515991 CGTGCCAACACCCACTGT 60.516 61.111 0.00 0.00 44.40 3.55
1645 4242 3.717294 AAGGGGTTCGGCTGCGAT 61.717 61.111 0.00 0.00 0.00 4.58
2332 5239 1.608590 ACCACACATGTGCAAGCTAAC 59.391 47.619 25.68 0.00 44.34 2.34
2445 5389 1.336125 GGCATCTGATGGTTAAGCTGC 59.664 52.381 18.60 6.04 35.36 5.25
2449 5395 4.336433 GCATCTGATGGTTAAGCTGCTTAA 59.664 41.667 26.31 26.31 33.75 1.85
2513 5465 3.945285 GCTAAGCAATGGTAAGGTAGCAA 59.055 43.478 8.47 0.00 39.89 3.91
2551 5503 2.501723 GAGGGTAGGAATGCTTCACTCA 59.498 50.000 5.83 0.00 0.00 3.41
2592 5610 8.210946 TGGCCTAAATAGTACTACTAGTAACGA 58.789 37.037 4.31 0.00 33.66 3.85
2965 6263 4.079443 TCAAAGAGTTTTTCCCCCTCTCAA 60.079 41.667 0.00 0.00 34.55 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 164 3.541242 AGAGCCCTAGACATAGCAGAT 57.459 47.619 0.00 0.00 0.00 2.90
231 235 9.308000 AGTACCAAAATCCATCATTCTGTTAAA 57.692 29.630 0.00 0.00 0.00 1.52
240 244 5.242393 GCATGCTAGTACCAAAATCCATCAT 59.758 40.000 11.37 0.00 0.00 2.45
256 260 4.541085 TGAACGAATTGATGCATGCTAG 57.459 40.909 20.33 0.00 0.00 3.42
257 261 4.155644 TGTTGAACGAATTGATGCATGCTA 59.844 37.500 20.33 5.73 0.00 3.49
259 263 3.244156 TGTTGAACGAATTGATGCATGC 58.756 40.909 11.82 11.82 0.00 4.06
260 264 5.181235 GTTGTTGAACGAATTGATGCATG 57.819 39.130 2.46 0.00 0.00 4.06
281 285 3.057946 GGAACTAACAAGTACTCGTCCGT 60.058 47.826 0.00 0.00 0.00 4.69
283 287 4.483311 CTGGAACTAACAAGTACTCGTCC 58.517 47.826 0.00 0.00 0.00 4.79
286 290 3.909430 TGCTGGAACTAACAAGTACTCG 58.091 45.455 0.00 0.00 0.00 4.18
305 346 5.615289 ACCTCTTCCATGTACTAATCATGC 58.385 41.667 0.00 0.00 40.63 4.06
336 377 4.641541 CCAAAGATCATACATCCAACAGCA 59.358 41.667 0.00 0.00 0.00 4.41
350 427 3.965379 TTACGTGCTACCCAAAGATCA 57.035 42.857 0.00 0.00 0.00 2.92
413 492 2.667969 TCTTGTGAATGCGATCGTGAAG 59.332 45.455 17.81 8.37 0.00 3.02
442 521 2.662596 TGACATGCGGGTCAGACC 59.337 61.111 11.70 11.70 42.56 3.85
477 556 3.741344 AGTCGAATTCGGTCAAGTTGAAG 59.259 43.478 26.47 5.22 40.29 3.02
508 587 3.060940 CACAGCTAATATTGTCGTGCGAG 60.061 47.826 0.00 0.00 0.00 5.03
510 589 2.603110 ACACAGCTAATATTGTCGTGCG 59.397 45.455 0.00 0.00 0.00 5.34
552 631 2.065993 AGTCATGGAACTTGTCGTCG 57.934 50.000 0.00 0.00 0.00 5.12
657 2366 5.712917 GGGTATGATGGTCCAGTTAAAAACA 59.287 40.000 0.00 0.00 0.00 2.83
658 2367 5.949952 AGGGTATGATGGTCCAGTTAAAAAC 59.050 40.000 0.00 0.00 0.00 2.43
691 2400 6.051717 GCTTGAGATTAAGATGTGCCTCTTA 58.948 40.000 0.00 0.00 36.82 2.10
822 2890 5.681337 TGCTGATAATGTTCGTTTTGACA 57.319 34.783 0.00 0.00 0.00 3.58
875 2943 1.068753 CCAGCAGAGCATACCCGAG 59.931 63.158 0.00 0.00 0.00 4.63
983 3053 4.568359 CCTTCATGGTCATTTCTAGTCACG 59.432 45.833 0.00 0.00 0.00 4.35
1033 3103 2.266055 CTTCACCTCCTCGGCACC 59.734 66.667 0.00 0.00 35.61 5.01
1186 3256 2.614013 GGGCTTGAGGGGGAGGAA 60.614 66.667 0.00 0.00 0.00 3.36
1226 3296 4.989279 AATTATCGCTTTGGTGCAAGAT 57.011 36.364 0.00 0.00 0.00 2.40
1255 3327 1.145119 AGAGGGTGTTGGGGTTCTTTC 59.855 52.381 0.00 0.00 0.00 2.62
1259 3331 1.145119 AGAAAGAGGGTGTTGGGGTTC 59.855 52.381 0.00 0.00 0.00 3.62
1264 3336 4.223923 ACAGAGATAGAAAGAGGGTGTTGG 59.776 45.833 0.00 0.00 0.00 3.77
1268 3340 4.399618 TCGAACAGAGATAGAAAGAGGGTG 59.600 45.833 0.00 0.00 0.00 4.61
1286 3363 6.237701 CGAATCTCAAAGAAATCCTCTCGAAC 60.238 42.308 0.00 0.00 31.02 3.95
1337 3415 2.113860 AATGTCTTCCATCCACGTGG 57.886 50.000 29.26 29.26 40.76 4.94
1579 4175 3.177884 ACCTTGTCCAGCTGGCCA 61.178 61.111 28.91 21.82 34.44 5.36
1645 4242 3.445888 TGGAACACCACGTAGCGA 58.554 55.556 0.00 0.00 0.00 4.93
1801 4406 2.183555 CTCCAAGACCGGCCGTAC 59.816 66.667 26.12 17.28 0.00 3.67
2332 5239 6.098695 ACCATAATCTTGATTGATTGGGTTGG 59.901 38.462 17.71 0.00 39.83 3.77
2449 5395 8.918116 TCAAACTGATCTAGTACTGATATTGCT 58.082 33.333 5.39 0.00 39.18 3.91
2478 5425 5.297776 CCATTGCTTAGCTGCATTACTACTT 59.702 40.000 5.60 0.00 42.96 2.24
2505 5452 7.036220 CGCTTAGCTACATATTATTGCTACCT 58.964 38.462 1.76 0.00 36.19 3.08
2513 5465 6.321690 CCTACCCTCGCTTAGCTACATATTAT 59.678 42.308 1.76 0.00 0.00 1.28
2592 5610 7.506114 TCAGATCAAGTACAAACCAGTAACTT 58.494 34.615 0.00 0.00 0.00 2.66
2965 6263 3.297134 ACACACAACTTGACCCATCTT 57.703 42.857 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.