Multiple sequence alignment - TraesCS7A01G292300

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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 TraesCS7A01G292300 chr7A 100.000 3157 0 0 1 3157 366869296 366872452 0.000000e+00 5830.0
1 TraesCS7A01G292300 chr7A 93.767 1123 63 3 213 1328 153713115 153711993 0.000000e+00 1679.0
2 TraesCS7A01G292300 chr7A 81.462 383 60 7 1339 1715 718239116 718239493 1.420000e-78 303.0
3 TraesCS7A01G292300 chr6B 95.541 1794 62 11 1253 3035 701485727 701487513 0.000000e+00 2854.0
4 TraesCS7A01G292300 chr7D 94.472 1610 66 11 1329 2921 227690703 227692306 0.000000e+00 2459.0
5 TraesCS7A01G292300 chr7D 91.585 820 38 13 2131 2921 8373974 8374791 0.000000e+00 1103.0
6 TraesCS7A01G292300 chr7D 93.575 358 10 4 1738 2094 8373631 8373976 3.610000e-144 521.0
7 TraesCS7A01G292300 chr7D 94.357 319 15 3 1434 1751 8371410 8371726 1.320000e-133 486.0
8 TraesCS7A01G292300 chr5B 93.039 1609 67 15 1329 2921 15933471 15931892 0.000000e+00 2309.0
9 TraesCS7A01G292300 chr5B 93.678 1123 62 5 213 1328 492713110 492711990 0.000000e+00 1672.0
10 TraesCS7A01G292300 chr5B 96.825 378 10 1 2559 2934 55056066 55055689 5.750000e-177 630.0
11 TraesCS7A01G292300 chr5B 97.010 301 9 0 1 301 55089953 55089653 1.010000e-139 507.0
12 TraesCS7A01G292300 chr5B 97.656 256 6 0 2902 3157 120042784 120043039 1.040000e-119 440.0
13 TraesCS7A01G292300 chr5B 96.875 256 8 0 2902 3157 55055690 55055435 2.250000e-116 429.0
14 TraesCS7A01G292300 chr5B 82.289 463 71 11 1737 2194 700648106 700648562 1.060000e-104 390.0
15 TraesCS7A01G292300 chr3D 93.708 1335 65 6 1 1328 226020988 226022310 0.000000e+00 1982.0
16 TraesCS7A01G292300 chr3D 94.394 1106 55 3 230 1328 474129693 474128588 0.000000e+00 1692.0
17 TraesCS7A01G292300 chr3D 94.394 1106 55 3 230 1328 573315457 573314352 0.000000e+00 1692.0
18 TraesCS7A01G292300 chr3D 96.721 244 8 0 2914 3157 226023529 226023772 1.050000e-109 407.0
19 TraesCS7A01G292300 chr3B 91.835 1335 97 7 1 1328 254607553 254606224 0.000000e+00 1851.0
20 TraesCS7A01G292300 chr3B 93.333 45 3 0 2345 2389 29233432 29233388 2.030000e-07 67.6
21 TraesCS7A01G292300 chr2D 93.939 1122 62 3 213 1328 573507154 573508275 0.000000e+00 1690.0
22 TraesCS7A01G292300 chr2D 95.902 244 10 0 2914 3157 467629532 467629289 2.280000e-106 396.0
23 TraesCS7A01G292300 chr1A 93.945 1123 61 3 213 1328 29181991 29183113 0.000000e+00 1690.0
24 TraesCS7A01G292300 chr1A 93.333 45 2 1 2346 2390 42645388 42645431 7.310000e-07 65.8
25 TraesCS7A01G292300 chr4A 93.856 1123 62 3 213 1328 49449428 49450550 0.000000e+00 1685.0
26 TraesCS7A01G292300 chr7B 91.385 650 29 5 1788 2430 657228338 657228967 0.000000e+00 865.0
27 TraesCS7A01G292300 chr7B 95.625 480 18 2 2438 2915 657229130 657229608 0.000000e+00 767.0
28 TraesCS7A01G292300 chr7B 92.548 416 21 7 1383 1792 657226681 657227092 3.510000e-164 588.0
29 TraesCS7A01G292300 chr4B 96.021 377 14 1 2559 2934 302519274 302519650 2.080000e-171 612.0
30 TraesCS7A01G292300 chr4B 96.094 256 10 0 2902 3157 302519649 302519904 4.870000e-113 418.0
31 TraesCS7A01G292300 chr4B 81.330 391 52 12 1330 1714 227108541 227108916 6.620000e-77 298.0
32 TraesCS7A01G292300 chr3A 84.420 629 66 17 1734 2336 696048366 696048988 9.750000e-165 590.0
33 TraesCS7A01G292300 chr3A 85.086 523 58 11 1731 2237 628705904 628706422 1.680000e-142 516.0
34 TraesCS7A01G292300 chr3A 86.053 380 39 8 2547 2915 696049176 696049552 2.280000e-106 396.0
35 TraesCS7A01G292300 chr3A 85.789 380 43 8 2544 2915 628711262 628711638 2.950000e-105 392.0
36 TraesCS7A01G292300 chr4D 97.951 244 5 0 2914 3157 197323608 197323365 1.050000e-114 424.0
37 TraesCS7A01G292300 chr4D 97.131 244 7 0 2914 3157 12845364 12845607 2.270000e-111 412.0
38 TraesCS7A01G292300 chr6A 97.479 238 6 0 2920 3157 33172305 33172068 1.050000e-109 407.0
39 TraesCS7A01G292300 chr2B 81.522 460 77 8 1737 2194 488987173 488986720 3.850000e-99 372.0
40 TraesCS7A01G292300 chr2B 95.349 43 2 0 2347 2389 106941678 106941636 5.650000e-08 69.4
41 TraesCS7A01G292300 chr1B 95.455 44 2 0 2346 2389 156597608 156597651 1.570000e-08 71.3


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 TraesCS7A01G292300 chr7A 366869296 366872452 3156 False 5830.000000 5830 100.000000 1 3157 1 chr7A.!!$F1 3156
1 TraesCS7A01G292300 chr7A 153711993 153713115 1122 True 1679.000000 1679 93.767000 213 1328 1 chr7A.!!$R1 1115
2 TraesCS7A01G292300 chr6B 701485727 701487513 1786 False 2854.000000 2854 95.541000 1253 3035 1 chr6B.!!$F1 1782
3 TraesCS7A01G292300 chr7D 227690703 227692306 1603 False 2459.000000 2459 94.472000 1329 2921 1 chr7D.!!$F1 1592
4 TraesCS7A01G292300 chr7D 8371410 8374791 3381 False 703.333333 1103 93.172333 1434 2921 3 chr7D.!!$F2 1487
5 TraesCS7A01G292300 chr5B 15931892 15933471 1579 True 2309.000000 2309 93.039000 1329 2921 1 chr5B.!!$R1 1592
6 TraesCS7A01G292300 chr5B 492711990 492713110 1120 True 1672.000000 1672 93.678000 213 1328 1 chr5B.!!$R3 1115
7 TraesCS7A01G292300 chr5B 55055435 55056066 631 True 529.500000 630 96.850000 2559 3157 2 chr5B.!!$R4 598
8 TraesCS7A01G292300 chr3D 474128588 474129693 1105 True 1692.000000 1692 94.394000 230 1328 1 chr3D.!!$R1 1098
9 TraesCS7A01G292300 chr3D 573314352 573315457 1105 True 1692.000000 1692 94.394000 230 1328 1 chr3D.!!$R2 1098
10 TraesCS7A01G292300 chr3D 226020988 226023772 2784 False 1194.500000 1982 95.214500 1 3157 2 chr3D.!!$F1 3156
11 TraesCS7A01G292300 chr3B 254606224 254607553 1329 True 1851.000000 1851 91.835000 1 1328 1 chr3B.!!$R2 1327
12 TraesCS7A01G292300 chr2D 573507154 573508275 1121 False 1690.000000 1690 93.939000 213 1328 1 chr2D.!!$F1 1115
13 TraesCS7A01G292300 chr1A 29181991 29183113 1122 False 1690.000000 1690 93.945000 213 1328 1 chr1A.!!$F1 1115
14 TraesCS7A01G292300 chr4A 49449428 49450550 1122 False 1685.000000 1685 93.856000 213 1328 1 chr4A.!!$F1 1115
15 TraesCS7A01G292300 chr7B 657226681 657229608 2927 False 740.000000 865 93.186000 1383 2915 3 chr7B.!!$F1 1532
16 TraesCS7A01G292300 chr4B 302519274 302519904 630 False 515.000000 612 96.057500 2559 3157 2 chr4B.!!$F2 598
17 TraesCS7A01G292300 chr3A 628705904 628706422 518 False 516.000000 516 85.086000 1731 2237 1 chr3A.!!$F1 506
18 TraesCS7A01G292300 chr3A 696048366 696049552 1186 False 493.000000 590 85.236500 1734 2915 2 chr3A.!!$F3 1181

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
635 646 0.380733 TGATGCTCGCTAGTACGTGG 59.619 55.000 0.0 0.0 0.00 4.94 F
2117 5908 1.066430 CCCTTCGCTGGCAACTTACTA 60.066 52.381 0.0 0.0 37.61 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 5933 0.328258 ACAATTTAGGGCTCAGCGGT 59.672 50.000 0.0 0.0 0.0 5.68 R
3085 7210 9.170584 GCATAACAAAAACACTAAGAAAGAGAC 57.829 33.333 0.0 0.0 0.0 3.36 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
84 85 2.770827 CTCCCCAAGGAAACCCCC 59.229 66.667 0.00 0.00 43.40 5.40
189 198 2.579201 CAACCACCGCCTCGATCT 59.421 61.111 0.00 0.00 0.00 2.75
462 473 5.431765 CCTGATGTGAAGGTATAGCACTTT 58.568 41.667 4.48 0.00 33.83 2.66
477 488 2.590291 TTTCCGTTCTGCTGCGCA 60.590 55.556 10.98 10.98 36.92 6.09
498 509 1.945394 CGCCCTCTGAAATCTCAATGG 59.055 52.381 0.00 0.00 0.00 3.16
566 577 1.980052 CTGGGGTTCTTCTGCCGTA 59.020 57.895 0.00 0.00 0.00 4.02
567 578 0.541863 CTGGGGTTCTTCTGCCGTAT 59.458 55.000 0.00 0.00 0.00 3.06
607 618 7.573843 GCTGCTACAAGTGATAAATCTGTTTGT 60.574 37.037 0.00 10.11 33.45 2.83
623 634 7.421530 TCTGTTTGTTTAACTAGTGATGCTC 57.578 36.000 0.00 0.00 37.64 4.26
635 646 0.380733 TGATGCTCGCTAGTACGTGG 59.619 55.000 0.00 0.00 0.00 4.94
844 855 8.289618 CCTTTTCTTTCTCGACATTATTGACAA 58.710 33.333 0.00 0.00 0.00 3.18
913 926 9.868277 CTAGGAGGAATCATTTAACTATGCTAG 57.132 37.037 0.00 0.00 0.00 3.42
1156 1173 7.232534 TCAAGGTTGGTGCTTCATAATAACTTT 59.767 33.333 0.00 0.00 0.00 2.66
1352 1730 4.220693 TGCTGCATACTTAATCACCACT 57.779 40.909 0.00 0.00 0.00 4.00
1353 1731 4.588899 TGCTGCATACTTAATCACCACTT 58.411 39.130 0.00 0.00 0.00 3.16
1405 1853 9.935241 GTCATATATGTAGTTCATCTGTCCAAT 57.065 33.333 12.42 0.00 37.91 3.16
1445 1895 2.943369 ATTTGTGTGCCAGGCCACCA 62.943 55.000 23.05 14.01 34.85 4.17
1659 2118 2.872732 GGATCTCATGGATGCCACAAT 58.127 47.619 0.00 0.00 35.80 2.71
1679 2138 8.554528 CCACAATTGCACACAATAAATAAACAA 58.445 29.630 5.05 0.00 45.90 2.83
1803 5430 5.818678 TTTCTACTTAGCCCTCAGAAACA 57.181 39.130 0.00 0.00 31.96 2.83
1831 5458 5.262009 TGACTACTAGCCAACTACACTCAT 58.738 41.667 0.00 0.00 0.00 2.90
2117 5908 1.066430 CCCTTCGCTGGCAACTTACTA 60.066 52.381 0.00 0.00 37.61 1.82
2142 5933 0.106918 AGAAACCCAAGTGGACGCAA 60.107 50.000 0.00 0.00 37.39 4.85
2405 6226 2.774234 ACACTGGAGTATATGGCTTGCT 59.226 45.455 0.00 0.00 0.00 3.91
2425 6246 5.863965 TGCTAATCCCATCATGATTACGAA 58.136 37.500 5.16 0.00 34.43 3.85
2426 6247 6.475504 TGCTAATCCCATCATGATTACGAAT 58.524 36.000 5.16 0.00 34.43 3.34
2753 6807 2.959507 ACAAGGAAACAAAGCACACC 57.040 45.000 0.00 0.00 0.00 4.16
3085 7210 6.483640 GCTACATTTCTACTCCTAACCCATTG 59.516 42.308 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 2.040359 GGAGGGGAGGAGGAAGGG 60.040 72.222 0.00 0.00 0.00 3.95
84 85 1.074850 GAGGAGGGGAGGAGGAAGG 60.075 68.421 0.00 0.00 0.00 3.46
85 86 1.074850 GGAGGAGGGGAGGAGGAAG 60.075 68.421 0.00 0.00 0.00 3.46
86 87 1.550374 AGGAGGAGGGGAGGAGGAA 60.550 63.158 0.00 0.00 0.00 3.36
87 88 2.015726 GAGGAGGAGGGGAGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
88 89 2.612251 GAGGAGGAGGGGAGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
89 90 2.612251 GGAGGAGGAGGGGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
90 91 3.036959 GGGAGGAGGAGGGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
91 92 3.368501 TGGGAGGAGGAGGGGAGG 61.369 72.222 0.00 0.00 0.00 4.30
92 93 2.041405 GTGGGAGGAGGAGGGGAG 60.041 72.222 0.00 0.00 0.00 4.30
93 94 2.540910 AGTGGGAGGAGGAGGGGA 60.541 66.667 0.00 0.00 0.00 4.81
97 98 1.075600 GGAGGAGTGGGAGGAGGAG 60.076 68.421 0.00 0.00 0.00 3.69
189 198 1.204704 CGAACACTATCAGACCTGGCA 59.795 52.381 0.00 0.00 0.00 4.92
477 488 2.636830 CATTGAGATTTCAGAGGGCGT 58.363 47.619 0.00 0.00 34.15 5.68
498 509 4.396166 AGACTATACCAATTGTGCAACTGC 59.604 41.667 4.43 0.00 38.04 4.40
566 577 0.171903 GCAGCGCTGACCAAATTGAT 59.828 50.000 40.21 0.00 0.00 2.57
567 578 0.890542 AGCAGCGCTGACCAAATTGA 60.891 50.000 40.21 0.00 37.57 2.57
623 634 3.637998 ATACCAATCCACGTACTAGCG 57.362 47.619 0.00 0.00 37.94 4.26
635 646 7.865706 TCCTCTTTCAGCTAAAATACCAATC 57.134 36.000 0.00 0.00 0.00 2.67
749 760 1.227468 GGTTTATCCGAGGGGCGTC 60.227 63.158 0.00 0.00 38.67 5.19
844 855 0.820871 GTGATGAGAGCCCGAGACTT 59.179 55.000 0.00 0.00 0.00 3.01
913 926 5.246307 ACAGCAAGAAAACTACCCTATGAC 58.754 41.667 0.00 0.00 0.00 3.06
1156 1173 3.679980 GCAGAAGAAGCACGTTGATAGAA 59.320 43.478 0.00 0.00 0.00 2.10
1224 1241 5.939883 TTGATACACAAGATAAGCACAAGCT 59.060 36.000 0.00 0.00 42.53 3.74
1279 1296 2.370189 CGGCTTCCTCAATAGAAGGGAT 59.630 50.000 2.97 0.00 40.91 3.85
1405 1853 9.613428 ACAAATTAGTATTTATAGTGCAGAGCA 57.387 29.630 0.00 0.00 32.75 4.26
1445 1895 1.635487 AGACATGGGCACTACCACAAT 59.365 47.619 0.00 0.00 44.72 2.71
1623 2080 4.041321 TGAGATCCCAATTATCAGAGCTGG 59.959 45.833 0.00 0.00 0.00 4.85
1679 2138 6.209986 TCTGTTCAAGAAGGCATCATCAAATT 59.790 34.615 0.00 0.00 29.54 1.82
1803 5430 6.890814 AGTGTAGTTGGCTAGTAGTCATACTT 59.109 38.462 18.38 6.28 42.39 2.24
1971 5762 8.264347 ACCATGGTCTTAGTTTTTCAAACAATT 58.736 29.630 13.00 0.00 0.00 2.32
2113 5904 6.154021 GTCCACTTGGGTTTCTACATCTAGTA 59.846 42.308 0.00 0.00 38.11 1.82
2117 5908 3.306780 CGTCCACTTGGGTTTCTACATCT 60.307 47.826 0.00 0.00 38.11 2.90
2142 5933 0.328258 ACAATTTAGGGCTCAGCGGT 59.672 50.000 0.00 0.00 0.00 5.68
2271 6089 5.935789 TGAATGGTAAAAGTAGGAAAGGACG 59.064 40.000 0.00 0.00 0.00 4.79
2309 6129 9.330063 ACCTGACAACAAATATGATACATACAG 57.670 33.333 0.00 0.00 0.00 2.74
2425 6246 9.170734 CTCCAGCAGCAAACAACATATATATAT 57.829 33.333 0.00 0.00 0.00 0.86
2426 6247 8.374743 TCTCCAGCAGCAAACAACATATATATA 58.625 33.333 0.00 0.00 0.00 0.86
2753 6807 5.982516 TGGCAAAGCTAATTTAATTATGCGG 59.017 36.000 12.11 8.32 31.25 5.69
3085 7210 9.170584 GCATAACAAAAACACTAAGAAAGAGAC 57.829 33.333 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.