Multiple sequence alignment - TraesCS3B01G197200

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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 TraesCS3B01G197200 chr3B 100.000 2999 0 0 1 2999 224287890 224284892 0.000000e+00 5539.0
1 TraesCS3B01G197200 chr3B 95.874 3005 86 17 1 2999 224165407 224162435 0.000000e+00 4828.0
2 TraesCS3B01G197200 chr3B 89.891 3027 160 61 27 2999 223678853 223675919 0.000000e+00 3760.0
3 TraesCS3B01G197200 chr3B 93.064 692 24 6 798 1473 223558923 223558240 0.000000e+00 990.0
4 TraesCS3B01G197200 chr3B 92.979 527 27 3 1698 2220 223558131 223557611 0.000000e+00 760.0
5 TraesCS3B01G197200 chr3B 89.311 421 29 6 808 1213 223690763 223690344 5.730000e-142 514.0
6 TraesCS3B01G197200 chr3B 90.727 399 18 7 2620 2999 224319052 224318654 5.730000e-142 514.0
7 TraesCS3B01G197200 chr3B 84.194 310 43 5 339 644 499800444 499800137 2.260000e-76 296.0
8 TraesCS3B01G197200 chr3B 94.783 115 6 0 844 958 223653794 223653680 2.380000e-41 180.0
9 TraesCS3B01G197200 chr3B 93.220 59 4 0 1747 1805 469631876 469631934 1.480000e-13 87.9
10 TraesCS3B01G197200 chr3D 91.853 2283 92 38 776 2999 152852273 152850026 0.000000e+00 3099.0
11 TraesCS3B01G197200 chr3D 91.498 988 60 5 779 1745 152702662 152701678 0.000000e+00 1338.0
12 TraesCS3B01G197200 chr3D 84.942 1202 119 20 956 2122 149769996 149768822 0.000000e+00 1160.0
13 TraesCS3B01G197200 chr3D 90.786 814 45 16 2214 2999 153084044 153083233 0.000000e+00 1061.0
14 TraesCS3B01G197200 chr3D 87.215 876 71 14 950 1805 141410556 141411410 0.000000e+00 959.0
15 TraesCS3B01G197200 chr3D 93.246 533 25 4 1698 2220 152701800 152701269 0.000000e+00 774.0
16 TraesCS3B01G197200 chr3D 84.520 323 42 6 326 644 435710949 435710631 2.240000e-81 313.0
17 TraesCS3B01G197200 chr3D 83.974 312 40 8 339 644 47207969 47208276 1.050000e-74 291.0
18 TraesCS3B01G197200 chr3A 93.318 1302 60 7 841 2128 177671314 177672602 0.000000e+00 1897.0
19 TraesCS3B01G197200 chr3A 93.180 1217 66 7 1008 2220 177888055 177889258 0.000000e+00 1772.0
20 TraesCS3B01G197200 chr3A 83.615 1300 113 45 950 2209 159831955 159833194 0.000000e+00 1129.0
21 TraesCS3B01G197200 chr3A 89.889 811 36 18 2214 2999 177105075 177105864 0.000000e+00 1002.0
22 TraesCS3B01G197200 chr3A 83.290 1167 110 35 1012 2120 181104902 181106041 0.000000e+00 996.0
23 TraesCS3B01G197200 chr3A 88.193 559 53 10 776 1329 177647061 177647611 0.000000e+00 654.0
24 TraesCS3B01G197200 chr3A 93.865 163 8 2 2176 2336 177672706 177672868 8.300000e-61 244.0
25 TraesCS3B01G197200 chr6A 82.248 1290 125 48 956 2209 146441640 146440419 0.000000e+00 1018.0
26 TraesCS3B01G197200 chr6A 83.387 313 42 6 339 645 68503461 68503769 6.330000e-72 281.0
27 TraesCS3B01G197200 chr5D 88.350 309 32 3 339 644 344690139 344690446 4.720000e-98 368.0
28 TraesCS3B01G197200 chr5D 84.227 317 43 5 336 649 237258649 237258961 4.860000e-78 302.0
29 TraesCS3B01G197200 chr6D 86.984 315 34 6 339 649 177797254 177796943 6.150000e-92 348.0
30 TraesCS3B01G197200 chr6B 84.112 321 45 5 333 649 632504938 632505256 3.760000e-79 305.0


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 TraesCS3B01G197200 chr3B 224284892 224287890 2998 True 5539.0 5539 100.0000 1 2999 1 chr3B.!!$R5 2998
1 TraesCS3B01G197200 chr3B 224162435 224165407 2972 True 4828.0 4828 95.8740 1 2999 1 chr3B.!!$R4 2998
2 TraesCS3B01G197200 chr3B 223675919 223678853 2934 True 3760.0 3760 89.8910 27 2999 1 chr3B.!!$R2 2972
3 TraesCS3B01G197200 chr3B 223557611 223558923 1312 True 875.0 990 93.0215 798 2220 2 chr3B.!!$R8 1422
4 TraesCS3B01G197200 chr3D 152850026 152852273 2247 True 3099.0 3099 91.8530 776 2999 1 chr3D.!!$R2 2223
5 TraesCS3B01G197200 chr3D 149768822 149769996 1174 True 1160.0 1160 84.9420 956 2122 1 chr3D.!!$R1 1166
6 TraesCS3B01G197200 chr3D 153083233 153084044 811 True 1061.0 1061 90.7860 2214 2999 1 chr3D.!!$R3 785
7 TraesCS3B01G197200 chr3D 152701269 152702662 1393 True 1056.0 1338 92.3720 779 2220 2 chr3D.!!$R5 1441
8 TraesCS3B01G197200 chr3D 141410556 141411410 854 False 959.0 959 87.2150 950 1805 1 chr3D.!!$F2 855
9 TraesCS3B01G197200 chr3A 177888055 177889258 1203 False 1772.0 1772 93.1800 1008 2220 1 chr3A.!!$F4 1212
10 TraesCS3B01G197200 chr3A 159831955 159833194 1239 False 1129.0 1129 83.6150 950 2209 1 chr3A.!!$F1 1259
11 TraesCS3B01G197200 chr3A 177671314 177672868 1554 False 1070.5 1897 93.5915 841 2336 2 chr3A.!!$F6 1495
12 TraesCS3B01G197200 chr3A 177105075 177105864 789 False 1002.0 1002 89.8890 2214 2999 1 chr3A.!!$F2 785
13 TraesCS3B01G197200 chr3A 181104902 181106041 1139 False 996.0 996 83.2900 1012 2120 1 chr3A.!!$F5 1108
14 TraesCS3B01G197200 chr3A 177647061 177647611 550 False 654.0 654 88.1930 776 1329 1 chr3A.!!$F3 553
15 TraesCS3B01G197200 chr6A 146440419 146441640 1221 True 1018.0 1018 82.2480 956 2209 1 chr6A.!!$R1 1253

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
41 42 0.523966 GCTCGATATGAGGTCTCCGG 59.476 60.0 0.0 0.0 45.38 5.14 F
729 733 0.534412 CCGGAGTTGCTCTCACATCT 59.466 55.0 0.0 0.0 44.40 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1634 1706 1.964608 CTCCTTCTGCTGGATCGGCA 61.965 60.0 10.74 10.74 44.04 5.69 R
2590 2966 0.235926 GCAAGACTCGCCAACACTTC 59.764 55.0 0.00 0.00 0.00 3.01 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
35 36 2.439507 ACATTTGGGCTCGATATGAGGT 59.560 45.455 0.03 0.00 45.38 3.85
41 42 0.523966 GCTCGATATGAGGTCTCCGG 59.476 60.000 0.00 0.00 45.38 5.14
72 73 4.038271 TGATTTGAGGGCAGTTTGAGAT 57.962 40.909 0.00 0.00 0.00 2.75
75 76 0.694771 TGAGGGCAGTTTGAGATGCT 59.305 50.000 0.00 0.00 42.19 3.79
143 144 0.599060 CATTTAACGCGGGTTTGGGT 59.401 50.000 23.57 0.55 37.58 4.51
145 146 1.109609 TTTAACGCGGGTTTGGGTTT 58.890 45.000 23.57 0.00 41.60 3.27
163 164 2.024176 TTTTCGGCTGTAGATGCTCC 57.976 50.000 0.00 0.00 0.00 4.70
192 193 3.374042 AGAGTAGAGTAGAAGCAGCCA 57.626 47.619 0.00 0.00 0.00 4.75
199 200 1.902508 AGTAGAAGCAGCCAAGTAGCA 59.097 47.619 0.00 0.00 34.23 3.49
263 265 4.223923 TGGACATTCCAACAAAACCAACTT 59.776 37.500 0.00 0.00 45.00 2.66
282 284 4.844267 ACTTAACATGAACACGTGAAAGC 58.156 39.130 25.01 8.56 0.00 3.51
314 316 4.686554 GTCAAACGAGTCTTCTAGCACATT 59.313 41.667 0.00 0.00 0.00 2.71
331 333 3.577848 CACATTCATTGGTCCTTTTCCCA 59.422 43.478 0.00 0.00 0.00 4.37
352 354 3.686726 CACTAATCAGAGCAACTCCAACC 59.313 47.826 0.00 0.00 0.00 3.77
437 440 5.291971 GGCGTCCGTCCTATTTTAGATTTA 58.708 41.667 0.00 0.00 0.00 1.40
445 448 5.699915 GTCCTATTTTAGATTTAGGTCGGCC 59.300 44.000 0.00 0.00 35.13 6.13
446 449 5.367352 TCCTATTTTAGATTTAGGTCGGCCA 59.633 40.000 9.71 0.00 35.13 5.36
603 606 1.347062 TCACCACACAGTATGCTGGA 58.653 50.000 15.65 0.00 46.62 3.86
704 708 4.020378 CCGTTTTGGTCGGTGCGG 62.020 66.667 0.00 0.00 42.62 5.69
729 733 0.534412 CCGGAGTTGCTCTCACATCT 59.466 55.000 0.00 0.00 44.40 2.90
748 752 6.306356 CACATCTTTTGATTTGTCGATTGGAC 59.694 38.462 0.00 0.00 40.71 4.02
1593 1665 3.869272 GTTGAGCTGATGCGGCGG 61.869 66.667 9.78 0.00 45.42 6.13
1836 2019 0.921896 AGCCACACATGATAAGCCCT 59.078 50.000 0.00 0.00 0.00 5.19
1986 2190 1.445582 CGTGTGCCCCTACTTCGTC 60.446 63.158 0.00 0.00 0.00 4.20
2067 2316 3.873910 AGTGTAAATCGTGCTAGCCATT 58.126 40.909 13.29 5.07 0.00 3.16
2173 2431 6.992063 ATCTTGATGTAATTGGTGTCTGAC 57.008 37.500 0.00 0.00 0.00 3.51
2590 2966 5.065914 CCCCATGGATATGTGAAACTACAG 58.934 45.833 15.22 0.00 38.04 2.74
2759 3158 4.252073 TGTTCAACTTGCATGCTTTGTTT 58.748 34.783 20.33 2.11 0.00 2.83
2760 3159 4.329528 TGTTCAACTTGCATGCTTTGTTTC 59.670 37.500 20.33 12.95 0.00 2.78
2761 3160 3.456280 TCAACTTGCATGCTTTGTTTCC 58.544 40.909 20.33 0.00 0.00 3.13
2826 3244 6.890663 TCTGTTTGTTTTTCTTGAATGCTG 57.109 33.333 0.00 0.00 0.00 4.41
2897 3315 6.834168 TCAATGTTTTAGGGTTTCAGATCC 57.166 37.500 0.00 0.00 0.00 3.36
2986 3410 3.648339 TTTGGTCTCTGCTGCATTTTC 57.352 42.857 1.31 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.108138 CATCAGGTTGTCCGGAGACC 60.108 60.000 23.44 23.44 42.81 3.85
35 36 1.866015 ATCATCAGGTTGTCCGGAGA 58.134 50.000 3.06 0.00 40.87 3.71
41 42 2.424956 GCCCTCAAATCATCAGGTTGTC 59.575 50.000 0.00 0.00 0.00 3.18
72 73 0.393820 AAAAACGACCTACCCGAGCA 59.606 50.000 0.00 0.00 0.00 4.26
143 144 2.356135 GGAGCATCTACAGCCGAAAAA 58.644 47.619 0.00 0.00 33.73 1.94
145 146 0.178068 GGGAGCATCTACAGCCGAAA 59.822 55.000 0.00 0.00 33.73 3.46
187 188 4.445453 TGATGTATCTTGCTACTTGGCTG 58.555 43.478 0.00 0.00 0.00 4.85
192 193 9.899226 GTTTCTTTTTGATGTATCTTGCTACTT 57.101 29.630 0.00 0.00 0.00 2.24
199 200 8.912988 TGTTGGAGTTTCTTTTTGATGTATCTT 58.087 29.630 0.00 0.00 0.00 2.40
263 265 2.222213 CCGCTTTCACGTGTTCATGTTA 59.778 45.455 16.51 0.00 0.00 2.41
282 284 2.226912 AGACTCGTTTGACTCTTCTCCG 59.773 50.000 0.00 0.00 0.00 4.63
314 316 4.733077 TTAGTGGGAAAAGGACCAATGA 57.267 40.909 0.00 0.00 38.73 2.57
331 333 3.617531 CGGTTGGAGTTGCTCTGATTAGT 60.618 47.826 0.00 0.00 0.00 2.24
352 354 3.047877 GTCTGTTTGGGTCGGCCG 61.048 66.667 22.12 22.12 34.97 6.13
558 561 4.762765 TGTTTTGAAGCCGGTATTGTATGT 59.237 37.500 1.90 0.00 0.00 2.29
612 615 1.630244 GACATGTGTGCTGACCGCTC 61.630 60.000 1.15 0.00 40.11 5.03
646 650 2.052104 CCTGCCGACCCATTTTCCC 61.052 63.158 0.00 0.00 0.00 3.97
649 653 3.061848 CGCCTGCCGACCCATTTT 61.062 61.111 0.00 0.00 40.02 1.82
704 708 2.508663 GAGCAACTCCGGGCGTAC 60.509 66.667 0.00 0.00 34.54 3.67
729 733 7.737972 TTCTAGTCCAATCGACAAATCAAAA 57.262 32.000 0.00 0.00 44.66 2.44
748 752 0.529773 TGCGGTGGCGCTATTTCTAG 60.530 55.000 7.64 0.00 44.10 2.43
1508 1580 2.452114 CCTCCCAGTCCAGTCCCT 59.548 66.667 0.00 0.00 0.00 4.20
1634 1706 1.964608 CTCCTTCTGCTGGATCGGCA 61.965 60.000 10.74 10.74 44.04 5.69
1986 2190 2.554032 GTGGTTCATTCAGTTGGTCCAG 59.446 50.000 0.00 0.00 0.00 3.86
2150 2408 6.715280 AGTCAGACACCAATTACATCAAGAT 58.285 36.000 2.66 0.00 0.00 2.40
2258 2600 0.379669 GCAGAGAAATGGGTGCGATG 59.620 55.000 0.00 0.00 0.00 3.84
2590 2966 0.235926 GCAAGACTCGCCAACACTTC 59.764 55.000 0.00 0.00 0.00 3.01
2759 3158 6.182627 AGTTATGCTGAATTCAGACAATGGA 58.817 36.000 34.43 12.62 46.59 3.41
2760 3159 6.446781 AGTTATGCTGAATTCAGACAATGG 57.553 37.500 34.43 11.44 46.59 3.16
2761 3160 9.499585 CTTTAGTTATGCTGAATTCAGACAATG 57.500 33.333 34.43 17.63 46.59 2.82
2910 3328 6.950842 TGTCCTTCATTTGATATGAGACAGT 58.049 36.000 4.63 0.00 32.14 3.55


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

AutoCloner maintained by Alex Coulton.