Multiple sequence alignment - TraesCS7D01G427600

Loading Multiple Alignment...

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 TraesCS7D01G427600 chr7D 100.000 2420 0 0 1 2420 548608693 548611112 0.000000e+00 4470
1 TraesCS7D01G427600 chr7D 94.449 1189 52 6 232 1413 548617098 548618279 0.000000e+00 1818
2 TraesCS7D01G427600 chr7D 78.301 1931 320 50 279 2171 581271645 581273514 0.000000e+00 1153
3 TraesCS7D01G427600 chr7D 77.618 1528 247 56 279 1762 581284186 581285662 0.000000e+00 839
4 TraesCS7D01G427600 chr7D 78.362 1160 188 30 273 1424 581039864 581040968 0.000000e+00 693
5 TraesCS7D01G427600 chr7D 83.621 464 65 8 1823 2279 548619839 548620298 2.220000e-115 425
6 TraesCS7D01G427600 chr7D 85.909 220 24 6 1531 1748 548619624 548619838 6.730000e-56 228
7 TraesCS7D01G427600 chr7D 71.242 1151 242 49 278 1413 581452438 581453514 2.440000e-50 209
8 TraesCS7D01G427600 chr7D 91.781 73 2 2 1 69 548616630 548616702 5.510000e-17 99
9 TraesCS7D01G427600 chr7A 90.730 1424 110 9 1 1413 632518248 632519660 0.000000e+00 1879
10 TraesCS7D01G427600 chr7A 90.796 1282 80 12 1 1280 632383043 632384288 0.000000e+00 1679
11 TraesCS7D01G427600 chr7A 93.192 1087 53 9 1349 2420 632384317 632385397 0.000000e+00 1578
12 TraesCS7D01G427600 chr7A 77.681 914 164 20 519 1424 673013263 673014144 2.760000e-144 521
13 TraesCS7D01G427600 chr7A 74.283 1221 218 52 278 1458 721024714 721023550 6.180000e-116 427
14 TraesCS7D01G427600 chr7A 83.871 248 25 7 1503 1748 632519708 632519942 3.130000e-54 222
15 TraesCS7D01G427600 chr5D 76.498 1702 282 66 279 1899 289687142 289688806 0.000000e+00 819
16 TraesCS7D01G427600 chr7B 73.992 1315 274 45 279 1569 649404119 649405389 2.820000e-129 472
17 TraesCS7D01G427600 chr7B 76.875 800 151 25 278 1051 724982610 724981819 2.880000e-114 422
18 TraesCS7D01G427600 chr7B 73.397 1154 257 33 279 1413 649448474 649449596 3.770000e-103 385
19 TraesCS7D01G427600 chr7B 78.396 611 107 15 279 872 724168649 724169251 8.170000e-100 374
20 TraesCS7D01G427600 chr7B 72.743 1152 267 31 279 1413 649458039 649459160 6.410000e-91 344
21 TraesCS7D01G427600 chr7B 74.100 1000 176 42 1057 2007 648905751 648906716 3.860000e-88 335
22 TraesCS7D01G427600 chr7B 84.615 338 48 3 283 618 648904798 648905133 1.390000e-87 333
23 TraesCS7D01G427600 chr7B 79.124 388 71 6 305 688 648435061 648435442 2.390000e-65 259
24 TraesCS7D01G427600 chrUn 73.397 1154 257 33 279 1413 286625867 286626989 3.770000e-103 385
25 TraesCS7D01G427600 chrUn 74.806 643 110 36 1026 1656 87735025 87735627 2.400000e-60 243
26 TraesCS7D01G427600 chr4A 79.039 458 84 5 286 740 84934827 84935275 1.090000e-78 303


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 TraesCS7D01G427600 chr7D 548608693 548611112 2419 False 4470.0 4470 100.0000 1 2420 1 chr7D.!!$F1 2419
1 TraesCS7D01G427600 chr7D 581271645 581273514 1869 False 1153.0 1153 78.3010 279 2171 1 chr7D.!!$F3 1892
2 TraesCS7D01G427600 chr7D 581284186 581285662 1476 False 839.0 839 77.6180 279 1762 1 chr7D.!!$F4 1483
3 TraesCS7D01G427600 chr7D 581039864 581040968 1104 False 693.0 693 78.3620 273 1424 1 chr7D.!!$F2 1151
4 TraesCS7D01G427600 chr7D 548616630 548620298 3668 False 642.5 1818 88.9400 1 2279 4 chr7D.!!$F6 2278
5 TraesCS7D01G427600 chr7D 581452438 581453514 1076 False 209.0 209 71.2420 278 1413 1 chr7D.!!$F5 1135
6 TraesCS7D01G427600 chr7A 632383043 632385397 2354 False 1628.5 1679 91.9940 1 2420 2 chr7A.!!$F2 2419
7 TraesCS7D01G427600 chr7A 632518248 632519942 1694 False 1050.5 1879 87.3005 1 1748 2 chr7A.!!$F3 1747
8 TraesCS7D01G427600 chr7A 673013263 673014144 881 False 521.0 521 77.6810 519 1424 1 chr7A.!!$F1 905
9 TraesCS7D01G427600 chr7A 721023550 721024714 1164 True 427.0 427 74.2830 278 1458 1 chr7A.!!$R1 1180
10 TraesCS7D01G427600 chr5D 289687142 289688806 1664 False 819.0 819 76.4980 279 1899 1 chr5D.!!$F1 1620
11 TraesCS7D01G427600 chr7B 649404119 649405389 1270 False 472.0 472 73.9920 279 1569 1 chr7B.!!$F2 1290
12 TraesCS7D01G427600 chr7B 724981819 724982610 791 True 422.0 422 76.8750 278 1051 1 chr7B.!!$R1 773
13 TraesCS7D01G427600 chr7B 649448474 649449596 1122 False 385.0 385 73.3970 279 1413 1 chr7B.!!$F3 1134
14 TraesCS7D01G427600 chr7B 724168649 724169251 602 False 374.0 374 78.3960 279 872 1 chr7B.!!$F5 593
15 TraesCS7D01G427600 chr7B 649458039 649459160 1121 False 344.0 344 72.7430 279 1413 1 chr7B.!!$F4 1134
16 TraesCS7D01G427600 chr7B 648904798 648906716 1918 False 334.0 335 79.3575 283 2007 2 chr7B.!!$F6 1724
17 TraesCS7D01G427600 chrUn 286625867 286626989 1122 False 385.0 385 73.3970 279 1413 1 chrUn.!!$F2 1134
18 TraesCS7D01G427600 chrUn 87735025 87735627 602 False 243.0 243 74.8060 1026 1656 1 chrUn.!!$F1 630

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
121 126 0.178929 GTCGACTAGGGGATGGGGAT 60.179 60.0 8.7 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 3593 0.796312 CGCTCAAACACTACGCCAAT 59.204 50.0 0.0 0.0 0.0 3.16 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
109 114 1.748122 GCCTCACTCCCGTCGACTA 60.748 63.158 14.70 0.00 0.00 2.59
117 122 3.444737 CCGTCGACTAGGGGATGG 58.555 66.667 14.70 8.60 33.33 3.51
118 123 2.201022 CCGTCGACTAGGGGATGGG 61.201 68.421 14.70 0.00 36.00 4.00
119 124 2.201022 CGTCGACTAGGGGATGGGG 61.201 68.421 14.70 0.00 0.00 4.96
120 125 1.232216 GTCGACTAGGGGATGGGGA 59.768 63.158 8.70 0.00 0.00 4.81
121 126 0.178929 GTCGACTAGGGGATGGGGAT 60.179 60.000 8.70 0.00 0.00 3.85
209 214 4.227134 CCTCCCGCCTCCATGTCG 62.227 72.222 0.00 0.00 0.00 4.35
403 641 2.365635 CCCTCATCGACCACCCCT 60.366 66.667 0.00 0.00 0.00 4.79
464 724 2.618241 TCTACGACAACAAGTACACCGT 59.382 45.455 0.00 0.00 32.62 4.83
638 1125 2.182030 CGCCGAGGGTGAAGAGTC 59.818 66.667 0.00 0.00 34.74 3.36
835 1358 2.531206 GAGTGGCAGTGTATTCGTCTC 58.469 52.381 0.00 0.00 0.00 3.36
862 1385 5.104067 ACTGGAGGATGGGTTTATAAGGAAC 60.104 44.000 0.00 0.00 0.00 3.62
899 1422 1.213296 ATTAGGCCCATTGACCGTCT 58.787 50.000 0.00 0.00 0.00 4.18
1413 2008 3.475575 TGCAGAGTTACAGTCATTGCAA 58.524 40.909 0.00 0.00 37.17 4.08
1424 2020 6.092955 ACAGTCATTGCAAATTTGACATCT 57.907 33.333 25.66 9.34 38.09 2.90
1447 2052 5.001232 TGTCTGAGTTGGTGGCTTTATAAC 58.999 41.667 0.00 0.00 0.00 1.89
1544 3422 6.480763 TGGGCTATTGTTTTATCTGACTGAA 58.519 36.000 0.00 0.00 0.00 3.02
1546 3424 6.458888 GGGCTATTGTTTTATCTGACTGAAGC 60.459 42.308 0.00 0.00 0.00 3.86
1548 3426 7.185453 GCTATTGTTTTATCTGACTGAAGCAG 58.815 38.462 0.00 0.00 37.52 4.24
1611 3505 7.016153 AGTGAACTTGGGTGATTAGTTATCA 57.984 36.000 0.00 0.00 40.96 2.15
1616 3510 7.923414 ACTTGGGTGATTAGTTATCAAAGTC 57.077 36.000 3.09 0.00 44.62 3.01
1698 3593 5.662208 TCCTACCTCCATGTATTCGGTTAAA 59.338 40.000 0.00 0.00 0.00 1.52
1837 3770 7.363431 TGATCAGTTGTCTGCTAACGATATAG 58.637 38.462 0.00 0.00 41.10 1.31
1872 3805 8.730680 ACTGTGCTAATGGTATAACTTTTGAAG 58.269 33.333 2.73 0.50 0.00 3.02
1969 3907 6.095860 TGCTGATATCAAACATTAGCAAGCTT 59.904 34.615 6.90 0.00 40.72 3.74
2094 4044 6.492087 TGTTTGGTAGGCAGCTTAAAATAGTT 59.508 34.615 0.00 0.00 0.00 2.24
2171 4126 2.478370 CCAAGATGCCTGTAATGTTGCG 60.478 50.000 0.00 0.00 29.35 4.85
2190 4145 1.409064 CGCATAAGCTCCAGTCCAGTA 59.591 52.381 0.00 0.00 39.10 2.74
2204 4159 2.031682 GTCCAGTACAACTTTGCAGCAG 60.032 50.000 0.00 0.00 0.00 4.24
2323 4278 2.553904 CCAAGCCTCCACACAGATTTCT 60.554 50.000 0.00 0.00 0.00 2.52
2341 4296 1.967779 TCTGTTTCATCTCACGGTCCA 59.032 47.619 0.00 0.00 0.00 4.02
2356 4311 2.144078 TCCAGGACCTCGCACCAAA 61.144 57.895 0.00 0.00 0.00 3.28
2360 4315 0.822121 AGGACCTCGCACCAAAAACC 60.822 55.000 0.00 0.00 0.00 3.27
2396 4351 2.889512 GGAACCCACTCCCTTGATTTT 58.110 47.619 0.00 0.00 0.00 1.82
2398 4353 3.258372 GGAACCCACTCCCTTGATTTTTC 59.742 47.826 0.00 0.00 0.00 2.29
2400 4355 2.158519 ACCCACTCCCTTGATTTTTCGT 60.159 45.455 0.00 0.00 0.00 3.85
2404 4359 3.123621 CACTCCCTTGATTTTTCGTCTCG 59.876 47.826 0.00 0.00 0.00 4.04
2413 4368 2.719426 TTTTCGTCTCGTTCCTCTCC 57.281 50.000 0.00 0.00 0.00 3.71
2414 4369 0.886563 TTTCGTCTCGTTCCTCTCCC 59.113 55.000 0.00 0.00 0.00 4.30
2417 4372 1.305046 GTCTCGTTCCTCTCCCCCA 60.305 63.158 0.00 0.00 0.00 4.96
2418 4373 1.000486 TCTCGTTCCTCTCCCCCAG 60.000 63.158 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 76 1.668419 CGAGGCTTAACAGATTGGGG 58.332 55.000 0.00 0.00 0.00 4.96
113 118 1.889829 CTACGTCTGAGGATCCCCATC 59.110 57.143 8.55 0.00 33.88 3.51
114 119 1.481428 CCTACGTCTGAGGATCCCCAT 60.481 57.143 8.55 0.00 35.99 4.00
115 120 0.106167 CCTACGTCTGAGGATCCCCA 60.106 60.000 8.55 0.63 35.99 4.96
117 122 1.777941 AACCTACGTCTGAGGATCCC 58.222 55.000 8.55 0.11 37.53 3.85
118 123 2.758979 TGAAACCTACGTCTGAGGATCC 59.241 50.000 9.86 2.48 37.53 3.36
119 124 4.657436 ATGAAACCTACGTCTGAGGATC 57.343 45.455 9.86 7.86 37.53 3.36
120 125 4.712337 AGAATGAAACCTACGTCTGAGGAT 59.288 41.667 9.86 0.00 37.53 3.24
121 126 4.087182 AGAATGAAACCTACGTCTGAGGA 58.913 43.478 9.86 0.00 37.53 3.71
633 1120 0.886490 ACACGACGTAACGGGACTCT 60.886 55.000 5.85 0.00 39.16 3.24
638 1125 1.286354 ATTGCACACGACGTAACGGG 61.286 55.000 0.00 0.00 42.75 5.28
835 1358 5.594317 CCTTATAAACCCATCCTCCAGTTTG 59.406 44.000 0.00 0.00 34.46 2.93
862 1385 6.095377 GCCTAATTTGTTTGTTCCATCTCTG 58.905 40.000 0.00 0.00 0.00 3.35
903 1429 5.382618 AGCCATCAAGAAAGACAAATGTC 57.617 39.130 5.40 5.40 45.08 3.06
1424 2020 3.788227 ATAAAGCCACCAACTCAGACA 57.212 42.857 0.00 0.00 0.00 3.41
1447 2052 2.158449 GTGCTTGTCGAAGATCCACTTG 59.842 50.000 0.00 0.00 40.67 3.16
1485 2093 7.676683 ACATACCAAGTAGACTGTTCCATAT 57.323 36.000 0.00 0.00 0.00 1.78
1486 2094 7.490657 AACATACCAAGTAGACTGTTCCATA 57.509 36.000 0.00 0.00 0.00 2.74
1487 2095 6.374417 AACATACCAAGTAGACTGTTCCAT 57.626 37.500 0.00 0.00 0.00 3.41
1488 2096 5.818678 AACATACCAAGTAGACTGTTCCA 57.181 39.130 0.00 0.00 0.00 3.53
1499 2107 4.037923 CCAGTTCAAGCAAACATACCAAGT 59.962 41.667 0.00 0.00 0.00 3.16
1546 3424 5.911280 CACTCGAAATATAAAAGCATGCCTG 59.089 40.000 15.66 0.00 0.00 4.85
1548 3426 5.682862 CACACTCGAAATATAAAAGCATGCC 59.317 40.000 15.66 0.00 0.00 4.40
1611 3505 6.183360 GCAACAGAAAGTTCAGTACAGACTTT 60.183 38.462 16.29 16.29 38.74 2.66
1616 3510 4.024556 CAGGCAACAGAAAGTTCAGTACAG 60.025 45.833 0.00 0.00 38.74 2.74
1698 3593 0.796312 CGCTCAAACACTACGCCAAT 59.204 50.000 0.00 0.00 0.00 3.16
1837 3770 5.880054 ACCATTAGCACAGTTTGACATAC 57.120 39.130 0.00 0.00 0.00 2.39
1872 3805 7.617041 ACCATTAGCAGTAGAGAAAATTGAC 57.383 36.000 0.00 0.00 0.00 3.18
1883 3816 9.528018 TTTTTCTTTTCAAACCATTAGCAGTAG 57.472 29.630 0.00 0.00 0.00 2.57
1969 3907 5.125356 ACATGAATATCACGATCCAAGCAA 58.875 37.500 0.00 0.00 0.00 3.91
2094 4044 7.449827 CGAACAGTGTCGCTTATTTATGTAAA 58.550 34.615 0.00 0.00 33.66 2.01
2171 4126 2.168521 TGTACTGGACTGGAGCTTATGC 59.831 50.000 0.00 0.00 40.05 3.14
2204 4159 6.991485 TCGAAACTCAAAATTCAGAAATGC 57.009 33.333 0.00 0.00 0.00 3.56
2241 4196 3.349006 AGCCACGCTGTTGCTTCG 61.349 61.111 2.31 0.00 37.57 3.79
2262 4217 0.607217 TGTTGCAGAGCCATGACAGG 60.607 55.000 0.00 0.00 0.00 4.00
2323 4278 1.001974 CCTGGACCGTGAGATGAAACA 59.998 52.381 0.00 0.00 0.00 2.83
2341 4296 0.822121 GGTTTTTGGTGCGAGGTCCT 60.822 55.000 0.00 0.00 0.00 3.85
2349 4304 2.432874 AGTTACAAGGGGTTTTTGGTGC 59.567 45.455 0.00 0.00 0.00 5.01
2356 4311 1.202964 CCGGGAAGTTACAAGGGGTTT 60.203 52.381 0.00 0.00 0.00 3.27
2360 4315 0.694196 TTCCCGGGAAGTTACAAGGG 59.306 55.000 32.53 10.78 40.16 3.95
2396 4351 0.964358 GGGGAGAGGAACGAGACGAA 60.964 60.000 0.00 0.00 0.00 3.85
2398 4353 2.416432 GGGGGAGAGGAACGAGACG 61.416 68.421 0.00 0.00 0.00 4.18
2400 4355 1.000486 CTGGGGGAGAGGAACGAGA 60.000 63.158 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.