Multiple sequence alignment - TraesCS6B01G155200

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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 TraesCS6B01G155200 chr6B 100.000 2564 0 0 415 2978 158154512 158157075 0.000000e+00 4735
1 TraesCS6B01G155200 chr6B 100.000 137 0 0 1 137 158154098 158154234 1.370000e-63 254
2 TraesCS6B01G155200 chr2B 93.339 2567 161 8 415 2978 385154909 385152350 0.000000e+00 3784
3 TraesCS6B01G155200 chr3B 92.443 2567 182 9 415 2978 541570178 541572735 0.000000e+00 3655
4 TraesCS6B01G155200 chr3B 89.441 2538 256 10 443 2975 466654528 466657058 0.000000e+00 3192
5 TraesCS6B01G155200 chr3B 84.354 147 12 3 1 136 541569555 541569701 1.860000e-27 134
6 TraesCS6B01G155200 chr4B 90.955 2565 223 6 415 2975 613914733 613917292 0.000000e+00 3443
7 TraesCS6B01G155200 chr4B 87.980 2346 259 15 638 2975 436303575 436301245 0.000000e+00 2748
8 TraesCS6B01G155200 chr3D 88.834 2418 246 19 568 2975 324402193 324404596 0.000000e+00 2948
9 TraesCS6B01G155200 chr5D 85.742 2574 343 19 415 2978 110339693 110342252 0.000000e+00 2699
10 TraesCS6B01G155200 chr5D 86.190 2462 329 11 523 2978 438819403 438816947 0.000000e+00 2652
11 TraesCS6B01G155200 chr2D 85.636 2541 326 31 444 2978 326414290 326411783 0.000000e+00 2634


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 TraesCS6B01G155200 chr6B 158154098 158157075 2977 False 2494.5 4735 100.0000 1 2978 2 chr6B.!!$F1 2977
1 TraesCS6B01G155200 chr2B 385152350 385154909 2559 True 3784.0 3784 93.3390 415 2978 1 chr2B.!!$R1 2563
2 TraesCS6B01G155200 chr3B 466654528 466657058 2530 False 3192.0 3192 89.4410 443 2975 1 chr3B.!!$F1 2532
3 TraesCS6B01G155200 chr3B 541569555 541572735 3180 False 1894.5 3655 88.3985 1 2978 2 chr3B.!!$F2 2977
4 TraesCS6B01G155200 chr4B 613914733 613917292 2559 False 3443.0 3443 90.9550 415 2975 1 chr4B.!!$F1 2560
5 TraesCS6B01G155200 chr4B 436301245 436303575 2330 True 2748.0 2748 87.9800 638 2975 1 chr4B.!!$R1 2337
6 TraesCS6B01G155200 chr3D 324402193 324404596 2403 False 2948.0 2948 88.8340 568 2975 1 chr3D.!!$F1 2407
7 TraesCS6B01G155200 chr5D 110339693 110342252 2559 False 2699.0 2699 85.7420 415 2978 1 chr5D.!!$F1 2563
8 TraesCS6B01G155200 chr5D 438816947 438819403 2456 True 2652.0 2652 86.1900 523 2978 1 chr5D.!!$R1 2455
9 TraesCS6B01G155200 chr2D 326411783 326414290 2507 True 2634.0 2634 85.6360 444 2978 1 chr2D.!!$R1 2534

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
973 1197 1.046472 TCACCCCGCGATCCTATGTT 61.046 55.000 8.23 0.0 0.0 2.71 F
1483 1711 1.071471 CGGGTCAAGGTGAAGTGCT 59.929 57.895 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
1962 2191 0.615850 GAGGTCAAACCAGGAGGGAG 59.384 60.000 0.00 0.0 41.95 4.30 R
2824 3055 1.905215 CATGGAGGGAGAACTCAGTGT 59.095 52.381 4.23 0.0 39.27 3.55 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
40 41 2.150719 TTTCCTCGCCAACCCTCCA 61.151 57.895 0.00 0.00 0.00 3.86
48 49 4.366684 CAACCCTCCACCAGCCCC 62.367 72.222 0.00 0.00 0.00 5.80
69 70 2.122189 CCTCCATCTCCCCTCCCC 60.122 72.222 0.00 0.00 0.00 4.81
70 71 2.525381 CTCCATCTCCCCTCCCCG 60.525 72.222 0.00 0.00 0.00 5.73
73 74 3.227276 CATCTCCCCTCCCCGACG 61.227 72.222 0.00 0.00 0.00 5.12
477 688 4.748798 CCTCCCCCTGCCAGTCCT 62.749 72.222 0.00 0.00 0.00 3.85
684 895 4.351938 CCGACTCCAACGCCACGA 62.352 66.667 0.00 0.00 0.00 4.35
885 1109 2.972505 CCGCCGTGCTTCAACTGT 60.973 61.111 0.00 0.00 0.00 3.55
925 1149 4.008669 TGGCATGCCCCAACCCAT 62.009 61.111 33.44 0.00 34.56 4.00
936 1160 1.586422 CCAACCCATCGATGTGCTAG 58.414 55.000 23.27 8.03 0.00 3.42
973 1197 1.046472 TCACCCCGCGATCCTATGTT 61.046 55.000 8.23 0.00 0.00 2.71
1290 1518 1.806542 CTCAACGGGATTGTGGTGAAG 59.193 52.381 0.00 0.00 39.54 3.02
1362 1590 2.502492 GCTCCTCATCGCCAGCCTA 61.502 63.158 0.00 0.00 0.00 3.93
1366 1594 1.750930 CTCATCGCCAGCCTACCAT 59.249 57.895 0.00 0.00 0.00 3.55
1408 1636 3.262420 GTCATTCGCAGTATGTCCAAGT 58.738 45.455 0.00 0.00 39.31 3.16
1483 1711 1.071471 CGGGTCAAGGTGAAGTGCT 59.929 57.895 0.00 0.00 0.00 4.40
1520 1748 2.432628 CACCACGCTTCGGGTCTC 60.433 66.667 0.00 0.00 34.45 3.36
1645 1873 2.184322 CCGATGACTCCCACCACG 59.816 66.667 0.00 0.00 0.00 4.94
2207 2437 4.415332 CAGACGGTGGCGTACGCT 62.415 66.667 36.24 19.18 41.60 5.07
2295 2525 4.065281 CGGCGGACTCCTCGGTTT 62.065 66.667 0.00 0.00 0.00 3.27
2323 2553 4.193334 CGAGCGTGCGGAGATCCA 62.193 66.667 0.00 0.00 35.14 3.41
2392 2622 5.532779 CCAGCTCTTCTAGTTGTTCCTTTTT 59.467 40.000 0.00 0.00 34.78 1.94
2582 2813 3.782443 GAATCGACCGCCACCCCT 61.782 66.667 0.00 0.00 0.00 4.79
2625 2856 2.286121 ACGGGGTGATCCATGGGT 60.286 61.111 13.02 3.70 37.22 4.51
2743 2974 2.508439 GAACATCCGCGGCTTCGA 60.508 61.111 23.51 2.08 35.61 3.71
2824 3055 0.971959 GCCATCCAGGAAACCATGCA 60.972 55.000 0.00 0.00 41.22 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
463 673 3.721706 GTCAGGACTGGCAGGGGG 61.722 72.222 20.34 5.44 34.82 5.40
573 784 4.974438 AGACAACCGGGCCTCCCA 62.974 66.667 6.32 0.00 45.83 4.37
738 950 2.035626 CCGGTTCCCATTGCCACT 59.964 61.111 0.00 0.00 0.00 4.00
885 1109 3.842925 GAAGTGCCCGGTCAAGCCA 62.843 63.158 0.00 0.00 36.97 4.75
925 1149 0.532115 TTGCAGAGCTAGCACATCGA 59.468 50.000 18.83 3.62 42.54 3.59
936 1160 3.130160 CCGGCTTCCTTGCAGAGC 61.130 66.667 0.00 5.26 35.71 4.09
989 1213 3.161067 CCGTACATCATGATCTCCTCCT 58.839 50.000 4.86 0.00 0.00 3.69
1189 1417 2.972505 CGTGAAGGCGTTGGCAGT 60.973 61.111 0.00 0.00 42.47 4.40
1247 1475 1.800805 CAAGGTGATCTTGTCGCTGT 58.199 50.000 0.00 0.00 45.81 4.40
1290 1518 2.725008 CACCTCGGCTCGGAGATC 59.275 66.667 9.69 0.00 36.08 2.75
1366 1594 2.731571 GCTCAGACCGGGCCACATA 61.732 63.158 1.76 0.00 0.00 2.29
1385 1613 1.831106 TGGACATACTGCGAATGACCT 59.169 47.619 12.73 0.00 39.14 3.85
1520 1748 1.542544 GTATCCGTCGTCGTTGAAGG 58.457 55.000 0.71 5.56 38.66 3.46
1618 1846 1.497223 GAGTCATCGGCATCAGCAGC 61.497 60.000 0.00 0.00 44.61 5.25
1716 1944 3.621805 TTGACTGGCTCGCGGGAA 61.622 61.111 12.03 0.00 0.00 3.97
1962 2191 0.615850 GAGGTCAAACCAGGAGGGAG 59.384 60.000 0.00 0.00 41.95 4.30
1967 2197 2.221299 CGGGGAGGTCAAACCAGGA 61.221 63.158 0.00 0.00 41.95 3.86
2392 2622 2.202878 GTATGGCCTCAAGCGCGA 60.203 61.111 12.10 0.00 45.17 5.87
2824 3055 1.905215 CATGGAGGGAGAACTCAGTGT 59.095 52.381 4.23 0.00 39.27 3.55
2925 3156 4.286707 GTGGCATCCTTTACCCCTAAAAT 58.713 43.478 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.