Multiple sequence alignment - TraesCS4B01G170700

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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 TraesCS4B01G170700 chr4B 100.000 4125 0 0 1 4125 373980748 373984872 0.000000e+00 7618.0
1 TraesCS4B01G170700 chr4D 97.941 2622 45 5 601 3221 300782939 300785552 0.000000e+00 4534.0
2 TraesCS4B01G170700 chr4D 93.689 618 23 8 1 612 300782314 300782921 0.000000e+00 911.0
3 TraesCS4B01G170700 chr4A 94.928 2642 87 31 601 3221 182219734 182217119 0.000000e+00 4093.0
4 TraesCS4B01G170700 chr4A 93.740 623 22 9 1 615 182220362 182219749 0.000000e+00 918.0
5 TraesCS4B01G170700 chr1A 97.286 921 9 2 3221 4125 710284 709364 0.000000e+00 1548.0
6 TraesCS4B01G170700 chr2D 78.087 575 116 9 1096 1665 56202690 56202121 5.070000e-94 355.0
7 TraesCS4B01G170700 chr2A 78.049 574 116 9 1097 1665 57831978 57831410 1.820000e-93 353.0
8 TraesCS4B01G170700 chr2B 77.453 581 121 9 1096 1671 88932537 88931962 5.110000e-89 339.0
9 TraesCS4B01G170700 chr5D 100.000 29 0 0 3221 3249 318009672 318009700 2.000000e-03 54.7


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 TraesCS4B01G170700 chr4B 373980748 373984872 4124 False 7618.0 7618 100.000 1 4125 1 chr4B.!!$F1 4124
1 TraesCS4B01G170700 chr4D 300782314 300785552 3238 False 2722.5 4534 95.815 1 3221 2 chr4D.!!$F1 3220
2 TraesCS4B01G170700 chr4A 182217119 182220362 3243 True 2505.5 4093 94.334 1 3221 2 chr4A.!!$R1 3220
3 TraesCS4B01G170700 chr1A 709364 710284 920 True 1548.0 1548 97.286 3221 4125 1 chr1A.!!$R1 904
4 TraesCS4B01G170700 chr2D 56202121 56202690 569 True 355.0 355 78.087 1096 1665 1 chr2D.!!$R1 569
5 TraesCS4B01G170700 chr2A 57831410 57831978 568 True 353.0 353 78.049 1097 1665 1 chr2A.!!$R1 568
6 TraesCS4B01G170700 chr2B 88931962 88932537 575 True 339.0 339 77.453 1096 1671 1 chr2B.!!$R1 575

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
894 935 0.041833 TCCCTTAGACAGAGCTGCCT 59.958 55.0 0.0 0.0 0.0 4.75 F
2235 2281 0.321671 CTGTGGAGTATATGGCCCCG 59.678 60.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2732 2798 0.835941 AGGCATCAGTCATGTCTCCC 59.164 55.0 0.0 0.0 44.86 4.30 R
3687 3754 0.106149 CGGGGGTAATAGTGGTGAGC 59.894 60.0 0.0 0.0 0.00 4.26 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
38 39 0.390860 GGATCTGTGGCGCTCATAGT 59.609 55.000 7.64 2.86 36.22 2.12
53 54 0.764752 ATAGTGGGCAGGGGCTAGTC 60.765 60.000 0.00 0.00 40.87 2.59
83 85 2.620585 GGGATTTAGCTGATGCCTTGAC 59.379 50.000 13.08 0.00 40.80 3.18
86 88 3.439857 TTTAGCTGATGCCTTGACCTT 57.560 42.857 0.00 0.00 40.80 3.50
123 125 2.673368 CCTTCTGAGTGTAATTCGGTGC 59.327 50.000 0.00 0.00 29.93 5.01
124 126 1.990799 TCTGAGTGTAATTCGGTGCG 58.009 50.000 0.00 0.00 29.93 5.34
139 141 6.996562 TTCGGTGCGTGTATATTATGTTAG 57.003 37.500 0.00 0.00 0.00 2.34
144 146 8.329583 CGGTGCGTGTATATTATGTTAGAAAAA 58.670 33.333 0.00 0.00 0.00 1.94
145 147 9.646336 GGTGCGTGTATATTATGTTAGAAAAAG 57.354 33.333 0.00 0.00 0.00 2.27
164 166 9.281371 AGAAAAAGTACTCCTATGGTTTTGTAC 57.719 33.333 0.00 0.00 0.00 2.90
233 235 6.560253 TTTGTGAGCTCTCCAATAAGTTTC 57.440 37.500 16.19 0.00 0.00 2.78
289 294 1.396653 GTCCCCATTCTTGGCAGATG 58.603 55.000 0.00 0.00 42.15 2.90
308 313 5.813672 CAGATGGGAATGCCAATTTTAGTTG 59.186 40.000 0.00 0.00 35.15 3.16
505 511 8.960075 GCAAATTACTTTTAGAACACGCTTTAA 58.040 29.630 0.00 0.00 0.00 1.52
530 536 5.839621 TGTCTTTACGTTTAGTCTCTGCTT 58.160 37.500 0.00 0.00 0.00 3.91
540 546 8.251721 ACGTTTAGTCTCTGCTTAAGATAACAT 58.748 33.333 6.67 0.00 33.29 2.71
568 574 4.261322 CCCTACCGATTCAATTTGCAGATG 60.261 45.833 0.00 0.00 0.00 2.90
587 593 6.183360 GCAGATGAGCACATGGTTTTATACTT 60.183 38.462 0.00 0.00 36.82 2.24
894 935 0.041833 TCCCTTAGACAGAGCTGCCT 59.958 55.000 0.00 0.00 0.00 4.75
969 1010 2.622436 ACCGCTAGCTTTCATCAAGAC 58.378 47.619 13.93 0.00 33.80 3.01
1044 1085 5.060506 TCAGTTACAACAACCCATACACAG 58.939 41.667 0.00 0.00 0.00 3.66
1761 1802 7.039270 CCAGTGCTAAAACCAAAACTTACTTT 58.961 34.615 0.00 0.00 0.00 2.66
1860 1901 9.923143 ACAAGGCTTGTTTAGGTAATTTAATTC 57.077 29.630 26.54 0.00 42.22 2.17
2235 2281 0.321671 CTGTGGAGTATATGGCCCCG 59.678 60.000 0.00 0.00 0.00 5.73
2564 2611 2.805657 GCTACGTTCACCTTGACCTTGT 60.806 50.000 0.00 0.00 0.00 3.16
2732 2798 2.502947 TGATCCCTGGATGTCTCTTGTG 59.497 50.000 2.75 0.00 34.60 3.33
2756 2822 3.079578 AGACATGACTGATGCCTTGTTG 58.920 45.455 0.00 0.00 35.15 3.33
2812 2878 3.906720 TGCCCTTACTATCTCAACACC 57.093 47.619 0.00 0.00 0.00 4.16
3025 3092 1.447643 GAGTATGCCCGTGCTGGAT 59.552 57.895 0.00 0.00 42.00 3.41
3267 3334 3.597255 TGGAACACAAGAACACACGTAA 58.403 40.909 0.00 0.00 0.00 3.18
3356 3423 3.758023 TGGAAAGCATTGATGTCGATGTT 59.242 39.130 10.97 3.46 39.42 2.71
3561 3628 6.762187 TGAGAAAATTCATGTGTGCACAAAAT 59.238 30.769 23.59 15.62 45.41 1.82
3687 3754 1.482593 ACCTCTCTCACCATTTAGGCG 59.517 52.381 0.00 0.00 43.14 5.52
3790 3873 1.126488 GCTCAGTCCATCTCCATCCA 58.874 55.000 0.00 0.00 0.00 3.41
3791 3874 1.698532 GCTCAGTCCATCTCCATCCAT 59.301 52.381 0.00 0.00 0.00 3.41
3811 3894 2.852449 TGCCAGACACAATTTTCCGTA 58.148 42.857 0.00 0.00 0.00 4.02
3833 3916 2.818274 CCCTTAGCAACGGTCGCC 60.818 66.667 0.00 0.00 0.00 5.54
3981 4064 7.221450 AGCACTTCAGGTACTAAACATAACAA 58.779 34.615 0.00 0.00 36.02 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 4.715130 ACGACTAGCCCCTGCCCA 62.715 66.667 0.00 0.00 38.69 5.36
53 54 3.194861 TCAGCTAAATCCCAAATCGACG 58.805 45.455 0.00 0.00 0.00 5.12
83 85 3.968265 AGGACACAATTACCATGGAAGG 58.032 45.455 21.47 5.44 0.00 3.46
86 88 4.288366 TCAGAAGGACACAATTACCATGGA 59.712 41.667 21.47 0.00 0.00 3.41
139 141 8.225777 CGTACAAAACCATAGGAGTACTTTTTC 58.774 37.037 0.00 0.00 32.01 2.29
144 146 4.774200 ACCGTACAAAACCATAGGAGTACT 59.226 41.667 0.00 0.00 32.01 2.73
145 147 5.077134 ACCGTACAAAACCATAGGAGTAC 57.923 43.478 0.00 0.00 0.00 2.73
146 148 5.743636 AACCGTACAAAACCATAGGAGTA 57.256 39.130 0.00 0.00 0.00 2.59
147 149 4.628963 AACCGTACAAAACCATAGGAGT 57.371 40.909 0.00 0.00 0.00 3.85
148 150 7.619964 AATTAACCGTACAAAACCATAGGAG 57.380 36.000 0.00 0.00 0.00 3.69
149 151 7.094291 CCAAATTAACCGTACAAAACCATAGGA 60.094 37.037 0.00 0.00 0.00 2.94
150 152 7.030768 CCAAATTAACCGTACAAAACCATAGG 58.969 38.462 0.00 0.00 0.00 2.57
151 153 7.030768 CCCAAATTAACCGTACAAAACCATAG 58.969 38.462 0.00 0.00 0.00 2.23
164 166 3.672241 GCAGCTAACACCCAAATTAACCG 60.672 47.826 0.00 0.00 0.00 4.44
263 266 1.375523 AAGAATGGGGACGCGTGTC 60.376 57.895 20.70 20.76 44.72 3.67
264 267 1.671054 CAAGAATGGGGACGCGTGT 60.671 57.895 20.70 0.00 0.00 4.49
265 268 2.398554 CCAAGAATGGGGACGCGTG 61.399 63.158 20.70 0.00 43.51 5.34
289 294 3.872696 CCCAACTAAAATTGGCATTCCC 58.127 45.455 0.00 0.00 46.77 3.97
308 313 1.379527 CCTATCCAAACACGAAGCCC 58.620 55.000 0.00 0.00 0.00 5.19
505 511 5.009811 AGCAGAGACTAAACGTAAAGACAGT 59.990 40.000 4.23 0.00 0.00 3.55
558 564 2.453521 ACCATGTGCTCATCTGCAAAT 58.546 42.857 0.00 0.00 45.12 2.32
605 614 9.569122 ACAAATAAGGAAGCTTGTACTAAGAAA 57.431 29.630 2.10 0.00 30.41 2.52
846 887 3.142951 TCCACAAATACCCAAGACAACG 58.857 45.455 0.00 0.00 0.00 4.10
921 962 0.393808 GGCTTCCCGCTACCAATTCA 60.394 55.000 0.00 0.00 39.13 2.57
969 1010 4.392940 ACCAGGATTCAACACTTTGAGAG 58.607 43.478 0.00 0.00 42.79 3.20
987 1028 3.084786 GGAAACCATCTTCAGGAACCAG 58.915 50.000 0.00 0.00 0.00 4.00
1711 1752 6.690098 GCAGATGCAAAACACTACAGATAATG 59.310 38.462 0.00 0.00 41.59 1.90
1761 1802 5.651139 AGATAAAGTCGGTACTTAGTCTGCA 59.349 40.000 0.00 0.00 45.37 4.41
1860 1901 7.231519 TGGATAGGTGTACAGATGAGATTACAG 59.768 40.741 0.00 0.00 0.00 2.74
1874 1920 5.109903 GTTGTCACATCTGGATAGGTGTAC 58.890 45.833 0.00 0.00 46.37 2.90
2089 2135 2.791560 CTGGCGATCATAACACGAAGAG 59.208 50.000 0.00 0.00 0.00 2.85
2235 2281 1.821136 CCTCTGCCCTGAACAATTTCC 59.179 52.381 0.00 0.00 0.00 3.13
2379 2425 7.035004 GTGTGCAAAGAAAAATATATCAGGCA 58.965 34.615 0.00 0.00 0.00 4.75
2732 2798 0.835941 AGGCATCAGTCATGTCTCCC 59.164 55.000 0.00 0.00 44.86 4.30
2756 2822 8.669243 CAAGTCATCTAGATTTAACTTCCAACC 58.331 37.037 16.56 0.00 0.00 3.77
3168 3235 5.240891 TCATCTTACTGTCTTGAGCAAAGG 58.759 41.667 0.00 0.00 36.46 3.11
3246 3313 2.102070 ACGTGTGTTCTTGTGTTCCA 57.898 45.000 0.00 0.00 0.00 3.53
3356 3423 2.610859 GGAGGGCAAGGGAGGACA 60.611 66.667 0.00 0.00 0.00 4.02
3687 3754 0.106149 CGGGGGTAATAGTGGTGAGC 59.894 60.000 0.00 0.00 0.00 4.26
3790 3873 2.238521 ACGGAAAATTGTGTCTGGCAT 58.761 42.857 0.00 0.00 0.00 4.40
3791 3874 1.686355 ACGGAAAATTGTGTCTGGCA 58.314 45.000 0.00 0.00 0.00 4.92
3811 3894 1.750297 ACCGTTGCTAAGGGTTCGT 59.250 52.632 5.06 0.00 46.85 3.85
3833 3916 0.969894 GGTAGGGATGGAGGATGACG 59.030 60.000 0.00 0.00 0.00 4.35
3981 4064 8.908786 TTGATTGAAAGTGTCTGACTAGATTT 57.091 30.769 9.51 4.87 34.94 2.17


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

AutoCloner maintained by Alex Coulton.