Multiple sequence alignment - TraesCS7A01G038700

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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 TraesCS7A01G038700 chr7A 100.000 2222 0 0 1 2222 17368998 17371219 0.000000e+00 4104.0
1 TraesCS7A01G038700 chr7A 82.000 100 16 2 2063 2161 54868054 54867956 1.410000e-12 84.2
2 TraesCS7A01G038700 chr5A 96.913 1555 43 5 1 1551 23905548 23903995 0.000000e+00 2601.0
3 TraesCS7A01G038700 chr5A 95.517 1539 65 4 1 1537 33881955 33880419 0.000000e+00 2457.0
4 TraesCS7A01G038700 chr5A 79.365 126 19 5 2036 2160 3164096 3163977 5.090000e-12 82.4
5 TraesCS7A01G038700 chr3A 95.912 1541 58 4 1 1537 11605919 11604380 0.000000e+00 2492.0
6 TraesCS7A01G038700 chr3A 95.847 1541 59 4 1 1537 11599031 11597492 0.000000e+00 2486.0
7 TraesCS7A01G038700 chr3A 95.452 1539 65 4 1 1537 684743942 684745477 0.000000e+00 2449.0
8 TraesCS7A01G038700 chr3A 95.387 1539 65 4 1 1537 459623244 459621710 0.000000e+00 2444.0
9 TraesCS7A01G038700 chr4B 95.517 1539 64 4 1 1537 604142986 604144521 0.000000e+00 2455.0
10 TraesCS7A01G038700 chr4B 95.387 1539 65 4 1 1537 85985498 85987032 0.000000e+00 2444.0
11 TraesCS7A01G038700 chr4B 82.796 93 14 2 2063 2154 100941383 100941292 5.090000e-12 82.4
12 TraesCS7A01G038700 chr4B 100.000 29 0 0 1838 1866 240119725 240119697 1.000000e-03 54.7
13 TraesCS7A01G038700 chr2B 95.192 1539 69 4 1 1537 721723156 721724691 0.000000e+00 2427.0
14 TraesCS7A01G038700 chr2B 81.897 116 15 5 2050 2161 36628070 36627957 2.350000e-15 93.5
15 TraesCS7A01G038700 chr2B 82.022 89 14 2 2067 2154 277252236 277252323 8.510000e-10 75.0
16 TraesCS7A01G038700 chr7D 90.364 467 17 6 1779 2222 17872853 17873314 2.460000e-164 588.0
17 TraesCS7A01G038700 chr7D 92.245 245 9 2 1539 1783 17872582 17872816 2.730000e-89 339.0
18 TraesCS7A01G038700 chr4D 84.615 104 12 4 2053 2154 505493850 505493951 1.400000e-17 100.0
19 TraesCS7A01G038700 chr6D 78.621 145 23 7 2022 2161 25832553 25832412 3.040000e-14 89.8
20 TraesCS7A01G038700 chr7B 78.740 127 18 7 2031 2154 99093110 99093230 2.370000e-10 76.8
21 TraesCS7A01G038700 chr5B 80.208 96 15 4 2063 2156 578793883 578793976 3.960000e-08 69.4
22 TraesCS7A01G038700 chr6A 100.000 29 0 0 1838 1866 479397176 479397148 1.000000e-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 TraesCS7A01G038700 chr7A 17368998 17371219 2221 False 4104.0 4104 100.0000 1 2222 1 chr7A.!!$F1 2221
1 TraesCS7A01G038700 chr5A 23903995 23905548 1553 True 2601.0 2601 96.9130 1 1551 1 chr5A.!!$R2 1550
2 TraesCS7A01G038700 chr5A 33880419 33881955 1536 True 2457.0 2457 95.5170 1 1537 1 chr5A.!!$R3 1536
3 TraesCS7A01G038700 chr3A 11604380 11605919 1539 True 2492.0 2492 95.9120 1 1537 1 chr3A.!!$R2 1536
4 TraesCS7A01G038700 chr3A 11597492 11599031 1539 True 2486.0 2486 95.8470 1 1537 1 chr3A.!!$R1 1536
5 TraesCS7A01G038700 chr3A 684743942 684745477 1535 False 2449.0 2449 95.4520 1 1537 1 chr3A.!!$F1 1536
6 TraesCS7A01G038700 chr3A 459621710 459623244 1534 True 2444.0 2444 95.3870 1 1537 1 chr3A.!!$R3 1536
7 TraesCS7A01G038700 chr4B 604142986 604144521 1535 False 2455.0 2455 95.5170 1 1537 1 chr4B.!!$F2 1536
8 TraesCS7A01G038700 chr4B 85985498 85987032 1534 False 2444.0 2444 95.3870 1 1537 1 chr4B.!!$F1 1536
9 TraesCS7A01G038700 chr2B 721723156 721724691 1535 False 2427.0 2427 95.1920 1 1537 1 chr2B.!!$F2 1536
10 TraesCS7A01G038700 chr7D 17872582 17873314 732 False 463.5 588 91.3045 1539 2222 2 chr7D.!!$F1 683

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
969 972 4.02165 GACACTTTGTCGGCGTGA 57.978 55.556 6.85 0.0 37.67 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 2155 3.073101 GCTCGGACCTAACCCGGT 61.073 66.667 0.0 0.0 46.47 5.28 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
51 52 8.260114 TCTTCAAGTTTGATGACTGCAGATATA 58.740 33.333 23.35 3.47 36.72 0.86
366 367 4.055360 CAACAGTTACGGAGTCATGTGAA 58.945 43.478 0.00 0.00 43.93 3.18
367 368 4.537135 ACAGTTACGGAGTCATGTGAAT 57.463 40.909 0.00 0.00 43.93 2.57
494 495 6.035435 TGTTAAAGTGACGCGTGTAAAGTTTA 59.965 34.615 20.70 15.28 0.00 2.01
546 548 4.227197 CAACCTATCCCTGGAGATAGTGT 58.773 47.826 20.96 17.18 42.82 3.55
615 617 6.184580 ACGTAAAACACACACTGATCAAAA 57.815 33.333 0.00 0.00 0.00 2.44
765 767 6.597280 GGAAATAGACTCTGCATCTTGACTTT 59.403 38.462 0.00 0.00 0.00 2.66
775 777 6.936335 TCTGCATCTTGACTTTTTCAGTATCA 59.064 34.615 0.00 0.00 35.01 2.15
969 972 4.021650 GACACTTTGTCGGCGTGA 57.978 55.556 6.85 0.00 37.67 4.35
1170 1173 1.524621 GGCTAGCGTGCATGATGGT 60.525 57.895 10.93 0.00 34.04 3.55
1211 1214 5.573380 AGCTTTCTAATAGGATGGATGCA 57.427 39.130 0.00 0.00 0.00 3.96
1668 1673 6.444633 CAAAGTAGTAGGTCTTGAGTTCGAA 58.555 40.000 0.00 0.00 0.00 3.71
1722 1727 2.738846 CAGACGAACCAAACAGATCAGG 59.261 50.000 0.00 0.00 0.00 3.86
1725 1730 4.039973 AGACGAACCAAACAGATCAGGTTA 59.960 41.667 0.00 0.00 43.94 2.85
1746 1751 2.352805 GCCAGCTAGTTGTGGGCT 59.647 61.111 5.81 0.00 41.39 5.19
1777 1782 4.785453 GCCTAGGTTGGCGCTGCT 62.785 66.667 11.31 0.00 43.74 4.24
1810 1856 5.626142 TCTGTAATTTTAGCACCACCTTGA 58.374 37.500 0.00 0.00 0.00 3.02
1849 1895 6.811253 TGCTGTAATTTTAGTACCACCTTG 57.189 37.500 0.00 0.00 0.00 3.61
1983 2032 9.908747 TCTTAGTATCTCTTGTAACTAGCTCTT 57.091 33.333 0.00 0.00 0.00 2.85
2036 2092 3.118956 TCGGGCATTTCTTGTTGTTGTTT 60.119 39.130 0.00 0.00 0.00 2.83
2037 2093 3.620821 CGGGCATTTCTTGTTGTTGTTTT 59.379 39.130 0.00 0.00 0.00 2.43
2071 2127 5.351948 TGTATGCTGCTTGTGTAATCCTA 57.648 39.130 0.00 0.00 0.00 2.94
2099 2155 6.201806 CGGTTGATGGCTTTGTTAATTCAAAA 59.798 34.615 0.00 0.00 36.96 2.44
2123 2179 2.169978 GGGTTAGGTCCGAGCATACTTT 59.830 50.000 0.00 0.00 0.00 2.66
2126 2182 4.340381 GGTTAGGTCCGAGCATACTTTAGA 59.660 45.833 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.735315 TCAAACTTGAAGACATGTTGTTTAAGA 58.265 29.630 22.60 10.82 41.36 2.10
51 52 3.758023 TGTGCAGTTTCGAATGATCCAAT 59.242 39.130 0.00 0.00 0.00 3.16
341 342 4.056050 ACATGACTCCGTAACTGTTGTTC 58.944 43.478 0.00 0.00 37.59 3.18
546 548 1.845664 TGGGTTGCACCTGCCTAGA 60.846 57.895 0.00 0.00 38.64 2.43
615 617 9.135189 TGATTAGAATTGCCTTATTTGTGCTAT 57.865 29.630 0.00 0.00 0.00 2.97
775 777 7.540474 TGTCTTACAAAGTAGGATCAAGAGT 57.460 36.000 0.00 0.00 0.00 3.24
935 938 0.391130 GTCTATTCAGCGGGTGCACA 60.391 55.000 20.43 0.00 46.23 4.57
969 972 3.996124 AGCTCCGTTCGCAGCACT 61.996 61.111 10.67 0.00 38.18 4.40
1184 1187 7.826252 GCATCCATCCTATTAGAAAGCTAATCA 59.174 37.037 0.00 0.00 44.20 2.57
1211 1214 9.726438 CCATCCTATTAAAAACTTATCTCGGAT 57.274 33.333 0.00 0.00 0.00 4.18
1556 1561 5.549742 AACAGAATTGGGCATTTTTCTGA 57.450 34.783 19.31 0.00 44.97 3.27
1698 1703 0.834612 TCTGTTTGGTTCGTCTGGGT 59.165 50.000 0.00 0.00 0.00 4.51
1699 1704 2.076863 GATCTGTTTGGTTCGTCTGGG 58.923 52.381 0.00 0.00 0.00 4.45
1700 1705 2.738846 CTGATCTGTTTGGTTCGTCTGG 59.261 50.000 0.00 0.00 0.00 3.86
1701 1706 2.738846 CCTGATCTGTTTGGTTCGTCTG 59.261 50.000 0.00 0.00 0.00 3.51
1702 1707 2.368875 ACCTGATCTGTTTGGTTCGTCT 59.631 45.455 0.00 0.00 0.00 4.18
1703 1708 2.767505 ACCTGATCTGTTTGGTTCGTC 58.232 47.619 0.00 0.00 0.00 4.20
1704 1709 2.930826 ACCTGATCTGTTTGGTTCGT 57.069 45.000 0.00 0.00 0.00 3.85
1705 1710 4.154195 CCTTAACCTGATCTGTTTGGTTCG 59.846 45.833 6.53 0.00 42.14 3.95
1706 1711 4.459337 CCCTTAACCTGATCTGTTTGGTTC 59.541 45.833 6.53 0.00 42.14 3.62
1707 1712 4.407365 CCCTTAACCTGATCTGTTTGGTT 58.593 43.478 6.53 0.00 44.03 3.67
1708 1713 3.814316 GCCCTTAACCTGATCTGTTTGGT 60.814 47.826 6.53 0.00 0.00 3.67
1722 1727 2.084546 CACAACTAGCTGGCCCTTAAC 58.915 52.381 0.00 0.00 0.00 2.01
1725 1730 1.380302 CCACAACTAGCTGGCCCTT 59.620 57.895 0.00 0.00 0.00 3.95
1787 1833 5.626142 TCAAGGTGGTGCTAAAATTACAGA 58.374 37.500 0.00 0.00 0.00 3.41
1983 2032 6.112734 ACACTCTGAACTTACAACACATCAA 58.887 36.000 0.00 0.00 0.00 2.57
2036 2092 6.007936 AGCAGCATACAAATAACACGAAAA 57.992 33.333 0.00 0.00 0.00 2.29
2037 2093 5.621197 AGCAGCATACAAATAACACGAAA 57.379 34.783 0.00 0.00 0.00 3.46
2043 2099 7.432252 GGATTACACAAGCAGCATACAAATAAC 59.568 37.037 0.00 0.00 0.00 1.89
2045 2101 6.828273 AGGATTACACAAGCAGCATACAAATA 59.172 34.615 0.00 0.00 0.00 1.40
2046 2102 5.653769 AGGATTACACAAGCAGCATACAAAT 59.346 36.000 0.00 0.00 0.00 2.32
2099 2155 3.073101 GCTCGGACCTAACCCGGT 61.073 66.667 0.00 0.00 46.47 5.28
2117 2173 3.321396 GGCTTAGCCCGAGTCTAAAGTAT 59.679 47.826 13.12 0.00 44.06 2.12
2162 2231 7.818446 CCAATCCAACATCTGAGACTATCTATG 59.182 40.741 0.00 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.