Multiple sequence alignment - TraesCS1A01G372300

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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 TraesCS1A01G372300 chr1A 100.000 2643 0 0 537 3179 548788871 548791513 0.000000e+00 4881.0
1 TraesCS1A01G372300 chr1A 89.608 1251 105 13 936 2178 548733310 548734543 0.000000e+00 1567.0
2 TraesCS1A01G372300 chr1A 89.861 1223 90 17 962 2178 548772382 548773576 0.000000e+00 1541.0
3 TraesCS1A01G372300 chr1A 100.000 211 0 0 1 211 548788335 548788545 1.070000e-104 390.0
4 TraesCS1A01G372300 chr1A 79.290 169 27 6 2991 3154 64410281 64410446 9.320000e-21 111.0
5 TraesCS1A01G372300 chr1D 93.920 2681 106 18 537 3178 454812286 454814948 0.000000e+00 3995.0
6 TraesCS1A01G372300 chr1D 87.777 1489 122 34 710 2178 454768817 454770265 0.000000e+00 1687.0
7 TraesCS1A01G372300 chr1D 87.659 1491 102 40 712 2178 454458700 454457268 0.000000e+00 1659.0
8 TraesCS1A01G372300 chr1D 88.174 1353 97 26 846 2178 454493944 454492635 0.000000e+00 1554.0
9 TraesCS1A01G372300 chr1D 88.732 213 22 1 1 211 454811861 454812073 3.150000e-65 259.0
10 TraesCS1A01G372300 chr1D 81.897 116 18 3 2980 3093 107183086 107182972 9.390000e-16 95.3
11 TraesCS1A01G372300 chr1B 93.586 2401 99 25 586 2961 625144815 625147185 0.000000e+00 3530.0
12 TraesCS1A01G372300 chr1B 88.204 1492 112 32 710 2178 625082314 625083764 0.000000e+00 1722.0
13 TraesCS1A01G372300 chr1B 88.922 1354 102 25 832 2174 624970683 624971999 0.000000e+00 1626.0
14 TraesCS1A01G372300 chr1B 85.153 229 26 3 1955 2178 625051984 625052209 8.870000e-56 228.0
15 TraesCS1A01G372300 chr2A 90.826 109 10 0 2 110 434580091 434580199 2.560000e-31 147.0
16 TraesCS1A01G372300 chr3B 89.908 109 11 0 2 110 680975352 680975460 1.190000e-29 141.0
17 TraesCS1A01G372300 chr3B 96.875 32 1 0 537 568 650837704 650837735 2.000000e-03 54.7
18 TraesCS1A01G372300 chr4B 87.179 117 12 3 2991 3106 659694120 659694006 2.570000e-26 130.0
19 TraesCS1A01G372300 chr4B 86.239 109 15 0 2 110 591266090 591265982 5.570000e-23 119.0
20 TraesCS1A01G372300 chr4B 100.000 30 0 0 539 568 620060532 620060561 4.430000e-04 56.5
21 TraesCS1A01G372300 chr2B 88.073 109 13 0 2 110 366976621 366976513 2.570000e-26 130.0
22 TraesCS1A01G372300 chr2B 85.321 109 16 0 2 110 636216131 636216023 2.590000e-21 113.0
23 TraesCS1A01G372300 chr7D 87.156 109 14 0 2 110 285227497 285227389 1.200000e-24 124.0
24 TraesCS1A01G372300 chr7D 83.636 110 14 4 2992 3099 462277964 462277857 2.020000e-17 100.0
25 TraesCS1A01G372300 chr5B 87.037 108 14 0 2 109 181571111 181571004 4.310000e-24 122.0
26 TraesCS1A01G372300 chr5B 87.156 109 13 1 2 110 617437618 617437725 4.310000e-24 122.0
27 TraesCS1A01G372300 chr5B 85.470 117 12 5 2976 3090 283520568 283520455 2.000000e-22 117.0
28 TraesCS1A01G372300 chr3A 79.042 167 29 6 2992 3154 94185726 94185890 3.350000e-20 110.0
29 TraesCS1A01G372300 chr6B 81.356 118 17 5 2974 3088 369014299 369014184 1.210000e-14 91.6
30 TraesCS1A01G372300 chr6A 81.197 117 19 3 2974 3088 287242719 287242604 1.210000e-14 91.6
31 TraesCS1A01G372300 chr6A 94.595 37 1 1 540 575 60973804 60973768 4.430000e-04 56.5
32 TraesCS1A01G372300 chrUn 97.297 37 1 0 537 573 470559199 470559163 2.650000e-06 63.9
33 TraesCS1A01G372300 chr5A 92.308 39 3 0 537 575 487808280 487808318 4.430000e-04 56.5
34 TraesCS1A01G372300 chr7A 96.875 32 1 0 537 568 101305927 101305958 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 TraesCS1A01G372300 chr1A 548788335 548791513 3178 False 2635.5 4881 100.000 1 3179 2 chr1A.!!$F4 3178
1 TraesCS1A01G372300 chr1A 548733310 548734543 1233 False 1567.0 1567 89.608 936 2178 1 chr1A.!!$F2 1242
2 TraesCS1A01G372300 chr1A 548772382 548773576 1194 False 1541.0 1541 89.861 962 2178 1 chr1A.!!$F3 1216
3 TraesCS1A01G372300 chr1D 454811861 454814948 3087 False 2127.0 3995 91.326 1 3178 2 chr1D.!!$F2 3177
4 TraesCS1A01G372300 chr1D 454768817 454770265 1448 False 1687.0 1687 87.777 710 2178 1 chr1D.!!$F1 1468
5 TraesCS1A01G372300 chr1D 454457268 454458700 1432 True 1659.0 1659 87.659 712 2178 1 chr1D.!!$R2 1466
6 TraesCS1A01G372300 chr1D 454492635 454493944 1309 True 1554.0 1554 88.174 846 2178 1 chr1D.!!$R3 1332
7 TraesCS1A01G372300 chr1B 625144815 625147185 2370 False 3530.0 3530 93.586 586 2961 1 chr1B.!!$F4 2375
8 TraesCS1A01G372300 chr1B 625082314 625083764 1450 False 1722.0 1722 88.204 710 2178 1 chr1B.!!$F3 1468
9 TraesCS1A01G372300 chr1B 624970683 624971999 1316 False 1626.0 1626 88.922 832 2174 1 chr1B.!!$F1 1342

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
74 75 0.179200 AACGCGCATCACCGAAAATC 60.179 50.000 5.73 0.0 0.0 2.17 F
77 78 1.295792 GCGCATCACCGAAAATCCTA 58.704 50.000 0.30 0.0 0.0 2.94 F
1753 1808 1.337071 TGCTTCTCAACTTCGACGACT 59.663 47.619 0.00 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 1953 0.723981 GTCGATGAAGAGCTGGTTGC 59.276 55.000 0.00 0.00 43.29 4.17 R
2093 2172 1.162800 GGCGTCCATGGATCTCTTGC 61.163 60.000 19.62 14.37 0.00 4.01 R
2713 2817 1.379443 CCAGGTGAGGTGCATGCAT 60.379 57.895 25.64 8.94 0.00 3.96 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
69 70 1.080366 ACTAAACGCGCATCACCGA 60.080 52.632 5.73 0.00 0.00 4.69
74 75 0.179200 AACGCGCATCACCGAAAATC 60.179 50.000 5.73 0.00 0.00 2.17
76 77 1.705337 CGCGCATCACCGAAAATCCT 61.705 55.000 8.75 0.00 0.00 3.24
77 78 1.295792 GCGCATCACCGAAAATCCTA 58.704 50.000 0.30 0.00 0.00 2.94
109 110 3.002656 CAGTAATAAATGCGAGCACCAGG 59.997 47.826 0.00 0.00 0.00 4.45
113 114 4.790962 ATGCGAGCACCAGGGCTG 62.791 66.667 0.00 0.00 45.99 4.85
128 131 1.490490 GGGCTGAGGATACCAATGTCA 59.510 52.381 0.00 0.00 37.17 3.58
131 134 3.181451 GGCTGAGGATACCAATGTCATCA 60.181 47.826 0.00 0.00 34.82 3.07
574 577 7.981789 TCGACTGAGACTTAGCAAAATTGATAT 59.018 33.333 0.00 0.00 0.00 1.63
1011 1060 1.521457 GATTCGGATGGACAGCGCA 60.521 57.895 11.47 0.00 0.00 6.09
1369 1418 4.697756 CCAACTTCCGCCCGCTCA 62.698 66.667 0.00 0.00 0.00 4.26
1413 1462 3.832492 GAGCTCCGCTTCCTCGCT 61.832 66.667 0.87 0.00 39.88 4.93
1680 1735 2.607892 GCACGCCGAGAAGCACTTT 61.608 57.895 0.00 0.00 0.00 2.66
1753 1808 1.337071 TGCTTCTCAACTTCGACGACT 59.663 47.619 0.00 0.00 0.00 4.18
1824 1879 1.741770 CTACGTGCTCACCAAGGGC 60.742 63.158 0.00 0.00 0.00 5.19
1893 1948 1.605058 GGTTCTACCGCTCTGCCTCA 61.605 60.000 0.00 0.00 0.00 3.86
2093 2172 0.896940 AGCATGGTGCCCAAGACAAG 60.897 55.000 0.00 0.00 46.52 3.16
2216 2304 0.952010 CCATGGTTGCTTTGCTTGCC 60.952 55.000 2.57 0.00 0.00 4.52
2231 2319 2.027837 GCTTGCCTCCAAATTTCCATGT 60.028 45.455 0.00 0.00 0.00 3.21
2312 2402 8.198109 TCTCATACACAAGTTAGCTCTAAATCC 58.802 37.037 0.00 0.00 0.00 3.01
2368 2458 2.032030 CGTTCTCGAAATGGCAAGTGTT 60.032 45.455 0.00 0.00 39.71 3.32
2488 2580 5.898174 TGCATATTTGGAGCTTTTCATCTG 58.102 37.500 0.00 0.00 0.00 2.90
2491 2583 1.549203 TTGGAGCTTTTCATCTGGCC 58.451 50.000 0.00 0.00 0.00 5.36
2501 2593 0.624206 TCATCTGGCCATCCCCTTCA 60.624 55.000 5.51 0.00 0.00 3.02
2514 2606 1.341383 CCCCTTCATCTCCCAAACTGG 60.341 57.143 0.00 0.00 37.25 4.00
2529 2621 1.817099 CTGGGATGCAAGGAGACGC 60.817 63.158 0.00 0.00 0.00 5.19
2647 2747 2.036731 AGGTGCATGCATGTGGCT 59.963 55.556 25.64 6.13 45.15 4.75
2649 2749 2.101575 GTGCATGCATGTGGCTCG 59.898 61.111 25.64 0.81 45.15 5.03
2712 2816 3.581755 GCCCATAATTGTATGCATGCAG 58.418 45.455 26.69 8.64 36.53 4.41
2713 2817 3.256383 GCCCATAATTGTATGCATGCAGA 59.744 43.478 26.69 19.87 36.53 4.26
2714 2818 4.081862 GCCCATAATTGTATGCATGCAGAT 60.082 41.667 26.69 12.95 36.53 2.90
2715 2819 5.407502 CCCATAATTGTATGCATGCAGATG 58.592 41.667 26.69 18.94 36.53 2.90
2825 2929 1.269723 GAAACTAAAGTGGGCACTGGC 59.730 52.381 0.00 0.00 41.58 4.85
2967 3071 8.480853 CGTTCGAAATTTTCCTAGATCTATGAC 58.519 37.037 7.18 0.00 0.00 3.06
2969 3073 9.534565 TTCGAAATTTTCCTAGATCTATGACTG 57.465 33.333 7.18 0.00 0.00 3.51
2971 3075 9.319143 CGAAATTTTCCTAGATCTATGACTGTT 57.681 33.333 7.18 1.14 0.00 3.16
2978 3083 8.053776 TCCTAGATCTATGACTGTTAAGGGTA 57.946 38.462 2.11 0.00 0.00 3.69
3030 3144 7.857404 TCAGTGGGGTCCAAAATATTTTTAA 57.143 32.000 10.77 0.00 34.18 1.52
3034 3148 5.046520 TGGGGTCCAAAATATTTTTAACCCG 60.047 40.000 31.41 15.59 45.05 5.28
3040 3154 6.874664 TCCAAAATATTTTTAACCCGGAAAGC 59.125 34.615 10.77 0.00 0.00 3.51
3170 3284 6.589523 TGCAAATTTTCACATATTTCGGAAGG 59.410 34.615 0.00 0.00 0.00 3.46
3178 3292 5.182380 TCACATATTTCGGAAGGTCCAAAAC 59.818 40.000 0.00 0.00 35.91 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.595310 GAGCCGCCTACGATGACTTC 60.595 60.000 0.00 0.00 43.93 3.01
9 10 1.779025 TACGAGCCGCCTACGATGAC 61.779 60.000 8.73 0.00 43.93 3.06
40 41 1.336517 CGCGTTTAGTGGGAAGAGACA 60.337 52.381 0.00 0.00 0.00 3.41
54 55 0.239879 ATTTTCGGTGATGCGCGTTT 59.760 45.000 8.43 0.00 0.00 3.60
77 78 9.463443 GCTCGCATTTATTACTGGATTTAATTT 57.537 29.630 0.00 0.00 0.00 1.82
100 101 1.050988 TATCCTCAGCCCTGGTGCTC 61.051 60.000 6.69 0.00 40.32 4.26
109 110 3.181451 TGATGACATTGGTATCCTCAGCC 60.181 47.826 0.00 0.00 0.00 4.85
113 114 4.696479 AGGTGATGACATTGGTATCCTC 57.304 45.455 0.00 0.00 0.00 3.71
147 150 3.117284 ACTGAAACCTAACCACACCCATT 60.117 43.478 0.00 0.00 0.00 3.16
149 152 1.847737 ACTGAAACCTAACCACACCCA 59.152 47.619 0.00 0.00 0.00 4.51
150 153 2.501261 GACTGAAACCTAACCACACCC 58.499 52.381 0.00 0.00 0.00 4.61
550 553 9.323985 AGATATCAATTTTGCTAAGTCTCAGTC 57.676 33.333 5.32 0.00 0.00 3.51
675 680 4.469657 ACTCCATGCTGGTGTTTCTTTTA 58.530 39.130 4.66 0.00 41.00 1.52
934 958 6.097129 GGGAGAGAAGTAGAGCTTAGCTAAAA 59.903 42.308 6.75 0.00 39.88 1.52
1011 1060 1.004440 GTCCACGAGGCAGCTTCTT 60.004 57.895 2.62 0.00 33.74 2.52
1647 1702 0.735978 CGTGCTGCTTCGGTATCACA 60.736 55.000 0.00 0.00 0.00 3.58
1680 1735 0.972983 CGGAAGGAAGCTGGAGAGGA 60.973 60.000 0.00 0.00 0.00 3.71
1824 1879 1.580845 CCTTGACAAAGCGGCTCCAG 61.581 60.000 1.45 0.00 31.51 3.86
1836 1891 2.069776 CAGGCCCTTCTCCTTGACA 58.930 57.895 0.00 0.00 0.00 3.58
1898 1953 0.723981 GTCGATGAAGAGCTGGTTGC 59.276 55.000 0.00 0.00 43.29 4.17
2093 2172 1.162800 GGCGTCCATGGATCTCTTGC 61.163 60.000 19.62 14.37 0.00 4.01
2180 2268 1.808411 TGGAGGAAAAACGCTAGCTG 58.192 50.000 13.93 9.03 0.00 4.24
2216 2304 7.396540 AAGCTACTAACATGGAAATTTGGAG 57.603 36.000 0.00 0.00 0.00 3.86
2368 2458 3.410631 TTGGTAGCATTTCTTCGGTGA 57.589 42.857 0.00 0.00 0.00 4.02
2488 2580 1.458045 GGAGATGAAGGGGATGGCC 59.542 63.158 0.00 0.00 0.00 5.36
2491 2583 2.243221 AGTTTGGGAGATGAAGGGGATG 59.757 50.000 0.00 0.00 0.00 3.51
2514 2606 2.892425 CGGCGTCTCCTTGCATCC 60.892 66.667 0.00 0.00 0.00 3.51
2529 2621 1.705337 AAATCGCGACATGAAGCCGG 61.705 55.000 12.93 0.00 0.00 6.13
2535 2635 2.164422 AGAGAGTCAAATCGCGACATGA 59.836 45.455 12.93 16.58 35.77 3.07
2647 2747 4.617520 TTCTGCACTTGCGGCCGA 62.618 61.111 33.48 11.82 46.62 5.54
2649 2749 2.256461 CTTTCTGCACTTGCGGCC 59.744 61.111 5.08 0.00 46.62 6.13
2658 2758 2.927856 TCCCGGAGCCTTTCTGCA 60.928 61.111 0.73 0.00 31.94 4.41
2712 2816 1.381928 CCAGGTGAGGTGCATGCATC 61.382 60.000 25.64 24.66 0.00 3.91
2713 2817 1.379443 CCAGGTGAGGTGCATGCAT 60.379 57.895 25.64 8.94 0.00 3.96
2714 2818 2.034532 CCAGGTGAGGTGCATGCA 59.965 61.111 18.46 18.46 0.00 3.96
2715 2819 3.446570 GCCAGGTGAGGTGCATGC 61.447 66.667 11.82 11.82 0.00 4.06
2716 2820 2.753043 GGCCAGGTGAGGTGCATG 60.753 66.667 0.00 0.00 0.00 4.06
2825 2929 2.802247 CACCTGTCACATACACACAGTG 59.198 50.000 0.00 0.00 36.57 3.66
3030 3144 3.249189 TGCTCTGGCTTTCCGGGT 61.249 61.111 0.00 0.00 39.31 5.28
3034 3148 2.119801 TGAATCTGCTCTGGCTTTCC 57.880 50.000 0.00 0.00 39.59 3.13
3040 3154 8.464404 TCTGAAATTAATTTGAATCTGCTCTGG 58.536 33.333 17.98 0.00 0.00 3.86
3154 3268 4.561500 TTGGACCTTCCGAAATATGTGA 57.438 40.909 0.00 0.00 40.17 3.58


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

AutoCloner maintained by Alex Coulton.