Multiple sequence alignment - TraesCS7D01G286600

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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 TraesCS7D01G286600 chr7D 100.000 3627 0 0 1 3627 309914926 309911300 0.000000e+00 6698.0
1 TraesCS7D01G286600 chr7B 95.750 2753 111 4 1 2750 304522801 304525550 0.000000e+00 4431.0
2 TraesCS7D01G286600 chr7B 90.335 538 29 10 2710 3244 304525551 304526068 0.000000e+00 684.0
3 TraesCS7D01G286600 chr7B 91.003 389 28 7 3244 3627 304529538 304529924 5.370000e-143 518.0
4 TraesCS7D01G286600 chr7A 96.803 2565 80 2 684 3247 349686610 349684047 0.000000e+00 4281.0
5 TraesCS7D01G286600 chr7A 88.596 342 24 4 3287 3627 349683800 349683473 5.640000e-108 401.0
6 TraesCS7D01G286600 chr7A 94.286 35 1 1 419 452 10224738 10224704 7.000000e-03 52.8
7 TraesCS7D01G286600 chr2B 77.778 1053 215 16 1545 2586 390925527 390926571 6.610000e-177 630.0
8 TraesCS7D01G286600 chr2B 77.168 1038 219 17 1545 2573 231233874 231234902 4.030000e-164 588.0
9 TraesCS7D01G286600 chr2B 80.000 245 45 4 1305 1547 231233404 231233646 1.030000e-40 178.0
10 TraesCS7D01G286600 chr2B 87.879 66 8 0 1074 1139 484591452 484591517 1.080000e-10 78.7
11 TraesCS7D01G286600 chr2D 77.821 1037 213 14 1560 2586 323076889 323077918 3.070000e-175 625.0
12 TraesCS7D01G286600 chr2D 77.647 1020 210 17 1566 2576 166609436 166608426 4.010000e-169 604.0
13 TraesCS7D01G286600 chr2D 80.816 245 43 4 1305 1547 166609926 166609684 4.780000e-44 189.0
14 TraesCS7D01G286600 chr2D 92.308 39 1 2 415 452 24262683 24262720 2.000000e-03 54.7
15 TraesCS7D01G286600 chr2A 77.767 1039 210 18 1560 2586 407740526 407739497 1.430000e-173 619.0
16 TraesCS7D01G286600 chr2A 80.816 245 43 4 1305 1547 183550321 183550563 4.780000e-44 189.0
17 TraesCS7D01G286600 chr2A 87.879 66 8 0 1074 1139 578117870 578117935 1.080000e-10 78.7
18 TraesCS7D01G286600 chr6D 73.429 1114 267 27 1494 2588 88503115 88504218 1.220000e-104 390.0
19 TraesCS7D01G286600 chr6D 100.000 28 0 0 1304 1331 88502925 88502952 7.000000e-03 52.8
20 TraesCS7D01G286600 chr6A 72.456 1307 319 39 1304 2585 106455573 106456863 7.350000e-102 381.0
21 TraesCS7D01G286600 chr5D 88.298 94 11 0 1043 1136 1887287 1887194 2.960000e-21 113.0
22 TraesCS7D01G286600 chr5B 87.059 85 9 2 1053 1136 764837 764754 1.070000e-15 95.3
23 TraesCS7D01G286600 chr4B 88.136 59 7 0 1077 1135 640027282 640027224 1.810000e-08 71.3
24 TraesCS7D01G286600 chr5A 93.182 44 3 0 1092 1135 678583821 678583778 8.410000e-07 65.8
25 TraesCS7D01G286600 chr4D 93.182 44 3 0 1092 1135 498063179 498063136 8.410000e-07 65.8
26 TraesCS7D01G286600 chr3A 92.308 39 1 2 415 452 164412359 164412396 2.000000e-03 54.7
27 TraesCS7D01G286600 chr3A 92.308 39 1 2 415 452 565473193 565473156 2.000000e-03 54.7
28 TraesCS7D01G286600 chr1B 92.308 39 1 2 415 452 91553596 91553633 2.000000e-03 54.7
29 TraesCS7D01G286600 chr3D 100.000 28 0 0 425 452 419931099 419931126 7.000000e-03 52.8


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 TraesCS7D01G286600 chr7D 309911300 309914926 3626 True 6698.000000 6698 100.000000 1 3627 1 chr7D.!!$R1 3626
1 TraesCS7D01G286600 chr7B 304522801 304529924 7123 False 1877.666667 4431 92.362667 1 3627 3 chr7B.!!$F1 3626
2 TraesCS7D01G286600 chr7A 349683473 349686610 3137 True 2341.000000 4281 92.699500 684 3627 2 chr7A.!!$R2 2943
3 TraesCS7D01G286600 chr2B 390925527 390926571 1044 False 630.000000 630 77.778000 1545 2586 1 chr2B.!!$F1 1041
4 TraesCS7D01G286600 chr2B 231233404 231234902 1498 False 383.000000 588 78.584000 1305 2573 2 chr2B.!!$F3 1268
5 TraesCS7D01G286600 chr2D 323076889 323077918 1029 False 625.000000 625 77.821000 1560 2586 1 chr2D.!!$F2 1026
6 TraesCS7D01G286600 chr2D 166608426 166609926 1500 True 396.500000 604 79.231500 1305 2576 2 chr2D.!!$R1 1271
7 TraesCS7D01G286600 chr2A 407739497 407740526 1029 True 619.000000 619 77.767000 1560 2586 1 chr2A.!!$R1 1026
8 TraesCS7D01G286600 chr6D 88502925 88504218 1293 False 221.400000 390 86.714500 1304 2588 2 chr6D.!!$F1 1284
9 TraesCS7D01G286600 chr6A 106455573 106456863 1290 False 381.000000 381 72.456000 1304 2585 1 chr6A.!!$F1 1281

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
176 177 0.103390 TTCGAACTTCACACGAGCCA 59.897 50.0 0.00 0.0 37.36 4.75 F
256 257 0.179004 ATGCAGGGGACGAACACAAA 60.179 50.0 0.00 0.0 0.00 2.83 F
257 258 0.394488 TGCAGGGGACGAACACAAAA 60.394 50.0 0.00 0.0 0.00 2.44 F
2089 2343 0.673437 CGGGGCTTGTCAACATGTTT 59.327 50.0 8.77 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2089 2343 0.107268 CGATGGAGATGATGGTGGCA 59.893 55.000 0.0 0.0 0.0 4.92 R
2350 2604 2.759973 CTCTGCCCTGCCGACCTA 60.760 66.667 0.0 0.0 0.0 3.08 R
2392 2646 1.355381 TGCCCAATGATGAAGGTGAGT 59.645 47.619 0.0 0.0 0.0 3.41 R
3498 7271 0.754957 CTCGGGAGATGAGCAGACCT 60.755 60.000 0.0 0.0 38.8 3.85 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
27 28 1.092921 TTCACGCGACTTGCAAACCT 61.093 50.000 15.93 0.00 46.97 3.50
55 56 8.837099 ATAGGATTGGTGGAATTTGATGTAAA 57.163 30.769 0.00 0.00 0.00 2.01
60 61 9.657419 GATTGGTGGAATTTGATGTAAAGAATT 57.343 29.630 0.00 0.00 0.00 2.17
61 62 8.830201 TTGGTGGAATTTGATGTAAAGAATTG 57.170 30.769 0.00 0.00 0.00 2.32
152 153 4.620086 TTCTGTATAGAAGGGGAGGTCA 57.380 45.455 0.00 0.00 37.99 4.02
154 155 4.742012 TCTGTATAGAAGGGGAGGTCATC 58.258 47.826 0.00 0.00 0.00 2.92
156 157 4.223953 TGTATAGAAGGGGAGGTCATCAC 58.776 47.826 0.00 0.00 0.00 3.06
159 160 2.192263 AGAAGGGGAGGTCATCACTTC 58.808 52.381 11.15 11.15 40.78 3.01
170 171 3.184581 GGTCATCACTTCGAACTTCACAC 59.815 47.826 0.00 0.00 0.00 3.82
176 177 0.103390 TTCGAACTTCACACGAGCCA 59.897 50.000 0.00 0.00 37.36 4.75
195 196 6.806249 CGAGCCAAAATATTTTTAGTTGCTCA 59.194 34.615 25.85 0.00 0.00 4.26
253 254 2.040544 CCATGCAGGGGACGAACAC 61.041 63.158 10.25 0.00 0.00 3.32
255 256 0.888736 CATGCAGGGGACGAACACAA 60.889 55.000 0.00 0.00 0.00 3.33
256 257 0.179004 ATGCAGGGGACGAACACAAA 60.179 50.000 0.00 0.00 0.00 2.83
257 258 0.394488 TGCAGGGGACGAACACAAAA 60.394 50.000 0.00 0.00 0.00 2.44
258 259 0.741915 GCAGGGGACGAACACAAAAA 59.258 50.000 0.00 0.00 0.00 1.94
259 260 1.269051 GCAGGGGACGAACACAAAAAG 60.269 52.381 0.00 0.00 0.00 2.27
277 281 4.090588 TGGGAAACTAGGCGGCGG 62.091 66.667 9.78 3.12 0.00 6.13
279 283 4.468689 GGAAACTAGGCGGCGGCT 62.469 66.667 37.55 37.55 42.39 5.52
305 309 7.226720 TCAGAACAAGAAACTACAGGATTGAAC 59.773 37.037 0.00 0.00 0.00 3.18
316 320 5.909621 ACAGGATTGAACTGATTGATTGG 57.090 39.130 0.00 0.00 39.24 3.16
358 362 5.595542 ACGAATGGTGATTGGATTGATTGAT 59.404 36.000 0.00 0.00 0.00 2.57
639 643 7.377766 TCACATAAATGAGTTTAGCACTTCC 57.622 36.000 0.00 0.00 35.01 3.46
656 660 3.072622 ACTTCCCAAGTTCTTGGTCTACC 59.927 47.826 24.22 0.00 39.04 3.18
657 661 1.982958 TCCCAAGTTCTTGGTCTACCC 59.017 52.381 24.22 0.00 40.46 3.69
659 663 1.985895 CCAAGTTCTTGGTCTACCCCT 59.014 52.381 19.86 0.00 37.32 4.79
796 800 2.357637 TGATGCACTAATTTTAGCGCCC 59.642 45.455 2.29 2.02 37.87 6.13
978 982 1.839994 GGTCTCTTCCATCCATCACCA 59.160 52.381 0.00 0.00 0.00 4.17
1023 1027 2.516225 GGGGGCGTGGTGATAAGC 60.516 66.667 0.00 0.00 0.00 3.09
1098 1102 2.752238 CTCGTCGCCTCCTCTGGT 60.752 66.667 0.00 0.00 0.00 4.00
1159 1163 4.858692 CCGCCAATTACTTCATTGAAACAG 59.141 41.667 0.01 0.00 36.39 3.16
1390 1394 2.738643 GCTAGCAACATCGTTCCTAGCA 60.739 50.000 19.93 0.00 46.24 3.49
1846 2097 2.264794 GGAACCTCGGACGTGCAT 59.735 61.111 8.11 0.00 0.00 3.96
1858 2109 2.543861 GGACGTGCATGATGAGTACGAT 60.544 50.000 14.17 7.69 38.08 3.73
2089 2343 0.673437 CGGGGCTTGTCAACATGTTT 59.327 50.000 8.77 0.00 0.00 2.83
2350 2604 1.741770 GGTGTTCGCGCTGGAGATT 60.742 57.895 5.56 0.00 0.00 2.40
2431 2685 1.675641 GGCGTTCCTCACCATGCTT 60.676 57.895 0.00 0.00 0.00 3.91
2637 2891 1.015868 GGCGTCTAGTCTAGCGTCTT 58.984 55.000 18.52 0.00 30.95 3.01
2777 3072 8.651589 TCAAGAGAGATGTTTTAGGAAGTCTA 57.348 34.615 0.00 0.00 0.00 2.59
2831 3126 5.422214 AGTGATTTCCCGTTGTAGAGAAT 57.578 39.130 0.00 0.00 0.00 2.40
2916 3211 8.870879 ACATTGTAAGCGATAGAGTTTAAAGTC 58.129 33.333 14.15 14.15 39.76 3.01
2917 3214 8.869897 CATTGTAAGCGATAGAGTTTAAAGTCA 58.130 33.333 22.06 10.58 39.76 3.41
2985 3282 2.305635 TCTGGGCTGAGCTAATGTTTCA 59.694 45.455 3.72 0.00 0.00 2.69
3043 3340 4.645956 GCTGAACGTCAAATGATCTTCAG 58.354 43.478 19.12 19.12 40.15 3.02
3070 3367 8.944138 TGAGAAATGAATATATAACACCTCCCA 58.056 33.333 0.00 0.00 0.00 4.37
3078 3375 2.963599 TAACACCTCCCAAAGAACCC 57.036 50.000 0.00 0.00 0.00 4.11
3092 3389 0.108945 GAACCCGAGTTACCACTCCG 60.109 60.000 0.00 0.00 46.19 4.63
3166 3463 2.372837 GGAGGTTACCAGGGTGTGTTTA 59.627 50.000 3.51 0.00 0.00 2.01
3168 3465 3.817084 GAGGTTACCAGGGTGTGTTTAAC 59.183 47.826 3.51 0.00 0.00 2.01
3175 3472 4.471747 ACCAGGGTGTGTTTAACCAAAAAT 59.528 37.500 0.00 0.00 39.65 1.82
3176 3473 5.045505 ACCAGGGTGTGTTTAACCAAAAATT 60.046 36.000 0.00 0.00 39.65 1.82
3236 3536 0.248336 TCATGTCTACGGCGCGTAAG 60.248 55.000 6.90 1.52 41.82 2.34
3256 7026 9.635520 GCGTAAGTACCATATTATTCACATAGT 57.364 33.333 0.00 0.00 41.68 2.12
3280 7051 7.951245 AGTAATTACCAGGGGTATGTTTCAAAA 59.049 33.333 12.05 0.00 38.05 2.44
3282 7053 4.948341 ACCAGGGGTATGTTTCAAAAAC 57.052 40.909 0.00 0.00 32.11 2.43
3284 7055 4.717280 ACCAGGGGTATGTTTCAAAAACAA 59.283 37.500 9.10 0.00 32.11 2.83
3285 7056 5.189934 ACCAGGGGTATGTTTCAAAAACAAA 59.810 36.000 9.10 0.00 32.11 2.83
3473 7246 1.267532 CCGTCATGCGACTAAACATGC 60.268 52.381 10.48 0.00 42.72 4.06
3512 7285 3.639162 CGTGAGGTCTGCTCATCTC 57.361 57.895 0.00 0.00 33.08 2.75
3516 7289 0.753479 GAGGTCTGCTCATCTCCCGA 60.753 60.000 0.00 0.00 0.00 5.14
3590 7364 4.154195 AGCGTGGCTATGTTCTAAAACTTG 59.846 41.667 0.00 0.00 36.99 3.16
3609 7383 1.139163 GTTTTCCCGCGTCGAAGTTA 58.861 50.000 4.92 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.249531 TAGGTTTGCAAGTCGCGTGA 60.250 50.000 5.77 0.00 46.97 4.35
55 56 3.203040 CCCAATAGTCCCACCTCAATTCT 59.797 47.826 0.00 0.00 0.00 2.40
60 61 2.841881 GTTACCCAATAGTCCCACCTCA 59.158 50.000 0.00 0.00 0.00 3.86
61 62 2.841881 TGTTACCCAATAGTCCCACCTC 59.158 50.000 0.00 0.00 0.00 3.85
138 139 3.375699 GAAGTGATGACCTCCCCTTCTA 58.624 50.000 0.00 0.00 32.29 2.10
143 144 0.902531 TTCGAAGTGATGACCTCCCC 59.097 55.000 0.00 0.00 0.00 4.81
152 153 3.309388 CTCGTGTGAAGTTCGAAGTGAT 58.691 45.455 6.19 0.00 33.32 3.06
154 155 1.190323 GCTCGTGTGAAGTTCGAAGTG 59.810 52.381 6.19 0.00 33.32 3.16
156 157 0.784778 GGCTCGTGTGAAGTTCGAAG 59.215 55.000 0.00 0.00 33.32 3.79
159 160 0.934496 TTTGGCTCGTGTGAAGTTCG 59.066 50.000 0.00 0.00 0.00 3.95
170 171 6.806249 TGAGCAACTAAAAATATTTTGGCTCG 59.194 34.615 25.86 15.07 0.00 5.03
253 254 2.030274 CCGCCTAGTTTCCCACTTTTTG 60.030 50.000 0.00 0.00 36.88 2.44
255 256 1.905637 CCGCCTAGTTTCCCACTTTT 58.094 50.000 0.00 0.00 36.88 2.27
256 257 0.608308 GCCGCCTAGTTTCCCACTTT 60.608 55.000 0.00 0.00 36.88 2.66
257 258 1.002502 GCCGCCTAGTTTCCCACTT 60.003 57.895 0.00 0.00 36.88 3.16
258 259 2.669240 GCCGCCTAGTTTCCCACT 59.331 61.111 0.00 0.00 39.87 4.00
259 260 2.818274 CGCCGCCTAGTTTCCCAC 60.818 66.667 0.00 0.00 0.00 4.61
263 267 2.890961 GAGCCGCCGCCTAGTTTC 60.891 66.667 0.00 0.00 34.57 2.78
277 281 4.632153 TCCTGTAGTTTCTTGTTCTGAGC 58.368 43.478 0.00 0.00 0.00 4.26
279 283 6.826668 TCAATCCTGTAGTTTCTTGTTCTGA 58.173 36.000 0.00 0.00 0.00 3.27
336 340 7.494211 TCAATCAATCAATCCAATCACCATTC 58.506 34.615 0.00 0.00 0.00 2.67
337 341 7.426606 TCAATCAATCAATCCAATCACCATT 57.573 32.000 0.00 0.00 0.00 3.16
378 382 2.265182 CGTTGTTGGTCCGCCCATT 61.265 57.895 0.00 0.00 44.74 3.16
415 419 8.939932 CCTACTAATAAAGGGAGGAAGATTTCT 58.060 37.037 0.00 0.00 35.42 2.52
456 460 7.921745 TGTTGTTTATACAAAAAGCAGGGTTAC 59.078 33.333 0.00 0.00 45.33 2.50
460 464 7.151308 TGATGTTGTTTATACAAAAAGCAGGG 58.849 34.615 0.00 0.00 45.33 4.45
463 467 8.147058 ACCATGATGTTGTTTATACAAAAAGCA 58.853 29.630 0.00 2.55 45.33 3.91
464 468 8.532977 ACCATGATGTTGTTTATACAAAAAGC 57.467 30.769 0.00 0.00 45.33 3.51
547 551 2.125326 CCATACCTCGGTCCGCTCA 61.125 63.158 6.34 0.00 0.00 4.26
616 620 6.150976 TGGGAAGTGCTAAACTCATTTATGTG 59.849 38.462 0.00 0.00 38.56 3.21
939 943 2.037381 ACCAAACGAGGAGGAAGAAGAC 59.963 50.000 0.00 0.00 0.00 3.01
978 982 1.550524 TCTGCGAACAGGCTAGACAAT 59.449 47.619 0.00 0.00 44.59 2.71
1159 1163 7.367285 TGCCAGTTAGTTGTATTTCATTTCAC 58.633 34.615 0.00 0.00 0.00 3.18
1342 1346 2.231478 CAGGTACAGTGAGGACGTGAAT 59.769 50.000 0.00 0.00 32.12 2.57
1837 2085 1.200483 CGTACTCATCATGCACGTCC 58.800 55.000 0.00 0.00 0.00 4.79
1846 2097 3.181476 CCACCATGTCATCGTACTCATCA 60.181 47.826 0.00 0.00 0.00 3.07
1858 2109 4.720902 CTGGCGGCCACCATGTCA 62.721 66.667 19.77 0.00 39.54 3.58
2077 2331 1.478631 TGGTGGCAAACATGTTGACA 58.521 45.000 12.82 11.82 34.56 3.58
2089 2343 0.107268 CGATGGAGATGATGGTGGCA 59.893 55.000 0.00 0.00 0.00 4.92
2350 2604 2.759973 CTCTGCCCTGCCGACCTA 60.760 66.667 0.00 0.00 0.00 3.08
2392 2646 1.355381 TGCCCAATGATGAAGGTGAGT 59.645 47.619 0.00 0.00 0.00 3.41
2431 2685 0.534203 GGCCGAACTTGAGGTGACAA 60.534 55.000 0.00 0.00 0.00 3.18
2637 2891 3.187637 ACACGCTCGCTAAATAAAAAGCA 59.812 39.130 0.00 0.00 38.70 3.91
2777 3072 8.585471 ATGTCCATCTCTACATTTCAATTTGT 57.415 30.769 0.00 0.00 32.43 2.83
2818 3113 8.480643 AAAGAAGACAATATTCTCTACAACGG 57.519 34.615 0.00 0.00 35.98 4.44
2916 3211 4.697514 TGAGGTCTTGAGTTCAACTCTTG 58.302 43.478 18.49 10.84 45.27 3.02
2917 3214 4.742138 GCTGAGGTCTTGAGTTCAACTCTT 60.742 45.833 18.49 0.00 45.27 2.85
2985 3282 1.135517 ACAACGACGCAAAGCTTTGTT 60.136 42.857 33.47 23.52 40.24 2.83
3043 3340 9.220767 GGGAGGTGTTATATATTCATTTCTCAC 57.779 37.037 0.00 0.00 0.00 3.51
3070 3367 3.397849 GAGTGGTAACTCGGGTTCTTT 57.602 47.619 2.54 0.00 43.35 2.52
3092 3389 6.929049 TGCAGGCATGATAAGTTACATACTAC 59.071 38.462 0.62 0.00 35.54 2.73
3166 3463 8.630037 ACTTTGATCGAGAGTTAATTTTTGGTT 58.370 29.630 3.20 0.00 0.00 3.67
3175 3472 6.750501 CCGTGATAACTTTGATCGAGAGTTAA 59.249 38.462 15.09 2.93 38.80 2.01
3176 3473 6.127814 ACCGTGATAACTTTGATCGAGAGTTA 60.128 38.462 14.07 14.07 39.41 2.24
3256 7026 8.586744 GTTTTTGAAACATACCCCTGGTAATTA 58.413 33.333 0.00 0.00 41.85 1.40
3372 7144 8.605746 GCATGTTGAAATATACACCGTAAACTA 58.394 33.333 0.00 0.00 0.00 2.24
3498 7271 0.754957 CTCGGGAGATGAGCAGACCT 60.755 60.000 0.00 0.00 38.80 3.85
3532 7305 8.720562 TGTAAAGAACATAACATGTCATGTCAG 58.279 33.333 15.09 13.28 44.07 3.51
3538 7311 8.669946 TTCTGTGTAAAGAACATAACATGTCA 57.330 30.769 0.00 0.00 44.07 3.58
3590 7364 1.139163 TAACTTCGACGCGGGAAAAC 58.861 50.000 12.47 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.