Multiple sequence alignment - TraesCS1D01G318600

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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 TraesCS1D01G318600 chr1D 100.000 3155 0 0 1 3155 412896768 412899922 0.000000e+00 5827.0
1 TraesCS1D01G318600 chr1D 97.070 2662 57 7 507 3155 412683568 412686221 0.000000e+00 4464.0
2 TraesCS1D01G318600 chr1D 97.226 2091 24 6 623 2702 412814078 412816145 0.000000e+00 3509.0
3 TraesCS1D01G318600 chr1D 90.878 2017 120 30 696 2675 412641928 412643917 0.000000e+00 2647.0
4 TraesCS1D01G318600 chr1D 92.153 1886 86 28 696 2546 412745906 412747764 0.000000e+00 2606.0
5 TraesCS1D01G318600 chr1D 92.153 1886 86 28 696 2546 412763069 412764927 0.000000e+00 2606.0
6 TraesCS1D01G318600 chr1D 94.451 1586 56 12 696 2268 412660192 412661758 0.000000e+00 2412.0
7 TraesCS1D01G318600 chr1D 96.768 495 13 1 1 495 412683091 412683582 0.000000e+00 822.0
8 TraesCS1D01G318600 chr1D 97.450 353 6 3 2805 3155 412816138 412816489 1.620000e-167 599.0
9 TraesCS1D01G318600 chr1D 90.722 388 29 4 551 935 413061282 413061665 7.810000e-141 510.0
10 TraesCS1D01G318600 chr1B 92.701 2192 112 20 998 3155 556251420 556253597 0.000000e+00 3118.0
11 TraesCS1D01G318600 chr1B 93.537 1903 86 17 696 2579 556662844 556664728 0.000000e+00 2798.0
12 TraesCS1D01G318600 chr1B 91.927 1982 110 22 1199 3155 556834311 556836267 0.000000e+00 2728.0
13 TraesCS1D01G318600 chr1B 91.927 1982 110 22 1199 3155 556862732 556864688 0.000000e+00 2728.0
14 TraesCS1D01G318600 chr1B 91.640 1543 82 28 998 2520 556297340 556298855 0.000000e+00 2091.0
15 TraesCS1D01G318600 chr1B 88.436 1228 95 19 513 1723 556968932 556970129 0.000000e+00 1437.0
16 TraesCS1D01G318600 chr1B 86.792 583 36 18 2592 3155 556666532 556667092 2.080000e-171 612.0
17 TraesCS1D01G318600 chr1B 88.056 360 36 3 579 935 556965928 556966283 1.350000e-113 420.0
18 TraesCS1D01G318600 chr1B 79.139 302 42 10 2674 2960 295427776 295427481 4.150000e-44 189.0
19 TraesCS1D01G318600 chr1B 79.435 248 31 13 2237 2474 556306456 556306693 1.170000e-34 158.0
20 TraesCS1D01G318600 chr1A 92.975 1765 73 23 696 2440 509849710 509847977 0.000000e+00 2525.0
21 TraesCS1D01G318600 chr1A 94.063 1617 63 16 696 2305 509720185 509718595 0.000000e+00 2423.0
22 TraesCS1D01G318600 chr1A 90.924 1201 74 14 1758 2929 510111533 510112727 0.000000e+00 1581.0
23 TraesCS1D01G318600 chr1A 90.758 1201 66 16 1758 2929 509541974 509540790 0.000000e+00 1561.0
24 TraesCS1D01G318600 chr1A 88.945 398 37 3 553 947 509494029 509493636 4.730000e-133 484.0
25 TraesCS1D01G318600 chr1A 89.637 386 33 4 553 935 510184758 510185139 4.730000e-133 484.0
26 TraesCS1D01G318600 chr1A 86.486 222 28 1 1 220 554878475 554878696 3.140000e-60 243.0
27 TraesCS1D01G318600 chr1A 91.333 150 10 3 2983 3129 509540803 509540654 5.340000e-48 202.0
28 TraesCS1D01G318600 chr1A 83.688 141 16 4 517 650 509704021 509703881 3.300000e-25 126.0
29 TraesCS1D01G318600 chr1A 83.459 133 15 4 525 650 509777242 509777110 1.990000e-22 117.0
30 TraesCS1D01G318600 chr1A 76.800 125 26 3 89 211 429127495 429127372 2.030000e-07 67.6
31 TraesCS1D01G318600 chr1A 100.000 28 0 0 2673 2700 416772666 416772693 6.000000e-03 52.8
32 TraesCS1D01G318600 chr3B 87.129 202 21 5 9 207 365214406 365214605 1.140000e-54 224.0
33 TraesCS1D01G318600 chr3B 75.524 286 50 14 2673 2948 243429656 243429931 4.270000e-24 122.0
34 TraesCS1D01G318600 chr5B 85.644 202 27 1 1 200 233920566 233920767 8.870000e-51 211.0
35 TraesCS1D01G318600 chr5B 75.962 312 55 14 2674 2974 227281997 227281695 3.280000e-30 143.0
36 TraesCS1D01G318600 chr2B 79.863 293 37 10 2684 2960 19981544 19981830 8.930000e-46 195.0
37 TraesCS1D01G318600 chr2A 85.795 176 21 4 7 180 388461651 388461478 1.930000e-42 183.0
38 TraesCS1D01G318600 chr2A 78.231 147 27 5 81 223 423174917 423174772 4.330000e-14 89.8
39 TraesCS1D01G318600 chr6D 77.211 294 52 9 2674 2960 210072982 210072697 1.170000e-34 158.0
40 TraesCS1D01G318600 chr6D 89.062 128 12 2 9 134 272126939 272127066 1.170000e-34 158.0
41 TraesCS1D01G318600 chrUn 82.979 141 19 2 2674 2814 271933848 271933713 4.270000e-24 122.0
42 TraesCS1D01G318600 chr7B 77.372 137 21 9 81 211 592001189 592001321 4.370000e-09 73.1


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 TraesCS1D01G318600 chr1D 412896768 412899922 3154 False 5827.0 5827 100.0000 1 3155 1 chr1D.!!$F5 3154
1 TraesCS1D01G318600 chr1D 412641928 412643917 1989 False 2647.0 2647 90.8780 696 2675 1 chr1D.!!$F1 1979
2 TraesCS1D01G318600 chr1D 412683091 412686221 3130 False 2643.0 4464 96.9190 1 3155 2 chr1D.!!$F7 3154
3 TraesCS1D01G318600 chr1D 412745906 412747764 1858 False 2606.0 2606 92.1530 696 2546 1 chr1D.!!$F3 1850
4 TraesCS1D01G318600 chr1D 412763069 412764927 1858 False 2606.0 2606 92.1530 696 2546 1 chr1D.!!$F4 1850
5 TraesCS1D01G318600 chr1D 412660192 412661758 1566 False 2412.0 2412 94.4510 696 2268 1 chr1D.!!$F2 1572
6 TraesCS1D01G318600 chr1D 412814078 412816489 2411 False 2054.0 3509 97.3380 623 3155 2 chr1D.!!$F8 2532
7 TraesCS1D01G318600 chr1B 556251420 556253597 2177 False 3118.0 3118 92.7010 998 3155 1 chr1B.!!$F1 2157
8 TraesCS1D01G318600 chr1B 556834311 556836267 1956 False 2728.0 2728 91.9270 1199 3155 1 chr1B.!!$F4 1956
9 TraesCS1D01G318600 chr1B 556862732 556864688 1956 False 2728.0 2728 91.9270 1199 3155 1 chr1B.!!$F5 1956
10 TraesCS1D01G318600 chr1B 556297340 556298855 1515 False 2091.0 2091 91.6400 998 2520 1 chr1B.!!$F2 1522
11 TraesCS1D01G318600 chr1B 556662844 556667092 4248 False 1705.0 2798 90.1645 696 3155 2 chr1B.!!$F6 2459
12 TraesCS1D01G318600 chr1B 556965928 556970129 4201 False 928.5 1437 88.2460 513 1723 2 chr1B.!!$F7 1210
13 TraesCS1D01G318600 chr1A 509847977 509849710 1733 True 2525.0 2525 92.9750 696 2440 1 chr1A.!!$R6 1744
14 TraesCS1D01G318600 chr1A 509718595 509720185 1590 True 2423.0 2423 94.0630 696 2305 1 chr1A.!!$R4 1609
15 TraesCS1D01G318600 chr1A 510111533 510112727 1194 False 1581.0 1581 90.9240 1758 2929 1 chr1A.!!$F2 1171
16 TraesCS1D01G318600 chr1A 509540654 509541974 1320 True 881.5 1561 91.0455 1758 3129 2 chr1A.!!$R7 1371

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
480 481 2.397044 TGCCTGGAAAAATCCCAAGT 57.603 45.0 0.0 0.0 32.53 3.16 F
1488 1522 0.807667 CGCAGTATGGCTGGTGAGTC 60.808 60.0 0.0 0.0 45.14 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 2174 0.602638 CGTTGAGGCTGGCACACTTA 60.603 55.000 3.38 0.0 0.00 2.24 R
2724 5290 1.074248 TTTTTCCTCCGCCTGGACC 59.926 57.895 0.00 0.0 40.17 4.46 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
79 80 2.501723 TGCTCCTCTCATAAAGGGTGTC 59.498 50.000 0.00 0.00 34.46 3.67
119 120 2.880268 GGTTGTAAGTTTGTAACCCGCT 59.120 45.455 0.00 0.00 37.25 5.52
193 194 3.639952 AGTCTTACTACCCGCCTACATT 58.360 45.455 0.00 0.00 0.00 2.71
196 197 4.339247 GTCTTACTACCCGCCTACATTACA 59.661 45.833 0.00 0.00 0.00 2.41
480 481 2.397044 TGCCTGGAAAAATCCCAAGT 57.603 45.000 0.00 0.00 32.53 3.16
481 482 3.534357 TGCCTGGAAAAATCCCAAGTA 57.466 42.857 0.00 0.00 32.53 2.24
482 483 4.059773 TGCCTGGAAAAATCCCAAGTAT 57.940 40.909 0.00 0.00 32.53 2.12
483 484 5.199982 TGCCTGGAAAAATCCCAAGTATA 57.800 39.130 0.00 0.00 32.53 1.47
484 485 5.776358 TGCCTGGAAAAATCCCAAGTATAT 58.224 37.500 0.00 0.00 32.53 0.86
485 486 6.916909 TGCCTGGAAAAATCCCAAGTATATA 58.083 36.000 0.00 0.00 32.53 0.86
486 487 7.534852 TGCCTGGAAAAATCCCAAGTATATAT 58.465 34.615 0.00 0.00 32.53 0.86
487 488 8.674173 TGCCTGGAAAAATCCCAAGTATATATA 58.326 33.333 0.00 0.00 32.53 0.86
488 489 9.700831 GCCTGGAAAAATCCCAAGTATATATAT 57.299 33.333 0.00 0.00 32.53 0.86
1376 1410 4.379243 AACCAGACGCTGCGAGGG 62.379 66.667 30.47 25.50 0.00 4.30
1488 1522 0.807667 CGCAGTATGGCTGGTGAGTC 60.808 60.000 0.00 0.00 45.14 3.36
1506 1551 6.094603 GGTGAGTCGACTACTAGACCATTTTA 59.905 42.308 20.09 0.00 39.29 1.52
1824 2141 2.680352 AGCGACATCGACCCCACT 60.680 61.111 5.26 0.00 43.02 4.00
1857 2174 2.698855 ACATGATGCGGCTAAAGAGT 57.301 45.000 0.00 0.00 0.00 3.24
2163 2480 3.086282 GGTCAACCATTAAACCACCGAT 58.914 45.455 0.00 0.00 35.64 4.18
2371 2699 5.465724 GGAGATTATTCATGTCACGGTTACC 59.534 44.000 0.00 0.00 0.00 2.85
2714 5280 6.019801 GTGTATAAGTCATCTAAGGTTGTGCG 60.020 42.308 0.00 0.00 0.00 5.34
2715 5281 1.726853 AGTCATCTAAGGTTGTGCGC 58.273 50.000 0.00 0.00 0.00 6.09
2717 5283 0.613260 TCATCTAAGGTTGTGCGCCT 59.387 50.000 4.18 0.00 38.11 5.52
2718 5284 0.729116 CATCTAAGGTTGTGCGCCTG 59.271 55.000 4.18 0.00 36.30 4.85
2720 5286 0.320421 TCTAAGGTTGTGCGCCTGAC 60.320 55.000 4.18 0.00 36.30 3.51
2721 5287 0.602638 CTAAGGTTGTGCGCCTGACA 60.603 55.000 4.18 0.00 36.30 3.58
2724 5290 2.633657 GTTGTGCGCCTGACACTG 59.366 61.111 4.18 0.00 38.86 3.66
2725 5291 2.591429 TTGTGCGCCTGACACTGG 60.591 61.111 4.18 0.00 38.86 4.00
2727 5293 3.044305 GTGCGCCTGACACTGGTC 61.044 66.667 4.18 0.00 44.57 4.02
3058 6724 4.814771 TGCATTTGAGCTCATGTCTAGATG 59.185 41.667 19.04 13.14 34.99 2.90
3101 6768 4.026228 GGCGTTTTAGACCTAAGAATACGC 60.026 45.833 19.87 19.87 40.37 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 4.721776 ACACCCTTTATGAGAGGAGCATAA 59.278 41.667 0.00 0.00 36.67 1.90
60 61 2.101582 CCGACACCCTTTATGAGAGGAG 59.898 54.545 0.00 0.00 36.33 3.69
119 120 7.773489 TGAGAGAGAAGATGAAAGAAGAGAA 57.227 36.000 0.00 0.00 0.00 2.87
168 169 5.016173 TGTAGGCGGGTAGTAAGACTTTAA 58.984 41.667 0.00 0.00 0.00 1.52
169 170 4.599041 TGTAGGCGGGTAGTAAGACTTTA 58.401 43.478 0.00 0.00 0.00 1.85
170 171 3.434309 TGTAGGCGGGTAGTAAGACTTT 58.566 45.455 0.00 0.00 0.00 2.66
1376 1410 1.014564 CCCTCTCGACAAAGCCGAAC 61.015 60.000 0.00 0.00 35.48 3.95
1488 1522 8.592998 GTCATTTGTAAAATGGTCTAGTAGTCG 58.407 37.037 11.65 0.00 0.00 4.18
1824 2141 0.970427 TCATGTACTGCGGCTCCAGA 60.970 55.000 10.42 0.00 36.67 3.86
1857 2174 0.602638 CGTTGAGGCTGGCACACTTA 60.603 55.000 3.38 0.00 0.00 2.24
2099 2416 2.348998 CTTGGCTTCCGGTGAGCT 59.651 61.111 24.50 0.00 40.01 4.09
2163 2480 4.523083 AGTCAAAACAGCCTTGTACTTCA 58.477 39.130 0.00 0.00 36.23 3.02
2371 2699 8.742554 AACAAAGACAAACTTAGACAAAACTG 57.257 30.769 0.00 0.00 37.93 3.16
2634 5198 3.524014 TGCTTGTGCACTTGGTGG 58.476 55.556 19.41 3.00 45.31 4.61
2714 5280 2.348998 CCTGGACCAGTGTCAGGC 59.651 66.667 20.24 0.00 43.65 4.85
2715 5281 2.348998 GCCTGGACCAGTGTCAGG 59.651 66.667 20.24 15.85 43.65 3.86
2717 5283 3.625897 CCGCCTGGACCAGTGTCA 61.626 66.667 20.24 0.00 43.65 3.58
2718 5284 3.302347 CTCCGCCTGGACCAGTGTC 62.302 68.421 20.24 7.98 40.17 3.67
2720 5286 4.087892 CCTCCGCCTGGACCAGTG 62.088 72.222 20.24 12.43 40.17 3.66
2721 5287 3.846405 TTCCTCCGCCTGGACCAGT 62.846 63.158 20.24 0.00 40.17 4.00
2724 5290 1.074248 TTTTTCCTCCGCCTGGACC 59.926 57.895 0.00 0.00 40.17 4.46
2725 5291 4.813346 TTTTTCCTCCGCCTGGAC 57.187 55.556 0.00 0.00 40.17 4.02
3101 6768 2.092375 AGGAGGAAAATTAAGGAGGCCG 60.092 50.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.