Multiple sequence alignment - TraesCS1D01G339200

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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 TraesCS1D01G339200 chr1D 100.000 3458 0 0 1 3458 429024188 429027645 0.000000e+00 6386.0
1 TraesCS1D01G339200 chr1D 90.730 3495 194 57 1 3454 429490990 429494395 0.000000e+00 4540.0
2 TraesCS1D01G339200 chr1B 94.336 2560 119 13 905 3458 580537520 580540059 0.000000e+00 3901.0
3 TraesCS1D01G339200 chr1B 77.525 1406 270 35 999 2393 589225986 589224616 0.000000e+00 804.0
4 TraesCS1D01G339200 chr1B 87.071 495 42 9 1 484 580530651 580531134 1.090000e-149 540.0
5 TraesCS1D01G339200 chr1B 90.367 218 7 5 558 773 580531717 580531922 1.220000e-69 274.0
6 TraesCS1D01G339200 chr1B 87.766 188 23 0 1 188 580532753 580532940 1.620000e-53 220.0
7 TraesCS1D01G339200 chr1A 91.648 2263 134 24 268 2500 526756813 526759050 0.000000e+00 3081.0
8 TraesCS1D01G339200 chr1A 77.163 1410 260 46 1001 2391 441032364 441033730 0.000000e+00 763.0
9 TraesCS1D01G339200 chr1A 83.750 720 76 16 2775 3457 526918602 526919317 0.000000e+00 643.0
10 TraesCS1D01G339200 chr1A 79.057 530 93 8 2565 3092 558888477 558888990 7.100000e-92 348.0
11 TraesCS1D01G339200 chr1A 93.000 100 6 1 2541 2640 526763385 526763483 1.000000e-30 145.0
12 TraesCS1D01G339200 chr1A 100.000 30 0 0 2510 2539 526763319 526763348 4.820000e-04 56.5
13 TraesCS1D01G339200 chr7D 80.259 1469 248 30 1004 2451 92762469 92763916 0.000000e+00 1068.0
14 TraesCS1D01G339200 chr7B 80.153 1436 254 23 1010 2440 45176949 45175540 0.000000e+00 1044.0
15 TraesCS1D01G339200 chr7A 80.132 1213 210 26 1004 2197 94914811 94916011 0.000000e+00 876.0
16 TraesCS1D01G339200 chr2A 74.927 1033 202 48 1330 2341 179348073 179349069 1.480000e-113 420.0
17 TraesCS1D01G339200 chr5D 72.507 1444 325 57 1019 2420 431970290 431971703 5.380000e-108 401.0
18 TraesCS1D01G339200 chr5A 72.268 1446 325 58 1019 2420 547060457 547061870 2.520000e-101 379.0
19 TraesCS1D01G339200 chr5A 87.671 73 7 2 2548 2618 229519177 229519249 2.210000e-12 84.2
20 TraesCS1D01G339200 chr6A 82.500 400 59 9 2570 2966 506324304 506323913 1.190000e-89 340.0
21 TraesCS1D01G339200 chr6A 77.876 565 84 23 2833 3364 49472598 49472042 2.590000e-81 313.0
22 TraesCS1D01G339200 chr6D 78.136 590 82 26 2678 3236 296204761 296204188 7.150000e-87 331.0
23 TraesCS1D01G339200 chr6B 75.426 704 106 38 2570 3238 550146677 550146006 2.630000e-71 279.0
24 TraesCS1D01G339200 chr6B 80.072 276 37 12 2569 2843 88733641 88733383 4.560000e-44 189.0
25 TraesCS1D01G339200 chr3B 75.276 453 92 17 2563 3012 428135552 428135987 7.570000e-47 198.0
26 TraesCS1D01G339200 chr5B 84.884 86 11 2 2990 3074 248804107 248804191 6.150000e-13 86.1
27 TraesCS1D01G339200 chr5B 84.706 85 12 1 2990 3074 248926950 248926867 2.210000e-12 84.2
28 TraesCS1D01G339200 chr5B 100.000 30 0 0 436 465 270665916 270665945 4.820000e-04 56.5
29 TraesCS1D01G339200 chr2D 88.235 51 6 0 429 479 27275671 27275721 1.040000e-05 62.1


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 TraesCS1D01G339200 chr1D 429024188 429027645 3457 False 6386.000000 6386 100.000000 1 3458 1 chr1D.!!$F1 3457
1 TraesCS1D01G339200 chr1D 429490990 429494395 3405 False 4540.000000 4540 90.730000 1 3454 1 chr1D.!!$F2 3453
2 TraesCS1D01G339200 chr1B 580537520 580540059 2539 False 3901.000000 3901 94.336000 905 3458 1 chr1B.!!$F1 2553
3 TraesCS1D01G339200 chr1B 589224616 589225986 1370 True 804.000000 804 77.525000 999 2393 1 chr1B.!!$R1 1394
4 TraesCS1D01G339200 chr1B 580530651 580532940 2289 False 344.666667 540 88.401333 1 773 3 chr1B.!!$F2 772
5 TraesCS1D01G339200 chr1A 526756813 526759050 2237 False 3081.000000 3081 91.648000 268 2500 1 chr1A.!!$F2 2232
6 TraesCS1D01G339200 chr1A 441032364 441033730 1366 False 763.000000 763 77.163000 1001 2391 1 chr1A.!!$F1 1390
7 TraesCS1D01G339200 chr1A 526918602 526919317 715 False 643.000000 643 83.750000 2775 3457 1 chr1A.!!$F3 682
8 TraesCS1D01G339200 chr1A 558888477 558888990 513 False 348.000000 348 79.057000 2565 3092 1 chr1A.!!$F4 527
9 TraesCS1D01G339200 chr7D 92762469 92763916 1447 False 1068.000000 1068 80.259000 1004 2451 1 chr7D.!!$F1 1447
10 TraesCS1D01G339200 chr7B 45175540 45176949 1409 True 1044.000000 1044 80.153000 1010 2440 1 chr7B.!!$R1 1430
11 TraesCS1D01G339200 chr7A 94914811 94916011 1200 False 876.000000 876 80.132000 1004 2197 1 chr7A.!!$F1 1193
12 TraesCS1D01G339200 chr2A 179348073 179349069 996 False 420.000000 420 74.927000 1330 2341 1 chr2A.!!$F1 1011
13 TraesCS1D01G339200 chr5D 431970290 431971703 1413 False 401.000000 401 72.507000 1019 2420 1 chr5D.!!$F1 1401
14 TraesCS1D01G339200 chr5A 547060457 547061870 1413 False 379.000000 379 72.268000 1019 2420 1 chr5A.!!$F2 1401
15 TraesCS1D01G339200 chr6A 49472042 49472598 556 True 313.000000 313 77.876000 2833 3364 1 chr6A.!!$R1 531
16 TraesCS1D01G339200 chr6D 296204188 296204761 573 True 331.000000 331 78.136000 2678 3236 1 chr6D.!!$R1 558
17 TraesCS1D01G339200 chr6B 550146006 550146677 671 True 279.000000 279 75.426000 2570 3238 1 chr6B.!!$R2 668

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
487 499 2.228138 ACGTTGGTTCGCTCTACAAA 57.772 45.0 0.00 0.00 0.0 2.83 F
1233 1830 1.949847 ATCTCCCGGACGTCAAGCTG 61.950 60.0 18.91 4.39 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2436 3129 2.044848 ACGTTGGGCAACACCACA 60.045 55.556 0.00 0.0 41.03 4.17 R
2554 3252 1.000274 GAAAAAGCGCCACACTCCATT 60.000 47.619 2.29 0.0 0.00 3.16 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
85 86 6.876789 ACAACAACTATTTACCGATGTGATGA 59.123 34.615 0.00 0.00 0.00 2.92
258 260 5.885912 AGGTGCCGATTACAATCACTTTTAT 59.114 36.000 3.07 0.00 35.11 1.40
259 261 5.971202 GGTGCCGATTACAATCACTTTTATG 59.029 40.000 3.07 0.00 35.11 1.90
260 262 6.183360 GGTGCCGATTACAATCACTTTTATGA 60.183 38.462 3.07 0.00 35.11 2.15
261 263 7.417612 GTGCCGATTACAATCACTTTTATGAT 58.582 34.615 3.07 0.00 41.20 2.45
262 264 7.376866 GTGCCGATTACAATCACTTTTATGATG 59.623 37.037 3.07 0.00 39.32 3.07
263 265 7.281999 TGCCGATTACAATCACTTTTATGATGA 59.718 33.333 3.07 0.00 39.32 2.92
264 266 8.292448 GCCGATTACAATCACTTTTATGATGAT 58.708 33.333 3.07 0.00 39.32 2.45
265 267 9.603298 CCGATTACAATCACTTTTATGATGATG 57.397 33.333 3.07 0.00 39.32 3.07
286 288 8.442632 TGATGATGATGATGATGATGATGATG 57.557 34.615 0.00 0.00 0.00 3.07
297 299 7.005709 TGATGATGATGATGAGCACTTAGAT 57.994 36.000 0.00 0.00 0.00 1.98
407 409 3.436704 TGAACTCTAGGAAAATGCAAGCG 59.563 43.478 0.00 0.00 0.00 4.68
424 426 4.201950 GCAAGCGTCAATATCAAGTCCAAT 60.202 41.667 0.00 0.00 0.00 3.16
487 499 2.228138 ACGTTGGTTCGCTCTACAAA 57.772 45.000 0.00 0.00 0.00 2.83
526 1089 9.844257 CTTGAGAATTAGAAATAATGAGAGGGT 57.156 33.333 0.00 0.00 0.00 4.34
605 1170 4.125124 TGGTGGAATTCATGGGAGAAAA 57.875 40.909 7.93 0.00 0.00 2.29
667 1232 4.045636 GGCAAACCTACCAATGCTAATG 57.954 45.455 0.00 0.00 38.79 1.90
668 1233 3.447742 GCAAACCTACCAATGCTAATGC 58.552 45.455 0.00 0.00 35.93 3.56
669 1234 3.737972 GCAAACCTACCAATGCTAATGCC 60.738 47.826 0.00 0.00 38.71 4.40
670 1235 3.380471 AACCTACCAATGCTAATGCCA 57.620 42.857 0.00 0.00 38.71 4.92
671 1236 3.600448 ACCTACCAATGCTAATGCCAT 57.400 42.857 0.00 0.00 38.71 4.40
750 1315 6.529477 CCAACGCTAGTGATGATGTATGATAG 59.471 42.308 14.53 0.00 0.00 2.08
751 1316 6.825944 ACGCTAGTGATGATGTATGATAGT 57.174 37.500 10.99 0.00 0.00 2.12
819 1384 6.014840 ACTCTAGGAAGTCACCGTTATTCAAA 60.015 38.462 0.00 0.00 34.73 2.69
821 1386 7.039882 TCTAGGAAGTCACCGTTATTCAAATC 58.960 38.462 0.00 0.00 34.73 2.17
832 1397 5.450412 CCGTTATTCAAATCTCCAACATGGG 60.450 44.000 0.00 0.00 38.32 4.00
862 1427 3.241022 CGTTATCGTCGTTCCGTACAAAC 60.241 47.826 0.00 0.00 0.00 2.93
893 1472 6.775629 ACTTATTTGCAAGGAAAGACCAACTA 59.224 34.615 18.70 0.00 42.04 2.24
1233 1830 1.949847 ATCTCCCGGACGTCAAGCTG 61.950 60.000 18.91 4.39 0.00 4.24
1325 1922 3.251972 GCAGCTATAATTGGCTTGACCTC 59.748 47.826 0.00 0.00 37.63 3.85
2513 3211 5.351465 TGATGTTTCTTCTTATTCGAGTGCC 59.649 40.000 0.00 0.00 0.00 5.01
2539 3237 5.825679 AGTAATTACTGCGGGCAAATAATCA 59.174 36.000 17.35 0.00 34.72 2.57
2554 3252 7.372714 GCAAATAATCATGGATCATAGCAACA 58.627 34.615 0.00 0.00 0.00 3.33
2625 3332 5.804639 AGATGCAATAACACTAGGTTGTCA 58.195 37.500 0.00 0.00 40.73 3.58
2660 3367 5.163163 CCCAGGATCATTTCTTCTATGTCCA 60.163 44.000 0.00 0.00 31.39 4.02
2674 3381 2.293677 TGTCCAAATCATCCGACGAG 57.706 50.000 0.00 0.00 0.00 4.18
2675 3382 1.134818 TGTCCAAATCATCCGACGAGG 60.135 52.381 0.00 0.00 42.97 4.63
2683 3390 3.991999 TCCGACGAGGACGACAAT 58.008 55.556 0.00 0.00 45.98 2.71
2734 3443 2.738147 ACGCTCGTGAATTTCTCCG 58.262 52.632 0.00 0.91 0.00 4.63
2749 3458 3.095912 TCTCCGGAATCTCACAGGTTA 57.904 47.619 5.23 0.00 0.00 2.85
2809 3519 2.668212 CCGAAGCAAAGCCGACCA 60.668 61.111 0.00 0.00 0.00 4.02
2822 3532 0.400594 CCGACCACCCCTTTCTTCTT 59.599 55.000 0.00 0.00 0.00 2.52
2965 3679 0.593008 GGTGCCGAAAACAACCGAAC 60.593 55.000 0.00 0.00 0.00 3.95
3249 4096 1.135774 GCGGAAATGTTCGGGACTTTC 60.136 52.381 0.00 0.00 0.00 2.62
3250 4097 2.423577 CGGAAATGTTCGGGACTTTCT 58.576 47.619 9.62 0.00 31.64 2.52
3291 4141 9.849166 AAAATTATGAAATGACCGATTTTACGT 57.151 25.926 0.00 0.00 34.18 3.57
3443 4334 6.545666 TGATTCGAATTATGTTAACCTGGCAT 59.454 34.615 12.81 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.123344 AGTTGTGTAGGCGAAAAATCATACC 59.877 40.000 0.00 0.00 0.00 2.73
85 86 5.793817 TCTAAACGTGCATCATAGGCATAT 58.206 37.500 0.00 0.00 44.11 1.78
193 194 9.060347 ACTAAATTGTAATAGGCATCACATCAG 57.940 33.333 0.00 0.00 0.00 2.90
258 260 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
259 261 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
260 262 9.064706 CATCATCATCATCATCATCATCATCAT 57.935 33.333 0.00 0.00 0.00 2.45
261 263 8.267183 TCATCATCATCATCATCATCATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
262 264 8.668510 TCATCATCATCATCATCATCATCATC 57.331 34.615 0.00 0.00 0.00 2.92
263 265 7.228308 GCTCATCATCATCATCATCATCATCAT 59.772 37.037 0.00 0.00 0.00 2.45
264 266 6.540189 GCTCATCATCATCATCATCATCATCA 59.460 38.462 0.00 0.00 0.00 3.07
265 267 6.540189 TGCTCATCATCATCATCATCATCATC 59.460 38.462 0.00 0.00 0.00 2.92
266 268 6.317391 GTGCTCATCATCATCATCATCATCAT 59.683 38.462 0.00 0.00 0.00 2.45
297 299 8.153221 TGTATTTGTAGGGATCAAAAGGACTA 57.847 34.615 0.00 0.00 38.11 2.59
424 426 7.839705 AGGACAGTGATATTCCTAGTTCAAGTA 59.160 37.037 0.00 0.00 38.03 2.24
518 1081 3.387962 AGATGCCATCTTTACCCTCTCA 58.612 45.455 0.08 0.00 35.76 3.27
529 1092 2.705658 TCCACCGATAAAGATGCCATCT 59.294 45.455 0.08 0.08 42.61 2.90
530 1093 3.126001 TCCACCGATAAAGATGCCATC 57.874 47.619 0.00 0.00 0.00 3.51
531 1094 3.576078 TTCCACCGATAAAGATGCCAT 57.424 42.857 0.00 0.00 0.00 4.40
605 1170 1.196012 GGTCCTCTCATCGGGTCTTT 58.804 55.000 0.00 0.00 0.00 2.52
666 1231 5.991606 CGTCCTCTTCTAATTATCAATGGCA 59.008 40.000 0.00 0.00 0.00 4.92
667 1232 5.992217 ACGTCCTCTTCTAATTATCAATGGC 59.008 40.000 0.00 0.00 0.00 4.40
668 1233 7.326305 CGTACGTCCTCTTCTAATTATCAATGG 59.674 40.741 7.22 0.00 0.00 3.16
669 1234 7.861372 ACGTACGTCCTCTTCTAATTATCAATG 59.139 37.037 16.72 0.00 0.00 2.82
670 1235 7.861372 CACGTACGTCCTCTTCTAATTATCAAT 59.139 37.037 19.94 0.00 0.00 2.57
671 1236 7.191551 CACGTACGTCCTCTTCTAATTATCAA 58.808 38.462 19.94 0.00 0.00 2.57
788 1353 3.526534 GGTGACTTCCTAGAGTTGCATC 58.473 50.000 0.00 0.00 0.00 3.91
819 1384 0.994247 TGTGAGCCCATGTTGGAGAT 59.006 50.000 0.00 0.00 40.96 2.75
821 1386 1.386533 GATGTGAGCCCATGTTGGAG 58.613 55.000 0.00 0.00 40.96 3.86
832 1397 1.823828 ACGACGATAACGATGTGAGC 58.176 50.000 0.00 0.00 42.66 4.26
862 1427 7.078228 GTCTTTCCTTGCAAATAAGTACAGTG 58.922 38.462 0.00 0.00 0.00 3.66
872 1437 6.458210 CATTAGTTGGTCTTTCCTTGCAAAT 58.542 36.000 0.00 0.00 37.07 2.32
874 1439 4.280677 CCATTAGTTGGTCTTTCCTTGCAA 59.719 41.667 0.00 0.00 40.99 4.08
893 1472 0.921896 CCCATGAGTGAGACCCCATT 59.078 55.000 0.00 0.00 0.00 3.16
958 1545 2.032799 GTGGCTACTCGATCTGTCTCTG 59.967 54.545 0.00 0.00 0.00 3.35
2436 3129 2.044848 ACGTTGGGCAACACCACA 60.045 55.556 0.00 0.00 41.03 4.17
2513 3211 6.854496 TTATTTGCCCGCAGTAATTACTAG 57.146 37.500 17.62 13.96 34.13 2.57
2539 3237 4.825634 CACTCCATTGTTGCTATGATCCAT 59.174 41.667 0.00 0.00 0.00 3.41
2554 3252 1.000274 GAAAAAGCGCCACACTCCATT 60.000 47.619 2.29 0.00 0.00 3.16
2625 3332 1.739338 GATCCTGGGCGACGATGTCT 61.739 60.000 0.00 0.00 0.00 3.41
2674 3381 2.599082 GAGTTCATCGTCATTGTCGTCC 59.401 50.000 3.38 0.00 0.00 4.79
2675 3382 2.599082 GGAGTTCATCGTCATTGTCGTC 59.401 50.000 3.38 0.00 0.00 4.20
2676 3383 2.029380 TGGAGTTCATCGTCATTGTCGT 60.029 45.455 3.38 0.00 0.00 4.34
2683 3390 3.452264 AGATGGATTGGAGTTCATCGTCA 59.548 43.478 0.00 0.00 40.43 4.35
2734 3443 7.698130 CGATTCAATTTTAACCTGTGAGATTCC 59.302 37.037 0.00 0.00 0.00 3.01
2749 3458 6.624423 CCCACTGATCTTTCGATTCAATTTT 58.376 36.000 0.00 0.00 0.00 1.82
2809 3519 2.075837 CGGGGAAGAAGAAAGGGGT 58.924 57.895 0.00 0.00 0.00 4.95
2965 3679 1.227823 TGGTCTTGTTGCCGACAGG 60.228 57.895 0.00 0.00 39.94 4.00
3238 4085 3.181483 GCGGTATCTTAGAAAGTCCCGAA 60.181 47.826 14.09 0.00 36.75 4.30
3274 4122 8.433421 AATAGATCACGTAAAATCGGTCATTT 57.567 30.769 0.00 0.00 36.12 2.32
3291 4141 4.611119 TCGGCCCCGAATAGATCA 57.389 55.556 6.99 0.00 46.01 2.92


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

AutoCloner maintained by Alex Coulton.