Multiple sequence alignment - TraesCS7D01G417000

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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 TraesCS7D01G417000 chr7D 100.000 4040 0 0 1 4040 535756445 535752406 0.000000e+00 7461
1 TraesCS7D01G417000 chr7D 85.748 842 105 10 2577 3413 535757319 535758150 0.000000e+00 876
2 TraesCS7D01G417000 chr7D 80.569 422 46 19 3636 4028 535758772 535759186 3.950000e-75 292
3 TraesCS7D01G417000 chr7B 91.653 3738 169 59 369 3992 577756707 577752999 0.000000e+00 5042
4 TraesCS7D01G417000 chr7B 83.794 506 68 8 2730 3231 577758083 577758578 6.110000e-128 468
5 TraesCS7D01G417000 chr7B 89.496 238 10 3 37 259 577757215 577756978 1.840000e-73 287
6 TraesCS7D01G417000 chr7A 93.447 3235 143 36 550 3745 617688358 617691562 0.000000e+00 4735
7 TraesCS7D01G417000 chr7A 84.248 838 118 9 2580 3413 617687152 617686325 0.000000e+00 804
8 TraesCS7D01G417000 chr7A 92.739 303 14 3 3722 4017 617691582 617691883 8.020000e-117 431
9 TraesCS7D01G417000 chr7A 83.600 250 25 10 2 248 617688028 617688264 1.890000e-53 220
10 TraesCS7D01G417000 chr7A 84.024 169 23 3 3636 3801 617685739 617685572 4.180000e-35 159
11 TraesCS7D01G417000 chr6D 75.921 2035 425 50 1039 3051 75377274 75375283 0.000000e+00 983
12 TraesCS7D01G417000 chr6A 75.481 2027 446 38 1040 3051 91429167 91427177 0.000000e+00 942
13 TraesCS7D01G417000 chr6B 76.127 1864 404 32 1039 2889 149060031 149058196 0.000000e+00 939


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 TraesCS7D01G417000 chr7D 535752406 535756445 4039 True 7461.000000 7461 100.000000 1 4040 1 chr7D.!!$R1 4039
1 TraesCS7D01G417000 chr7D 535757319 535759186 1867 False 584.000000 876 83.158500 2577 4028 2 chr7D.!!$F1 1451
2 TraesCS7D01G417000 chr7B 577752999 577757215 4216 True 2664.500000 5042 90.574500 37 3992 2 chr7B.!!$R1 3955
3 TraesCS7D01G417000 chr7A 617688028 617691883 3855 False 1795.333333 4735 89.928667 2 4017 3 chr7A.!!$F1 4015
4 TraesCS7D01G417000 chr7A 617685572 617687152 1580 True 481.500000 804 84.136000 2580 3801 2 chr7A.!!$R1 1221
5 TraesCS7D01G417000 chr6D 75375283 75377274 1991 True 983.000000 983 75.921000 1039 3051 1 chr6D.!!$R1 2012
6 TraesCS7D01G417000 chr6A 91427177 91429167 1990 True 942.000000 942 75.481000 1040 3051 1 chr6A.!!$R1 2011
7 TraesCS7D01G417000 chr6B 149058196 149060031 1835 True 939.000000 939 76.127000 1039 2889 1 chr6B.!!$R1 1850

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
367 530 0.604578 CGGAAAGTAGTCCCCACGAA 59.395 55.000 0.0 0.0 33.74 3.85 F
611 855 1.079057 GTTTCGACTCTCCCAGCCC 60.079 63.158 0.0 0.0 0.00 5.19 F
2292 2599 0.847373 TCCCCAAGTACTGCAACCAA 59.153 50.000 0.0 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1795 1.228459 GGGGACGCCCTTGAGTTTT 60.228 57.895 13.58 0.0 44.66 2.43 R
2454 2761 2.937469 AGAGAGATGACAGCGTCTTG 57.063 50.000 9.49 0.0 40.42 3.02 R
3255 3569 1.991070 CCCCCATATGCTCTGAGGAAT 59.009 52.381 2.14 0.0 0.00 3.01 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
42 43 3.001406 ACCCAGGTAGACACGGCC 61.001 66.667 0.00 0.00 0.00 6.13
155 174 0.835941 GTCCATCCATCCAGCAGAGT 59.164 55.000 0.00 0.00 0.00 3.24
252 285 3.425404 CAATAATTGCGGTGAAACTCGG 58.575 45.455 0.00 0.00 36.74 4.63
259 292 1.593209 GGTGAAACTCGGACGCACA 60.593 57.895 0.00 0.00 36.74 4.57
261 294 1.300620 TGAAACTCGGACGCACAGG 60.301 57.895 0.00 0.00 0.00 4.00
262 295 2.027625 GAAACTCGGACGCACAGGG 61.028 63.158 0.00 0.00 0.00 4.45
360 523 2.884207 CCGCGCGGAAAGTAGTCC 60.884 66.667 44.86 0.00 37.50 3.85
361 524 2.884207 CGCGCGGAAAGTAGTCCC 60.884 66.667 24.84 0.00 33.74 4.46
363 526 2.975536 CGCGGAAAGTAGTCCCCA 59.024 61.111 0.00 0.00 33.74 4.96
364 527 1.447314 CGCGGAAAGTAGTCCCCAC 60.447 63.158 0.00 0.00 33.74 4.61
365 528 1.447314 GCGGAAAGTAGTCCCCACG 60.447 63.158 0.00 0.00 33.74 4.94
366 529 1.880819 GCGGAAAGTAGTCCCCACGA 61.881 60.000 0.00 0.00 33.74 4.35
367 530 0.604578 CGGAAAGTAGTCCCCACGAA 59.395 55.000 0.00 0.00 33.74 3.85
385 585 4.344865 GCAGAGGGCCACGGGAAA 62.345 66.667 6.18 0.00 36.11 3.13
387 587 1.675641 CAGAGGGCCACGGGAAAAG 60.676 63.158 6.18 0.00 0.00 2.27
388 588 2.361230 GAGGGCCACGGGAAAAGG 60.361 66.667 6.18 0.00 0.00 3.11
462 673 1.680989 AATTACCCAACCTGCGGCC 60.681 57.895 0.00 0.00 0.00 6.13
515 726 2.871637 GCCAGCCCCACAATTTCTTTTC 60.872 50.000 0.00 0.00 0.00 2.29
554 772 2.813726 CCAACCACAGACCGGACCA 61.814 63.158 9.46 0.00 0.00 4.02
556 774 3.178540 AACCACAGACCGGACCAGC 62.179 63.158 9.46 0.00 0.00 4.85
557 775 4.394712 CCACAGACCGGACCAGCC 62.395 72.222 9.46 0.00 0.00 4.85
560 778 3.636231 CAGACCGGACCAGCCCAA 61.636 66.667 9.46 0.00 0.00 4.12
611 855 1.079057 GTTTCGACTCTCCCAGCCC 60.079 63.158 0.00 0.00 0.00 5.19
612 856 1.229209 TTTCGACTCTCCCAGCCCT 60.229 57.895 0.00 0.00 0.00 5.19
613 857 1.258445 TTTCGACTCTCCCAGCCCTC 61.258 60.000 0.00 0.00 0.00 4.30
761 1027 4.699522 GTCACCCACCTCCACGGC 62.700 72.222 0.00 0.00 35.61 5.68
812 1084 4.101077 CTCCCTCCCTCCCTGCCT 62.101 72.222 0.00 0.00 0.00 4.75
981 1288 2.187946 CATTCGGAGGGCGAGCTT 59.812 61.111 0.00 0.00 0.00 3.74
988 1295 3.642778 GAGGGCGAGCTTGTGCGTA 62.643 63.158 2.14 0.00 45.42 4.42
990 1297 3.188786 GGCGAGCTTGTGCGTAGG 61.189 66.667 2.14 0.00 45.42 3.18
1233 1540 4.402528 CCCAACATCGACCGGGCA 62.403 66.667 8.76 0.00 0.00 5.36
1616 1923 1.381191 TCGCTATGCAGGAGGACCA 60.381 57.895 0.00 0.00 38.94 4.02
1734 2041 3.775654 GGGCGGCTCAGCTACTGT 61.776 66.667 9.56 0.00 37.29 3.55
1818 2125 3.006430 TCGATTACTTGCAAGACCAGACA 59.994 43.478 32.50 7.88 0.00 3.41
2067 2374 1.467734 CTGAGGCTGCTTGATGTGTTC 59.532 52.381 0.00 0.00 0.00 3.18
2232 2539 3.176578 CTGCAGCGCAAAATGCCG 61.177 61.111 11.47 2.87 41.12 5.69
2292 2599 0.847373 TCCCCAAGTACTGCAACCAA 59.153 50.000 0.00 0.00 0.00 3.67
2454 2761 1.095807 GGGCAAAGGCGTATGAGGAC 61.096 60.000 0.00 0.00 42.47 3.85
2763 3072 0.318441 CCGCGTGGATCATACCAGAT 59.682 55.000 10.20 0.00 40.85 2.90
3146 3459 3.202706 GGCGTTGAAGATCCCGGC 61.203 66.667 0.00 0.00 38.68 6.13
3161 3474 1.523711 CGGCTGTGCGGGATACATT 60.524 57.895 0.00 0.00 39.74 2.71
3174 3487 3.673809 GGGATACATTGTAATCGCTCGAC 59.326 47.826 0.00 0.00 39.74 4.20
3255 3569 3.245264 GGGGGAGAAGGAAACTGAAATCA 60.245 47.826 0.00 0.00 42.68 2.57
3273 3587 4.571369 ATCATTCCTCAGAGCATATGGG 57.429 45.455 4.56 0.00 0.00 4.00
3290 3604 2.039724 GGGTCCCCTTCCCCTAGG 60.040 72.222 0.06 0.06 39.08 3.02
3307 3621 2.134789 AGGCCATTCTCTTCGCATTT 57.865 45.000 5.01 0.00 0.00 2.32
3508 4067 6.939622 TGACAGTGATCAATTGACTGACTAT 58.060 36.000 24.71 11.71 39.64 2.12
3555 4115 2.096417 CGAAGTTTCGGTTCCACATGTC 60.096 50.000 6.38 0.00 46.30 3.06
3556 4116 2.930826 AGTTTCGGTTCCACATGTCT 57.069 45.000 0.00 0.00 0.00 3.41
3570 4130 7.264373 TCCACATGTCTTTTCTTTCTCTTTC 57.736 36.000 0.00 0.00 0.00 2.62
3634 4389 1.603802 CAGATAAATCATGCGCCCGTT 59.396 47.619 4.18 0.00 0.00 4.44
3681 4437 8.939201 TGAGTGTTTCATGCAAAAAGAATTAA 57.061 26.923 0.00 0.00 0.00 1.40
3707 4463 3.577805 AGTTTACCTTGCTTGGTGAGT 57.422 42.857 10.70 1.50 41.05 3.41
3792 4592 1.691976 TGTCCGGTCACAGAAGAATGT 59.308 47.619 0.00 0.00 0.00 2.71
3939 4764 8.721478 AGATGTTGTGTCAGTATTTGTAATCAC 58.279 33.333 0.00 0.00 0.00 3.06
4018 4849 8.609176 CATCATCATGAAGGGCTTAAAAATTTG 58.391 33.333 0.00 0.00 30.57 2.32
4019 4850 7.905265 TCATCATGAAGGGCTTAAAAATTTGA 58.095 30.769 0.00 0.00 0.00 2.69
4020 4851 7.818930 TCATCATGAAGGGCTTAAAAATTTGAC 59.181 33.333 0.00 0.00 0.00 3.18
4021 4852 6.155827 TCATGAAGGGCTTAAAAATTTGACG 58.844 36.000 0.00 0.00 0.00 4.35
4022 4853 5.776173 TGAAGGGCTTAAAAATTTGACGA 57.224 34.783 0.00 0.00 0.00 4.20
4023 4854 6.339587 TGAAGGGCTTAAAAATTTGACGAT 57.660 33.333 0.00 0.00 0.00 3.73
4024 4855 6.155827 TGAAGGGCTTAAAAATTTGACGATG 58.844 36.000 0.00 0.00 0.00 3.84
4025 4856 5.722021 AGGGCTTAAAAATTTGACGATGT 57.278 34.783 0.00 0.00 0.00 3.06
4027 4858 5.925969 AGGGCTTAAAAATTTGACGATGTTG 59.074 36.000 0.00 0.00 0.00 3.33
4028 4859 5.694458 GGGCTTAAAAATTTGACGATGTTGT 59.306 36.000 0.00 0.00 0.00 3.32
4029 4860 6.864165 GGGCTTAAAAATTTGACGATGTTGTA 59.136 34.615 0.00 0.00 0.00 2.41
4030 4861 7.382759 GGGCTTAAAAATTTGACGATGTTGTAA 59.617 33.333 0.00 0.00 0.00 2.41
4031 4862 8.756864 GGCTTAAAAATTTGACGATGTTGTAAA 58.243 29.630 0.00 0.00 0.00 2.01
4039 4870 9.638239 AATTTGACGATGTTGTAAATATTTGCT 57.362 25.926 15.93 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.701663 CACGCCAGTGGAGTTCAT 57.298 55.556 16.77 0.00 44.34 2.57
136 138 0.835941 ACTCTGCTGGATGGATGGAC 59.164 55.000 0.00 0.00 0.00 4.02
140 142 0.469070 GCTCACTCTGCTGGATGGAT 59.531 55.000 0.00 0.00 0.00 3.41
208 237 3.614616 CCTACGCTCACTTCAATCTGTTC 59.385 47.826 0.00 0.00 0.00 3.18
252 285 2.047560 GGTACACCCCTGTGCGTC 60.048 66.667 0.00 0.00 46.86 5.19
259 292 0.766674 TTGCTGTCAGGTACACCCCT 60.767 55.000 1.14 0.00 36.42 4.79
261 294 0.949105 CGTTGCTGTCAGGTACACCC 60.949 60.000 1.14 0.00 36.42 4.61
262 295 0.949105 CCGTTGCTGTCAGGTACACC 60.949 60.000 1.14 0.00 33.45 4.16
264 297 1.301401 GCCGTTGCTGTCAGGTACA 60.301 57.895 1.14 0.00 36.42 2.90
265 298 1.301401 TGCCGTTGCTGTCAGGTAC 60.301 57.895 1.14 0.00 38.71 3.34
266 299 1.301401 GTGCCGTTGCTGTCAGGTA 60.301 57.895 1.14 0.00 38.71 3.08
298 373 4.685467 TTCCCGGTTCGGTTCGGC 62.685 66.667 0.00 0.00 46.80 5.54
306 381 2.674084 CGCCGTTTCTTCCCGGTTC 61.674 63.158 0.00 0.00 45.91 3.62
307 382 2.667199 CGCCGTTTCTTCCCGGTT 60.667 61.111 0.00 0.00 45.91 4.44
308 383 3.618750 TCGCCGTTTCTTCCCGGT 61.619 61.111 0.00 0.00 45.91 5.28
309 384 3.116531 GTCGCCGTTTCTTCCCGG 61.117 66.667 0.00 0.00 46.90 5.73
310 385 3.475774 CGTCGCCGTTTCTTCCCG 61.476 66.667 0.00 0.00 0.00 5.14
311 386 3.116531 CCGTCGCCGTTTCTTCCC 61.117 66.667 0.00 0.00 0.00 3.97
348 511 0.604578 TTCGTGGGGACTACTTTCCG 59.395 55.000 0.00 0.00 36.38 4.30
354 517 0.173708 CTCTGCTTCGTGGGGACTAC 59.826 60.000 0.00 0.00 0.00 2.73
355 518 0.970937 CCTCTGCTTCGTGGGGACTA 60.971 60.000 0.00 0.00 0.00 2.59
358 521 3.003173 CCCTCTGCTTCGTGGGGA 61.003 66.667 0.00 0.00 39.42 4.81
360 523 4.785453 GGCCCTCTGCTTCGTGGG 62.785 72.222 0.00 0.00 40.92 4.61
361 524 4.020617 TGGCCCTCTGCTTCGTGG 62.021 66.667 0.00 0.00 40.92 4.94
363 526 4.379243 CGTGGCCCTCTGCTTCGT 62.379 66.667 0.00 0.00 40.92 3.85
365 528 4.785453 CCCGTGGCCCTCTGCTTC 62.785 72.222 0.00 0.00 40.92 3.86
384 584 2.983592 CTTTGCGTCGGGGCCTTT 60.984 61.111 0.84 0.00 0.00 3.11
385 585 4.265056 ACTTTGCGTCGGGGCCTT 62.265 61.111 0.84 0.00 0.00 4.35
388 588 3.423154 CTCACTTTGCGTCGGGGC 61.423 66.667 0.00 0.00 0.00 5.80
396 599 2.459934 CGGGTTTTGTTCTCACTTTGC 58.540 47.619 0.00 0.00 0.00 3.68
497 708 5.368145 GAAAAGAAAAGAAATTGTGGGGCT 58.632 37.500 0.00 0.00 0.00 5.19
498 709 4.211164 CGAAAAGAAAAGAAATTGTGGGGC 59.789 41.667 0.00 0.00 0.00 5.80
499 710 5.462068 GTCGAAAAGAAAAGAAATTGTGGGG 59.538 40.000 0.00 0.00 0.00 4.96
500 711 6.273071 AGTCGAAAAGAAAAGAAATTGTGGG 58.727 36.000 0.00 0.00 0.00 4.61
515 726 1.566018 GCGTGGGTGGAGTCGAAAAG 61.566 60.000 0.00 0.00 0.00 2.27
611 855 2.956333 AGTTTTTGGACGGGAAAAGGAG 59.044 45.455 0.00 0.00 0.00 3.69
612 856 2.953648 GAGTTTTTGGACGGGAAAAGGA 59.046 45.455 0.00 0.00 0.00 3.36
613 857 2.956333 AGAGTTTTTGGACGGGAAAAGG 59.044 45.455 0.00 0.00 0.00 3.11
670 932 2.364317 TGGAGCGGGGAGGAGAAG 60.364 66.667 0.00 0.00 0.00 2.85
718 984 1.452833 GGGAAGATGGGTGCTCTGC 60.453 63.158 0.00 0.00 0.00 4.26
721 987 1.452833 GCTGGGAAGATGGGTGCTC 60.453 63.158 0.00 0.00 0.00 4.26
811 1083 1.399471 GCGTACTACTTATCCGCGGAG 60.399 57.143 33.87 22.13 34.66 4.63
812 1084 0.588252 GCGTACTACTTATCCGCGGA 59.412 55.000 33.12 33.12 34.66 5.54
814 1086 1.003116 AGTGCGTACTACTTATCCGCG 60.003 52.381 3.62 0.00 46.77 6.46
815 1087 2.648426 GAGTGCGTACTACTTATCCGC 58.352 52.381 6.01 0.00 44.27 5.54
865 1137 4.776322 CAATCTGCCGGCCGGTGA 62.776 66.667 42.53 36.97 37.65 4.02
1005 1312 2.368192 TCCGCCCCCTGATCCATT 60.368 61.111 0.00 0.00 0.00 3.16
1488 1795 1.228459 GGGGACGCCCTTGAGTTTT 60.228 57.895 13.58 0.00 44.66 2.43
1818 2125 3.397439 AGCGCCTGAGCATCCTGT 61.397 61.111 2.29 0.00 39.83 4.00
2067 2374 4.891627 TCTGAGCTTACTGAGAGAATCG 57.108 45.455 0.00 0.00 42.67 3.34
2454 2761 2.937469 AGAGAGATGACAGCGTCTTG 57.063 50.000 9.49 0.00 40.42 3.02
2763 3072 1.126488 CCCTCTGCTGCAGATCCTTA 58.874 55.000 30.50 9.41 39.92 2.69
3146 3459 3.184379 CGATTACAATGTATCCCGCACAG 59.816 47.826 0.00 0.00 0.00 3.66
3156 3469 3.678915 TCGTCGAGCGATTACAATGTA 57.321 42.857 6.09 0.00 45.68 2.29
3174 3487 2.992543 GCTCCAGCAGCTCTTATTATCG 59.007 50.000 0.00 0.00 45.83 2.92
3255 3569 1.991070 CCCCCATATGCTCTGAGGAAT 59.009 52.381 2.14 0.00 0.00 3.01
3290 3604 2.927553 ACAAATGCGAAGAGAATGGC 57.072 45.000 0.00 0.00 0.00 4.40
3508 4067 7.609097 AGATAGACTGATTTCTTGCCTCATA 57.391 36.000 0.00 0.00 0.00 2.15
3634 4389 2.779951 TTCAGAAGCTAGCGCCGCAA 62.780 55.000 13.36 3.91 36.60 4.85
3681 4437 6.717289 TCACCAAGCAAGGTAAACTATACAT 58.283 36.000 0.00 0.00 40.77 2.29
3686 4442 4.699925 ACTCACCAAGCAAGGTAAACTA 57.300 40.909 0.00 0.00 40.77 2.24
3792 4592 4.858692 GCGTACAAGGTACGAATTTCAGTA 59.141 41.667 27.21 0.00 42.94 2.74


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

AutoCloner maintained by Alex Coulton.