Multiple sequence alignment - TraesCS6A01G024000

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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 TraesCS6A01G024000 chr6A 100.000 4443 0 0 1 4443 11962972 11967414 0.000000e+00 8205.0
1 TraesCS6A01G024000 chr6D 93.320 4521 194 57 2 4441 10413547 10418040 0.000000e+00 6577.0
2 TraesCS6A01G024000 chr6B 94.757 3452 150 18 683 4108 19125142 19128588 0.000000e+00 5343.0
3 TraesCS6A01G024000 chr6B 88.857 350 31 7 4096 4443 19129442 19129785 1.480000e-114 424.0
4 TraesCS6A01G024000 chr6B 81.289 481 53 19 2 463 19124279 19124741 5.470000e-94 355.0
5 TraesCS6A01G024000 chr2B 95.000 40 1 1 303 342 779043653 779043615 1.330000e-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 TraesCS6A01G024000 chr6A 11962972 11967414 4442 False 8205.000000 8205 100.000 1 4443 1 chr6A.!!$F1 4442
1 TraesCS6A01G024000 chr6D 10413547 10418040 4493 False 6577.000000 6577 93.320 2 4441 1 chr6D.!!$F1 4439
2 TraesCS6A01G024000 chr6B 19124279 19129785 5506 False 2040.666667 5343 88.301 2 4443 3 chr6B.!!$F1 4441

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
608 679 0.107831 CAGTGTCCCGAACCCAGAAA 59.892 55.0 0.00 0.00 0.00 2.52 F
1922 2224 0.885196 GTTTGGCGGCTGTGGATTTA 59.115 50.0 11.43 0.00 0.00 1.40 F
2399 2701 0.465097 ACCATCTGTATGCCTGCAGC 60.465 55.0 8.66 4.57 44.14 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2125 2427 0.245539 CTCGTTTCCCGCTCTTACCA 59.754 55.0 0.0 0.0 36.19 3.25 R
3271 3578 0.300491 CGTGATGATTACCCGTTGCG 59.700 55.0 0.0 0.0 0.00 4.85 R
3493 3800 0.742281 CACGGAGCCATCAGAAGTGG 60.742 60.0 0.0 0.0 39.80 4.00 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
22 23 0.826715 TCCTCATCGAAGGCTCCTTG 59.173 55.000 5.80 0.00 36.26 3.61
47 48 1.021202 ATGTTGTTGTCGTGTGGTGG 58.979 50.000 0.00 0.00 0.00 4.61
117 133 3.324108 GGACAAGGGGGCACGGTA 61.324 66.667 0.00 0.00 0.00 4.02
133 149 3.299977 TAGTCAGTGGGCGCGTGT 61.300 61.111 8.43 0.00 0.00 4.49
149 165 6.175087 GGCGCGTGTCATTTAAAAATTATTG 58.825 36.000 8.43 0.00 0.00 1.90
294 312 9.739276 ATATGTTGGTGACATCTAAGAGAAAAA 57.261 29.630 0.00 0.00 45.88 1.94
295 313 8.641498 ATGTTGGTGACATCTAAGAGAAAAAT 57.359 30.769 0.00 0.00 45.88 1.82
378 398 8.649841 CAAAAGTATATTTCAATGTGTGCTTGG 58.350 33.333 0.00 0.00 0.00 3.61
575 632 3.665443 CCCATAGTCCTTTTCCCTCCTA 58.335 50.000 0.00 0.00 0.00 2.94
585 655 9.696572 AGTCCTTTTCCCTCCTATTATTTTAAC 57.303 33.333 0.00 0.00 0.00 2.01
605 676 2.358737 GCAGTGTCCCGAACCCAG 60.359 66.667 0.00 0.00 0.00 4.45
608 679 0.107831 CAGTGTCCCGAACCCAGAAA 59.892 55.000 0.00 0.00 0.00 2.52
611 682 1.810755 GTGTCCCGAACCCAGAAATTC 59.189 52.381 0.00 0.00 0.00 2.17
621 692 1.940613 CCCAGAAATTCGATTCCGTCC 59.059 52.381 0.00 0.00 37.05 4.79
622 693 1.593006 CCAGAAATTCGATTCCGTCCG 59.407 52.381 0.00 0.00 37.05 4.79
623 694 2.268298 CAGAAATTCGATTCCGTCCGT 58.732 47.619 0.00 0.00 37.05 4.69
624 695 2.281762 CAGAAATTCGATTCCGTCCGTC 59.718 50.000 0.00 0.00 37.05 4.79
829 1096 2.992689 TTCTCCGGCTGGTACGCA 60.993 61.111 12.43 0.00 36.30 5.24
896 1166 2.047274 CCACGATTGACGGGCAGT 60.047 61.111 0.00 0.00 44.90 4.40
911 1181 4.664677 AGTGGCGCCGTGAGTGTC 62.665 66.667 23.90 4.39 0.00 3.67
923 1193 0.895530 TGAGTGTCTCGGATTCCCAC 59.104 55.000 0.00 0.00 32.35 4.61
940 1210 2.500504 CCCACCCTAGTTCTGTCCTTAC 59.499 54.545 0.00 0.00 0.00 2.34
1277 1560 4.932200 GCAGAATTGAGCACTAGTACTGTT 59.068 41.667 5.39 0.00 0.00 3.16
1296 1579 2.672961 TGTGGTAAGATCTTGCTCGG 57.327 50.000 20.91 0.00 0.00 4.63
1363 1646 7.100458 ACCCATTGTTCATTACTAATTCAGC 57.900 36.000 0.00 0.00 0.00 4.26
1375 1658 9.770503 CATTACTAATTCAGCATTGCTCATATC 57.229 33.333 8.54 0.00 36.40 1.63
1394 1677 7.099120 TCATATCATATGTGGCACATGTACTC 58.901 38.462 36.61 1.73 44.52 2.59
1396 1679 3.132111 TCATATGTGGCACATGTACTCGT 59.868 43.478 36.61 16.22 44.52 4.18
1398 1681 1.790755 TGTGGCACATGTACTCGTTC 58.209 50.000 17.96 0.00 44.52 3.95
1442 1726 8.523915 ATTGCTAGTCAATTTCATTGGATACA 57.476 30.769 6.58 0.00 44.12 2.29
1443 1727 9.139734 ATTGCTAGTCAATTTCATTGGATACAT 57.860 29.630 6.58 0.00 44.83 2.29
1688 1990 0.951040 CTTGGTCGGAGCACAGGTTC 60.951 60.000 9.78 0.00 0.00 3.62
1888 2190 2.260844 TGTTGAGGCAAAGACCAGAG 57.739 50.000 0.00 0.00 0.00 3.35
1922 2224 0.885196 GTTTGGCGGCTGTGGATTTA 59.115 50.000 11.43 0.00 0.00 1.40
2119 2421 4.926140 TGATAGCACAGAATCATCGAGT 57.074 40.909 0.00 0.00 0.00 4.18
2350 2652 6.472486 TCAGCGATAAAACGTAAGAGAATCTG 59.528 38.462 0.00 0.00 39.76 2.90
2399 2701 0.465097 ACCATCTGTATGCCTGCAGC 60.465 55.000 8.66 4.57 44.14 5.25
2407 2709 1.399791 GTATGCCTGCAGCTTTGAGAC 59.600 52.381 8.66 0.00 44.23 3.36
2426 2728 5.762711 TGAGACAGCATGCTAAGTTGTTAAA 59.237 36.000 22.19 1.53 42.53 1.52
2453 2755 7.853929 TGCGAAGATTGTTTTAAACTGACTAAC 59.146 33.333 9.33 0.00 0.00 2.34
2684 2986 3.383185 CCAGTTGGAAGTTTTGGCAGTTA 59.617 43.478 0.00 0.00 37.39 2.24
2692 2994 8.466617 TGGAAGTTTTGGCAGTTATTTTACTA 57.533 30.769 0.00 0.00 0.00 1.82
2841 3144 2.232208 TGCTGTTCGAGATGATGACTGT 59.768 45.455 0.00 0.00 0.00 3.55
2871 3175 5.711698 TGATCCTGAACCCTTTAACCTTTT 58.288 37.500 0.00 0.00 0.00 2.27
3086 3391 4.570772 CAGGAAACCACAATATCAGGTACG 59.429 45.833 0.00 0.00 34.63 3.67
3110 3416 7.041780 ACGTCAATAGCTGGTGAAATATGAATC 60.042 37.037 0.00 0.00 0.00 2.52
3112 3418 8.502387 GTCAATAGCTGGTGAAATATGAATCTC 58.498 37.037 0.00 0.00 0.00 2.75
3118 3424 6.017275 GCTGGTGAAATATGAATCTCAGAAGG 60.017 42.308 0.00 0.00 0.00 3.46
3119 3425 6.359804 TGGTGAAATATGAATCTCAGAAGGG 58.640 40.000 0.00 0.00 0.00 3.95
3134 3440 4.513692 TCAGAAGGGTGACAACGTTTAATG 59.486 41.667 0.00 0.99 0.00 1.90
3150 3456 6.639279 ACGTTTAATGCATTTTTATATCCCGC 59.361 34.615 18.75 0.00 0.00 6.13
3151 3457 6.088883 CGTTTAATGCATTTTTATATCCCGCC 59.911 38.462 18.75 0.00 0.00 6.13
3165 3471 1.376812 CCGCCCTCTTACGCCTTTT 60.377 57.895 0.00 0.00 0.00 2.27
3183 3490 5.523552 GCCTTTTGTTTTTCAGTTGTGCTAT 59.476 36.000 0.00 0.00 0.00 2.97
3271 3578 2.117910 GGTTCTAGAACGCTCGTATGC 58.882 52.381 25.44 7.99 42.02 3.14
3493 3800 1.333619 TGTCTCAAGGCGTTTTCTTGC 59.666 47.619 0.00 0.00 40.82 4.01
3587 3894 2.169789 CAGCTGGCCGTCGATCAAG 61.170 63.158 5.57 0.00 0.00 3.02
3650 3957 7.642669 CATCTACAAAGAAACTCTGCTTCAAA 58.357 34.615 0.00 0.00 34.73 2.69
3659 3966 1.268899 CTCTGCTTCAAAGTGGCTTGG 59.731 52.381 0.00 0.00 0.00 3.61
3667 3974 1.675720 AAAGTGGCTTGGCGCAGTTT 61.676 50.000 10.83 0.00 41.67 2.66
3782 4089 4.510340 GTGACAGTCTCGTGTTGGTTTTAT 59.490 41.667 1.31 0.00 0.00 1.40
3785 4092 4.682860 ACAGTCTCGTGTTGGTTTTATACG 59.317 41.667 0.00 0.00 36.20 3.06
3830 4137 2.202878 GTTGCGCCGCTATCCTCA 60.203 61.111 11.67 0.00 0.00 3.86
3838 4145 1.531739 CCGCTATCCTCAGGGCTCTC 61.532 65.000 0.00 0.00 0.00 3.20
3906 4213 8.184192 CGGAGTGCAGTATTTTCTCAAATAATT 58.816 33.333 0.00 0.00 36.75 1.40
3987 4294 5.815233 AATCTGTCCGATCCTTGTATGAT 57.185 39.130 0.00 0.00 0.00 2.45
4009 4316 5.676532 TGATAAACACGGTTCGTTGATTT 57.323 34.783 0.00 0.00 38.32 2.17
4104 5277 7.526608 GCACAGCACATTCAGTTTATTAGTTA 58.473 34.615 0.00 0.00 0.00 2.24
4168 5341 8.785329 TTTTCTTTTTATGCAGTTTGGACTTT 57.215 26.923 0.00 0.00 32.54 2.66
4209 5382 1.344763 CCAGGCCTAGAAATACGAGGG 59.655 57.143 3.98 0.00 40.88 4.30
4216 5401 1.421480 AGAAATACGAGGGGTAGGGC 58.579 55.000 0.00 0.00 33.84 5.19
4218 5403 2.036428 AAATACGAGGGGTAGGGCGC 62.036 60.000 0.00 0.00 33.84 6.53
4219 5404 3.744003 ATACGAGGGGTAGGGCGCA 62.744 63.158 10.83 0.00 33.84 6.09
4372 5558 9.476202 AATTTTCGGTTTTCTTTCTTCTATTGG 57.524 29.630 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.680522 GGAGCCTTCGATGAGGAGCA 61.681 60.000 7.36 0.00 39.25 4.26
22 23 3.059868 CCACACGACAACAACATAGTGAC 60.060 47.826 0.00 0.00 34.16 3.67
47 48 1.456331 CCCCATCCTCACCATTGGC 60.456 63.158 1.54 0.00 0.00 4.52
104 105 2.203877 TGACTACCGTGCCCCCTT 60.204 61.111 0.00 0.00 0.00 3.95
117 133 4.664677 GACACGCGCCCACTGACT 62.665 66.667 5.73 0.00 0.00 3.41
305 323 7.391148 AAACTATGCGGACATTTTTCTACAT 57.609 32.000 0.00 0.00 37.74 2.29
575 632 3.697542 GGGACACTGCGGGTTAAAATAAT 59.302 43.478 0.00 0.00 0.00 1.28
605 676 2.264813 TGACGGACGGAATCGAATTTC 58.735 47.619 0.00 0.00 40.11 2.17
608 679 2.373540 TTTGACGGACGGAATCGAAT 57.626 45.000 0.00 0.00 40.11 3.34
611 682 2.063266 TCTTTTTGACGGACGGAATCG 58.937 47.619 0.00 0.00 43.02 3.34
621 692 2.400408 CGGCGATGTTTTCTTTTTGACG 59.600 45.455 0.00 0.00 0.00 4.35
622 693 2.153057 GCGGCGATGTTTTCTTTTTGAC 59.847 45.455 12.98 0.00 0.00 3.18
623 694 2.389998 GCGGCGATGTTTTCTTTTTGA 58.610 42.857 12.98 0.00 0.00 2.69
624 695 1.455408 GGCGGCGATGTTTTCTTTTTG 59.545 47.619 12.98 0.00 0.00 2.44
829 1096 1.627297 GGGAGAAGATCGGGCTGGTT 61.627 60.000 0.00 0.00 0.00 3.67
873 1140 1.301401 CCGTCAATCGTGGTGTGGT 60.301 57.895 0.00 0.00 37.94 4.16
896 1166 4.357947 GAGACACTCACGGCGCCA 62.358 66.667 28.98 5.90 0.00 5.69
906 1176 1.265454 GGGTGGGAATCCGAGACACT 61.265 60.000 6.41 0.00 35.24 3.55
911 1181 1.413077 GAACTAGGGTGGGAATCCGAG 59.587 57.143 0.00 0.00 35.24 4.63
923 1193 4.527038 TCTTGTGTAAGGACAGAACTAGGG 59.473 45.833 0.00 0.00 34.12 3.53
940 1210 1.135859 GCACAGAGGCGAAATCTTGTG 60.136 52.381 0.00 0.00 33.11 3.33
976 1247 5.821995 TCTCCGCATCAATCAACAATTATCA 59.178 36.000 0.00 0.00 0.00 2.15
984 1255 4.063689 AGATCATCTCCGCATCAATCAAC 58.936 43.478 0.00 0.00 0.00 3.18
1092 1375 0.393132 GAAGAAAAGGGGGAGCTCCG 60.393 60.000 26.36 0.00 36.71 4.63
1129 1412 8.956426 CCAAGGCAGTAAAATTATAAGTTCAGA 58.044 33.333 0.00 0.00 0.00 3.27
1253 1536 3.549471 CAGTACTAGTGCTCAATTCTGCG 59.451 47.826 10.90 0.00 0.00 5.18
1277 1560 2.094182 GTCCGAGCAAGATCTTACCACA 60.094 50.000 7.86 0.00 0.00 4.17
1325 1608 8.472007 TGAACAATGGGTTACATCTACTTTTT 57.528 30.769 0.00 0.00 40.63 1.94
1363 1646 5.182380 TGTGCCACATATGATATGAGCAATG 59.818 40.000 25.02 12.31 35.15 2.82
1375 1658 3.457234 ACGAGTACATGTGCCACATATG 58.543 45.455 10.53 3.23 36.53 1.78
1431 1715 8.262601 ACCTATCAGTACAATGTATCCAATGA 57.737 34.615 0.00 0.00 0.00 2.57
1442 1726 7.831193 AGCAAAATTCAGACCTATCAGTACAAT 59.169 33.333 0.00 0.00 0.00 2.71
1443 1727 7.168219 AGCAAAATTCAGACCTATCAGTACAA 58.832 34.615 0.00 0.00 0.00 2.41
1445 1729 7.334421 TGAAGCAAAATTCAGACCTATCAGTAC 59.666 37.037 0.00 0.00 34.31 2.73
1446 1730 7.394016 TGAAGCAAAATTCAGACCTATCAGTA 58.606 34.615 0.00 0.00 34.31 2.74
1447 1731 6.240894 TGAAGCAAAATTCAGACCTATCAGT 58.759 36.000 0.00 0.00 34.31 3.41
1664 1966 2.828868 TGCTCCGACCAAGCAAGT 59.171 55.556 0.00 0.00 46.29 3.16
1688 1990 4.148166 TCAATTCGTTGAATTTCGCTTCG 58.852 39.130 2.16 0.00 39.82 3.79
1750 2052 0.960364 TTGTTGATGAGCCGCCTTCC 60.960 55.000 0.00 0.00 0.00 3.46
1888 2190 1.608283 CCAAACAGAACCTCCCTCGTC 60.608 57.143 0.00 0.00 0.00 4.20
1922 2224 3.588842 TGAAGTGAAGGGATGTCAGGAAT 59.411 43.478 0.00 0.00 0.00 3.01
2119 2421 0.975556 TCCCGCTCTTACCATGCAGA 60.976 55.000 0.00 0.00 0.00 4.26
2125 2427 0.245539 CTCGTTTCCCGCTCTTACCA 59.754 55.000 0.00 0.00 36.19 3.25
2181 2483 2.035321 GTCGATGATCTTGGAGGAGGAC 59.965 54.545 0.00 0.00 0.00 3.85
2302 2604 6.809689 TGATGATGACATTCTTTGAATTGTGC 59.190 34.615 0.00 0.00 36.82 4.57
2356 2658 6.605594 GTGGGATAGGACATTCCATAAACAAA 59.394 38.462 0.00 0.00 39.61 2.83
2399 2701 4.214971 ACAACTTAGCATGCTGTCTCAAAG 59.785 41.667 30.42 24.06 0.00 2.77
2407 2709 4.263677 CGCATTTAACAACTTAGCATGCTG 59.736 41.667 30.42 16.80 32.74 4.41
2426 2728 6.970484 AGTCAGTTTAAAACAATCTTCGCAT 58.030 32.000 0.00 0.00 0.00 4.73
2790 3093 6.981762 ATGTTGAACAAATGTGCAGAAAAA 57.018 29.167 0.62 0.00 34.53 1.94
2841 3144 4.934797 AAGGGTTCAGGATCAATCTCAA 57.065 40.909 0.00 0.00 0.00 3.02
3032 3337 4.917906 ACACCTCTTTTCAATAGCCTCT 57.082 40.909 0.00 0.00 0.00 3.69
3086 3391 8.388484 AGATTCATATTTCACCAGCTATTGAC 57.612 34.615 0.00 0.00 0.00 3.18
3110 3416 2.240493 AACGTTGTCACCCTTCTGAG 57.760 50.000 0.00 0.00 0.00 3.35
3112 3418 4.783242 CATTAAACGTTGTCACCCTTCTG 58.217 43.478 0.00 0.00 0.00 3.02
3118 3424 5.898630 AAAATGCATTAAACGTTGTCACC 57.101 34.783 13.39 0.00 0.00 4.02
3134 3440 3.421844 AGAGGGCGGGATATAAAAATGC 58.578 45.455 0.00 0.00 0.00 3.56
3146 3452 2.814913 AAAAGGCGTAAGAGGGCGGG 62.815 60.000 0.00 0.00 43.02 6.13
3150 3456 4.202070 TGAAAAACAAAAGGCGTAAGAGGG 60.202 41.667 0.00 0.00 43.02 4.30
3151 3457 4.927422 TGAAAAACAAAAGGCGTAAGAGG 58.073 39.130 0.00 0.00 43.02 3.69
3165 3471 4.642437 TCCACATAGCACAACTGAAAAACA 59.358 37.500 0.00 0.00 0.00 2.83
3183 3490 2.846206 ACTAGCAATTCCAGGATCCACA 59.154 45.455 15.82 0.00 0.00 4.17
3271 3578 0.300491 CGTGATGATTACCCGTTGCG 59.700 55.000 0.00 0.00 0.00 4.85
3493 3800 0.742281 CACGGAGCCATCAGAAGTGG 60.742 60.000 0.00 0.00 39.80 4.00
3587 3894 8.540492 CCTGTGTAATATACATCGAAGAACAAC 58.460 37.037 0.00 0.00 43.58 3.32
3626 3933 7.500559 ACTTTGAAGCAGAGTTTCTTTGTAGAT 59.499 33.333 0.00 0.00 0.00 1.98
3785 4092 3.120130 CCAATGGATGTGCAAAAACATGC 60.120 43.478 0.00 2.30 46.58 4.06
3830 4137 1.950748 ATACAGACCCCGAGAGCCCT 61.951 60.000 0.00 0.00 0.00 5.19
3838 4145 2.036958 TGCAATGAATACAGACCCCG 57.963 50.000 0.00 0.00 0.00 5.73
3987 4294 5.676532 AAATCAACGAACCGTGTTTATCA 57.323 34.783 0.00 0.00 39.99 2.15
4196 5369 2.601905 GCCCTACCCCTCGTATTTCTA 58.398 52.381 0.00 0.00 0.00 2.10
4344 5530 9.476202 AATAGAAGAAAGAAAACCGAAAATTGG 57.524 29.630 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.