Multiple sequence alignment - TraesCS7D01G143700

Loading Multiple Alignment...

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 TraesCS7D01G143700 chr7D 100.000 3573 0 0 1 3573 91809031 91812603 0.000000e+00 6599.0
1 TraesCS7D01G143700 chr7D 82.948 563 82 8 2297 2846 579142646 579143207 2.860000e-136 496.0
2 TraesCS7D01G143700 chr7D 100.000 241 0 0 3879 4119 91812909 91813149 2.920000e-121 446.0
3 TraesCS7D01G143700 chr7D 78.846 260 35 12 1677 1923 579142086 579142338 1.530000e-34 158.0
4 TraesCS7D01G143700 chr7B 95.479 3340 120 12 246 3573 42779672 42776352 0.000000e+00 5302.0
5 TraesCS7D01G143700 chr7B 81.172 563 92 8 2297 2846 643339900 643340461 1.360000e-119 440.0
6 TraesCS7D01G143700 chr7B 83.190 232 20 7 3897 4119 42776273 42776052 1.170000e-45 195.0
7 TraesCS7D01G143700 chr7B 79.216 255 33 12 1677 1918 643339349 643339596 4.260000e-35 159.0
8 TraesCS7D01G143700 chr7A 96.862 2581 63 8 673 3248 93487834 93490401 0.000000e+00 4301.0
9 TraesCS7D01G143700 chr7A 91.826 575 27 12 1 563 93486949 93487515 0.000000e+00 784.0
10 TraesCS7D01G143700 chr7A 94.469 452 22 3 1 449 93460588 93461039 0.000000e+00 693.0
11 TraesCS7D01G143700 chr7A 93.548 310 16 1 546 851 93475191 93475500 3.750000e-125 459.0
12 TraesCS7D01G143700 chr7A 92.667 300 18 3 3274 3573 93490682 93490977 2.940000e-116 429.0
13 TraesCS7D01G143700 chr7A 84.000 250 20 8 3879 4119 93491038 93491276 5.360000e-54 222.0
14 TraesCS7D01G143700 chr7A 91.729 133 11 0 540 672 93487559 93487691 7.030000e-43 185.0
15 TraesCS7D01G143700 chr5A 81.383 564 100 3 2289 2848 567782263 567782825 4.850000e-124 455.0
16 TraesCS7D01G143700 chr5A 76.853 769 116 39 1210 1938 567781223 567781969 1.080000e-100 377.0
17 TraesCS7D01G143700 chr5D 76.197 773 127 37 1202 1938 449014967 449015718 5.060000e-94 355.0
18 TraesCS7D01G143700 chr3D 79.568 509 90 9 2368 2864 598465199 598464693 6.550000e-93 351.0
19 TraesCS7D01G143700 chr3D 79.917 483 92 3 2368 2846 571706793 571707274 2.360000e-92 350.0
20 TraesCS7D01G143700 chr6D 79.487 507 93 7 2368 2864 63716787 63716282 2.360000e-92 350.0
21 TraesCS7D01G143700 chr6B 72.505 491 109 24 2375 2852 213398917 213399394 7.180000e-28 135.0
22 TraesCS7D01G143700 chr1D 97.436 39 1 0 1301 1339 487351026 487351064 2.660000e-07 67.6
23 TraesCS7D01G143700 chr3B 94.872 39 2 0 1301 1339 59464143 59464181 1.240000e-05 62.1
24 TraesCS7D01G143700 chr6A 96.970 33 1 0 1721 1753 162349907 162349875 5.750000e-04 56.5


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 TraesCS7D01G143700 chr7D 91809031 91813149 4118 False 3522.5 6599 100.0000 1 4119 2 chr7D.!!$F1 4118
1 TraesCS7D01G143700 chr7D 579142086 579143207 1121 False 327.0 496 80.8970 1677 2846 2 chr7D.!!$F2 1169
2 TraesCS7D01G143700 chr7B 42776052 42779672 3620 True 2748.5 5302 89.3345 246 4119 2 chr7B.!!$R1 3873
3 TraesCS7D01G143700 chr7B 643339349 643340461 1112 False 299.5 440 80.1940 1677 2846 2 chr7B.!!$F1 1169
4 TraesCS7D01G143700 chr7A 93486949 93491276 4327 False 1184.2 4301 91.4168 1 4119 5 chr7A.!!$F3 4118
5 TraesCS7D01G143700 chr5A 567781223 567782825 1602 False 416.0 455 79.1180 1210 2848 2 chr5A.!!$F1 1638
6 TraesCS7D01G143700 chr5D 449014967 449015718 751 False 355.0 355 76.1970 1202 1938 1 chr5D.!!$F1 736
7 TraesCS7D01G143700 chr3D 598464693 598465199 506 True 351.0 351 79.5680 2368 2864 1 chr3D.!!$R1 496
8 TraesCS7D01G143700 chr6D 63716282 63716787 505 True 350.0 350 79.4870 2368 2864 1 chr6D.!!$R1 496

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
27 28 0.459585 TTTAGCGGCCTAGAACAGCG 60.460 55.000 0.00 0.0 0.00 5.18 F
1166 1414 0.249657 GATCAAGAGGGTAGCGGCAG 60.250 60.000 1.45 0.0 0.00 4.85 F
2097 2423 2.123428 GGGCATGGCATCGAAGCTT 61.123 57.895 22.06 0.0 34.17 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1956 2249 0.322277 CATGGTCTTGTGCCTCTGCT 60.322 55.000 0.0 0.0 38.71 4.24 R
2587 2924 2.578178 CTCGCCGTCGCTCTTCAG 60.578 66.667 0.0 0.0 35.26 3.02 R
3373 3975 0.605589 GCATCGACCATCCCTCTAGG 59.394 60.000 0.0 0.0 0.00 3.02 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 0.459585 TTTAGCGGCCTAGAACAGCG 60.460 55.000 0.00 0.00 0.00 5.18
173 175 8.657074 ATTTCATGATGTATCTTTTGGCATTG 57.343 30.769 0.00 0.00 0.00 2.82
198 200 8.077386 TGGTTTTGGTTTTCATTTATAGACGTC 58.923 33.333 7.70 7.70 0.00 4.34
202 204 8.929827 TTGGTTTTCATTTATAGACGTCGATA 57.070 30.769 13.57 13.57 0.00 2.92
277 279 8.451908 AAGCAAATATACTTACATGTTCCTCC 57.548 34.615 2.30 0.00 0.00 4.30
367 373 6.831664 AGTTTGGTCACCAGATTCCTATAT 57.168 37.500 0.00 0.00 33.81 0.86
425 442 9.206690 AGAATCTCAACATGATCTCTAACCTTA 57.793 33.333 0.00 0.00 0.00 2.69
426 443 9.995003 GAATCTCAACATGATCTCTAACCTTAT 57.005 33.333 0.00 0.00 0.00 1.73
886 1126 5.966853 TTTTCAAAGGAAAAGAACCCCAT 57.033 34.783 0.00 0.00 45.51 4.00
982 1222 1.815613 CCAGCTACCATCGATCGATCT 59.184 52.381 27.20 17.64 31.62 2.75
985 1225 3.935828 CAGCTACCATCGATCGATCTCTA 59.064 47.826 27.20 14.78 31.62 2.43
986 1226 4.574421 CAGCTACCATCGATCGATCTCTAT 59.426 45.833 27.20 13.17 31.62 1.98
988 1228 4.024387 GCTACCATCGATCGATCTCTATCC 60.024 50.000 27.20 9.31 31.62 2.59
990 1230 3.692101 ACCATCGATCGATCTCTATCCAC 59.308 47.826 27.20 0.00 31.62 4.02
991 1231 3.944650 CCATCGATCGATCTCTATCCACT 59.055 47.826 27.20 0.19 31.62 4.00
992 1232 5.119694 CCATCGATCGATCTCTATCCACTA 58.880 45.833 27.20 0.00 31.62 2.74
993 1233 5.007234 CCATCGATCGATCTCTATCCACTAC 59.993 48.000 27.20 0.00 31.62 2.73
994 1234 5.408880 TCGATCGATCTCTATCCACTACT 57.591 43.478 22.43 0.00 0.00 2.57
995 1235 6.527057 TCGATCGATCTCTATCCACTACTA 57.473 41.667 22.43 0.00 0.00 1.82
996 1236 6.331845 TCGATCGATCTCTATCCACTACTAC 58.668 44.000 22.43 0.00 0.00 2.73
997 1237 6.153170 TCGATCGATCTCTATCCACTACTACT 59.847 42.308 22.43 0.00 0.00 2.57
998 1238 7.338957 TCGATCGATCTCTATCCACTACTACTA 59.661 40.741 22.43 0.00 0.00 1.82
1158 1400 1.333636 CCAGCTCCGATCAAGAGGGT 61.334 60.000 10.82 0.00 0.00 4.34
1164 1412 1.300233 CGATCAAGAGGGTAGCGGC 60.300 63.158 0.00 0.00 0.00 6.53
1165 1413 1.823295 GATCAAGAGGGTAGCGGCA 59.177 57.895 1.45 0.00 0.00 5.69
1166 1414 0.249657 GATCAAGAGGGTAGCGGCAG 60.250 60.000 1.45 0.00 0.00 4.85
1167 1415 2.317149 ATCAAGAGGGTAGCGGCAGC 62.317 60.000 0.00 0.00 45.58 5.25
1707 1973 4.221422 GCGCACGGGCTGATCCTA 62.221 66.667 8.62 0.00 38.10 2.94
1956 2249 3.680786 CCGGCAGAGGACACGACA 61.681 66.667 0.00 0.00 0.00 4.35
2097 2423 2.123428 GGGCATGGCATCGAAGCTT 61.123 57.895 22.06 0.00 34.17 3.74
2229 2555 2.173669 ATTCTTCATGTCCGGCGCG 61.174 57.895 0.00 0.00 0.00 6.86
2775 3115 2.039405 GCAGCTGCTCACCTTCCTG 61.039 63.158 31.33 0.00 38.21 3.86
2955 3301 1.134788 CCTTTCTGGATTCGGCTACGT 60.135 52.381 0.00 0.00 38.70 3.57
3000 3347 4.278975 TGGTTTGGCATTGGTATTTTCC 57.721 40.909 0.00 0.00 0.00 3.13
3138 3485 9.689234 TTTTCCATTAAAATTACCGAGAGCGGC 62.689 40.741 3.97 0.00 45.52 6.53
3207 3554 5.945784 AGATTTGAAATCTCGGTTGGAATCA 59.054 36.000 14.34 0.00 0.00 2.57
3288 3890 2.551032 GGGACACTTAGGGTTTCAAACG 59.449 50.000 0.00 0.00 0.00 3.60
3290 3892 4.379652 GGACACTTAGGGTTTCAAACGTA 58.620 43.478 0.00 0.00 0.00 3.57
3291 3893 4.212004 GGACACTTAGGGTTTCAAACGTAC 59.788 45.833 0.00 0.00 0.00 3.67
3292 3894 5.027293 ACACTTAGGGTTTCAAACGTACT 57.973 39.130 0.00 0.00 0.00 2.73
3293 3895 5.052481 ACACTTAGGGTTTCAAACGTACTC 58.948 41.667 0.00 0.00 0.00 2.59
3294 3896 4.149396 CACTTAGGGTTTCAAACGTACTCG 59.851 45.833 0.00 0.00 43.34 4.18
3295 3897 1.505425 AGGGTTTCAAACGTACTCGC 58.495 50.000 0.00 0.00 41.18 5.03
3317 3919 4.307432 CACTGTGGCGGTTATAAGATAGG 58.693 47.826 0.00 0.00 0.00 2.57
3319 3921 2.038033 TGTGGCGGTTATAAGATAGGGC 59.962 50.000 0.00 0.00 0.00 5.19
3373 3975 1.597461 CTCACCCTCCCTCCGAAAC 59.403 63.158 0.00 0.00 0.00 2.78
3445 4047 2.632028 CAGCCAGCAGTAGGATAGATGT 59.368 50.000 0.00 0.00 0.00 3.06
3540 4142 3.121929 AGGCTGAGTTAGGGAGAATCA 57.878 47.619 0.00 0.00 36.25 2.57
3547 4149 4.715297 TGAGTTAGGGAGAATCAGGGTTAC 59.285 45.833 0.00 0.00 36.25 2.50
3551 4153 2.023695 AGGGAGAATCAGGGTTACGGTA 60.024 50.000 0.00 0.00 36.25 4.02
4023 4634 2.990066 AGAACTGGAGAAATAGGCCG 57.010 50.000 0.00 0.00 0.00 6.13
4027 4638 2.463752 ACTGGAGAAATAGGCCGTACA 58.536 47.619 0.00 0.00 0.00 2.90
4040 4651 0.460311 CCGTACACCAGATCTCCCAC 59.540 60.000 0.00 0.00 0.00 4.61
4048 4659 2.268920 GATCTCCCACAAGGCGCA 59.731 61.111 10.83 0.00 34.51 6.09
4052 4663 0.326595 TCTCCCACAAGGCGCATTAA 59.673 50.000 7.11 0.00 34.51 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 5.116882 GTGGATGTAGGGAGAATGTGTTAC 58.883 45.833 0.00 0.00 0.00 2.50
150 152 6.154877 ACCAATGCCAAAAGATACATCATGAA 59.845 34.615 0.00 0.00 0.00 2.57
158 160 5.304778 ACCAAAACCAATGCCAAAAGATAC 58.695 37.500 0.00 0.00 0.00 2.24
164 166 4.335416 TGAAAACCAAAACCAATGCCAAA 58.665 34.783 0.00 0.00 0.00 3.28
173 175 7.269724 CGACGTCTATAAATGAAAACCAAAACC 59.730 37.037 14.70 0.00 0.00 3.27
226 228 9.810545 TTGTTTCTAAGTCAACCATTTTAAAGG 57.189 29.630 0.00 0.00 0.00 3.11
277 279 8.922058 ATTCAATGAAATTTCTTCAATCCGAG 57.078 30.769 18.64 0.00 31.22 4.63
345 347 9.220767 GATTATATAGGAATCTGGTGACCAAAC 57.779 37.037 5.53 0.00 30.80 2.93
367 373 8.109634 GGAATAAAAGGGCATAGAGATGGATTA 58.890 37.037 0.00 0.00 33.26 1.75
428 445 8.181573 GCAATGGACGTCTCAAAGAAAATATAA 58.818 33.333 16.46 0.00 0.00 0.98
429 446 7.335673 TGCAATGGACGTCTCAAAGAAAATATA 59.664 33.333 16.46 0.00 0.00 0.86
430 447 6.150976 TGCAATGGACGTCTCAAAGAAAATAT 59.849 34.615 16.46 0.00 0.00 1.28
431 448 5.471797 TGCAATGGACGTCTCAAAGAAAATA 59.528 36.000 16.46 0.00 0.00 1.40
432 449 4.278170 TGCAATGGACGTCTCAAAGAAAAT 59.722 37.500 16.46 0.00 0.00 1.82
541 568 6.663093 TGGCATGTACTTTGAATTCCTACAAT 59.337 34.615 2.27 0.00 0.00 2.71
564 658 3.119849 GGGAAAACACACGATTGAGATGG 60.120 47.826 0.00 0.00 0.00 3.51
1016 1258 3.004734 GGTTGTTGCTTGTTATGCTCACT 59.995 43.478 0.00 0.00 0.00 3.41
1701 1967 2.871182 TGAGCATGTCACGTAGGATC 57.129 50.000 0.00 0.00 0.00 3.36
1707 1973 1.080435 CGAGCATGAGCATGTCACGT 61.080 55.000 11.68 0.00 45.49 4.49
1956 2249 0.322277 CATGGTCTTGTGCCTCTGCT 60.322 55.000 0.00 0.00 38.71 4.24
2278 2604 3.842923 CTCGATCAGCGGTGGCCT 61.843 66.667 15.67 0.00 41.24 5.19
2542 2877 4.003788 CAGAAGGGCCACGTCGGT 62.004 66.667 6.18 0.00 36.97 4.69
2587 2924 2.578178 CTCGCCGTCGCTCTTCAG 60.578 66.667 0.00 0.00 35.26 3.02
2775 3115 2.596631 AGCATCATGATGGCGGCC 60.597 61.111 31.62 13.32 39.16 6.13
2955 3301 3.447944 ACACATGCATGCCAATTATGTCA 59.552 39.130 26.53 0.00 30.15 3.58
3000 3347 3.837213 AAAAATGCACATCCACTCTCG 57.163 42.857 0.00 0.00 0.00 4.04
3207 3554 3.555586 GCACCAAGAAATTGCATGGTCTT 60.556 43.478 10.52 2.82 44.12 3.01
3294 3896 2.018542 TCTTATAACCGCCACAGTGC 57.981 50.000 0.00 0.00 0.00 4.40
3295 3897 4.307432 CCTATCTTATAACCGCCACAGTG 58.693 47.826 0.00 0.00 0.00 3.66
3317 3919 1.456705 TGGTGTCAAAACCCCAGCC 60.457 57.895 0.00 0.00 39.70 4.85
3347 3949 3.081409 GGAGGGTGAGGCGGCTTA 61.081 66.667 14.76 6.01 0.00 3.09
3366 3968 1.007963 ACCATCCCTCTAGGTTTCGGA 59.992 52.381 0.00 0.00 36.75 4.55
3369 3971 2.385803 TCGACCATCCCTCTAGGTTTC 58.614 52.381 0.00 0.00 35.36 2.78
3373 3975 0.605589 GCATCGACCATCCCTCTAGG 59.394 60.000 0.00 0.00 0.00 3.02
3400 4002 3.200825 AGCAGTTACCATGTTGCCTCTAT 59.799 43.478 0.00 0.00 37.26 1.98
3540 4142 1.821136 CCTTTCGACTACCGTAACCCT 59.179 52.381 0.00 0.00 39.75 4.34
3547 4149 3.308438 TTTCCTTCCTTTCGACTACCG 57.692 47.619 0.00 0.00 40.25 4.02
3946 4548 9.836864 AGAAGATTTGTACATCACTGCATTATA 57.163 29.630 0.00 0.00 0.00 0.98
3947 4549 8.618677 CAGAAGATTTGTACATCACTGCATTAT 58.381 33.333 0.00 0.00 0.00 1.28
3948 4550 7.414429 GCAGAAGATTTGTACATCACTGCATTA 60.414 37.037 25.76 0.00 45.14 1.90
3949 4551 6.624423 GCAGAAGATTTGTACATCACTGCATT 60.624 38.462 25.76 5.48 45.14 3.56
3950 4552 5.163683 GCAGAAGATTTGTACATCACTGCAT 60.164 40.000 25.76 5.53 45.14 3.96
3951 4553 4.154737 GCAGAAGATTTGTACATCACTGCA 59.845 41.667 25.76 0.00 45.14 4.41
3952 4554 4.154737 TGCAGAAGATTTGTACATCACTGC 59.845 41.667 24.91 24.91 45.53 4.40
3953 4555 5.868043 TGCAGAAGATTTGTACATCACTG 57.132 39.130 0.00 7.66 35.15 3.66
3954 4556 8.743085 AATATGCAGAAGATTTGTACATCACT 57.257 30.769 0.00 0.00 0.00 3.41
3955 4557 8.834465 AGAATATGCAGAAGATTTGTACATCAC 58.166 33.333 0.00 0.00 0.00 3.06
4000 4611 4.459337 CGGCCTATTTCTCCAGTTCTTTTT 59.541 41.667 0.00 0.00 0.00 1.94
4003 4614 2.572104 ACGGCCTATTTCTCCAGTTCTT 59.428 45.455 0.00 0.00 0.00 2.52
4018 4629 1.043673 GGAGATCTGGTGTACGGCCT 61.044 60.000 0.00 0.00 0.00 5.19
4023 4634 2.093447 CCTTGTGGGAGATCTGGTGTAC 60.093 54.545 0.00 0.00 37.23 2.90
4027 4638 1.903877 CGCCTTGTGGGAGATCTGGT 61.904 60.000 0.00 0.00 37.02 4.00
4040 4651 1.013596 TGTCCGATTAATGCGCCTTG 58.986 50.000 4.18 0.00 0.00 3.61
4048 4659 9.734620 CATGTTAATGTTGATTGTCCGATTAAT 57.265 29.630 0.00 0.00 0.00 1.40
4052 4663 6.823182 TCTCATGTTAATGTTGATTGTCCGAT 59.177 34.615 0.00 0.00 35.15 4.18


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

AutoCloner maintained by Alex Coulton.