Multiple sequence alignment - TraesCS4D01G116200

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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 TraesCS4D01G116200 chr4D 100.000 3402 0 0 1 3402 97375231 97378632 0.000000e+00 6283
1 TraesCS4D01G116200 chr4D 81.536 742 117 12 2639 3364 97382759 97383496 8.130000e-166 593
2 TraesCS4D01G116200 chr4B 91.323 3446 196 44 1 3387 139021409 139024810 0.000000e+00 4612
3 TraesCS4D01G116200 chr4A 93.485 2410 111 22 160 2533 478869159 478866760 0.000000e+00 3539
4 TraesCS4D01G116200 chr4A 79.380 742 121 15 2642 3367 478752732 478752007 8.480000e-136 494
5 TraesCS4D01G116200 chr4A 98.266 173 3 0 1 173 478869352 478869180 1.530000e-78 303
6 TraesCS4D01G116200 chr4A 85.096 208 29 2 3169 3375 478866582 478866376 9.560000e-51 211
7 TraesCS4D01G116200 chr4A 91.241 137 5 4 3045 3181 478866733 478866604 2.700000e-41 180


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 TraesCS4D01G116200 chr4D 97375231 97378632 3401 False 6283.00 6283 100.000 1 3402 1 chr4D.!!$F1 3401
1 TraesCS4D01G116200 chr4D 97382759 97383496 737 False 593.00 593 81.536 2639 3364 1 chr4D.!!$F2 725
2 TraesCS4D01G116200 chr4B 139021409 139024810 3401 False 4612.00 4612 91.323 1 3387 1 chr4B.!!$F1 3386
3 TraesCS4D01G116200 chr4A 478866376 478869352 2976 True 1058.25 3539 92.022 1 3375 4 chr4A.!!$R2 3374
4 TraesCS4D01G116200 chr4A 478752007 478752732 725 True 494.00 494 79.380 2642 3367 1 chr4A.!!$R1 725

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
412 467 0.176680 CTCGACATACCAGCTGGCTT 59.823 55.0 33.06 17.52 39.32 4.35 F
812 874 0.234884 GTTCCACGTACTGCTTGTGC 59.765 55.0 0.00 0.00 40.20 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1860 1941 0.251916 TCATCACAGGGCCTAAACCG 59.748 55.0 5.28 0.0 0.0 4.44 R
2604 2735 0.179034 GGCCCAGATCAGCGAGAAAT 60.179 55.0 0.00 0.0 0.0 2.17 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
220 255 2.822561 TCACAAAACTGCACAGGAAACA 59.177 40.909 2.21 0.00 0.00 2.83
228 263 4.074970 ACTGCACAGGAAACATTAAGGAG 58.925 43.478 2.21 0.00 0.00 3.69
230 265 4.326826 TGCACAGGAAACATTAAGGAGAG 58.673 43.478 0.00 0.00 0.00 3.20
267 316 3.379688 GCATCAGGGGAAAAGAAGATGAC 59.620 47.826 0.00 0.00 35.98 3.06
296 345 1.474879 TCGTAATGATGCAGACACCGA 59.525 47.619 0.00 2.16 0.00 4.69
412 467 0.176680 CTCGACATACCAGCTGGCTT 59.823 55.000 33.06 17.52 39.32 4.35
711 769 7.493320 CCATGCAGCAACTACATTGATAAATTT 59.507 33.333 0.00 0.00 41.23 1.82
724 782 6.954616 TTGATAAATTTCTCACGCGTCTTA 57.045 33.333 9.86 0.00 0.00 2.10
812 874 0.234884 GTTCCACGTACTGCTTGTGC 59.765 55.000 0.00 0.00 40.20 4.57
877 939 5.357878 TGAAAAGAAATATGGAAGCGAGCAT 59.642 36.000 0.00 0.00 0.00 3.79
979 1047 1.512230 CACCACCATTGCCAATCCG 59.488 57.895 0.00 0.00 0.00 4.18
1107 1175 1.816961 GCCATCATCGCCTTCCTCAAT 60.817 52.381 0.00 0.00 0.00 2.57
1219 1287 7.330208 CCAAGGCAAGAACTCTCAAATTTATTG 59.670 37.037 0.00 0.00 0.00 1.90
1363 1441 2.622064 AGAAACACGAAAGACCTGCT 57.378 45.000 0.00 0.00 0.00 4.24
1380 1458 4.393155 TTCTGCATGCGACGGGCT 62.393 61.111 14.09 0.00 44.05 5.19
1413 1491 1.332375 CGTCCATCGTGGTTTGTTTGT 59.668 47.619 4.33 0.00 39.03 2.83
1470 1548 2.880879 CCGCATGTCTCCGTCACG 60.881 66.667 0.00 0.00 0.00 4.35
1541 1619 1.293924 GACGCCACTCTCATGATTGG 58.706 55.000 11.97 11.97 43.44 3.16
1560 1638 3.211045 TGGCGCTTCTAAAGTTCAGTTT 58.789 40.909 7.64 0.00 0.00 2.66
1576 1657 8.920509 AGTTCAGTTTAAGTTTTAAAATGCGT 57.079 26.923 13.75 0.00 33.94 5.24
1765 1846 2.125106 GAGCCCACACCGACATCC 60.125 66.667 0.00 0.00 0.00 3.51
1840 1921 0.609131 CCGCCTTCCTTTGTGTCCAT 60.609 55.000 0.00 0.00 0.00 3.41
1886 1967 3.737559 AGGCCCTGTGATGAATAAACA 57.262 42.857 0.00 0.00 0.00 2.83
2050 2131 0.178903 TCCTGGCCTTCCTGTACACT 60.179 55.000 3.32 0.00 0.00 3.55
2065 2146 4.680537 ACTGGGACCCTCGACGCT 62.681 66.667 13.00 0.00 0.00 5.07
2308 2389 1.070786 GCAGGTGGTGTTCTCCGAA 59.929 57.895 0.00 0.00 0.00 4.30
2504 2621 2.305635 TGCAAGAGTAATTCAGGCTCCA 59.694 45.455 0.00 0.00 0.00 3.86
2553 2670 0.308376 GACTAGTCGAGGCGTCCATC 59.692 60.000 7.22 0.00 0.00 3.51
2571 2688 6.319152 CGTCCATCTAAAGTCTTTCTCCTCTA 59.681 42.308 0.00 0.00 0.00 2.43
2573 2690 8.700973 GTCCATCTAAAGTCTTTCTCCTCTATT 58.299 37.037 0.00 0.00 0.00 1.73
2582 2699 7.415086 AGTCTTTCTCCTCTATTCTAGAACCA 58.585 38.462 7.48 0.00 33.75 3.67
2587 2704 6.503944 TCTCCTCTATTCTAGAACCAAACCT 58.496 40.000 7.48 0.00 33.75 3.50
2624 2755 1.552799 TTTCTCGCTGATCTGGGCCA 61.553 55.000 5.85 5.85 0.00 5.36
2628 2759 2.124403 GCTGATCTGGGCCACTGG 60.124 66.667 0.00 0.00 0.00 4.00
2657 2788 1.002624 GGCATGGACCAGACGGAAA 60.003 57.895 0.00 0.00 35.59 3.13
2821 2954 5.276461 TGCACGGTATCTTCATCAACTAT 57.724 39.130 0.00 0.00 0.00 2.12
2822 2955 5.049828 TGCACGGTATCTTCATCAACTATG 58.950 41.667 0.00 0.00 36.88 2.23
2824 2957 5.523916 GCACGGTATCTTCATCAACTATGTT 59.476 40.000 0.00 0.00 36.89 2.71
2832 2965 8.939201 ATCTTCATCAACTATGTTGACTACAG 57.061 34.615 14.23 8.96 40.83 2.74
2902 3035 1.079503 GCAACCTAGACTTCTTGCCG 58.920 55.000 0.00 0.00 34.21 5.69
2960 3093 2.742053 TGCAACGGTCTCTTGCTTTATC 59.258 45.455 8.84 0.00 43.76 1.75
2967 3100 1.136305 TCTCTTGCTTTATCGGGGTCG 59.864 52.381 0.00 0.00 37.82 4.79
2995 3131 1.228033 GTTGTACGTGGCCAACCCT 60.228 57.895 7.24 0.00 35.93 4.34
3004 3140 3.305516 GCCAACCCTGCCACAAGG 61.306 66.667 0.00 0.00 37.05 3.61
3044 3180 0.034896 CAAGGGTGGCGACTACAAGT 59.965 55.000 0.00 0.00 0.00 3.16
3117 3259 2.590282 TCGATCCCATATGTACCCGA 57.410 50.000 1.24 3.05 0.00 5.14
3118 3260 2.443416 TCGATCCCATATGTACCCGAG 58.557 52.381 1.24 0.00 0.00 4.63
3119 3261 2.040679 TCGATCCCATATGTACCCGAGA 59.959 50.000 1.24 0.00 0.00 4.04
3120 3262 2.823747 CGATCCCATATGTACCCGAGAA 59.176 50.000 1.24 0.00 0.00 2.87
3121 3263 3.119459 CGATCCCATATGTACCCGAGAAG 60.119 52.174 1.24 0.00 0.00 2.85
3122 3264 2.605257 TCCCATATGTACCCGAGAAGG 58.395 52.381 1.24 0.00 40.63 3.46
3163 3305 1.213619 TGGAATGGCCACCATCCTCA 61.214 55.000 26.12 11.20 44.40 3.86
3204 3380 2.930040 CGTCTAGTACAAGGCAATGGTG 59.070 50.000 0.00 0.00 0.00 4.17
3266 3442 2.547211 GTGGCTAACGCTCGACTAGATA 59.453 50.000 0.00 0.00 36.09 1.98
3273 3449 2.867368 ACGCTCGACTAGATACACTGAG 59.133 50.000 0.00 0.00 0.00 3.35
3276 3452 3.206964 CTCGACTAGATACACTGAGGCA 58.793 50.000 0.00 0.00 0.00 4.75
3278 3454 3.628032 TCGACTAGATACACTGAGGCAAG 59.372 47.826 0.00 0.00 0.00 4.01
3279 3455 3.378742 CGACTAGATACACTGAGGCAAGT 59.621 47.826 0.00 0.00 0.00 3.16
3286 3471 0.107456 CACTGAGGCAAGTGTGGAGT 59.893 55.000 11.10 0.00 42.21 3.85
3290 3475 0.886490 GAGGCAAGTGTGGAGTGGTG 60.886 60.000 0.00 0.00 0.00 4.17
3292 3477 2.896801 GCAAGTGTGGAGTGGTGCG 61.897 63.158 0.00 0.00 0.00 5.34
3343 3528 6.173339 AGGATCACTTTATGTTCATTGTCGT 58.827 36.000 0.00 0.00 0.00 4.34
3349 3534 1.603456 ATGTTCATTGTCGTGGTGCA 58.397 45.000 0.00 0.00 0.00 4.57
3352 3537 2.031245 TGTTCATTGTCGTGGTGCATTC 60.031 45.455 0.00 0.00 0.00 2.67
3357 3542 3.109547 TCGTGGTGCATTCGTCGC 61.110 61.111 0.00 0.00 0.00 5.19
3367 3552 2.224185 TGCATTCGTCGCCAGGTAATAT 60.224 45.455 0.00 0.00 0.00 1.28
3375 3560 4.280461 GTCGCCAGGTAATATATCGATCG 58.720 47.826 9.36 9.36 0.00 3.69
3379 3564 5.505819 CGCCAGGTAATATATCGATCGTGAT 60.506 44.000 15.94 11.83 0.00 3.06
3380 3565 5.687730 GCCAGGTAATATATCGATCGTGATG 59.312 44.000 15.94 1.45 0.00 3.07
3387 3572 9.025020 GTAATATATCGATCGTGATGCATCTTT 57.975 33.333 26.32 9.28 0.00 2.52
3388 3573 5.774878 ATATCGATCGTGATGCATCTTTG 57.225 39.130 26.32 15.87 0.00 2.77
3389 3574 2.892374 TCGATCGTGATGCATCTTTGT 58.108 42.857 26.32 11.01 0.00 2.83
3390 3575 2.604462 TCGATCGTGATGCATCTTTGTG 59.396 45.455 26.32 12.45 0.00 3.33
3391 3576 2.604462 CGATCGTGATGCATCTTTGTGA 59.396 45.455 26.32 16.27 0.00 3.58
3392 3577 3.062504 CGATCGTGATGCATCTTTGTGAA 59.937 43.478 26.32 2.27 0.00 3.18
3393 3578 4.435917 CGATCGTGATGCATCTTTGTGAAA 60.436 41.667 26.32 1.49 0.00 2.69
3394 3579 4.145876 TCGTGATGCATCTTTGTGAAAC 57.854 40.909 26.32 12.91 37.35 2.78
3395 3580 3.058293 TCGTGATGCATCTTTGTGAAACC 60.058 43.478 26.32 0.00 34.36 3.27
3396 3581 3.304592 CGTGATGCATCTTTGTGAAACCA 60.305 43.478 26.32 0.12 34.36 3.67
3397 3582 4.616604 CGTGATGCATCTTTGTGAAACCAT 60.617 41.667 26.32 0.00 34.36 3.55
3398 3583 4.860907 GTGATGCATCTTTGTGAAACCATC 59.139 41.667 26.32 0.00 34.36 3.51
3399 3584 4.768448 TGATGCATCTTTGTGAAACCATCT 59.232 37.500 26.32 0.00 34.36 2.90
3400 3585 5.244402 TGATGCATCTTTGTGAAACCATCTT 59.756 36.000 26.32 0.00 34.36 2.40
3401 3586 5.534207 TGCATCTTTGTGAAACCATCTTT 57.466 34.783 0.00 0.00 34.36 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 212 1.857217 CAGCTGTCGCTAATGCAGTAG 59.143 52.381 16.68 16.68 46.99 2.57
189 224 2.663879 GCAGTTTTGTGATCAGCTGTCG 60.664 50.000 14.67 0.00 0.00 4.35
220 255 8.523658 GCCAAAGTGTTATTTTCTCTCCTTAAT 58.476 33.333 0.00 0.00 0.00 1.40
228 263 6.095377 CCTGATGCCAAAGTGTTATTTTCTC 58.905 40.000 0.00 0.00 0.00 2.87
230 265 5.170748 CCCTGATGCCAAAGTGTTATTTTC 58.829 41.667 0.00 0.00 0.00 2.29
330 383 0.317770 GATCTCGGCAGAAGAGAGCG 60.318 60.000 2.38 0.00 46.43 5.03
412 467 4.998672 GCCAACTACTATGTACCAAACACA 59.001 41.667 0.00 0.00 42.09 3.72
711 769 3.678072 CCAAAAGATTAAGACGCGTGAGA 59.322 43.478 20.70 0.00 0.00 3.27
724 782 8.786826 TCATAACGAATGTACTCCAAAAGATT 57.213 30.769 0.00 0.00 36.89 2.40
812 874 2.010145 TGCTAGCCGACTAAAGCAAG 57.990 50.000 13.29 0.00 29.38 4.01
866 928 0.745845 ATGGTGTGATGCTCGCTTCC 60.746 55.000 2.84 0.00 0.00 3.46
877 939 0.325671 GAGGGAGGAGGATGGTGTGA 60.326 60.000 0.00 0.00 0.00 3.58
979 1047 1.208706 CTTCCTCCTCCCTTCCCTTC 58.791 60.000 0.00 0.00 0.00 3.46
983 1051 0.182299 CATGCTTCCTCCTCCCTTCC 59.818 60.000 0.00 0.00 0.00 3.46
984 1052 0.182299 CCATGCTTCCTCCTCCCTTC 59.818 60.000 0.00 0.00 0.00 3.46
985 1053 0.253347 TCCATGCTTCCTCCTCCCTT 60.253 55.000 0.00 0.00 0.00 3.95
986 1054 0.985490 GTCCATGCTTCCTCCTCCCT 60.985 60.000 0.00 0.00 0.00 4.20
987 1055 0.985490 AGTCCATGCTTCCTCCTCCC 60.985 60.000 0.00 0.00 0.00 4.30
1219 1287 3.853355 ACATTGGAGACCATGAGGATC 57.147 47.619 0.00 0.00 38.69 3.36
1363 1441 4.393155 AGCCCGTCGCATGCAGAA 62.393 61.111 19.57 0.00 41.38 3.02
1380 1458 5.345702 CACGATGGACGAACTAATTAAGGA 58.654 41.667 0.00 0.00 45.77 3.36
1470 1548 3.184541 GTTCAGACATGCATGCAATTCC 58.815 45.455 26.68 13.92 0.00 3.01
1541 1619 5.986936 ACTTAAACTGAACTTTAGAAGCGC 58.013 37.500 0.00 0.00 0.00 5.92
1576 1657 5.018809 ACTTCCCGGTGTTACTGATTACTA 58.981 41.667 0.00 0.00 0.00 1.82
1577 1658 3.836562 ACTTCCCGGTGTTACTGATTACT 59.163 43.478 0.00 0.00 0.00 2.24
1578 1659 4.179298 GACTTCCCGGTGTTACTGATTAC 58.821 47.826 0.00 0.00 0.00 1.89
1765 1846 1.812571 CCCATTTCCAGGTTTGACGAG 59.187 52.381 0.00 0.00 0.00 4.18
1812 1893 4.021925 GGAAGGCGGCTCACCAGT 62.022 66.667 23.32 4.42 34.57 4.00
1860 1941 0.251916 TCATCACAGGGCCTAAACCG 59.748 55.000 5.28 0.00 0.00 4.44
1886 1967 2.025898 CACGGCCGGGGTTAATTATTT 58.974 47.619 31.76 0.00 0.00 1.40
2008 2089 4.838486 GAGAGCTCGTCGTGGGCG 62.838 72.222 8.37 0.00 39.92 6.13
2308 2389 1.881602 GGCGAAGTCGTGGTACTCT 59.118 57.895 2.25 0.00 42.22 3.24
2504 2621 1.792757 TTGCCCAGCCCTGAACTGAT 61.793 55.000 0.00 0.00 37.32 2.90
2536 2653 1.880271 TAGATGGACGCCTCGACTAG 58.120 55.000 0.00 0.00 0.00 2.57
2544 2661 3.863041 AGAAAGACTTTAGATGGACGCC 58.137 45.455 0.00 0.00 0.00 5.68
2571 2688 5.176592 GCGTCTAAGGTTTGGTTCTAGAAT 58.823 41.667 8.75 0.00 0.00 2.40
2573 2690 3.366679 CGCGTCTAAGGTTTGGTTCTAGA 60.367 47.826 0.00 0.00 0.00 2.43
2576 2693 1.792006 CGCGTCTAAGGTTTGGTTCT 58.208 50.000 0.00 0.00 0.00 3.01
2582 2699 3.116531 GCGGCGCGTCTAAGGTTT 61.117 61.111 19.09 0.00 0.00 3.27
2604 2735 0.179034 GGCCCAGATCAGCGAGAAAT 60.179 55.000 0.00 0.00 0.00 2.17
2624 2755 4.008933 GCCTCCACGCAGACCAGT 62.009 66.667 0.00 0.00 0.00 4.00
2628 2759 2.821366 CCATGCCTCCACGCAGAC 60.821 66.667 0.00 0.00 43.26 3.51
2821 2954 2.345991 GGGCGCCTGTAGTCAACA 59.654 61.111 28.56 0.00 36.42 3.33
2822 2955 2.813908 CGGGCGCCTGTAGTCAAC 60.814 66.667 27.83 5.19 0.00 3.18
2878 3011 3.556004 GCAAGAAGTCTAGGTTGCAGTCT 60.556 47.826 8.25 0.00 43.86 3.24
2921 3054 1.091771 CAGTGATCGGCGATTGGCTT 61.092 55.000 24.81 0.00 42.94 4.35
2960 3093 4.430765 CAAGTCCGTCCGACCCCG 62.431 72.222 0.00 0.00 43.08 5.73
2967 3100 1.134226 CACGTACAACAAGTCCGTCC 58.866 55.000 0.00 0.00 41.08 4.79
3004 3140 3.077617 GCAGAGATCTTCCCACTGC 57.922 57.895 15.23 15.23 44.88 4.40
3039 3175 2.445525 ACAAGGTATGGGTTCCACTTGT 59.554 45.455 12.64 12.64 40.83 3.16
3121 3263 1.541588 GAATCTTGTGCAAGGTCCACC 59.458 52.381 11.47 0.00 38.88 4.61
3122 3264 1.541588 GGAATCTTGTGCAAGGTCCAC 59.458 52.381 20.60 8.51 40.10 4.02
3129 3271 4.459390 CATTCCATGGAATCTTGTGCAA 57.541 40.909 32.87 7.45 42.30 4.08
3163 3305 5.127845 AGACGAGAACACATCTAACATCCAT 59.872 40.000 0.00 0.00 38.96 3.41
3204 3380 0.799393 GCGGAGAAAAGACCTCTTGC 59.201 55.000 0.00 0.00 36.12 4.01
3253 3429 2.222213 CCTCAGTGTATCTAGTCGAGCG 59.778 54.545 0.00 0.00 0.00 5.03
3273 3449 2.555547 GCACCACTCCACACTTGCC 61.556 63.158 0.00 0.00 0.00 4.52
3276 3452 1.069765 CTCGCACCACTCCACACTT 59.930 57.895 0.00 0.00 0.00 3.16
3278 3454 2.357517 CCTCGCACCACTCCACAC 60.358 66.667 0.00 0.00 0.00 3.82
3279 3455 2.842462 ACCTCGCACCACTCCACA 60.842 61.111 0.00 0.00 0.00 4.17
3286 3471 1.110518 TATATCGCCACCTCGCACCA 61.111 55.000 0.00 0.00 0.00 4.17
3290 3475 0.314302 ACACTATATCGCCACCTCGC 59.686 55.000 0.00 0.00 0.00 5.03
3292 3477 4.785511 ATACACACTATATCGCCACCTC 57.214 45.455 0.00 0.00 0.00 3.85
3343 3528 2.741985 CTGGCGACGAATGCACCA 60.742 61.111 0.00 0.00 0.00 4.17
3349 3534 4.397103 TCGATATATTACCTGGCGACGAAT 59.603 41.667 0.00 0.00 0.00 3.34
3352 3537 3.752412 TCGATATATTACCTGGCGACG 57.248 47.619 0.00 0.00 0.00 5.12
3357 3542 5.687730 GCATCACGATCGATATATTACCTGG 59.312 44.000 24.34 0.00 0.00 4.45
3367 3552 4.445385 CACAAAGATGCATCACGATCGATA 59.555 41.667 27.81 9.48 0.00 2.92
3375 3560 4.241590 TGGTTTCACAAAGATGCATCAC 57.758 40.909 27.81 14.19 0.00 3.06
3379 3564 5.534207 AAAGATGGTTTCACAAAGATGCA 57.466 34.783 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.