Multiple sequence alignment - TraesCS7B01G120200

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 TraesCS7B01G120200 chr7B 100.000 2277 0 0 1 2277 139619347 139617071 0 4205
1 TraesCS7B01G120200 chr7B 96.004 2277 84 3 1 2277 698126662 698124393 0 3694
2 TraesCS7B01G120200 chr7B 95.608 2277 94 2 1 2277 716795567 716793297 0 3646
3 TraesCS7B01G120200 chr1D 96.355 2277 82 1 1 2277 212429140 212431415 0 3744
4 TraesCS7B01G120200 chrUn 96.311 2277 83 1 1 2277 257944383 257946658 0 3738
5 TraesCS7B01G120200 chrUn 96.047 2277 84 2 1 2277 233524997 233522727 0 3701
6 TraesCS7B01G120200 chr7A 95.872 2277 88 2 1 2277 60095927 60093657 0 3679
7 TraesCS7B01G120200 chr7A 95.608 2277 99 1 1 2277 211237863 211235588 0 3650
8 TraesCS7B01G120200 chr2D 95.784 2277 93 3 1 2277 637308434 637306161 0 3670
9 TraesCS7B01G120200 chr4D 95.740 2277 96 1 1 2277 123689233 123691508 0 3666


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 TraesCS7B01G120200 chr7B 139617071 139619347 2276 True 4205 4205 100.000 1 2277 1 chr7B.!!$R1 2276
1 TraesCS7B01G120200 chr7B 698124393 698126662 2269 True 3694 3694 96.004 1 2277 1 chr7B.!!$R2 2276
2 TraesCS7B01G120200 chr7B 716793297 716795567 2270 True 3646 3646 95.608 1 2277 1 chr7B.!!$R3 2276
3 TraesCS7B01G120200 chr1D 212429140 212431415 2275 False 3744 3744 96.355 1 2277 1 chr1D.!!$F1 2276
4 TraesCS7B01G120200 chrUn 257944383 257946658 2275 False 3738 3738 96.311 1 2277 1 chrUn.!!$F1 2276
5 TraesCS7B01G120200 chrUn 233522727 233524997 2270 True 3701 3701 96.047 1 2277 1 chrUn.!!$R1 2276
6 TraesCS7B01G120200 chr7A 60093657 60095927 2270 True 3679 3679 95.872 1 2277 1 chr7A.!!$R1 2276
7 TraesCS7B01G120200 chr7A 211235588 211237863 2275 True 3650 3650 95.608 1 2277 1 chr7A.!!$R2 2276
8 TraesCS7B01G120200 chr2D 637306161 637308434 2273 True 3670 3670 95.784 1 2277 1 chr2D.!!$R1 2276
9 TraesCS7B01G120200 chr4D 123689233 123691508 2275 False 3666 3666 95.740 1 2277 1 chr4D.!!$F1 2276

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
998 999 0.032267 GATCCGCTTACCGAGGAAGG 59.968 60.0 0.0 0.0 45.11 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 2055 0.90818 CTTTCCCCTGGTAGTCCCGT 60.908 60.0 0.0 0.0 35.15 5.28 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
46 47 7.248743 AGATCATGTTGTTCATTGGGAATTT 57.751 32.000 0.00 0.00 37.93 1.82
70 71 0.250513 GGGGAGAACGAGCAGACATT 59.749 55.000 0.00 0.00 0.00 2.71
192 193 5.164022 GCAAGCAAATTCGGAAATGAAAGAG 60.164 40.000 10.10 0.00 0.00 2.85
195 196 4.082245 GCAAATTCGGAAATGAAAGAGGGA 60.082 41.667 10.10 0.00 0.00 4.20
222 223 4.606961 GAAAGAACAAGCAACGGATTTCA 58.393 39.130 0.00 0.00 0.00 2.69
271 272 4.036380 CGTTTTCTTGCTCCTTGGTACTTT 59.964 41.667 0.00 0.00 0.00 2.66
288 289 6.998074 TGGTACTTTTCTGATCAATCACACTT 59.002 34.615 0.00 0.00 32.50 3.16
347 348 6.973843 TGAACCGCTTACTAATCACGTATAT 58.026 36.000 0.00 0.00 0.00 0.86
404 405 1.603172 CGTCTTGGTCTCGCTCACTTT 60.603 52.381 0.00 0.00 0.00 2.66
421 422 0.753867 TTTGCCCGCCTATCGTATCA 59.246 50.000 0.00 0.00 36.19 2.15
457 458 0.672342 CAAGCAACAGCTTCTGCCTT 59.328 50.000 12.20 4.94 46.35 4.35
522 523 4.445452 TGTAGTAGTCGGCCTTTGTTAG 57.555 45.455 0.00 0.00 0.00 2.34
542 543 1.641577 GCTTCGCCAGAAACGACTAT 58.358 50.000 0.00 0.00 39.67 2.12
545 546 3.512680 CTTCGCCAGAAACGACTATTCT 58.487 45.455 0.00 0.00 39.67 2.40
650 651 3.540314 AGATGGAGAGTAAGCAAGCTG 57.460 47.619 0.00 0.00 0.00 4.24
653 654 0.036010 GGAGAGTAAGCAAGCTGCCA 60.036 55.000 0.00 0.00 46.52 4.92
708 709 1.378250 CCCTTCCTGCCTGCTTCAG 60.378 63.158 0.00 0.00 0.00 3.02
728 729 5.719173 TCAGTTGATGTGAATGATCGTGTA 58.281 37.500 0.00 0.00 0.00 2.90
732 733 6.818142 AGTTGATGTGAATGATCGTGTATTCA 59.182 34.615 2.85 2.85 40.06 2.57
741 742 8.124199 TGAATGATCGTGTATTCAACATCAATG 58.876 33.333 4.22 0.00 41.10 2.82
750 751 5.892160 ATTCAACATCAATGTCAGTCTGG 57.108 39.130 0.00 0.00 40.80 3.86
751 752 4.622260 TCAACATCAATGTCAGTCTGGA 57.378 40.909 0.00 0.00 40.80 3.86
815 816 0.600057 TCGGATGATGAGGATGAGCG 59.400 55.000 0.00 0.00 0.00 5.03
980 981 0.325296 ATACTCCCCAGCTTCCACGA 60.325 55.000 0.00 0.00 0.00 4.35
998 999 0.032267 GATCCGCTTACCGAGGAAGG 59.968 60.000 0.00 0.00 45.11 3.46
1102 1103 4.402155 TCGTACGGTTCATAGTTGGGTATT 59.598 41.667 16.52 0.00 0.00 1.89
1129 1130 1.133025 CTCATGGATTGTTGGGAACGC 59.867 52.381 0.00 0.00 0.00 4.84
1333 1334 0.038526 AGGAATGTTCGCGTCTCGTT 60.039 50.000 5.77 5.58 39.67 3.85
1343 1344 2.720758 CGTCTCGTTGCAAGGCTCG 61.721 63.158 14.22 13.31 0.00 5.03
1392 1393 3.636231 CAGTCCGGGGCACAAGGA 61.636 66.667 0.00 0.00 33.32 3.36
1413 1414 2.678786 CTGGTACTACCCAGGTGCA 58.321 57.895 2.59 0.00 46.89 4.57
1419 1420 2.568623 ACTACCCAGGTGCAAAGAAG 57.431 50.000 0.00 0.00 0.00 2.85
1577 1578 0.319555 TTTCAGAGAAGTGGCGGTCG 60.320 55.000 0.00 0.00 0.00 4.79
1589 1590 1.389609 GGCGGTCGGAATCCACTCTA 61.390 60.000 0.00 0.00 0.00 2.43
1615 1616 8.232913 ACAAAAGAAAATAACAGACTAAGCCA 57.767 30.769 0.00 0.00 0.00 4.75
1695 1697 2.894126 CAGATCGGCCATAGGAGTACTT 59.106 50.000 2.24 0.00 0.00 2.24
1756 1758 1.287503 GCCGCCCGTTTTCATTTCA 59.712 52.632 0.00 0.00 0.00 2.69
1770 1772 2.041081 TCATTTCATGAAAGTCCCCGGT 59.959 45.455 24.17 4.11 36.11 5.28
1772 1774 4.080015 TCATTTCATGAAAGTCCCCGGTAT 60.080 41.667 24.17 2.71 36.11 2.73
1813 1815 1.014564 GCGCGTTCTGCTTCTTAGGT 61.015 55.000 8.43 0.00 43.27 3.08
1821 1823 4.377839 TCTGCTTCTTAGGTCGATGAAG 57.622 45.455 0.00 0.00 38.96 3.02
1851 1853 3.558411 GATCGTGCGTGGCAGCTC 61.558 66.667 9.68 5.91 40.08 4.09
1937 1939 4.610333 CAAAGCTAAATAGGAAAGGGGGT 58.390 43.478 0.00 0.00 0.00 4.95
2038 2040 3.283751 AGAAAGATGAGACGAGACGGAT 58.716 45.455 0.00 0.00 0.00 4.18
2075 2077 0.914902 GGACTACCAGGGGAAAGCCT 60.915 60.000 0.00 0.00 35.97 4.58
2076 2078 1.624391 GGACTACCAGGGGAAAGCCTA 60.624 57.143 0.00 0.00 35.97 3.93
2086 2088 1.145598 GAAAGCCTACCCCCGCTAC 59.854 63.158 0.00 0.00 34.11 3.58
2087 2089 1.306739 AAAGCCTACCCCCGCTACT 60.307 57.895 0.00 0.00 34.11 2.57
2113 2115 7.468141 AACATAGATATCTATTCTCGGTGCA 57.532 36.000 20.53 0.00 37.07 4.57
2187 2189 0.712380 ACTTGGGATGGGAATGGCTT 59.288 50.000 0.00 0.00 0.00 4.35
2234 2236 1.680651 CTCCAGTCCAGTCGCCTCT 60.681 63.158 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 1.005569 TCTGCTCGTTCTCCCCTCTTA 59.994 52.381 0.00 0.00 0.00 2.10
92 93 5.956068 TGATGACGAATTCCATGAAAACA 57.044 34.783 0.00 0.00 0.00 2.83
96 97 5.297527 CCATCTTGATGACGAATTCCATGAA 59.702 40.000 11.76 0.00 0.00 2.57
192 193 2.706890 TGCTTGTTCTTTCGGTATCCC 58.293 47.619 0.00 0.00 0.00 3.85
195 196 2.482721 CCGTTGCTTGTTCTTTCGGTAT 59.517 45.455 0.00 0.00 33.20 2.73
222 223 2.014068 GCTTTAGCAAGGGATGAGCGT 61.014 52.381 0.00 0.00 41.59 5.07
271 272 9.288576 ACTAATGAAAAGTGTGATTGATCAGAA 57.711 29.630 0.00 0.00 37.51 3.02
311 312 1.144969 GCGGTTCAAGACATCGAACA 58.855 50.000 0.00 0.00 42.67 3.18
347 348 2.686119 GTGAAGGGGGCCTACTATACA 58.314 52.381 0.84 1.88 31.13 2.29
404 405 1.964448 CTGATACGATAGGCGGGCA 59.036 57.895 3.78 0.00 46.49 5.36
457 458 0.530744 AGCGATAGTGAAGCCGTCAA 59.469 50.000 0.00 0.00 38.23 3.18
535 536 3.491104 GCATTCGGGAAGAGAATAGTCGT 60.491 47.826 0.00 0.00 36.64 4.34
542 543 1.573108 AGAGGCATTCGGGAAGAGAA 58.427 50.000 0.00 0.00 0.00 2.87
545 546 1.909302 AGAAAGAGGCATTCGGGAAGA 59.091 47.619 0.00 0.00 32.04 2.87
653 654 7.122838 CGTTTAACGAATGCAATGCAAGCAT 62.123 40.000 20.44 20.44 46.05 3.79
708 709 7.003939 TGAATACACGATCATTCACATCAAC 57.996 36.000 2.85 0.00 36.49 3.18
728 729 5.563592 TCCAGACTGACATTGATGTTGAAT 58.436 37.500 3.32 0.00 41.95 2.57
732 733 6.550938 TCTATCCAGACTGACATTGATGTT 57.449 37.500 3.32 0.00 41.95 2.71
741 742 7.890515 TCAATGACATATCTATCCAGACTGAC 58.109 38.462 3.32 0.00 32.25 3.51
785 786 8.790718 CATCCTCATCATCCGAAAAGAAAATAT 58.209 33.333 0.00 0.00 0.00 1.28
815 816 5.763204 TCCAAAATTATGTTAGGATCGGCTC 59.237 40.000 0.00 0.00 0.00 4.70
980 981 1.400530 CCCTTCCTCGGTAAGCGGAT 61.401 60.000 0.00 0.00 33.07 4.18
1069 1070 0.108804 AACCGTACGAGCACATCCTG 60.109 55.000 18.76 0.00 0.00 3.86
1102 1103 6.264771 TCCCAACAATCCATGAGAATATCA 57.735 37.500 0.00 0.00 43.70 2.15
1129 1130 8.043710 AGAAAGGCATATTTCGAATATAGAGGG 58.956 37.037 0.00 0.00 42.73 4.30
1291 1292 1.841556 TTGCAGTTCCCTCCGGTCT 60.842 57.895 0.00 0.00 0.00 3.85
1322 1323 2.733218 CCTTGCAACGAGACGCGA 60.733 61.111 15.93 0.00 44.57 5.87
1333 1334 1.388547 AACTCAAAACGAGCCTTGCA 58.611 45.000 0.00 0.00 46.63 4.08
1343 1344 4.560716 GCCCTATGACCCAAAACTCAAAAC 60.561 45.833 0.00 0.00 0.00 2.43
1520 1521 1.220236 CTCTCTCCTCCCTCCTTGGAT 59.780 57.143 0.00 0.00 38.35 3.41
1589 1590 8.691797 TGGCTTAGTCTGTTATTTTCTTTTGTT 58.308 29.630 0.00 0.00 0.00 2.83
1630 1632 1.295423 CCGTCCCGTGTGGAGAATT 59.705 57.895 0.00 0.00 46.38 2.17
1695 1697 0.105401 TGCCCTGGTGTATATCCCGA 60.105 55.000 0.00 0.00 0.00 5.14
1756 1758 3.339713 TCCTATACCGGGGACTTTCAT 57.660 47.619 6.32 0.00 0.00 2.57
1770 1772 4.274794 TCACCTACAGCCCTTTCCTATA 57.725 45.455 0.00 0.00 0.00 1.31
1772 1774 2.634639 TCACCTACAGCCCTTTCCTA 57.365 50.000 0.00 0.00 0.00 2.94
1813 1815 4.368577 CCCATGGGAACGACTTCATCGA 62.369 54.545 28.27 0.00 45.80 3.59
1829 1831 3.576356 GCCACGCACGATCCCATG 61.576 66.667 0.00 0.00 0.00 3.66
1851 1853 4.564372 CCGCCTTTCATCATCATCTATACG 59.436 45.833 0.00 0.00 0.00 3.06
1885 1887 6.322931 TGCCTATTATGAGAATAGGTCCTGA 58.677 40.000 22.68 4.39 46.94 3.86
1887 1889 5.188751 GCTGCCTATTATGAGAATAGGTCCT 59.811 44.000 22.68 0.00 46.94 3.85
1937 1939 2.807967 CGAAAAAGGCAGTCATCAGTCA 59.192 45.455 0.00 0.00 0.00 3.41
2038 2040 1.300620 CCGTTGCGTCCTCTGACAA 60.301 57.895 0.00 0.00 41.85 3.18
2053 2055 0.908180 CTTTCCCCTGGTAGTCCCGT 60.908 60.000 0.00 0.00 35.15 5.28
2075 2077 4.183223 TCTATGTTAAGTAGCGGGGGTA 57.817 45.455 0.00 0.00 0.00 3.69
2076 2078 3.036452 TCTATGTTAAGTAGCGGGGGT 57.964 47.619 0.00 0.00 0.00 4.95
2086 2088 9.509855 GCACCGAGAATAGATATCTATGTTAAG 57.490 37.037 23.03 15.16 39.02 1.85
2087 2089 9.020731 TGCACCGAGAATAGATATCTATGTTAA 57.979 33.333 23.03 0.00 39.02 2.01
2187 2189 3.015675 TCAAATGATGCATGTGGGCTA 57.984 42.857 2.46 0.00 30.57 3.93
2234 2236 1.142667 TGGTTGACAAGCCACTGATCA 59.857 47.619 14.49 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.