Multiple sequence alignment - TraesCS2D01G422100

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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 TraesCS2D01G422100 chr2D 100.000 3484 0 0 1 3484 535574212 535570729 0.000000e+00 6434.0
1 TraesCS2D01G422100 chr2D 92.135 89 7 0 3104 3192 535571021 535570933 3.650000e-25 126.0
2 TraesCS2D01G422100 chr2D 92.135 89 7 0 3192 3280 535571109 535571021 3.650000e-25 126.0
3 TraesCS2D01G422100 chr2A 92.944 2395 95 28 1 2351 678673856 678671492 0.000000e+00 3419.0
4 TraesCS2D01G422100 chr2A 94.221 1142 50 11 2348 3484 678671461 678670331 0.000000e+00 1729.0
5 TraesCS2D01G422100 chr2A 81.321 530 59 20 2633 3150 678670074 678669573 9.060000e-106 394.0
6 TraesCS2D01G422100 chr2A 80.934 257 26 9 3237 3484 678668792 678668550 7.680000e-42 182.0
7 TraesCS2D01G422100 chr2A 91.398 93 8 0 3104 3196 678670623 678670531 1.020000e-25 128.0
8 TraesCS2D01G422100 chr2A 90.698 86 8 0 3192 3277 678670713 678670628 7.900000e-22 115.0
9 TraesCS2D01G422100 chr2A 93.182 44 3 0 3149 3192 678668792 678668749 8.070000e-07 65.8
10 TraesCS2D01G422100 chr2B 90.624 2389 144 42 1 2351 636778280 636775934 0.000000e+00 3097.0
11 TraesCS2D01G422100 chr2B 94.118 867 33 8 2630 3484 636775369 636774509 0.000000e+00 1303.0
12 TraesCS2D01G422100 chr2B 92.414 290 17 3 2348 2634 636775903 636775616 3.240000e-110 409.0
13 TraesCS2D01G422100 chr2B 80.374 535 58 24 2633 3150 636774252 636773748 2.560000e-96 363.0
14 TraesCS2D01G422100 chr2B 92.135 89 7 0 3192 3280 636774893 636774805 3.650000e-25 126.0
15 TraesCS2D01G422100 chr2B 90.244 82 8 0 3111 3192 636774800 636774719 1.320000e-19 108.0
16 TraesCS2D01G422100 chr2B 93.182 44 3 0 3149 3192 636772952 636772909 8.070000e-07 65.8


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 TraesCS2D01G422100 chr2D 535570729 535574212 3483 True 2228.666667 6434 94.756667 1 3484 3 chr2D.!!$R1 3483
1 TraesCS2D01G422100 chr2A 678668550 678673856 5306 True 861.828571 3419 89.242571 1 3484 7 chr2A.!!$R1 3483
2 TraesCS2D01G422100 chr2B 636772909 636778280 5371 True 781.685714 3097 90.441571 1 3484 7 chr2B.!!$R1 3483

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
382 383 0.44426 GGCGCTTGAAGCAGTAGAAC 59.556 55.0 18.22 0.0 42.58 3.01 F
1176 1209 0.17915 CTTCGTCTTCCTCTGCCTCG 60.179 60.0 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 1685 0.536260 AGAGTGCTGCATCTGAGACC 59.464 55.000 5.27 0.00 0.00 3.85 R
3059 3432 3.069586 TCACGTCCTTCATGAAGTCAACT 59.930 43.478 29.03 13.52 36.72 3.16 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
84 85 1.004745 GTCAAGCCTCCCTGATTTGGA 59.995 52.381 0.00 0.00 0.00 3.53
295 296 3.689002 CTTGAAGGCGAGCCCCCTC 62.689 68.421 10.95 6.05 36.58 4.30
330 331 2.356278 GAGGGCATTGCAGGTGGA 59.644 61.111 11.39 0.00 0.00 4.02
346 347 2.359169 GGACGTCTGGAGGCCATGA 61.359 63.158 16.46 0.00 30.82 3.07
358 359 2.436646 CCATGAAAGCCGGCGTCT 60.437 61.111 26.84 14.89 0.00 4.18
382 383 0.444260 GGCGCTTGAAGCAGTAGAAC 59.556 55.000 18.22 0.00 42.58 3.01
451 452 1.000771 GGTCTTGGGGAAAGAGGCC 60.001 63.158 0.00 0.00 45.69 5.19
1006 1016 2.152297 CTGCGTGGTCACTCTCAGCT 62.152 60.000 0.00 0.00 0.00 4.24
1016 1026 0.323360 ACTCTCAGCTCTTCTCGGCT 60.323 55.000 0.00 0.00 39.60 5.52
1021 1031 2.355946 AGCTCTTCTCGGCTGTTCA 58.644 52.632 0.00 0.00 37.41 3.18
1034 1044 3.430218 CGGCTGTTCAGAAGTAGTTGAAG 59.570 47.826 3.84 0.00 34.25 3.02
1067 1077 2.184167 CACGGCCCAAACGTCAACT 61.184 57.895 0.00 0.00 43.58 3.16
1072 1082 1.165270 GCCCAAACGTCAACTAGCAT 58.835 50.000 0.00 0.00 0.00 3.79
1073 1083 1.135689 GCCCAAACGTCAACTAGCATG 60.136 52.381 0.00 0.00 0.00 4.06
1074 1084 1.468520 CCCAAACGTCAACTAGCATGG 59.531 52.381 0.00 0.00 0.00 3.66
1075 1085 1.468520 CCAAACGTCAACTAGCATGGG 59.531 52.381 0.00 0.00 0.00 4.00
1076 1086 1.468520 CAAACGTCAACTAGCATGGGG 59.531 52.381 0.00 0.00 0.00 4.96
1092 1121 0.475044 GGGGATACACGGCCCAAATA 59.525 55.000 0.00 0.00 46.57 1.40
1125 1158 2.205462 ATCATCCCCCTCCTCCCG 59.795 66.667 0.00 0.00 0.00 5.14
1132 1165 2.365105 CCCTCCTCCCGTGGCTTA 60.365 66.667 0.00 0.00 0.00 3.09
1151 1184 2.366640 ATTCGCTGCTACTCCTCCTA 57.633 50.000 0.00 0.00 0.00 2.94
1176 1209 0.179150 CTTCGTCTTCCTCTGCCTCG 60.179 60.000 0.00 0.00 0.00 4.63
1219 1269 3.164269 CCCCCTCCAGATCGGTGG 61.164 72.222 14.16 14.16 46.52 4.61
1244 1294 3.357079 CGCCCTGTTTGCTTCGCT 61.357 61.111 0.00 0.00 0.00 4.93
1268 1318 3.875727 CACCAGATCAAGTAAGCTCCATG 59.124 47.826 0.00 0.00 0.00 3.66
1274 1324 0.995024 AAGTAAGCTCCATGCCCTGT 59.005 50.000 0.00 0.00 44.23 4.00
1276 1326 0.543749 GTAAGCTCCATGCCCTGTCT 59.456 55.000 0.00 0.00 44.23 3.41
1291 1341 4.647611 CCCTGTCTGTGTGTAATTTGGTA 58.352 43.478 0.00 0.00 0.00 3.25
1294 1344 6.208599 CCCTGTCTGTGTGTAATTTGGTATTT 59.791 38.462 0.00 0.00 0.00 1.40
1343 1393 3.040655 TCCACCGAGATGGAATTAGGA 57.959 47.619 1.01 0.00 46.08 2.94
1344 1394 3.380393 TCCACCGAGATGGAATTAGGAA 58.620 45.455 1.01 0.00 46.08 3.36
1345 1395 3.973973 TCCACCGAGATGGAATTAGGAAT 59.026 43.478 1.01 0.00 46.08 3.01
1386 1437 6.507900 TGATTCGAGTCCTTGATTAGATGAC 58.492 40.000 5.38 0.00 0.00 3.06
1390 1441 4.339530 CGAGTCCTTGATTAGATGACTGGA 59.660 45.833 0.00 0.00 36.48 3.86
1408 1474 4.128643 CTGGAAGTAGTAGTAGTCCTCCG 58.871 52.174 8.18 0.00 0.00 4.63
1515 1581 4.436242 TTTCGTTCAGTAATCGCTCTCT 57.564 40.909 0.00 0.00 0.00 3.10
1604 1672 1.478916 GGAGGAGTGGACTGTAGAAGC 59.521 57.143 0.00 0.00 0.00 3.86
1617 1685 6.412362 ACTGTAGAAGCAGATAAGTATGGG 57.588 41.667 0.00 0.00 39.62 4.00
1627 1701 5.568423 GCAGATAAGTATGGGGTCTCAGATG 60.568 48.000 0.00 0.00 0.00 2.90
1683 1762 1.906574 AGGTCAGATTGGGTAGCGAAA 59.093 47.619 0.00 0.00 0.00 3.46
1694 1773 2.159627 GGGTAGCGAAATCACAGTTGTG 59.840 50.000 5.91 5.91 46.91 3.33
1697 1776 0.593128 GCGAAATCACAGTTGTGGCT 59.407 50.000 11.98 0.00 45.65 4.75
1737 1816 7.282224 TGTTTGCTTGTCTAAGATGTTTACTGT 59.718 33.333 0.00 0.00 35.92 3.55
1828 1907 6.757947 GCATGCTTATCTTGCCTTTTTATCAA 59.242 34.615 11.37 0.00 39.24 2.57
1830 1909 6.321717 TGCTTATCTTGCCTTTTTATCAACG 58.678 36.000 0.00 0.00 0.00 4.10
1831 1910 6.072175 TGCTTATCTTGCCTTTTTATCAACGT 60.072 34.615 0.00 0.00 0.00 3.99
1832 1911 6.806739 GCTTATCTTGCCTTTTTATCAACGTT 59.193 34.615 0.00 0.00 0.00 3.99
1833 1912 7.008357 GCTTATCTTGCCTTTTTATCAACGTTC 59.992 37.037 0.00 0.00 0.00 3.95
1834 1913 6.575162 ATCTTGCCTTTTTATCAACGTTCT 57.425 33.333 0.00 0.00 0.00 3.01
1835 1914 5.757886 TCTTGCCTTTTTATCAACGTTCTG 58.242 37.500 0.00 0.00 0.00 3.02
1943 2022 8.966155 TCATGTATGGGTTTATCTACCAGATA 57.034 34.615 0.00 0.00 40.09 1.98
1960 2039 6.493166 ACCAGATATTTCCAGGTTTGATTGA 58.507 36.000 0.00 0.00 29.09 2.57
1969 2048 3.119245 CCAGGTTTGATTGATGCTCCTTG 60.119 47.826 0.00 0.00 0.00 3.61
1987 2066 9.976511 TGCTCCTTGTACATTATGTTATACTAC 57.023 33.333 2.23 0.00 0.00 2.73
1988 2067 9.420551 GCTCCTTGTACATTATGTTATACTACC 57.579 37.037 2.23 0.00 0.00 3.18
2017 2096 5.878332 TTTGTATGGTACTGAAGCACATG 57.122 39.130 0.00 0.00 38.70 3.21
2019 2098 2.495155 ATGGTACTGAAGCACATGCA 57.505 45.000 6.64 0.00 45.16 3.96
2026 2105 5.240183 GGTACTGAAGCACATGCATTCATAT 59.760 40.000 6.64 7.20 45.16 1.78
2300 2379 0.989890 GCCGTAGCGTAACTTGAGTG 59.010 55.000 0.00 0.00 0.00 3.51
2351 2430 4.422057 TCCAGAGTCAGTTGGGTTATGTA 58.578 43.478 0.00 0.00 35.13 2.29
2352 2431 4.466370 TCCAGAGTCAGTTGGGTTATGTAG 59.534 45.833 0.00 0.00 35.13 2.74
2354 2433 5.411781 CAGAGTCAGTTGGGTTATGTAGTC 58.588 45.833 0.00 0.00 0.00 2.59
2355 2434 5.047306 CAGAGTCAGTTGGGTTATGTAGTCA 60.047 44.000 0.00 0.00 0.00 3.41
2359 2472 4.836175 TCAGTTGGGTTATGTAGTCACTGA 59.164 41.667 0.00 0.00 0.00 3.41
2482 2595 9.558396 GAGAAAGACTCCTGATCATAAATTCAT 57.442 33.333 0.00 0.00 39.53 2.57
2524 2637 4.738124 TCTGTCAGATCTTCTTTAGCACG 58.262 43.478 0.00 0.00 0.00 5.34
2716 3084 4.406069 CAGACAATGTATTCGGCTTGTTG 58.594 43.478 0.00 0.00 32.28 3.33
3161 3534 5.752955 GTCTTGTGTGTAAAACATTGCCATT 59.247 36.000 0.00 0.00 41.97 3.16
3253 3628 5.219633 GTGTGTAAAACATTGTCATGGTCC 58.780 41.667 0.00 0.00 41.97 4.46
3280 3655 4.948062 ACCCTTACCTTGAAATTAGCCT 57.052 40.909 0.00 0.00 0.00 4.58
3375 3757 4.036734 TCCTCTGTGTCATTTGTTTGCTTC 59.963 41.667 0.00 0.00 0.00 3.86
3477 3859 8.847196 GTTACTTTGTACTTTCTCCCTGAAAAT 58.153 33.333 0.00 0.00 43.25 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 2.299993 CACTATGGTCGATGTGCTGT 57.700 50.000 0.00 0.00 0.00 4.40
133 134 2.092753 TGAAATGAGACAGAGGGATGGC 60.093 50.000 0.00 0.00 0.00 4.40
330 331 0.036010 CTTTCATGGCCTCCAGACGT 60.036 55.000 3.32 0.00 36.75 4.34
358 359 3.939837 CTGCTTCAAGCGCCTCCGA 62.940 63.158 2.29 0.00 46.26 4.55
536 537 1.448922 CCCTCCGACGATCTGTCCTC 61.449 65.000 0.00 0.00 45.23 3.71
781 782 3.728373 GCCGACCCCACCATCCTT 61.728 66.667 0.00 0.00 0.00 3.36
969 970 3.226429 GATATGCTCCTCCGCGCCA 62.226 63.158 0.00 0.00 0.00 5.69
997 998 0.323360 AGCCGAGAAGAGCTGAGAGT 60.323 55.000 0.00 0.00 38.11 3.24
1006 1016 1.964223 ACTTCTGAACAGCCGAGAAGA 59.036 47.619 13.51 0.00 43.65 2.87
1016 1026 4.345257 AGGCTCTTCAACTACTTCTGAACA 59.655 41.667 0.00 0.00 0.00 3.18
1021 1031 3.898123 TCACAGGCTCTTCAACTACTTCT 59.102 43.478 0.00 0.00 0.00 2.85
1067 1077 1.752198 GCCGTGTATCCCCATGCTA 59.248 57.895 0.00 0.00 0.00 3.49
1072 1082 1.576368 ATTTGGGCCGTGTATCCCCA 61.576 55.000 0.00 0.00 46.73 4.96
1073 1083 0.475044 TATTTGGGCCGTGTATCCCC 59.525 55.000 0.00 0.00 41.92 4.81
1074 1084 2.433436 GATATTTGGGCCGTGTATCCC 58.567 52.381 0.00 0.00 42.93 3.85
1075 1085 2.073816 CGATATTTGGGCCGTGTATCC 58.926 52.381 0.00 0.00 0.00 2.59
1076 1086 2.993899 CTCGATATTTGGGCCGTGTATC 59.006 50.000 0.00 5.49 0.00 2.24
1125 1158 1.861575 GAGTAGCAGCGAATAAGCCAC 59.138 52.381 0.00 0.00 38.01 5.01
1132 1165 1.957877 GTAGGAGGAGTAGCAGCGAAT 59.042 52.381 0.00 0.00 0.00 3.34
1151 1184 0.410270 AGAGGAAGACGAAGGGAGGT 59.590 55.000 0.00 0.00 0.00 3.85
1176 1209 3.090532 AGGGGGCGATCTGGTTCC 61.091 66.667 0.00 0.00 0.00 3.62
1219 1269 2.034221 AAACAGGGCGCTCCTTCC 59.966 61.111 13.96 3.05 45.47 3.46
1244 1294 2.355108 GGAGCTTACTTGATCTGGTGCA 60.355 50.000 0.00 0.00 0.00 4.57
1268 1318 2.228822 CCAAATTACACACAGACAGGGC 59.771 50.000 0.00 0.00 0.00 5.19
1343 1393 8.792633 TCGAATCAATCAACCTAGAAAACAATT 58.207 29.630 0.00 0.00 0.00 2.32
1344 1394 8.335532 TCGAATCAATCAACCTAGAAAACAAT 57.664 30.769 0.00 0.00 0.00 2.71
1345 1395 7.444183 ACTCGAATCAATCAACCTAGAAAACAA 59.556 33.333 0.00 0.00 0.00 2.83
1386 1437 4.128643 CGGAGGACTACTACTACTTCCAG 58.871 52.174 0.00 0.00 0.00 3.86
1408 1474 4.640647 AGCTACCAAAATTTAGCAGCCTAC 59.359 41.667 12.08 0.00 42.78 3.18
1416 1482 7.384932 CCAAAGGTTGAAGCTACCAAAATTTAG 59.615 37.037 6.91 0.91 38.16 1.85
1453 1519 4.953579 TGGTTAAACCACAGAAAAGCTCTT 59.046 37.500 0.00 0.00 44.79 2.85
1515 1581 2.034179 CGTACTGATTCATAGGCACGGA 59.966 50.000 0.00 0.00 0.00 4.69
1604 1672 5.568423 GCATCTGAGACCCCATACTTATCTG 60.568 48.000 0.00 0.00 0.00 2.90
1617 1685 0.536260 AGAGTGCTGCATCTGAGACC 59.464 55.000 5.27 0.00 0.00 3.85
1627 1701 2.544486 CCCAAACTTTTCAGAGTGCTGC 60.544 50.000 0.00 0.00 42.01 5.25
1694 1773 2.322355 ACACAGCTCATATGACAGCC 57.678 50.000 12.09 0.00 36.17 4.85
1697 1776 3.678289 AGCAAACACAGCTCATATGACA 58.322 40.909 0.00 0.00 38.01 3.58
1737 1816 5.911378 TGGTTGCAGATATTAAATGTGCA 57.089 34.783 14.18 14.18 42.24 4.57
1834 1913 1.361204 TGCTTCTCCTGATGGGAACA 58.639 50.000 0.00 0.00 44.58 3.18
1835 1914 2.496899 TTGCTTCTCCTGATGGGAAC 57.503 50.000 0.00 0.00 44.58 3.62
1943 2022 4.161001 GGAGCATCAATCAAACCTGGAAAT 59.839 41.667 0.00 0.00 36.25 2.17
1986 2065 7.499232 GCTTCAGTACCATACAAAATATCAGGT 59.501 37.037 0.00 0.00 0.00 4.00
1987 2066 7.498900 TGCTTCAGTACCATACAAAATATCAGG 59.501 37.037 0.00 0.00 0.00 3.86
1988 2067 8.338259 GTGCTTCAGTACCATACAAAATATCAG 58.662 37.037 0.00 0.00 0.00 2.90
1990 2069 8.208718 TGTGCTTCAGTACCATACAAAATATC 57.791 34.615 0.00 0.00 0.00 1.63
1991 2070 8.623903 CATGTGCTTCAGTACCATACAAAATAT 58.376 33.333 0.00 0.00 0.00 1.28
1992 2071 7.415095 GCATGTGCTTCAGTACCATACAAAATA 60.415 37.037 0.00 0.00 38.21 1.40
2300 2379 5.197451 TGTGTATCATGGACATAAAACCCC 58.803 41.667 4.91 0.00 0.00 4.95
2355 2434 7.013369 GGTTCCATAACTCTGAAAGTTTTCAGT 59.987 37.037 25.59 14.51 46.26 3.41
2482 2595 7.618117 TGACAGAATTAGTGAAGGTATAGGACA 59.382 37.037 0.00 0.00 0.00 4.02
2495 2608 8.816144 GCTAAAGAAGATCTGACAGAATTAGTG 58.184 37.037 9.70 0.00 0.00 2.74
2582 2699 6.039829 AGGACAAAAGGAGACTCAATGTTTTC 59.960 38.462 4.53 0.00 42.68 2.29
2598 2715 9.678941 GGACTAAATCAAACTAAAGGACAAAAG 57.321 33.333 0.00 0.00 0.00 2.27
2959 3332 4.968719 TGTTATCCTTCTATCCAGCTCCAA 59.031 41.667 0.00 0.00 0.00 3.53
3059 3432 3.069586 TCACGTCCTTCATGAAGTCAACT 59.930 43.478 29.03 13.52 36.72 3.16
3375 3757 7.120432 AGCTAAAGTAAGCAAAGATTCTGAAGG 59.880 37.037 0.00 0.00 45.30 3.46


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

AutoCloner maintained by Alex Coulton.