Multiple sequence alignment - TraesCS6B01G096800

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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 TraesCS6B01G096800 chr6B 100.000 3404 0 0 1 3404 73072375 73075778 0.000000e+00 6287.0
1 TraesCS6B01G096800 chr6B 96.741 1381 23 9 2025 3404 73102894 73104253 0.000000e+00 2281.0
2 TraesCS6B01G096800 chr6B 99.494 989 3 2 4 991 676474205 676473218 0.000000e+00 1797.0
3 TraesCS6B01G096800 chr6B 82.238 1233 200 12 1226 2454 73164113 73162896 0.000000e+00 1046.0
4 TraesCS6B01G096800 chr6B 82.167 1043 179 5 1226 2266 37632822 37633859 0.000000e+00 889.0
5 TraesCS6B01G096800 chr6B 81.171 1025 186 6 1226 2247 36355268 36354248 0.000000e+00 817.0
6 TraesCS6B01G096800 chr6A 91.724 2163 129 28 1128 3255 39426795 39428942 0.000000e+00 2957.0
7 TraesCS6B01G096800 chr6A 92.913 127 8 1 993 1118 39426593 39426719 2.090000e-42 183.0
8 TraesCS6B01G096800 chr6D 91.724 2030 116 27 1128 3116 35456503 35458521 0.000000e+00 2771.0
9 TraesCS6B01G096800 chr6D 82.230 1193 195 11 1226 2416 35492234 35491057 0.000000e+00 1013.0
10 TraesCS6B01G096800 chr6D 88.112 143 10 5 3117 3255 35467023 35467162 2.720000e-36 163.0
11 TraesCS6B01G096800 chr7A 99.798 988 2 0 1 988 108591835 108592822 0.000000e+00 1814.0
12 TraesCS6B01G096800 chr7A 99.596 989 4 0 1 989 31974456 31975444 0.000000e+00 1805.0
13 TraesCS6B01G096800 chr7A 99.596 989 2 2 1 988 40255512 40256499 0.000000e+00 1803.0
14 TraesCS6B01G096800 chr7A 79.903 826 160 6 1322 2144 733434299 733433477 4.860000e-168 601.0
15 TraesCS6B01G096800 chr7B 99.697 990 2 1 1 990 745671359 745672347 0.000000e+00 1810.0
16 TraesCS6B01G096800 chr7B 99.696 988 2 1 1 988 703047154 703046168 0.000000e+00 1807.0
17 TraesCS6B01G096800 chr7B 78.364 929 197 4 1315 2241 720223526 720222600 1.750000e-167 599.0
18 TraesCS6B01G096800 chr5B 99.696 988 3 0 1 988 660602235 660603222 0.000000e+00 1808.0
19 TraesCS6B01G096800 chr5B 86.207 58 8 0 2348 2405 546094053 546093996 2.840000e-06 63.9
20 TraesCS6B01G096800 chr4B 99.595 988 2 2 1 988 621084254 621083269 0.000000e+00 1801.0
21 TraesCS6B01G096800 chr3B 99.496 992 1 1 1 988 6154106 6155097 0.000000e+00 1801.0
22 TraesCS6B01G096800 chr5D 77.357 1029 217 14 1226 2246 447634319 447635339 2.260000e-166 595.0


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 TraesCS6B01G096800 chr6B 73072375 73075778 3403 False 6287 6287 100.0000 1 3404 1 chr6B.!!$F2 3403
1 TraesCS6B01G096800 chr6B 73102894 73104253 1359 False 2281 2281 96.7410 2025 3404 1 chr6B.!!$F3 1379
2 TraesCS6B01G096800 chr6B 676473218 676474205 987 True 1797 1797 99.4940 4 991 1 chr6B.!!$R3 987
3 TraesCS6B01G096800 chr6B 73162896 73164113 1217 True 1046 1046 82.2380 1226 2454 1 chr6B.!!$R2 1228
4 TraesCS6B01G096800 chr6B 37632822 37633859 1037 False 889 889 82.1670 1226 2266 1 chr6B.!!$F1 1040
5 TraesCS6B01G096800 chr6B 36354248 36355268 1020 True 817 817 81.1710 1226 2247 1 chr6B.!!$R1 1021
6 TraesCS6B01G096800 chr6A 39426593 39428942 2349 False 1570 2957 92.3185 993 3255 2 chr6A.!!$F1 2262
7 TraesCS6B01G096800 chr6D 35456503 35458521 2018 False 2771 2771 91.7240 1128 3116 1 chr6D.!!$F1 1988
8 TraesCS6B01G096800 chr6D 35491057 35492234 1177 True 1013 1013 82.2300 1226 2416 1 chr6D.!!$R1 1190
9 TraesCS6B01G096800 chr7A 108591835 108592822 987 False 1814 1814 99.7980 1 988 1 chr7A.!!$F3 987
10 TraesCS6B01G096800 chr7A 31974456 31975444 988 False 1805 1805 99.5960 1 989 1 chr7A.!!$F1 988
11 TraesCS6B01G096800 chr7A 40255512 40256499 987 False 1803 1803 99.5960 1 988 1 chr7A.!!$F2 987
12 TraesCS6B01G096800 chr7A 733433477 733434299 822 True 601 601 79.9030 1322 2144 1 chr7A.!!$R1 822
13 TraesCS6B01G096800 chr7B 745671359 745672347 988 False 1810 1810 99.6970 1 990 1 chr7B.!!$F1 989
14 TraesCS6B01G096800 chr7B 703046168 703047154 986 True 1807 1807 99.6960 1 988 1 chr7B.!!$R1 987
15 TraesCS6B01G096800 chr7B 720222600 720223526 926 True 599 599 78.3640 1315 2241 1 chr7B.!!$R2 926
16 TraesCS6B01G096800 chr5B 660602235 660603222 987 False 1808 1808 99.6960 1 988 1 chr5B.!!$F1 987
17 TraesCS6B01G096800 chr4B 621083269 621084254 985 True 1801 1801 99.5950 1 988 1 chr4B.!!$R1 987
18 TraesCS6B01G096800 chr3B 6154106 6155097 991 False 1801 1801 99.4960 1 988 1 chr3B.!!$F1 987
19 TraesCS6B01G096800 chr5D 447634319 447635339 1020 False 595 595 77.3570 1226 2246 1 chr5D.!!$F1 1020

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
106 107 1.734163 TGCGCTCTATATCGATCGGA 58.266 50.000 16.41 4.00 0.0 4.55 F
1485 1560 2.440247 GGTAGTGGTGGGCATGGC 60.440 66.667 11.56 11.56 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1639 1715 0.834612 AGTGGGACTTCCGTGTCAAA 59.165 50.0 0.00 0.00 38.61 2.69 R
3324 3463 0.036010 ACAGGCCTGAATCGACAAGG 60.036 55.0 39.19 8.37 0.00 3.61 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
106 107 1.734163 TGCGCTCTATATCGATCGGA 58.266 50.000 16.41 4.00 0.00 4.55
1084 1092 3.512329 TCAAGACAAGCGGTACCTATTCA 59.488 43.478 10.90 0.00 0.00 2.57
1099 1107 9.921637 GGTACCTATTCATTTTGTCATTTGAAA 57.078 29.630 4.06 0.00 32.35 2.69
1219 1294 4.006319 GACAGTGCTTATCTTTTCCAGCT 58.994 43.478 0.00 0.00 33.15 4.24
1220 1295 3.755378 ACAGTGCTTATCTTTTCCAGCTG 59.245 43.478 6.78 6.78 33.15 4.24
1247 1322 3.375299 AGCGTCATTATTGGAGTTGCTTC 59.625 43.478 0.00 0.00 0.00 3.86
1420 1495 5.356190 TCAGAGAAAATGATCATGACCTTGC 59.644 40.000 9.46 0.00 0.00 4.01
1455 1530 6.993902 AGAAGGCAACAAACAATTTTGATCAT 59.006 30.769 0.00 0.00 44.38 2.45
1485 1560 2.440247 GGTAGTGGTGGGCATGGC 60.440 66.667 11.56 11.56 0.00 4.40
1639 1715 6.717540 TGTGGTAAAACTATATGGTTGTTGCT 59.282 34.615 5.10 0.00 0.00 3.91
1644 1720 9.124807 GTAAAACTATATGGTTGTTGCTTTGAC 57.875 33.333 5.10 0.00 0.00 3.18
1675 1751 4.813161 TCCCACTATTAGTCTACGAGTTCG 59.187 45.833 0.00 0.00 46.33 3.95
2126 2202 4.229876 GCAGAAGGCAATTTGTCACTAAC 58.770 43.478 3.49 0.00 43.97 2.34
2185 2261 6.914757 CCTAATTGAAGAAATCGCTGGAATTC 59.085 38.462 0.00 0.00 33.17 2.17
2596 2687 7.525688 TCATTCTAGTCGATTTGTTTAGCAG 57.474 36.000 0.00 0.00 0.00 4.24
2602 2693 4.220821 AGTCGATTTGTTTAGCAGAGAGGA 59.779 41.667 0.00 0.00 0.00 3.71
2718 2811 0.609957 TTGGCTTCATGGAGTGCCTG 60.610 55.000 2.16 0.00 45.11 4.85
3274 3413 5.480772 ACAAACGAGAGGAGAGATTTAGGAA 59.519 40.000 0.00 0.00 0.00 3.36
3275 3414 6.155393 ACAAACGAGAGGAGAGATTTAGGAAT 59.845 38.462 0.00 0.00 0.00 3.01
3284 3423 8.517323 AGGAGAGATTTAGGAATATGGTTCAT 57.483 34.615 0.00 0.00 0.00 2.57
3285 3424 8.601546 AGGAGAGATTTAGGAATATGGTTCATC 58.398 37.037 0.00 0.00 0.00 2.92
3298 3437 2.325583 GTTCATCCGAACCTATGCCA 57.674 50.000 0.00 0.00 44.92 4.92
3299 3438 2.213499 GTTCATCCGAACCTATGCCAG 58.787 52.381 0.00 0.00 44.92 4.85
3300 3439 1.496060 TCATCCGAACCTATGCCAGT 58.504 50.000 0.00 0.00 0.00 4.00
3301 3440 1.138859 TCATCCGAACCTATGCCAGTG 59.861 52.381 0.00 0.00 0.00 3.66
3302 3441 0.179045 ATCCGAACCTATGCCAGTGC 60.179 55.000 0.00 0.00 38.26 4.40
3304 3443 1.078497 CGAACCTATGCCAGTGCCA 60.078 57.895 0.00 0.00 36.33 4.92
3305 3444 0.464373 CGAACCTATGCCAGTGCCAT 60.464 55.000 0.00 0.00 36.33 4.40
3306 3445 1.767759 GAACCTATGCCAGTGCCATT 58.232 50.000 0.00 0.00 36.33 3.16
3307 3446 1.678101 GAACCTATGCCAGTGCCATTC 59.322 52.381 0.00 0.00 36.33 2.67
3308 3447 0.464373 ACCTATGCCAGTGCCATTCG 60.464 55.000 0.00 0.00 36.33 3.34
3309 3448 0.179048 CCTATGCCAGTGCCATTCGA 60.179 55.000 0.00 0.00 36.33 3.71
3310 3449 1.544093 CCTATGCCAGTGCCATTCGAT 60.544 52.381 0.00 0.00 36.33 3.59
3311 3450 1.802960 CTATGCCAGTGCCATTCGATC 59.197 52.381 0.00 0.00 36.33 3.69
3312 3451 0.182061 ATGCCAGTGCCATTCGATCT 59.818 50.000 0.00 0.00 36.33 2.75
3313 3452 0.829990 TGCCAGTGCCATTCGATCTA 59.170 50.000 0.00 0.00 36.33 1.98
3314 3453 1.417517 TGCCAGTGCCATTCGATCTAT 59.582 47.619 0.00 0.00 36.33 1.98
3315 3454 1.802960 GCCAGTGCCATTCGATCTATG 59.197 52.381 0.00 0.00 0.00 2.23
3316 3455 2.548707 GCCAGTGCCATTCGATCTATGA 60.549 50.000 6.32 0.00 0.00 2.15
3317 3456 3.062763 CCAGTGCCATTCGATCTATGAC 58.937 50.000 6.32 0.00 0.00 3.06
3318 3457 3.493176 CCAGTGCCATTCGATCTATGACA 60.493 47.826 6.32 0.00 0.00 3.58
3319 3458 3.739810 CAGTGCCATTCGATCTATGACAG 59.260 47.826 6.32 0.00 0.00 3.51
3320 3459 2.478134 GTGCCATTCGATCTATGACAGC 59.522 50.000 6.32 3.17 0.00 4.40
3321 3460 2.366590 TGCCATTCGATCTATGACAGCT 59.633 45.455 6.32 0.00 0.00 4.24
3322 3461 2.992543 GCCATTCGATCTATGACAGCTC 59.007 50.000 6.32 0.00 0.00 4.09
3323 3462 3.583806 CCATTCGATCTATGACAGCTCC 58.416 50.000 6.32 0.00 0.00 4.70
3324 3463 3.583806 CATTCGATCTATGACAGCTCCC 58.416 50.000 0.00 0.00 0.00 4.30
3325 3464 1.621992 TCGATCTATGACAGCTCCCC 58.378 55.000 0.00 0.00 0.00 4.81
3356 3495 4.088634 TCAGGCCTGTTTAGCATTCAAAT 58.911 39.130 31.58 0.00 0.00 2.32
3358 3497 4.628333 CAGGCCTGTTTAGCATTCAAATTG 59.372 41.667 25.53 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
991 999 1.141019 CATCACCCATTGCTGCTGC 59.859 57.895 8.89 8.89 40.20 5.25
1000 1008 1.690219 GGGCTCGTCTCATCACCCAT 61.690 60.000 0.00 0.00 37.30 4.00
1052 1060 1.215014 CTTGTCTTGACGACGCAGCA 61.215 55.000 0.00 0.00 45.87 4.41
1055 1063 2.300066 CGCTTGTCTTGACGACGCA 61.300 57.895 0.00 0.00 45.87 5.24
1069 1077 5.250200 TGACAAAATGAATAGGTACCGCTT 58.750 37.500 6.18 3.83 0.00 4.68
1115 1123 8.918202 AGAGAAACTGATACATTTTTGTGGTA 57.082 30.769 0.00 0.00 0.00 3.25
1116 1124 7.823745 AGAGAAACTGATACATTTTTGTGGT 57.176 32.000 0.00 0.00 0.00 4.16
1117 1125 9.994432 GATAGAGAAACTGATACATTTTTGTGG 57.006 33.333 0.00 0.00 0.00 4.17
1182 1257 7.759489 AAGCACTGTCATTTATTTTCTACCA 57.241 32.000 0.00 0.00 0.00 3.25
1193 1268 6.571150 GCTGGAAAAGATAAGCACTGTCATTT 60.571 38.462 0.00 0.00 35.69 2.32
1202 1277 3.719268 TCCAGCTGGAAAAGATAAGCA 57.281 42.857 33.41 5.54 42.18 3.91
1219 1294 3.197766 ACTCCAATAATGACGCTCTTCCA 59.802 43.478 0.00 0.00 0.00 3.53
1220 1295 3.798202 ACTCCAATAATGACGCTCTTCC 58.202 45.455 0.00 0.00 0.00 3.46
1247 1322 1.838073 AAGTACAAGGCCCGTCCCAG 61.838 60.000 0.00 0.00 34.51 4.45
1420 1495 3.325293 TGTTGCCTTCTCTAGCTCTTG 57.675 47.619 0.00 0.00 0.00 3.02
1455 1530 4.078537 CACCACTACCAATTTCATGACCA 58.921 43.478 0.00 0.00 0.00 4.02
1485 1560 5.413213 TGACAAAATCCCTTTATACACGGTG 59.587 40.000 6.58 6.58 0.00 4.94
1639 1715 0.834612 AGTGGGACTTCCGTGTCAAA 59.165 50.000 0.00 0.00 38.61 2.69
1644 1720 3.700038 AGACTAATAGTGGGACTTCCGTG 59.300 47.826 0.00 0.00 38.76 4.94
1675 1751 4.755411 TCACGAAGAGTTCCATTGGATAC 58.245 43.478 6.15 7.90 0.00 2.24
1767 1843 7.323052 TGAGTGAAGATAGGCTAGAGATCTA 57.677 40.000 0.00 0.00 29.71 1.98
2126 2202 8.781196 CCTCATTCATAACTTGTGGATCTAATG 58.219 37.037 0.00 0.00 0.00 1.90
2185 2261 6.741992 TCTTAATTTCACACATGCTACTGG 57.258 37.500 0.00 0.00 0.00 4.00
3284 3423 1.220749 GCACTGGCATAGGTTCGGA 59.779 57.895 0.00 0.00 40.72 4.55
3285 3424 1.819632 GGCACTGGCATAGGTTCGG 60.820 63.158 0.00 0.00 43.71 4.30
3298 3437 3.801638 GCTGTCATAGATCGAATGGCACT 60.802 47.826 12.59 0.00 34.16 4.40
3299 3438 2.478134 GCTGTCATAGATCGAATGGCAC 59.522 50.000 12.59 7.84 34.16 5.01
3300 3439 2.366590 AGCTGTCATAGATCGAATGGCA 59.633 45.455 14.93 14.93 36.64 4.92
3301 3440 2.992543 GAGCTGTCATAGATCGAATGGC 59.007 50.000 8.30 8.30 31.29 4.40
3302 3441 3.583806 GGAGCTGTCATAGATCGAATGG 58.416 50.000 0.00 0.00 42.76 3.16
3304 3443 2.564947 GGGGAGCTGTCATAGATCGAAT 59.435 50.000 0.00 0.00 42.76 3.34
3305 3444 1.964223 GGGGAGCTGTCATAGATCGAA 59.036 52.381 0.00 0.00 42.76 3.71
3306 3445 1.145945 AGGGGAGCTGTCATAGATCGA 59.854 52.381 0.00 0.00 42.76 3.59
3307 3446 1.626686 AGGGGAGCTGTCATAGATCG 58.373 55.000 0.00 0.00 42.76 3.69
3308 3447 2.703007 ACAAGGGGAGCTGTCATAGATC 59.297 50.000 0.00 0.00 41.11 2.75
3309 3448 2.703007 GACAAGGGGAGCTGTCATAGAT 59.297 50.000 0.00 0.00 41.35 1.98
3310 3449 2.111384 GACAAGGGGAGCTGTCATAGA 58.889 52.381 0.00 0.00 41.35 1.98
3311 3450 1.202463 CGACAAGGGGAGCTGTCATAG 60.202 57.143 0.00 0.00 41.71 2.23
3312 3451 0.824109 CGACAAGGGGAGCTGTCATA 59.176 55.000 0.00 0.00 41.71 2.15
3313 3452 0.904865 TCGACAAGGGGAGCTGTCAT 60.905 55.000 0.00 0.00 41.71 3.06
3314 3453 0.904865 ATCGACAAGGGGAGCTGTCA 60.905 55.000 0.00 0.00 41.71 3.58
3315 3454 0.250513 AATCGACAAGGGGAGCTGTC 59.749 55.000 0.00 0.00 38.87 3.51
3316 3455 0.250513 GAATCGACAAGGGGAGCTGT 59.749 55.000 0.00 0.00 0.00 4.40
3317 3456 0.250234 TGAATCGACAAGGGGAGCTG 59.750 55.000 0.00 0.00 0.00 4.24
3318 3457 0.539051 CTGAATCGACAAGGGGAGCT 59.461 55.000 0.00 0.00 0.00 4.09
3319 3458 0.462759 CCTGAATCGACAAGGGGAGC 60.463 60.000 0.00 0.00 0.00 4.70
3320 3459 0.462759 GCCTGAATCGACAAGGGGAG 60.463 60.000 10.87 0.00 0.00 4.30
3321 3460 1.602237 GCCTGAATCGACAAGGGGA 59.398 57.895 10.87 0.00 0.00 4.81
3322 3461 1.452108 GGCCTGAATCGACAAGGGG 60.452 63.158 10.87 1.45 0.00 4.79
3323 3462 0.745845 CAGGCCTGAATCGACAAGGG 60.746 60.000 29.88 0.00 0.00 3.95
3324 3463 0.036010 ACAGGCCTGAATCGACAAGG 60.036 55.000 39.19 8.37 0.00 3.61
3325 3464 1.813513 AACAGGCCTGAATCGACAAG 58.186 50.000 39.19 8.96 0.00 3.16


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

AutoCloner maintained by Alex Coulton.