Multiple sequence alignment - TraesCS3A01G315900

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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 TraesCS3A01G315900 chr3A 100.000 4025 0 0 1 4025 556672230 556668206 0.000000e+00 7433.0
1 TraesCS3A01G315900 chr3A 84.328 134 17 4 16 146 708335806 708335938 1.170000e-25 128.0
2 TraesCS3A01G315900 chr3B 96.467 2661 71 9 688 3345 561093133 561095773 0.000000e+00 4372.0
3 TraesCS3A01G315900 chr3B 95.372 605 19 4 3425 4025 561095772 561096371 0.000000e+00 953.0
4 TraesCS3A01G315900 chr3B 81.818 143 22 3 2 141 59165852 59165711 2.540000e-22 117.0
5 TraesCS3A01G315900 chr3D 97.083 2228 59 4 1118 3345 429095166 429097387 0.000000e+00 3749.0
6 TraesCS3A01G315900 chr3D 91.191 806 53 9 10 809 429092391 429093184 0.000000e+00 1079.0
7 TraesCS3A01G315900 chr3D 96.674 481 15 1 3546 4025 429097591 429098071 0.000000e+00 798.0
8 TraesCS3A01G315900 chr3D 86.824 296 7 8 808 1085 429094580 429094861 6.540000e-78 302.0
9 TraesCS3A01G315900 chr3D 95.200 125 5 1 3425 3548 429097386 429097510 3.170000e-46 196.0
10 TraesCS3A01G315900 chr3D 96.591 88 1 1 3344 3429 54370497 54370410 1.170000e-30 145.0
11 TraesCS3A01G315900 chr6D 98.795 83 1 0 3344 3426 185368083 185368165 9.010000e-32 148.0
12 TraesCS3A01G315900 chr6D 96.629 89 1 1 3343 3429 78083078 78083166 3.240000e-31 147.0
13 TraesCS3A01G315900 chr2B 94.624 93 5 0 3343 3435 397433482 397433390 1.170000e-30 145.0
14 TraesCS3A01G315900 chr5D 94.624 93 3 1 3344 3434 545227872 545227780 4.190000e-30 143.0
15 TraesCS3A01G315900 chr5D 82.781 151 23 3 2 150 546006740 546006591 9.080000e-27 132.0
16 TraesCS3A01G315900 chr4A 94.681 94 2 2 3343 3434 556767954 556768046 4.190000e-30 143.0
17 TraesCS3A01G315900 chr7D 86.260 131 16 2 17 146 624792191 624792320 1.510000e-29 141.0
18 TraesCS3A01G315900 chr2D 93.684 95 4 1 3343 3435 328357076 328356982 1.510000e-29 141.0
19 TraesCS3A01G315900 chr2D 88.696 115 7 5 3344 3455 386706997 386707108 7.020000e-28 135.0
20 TraesCS3A01G315900 chr6A 84.615 143 18 3 2 141 62622716 62622857 5.420000e-29 139.0
21 TraesCS3A01G315900 chr6A 79.195 149 24 6 2 146 18675824 18675679 3.310000e-16 97.1
22 TraesCS3A01G315900 chr1D 90.654 107 7 2 3340 3444 295954212 295954317 5.420000e-29 139.0
23 TraesCS3A01G315900 chr7A 83.333 150 19 6 2 146 720606749 720606897 2.520000e-27 134.0
24 TraesCS3A01G315900 chr1B 83.217 143 21 3 2 142 395207707 395207566 1.170000e-25 128.0


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 TraesCS3A01G315900 chr3A 556668206 556672230 4024 True 7433.0 7433 100.0000 1 4025 1 chr3A.!!$R1 4024
1 TraesCS3A01G315900 chr3B 561093133 561096371 3238 False 2662.5 4372 95.9195 688 4025 2 chr3B.!!$F1 3337
2 TraesCS3A01G315900 chr3D 429092391 429098071 5680 False 1224.8 3749 93.3944 10 4025 5 chr3D.!!$F1 4015

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
499 505 0.102300 GGCCATGTTGAAATACCGGC 59.898 55.0 0.00 0.0 35.78 6.13 F
507 513 0.178068 TGAAATACCGGCTGAGCTCC 59.822 55.0 12.15 0.0 0.00 4.70 F
2105 3810 0.320374 CTAAGGGGCTTGTGTCGTGA 59.680 55.0 0.00 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 3947 1.138859 TCCATACTCCGGCATCAGTTG 59.861 52.381 0.0 0.0 0.0 3.16 R
2253 3958 2.505819 ACCCACTGAACATCCATACTCC 59.494 50.000 0.0 0.0 0.0 3.85 R
3410 5116 1.203087 TGAACTACTCCTTCCGTCCCA 60.203 52.381 0.0 0.0 0.0 4.37 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
63 64 1.315257 AAACCGGTGCATCCATGAGC 61.315 55.000 8.52 0.00 35.57 4.26
147 151 9.037737 CAACATGAATATTTTCTTATGGCCTTG 57.962 33.333 3.32 0.00 32.78 3.61
154 158 3.439857 TTCTTATGGCCTTGAAGCAGT 57.560 42.857 3.32 0.00 0.00 4.40
160 164 1.277842 TGGCCTTGAAGCAGTCGATAA 59.722 47.619 3.32 0.00 0.00 1.75
190 194 1.073722 CCTCTCCTTGTGGCAGCAA 59.926 57.895 0.00 0.00 0.00 3.91
192 196 1.572085 CTCTCCTTGTGGCAGCAACG 61.572 60.000 0.00 0.00 0.00 4.10
208 212 4.436998 CGTCGTGGCCCTGGACTC 62.437 72.222 0.00 0.00 0.00 3.36
246 250 1.885850 GGGCTGTAATGGCGTACGG 60.886 63.158 18.39 0.00 34.07 4.02
247 251 1.153509 GGCTGTAATGGCGTACGGT 60.154 57.895 18.39 0.00 33.57 4.83
250 254 0.996462 CTGTAATGGCGTACGGTGTG 59.004 55.000 18.39 0.00 0.00 3.82
265 269 0.179150 GTGTGCCGTTGCTTTGTTGA 60.179 50.000 0.00 0.00 38.71 3.18
301 307 7.724287 AGCATATCATATCAGCGATAAGATGT 58.276 34.615 18.15 12.75 34.97 3.06
310 316 4.274705 TCAGCGATAAGATGTGAGAGAGAC 59.725 45.833 0.00 0.00 37.54 3.36
334 340 5.037383 AGGAAGAAAGACGAGAAAAGGTT 57.963 39.130 0.00 0.00 0.00 3.50
337 343 6.041751 AGGAAGAAAGACGAGAAAAGGTTAGA 59.958 38.462 0.00 0.00 0.00 2.10
338 344 6.366604 GGAAGAAAGACGAGAAAAGGTTAGAG 59.633 42.308 0.00 0.00 0.00 2.43
388 394 2.746279 TGAAAATGGTGTGTGGGTCT 57.254 45.000 0.00 0.00 0.00 3.85
397 403 3.523157 TGGTGTGTGGGTCTATGAATGAT 59.477 43.478 0.00 0.00 0.00 2.45
398 404 3.879295 GGTGTGTGGGTCTATGAATGATG 59.121 47.826 0.00 0.00 0.00 3.07
399 405 4.517285 GTGTGTGGGTCTATGAATGATGT 58.483 43.478 0.00 0.00 0.00 3.06
408 414 6.827251 GGGTCTATGAATGATGTGCATGATAT 59.173 38.462 0.00 0.00 37.28 1.63
452 458 1.388547 GCTGACAGTTTCCAACACCA 58.611 50.000 3.99 0.00 0.00 4.17
454 460 1.330521 CTGACAGTTTCCAACACCACG 59.669 52.381 0.00 0.00 0.00 4.94
473 479 2.199652 TCCTTTGCAACAAGGCCCG 61.200 57.895 11.71 0.00 36.15 6.13
490 496 2.094060 CGTATTGCGGCCATGTTGA 58.906 52.632 2.24 0.00 36.85 3.18
499 505 0.102300 GGCCATGTTGAAATACCGGC 59.898 55.000 0.00 0.00 35.78 6.13
504 510 1.448985 TGTTGAAATACCGGCTGAGC 58.551 50.000 0.00 0.00 0.00 4.26
506 512 1.666189 GTTGAAATACCGGCTGAGCTC 59.334 52.381 6.82 6.82 0.00 4.09
507 513 0.178068 TGAAATACCGGCTGAGCTCC 59.822 55.000 12.15 0.00 0.00 4.70
523 529 1.784525 CTCCCACAAAGACAGACGTC 58.215 55.000 7.70 7.70 42.95 4.34
524 530 1.068588 CTCCCACAAAGACAGACGTCA 59.931 52.381 19.50 0.00 45.23 4.35
526 532 0.852777 CCACAAAGACAGACGTCACG 59.147 55.000 19.50 10.93 45.23 4.35
528 534 1.255342 CACAAAGACAGACGTCACGTG 59.745 52.381 19.50 9.94 45.23 4.49
534 540 1.942223 CAGACGTCACGTGTGCGAA 60.942 57.895 30.08 6.09 43.41 4.70
539 545 2.202770 TCACGTGTGCGAAACGGT 60.203 55.556 16.51 0.00 45.20 4.83
556 562 7.346695 CGAAACGGTAGATAACACAAGAAAAA 58.653 34.615 0.00 0.00 0.00 1.94
558 564 9.326339 GAAACGGTAGATAACACAAGAAAAATC 57.674 33.333 0.00 0.00 0.00 2.17
560 566 8.029642 ACGGTAGATAACACAAGAAAAATCAG 57.970 34.615 0.00 0.00 0.00 2.90
561 567 7.660208 ACGGTAGATAACACAAGAAAAATCAGT 59.340 33.333 0.00 0.00 0.00 3.41
562 568 7.957484 CGGTAGATAACACAAGAAAAATCAGTG 59.043 37.037 0.00 0.00 36.34 3.66
574 580 6.215845 AGAAAAATCAGTGGGTTGAATTTCG 58.784 36.000 0.00 0.00 39.45 3.46
579 585 4.462133 TCAGTGGGTTGAATTTCGGTTAA 58.538 39.130 0.00 0.00 0.00 2.01
614 620 2.034436 TAGGTTCGAGGGAAGGGTTT 57.966 50.000 0.00 0.00 31.49 3.27
705 712 5.789574 TTTTAGGAAAAGGGCTGGAGATA 57.210 39.130 0.00 0.00 0.00 1.98
745 752 1.666311 CGACTTGTGAGTTCGAGGACC 60.666 57.143 0.00 0.00 35.88 4.46
757 764 1.154263 GAGGACCGAGTCACGAACG 60.154 63.158 6.41 0.00 45.77 3.95
762 769 1.211969 CCGAGTCACGAACGACCAT 59.788 57.895 0.14 0.00 45.77 3.55
763 770 0.448990 CCGAGTCACGAACGACCATA 59.551 55.000 0.14 0.00 45.77 2.74
764 771 1.531912 CGAGTCACGAACGACCATAC 58.468 55.000 0.14 0.00 45.77 2.39
788 795 2.614057 GACAAAATCGGATCGAGCCAAT 59.386 45.455 21.44 3.16 39.91 3.16
819 2223 0.320771 GAGCATGAGTCAACGGGTGT 60.321 55.000 0.00 0.00 0.00 4.16
832 2236 1.474077 ACGGGTGTGGTACGTAGATTC 59.526 52.381 0.00 0.00 39.30 2.52
981 2385 4.873129 CGACGCTACCGCCAGCAT 62.873 66.667 7.19 0.00 41.88 3.79
1063 2485 4.660938 GCCACCTCCACCACCACC 62.661 72.222 0.00 0.00 0.00 4.61
1064 2486 3.174987 CCACCTCCACCACCACCA 61.175 66.667 0.00 0.00 0.00 4.17
1520 3225 0.727457 CTGCTCGACGATATGCTCCG 60.727 60.000 0.00 0.00 0.00 4.63
1780 3485 4.335647 CCACCGTGCTCAAGGGCT 62.336 66.667 6.78 0.00 37.32 5.19
1857 3562 0.322816 AGAACTGCGTGCCCAATGAT 60.323 50.000 0.00 0.00 0.00 2.45
1914 3619 2.808206 GGGTATGGTGGAGAGGGCG 61.808 68.421 0.00 0.00 0.00 6.13
2103 3808 1.003718 GCTAAGGGGCTTGTGTCGT 60.004 57.895 0.00 0.00 0.00 4.34
2104 3809 1.298859 GCTAAGGGGCTTGTGTCGTG 61.299 60.000 0.00 0.00 0.00 4.35
2105 3810 0.320374 CTAAGGGGCTTGTGTCGTGA 59.680 55.000 0.00 0.00 0.00 4.35
2109 3814 3.712881 GGCTTGTGTCGTGACGGC 61.713 66.667 1.09 1.09 0.00 5.68
2160 3865 2.003301 GAGATGGTCCGAAAGAACTGC 58.997 52.381 0.00 0.00 31.28 4.40
2193 3898 7.558161 TGAGGTCACATTCAATACATTCATC 57.442 36.000 0.00 0.00 0.00 2.92
2253 3958 3.374988 TCAAGCTTATTCAACTGATGCCG 59.625 43.478 0.00 0.00 0.00 5.69
2478 4183 1.972872 AGGATTGCCCTCTAAATGCG 58.027 50.000 0.00 0.00 43.31 4.73
2817 4522 7.499232 GCTGGGATGTATAACAAGATACTGTTT 59.501 37.037 0.00 0.00 40.08 2.83
2925 4630 7.287005 TCGACCTACATTATACTCATTGAAGGT 59.713 37.037 1.48 1.48 36.36 3.50
2952 4657 2.040278 CCATGAGGGTCTGTTGAAGGAA 59.960 50.000 0.00 0.00 0.00 3.36
2957 4662 1.476833 GGGTCTGTTGAAGGAAGCACA 60.477 52.381 0.00 0.00 0.00 4.57
2980 4685 7.812669 CACAATATGTACTGAGTGAGTTGTACA 59.187 37.037 0.00 7.18 45.77 2.90
3007 4712 7.170998 CGAAAGGAGTTCTAAGCAAGAGTTTAA 59.829 37.037 0.00 0.00 35.05 1.52
3018 4723 6.319141 AGCAAGAGTTTAATTGAAGACCAC 57.681 37.500 0.00 0.00 0.00 4.16
3021 4726 6.672147 CAAGAGTTTAATTGAAGACCACCAG 58.328 40.000 0.00 0.00 0.00 4.00
3090 4795 6.810182 GTGAGAAAGAAAATTGTGCATATGCT 59.190 34.615 27.13 6.15 42.66 3.79
3108 4813 2.816087 TGCTTTGAGTCATGAGGCTTTC 59.184 45.455 0.00 0.00 0.00 2.62
3157 4862 1.106285 GGGCCTCATTTACAGCAAGG 58.894 55.000 0.84 0.00 0.00 3.61
3306 5012 2.033448 AACCGCGGGATTGCAGAA 59.967 55.556 31.76 0.00 34.15 3.02
3345 5051 9.803315 ATGTTTTTGAAACTTTCTCTTTCCTAC 57.197 29.630 3.22 0.00 0.00 3.18
3346 5052 9.020731 TGTTTTTGAAACTTTCTCTTTCCTACT 57.979 29.630 3.22 0.00 0.00 2.57
3347 5053 9.504710 GTTTTTGAAACTTTCTCTTTCCTACTC 57.495 33.333 3.22 0.00 0.00 2.59
3348 5054 7.803279 TTTGAAACTTTCTCTTTCCTACTCC 57.197 36.000 3.22 0.00 0.00 3.85
3349 5055 5.866207 TGAAACTTTCTCTTTCCTACTCCC 58.134 41.667 3.22 0.00 0.00 4.30
3350 5056 5.607171 TGAAACTTTCTCTTTCCTACTCCCT 59.393 40.000 3.22 0.00 0.00 4.20
3351 5057 5.748670 AACTTTCTCTTTCCTACTCCCTC 57.251 43.478 0.00 0.00 0.00 4.30
3352 5058 4.098155 ACTTTCTCTTTCCTACTCCCTCC 58.902 47.826 0.00 0.00 0.00 4.30
3353 5059 2.438800 TCTCTTTCCTACTCCCTCCG 57.561 55.000 0.00 0.00 0.00 4.63
3354 5060 1.639628 TCTCTTTCCTACTCCCTCCGT 59.360 52.381 0.00 0.00 0.00 4.69
3355 5061 2.025898 CTCTTTCCTACTCCCTCCGTC 58.974 57.143 0.00 0.00 0.00 4.79
3356 5062 1.112950 CTTTCCTACTCCCTCCGTCC 58.887 60.000 0.00 0.00 0.00 4.79
3357 5063 0.325016 TTTCCTACTCCCTCCGTCCC 60.325 60.000 0.00 0.00 0.00 4.46
3358 5064 1.512201 TTCCTACTCCCTCCGTCCCA 61.512 60.000 0.00 0.00 0.00 4.37
3359 5065 1.233369 CCTACTCCCTCCGTCCCAT 59.767 63.158 0.00 0.00 0.00 4.00
3360 5066 0.481567 CCTACTCCCTCCGTCCCATA 59.518 60.000 0.00 0.00 0.00 2.74
3361 5067 1.133262 CCTACTCCCTCCGTCCCATAA 60.133 57.143 0.00 0.00 0.00 1.90
3362 5068 2.492940 CCTACTCCCTCCGTCCCATAAT 60.493 54.545 0.00 0.00 0.00 1.28
3363 5069 3.245514 CCTACTCCCTCCGTCCCATAATA 60.246 52.174 0.00 0.00 0.00 0.98
3364 5070 3.339713 ACTCCCTCCGTCCCATAATAA 57.660 47.619 0.00 0.00 0.00 1.40
3365 5071 3.240302 ACTCCCTCCGTCCCATAATAAG 58.760 50.000 0.00 0.00 0.00 1.73
3366 5072 3.116862 ACTCCCTCCGTCCCATAATAAGA 60.117 47.826 0.00 0.00 0.00 2.10
3367 5073 3.507411 TCCCTCCGTCCCATAATAAGAG 58.493 50.000 0.00 0.00 0.00 2.85
3368 5074 2.028020 CCCTCCGTCCCATAATAAGAGC 60.028 54.545 0.00 0.00 0.00 4.09
3369 5075 2.352814 CCTCCGTCCCATAATAAGAGCG 60.353 54.545 0.00 0.00 0.00 5.03
3370 5076 2.296471 CTCCGTCCCATAATAAGAGCGT 59.704 50.000 0.00 0.00 0.00 5.07
3371 5077 2.696707 TCCGTCCCATAATAAGAGCGTT 59.303 45.455 0.00 0.00 0.00 4.84
3372 5078 3.133362 TCCGTCCCATAATAAGAGCGTTT 59.867 43.478 0.00 0.00 0.00 3.60
3373 5079 3.875134 CCGTCCCATAATAAGAGCGTTTT 59.125 43.478 0.00 0.00 0.00 2.43
3374 5080 4.334481 CCGTCCCATAATAAGAGCGTTTTT 59.666 41.667 0.00 0.00 0.00 1.94
3401 5107 4.743644 ACTAGTGTAGTGTCAAAAACGCTC 59.256 41.667 0.00 0.00 45.69 5.03
3402 5108 3.793559 AGTGTAGTGTCAAAAACGCTCT 58.206 40.909 0.00 0.00 45.69 4.09
3403 5109 4.189231 AGTGTAGTGTCAAAAACGCTCTT 58.811 39.130 0.00 0.00 45.69 2.85
3404 5110 5.353938 AGTGTAGTGTCAAAAACGCTCTTA 58.646 37.500 0.00 0.00 45.69 2.10
3405 5111 5.989777 AGTGTAGTGTCAAAAACGCTCTTAT 59.010 36.000 0.00 0.00 45.69 1.73
3406 5112 7.149973 AGTGTAGTGTCAAAAACGCTCTTATA 58.850 34.615 0.00 0.00 45.69 0.98
3407 5113 7.817962 AGTGTAGTGTCAAAAACGCTCTTATAT 59.182 33.333 0.00 0.00 45.69 0.86
3408 5114 8.440833 GTGTAGTGTCAAAAACGCTCTTATATT 58.559 33.333 0.00 0.00 45.69 1.28
3409 5115 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
3412 5118 8.612619 AGTGTCAAAAACGCTCTTATATTATGG 58.387 33.333 0.00 0.00 45.69 2.74
3413 5119 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
3414 5120 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
3415 5121 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
3416 5122 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
3417 5123 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
3418 5124 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
3419 5125 4.525487 ACGCTCTTATATTATGGGACGGAA 59.475 41.667 0.00 0.00 0.00 4.30
3420 5126 5.103000 CGCTCTTATATTATGGGACGGAAG 58.897 45.833 0.00 0.00 0.00 3.46
3421 5127 5.420409 GCTCTTATATTATGGGACGGAAGG 58.580 45.833 0.00 0.00 0.00 3.46
3422 5128 5.187186 GCTCTTATATTATGGGACGGAAGGA 59.813 44.000 0.00 0.00 0.00 3.36
3423 5129 6.628398 GCTCTTATATTATGGGACGGAAGGAG 60.628 46.154 0.00 0.00 0.00 3.69
3456 5163 6.636454 AGATGTGTTACCTTATTTCCCTCA 57.364 37.500 0.00 0.00 0.00 3.86
3526 5233 7.811117 TGTGCTTAATTAGTTGTACACCTTT 57.189 32.000 0.00 0.00 0.00 3.11
3527 5234 7.644490 TGTGCTTAATTAGTTGTACACCTTTG 58.356 34.615 0.00 0.00 0.00 2.77
3669 5460 8.638873 TCACTAACAGAAGTTATCTTGTTCAGA 58.361 33.333 0.00 0.00 39.36 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.857509 AGTCTGTCACACTCCTCTTAAC 57.142 45.455 0.00 0.00 0.00 2.01
130 134 5.951747 ACTGCTTCAAGGCCATAAGAAAATA 59.048 36.000 5.01 0.00 0.00 1.40
147 151 2.674796 AGGTGGTTATCGACTGCTTC 57.325 50.000 0.00 0.00 0.00 3.86
154 158 1.008693 AGGGGGTAAGGTGGTTATCGA 59.991 52.381 0.00 0.00 0.00 3.59
160 164 1.082392 GGAGAGGGGGTAAGGTGGT 59.918 63.158 0.00 0.00 0.00 4.16
192 196 4.436998 CGAGTCCAGGGCCACGAC 62.437 72.222 6.18 10.78 0.00 4.34
200 204 2.110967 CCAATGCTGCGAGTCCAGG 61.111 63.158 9.72 0.00 33.44 4.45
208 212 1.802636 CCAACCTACCAATGCTGCG 59.197 57.895 0.00 0.00 0.00 5.18
246 250 0.179150 TCAACAAAGCAACGGCACAC 60.179 50.000 0.00 0.00 44.61 3.82
247 251 0.743688 ATCAACAAAGCAACGGCACA 59.256 45.000 0.00 0.00 44.61 4.57
250 254 1.130955 CACATCAACAAAGCAACGGC 58.869 50.000 0.00 0.00 41.61 5.68
252 256 1.130955 GCCACATCAACAAAGCAACG 58.869 50.000 0.00 0.00 0.00 4.10
253 257 2.129607 CTGCCACATCAACAAAGCAAC 58.870 47.619 0.00 0.00 0.00 4.17
254 258 1.755959 ACTGCCACATCAACAAAGCAA 59.244 42.857 0.00 0.00 0.00 3.91
255 259 1.401761 ACTGCCACATCAACAAAGCA 58.598 45.000 0.00 0.00 0.00 3.91
256 260 2.514205 AACTGCCACATCAACAAAGC 57.486 45.000 0.00 0.00 0.00 3.51
265 269 6.714278 TGATATGATATGCTAACTGCCACAT 58.286 36.000 0.00 0.00 42.00 3.21
291 295 4.084066 CCTCGTCTCTCTCACATCTTATCG 60.084 50.000 0.00 0.00 0.00 2.92
301 307 3.754323 GTCTTTCTTCCTCGTCTCTCTCA 59.246 47.826 0.00 0.00 0.00 3.27
310 316 3.675698 CCTTTTCTCGTCTTTCTTCCTCG 59.324 47.826 0.00 0.00 0.00 4.63
334 340 9.585369 AGAAATATCTCATCTCACATGTCTCTA 57.415 33.333 0.00 0.00 0.00 2.43
371 377 4.380843 TCATAGACCCACACACCATTTT 57.619 40.909 0.00 0.00 0.00 1.82
397 403 3.996363 GCCTCGATTGTATATCATGCACA 59.004 43.478 0.00 0.00 0.00 4.57
398 404 3.061295 CGCCTCGATTGTATATCATGCAC 59.939 47.826 0.00 0.00 0.00 4.57
399 405 3.253230 CGCCTCGATTGTATATCATGCA 58.747 45.455 0.00 0.00 0.00 3.96
408 414 3.908189 TCGACCGCCTCGATTGTA 58.092 55.556 0.00 0.00 46.75 2.41
452 458 1.734388 GGCCTTGTTGCAAAGGACGT 61.734 55.000 19.41 0.00 45.38 4.34
473 479 2.645730 TTTCAACATGGCCGCAATAC 57.354 45.000 0.00 0.00 0.00 1.89
490 496 1.271840 TGGGAGCTCAGCCGGTATTT 61.272 55.000 17.19 0.00 0.00 1.40
499 505 1.345741 TCTGTCTTTGTGGGAGCTCAG 59.654 52.381 17.19 2.87 0.00 3.35
504 510 1.068588 TGACGTCTGTCTTTGTGGGAG 59.931 52.381 17.92 0.00 45.70 4.30
506 512 1.217882 GTGACGTCTGTCTTTGTGGG 58.782 55.000 17.92 0.00 45.70 4.61
507 513 0.852777 CGTGACGTCTGTCTTTGTGG 59.147 55.000 17.92 0.00 45.70 4.17
523 529 0.935831 TCTACCGTTTCGCACACGTG 60.936 55.000 15.48 15.48 41.18 4.49
524 530 0.038892 ATCTACCGTTTCGCACACGT 60.039 50.000 0.00 0.00 41.18 4.49
526 532 2.988493 TGTTATCTACCGTTTCGCACAC 59.012 45.455 0.00 0.00 0.00 3.82
528 534 2.988493 TGTGTTATCTACCGTTTCGCAC 59.012 45.455 0.00 0.00 0.00 5.34
534 540 8.385898 TGATTTTTCTTGTGTTATCTACCGTT 57.614 30.769 0.00 0.00 0.00 4.44
539 545 7.942341 ACCCACTGATTTTTCTTGTGTTATCTA 59.058 33.333 0.00 0.00 0.00 1.98
556 562 3.154827 ACCGAAATTCAACCCACTGAT 57.845 42.857 0.00 0.00 0.00 2.90
558 564 4.839668 TTAACCGAAATTCAACCCACTG 57.160 40.909 0.00 0.00 0.00 3.66
560 566 8.652463 CAAATATTTAACCGAAATTCAACCCAC 58.348 33.333 0.00 0.00 38.70 4.61
561 567 8.585881 TCAAATATTTAACCGAAATTCAACCCA 58.414 29.630 0.00 0.00 38.70 4.51
562 568 8.989653 TCAAATATTTAACCGAAATTCAACCC 57.010 30.769 0.00 0.00 38.70 4.11
597 603 1.678123 GCTAAACCCTTCCCTCGAACC 60.678 57.143 0.00 0.00 0.00 3.62
601 607 0.902531 TCAGCTAAACCCTTCCCTCG 59.097 55.000 0.00 0.00 0.00 4.63
614 620 6.163476 TCGTTTGAAGAATTAAGCTCAGCTA 58.837 36.000 0.00 0.00 38.25 3.32
705 712 0.830444 TGCACCGGTGGTCTAAGACT 60.830 55.000 34.58 0.00 31.02 3.24
745 752 1.129998 AGTATGGTCGTTCGTGACTCG 59.870 52.381 5.48 0.00 38.91 4.18
753 760 5.231568 CCGATTTTGTCTAGTATGGTCGTTC 59.768 44.000 0.00 0.00 0.00 3.95
757 764 5.629849 CGATCCGATTTTGTCTAGTATGGTC 59.370 44.000 0.00 0.00 0.00 4.02
762 769 4.261489 GGCTCGATCCGATTTTGTCTAGTA 60.261 45.833 0.00 0.00 34.61 1.82
763 770 3.491104 GGCTCGATCCGATTTTGTCTAGT 60.491 47.826 0.00 0.00 34.61 2.57
764 771 3.053455 GGCTCGATCCGATTTTGTCTAG 58.947 50.000 0.00 0.00 34.61 2.43
788 795 3.321648 ATGCTCACGCCTCACCCA 61.322 61.111 0.00 0.00 34.43 4.51
819 2223 1.402968 GAGCGGTGAATCTACGTACCA 59.597 52.381 0.00 0.00 32.75 3.25
832 2236 1.067060 TCTGATACGATTGGAGCGGTG 59.933 52.381 0.00 0.00 0.00 4.94
978 2382 1.449601 CGGGTAGTGGTGGTGATGC 60.450 63.158 0.00 0.00 0.00 3.91
981 2385 3.315949 GCCGGGTAGTGGTGGTGA 61.316 66.667 2.18 0.00 0.00 4.02
1443 3148 1.594293 CCGGATGATGGGCGTGTAC 60.594 63.158 0.00 0.00 0.00 2.90
1857 3562 5.011635 TCTGACTAGCATGTCAAAGGTAACA 59.988 40.000 11.85 0.00 44.98 2.41
1914 3619 5.106948 TGACATTTGCTGAAGAACTTCGATC 60.107 40.000 9.51 2.95 42.28 3.69
2104 3809 4.241555 ATGCTCCCATCGGCCGTC 62.242 66.667 27.15 7.22 0.00 4.79
2105 3810 4.552365 CATGCTCCCATCGGCCGT 62.552 66.667 27.15 10.00 0.00 5.68
2109 3814 2.124193 TTGGCATGCTCCCATCGG 60.124 61.111 18.92 0.00 31.26 4.18
2193 3898 3.942829 TCCTTTCTGGCACAAGATACAG 58.057 45.455 3.67 0.00 38.70 2.74
2242 3947 1.138859 TCCATACTCCGGCATCAGTTG 59.861 52.381 0.00 0.00 0.00 3.16
2253 3958 2.505819 ACCCACTGAACATCCATACTCC 59.494 50.000 0.00 0.00 0.00 3.85
2478 4183 3.866910 TCACAAGTACGTTGAAAGTCACC 59.133 43.478 0.00 0.00 38.60 4.02
2817 4522 4.365514 TTCACATCTTTTACAGAGGGCA 57.634 40.909 0.00 0.00 37.65 5.36
2952 4657 5.667539 ACTCACTCAGTACATATTGTGCT 57.332 39.130 0.00 0.00 44.11 4.40
2957 4662 7.027760 CGTGTACAACTCACTCAGTACATATT 58.972 38.462 0.00 0.00 45.70 1.28
2980 4685 4.039366 ACTCTTGCTTAGAACTCCTTTCGT 59.961 41.667 0.00 0.00 39.47 3.85
3018 4723 2.616842 GTGTGAACCACAACCTTACTGG 59.383 50.000 0.95 0.00 46.28 4.00
3021 4726 3.064820 CACAGTGTGAACCACAACCTTAC 59.935 47.826 18.83 0.00 46.28 2.34
3041 4746 6.708054 ACTCTTCAGTAATAAGGCATATGCAC 59.292 38.462 28.07 16.42 44.36 4.57
3090 4795 2.807967 CACGAAAGCCTCATGACTCAAA 59.192 45.455 0.00 0.00 0.00 2.69
3108 4813 6.036517 AGACTCAGCAGAATTTAATAAGCACG 59.963 38.462 0.00 0.00 0.00 5.34
3157 4862 2.774799 GCATGCCACCCGATTCCAC 61.775 63.158 6.36 0.00 0.00 4.02
3324 5030 6.771267 GGGAGTAGGAAAGAGAAAGTTTCAAA 59.229 38.462 17.65 0.00 35.90 2.69
3343 5049 4.106825 TCTTATTATGGGACGGAGGGAGTA 59.893 45.833 0.00 0.00 0.00 2.59
3344 5050 3.116862 TCTTATTATGGGACGGAGGGAGT 60.117 47.826 0.00 0.00 0.00 3.85
3345 5051 3.507411 TCTTATTATGGGACGGAGGGAG 58.493 50.000 0.00 0.00 0.00 4.30
3346 5052 3.507411 CTCTTATTATGGGACGGAGGGA 58.493 50.000 0.00 0.00 0.00 4.20
3347 5053 2.028020 GCTCTTATTATGGGACGGAGGG 60.028 54.545 0.00 0.00 0.00 4.30
3348 5054 2.352814 CGCTCTTATTATGGGACGGAGG 60.353 54.545 0.00 0.00 0.00 4.30
3349 5055 2.296471 ACGCTCTTATTATGGGACGGAG 59.704 50.000 0.00 0.00 0.00 4.63
3350 5056 2.313317 ACGCTCTTATTATGGGACGGA 58.687 47.619 0.00 0.00 0.00 4.69
3351 5057 2.814280 ACGCTCTTATTATGGGACGG 57.186 50.000 0.00 0.00 0.00 4.79
3352 5058 5.479716 AAAAACGCTCTTATTATGGGACG 57.520 39.130 0.00 0.00 0.00 4.79
3378 5084 4.690122 AGCGTTTTTGACACTACACTAGT 58.310 39.130 0.00 0.00 40.28 2.57
3379 5085 4.982916 AGAGCGTTTTTGACACTACACTAG 59.017 41.667 0.00 0.00 0.00 2.57
3380 5086 4.940463 AGAGCGTTTTTGACACTACACTA 58.060 39.130 0.00 0.00 0.00 2.74
3381 5087 3.793559 AGAGCGTTTTTGACACTACACT 58.206 40.909 0.00 0.00 0.00 3.55
3382 5088 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
3383 5089 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
3386 5092 8.612619 CCATAATATAAGAGCGTTTTTGACACT 58.387 33.333 0.00 0.00 0.00 3.55
3387 5093 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
3388 5094 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
3389 5095 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
3390 5096 7.042321 CGTCCCATAATATAAGAGCGTTTTTGA 60.042 37.037 0.00 0.00 0.00 2.69
3391 5097 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
3392 5098 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
3393 5099 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
3394 5100 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
3395 5101 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
3396 5102 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
3397 5103 4.713824 TCCGTCCCATAATATAAGAGCG 57.286 45.455 0.00 0.00 0.00 5.03
3398 5104 5.187186 TCCTTCCGTCCCATAATATAAGAGC 59.813 44.000 0.00 0.00 0.00 4.09
3399 5105 6.437793 ACTCCTTCCGTCCCATAATATAAGAG 59.562 42.308 0.00 0.00 0.00 2.85
3400 5106 6.320518 ACTCCTTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
3401 5107 6.607004 ACTCCTTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
3402 5108 7.243824 ACTACTCCTTCCGTCCCATAATATAA 58.756 38.462 0.00 0.00 0.00 0.98
3403 5109 6.797707 ACTACTCCTTCCGTCCCATAATATA 58.202 40.000 0.00 0.00 0.00 0.86
3404 5110 5.652324 ACTACTCCTTCCGTCCCATAATAT 58.348 41.667 0.00 0.00 0.00 1.28
3405 5111 5.070823 ACTACTCCTTCCGTCCCATAATA 57.929 43.478 0.00 0.00 0.00 0.98
3406 5112 3.924922 ACTACTCCTTCCGTCCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
3407 5113 3.393426 ACTACTCCTTCCGTCCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
3408 5114 3.294214 GAACTACTCCTTCCGTCCCATA 58.706 50.000 0.00 0.00 0.00 2.74
3409 5115 2.108970 GAACTACTCCTTCCGTCCCAT 58.891 52.381 0.00 0.00 0.00 4.00
3410 5116 1.203087 TGAACTACTCCTTCCGTCCCA 60.203 52.381 0.00 0.00 0.00 4.37
3411 5117 1.204231 GTGAACTACTCCTTCCGTCCC 59.796 57.143 0.00 0.00 0.00 4.46
3412 5118 2.169330 AGTGAACTACTCCTTCCGTCC 58.831 52.381 0.00 0.00 33.17 4.79
3413 5119 4.260170 TCTAGTGAACTACTCCTTCCGTC 58.740 47.826 0.00 0.00 40.89 4.79
3414 5120 4.298103 TCTAGTGAACTACTCCTTCCGT 57.702 45.455 0.00 0.00 40.89 4.69
3415 5121 4.641094 ACATCTAGTGAACTACTCCTTCCG 59.359 45.833 0.00 0.00 40.89 4.30
3526 5233 6.553953 TCTACATGCTAACAGGGTAATTCA 57.446 37.500 0.00 0.00 0.00 2.57
3527 5234 8.451908 AAATCTACATGCTAACAGGGTAATTC 57.548 34.615 0.00 0.00 0.00 2.17
3669 5460 4.823989 CCTTGGTCTTCACACTTCAAAGAT 59.176 41.667 0.00 0.00 32.11 2.40
3740 5531 3.687698 GGCCGTTACAAGTATGAACATGT 59.312 43.478 0.00 0.00 40.45 3.21
3754 5545 5.050567 CCTGTATCTTTTATTCGGCCGTTAC 60.051 44.000 27.15 13.27 0.00 2.50
3993 5787 3.736720 ACATGATTCATCGAGGACCATG 58.263 45.455 26.55 26.55 36.81 3.66
3994 5788 4.428294 AACATGATTCATCGAGGACCAT 57.572 40.909 0.00 3.74 0.00 3.55


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

AutoCloner maintained by Alex Coulton.