Multiple sequence alignment - TraesCS2A01G343200

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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 TraesCS2A01G343200 chr2A 100.000 4083 0 0 1 4083 580247965 580252047 0.000000e+00 7540.0
1 TraesCS2A01G343200 chr2A 88.618 123 11 3 16 138 413416065 413416184 3.290000e-31 147.0
2 TraesCS2A01G343200 chr2A 94.030 67 3 1 3807 3872 580251709 580251775 2.600000e-17 100.0
3 TraesCS2A01G343200 chr2A 94.030 67 3 1 3745 3811 580251771 580251836 2.600000e-17 100.0
4 TraesCS2A01G343200 chr2D 95.795 3948 111 18 138 4083 413259995 413263889 0.000000e+00 6320.0
5 TraesCS2A01G343200 chr2D 93.478 138 8 1 1 138 413259833 413259969 1.920000e-48 204.0
6 TraesCS2A01G343200 chr2D 94.030 67 3 1 3807 3872 413263551 413263617 2.600000e-17 100.0
7 TraesCS2A01G343200 chr2D 94.030 67 3 1 3745 3811 413263613 413263678 2.600000e-17 100.0
8 TraesCS2A01G343200 chr2B 95.808 3602 106 18 138 3736 486580852 486584411 0.000000e+00 5773.0
9 TraesCS2A01G343200 chr2B 96.011 351 14 0 3733 4083 486584491 486584841 4.580000e-159 571.0
10 TraesCS2A01G343200 chr2B 91.304 138 11 1 1 138 486580690 486580826 1.940000e-43 187.0
11 TraesCS2A01G343200 chr2B 97.015 67 1 1 3745 3811 486584565 486584630 1.200000e-20 111.0
12 TraesCS2A01G343200 chr2B 93.023 43 3 0 96 138 115903418 115903460 3.410000e-06 63.9
13 TraesCS2A01G343200 chr7A 91.241 137 11 1 2 138 39288231 39288366 6.970000e-43 185.0
14 TraesCS2A01G343200 chr7A 91.241 137 11 1 2 138 443987018 443987153 6.970000e-43 185.0
15 TraesCS2A01G343200 chr7D 100.000 37 0 0 105 141 574037709 574037673 7.320000e-08 69.4
16 TraesCS2A01G343200 chr7D 91.111 45 4 0 97 141 11323498 11323542 1.230000e-05 62.1
17 TraesCS2A01G343200 chr7B 97.297 37 1 0 105 141 645592014 645591978 3.410000e-06 63.9


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 TraesCS2A01G343200 chr2A 580247965 580252047 4082 False 2580.0 7540 96.02000 1 4083 3 chr2A.!!$F2 4082
1 TraesCS2A01G343200 chr2D 413259833 413263889 4056 False 1681.0 6320 94.33325 1 4083 4 chr2D.!!$F1 4082
2 TraesCS2A01G343200 chr2B 486580690 486584841 4151 False 1660.5 5773 95.03450 1 4083 4 chr2B.!!$F2 4082

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
158 185 0.242825 TTGCGACGGAGGAAGTACAG 59.757 55.000 0.00 0.0 0.0 2.74 F
213 240 1.534163 GGAGGTTCTGTTGTTAACGCC 59.466 52.381 0.26 0.0 0.0 5.68 F
1283 1323 0.605589 AAGCTACGCCCTGAACAACC 60.606 55.000 0.00 0.0 0.0 3.77 F
2205 2245 0.467290 GGTGGGAAGAGGTGTGCAAA 60.467 55.000 0.00 0.0 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1283 1323 0.384725 CGAACTGCGCTTTTGGTCAG 60.385 55.0 9.73 0.0 0.00 3.51 R
2205 2245 0.693049 ACTCCGAATGCAACCTTCCT 59.307 50.0 0.00 0.0 0.00 3.36 R
2857 2897 0.748367 CTGATGCTGTGCTGATGCCT 60.748 55.0 0.00 0.0 38.71 4.75 R
3417 3457 0.113776 AGTACCTGGACGTCCCAAGA 59.886 55.0 31.19 12.2 46.07 3.02 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
76 77 9.398170 CTGTATTTTGAACGATTTGTCATCTTT 57.602 29.630 0.00 0.00 0.00 2.52
92 93 4.641541 TCATCTTTATTGCCATCCAGTGTG 59.358 41.667 0.00 0.00 0.00 3.82
101 102 2.223923 GCCATCCAGTGTGAGCTACTAG 60.224 54.545 0.00 0.00 0.00 2.57
103 104 1.475403 TCCAGTGTGAGCTACTAGCC 58.525 55.000 4.32 0.00 43.77 3.93
122 123 4.793201 AGCCCTGTCCCAAATTATAAGAC 58.207 43.478 0.00 0.00 0.00 3.01
133 134 8.732531 TCCCAAATTATAAGACGTTTTTGGTAG 58.267 33.333 18.20 9.12 40.80 3.18
138 139 9.623000 AATTATAAGACGTTTTTGGTAGGCTAT 57.377 29.630 0.00 0.00 0.00 2.97
139 140 9.623000 ATTATAAGACGTTTTTGGTAGGCTATT 57.377 29.630 0.00 0.00 0.00 1.73
141 142 5.622770 AGACGTTTTTGGTAGGCTATTTG 57.377 39.130 0.00 0.00 0.00 2.32
142 143 4.082949 AGACGTTTTTGGTAGGCTATTTGC 60.083 41.667 0.00 0.00 41.94 3.68
143 144 3.168193 CGTTTTTGGTAGGCTATTTGCG 58.832 45.455 0.00 0.00 44.05 4.85
144 145 3.120130 CGTTTTTGGTAGGCTATTTGCGA 60.120 43.478 0.00 0.00 44.05 5.10
145 146 4.163552 GTTTTTGGTAGGCTATTTGCGAC 58.836 43.478 0.00 0.00 44.05 5.19
146 147 1.647346 TTGGTAGGCTATTTGCGACG 58.353 50.000 0.00 0.00 44.05 5.12
157 184 0.675083 TTTGCGACGGAGGAAGTACA 59.325 50.000 0.00 0.00 0.00 2.90
158 185 0.242825 TTGCGACGGAGGAAGTACAG 59.757 55.000 0.00 0.00 0.00 2.74
171 198 7.331791 GGAGGAAGTACAGTTTAACATCTGAT 58.668 38.462 0.00 0.00 35.84 2.90
182 209 1.575244 ACATCTGATCGAATGCACGG 58.425 50.000 6.96 0.00 0.00 4.94
191 218 5.984627 TGATCGAATGCACGGTTAATTATG 58.015 37.500 0.00 0.00 0.00 1.90
213 240 1.534163 GGAGGTTCTGTTGTTAACGCC 59.466 52.381 0.26 0.00 0.00 5.68
226 253 5.968528 TGTTAACGCCCTTCAAATATGTT 57.031 34.783 0.26 0.00 0.00 2.71
229 256 7.883217 TGTTAACGCCCTTCAAATATGTTAAA 58.117 30.769 0.26 0.00 33.63 1.52
297 324 2.693074 GGGACATGTTTGACAGTGGTTT 59.307 45.455 0.00 0.00 0.00 3.27
299 326 3.380004 GGACATGTTTGACAGTGGTTTCA 59.620 43.478 0.00 0.00 0.00 2.69
400 427 9.778741 TTAGTTCATCTTGAGTTTAGATTGTGT 57.221 29.630 0.00 0.00 30.05 3.72
401 428 8.682936 AGTTCATCTTGAGTTTAGATTGTGTT 57.317 30.769 0.00 0.00 30.05 3.32
402 429 8.562892 AGTTCATCTTGAGTTTAGATTGTGTTG 58.437 33.333 0.00 0.00 30.05 3.33
403 430 8.345565 GTTCATCTTGAGTTTAGATTGTGTTGT 58.654 33.333 0.00 0.00 30.05 3.32
404 431 9.554395 TTCATCTTGAGTTTAGATTGTGTTGTA 57.446 29.630 0.00 0.00 30.05 2.41
405 432 9.554395 TCATCTTGAGTTTAGATTGTGTTGTAA 57.446 29.630 0.00 0.00 30.05 2.41
406 433 9.599322 CATCTTGAGTTTAGATTGTGTTGTAAC 57.401 33.333 0.00 0.00 30.05 2.50
422 449 1.599542 GTAACGCCTCCATGAGCAATC 59.400 52.381 0.00 0.00 0.00 2.67
499 526 4.539870 CTGTTGCTAGTGGAATGTGTTTG 58.460 43.478 0.00 0.00 0.00 2.93
607 634 6.336842 AGCGACAGAGGTAGTTAAACTAAA 57.663 37.500 0.00 0.00 31.62 1.85
630 657 6.715347 AAACCACTTATTTCACTCAAGCTT 57.285 33.333 0.00 0.00 0.00 3.74
671 711 2.041216 GGGTATCAGTGGGTCAAAAGGT 59.959 50.000 0.00 0.00 0.00 3.50
672 712 3.499745 GGGTATCAGTGGGTCAAAAGGTT 60.500 47.826 0.00 0.00 0.00 3.50
673 713 4.263594 GGGTATCAGTGGGTCAAAAGGTTA 60.264 45.833 0.00 0.00 0.00 2.85
674 714 5.506708 GGTATCAGTGGGTCAAAAGGTTAT 58.493 41.667 0.00 0.00 0.00 1.89
675 715 5.357032 GGTATCAGTGGGTCAAAAGGTTATG 59.643 44.000 0.00 0.00 0.00 1.90
676 716 4.447138 TCAGTGGGTCAAAAGGTTATGT 57.553 40.909 0.00 0.00 0.00 2.29
677 717 4.798882 TCAGTGGGTCAAAAGGTTATGTT 58.201 39.130 0.00 0.00 0.00 2.71
678 718 4.582656 TCAGTGGGTCAAAAGGTTATGTTG 59.417 41.667 0.00 0.00 0.00 3.33
679 719 4.582656 CAGTGGGTCAAAAGGTTATGTTGA 59.417 41.667 0.00 0.00 0.00 3.18
680 720 5.068460 CAGTGGGTCAAAAGGTTATGTTGAA 59.932 40.000 0.00 0.00 33.29 2.69
681 721 5.659079 AGTGGGTCAAAAGGTTATGTTGAAA 59.341 36.000 0.00 0.00 33.29 2.69
682 722 6.326323 AGTGGGTCAAAAGGTTATGTTGAAAT 59.674 34.615 0.00 0.00 33.29 2.17
683 723 6.423604 GTGGGTCAAAAGGTTATGTTGAAATG 59.576 38.462 0.00 0.00 33.29 2.32
697 737 5.007682 TGTTGAAATGTTAGGACTTAGGGC 58.992 41.667 0.00 0.00 0.00 5.19
756 796 3.785486 GCATTTCTGTTATGCCCCTTTC 58.215 45.455 0.00 0.00 41.94 2.62
757 797 3.430790 GCATTTCTGTTATGCCCCTTTCC 60.431 47.826 0.00 0.00 41.94 3.13
758 798 3.825908 TTTCTGTTATGCCCCTTTCCT 57.174 42.857 0.00 0.00 0.00 3.36
759 799 3.825908 TTCTGTTATGCCCCTTTCCTT 57.174 42.857 0.00 0.00 0.00 3.36
760 800 3.825908 TCTGTTATGCCCCTTTCCTTT 57.174 42.857 0.00 0.00 0.00 3.11
789 829 7.860373 TGGAAAGATACACAAATTCGTCTTTTG 59.140 33.333 0.00 6.12 36.40 2.44
804 844 4.546570 GTCTTTTGGCATACAACTGGTTC 58.453 43.478 0.00 0.00 39.19 3.62
905 945 7.605449 CCAACACAATTCATTTTATCAGTCCT 58.395 34.615 0.00 0.00 0.00 3.85
1160 1200 8.944029 CAGTAATCCTGATATTATTTGCTCTGG 58.056 37.037 0.00 0.00 44.49 3.86
1211 1251 4.018870 TGGATAACAGCTTTGTGGATACCA 60.019 41.667 0.00 0.00 0.00 3.25
1283 1323 0.605589 AAGCTACGCCCTGAACAACC 60.606 55.000 0.00 0.00 0.00 3.77
1380 1420 6.642131 ACACAAAGCATGAATAACATCACAAC 59.358 34.615 0.00 0.00 37.07 3.32
1381 1421 5.858049 ACAAAGCATGAATAACATCACAACG 59.142 36.000 0.00 0.00 37.07 4.10
1382 1422 5.878332 AAGCATGAATAACATCACAACGA 57.122 34.783 0.00 0.00 37.07 3.85
1398 1438 2.743664 CAACGAGAGATGATGGTTGCAA 59.256 45.455 0.00 0.00 35.71 4.08
1408 1448 3.485394 TGATGGTTGCAAGCTTGTTCTA 58.515 40.909 27.31 15.19 0.00 2.10
1442 1482 5.440685 CAACACCTGATTTTTACTCGACAC 58.559 41.667 0.00 0.00 0.00 3.67
1449 1489 7.822334 ACCTGATTTTTACTCGACACATTATCA 59.178 33.333 0.00 0.00 0.00 2.15
1581 1621 1.251251 ATTCAGCCTCTGCAAACACC 58.749 50.000 0.00 0.00 41.13 4.16
2205 2245 0.467290 GGTGGGAAGAGGTGTGCAAA 60.467 55.000 0.00 0.00 0.00 3.68
2404 2444 2.711711 CACACCTCTGTGCAAAGCT 58.288 52.632 0.00 0.00 46.86 3.74
2602 2642 1.273048 TGCAGGATTGACAATTGTGGC 59.727 47.619 17.58 2.76 0.00 5.01
2623 2663 4.521130 CAAGAGTGCTCAAGGTAGTACA 57.479 45.455 2.06 0.00 34.85 2.90
2851 2891 3.069079 AGCATGACAAATGAGCACTCT 57.931 42.857 0.00 0.00 0.00 3.24
2857 2897 4.644498 TGACAAATGAGCACTCTTCATCA 58.356 39.130 0.00 0.00 0.00 3.07
2953 2993 1.825341 CTCCATGATGCCCTCGTCA 59.175 57.895 0.00 0.00 41.97 4.35
3106 3146 2.887783 TGTTTTCTCCGCCTGCAAATTA 59.112 40.909 0.00 0.00 0.00 1.40
3162 3202 7.010460 GTGTTGCCTATTGAATTTTATGCTTCC 59.990 37.037 0.00 0.00 0.00 3.46
3244 3284 4.097437 GGCAATTCTTCTGATCTGCATTCA 59.903 41.667 0.00 0.00 34.03 2.57
3301 3341 8.946085 CCAATAAGCCGTGTGTATTTGATATAT 58.054 33.333 0.00 0.00 0.00 0.86
3499 3540 8.058915 CGCTTCTTACTTTCTTATTAGTCATGC 58.941 37.037 0.00 0.00 0.00 4.06
3500 3541 8.058915 GCTTCTTACTTTCTTATTAGTCATGCG 58.941 37.037 0.00 0.00 0.00 4.73
3641 3684 1.203523 ACCACTTCGATGTCTCTCAGC 59.796 52.381 0.13 0.00 0.00 4.26
3653 3696 3.056250 TGTCTCTCAGCCTGATTGAACTC 60.056 47.826 0.00 0.00 0.00 3.01
3716 3759 2.825532 TGCCTGAAGGAAATACTTTGCC 59.174 45.455 0.00 0.00 37.39 4.52
3729 3772 6.809630 AATACTTTGCCTCTCAGAAAAGAC 57.190 37.500 4.61 0.00 34.47 3.01
3779 3905 7.268586 GCATACAAGGAGAAAACTAGATGAGA 58.731 38.462 0.00 0.00 0.00 3.27
3882 4008 2.279784 CGGGAGATGAAGCGAGCC 60.280 66.667 0.00 0.00 0.00 4.70
4010 4136 5.532779 ACTTGATCAAGAGTTTTGACTTCCC 59.467 40.000 36.15 0.00 40.79 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.969117 TCAAACTTGCAGCTTGTACAG 57.031 42.857 0.00 0.00 0.00 2.74
76 77 1.561076 AGCTCACACTGGATGGCAATA 59.439 47.619 0.00 0.00 0.00 1.90
92 93 0.397254 TGGGACAGGGCTAGTAGCTC 60.397 60.000 21.20 18.16 43.65 4.09
101 102 3.564225 CGTCTTATAATTTGGGACAGGGC 59.436 47.826 3.57 0.00 42.39 5.19
103 104 6.753107 AAACGTCTTATAATTTGGGACAGG 57.247 37.500 0.00 0.00 42.39 4.00
122 123 3.120130 TCGCAAATAGCCTACCAAAAACG 60.120 43.478 0.00 0.00 41.38 3.60
133 134 0.461339 TTCCTCCGTCGCAAATAGCC 60.461 55.000 0.00 0.00 41.38 3.93
138 139 0.675083 TGTACTTCCTCCGTCGCAAA 59.325 50.000 0.00 0.00 0.00 3.68
139 140 0.242825 CTGTACTTCCTCCGTCGCAA 59.757 55.000 0.00 0.00 0.00 4.85
141 142 0.243095 AACTGTACTTCCTCCGTCGC 59.757 55.000 0.00 0.00 0.00 5.19
142 143 2.719426 AAACTGTACTTCCTCCGTCG 57.281 50.000 0.00 0.00 0.00 5.12
143 144 4.874970 TGTTAAACTGTACTTCCTCCGTC 58.125 43.478 0.00 0.00 0.00 4.79
144 145 4.942761 TGTTAAACTGTACTTCCTCCGT 57.057 40.909 0.00 0.00 0.00 4.69
145 146 5.577164 CAGATGTTAAACTGTACTTCCTCCG 59.423 44.000 0.00 0.00 0.00 4.63
146 147 6.698380 TCAGATGTTAAACTGTACTTCCTCC 58.302 40.000 0.00 0.00 35.84 4.30
157 184 5.220472 CGTGCATTCGATCAGATGTTAAACT 60.220 40.000 0.00 0.00 0.00 2.66
158 185 4.957967 CGTGCATTCGATCAGATGTTAAAC 59.042 41.667 0.00 0.00 0.00 2.01
171 198 3.562141 CCCATAATTAACCGTGCATTCGA 59.438 43.478 0.00 0.00 0.00 3.71
182 209 5.949952 ACAACAGAACCTCCCCATAATTAAC 59.050 40.000 0.00 0.00 0.00 2.01
191 218 2.148768 CGTTAACAACAGAACCTCCCC 58.851 52.381 6.39 0.00 0.00 4.81
267 294 4.036262 TGTCAAACATGTCCCTTTTTCTCG 59.964 41.667 0.00 0.00 0.00 4.04
308 335 9.466497 TCTGAATAAATAAGCAAAACTCTGGAT 57.534 29.630 0.00 0.00 0.00 3.41
333 360 5.476945 ACCATAAACCCATGTTGTTCTCTTC 59.523 40.000 0.00 0.00 34.13 2.87
399 426 0.727398 GCTCATGGAGGCGTTACAAC 59.273 55.000 0.00 0.00 0.00 3.32
400 427 0.323302 TGCTCATGGAGGCGTTACAA 59.677 50.000 0.00 0.00 0.00 2.41
401 428 0.323302 TTGCTCATGGAGGCGTTACA 59.677 50.000 0.00 0.00 0.00 2.41
402 429 1.599542 GATTGCTCATGGAGGCGTTAC 59.400 52.381 0.00 0.00 0.00 2.50
403 430 1.486310 AGATTGCTCATGGAGGCGTTA 59.514 47.619 0.00 0.00 0.00 3.18
404 431 0.254178 AGATTGCTCATGGAGGCGTT 59.746 50.000 0.00 0.00 0.00 4.84
405 432 0.463295 CAGATTGCTCATGGAGGCGT 60.463 55.000 0.00 0.00 0.00 5.68
406 433 0.179065 TCAGATTGCTCATGGAGGCG 60.179 55.000 0.00 0.00 0.00 5.52
422 449 6.489022 ACCATCATCCATTTATGTCATGTCAG 59.511 38.462 0.00 0.00 0.00 3.51
499 526 2.493278 AGCACCAGTTACAATGCAATCC 59.507 45.455 0.00 0.00 40.63 3.01
607 634 6.507023 CAAGCTTGAGTGAAATAAGTGGTTT 58.493 36.000 22.31 0.00 0.00 3.27
630 657 0.804364 CCGCAGATGCTAAGTTTGCA 59.196 50.000 14.28 14.28 44.95 4.08
671 711 7.338449 GCCCTAAGTCCTAACATTTCAACATAA 59.662 37.037 0.00 0.00 0.00 1.90
672 712 6.826741 GCCCTAAGTCCTAACATTTCAACATA 59.173 38.462 0.00 0.00 0.00 2.29
673 713 5.652452 GCCCTAAGTCCTAACATTTCAACAT 59.348 40.000 0.00 0.00 0.00 2.71
674 714 5.007682 GCCCTAAGTCCTAACATTTCAACA 58.992 41.667 0.00 0.00 0.00 3.33
675 715 5.254115 AGCCCTAAGTCCTAACATTTCAAC 58.746 41.667 0.00 0.00 0.00 3.18
676 716 5.514500 AGCCCTAAGTCCTAACATTTCAA 57.486 39.130 0.00 0.00 0.00 2.69
677 717 6.385759 TGATAGCCCTAAGTCCTAACATTTCA 59.614 38.462 0.00 0.00 0.00 2.69
678 718 6.827727 TGATAGCCCTAAGTCCTAACATTTC 58.172 40.000 0.00 0.00 0.00 2.17
679 719 6.824958 TGATAGCCCTAAGTCCTAACATTT 57.175 37.500 0.00 0.00 0.00 2.32
680 720 7.394144 AATGATAGCCCTAAGTCCTAACATT 57.606 36.000 0.00 0.00 32.91 2.71
681 721 7.227156 CAAATGATAGCCCTAAGTCCTAACAT 58.773 38.462 0.00 0.00 0.00 2.71
682 722 6.591935 CAAATGATAGCCCTAAGTCCTAACA 58.408 40.000 0.00 0.00 0.00 2.41
683 723 5.470437 GCAAATGATAGCCCTAAGTCCTAAC 59.530 44.000 0.00 0.00 0.00 2.34
697 737 3.624900 CAGGAACATGCGCAAATGATAG 58.375 45.455 17.11 0.00 0.00 2.08
756 796 7.114811 CGAATTTGTGTATCTTTCCAACAAAGG 59.885 37.037 5.63 0.00 0.00 3.11
757 797 7.647715 ACGAATTTGTGTATCTTTCCAACAAAG 59.352 33.333 0.00 0.00 0.00 2.77
758 798 7.484975 ACGAATTTGTGTATCTTTCCAACAAA 58.515 30.769 0.00 2.17 0.00 2.83
759 799 7.012894 AGACGAATTTGTGTATCTTTCCAACAA 59.987 33.333 2.13 0.00 0.00 2.83
760 800 6.485313 AGACGAATTTGTGTATCTTTCCAACA 59.515 34.615 2.13 0.00 0.00 3.33
777 817 5.460646 CAGTTGTATGCCAAAAGACGAATT 58.539 37.500 0.00 0.00 34.07 2.17
804 844 5.738118 AAACATTTGTTTGGCATGAACTG 57.262 34.783 7.83 0.00 45.55 3.16
905 945 3.011818 CAGTTGACATCAAGCATAGGCA 58.988 45.455 0.67 0.00 44.61 4.75
1160 1200 2.691409 TAACACTATGACAGCTGGGC 57.309 50.000 19.93 10.32 0.00 5.36
1211 1251 4.520492 GTCATTCATCAGAGGTTGGTTTGT 59.480 41.667 0.00 0.00 0.00 2.83
1283 1323 0.384725 CGAACTGCGCTTTTGGTCAG 60.385 55.000 9.73 0.00 0.00 3.51
1339 1379 5.702865 CTTTGTGTACTTTCATCACCATGG 58.297 41.667 11.19 11.19 0.00 3.66
1380 1420 1.329906 GCTTGCAACCATCATCTCTCG 59.670 52.381 0.00 0.00 0.00 4.04
1381 1421 2.641305 AGCTTGCAACCATCATCTCTC 58.359 47.619 0.00 0.00 0.00 3.20
1382 1422 2.753452 CAAGCTTGCAACCATCATCTCT 59.247 45.455 14.65 0.00 0.00 3.10
1398 1438 1.351350 GACCCAACCCTAGAACAAGCT 59.649 52.381 0.00 0.00 0.00 3.74
1442 1482 2.425143 ACACCAGTGGGCTGATAATG 57.575 50.000 15.21 2.14 45.28 1.90
1449 1489 4.295201 TGACTTATATACACCAGTGGGCT 58.705 43.478 15.21 0.00 37.90 5.19
1498 1538 4.061596 CTGGGTCAGTGAAAGAGAAACTC 58.938 47.826 0.00 0.00 0.00 3.01
1666 1706 4.522971 CGGGGAGCAAAGAGTAGC 57.477 61.111 0.00 0.00 0.00 3.58
2205 2245 0.693049 ACTCCGAATGCAACCTTCCT 59.307 50.000 0.00 0.00 0.00 3.36
2404 2444 1.561076 CATCTCTTCCCACCACCATGA 59.439 52.381 0.00 0.00 0.00 3.07
2566 2606 2.961669 GCAACGCTTACCACCACCG 61.962 63.158 0.00 0.00 0.00 4.94
2602 2642 4.218635 TCTGTACTACCTTGAGCACTCTTG 59.781 45.833 0.00 0.00 0.00 3.02
2623 2663 1.542492 CATGGGCTTTGCAGAAGTCT 58.458 50.000 11.30 0.00 0.00 3.24
2851 2891 1.746470 CTGTGCTGATGCCTGATGAA 58.254 50.000 0.00 0.00 38.71 2.57
2857 2897 0.748367 CTGATGCTGTGCTGATGCCT 60.748 55.000 0.00 0.00 38.71 4.75
2953 2993 2.005960 GCACAGTAGGCTCCGACGAT 62.006 60.000 0.00 0.00 0.00 3.73
3106 3146 7.657336 CCTTTTATGTACAACCAAACTGACAT 58.343 34.615 0.00 0.00 0.00 3.06
3162 3202 9.073368 CATGAAATGTTTATCAAGCAAAGAGAG 57.927 33.333 0.00 0.00 40.20 3.20
3244 3284 1.003355 CTGACTGGACCGGCATGTT 60.003 57.895 0.00 0.00 0.00 2.71
3301 3341 9.995003 AATAATCCACAAGCAAATAAGAAACAA 57.005 25.926 0.00 0.00 0.00 2.83
3352 3392 2.489938 TACAAAACCCTGCCTAGCTG 57.510 50.000 0.00 0.00 0.00 4.24
3353 3393 3.518992 TTTACAAAACCCTGCCTAGCT 57.481 42.857 0.00 0.00 0.00 3.32
3412 3452 1.003118 CCTGGACGTCCCAAGATTTCA 59.997 52.381 31.19 8.71 46.07 2.69
3413 3453 1.003233 ACCTGGACGTCCCAAGATTTC 59.997 52.381 31.19 3.87 46.07 2.17
3416 3456 1.192428 GTACCTGGACGTCCCAAGAT 58.808 55.000 31.19 13.15 46.07 2.40
3417 3457 0.113776 AGTACCTGGACGTCCCAAGA 59.886 55.000 31.19 12.20 46.07 3.02
3418 3458 1.749634 CTAGTACCTGGACGTCCCAAG 59.250 57.143 31.19 21.91 46.07 3.61
3499 3540 1.076332 GATTTCGACACCCCAAGACG 58.924 55.000 0.00 0.00 0.00 4.18
3500 3541 1.076332 CGATTTCGACACCCCAAGAC 58.924 55.000 0.00 0.00 43.02 3.01
3575 3618 4.910956 GCATGGAGTGCGTAGACA 57.089 55.556 0.00 0.00 45.23 3.41
3583 3626 4.778534 AAAGAAACATCTGCATGGAGTG 57.221 40.909 14.43 13.44 33.82 3.51
3584 3627 5.069516 ACAAAAAGAAACATCTGCATGGAGT 59.930 36.000 14.43 0.00 33.82 3.85
3585 3628 5.535333 ACAAAAAGAAACATCTGCATGGAG 58.465 37.500 8.12 8.12 33.82 3.86
3586 3629 5.534207 ACAAAAAGAAACATCTGCATGGA 57.466 34.783 0.00 0.00 33.82 3.41
3641 3684 3.126831 GCAGGTATCGAGTTCAATCAGG 58.873 50.000 0.00 0.00 0.00 3.86
3653 3696 4.775058 AGATTAGCAGTAGCAGGTATCG 57.225 45.455 0.00 0.00 45.49 2.92
3716 3759 4.238761 TGGTACACGTCTTTTCTGAGAG 57.761 45.455 0.00 0.00 0.00 3.20
3779 3905 1.789523 TTAGGGCGGCTAGTCTCAAT 58.210 50.000 9.56 0.00 0.00 2.57
3882 4008 1.331214 ATGGCGGCTAATCCCAAATG 58.669 50.000 11.43 0.00 31.43 2.32
4010 4136 0.177604 CTCTGCCAGCTCCTACTTGG 59.822 60.000 0.00 0.00 35.06 3.61


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

AutoCloner maintained by Alex Coulton.