Multiple sequence alignment - TraesCS1B01G402000

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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 TraesCS1B01G402000 chr1B 100.000 2845 0 0 407 3251 632009386 632012230 0.000000e+00 5254.0
1 TraesCS1B01G402000 chr1B 100.000 246 0 0 1 246 632008980 632009225 3.820000e-124 455.0
2 TraesCS1B01G402000 chr1B 85.843 332 24 5 2535 2847 632001563 632001890 6.720000e-87 331.0
3 TraesCS1B01G402000 chr1B 76.880 359 51 20 2911 3250 632001891 632002236 1.200000e-39 174.0
4 TraesCS1B01G402000 chr1B 96.610 59 2 0 2858 2916 632009577 632009635 7.420000e-17 99.0
5 TraesCS1B01G402000 chr1B 96.610 59 2 0 598 656 632011837 632011895 7.420000e-17 99.0
6 TraesCS1B01G402000 chr1B 90.411 73 6 1 1713 1784 62389848 62389776 9.600000e-16 95.3
7 TraesCS1B01G402000 chr1B 98.113 53 1 0 2358 2410 632001230 632001282 3.450000e-15 93.5
8 TraesCS1B01G402000 chr1B 89.189 74 7 1 1710 1782 569427093 569427166 1.240000e-14 91.6
9 TraesCS1B01G402000 chr1D 94.893 2467 79 14 419 2853 460142583 460145034 0.000000e+00 3814.0
10 TraesCS1B01G402000 chr1D 97.947 341 6 1 2912 3251 460145044 460145384 1.000000e-164 590.0
11 TraesCS1B01G402000 chr1D 86.567 335 23 6 2535 2847 459890062 459890396 1.860000e-92 350.0
12 TraesCS1B01G402000 chr1D 85.311 354 29 12 2535 2866 262325340 262324988 8.640000e-91 344.0
13 TraesCS1B01G402000 chr1D 81.717 361 33 19 2911 3250 459890397 459890745 1.490000e-68 270.0
14 TraesCS1B01G402000 chr1D 86.719 128 12 4 2912 3034 262324992 262324865 1.570000e-28 137.0
15 TraesCS1B01G402000 chr1D 96.429 56 2 0 2355 2410 459889827 459889882 3.450000e-15 93.5
16 TraesCS1B01G402000 chr1D 98.039 51 1 0 2858 2908 460142763 460142813 4.470000e-14 89.8
17 TraesCS1B01G402000 chr2D 86.337 344 26 10 2535 2857 581827299 581827642 3.990000e-94 355.0
18 TraesCS1B01G402000 chr2D 81.183 186 18 11 2912 3080 581827647 581827832 2.030000e-27 134.0
19 TraesCS1B01G402000 chr2D 89.474 76 7 1 1710 1784 28789708 28789783 9.600000e-16 95.3
20 TraesCS1B01G402000 chr1A 86.350 337 23 11 2535 2853 551604802 551605133 2.400000e-91 346.0
21 TraesCS1B01G402000 chr1A 78.788 198 16 12 2355 2526 551604572 551604769 3.430000e-20 110.0
22 TraesCS1B01G402000 chr7A 89.286 84 7 2 1702 1784 691632762 691632680 1.600000e-18 104.0
23 TraesCS1B01G402000 chr5A 89.474 76 7 1 1710 1784 260411095 260411020 9.600000e-16 95.3
24 TraesCS1B01G402000 chr5A 89.333 75 7 1 1710 1783 552773922 552773996 3.450000e-15 93.5
25 TraesCS1B01G402000 chr3B 89.189 74 7 1 1710 1782 804973922 804973995 1.240000e-14 91.6
26 TraesCS1B01G402000 chr6B 86.420 81 10 1 1705 1784 646138919 646138999 1.610000e-13 87.9


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 TraesCS1B01G402000 chr1B 632008980 632012230 3250 False 1476.750000 5254 98.305000 1 3251 4 chr1B.!!$F3 3250
1 TraesCS1B01G402000 chr1D 460142583 460145384 2801 False 1497.933333 3814 96.959667 419 3251 3 chr1D.!!$F2 2832
2 TraesCS1B01G402000 chr1D 459889827 459890745 918 False 237.833333 350 88.237667 2355 3250 3 chr1D.!!$F1 895
3 TraesCS1B01G402000 chr2D 581827299 581827832 533 False 244.500000 355 83.760000 2535 3080 2 chr2D.!!$F2 545
4 TraesCS1B01G402000 chr1A 551604572 551605133 561 False 228.000000 346 82.569000 2355 2853 2 chr1A.!!$F1 498

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
913 917 0.173708 GTGCTACGGCTGCTTACTCT 59.826 55.0 0.0 0.0 39.59 3.24 F
1634 1638 0.034059 CTCCTGGCGTTGTGAGTCTT 59.966 55.0 0.0 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 2105 0.107848 ATCACCCATCCCGACGTTTC 60.108 55.0 0.0 0.0 0.00 2.78 R
2853 2959 0.257039 AATCGCTGGGAGGAGCAATT 59.743 50.0 0.0 0.0 39.07 2.32 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
38 39 3.793144 CCGAGCAGGCAAAGTCGC 61.793 66.667 0.00 0.00 0.00 5.19
109 110 2.666862 CAACACCAGCGCCGGTTA 60.667 61.111 13.98 0.00 37.07 2.85
110 111 2.667199 AACACCAGCGCCGGTTAC 60.667 61.111 13.98 0.00 37.07 2.50
111 112 4.692475 ACACCAGCGCCGGTTACC 62.692 66.667 13.98 0.00 37.07 2.85
121 122 2.493030 CGGTTACCGGCGACTCAT 59.507 61.111 17.00 0.00 44.15 2.90
122 123 1.876714 CGGTTACCGGCGACTCATG 60.877 63.158 17.00 0.00 44.15 3.07
123 124 2.171725 GGTTACCGGCGACTCATGC 61.172 63.158 9.30 0.00 0.00 4.06
124 125 1.447140 GTTACCGGCGACTCATGCA 60.447 57.895 9.30 0.00 0.00 3.96
125 126 1.153647 TTACCGGCGACTCATGCAG 60.154 57.895 9.30 0.00 0.00 4.41
126 127 3.716539 TACCGGCGACTCATGCAGC 62.717 63.158 9.30 0.00 0.00 5.25
127 128 4.827087 CCGGCGACTCATGCAGCT 62.827 66.667 9.30 0.00 0.00 4.24
128 129 3.561213 CGGCGACTCATGCAGCTG 61.561 66.667 10.11 10.11 0.00 4.24
129 130 3.873883 GGCGACTCATGCAGCTGC 61.874 66.667 31.89 31.89 42.50 5.25
139 140 3.368571 GCAGCTGCACCTCAACCC 61.369 66.667 33.36 0.00 41.59 4.11
140 141 3.052082 CAGCTGCACCTCAACCCG 61.052 66.667 0.00 0.00 0.00 5.28
141 142 4.335647 AGCTGCACCTCAACCCGG 62.336 66.667 1.02 0.00 0.00 5.73
143 144 4.722700 CTGCACCTCAACCCGGGG 62.723 72.222 27.92 12.73 0.00 5.73
164 165 2.423446 GCGGGTCAGCCTAGGATG 59.577 66.667 21.40 21.40 34.45 3.51
165 166 2.134287 GCGGGTCAGCCTAGGATGA 61.134 63.158 25.72 25.72 38.28 2.92
172 173 3.565764 TCAGCCTAGGATGACATTTGG 57.434 47.619 25.72 0.00 35.47 3.28
173 174 2.173356 TCAGCCTAGGATGACATTTGGG 59.827 50.000 25.72 0.00 35.47 4.12
174 175 2.173356 CAGCCTAGGATGACATTTGGGA 59.827 50.000 22.93 0.00 32.62 4.37
175 176 2.173569 AGCCTAGGATGACATTTGGGAC 59.826 50.000 14.75 0.00 0.00 4.46
176 177 2.749800 GCCTAGGATGACATTTGGGACC 60.750 54.545 14.75 0.00 0.00 4.46
177 178 2.509548 CCTAGGATGACATTTGGGACCA 59.490 50.000 1.05 0.00 0.00 4.02
178 179 3.053693 CCTAGGATGACATTTGGGACCAA 60.054 47.826 1.05 0.00 0.00 3.67
179 180 3.091633 AGGATGACATTTGGGACCAAG 57.908 47.619 3.73 0.00 37.24 3.61
180 181 1.478105 GGATGACATTTGGGACCAAGC 59.522 52.381 3.73 0.00 37.24 4.01
181 182 1.133025 GATGACATTTGGGACCAAGCG 59.867 52.381 3.73 2.51 37.24 4.68
182 183 0.893270 TGACATTTGGGACCAAGCGG 60.893 55.000 3.73 1.23 37.24 5.52
183 184 2.212900 GACATTTGGGACCAAGCGGC 62.213 60.000 3.73 0.00 37.24 6.53
184 185 1.978617 CATTTGGGACCAAGCGGCT 60.979 57.895 0.00 0.00 37.24 5.52
185 186 1.978617 ATTTGGGACCAAGCGGCTG 60.979 57.895 1.81 0.00 37.24 4.85
202 203 3.991999 GCTCAAGCATCACCAGCA 58.008 55.556 0.00 0.00 41.59 4.41
203 204 2.260247 GCTCAAGCATCACCAGCAA 58.740 52.632 0.00 0.00 41.59 3.91
204 205 0.599558 GCTCAAGCATCACCAGCAAA 59.400 50.000 0.00 0.00 41.59 3.68
205 206 1.000060 GCTCAAGCATCACCAGCAAAA 60.000 47.619 0.00 0.00 41.59 2.44
206 207 2.546373 GCTCAAGCATCACCAGCAAAAA 60.546 45.455 0.00 0.00 41.59 1.94
231 232 7.912056 AAAAAGAAAAAGAAAAGAAGCAGCT 57.088 28.000 0.00 0.00 0.00 4.24
232 233 6.898912 AAAGAAAAAGAAAAGAAGCAGCTG 57.101 33.333 10.11 10.11 0.00 4.24
233 234 4.366586 AGAAAAAGAAAAGAAGCAGCTGC 58.633 39.130 31.53 31.53 42.49 5.25
442 443 6.871844 TGAAGTTGAGATATCTGAACCTGAG 58.128 40.000 25.60 0.00 40.27 3.35
444 445 4.100808 AGTTGAGATATCTGAACCTGAGCC 59.899 45.833 25.60 5.18 40.27 4.70
450 451 0.833409 TCTGAACCTGAGCCTGCAGA 60.833 55.000 17.39 0.00 38.14 4.26
496 497 3.065306 CCTCAGGCCGTGTAACCA 58.935 61.111 0.00 0.00 0.00 3.67
497 498 1.373435 CCTCAGGCCGTGTAACCAA 59.627 57.895 0.00 0.00 0.00 3.67
559 561 3.018598 TCGGCATCGATGAGAAGAATC 57.981 47.619 29.20 8.15 40.88 2.52
582 584 4.779733 ACTCCCTCGCCATCGGGT 62.780 66.667 0.00 0.00 41.40 5.28
588 590 1.672854 CCTCGCCATCGGGTCACTAA 61.673 60.000 0.00 0.00 33.43 2.24
662 664 2.754658 AGCGATTCCCCGTCGTCT 60.755 61.111 0.00 0.00 40.98 4.18
709 713 0.257328 TCTCTCTCTCGCTCACCCAT 59.743 55.000 0.00 0.00 0.00 4.00
846 850 2.510012 TCATGCCGCTGCTTCTCG 60.510 61.111 0.70 0.00 38.71 4.04
884 888 0.733909 GCTGCTTTTCGTGGCCATTC 60.734 55.000 9.72 0.00 0.00 2.67
894 898 1.672030 TGGCCATTCTGTGTGCTCG 60.672 57.895 0.00 0.00 0.00 5.03
913 917 0.173708 GTGCTACGGCTGCTTACTCT 59.826 55.000 0.00 0.00 39.59 3.24
917 921 0.456221 TACGGCTGCTTACTCTGCTC 59.544 55.000 0.00 0.00 0.00 4.26
928 932 1.735920 CTCTGCTCCTGTGTCGTGC 60.736 63.158 0.00 0.00 0.00 5.34
929 933 2.029518 CTGCTCCTGTGTCGTGCA 59.970 61.111 0.00 0.00 0.00 4.57
930 934 2.025969 CTGCTCCTGTGTCGTGCAG 61.026 63.158 0.00 0.00 43.71 4.41
1030 1034 2.427320 GAGCCATAGCCATCGCCA 59.573 61.111 0.00 0.00 41.25 5.69
1041 1045 1.164662 CCATCGCCATCCTCTTGCTG 61.165 60.000 0.00 0.00 0.00 4.41
1107 1111 2.112297 TTGTCCGACAAGGGGTGC 59.888 61.111 9.99 0.00 41.52 5.01
1185 1189 6.115448 TCCTTTTTAGAGAAGGAGGTTGAG 57.885 41.667 1.61 0.00 45.81 3.02
1254 1258 1.508088 GCTCACCATTTTCTGCCCG 59.492 57.895 0.00 0.00 0.00 6.13
1257 1261 0.111446 TCACCATTTTCTGCCCGGAA 59.889 50.000 0.73 0.00 0.00 4.30
1293 1297 2.622436 GGGTTCACTCCGAGATTCAAG 58.378 52.381 1.33 0.00 0.00 3.02
1332 1336 2.675317 GCAGGTCGCACTTCTTCTGTAT 60.675 50.000 0.00 0.00 41.79 2.29
1452 1456 3.863780 GCATGCTCACCATCGATGTCTAT 60.864 47.826 23.27 3.94 29.71 1.98
1552 1556 1.139654 GCCTGGCTGTCTACATCATCA 59.860 52.381 12.43 0.00 0.00 3.07
1633 1637 1.668294 CTCCTGGCGTTGTGAGTCT 59.332 57.895 0.00 0.00 0.00 3.24
1634 1638 0.034059 CTCCTGGCGTTGTGAGTCTT 59.966 55.000 0.00 0.00 0.00 3.01
1635 1639 1.272490 CTCCTGGCGTTGTGAGTCTTA 59.728 52.381 0.00 0.00 0.00 2.10
1636 1640 1.689813 TCCTGGCGTTGTGAGTCTTAA 59.310 47.619 0.00 0.00 0.00 1.85
1637 1641 1.798813 CCTGGCGTTGTGAGTCTTAAC 59.201 52.381 0.00 0.00 0.00 2.01
1648 1652 6.274157 TGTGAGTCTTAACTTCATCTCCTC 57.726 41.667 0.00 0.00 35.28 3.71
1754 1758 5.388654 ACTCATCCAAAAGTCCAAACTGAT 58.611 37.500 0.00 0.00 35.36 2.90
1817 1821 4.288366 TGTCTGAATTTATCTGTGGGTGGA 59.712 41.667 0.00 0.00 0.00 4.02
1818 1822 5.222027 TGTCTGAATTTATCTGTGGGTGGAA 60.222 40.000 0.00 0.00 0.00 3.53
1931 1935 6.005823 TGACATTTCTGCCATATAATCAGGG 58.994 40.000 0.00 0.00 0.00 4.45
1965 1969 5.456619 CCAACTGATTATTAGGGAGATGCCA 60.457 44.000 0.00 0.00 38.95 4.92
2026 2030 6.755206 AGCAGGTGTAAATATATAGCGACAA 58.245 36.000 0.00 0.00 0.00 3.18
2273 2277 5.230942 AGAAGATCGTTTCGTGTCAAGATT 58.769 37.500 0.00 0.00 32.33 2.40
2274 2278 4.910746 AGATCGTTTCGTGTCAAGATTG 57.089 40.909 0.00 0.00 0.00 2.67
2292 2296 2.882927 TGCGCTACTACCTATGTTGG 57.117 50.000 9.73 0.00 0.00 3.77
2316 2334 3.927142 CGACAAGGACCTTAGTTCATGAC 59.073 47.826 6.38 0.00 0.00 3.06
2332 2350 7.521529 AGTTCATGACTGTTTCATTTACATCG 58.478 34.615 0.00 0.00 42.87 3.84
2338 2356 3.417101 TGTTTCATTTACATCGGCTGGT 58.583 40.909 0.00 0.00 0.00 4.00
2350 2368 3.965379 TCGGCTGGTCTAATGTTAACA 57.035 42.857 11.41 11.41 0.00 2.41
2356 2380 5.705905 GGCTGGTCTAATGTTAACAACTTCT 59.294 40.000 13.23 0.00 0.00 2.85
2374 2398 6.552445 ACTTCTACATTATCCTGCTCTGTT 57.448 37.500 0.00 0.00 0.00 3.16
2432 2466 3.845781 TCTCTGCCAAGAAACTTCAGT 57.154 42.857 0.00 0.00 30.03 3.41
2528 2587 5.973565 GCTTGATTGTTACCACATTCATAGC 59.026 40.000 12.86 12.86 41.00 2.97
2529 2588 6.404623 GCTTGATTGTTACCACATTCATAGCA 60.405 38.462 17.70 0.00 41.00 3.49
2599 2685 1.765314 AGAAGTGAGTGAGGTGCAACT 59.235 47.619 2.34 2.34 36.74 3.16
2667 2753 2.865119 TGTCATGTCCTGCTGTGATT 57.135 45.000 0.00 0.00 0.00 2.57
2687 2786 8.482128 TGTGATTGGTTTCAAGTAATTCCTTTT 58.518 29.630 0.00 0.00 36.19 2.27
2853 2959 4.374689 TGTTCTAAACCTGGCCATGTAA 57.625 40.909 14.55 2.05 0.00 2.41
2856 2962 5.777732 TGTTCTAAACCTGGCCATGTAAATT 59.222 36.000 14.55 7.85 0.00 1.82
2857 2963 5.913137 TCTAAACCTGGCCATGTAAATTG 57.087 39.130 14.55 5.56 0.00 2.32
2858 2964 3.333029 AAACCTGGCCATGTAAATTGC 57.667 42.857 14.55 0.00 0.00 3.56
2859 2965 2.236489 ACCTGGCCATGTAAATTGCT 57.764 45.000 12.49 0.00 0.00 3.91
2862 2968 2.381911 CTGGCCATGTAAATTGCTCCT 58.618 47.619 5.51 0.00 0.00 3.69
2863 2969 2.360165 CTGGCCATGTAAATTGCTCCTC 59.640 50.000 5.51 0.00 0.00 3.71
2864 2970 1.683385 GGCCATGTAAATTGCTCCTCC 59.317 52.381 0.00 0.00 0.00 4.30
2865 2971 1.683385 GCCATGTAAATTGCTCCTCCC 59.317 52.381 0.00 0.00 0.00 4.30
2866 2972 2.949963 GCCATGTAAATTGCTCCTCCCA 60.950 50.000 0.00 0.00 0.00 4.37
2867 2973 2.954318 CCATGTAAATTGCTCCTCCCAG 59.046 50.000 0.00 0.00 0.00 4.45
2868 2974 2.128771 TGTAAATTGCTCCTCCCAGC 57.871 50.000 0.00 0.00 40.13 4.85
2869 2975 1.017387 GTAAATTGCTCCTCCCAGCG 58.983 55.000 0.00 0.00 42.92 5.18
2870 2976 0.908910 TAAATTGCTCCTCCCAGCGA 59.091 50.000 0.00 0.00 42.92 4.93
2871 2977 0.257039 AAATTGCTCCTCCCAGCGAT 59.743 50.000 0.00 0.00 44.27 4.58
2872 2978 0.257039 AATTGCTCCTCCCAGCGATT 59.743 50.000 2.59 2.59 45.24 3.34
2873 2979 0.179034 ATTGCTCCTCCCAGCGATTC 60.179 55.000 0.00 0.00 40.14 2.52
2874 2980 2.110006 GCTCCTCCCAGCGATTCC 59.890 66.667 0.00 0.00 0.00 3.01
2875 2981 2.825264 CTCCTCCCAGCGATTCCC 59.175 66.667 0.00 0.00 0.00 3.97
2876 2982 2.768344 TCCTCCCAGCGATTCCCC 60.768 66.667 0.00 0.00 0.00 4.81
2877 2983 4.241555 CCTCCCAGCGATTCCCCG 62.242 72.222 0.00 0.00 0.00 5.73
2885 2991 4.587189 CGATTCCCCGCGGTCCTC 62.587 72.222 26.12 13.72 0.00 3.71
2886 2992 4.587189 GATTCCCCGCGGTCCTCG 62.587 72.222 26.12 8.02 42.76 4.63
2910 3016 4.496336 GCGGCTCCTCCCAGCAAT 62.496 66.667 0.00 0.00 41.65 3.56
2966 3072 1.985159 TCACAGGTCACAATTAGCCCT 59.015 47.619 0.00 0.00 0.00 5.19
3075 3203 9.935241 CATTATACTATGACTAGAACAATGCCT 57.065 33.333 0.00 0.00 0.00 4.75
3127 3255 6.425721 GGTGATAAATTCGATGATCCCGTTAA 59.574 38.462 4.83 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 3.793144 GCGACTTTGCCTGCTCGG 61.793 66.667 0.00 0.00 0.00 4.63
92 93 2.666862 TAACCGGCGCTGGTGTTG 60.667 61.111 40.30 14.94 42.89 3.33
93 94 2.667199 GTAACCGGCGCTGGTGTT 60.667 61.111 40.30 27.94 42.89 3.32
94 95 4.692475 GGTAACCGGCGCTGGTGT 62.692 66.667 40.30 29.28 42.89 4.16
105 106 2.171725 GCATGAGTCGCCGGTAACC 61.172 63.158 1.90 0.00 0.00 2.85
106 107 1.421410 CTGCATGAGTCGCCGGTAAC 61.421 60.000 1.90 1.09 0.00 2.50
107 108 1.153647 CTGCATGAGTCGCCGGTAA 60.154 57.895 1.90 0.00 0.00 2.85
108 109 2.494445 CTGCATGAGTCGCCGGTA 59.506 61.111 1.90 0.00 0.00 4.02
110 111 4.827087 AGCTGCATGAGTCGCCGG 62.827 66.667 1.02 0.00 0.00 6.13
111 112 3.561213 CAGCTGCATGAGTCGCCG 61.561 66.667 0.00 0.00 0.00 6.46
112 113 3.873883 GCAGCTGCATGAGTCGCC 61.874 66.667 33.36 0.00 41.59 5.54
122 123 3.368571 GGGTTGAGGTGCAGCTGC 61.369 66.667 31.89 31.89 42.50 5.25
123 124 3.052082 CGGGTTGAGGTGCAGCTG 61.052 66.667 25.60 10.11 0.00 4.24
124 125 4.335647 CCGGGTTGAGGTGCAGCT 62.336 66.667 20.31 20.31 0.00 4.24
126 127 4.722700 CCCCGGGTTGAGGTGCAG 62.723 72.222 21.85 0.00 0.00 4.41
147 148 2.134287 TCATCCTAGGCTGACCCGC 61.134 63.158 11.34 0.00 39.21 6.13
148 149 1.043116 TGTCATCCTAGGCTGACCCG 61.043 60.000 32.68 2.31 39.63 5.28
149 150 1.428869 ATGTCATCCTAGGCTGACCC 58.571 55.000 32.68 16.81 39.63 4.46
150 151 3.209410 CAAATGTCATCCTAGGCTGACC 58.791 50.000 32.68 20.00 39.63 4.02
151 152 3.209410 CCAAATGTCATCCTAGGCTGAC 58.791 50.000 30.55 30.55 40.45 3.51
152 153 2.173356 CCCAAATGTCATCCTAGGCTGA 59.827 50.000 11.34 11.34 0.00 4.26
153 154 2.173356 TCCCAAATGTCATCCTAGGCTG 59.827 50.000 6.25 6.25 0.00 4.85
154 155 2.173569 GTCCCAAATGTCATCCTAGGCT 59.826 50.000 2.96 0.00 0.00 4.58
155 156 2.576615 GTCCCAAATGTCATCCTAGGC 58.423 52.381 2.96 0.00 0.00 3.93
156 157 2.509548 TGGTCCCAAATGTCATCCTAGG 59.490 50.000 0.82 0.82 0.00 3.02
157 158 3.931907 TGGTCCCAAATGTCATCCTAG 57.068 47.619 0.00 0.00 0.00 3.02
158 159 3.624707 GCTTGGTCCCAAATGTCATCCTA 60.625 47.826 0.00 0.00 35.33 2.94
159 160 2.885554 GCTTGGTCCCAAATGTCATCCT 60.886 50.000 0.00 0.00 35.33 3.24
160 161 1.478105 GCTTGGTCCCAAATGTCATCC 59.522 52.381 0.00 0.00 35.33 3.51
161 162 1.133025 CGCTTGGTCCCAAATGTCATC 59.867 52.381 0.00 0.00 35.33 2.92
162 163 1.176527 CGCTTGGTCCCAAATGTCAT 58.823 50.000 0.00 0.00 35.33 3.06
163 164 0.893270 CCGCTTGGTCCCAAATGTCA 60.893 55.000 0.00 0.00 35.33 3.58
164 165 1.883021 CCGCTTGGTCCCAAATGTC 59.117 57.895 0.00 0.00 35.33 3.06
165 166 2.275380 GCCGCTTGGTCCCAAATGT 61.275 57.895 0.00 0.00 35.33 2.71
166 167 1.978617 AGCCGCTTGGTCCCAAATG 60.979 57.895 0.00 0.00 35.33 2.32
167 168 1.978617 CAGCCGCTTGGTCCCAAAT 60.979 57.895 0.00 0.00 35.33 2.32
168 169 2.597217 CAGCCGCTTGGTCCCAAA 60.597 61.111 0.00 0.00 35.33 3.28
185 186 0.599558 TTTGCTGGTGATGCTTGAGC 59.400 50.000 0.00 0.00 42.50 4.26
186 187 3.374220 TTTTTGCTGGTGATGCTTGAG 57.626 42.857 0.00 0.00 0.00 3.02
207 208 7.624974 GCAGCTGCTTCTTTTCTTTTTCTTTTT 60.625 33.333 31.33 0.00 38.21 1.94
208 209 6.183360 GCAGCTGCTTCTTTTCTTTTTCTTTT 60.183 34.615 31.33 0.00 38.21 2.27
209 210 5.292834 GCAGCTGCTTCTTTTCTTTTTCTTT 59.707 36.000 31.33 0.00 38.21 2.52
210 211 4.807834 GCAGCTGCTTCTTTTCTTTTTCTT 59.192 37.500 31.33 0.00 38.21 2.52
211 212 4.366586 GCAGCTGCTTCTTTTCTTTTTCT 58.633 39.130 31.33 0.00 38.21 2.52
212 213 4.705554 GCAGCTGCTTCTTTTCTTTTTC 57.294 40.909 31.33 0.00 38.21 2.29
406 407 5.110814 TCTCAACTTCAGGTTCCTCAAAA 57.889 39.130 0.00 0.00 35.74 2.44
407 408 4.771114 TCTCAACTTCAGGTTCCTCAAA 57.229 40.909 0.00 0.00 35.74 2.69
408 409 4.982241 ATCTCAACTTCAGGTTCCTCAA 57.018 40.909 0.00 0.00 35.74 3.02
409 410 5.960811 AGATATCTCAACTTCAGGTTCCTCA 59.039 40.000 0.00 0.00 35.74 3.86
410 411 6.097554 TCAGATATCTCAACTTCAGGTTCCTC 59.902 42.308 1.03 0.00 35.74 3.71
411 412 5.960811 TCAGATATCTCAACTTCAGGTTCCT 59.039 40.000 1.03 0.00 35.74 3.36
412 413 6.227298 TCAGATATCTCAACTTCAGGTTCC 57.773 41.667 1.03 0.00 35.74 3.62
413 414 6.536941 GGTTCAGATATCTCAACTTCAGGTTC 59.463 42.308 17.65 0.00 35.74 3.62
414 415 6.214412 AGGTTCAGATATCTCAACTTCAGGTT 59.786 38.462 17.65 0.00 38.93 3.50
415 416 5.723887 AGGTTCAGATATCTCAACTTCAGGT 59.276 40.000 17.65 0.00 0.00 4.00
416 417 6.047870 CAGGTTCAGATATCTCAACTTCAGG 58.952 44.000 17.65 0.00 0.00 3.86
417 418 6.871844 TCAGGTTCAGATATCTCAACTTCAG 58.128 40.000 17.65 6.96 0.00 3.02
425 426 3.554752 GCAGGCTCAGGTTCAGATATCTC 60.555 52.174 1.03 0.00 0.00 2.75
442 443 0.036022 ACTTTCAGTCCTCTGCAGGC 59.964 55.000 15.13 2.16 40.12 4.85
444 445 1.155042 GCACTTTCAGTCCTCTGCAG 58.845 55.000 7.63 7.63 41.10 4.41
450 451 0.888285 GCTGCTGCACTTTCAGTCCT 60.888 55.000 11.11 0.00 39.41 3.85
488 489 0.746923 GGGCCCTCGATTGGTTACAC 60.747 60.000 17.04 0.00 0.00 2.90
496 497 2.677228 CCACTTGGGCCCTCGATT 59.323 61.111 25.70 0.00 0.00 3.34
582 584 0.747255 GGAGCCGAGCAGATTAGTGA 59.253 55.000 0.00 0.00 0.00 3.41
588 590 2.841988 GGGAGGAGCCGAGCAGAT 60.842 66.667 0.00 0.00 37.63 2.90
649 651 4.007457 TCGAAGACGACGGGGAAT 57.993 55.556 0.00 0.00 43.81 3.01
722 726 2.473576 AACCCTAACCCTAGATCGCT 57.526 50.000 0.00 0.00 0.00 4.93
862 866 4.404654 GCCACGAAAAGCAGCGGG 62.405 66.667 0.00 0.00 0.00 6.13
884 888 2.088763 CCGTAGCACGAGCACACAG 61.089 63.158 7.77 1.92 46.05 3.66
894 898 0.173708 AGAGTAAGCAGCCGTAGCAC 59.826 55.000 0.00 0.00 43.56 4.40
913 917 2.029518 CTGCACGACACAGGAGCA 59.970 61.111 0.00 0.00 0.00 4.26
928 932 2.985456 GCTCAGTCCCTGTCCCTG 59.015 66.667 0.00 0.00 32.61 4.45
929 933 2.681778 CGCTCAGTCCCTGTCCCT 60.682 66.667 0.00 0.00 32.61 4.20
930 934 2.997897 ACGCTCAGTCCCTGTCCC 60.998 66.667 0.00 0.00 32.61 4.46
931 935 2.574399 GACGCTCAGTCCCTGTCC 59.426 66.667 0.00 0.00 43.95 4.02
949 953 1.959226 GGCAGAAGGAACGACGCAA 60.959 57.895 0.00 0.00 0.00 4.85
983 987 2.032030 GGCATGTGGTTAATTCGATCCG 60.032 50.000 0.00 0.00 0.00 4.18
1020 1024 1.147824 CAAGAGGATGGCGATGGCT 59.852 57.895 0.00 0.00 39.81 4.75
1030 1034 3.424105 GGGGGCCAGCAAGAGGAT 61.424 66.667 4.39 0.00 0.00 3.24
1141 1145 4.681978 GAACACCTCGCCCACGCT 62.682 66.667 0.00 0.00 39.84 5.07
1181 1185 2.091102 GAACACGTCGGGGGTCTCAA 62.091 60.000 0.00 0.00 0.00 3.02
1254 1258 3.195698 GCCACCGCATCGTCTTCC 61.196 66.667 0.00 0.00 34.03 3.46
1274 1278 3.594603 TCTTGAATCTCGGAGTGAACC 57.405 47.619 4.69 0.00 32.30 3.62
1275 1279 3.369451 GCTTCTTGAATCTCGGAGTGAAC 59.631 47.826 4.69 0.00 32.30 3.18
1320 1324 4.383552 GGCACTCCATGATACAGAAGAAGT 60.384 45.833 0.00 0.00 0.00 3.01
1332 1336 4.794439 CGCGACGGCACTCCATGA 62.794 66.667 0.00 0.00 39.92 3.07
1452 1456 6.263344 CGAAGAAAGTACCACGATATCTTCA 58.737 40.000 11.70 0.00 40.64 3.02
1552 1556 1.471287 TCTCGGAATCATCACGTCGTT 59.529 47.619 0.00 0.00 0.00 3.85
1633 1637 6.139671 AGCATAGAGGAGGAGATGAAGTTAA 58.860 40.000 0.00 0.00 0.00 2.01
1634 1638 5.710646 AGCATAGAGGAGGAGATGAAGTTA 58.289 41.667 0.00 0.00 0.00 2.24
1635 1639 4.555689 AGCATAGAGGAGGAGATGAAGTT 58.444 43.478 0.00 0.00 0.00 2.66
1636 1640 4.197559 AGCATAGAGGAGGAGATGAAGT 57.802 45.455 0.00 0.00 0.00 3.01
1637 1641 5.774690 ACTAAGCATAGAGGAGGAGATGAAG 59.225 44.000 2.38 0.00 33.15 3.02
1648 1652 6.879400 AGAGGTAACAAACTAAGCATAGAGG 58.121 40.000 2.38 0.00 41.41 3.69
1754 1758 8.567948 GTTGAAATTATTGTTTGTCTCTCTCCA 58.432 33.333 0.00 0.00 0.00 3.86
1817 1821 2.700897 AGTATGATCTAAGCAGCCCGTT 59.299 45.455 0.00 0.00 0.00 4.44
1818 1822 2.320781 AGTATGATCTAAGCAGCCCGT 58.679 47.619 0.00 0.00 0.00 5.28
1851 1855 2.545742 GCACATCCCCAAGTCACAAAAC 60.546 50.000 0.00 0.00 0.00 2.43
1965 1969 7.701539 TGGTTATGTTGCAGAATAAACTCAT 57.298 32.000 15.52 0.00 29.13 2.90
2038 2042 5.579511 GGTACGTGTGTAATCAAGCAGTAAT 59.420 40.000 0.00 0.00 30.94 1.89
2101 2105 0.107848 ATCACCCATCCCGACGTTTC 60.108 55.000 0.00 0.00 0.00 2.78
2175 2179 5.955355 GCAGGGGAGAGATAGATACAGTTAT 59.045 44.000 0.00 0.00 0.00 1.89
2273 2277 1.411246 CCCAACATAGGTAGTAGCGCA 59.589 52.381 11.47 0.00 0.00 6.09
2274 2278 1.872653 GCCCAACATAGGTAGTAGCGC 60.873 57.143 0.00 0.00 0.00 5.92
2292 2296 1.001633 TGAACTAAGGTCCTTGTCGCC 59.998 52.381 14.84 0.78 0.00 5.54
2316 2334 3.440173 ACCAGCCGATGTAAATGAAACAG 59.560 43.478 0.00 0.00 0.00 3.16
2332 2350 5.705905 AGAAGTTGTTAACATTAGACCAGCC 59.294 40.000 9.56 0.00 0.00 4.85
2350 2368 6.552445 ACAGAGCAGGATAATGTAGAAGTT 57.448 37.500 0.00 0.00 0.00 2.66
2356 2380 8.023021 AGTATGAAACAGAGCAGGATAATGTA 57.977 34.615 0.00 0.00 0.00 2.29
2374 2398 2.434336 AGGCAGCGATACCAAGTATGAA 59.566 45.455 0.00 0.00 0.00 2.57
2432 2466 6.693315 AACTCAAGCTACTTAACTTGCAAA 57.307 33.333 0.00 0.00 42.41 3.68
2528 2587 5.782047 TGGAGCAAAACCATTAGATTTGTG 58.218 37.500 0.00 0.00 36.63 3.33
2529 2588 6.014327 ACATGGAGCAAAACCATTAGATTTGT 60.014 34.615 0.00 0.00 44.51 2.83
2599 2685 0.599991 GACCACGACATGAGCACACA 60.600 55.000 0.00 0.00 0.00 3.72
2667 2753 7.340743 TGAGACAAAAGGAATTACTTGAAACCA 59.659 33.333 2.96 0.00 0.00 3.67
2687 2786 7.212274 CACCATGATATTACACAGATGAGACA 58.788 38.462 0.00 0.00 0.00 3.41
2853 2959 0.257039 AATCGCTGGGAGGAGCAATT 59.743 50.000 0.00 0.00 39.07 2.32
2856 2962 2.735772 GGAATCGCTGGGAGGAGCA 61.736 63.158 0.00 0.00 39.07 4.26
2857 2963 2.110006 GGAATCGCTGGGAGGAGC 59.890 66.667 0.00 0.00 35.46 4.70
2858 2964 2.812619 GGGGAATCGCTGGGAGGAG 61.813 68.421 0.00 0.00 0.00 3.69
2859 2965 2.768344 GGGGAATCGCTGGGAGGA 60.768 66.667 0.00 0.00 0.00 3.71
2868 2974 4.587189 GAGGACCGCGGGGAATCG 62.587 72.222 31.76 1.69 36.97 3.34
2869 2975 4.587189 CGAGGACCGCGGGGAATC 62.587 72.222 31.76 17.81 36.97 2.52
2893 2999 4.496336 ATTGCTGGGAGGAGCCGC 62.496 66.667 0.00 0.00 38.28 6.53
2894 3000 1.379044 AAATTGCTGGGAGGAGCCG 60.379 57.895 0.00 0.00 38.28 5.52
2895 3001 1.039785 GGAAATTGCTGGGAGGAGCC 61.040 60.000 0.00 0.00 38.28 4.70
2896 3002 1.039785 GGGAAATTGCTGGGAGGAGC 61.040 60.000 0.00 0.00 39.62 4.70
2897 3003 0.627986 AGGGAAATTGCTGGGAGGAG 59.372 55.000 0.00 0.00 0.00 3.69
2898 3004 0.332632 CAGGGAAATTGCTGGGAGGA 59.667 55.000 0.00 0.00 0.00 3.71
2899 3005 0.685458 CCAGGGAAATTGCTGGGAGG 60.685 60.000 0.00 0.00 33.61 4.30
2900 3006 2.892025 CCAGGGAAATTGCTGGGAG 58.108 57.895 0.00 0.00 33.61 4.30
2903 3009 2.361567 GCCCCAGGGAAATTGCTGG 61.362 63.158 7.25 0.00 37.50 4.85
2904 3010 2.361567 GGCCCCAGGGAAATTGCTG 61.362 63.158 7.25 0.00 37.50 4.41
2905 3011 2.039462 GGCCCCAGGGAAATTGCT 59.961 61.111 7.25 0.00 37.50 3.91
2906 3012 1.200760 AAAGGCCCCAGGGAAATTGC 61.201 55.000 7.25 0.00 37.50 3.56
2907 3013 0.904649 GAAAGGCCCCAGGGAAATTG 59.095 55.000 7.25 0.00 37.50 2.32
2908 3014 0.792960 AGAAAGGCCCCAGGGAAATT 59.207 50.000 7.25 0.00 37.50 1.82
2909 3015 0.792960 AAGAAAGGCCCCAGGGAAAT 59.207 50.000 7.25 0.00 37.50 2.17
2910 3016 0.565674 AAAGAAAGGCCCCAGGGAAA 59.434 50.000 7.25 0.00 37.50 3.13
3075 3203 0.872451 CGTAGCAACACACGGACACA 60.872 55.000 0.00 0.00 34.57 3.72
3127 3255 4.826556 AGAGAGAAACTTAAGCGCTCATT 58.173 39.130 12.06 0.00 31.98 2.57


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

AutoCloner maintained by Alex Coulton.