Multiple sequence alignment - TraesCS6B01G372400

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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 TraesCS6B01G372400 chr6B 100.000 2739 0 0 1 2739 645817182 645814444 0.000000e+00 5059.0
1 TraesCS6B01G372400 chr6B 84.286 280 32 9 260 527 285243206 285242927 2.090000e-66 263.0
2 TraesCS6B01G372400 chr6B 78.509 228 33 11 425 638 100604322 100604547 4.760000e-28 135.0
3 TraesCS6B01G372400 chr6A 93.358 1325 63 11 97 1418 573862670 573861368 0.000000e+00 1936.0
4 TraesCS6B01G372400 chr6A 94.812 1118 51 3 1327 2444 573861281 573860171 0.000000e+00 1736.0
5 TraesCS6B01G372400 chr6A 93.333 195 7 4 2550 2739 573859719 573859526 1.610000e-72 283.0
6 TraesCS6B01G372400 chr6A 98.913 92 1 0 1327 1418 573861370 573861279 6.070000e-37 165.0
7 TraesCS6B01G372400 chr6A 96.341 82 3 0 2473 2554 573860173 573860092 4.760000e-28 135.0
8 TraesCS6B01G372400 chr5D 78.187 1114 227 11 1058 2166 505401252 505402354 0.000000e+00 697.0
9 TraesCS6B01G372400 chr5D 81.391 489 70 14 51 525 422469136 422468655 1.990000e-101 379.0
10 TraesCS6B01G372400 chr5D 72.585 1149 267 35 1035 2166 505461497 505462614 1.570000e-87 333.0
11 TraesCS6B01G372400 chr5D 82.031 256 36 8 1035 1283 505420636 505420888 2.760000e-50 209.0
12 TraesCS6B01G372400 chr5D 71.683 505 128 13 1490 1988 505364175 505364670 2.860000e-25 126.0
13 TraesCS6B01G372400 chr5D 92.500 40 3 0 12 51 502745962 502746001 1.060000e-04 58.4
14 TraesCS6B01G372400 chr5B 77.482 1128 225 22 1053 2166 635462851 635463963 0.000000e+00 649.0
15 TraesCS6B01G372400 chr5B 79.184 490 77 13 170 638 441387884 441387399 1.580000e-82 316.0
16 TraesCS6B01G372400 chr5B 83.898 236 35 3 1053 1287 635510512 635510745 3.550000e-54 222.0
17 TraesCS6B01G372400 chr5B 82.101 257 34 10 1035 1283 635515172 635515424 2.760000e-50 209.0
18 TraesCS6B01G372400 chr5B 82.114 246 40 4 1058 1301 635466869 635467112 9.940000e-50 207.0
19 TraesCS6B01G372400 chr5A 77.984 1022 207 13 1058 2073 632881954 632882963 2.320000e-175 625.0
20 TraesCS6B01G372400 chr4A 82.922 486 74 4 51 527 585615438 585614953 1.950000e-116 429.0
21 TraesCS6B01G372400 chr7A 76.861 618 114 14 51 640 342762975 342763591 3.400000e-84 322.0
22 TraesCS6B01G372400 chr7D 78.615 491 88 10 51 527 318805767 318806254 2.650000e-80 309.0
23 TraesCS6B01G372400 chr1B 76.721 610 108 19 51 630 662028212 662027607 2.650000e-80 309.0
24 TraesCS6B01G372400 chr2A 78.137 526 80 16 142 638 454813722 454813203 4.430000e-78 302.0
25 TraesCS6B01G372400 chr2A 93.182 44 3 0 645 688 8042602 8042559 6.330000e-07 65.8
26 TraesCS6B01G372400 chr4D 78.163 490 91 11 51 527 30190392 30190878 5.730000e-77 298.0
27 TraesCS6B01G372400 chr4D 75.847 472 92 13 53 505 270612560 270613028 1.280000e-53 220.0
28 TraesCS6B01G372400 chr2D 77.989 527 78 19 142 638 343773733 343773215 2.060000e-76 296.0
29 TraesCS6B01G372400 chr2D 93.617 47 3 0 639 685 8983386 8983432 1.360000e-08 71.3
30 TraesCS6B01G372400 chr6D 79.810 421 56 12 246 638 157997075 157997494 2.080000e-71 279.0
31 TraesCS6B01G372400 chr6D 76.586 457 94 8 53 497 35216376 35216831 3.530000e-59 239.0
32 TraesCS6B01G372400 chr3D 75.822 517 86 20 153 638 583047165 583047673 2.740000e-55 226.0


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 TraesCS6B01G372400 chr6B 645814444 645817182 2738 True 5059 5059 100.0000 1 2739 1 chr6B.!!$R2 2738
1 TraesCS6B01G372400 chr6A 573859526 573862670 3144 True 851 1936 95.3514 97 2739 5 chr6A.!!$R1 2642
2 TraesCS6B01G372400 chr5D 505401252 505402354 1102 False 697 697 78.1870 1058 2166 1 chr5D.!!$F3 1108
3 TraesCS6B01G372400 chr5D 505461497 505462614 1117 False 333 333 72.5850 1035 2166 1 chr5D.!!$F5 1131
4 TraesCS6B01G372400 chr5B 635462851 635467112 4261 False 428 649 79.7980 1053 2166 2 chr5B.!!$F3 1113
5 TraesCS6B01G372400 chr5A 632881954 632882963 1009 False 625 625 77.9840 1058 2073 1 chr5A.!!$F1 1015
6 TraesCS6B01G372400 chr7A 342762975 342763591 616 False 322 322 76.8610 51 640 1 chr7A.!!$F1 589
7 TraesCS6B01G372400 chr1B 662027607 662028212 605 True 309 309 76.7210 51 630 1 chr1B.!!$R1 579
8 TraesCS6B01G372400 chr2A 454813203 454813722 519 True 302 302 78.1370 142 638 1 chr2A.!!$R2 496
9 TraesCS6B01G372400 chr2D 343773215 343773733 518 True 296 296 77.9890 142 638 1 chr2D.!!$R1 496
10 TraesCS6B01G372400 chr3D 583047165 583047673 508 False 226 226 75.8220 153 638 1 chr3D.!!$F1 485

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
387 400 0.033228 GCAGGTCCCAGATGAGATCG 59.967 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 2518 0.668706 GGATCATCGATGGACAGCCG 60.669 60.0 24.61 0.0 36.79 5.52 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
17 18 2.358737 CGTGGACAAGGTCAGGCC 60.359 66.667 0.00 0.00 33.68 5.19
18 19 2.358737 GTGGACAAGGTCAGGCCG 60.359 66.667 0.00 0.00 43.70 6.13
19 20 3.636231 TGGACAAGGTCAGGCCGG 61.636 66.667 0.00 0.00 43.70 6.13
20 21 4.410400 GGACAAGGTCAGGCCGGG 62.410 72.222 2.18 0.00 43.70 5.73
62 63 7.946381 TGGCTAGGTCTAGACATGATTATAG 57.054 40.000 23.91 11.22 45.67 1.31
74 75 7.114754 AGACATGATTATAGCATGGGGTATTG 58.885 38.462 17.03 0.00 45.62 1.90
84 85 0.035820 TGGGGTATTGTCTTGCCGAC 60.036 55.000 0.00 0.00 43.14 4.79
106 107 6.036844 CGACAATATCTATCATTCATGGGCAG 59.963 42.308 0.00 0.00 0.00 4.85
109 110 3.581265 TCTATCATTCATGGGCAGCAA 57.419 42.857 0.00 0.00 0.00 3.91
139 140 7.867909 TGAATACCATCAGTAAGCTAGAAATCG 59.132 37.037 0.00 0.00 33.70 3.34
149 150 6.713450 AGTAAGCTAGAAATCGGGAAACAAAA 59.287 34.615 0.00 0.00 0.00 2.44
242 244 1.450211 CCGTTGTTGGAGGTCCTGT 59.550 57.895 0.00 0.00 36.82 4.00
243 245 0.884704 CCGTTGTTGGAGGTCCTGTG 60.885 60.000 0.00 0.00 36.82 3.66
373 386 4.394712 GTGCCACGCCTAGCAGGT 62.395 66.667 4.45 0.00 40.28 4.00
387 400 0.033228 GCAGGTCCCAGATGAGATCG 59.967 60.000 0.00 0.00 0.00 3.69
554 584 5.391312 AGTTCTGGACCATTTGTTATTGC 57.609 39.130 0.00 0.00 0.00 3.56
643 674 9.515020 AACATTATAGTTTTGATTTATGTGCCG 57.485 29.630 0.00 0.00 0.00 5.69
733 764 4.292186 ACAACATCAAGGCACATAGTCT 57.708 40.909 0.00 0.00 0.00 3.24
734 765 4.256920 ACAACATCAAGGCACATAGTCTC 58.743 43.478 0.00 0.00 0.00 3.36
735 766 3.170791 ACATCAAGGCACATAGTCTCG 57.829 47.619 0.00 0.00 0.00 4.04
736 767 1.863454 CATCAAGGCACATAGTCTCGC 59.137 52.381 0.00 0.00 0.00 5.03
737 768 1.186200 TCAAGGCACATAGTCTCGCT 58.814 50.000 0.00 0.00 0.00 4.93
738 769 2.375146 TCAAGGCACATAGTCTCGCTA 58.625 47.619 0.00 0.00 0.00 4.26
739 770 2.758423 TCAAGGCACATAGTCTCGCTAA 59.242 45.455 0.00 0.00 32.72 3.09
770 801 2.592308 GCTTCTTCAGCCCCCGAT 59.408 61.111 0.00 0.00 43.65 4.18
874 905 2.275466 AGGGAGCCTGTTTAGCCTTAA 58.725 47.619 0.00 0.00 29.57 1.85
877 908 4.023980 GGGAGCCTGTTTAGCCTTAAATT 58.976 43.478 0.00 0.00 31.81 1.82
878 909 4.466370 GGGAGCCTGTTTAGCCTTAAATTT 59.534 41.667 0.00 0.00 31.81 1.82
917 948 0.109723 AGCTTGGCTAAACCGAACCA 59.890 50.000 0.00 0.00 43.94 3.67
934 965 0.738412 CCATGTACCCACGAACCGAC 60.738 60.000 0.00 0.00 0.00 4.79
938 969 3.271706 TACCCACGAACCGACGCAG 62.272 63.158 0.00 0.00 36.70 5.18
1008 1041 1.288932 CATCCTTCCCCACCCAAATCT 59.711 52.381 0.00 0.00 0.00 2.40
1041 1074 1.234529 CCCCAACCTTCCCCAAACA 59.765 57.895 0.00 0.00 0.00 2.83
1051 1084 2.750350 CCCAAACACTCGCCTCCT 59.250 61.111 0.00 0.00 0.00 3.69
1054 1087 1.674057 CAAACACTCGCCTCCTCCT 59.326 57.895 0.00 0.00 0.00 3.69
1102 1136 2.340328 GCCCGCGGATGGTTTCTTT 61.340 57.895 30.73 0.00 0.00 2.52
1303 1337 4.801221 GCCGCAAGCTTCTTCGCG 62.801 66.667 18.85 18.85 46.96 5.87
1483 1701 3.124921 CGTCGCATTCCCACACCC 61.125 66.667 0.00 0.00 0.00 4.61
1687 1905 3.370840 TCCCATCCAAATGTCCTCAAG 57.629 47.619 0.00 0.00 0.00 3.02
1852 2070 0.888619 CAGCAGAAGACGGTGGACTA 59.111 55.000 0.00 0.00 0.00 2.59
1978 2196 2.182842 GCTGCTACTTGATGGGGCG 61.183 63.158 0.00 0.00 0.00 6.13
1994 2212 1.446099 GCGCTCTCCATCACGTCAA 60.446 57.895 0.00 0.00 0.00 3.18
1997 2215 1.634702 GCTCTCCATCACGTCAACTC 58.365 55.000 0.00 0.00 0.00 3.01
2074 2298 3.939592 GGCTTGGTACCTACAGAATTGAC 59.060 47.826 14.36 0.00 0.00 3.18
2110 2334 2.938956 CCAGGATTGTATCTGGTCCC 57.061 55.000 0.00 0.00 44.03 4.46
2116 2340 2.109181 GTATCTGGTCCCGGCAGC 59.891 66.667 0.00 0.00 0.00 5.25
2130 2354 0.600057 GGCAGCAAAGTCTTTCCCTG 59.400 55.000 14.18 14.18 0.00 4.45
2146 2370 4.199002 TCCCTGCCAGAGATCTTACATA 57.801 45.455 0.00 0.00 0.00 2.29
2186 2410 4.256110 TGATTCTTAGTCCATGCACACAG 58.744 43.478 0.00 0.00 0.00 3.66
2196 2420 1.608109 CATGCACACAGCCTTGTACAA 59.392 47.619 8.28 8.28 44.83 2.41
2236 2460 7.773489 TGTTGGTCCATATTTTCTTGATGAA 57.227 32.000 0.00 0.00 0.00 2.57
2294 2518 5.595257 ACTTAACAGTAGCTACTAAGGCC 57.405 43.478 27.09 0.00 34.13 5.19
2326 2550 5.431179 TCGATGATCCATCCATCATGAAT 57.569 39.130 0.00 0.00 42.52 2.57
2396 2620 5.751028 GGTCTTCGAGTAAGGAAATGATCAG 59.249 44.000 0.09 0.00 35.75 2.90
2409 2633 0.107993 TGATCAGCAGTAGCAGCCAC 60.108 55.000 0.00 0.00 45.49 5.01
2432 2656 0.804989 GACGCAAAATGAGTCCCCAG 59.195 55.000 3.24 0.00 40.58 4.45
2442 2666 2.680352 GTCCCCAGACTCAGCGGA 60.680 66.667 0.00 0.00 40.10 5.54
2443 2667 2.060980 GTCCCCAGACTCAGCGGAT 61.061 63.158 0.00 0.00 40.10 4.18
2444 2668 1.306141 TCCCCAGACTCAGCGGATT 60.306 57.895 0.00 0.00 0.00 3.01
2445 2669 0.032515 TCCCCAGACTCAGCGGATTA 60.033 55.000 0.00 0.00 0.00 1.75
2446 2670 0.830648 CCCCAGACTCAGCGGATTAA 59.169 55.000 0.00 0.00 0.00 1.40
2447 2671 1.202580 CCCCAGACTCAGCGGATTAAG 60.203 57.143 0.00 0.00 0.00 1.85
2448 2672 1.576356 CCAGACTCAGCGGATTAAGC 58.424 55.000 0.00 0.00 0.00 3.09
2449 2673 1.576356 CAGACTCAGCGGATTAAGCC 58.424 55.000 0.00 0.00 34.64 4.35
2450 2674 0.466124 AGACTCAGCGGATTAAGCCC 59.534 55.000 3.70 0.00 34.64 5.19
2452 2676 0.179000 ACTCAGCGGATTAAGCCCTG 59.821 55.000 17.31 17.31 34.64 4.45
2453 2677 1.153168 TCAGCGGATTAAGCCCTGC 60.153 57.895 18.16 11.27 34.64 4.85
2454 2678 1.451927 CAGCGGATTAAGCCCTGCA 60.452 57.895 13.11 0.00 34.64 4.41
2455 2679 0.820891 CAGCGGATTAAGCCCTGCAT 60.821 55.000 13.11 0.00 34.64 3.96
2456 2680 0.106519 AGCGGATTAAGCCCTGCATT 60.107 50.000 11.46 0.00 34.64 3.56
2457 2681 0.312102 GCGGATTAAGCCCTGCATTC 59.688 55.000 3.70 0.00 0.00 2.67
2458 2682 0.588252 CGGATTAAGCCCTGCATTCG 59.412 55.000 3.70 0.00 0.00 3.34
2459 2683 1.680338 GGATTAAGCCCTGCATTCGT 58.320 50.000 0.00 0.00 0.00 3.85
2461 2685 3.211045 GGATTAAGCCCTGCATTCGTAA 58.789 45.455 0.00 0.00 0.00 3.18
2462 2686 3.003378 GGATTAAGCCCTGCATTCGTAAC 59.997 47.826 0.00 0.00 0.00 2.50
2463 2687 2.772077 TAAGCCCTGCATTCGTAACA 57.228 45.000 0.00 0.00 0.00 2.41
2464 2688 2.128771 AAGCCCTGCATTCGTAACAT 57.871 45.000 0.00 0.00 0.00 2.71
2467 2691 2.170607 AGCCCTGCATTCGTAACATAGT 59.829 45.455 0.00 0.00 0.00 2.12
2468 2692 2.287915 GCCCTGCATTCGTAACATAGTG 59.712 50.000 0.00 0.00 0.00 2.74
2525 3796 5.777802 AGATGCTACGGAAACATCTATCTG 58.222 41.667 10.41 0.00 46.58 2.90
2593 4478 2.320745 ACGGAAGTTCGTTTGGTCTT 57.679 45.000 0.00 0.00 46.40 3.01
2601 4486 4.461198 AGTTCGTTTGGTCTTGATTTCCT 58.539 39.130 0.00 0.00 0.00 3.36
2618 4503 3.981516 TCCTCATCTCCAGATACCTGT 57.018 47.619 0.00 0.00 38.74 4.00
2619 4504 3.570540 TCCTCATCTCCAGATACCTGTG 58.429 50.000 0.00 0.00 38.74 3.66
2698 4583 7.065443 TCACAATTTTTGCATGATTCAAACACA 59.935 29.630 0.00 0.00 33.66 3.72
2699 4584 7.164498 CACAATTTTTGCATGATTCAAACACAC 59.836 33.333 0.00 0.00 33.66 3.82
2733 5014 5.787953 TCATGAAAACTGGATTGAAAGCA 57.212 34.783 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.358737 CGGCCTGACCTTGTCCAC 60.359 66.667 0.00 0.00 35.61 4.02
2 3 3.636231 CCGGCCTGACCTTGTCCA 61.636 66.667 0.00 0.00 35.61 4.02
3 4 4.410400 CCCGGCCTGACCTTGTCC 62.410 72.222 0.00 0.00 35.61 4.02
34 35 2.088104 TGTCTAGACCTAGCCATGGG 57.912 55.000 20.11 0.00 33.32 4.00
35 36 3.234353 TCATGTCTAGACCTAGCCATGG 58.766 50.000 20.96 7.63 44.86 3.66
36 37 5.480642 AATCATGTCTAGACCTAGCCATG 57.519 43.478 20.11 17.33 45.64 3.66
37 38 7.069331 GCTATAATCATGTCTAGACCTAGCCAT 59.931 40.741 20.11 9.30 32.61 4.40
38 39 6.378564 GCTATAATCATGTCTAGACCTAGCCA 59.621 42.308 20.11 0.42 33.32 4.75
39 40 6.378564 TGCTATAATCATGTCTAGACCTAGCC 59.621 42.308 20.11 0.00 33.32 3.93
40 41 7.397892 TGCTATAATCATGTCTAGACCTAGC 57.602 40.000 20.11 14.17 33.32 3.42
41 42 8.412456 CCATGCTATAATCATGTCTAGACCTAG 58.588 40.741 20.11 9.81 39.60 3.02
42 43 7.343057 CCCATGCTATAATCATGTCTAGACCTA 59.657 40.741 20.11 2.70 39.60 3.08
43 44 6.155910 CCCATGCTATAATCATGTCTAGACCT 59.844 42.308 20.11 7.68 39.60 3.85
44 45 6.344500 CCCATGCTATAATCATGTCTAGACC 58.656 44.000 20.11 3.06 39.60 3.85
45 46 6.070538 ACCCCATGCTATAATCATGTCTAGAC 60.071 42.308 16.32 16.32 39.60 2.59
46 47 6.025539 ACCCCATGCTATAATCATGTCTAGA 58.974 40.000 11.48 0.00 39.60 2.43
47 48 6.305272 ACCCCATGCTATAATCATGTCTAG 57.695 41.667 11.48 0.00 39.60 2.43
48 49 7.995052 ATACCCCATGCTATAATCATGTCTA 57.005 36.000 11.48 0.00 39.60 2.59
49 50 6.898171 ATACCCCATGCTATAATCATGTCT 57.102 37.500 11.48 0.00 39.60 3.41
62 63 0.746659 GGCAAGACAATACCCCATGC 59.253 55.000 0.00 0.00 0.00 4.06
84 85 5.650703 TGCTGCCCATGAATGATAGATATTG 59.349 40.000 0.00 0.00 0.00 1.90
85 86 5.823312 TGCTGCCCATGAATGATAGATATT 58.177 37.500 0.00 0.00 0.00 1.28
86 87 5.446260 TGCTGCCCATGAATGATAGATAT 57.554 39.130 0.00 0.00 0.00 1.63
95 96 2.181125 TCACAATTGCTGCCCATGAAT 58.819 42.857 5.05 0.00 0.00 2.57
106 107 5.973565 GCTTACTGATGGTATTCACAATTGC 59.026 40.000 5.05 0.00 0.00 3.56
109 110 8.023021 TCTAGCTTACTGATGGTATTCACAAT 57.977 34.615 0.00 0.00 0.00 2.71
166 167 1.996292 TCCTTTCGACATGCTTCTCG 58.004 50.000 0.00 0.00 0.00 4.04
167 168 5.755375 TCAATATCCTTTCGACATGCTTCTC 59.245 40.000 0.00 0.00 0.00 2.87
242 244 3.494398 GGATTTCTTATCCCAGTAGCGCA 60.494 47.826 11.47 0.00 32.09 6.09
243 245 3.067833 GGATTTCTTATCCCAGTAGCGC 58.932 50.000 0.00 0.00 32.09 5.92
359 371 4.162690 GGGACCTGCTAGGCGTGG 62.163 72.222 2.50 0.00 39.63 4.94
362 374 2.136878 ATCTGGGACCTGCTAGGCG 61.137 63.158 2.50 0.00 39.63 5.52
373 386 1.194218 TGCAACGATCTCATCTGGGA 58.806 50.000 0.00 0.00 0.00 4.37
387 400 4.997395 TCTGTAGGTCTCAAGAAATGCAAC 59.003 41.667 0.00 0.00 0.00 4.17
529 543 7.014711 TGCAATAACAAATGGTCCAGAACTAAA 59.985 33.333 0.00 0.00 0.00 1.85
532 547 4.832266 TGCAATAACAAATGGTCCAGAACT 59.168 37.500 0.00 0.00 0.00 3.01
588 618 5.168647 TCGTACAACACAATAATCCCCTT 57.831 39.130 0.00 0.00 0.00 3.95
643 674 5.451937 GCCTATTCCCCTAAAACTGATTTGC 60.452 44.000 0.00 0.00 32.27 3.68
715 746 2.739932 GCGAGACTATGTGCCTTGATGT 60.740 50.000 0.00 0.00 0.00 3.06
733 764 2.163412 GCCACAAATGACCATTTAGCGA 59.837 45.455 7.56 0.00 38.84 4.93
734 765 2.164219 AGCCACAAATGACCATTTAGCG 59.836 45.455 7.56 0.00 38.84 4.26
735 766 3.874392 AGCCACAAATGACCATTTAGC 57.126 42.857 7.56 10.51 38.84 3.09
736 767 5.649782 AGAAGCCACAAATGACCATTTAG 57.350 39.130 7.56 5.79 38.84 1.85
737 768 5.538053 TGAAGAAGCCACAAATGACCATTTA 59.462 36.000 7.56 0.00 38.84 1.40
738 769 4.344679 TGAAGAAGCCACAAATGACCATTT 59.655 37.500 2.38 2.38 41.33 2.32
739 770 3.896888 TGAAGAAGCCACAAATGACCATT 59.103 39.130 0.00 0.00 0.00 3.16
917 948 1.213537 CGTCGGTTCGTGGGTACAT 59.786 57.895 0.00 0.00 0.00 2.29
955 986 1.367840 GAATCGAGTGCGGCCCTAT 59.632 57.895 0.00 0.00 38.28 2.57
1269 1303 4.148825 CCTCTTGGACGAGCCCCG 62.149 72.222 0.00 0.00 45.44 5.73
1303 1337 1.202698 AGGGTTGGAAGCGCAGATATC 60.203 52.381 11.47 0.00 0.00 1.63
1390 1605 4.857588 CAGTACTGGTCGTATGAGTCAAAC 59.142 45.833 15.49 0.00 0.00 2.93
1483 1701 2.159476 CCAGAGCAAACGATTGTCCATG 60.159 50.000 7.29 2.05 38.85 3.66
1687 1905 6.713520 CGAGCCACGGATATAACTATACTAC 58.286 44.000 0.00 0.00 38.46 2.73
1852 2070 1.077501 CACCATGGTGGCGAATCCT 60.078 57.895 33.56 0.00 42.67 3.24
1978 2196 1.067565 TGAGTTGACGTGATGGAGAGC 60.068 52.381 0.00 0.00 0.00 4.09
1994 2212 4.473444 ACACCACAAATTCCATCTTGAGT 58.527 39.130 0.00 0.00 0.00 3.41
1997 2215 3.742369 GCAACACCACAAATTCCATCTTG 59.258 43.478 0.00 0.00 0.00 3.02
2074 2298 1.743252 GGCTCGCCTTGACTTGAGG 60.743 63.158 0.00 0.00 37.35 3.86
2110 2334 0.890996 AGGGAAAGACTTTGCTGCCG 60.891 55.000 17.61 0.00 0.00 5.69
2116 2340 2.157738 CTCTGGCAGGGAAAGACTTTG 58.842 52.381 9.31 0.00 0.00 2.77
2130 2354 3.643792 ACCTGGTATGTAAGATCTCTGGC 59.356 47.826 0.00 0.00 0.00 4.85
2172 2396 0.892358 CAAGGCTGTGTGCATGGACT 60.892 55.000 18.75 0.00 45.15 3.85
2186 2410 6.435430 TCATAACACATGATTGTACAAGGC 57.565 37.500 14.65 9.13 33.76 4.35
2196 2420 6.436847 TGGACCAACAAATCATAACACATGAT 59.563 34.615 0.00 0.00 40.20 2.45
2231 2455 7.062839 CAGGCTTAATCTTAGTAGCGATTCATC 59.937 40.741 0.00 0.00 34.50 2.92
2236 2460 4.833380 TCCAGGCTTAATCTTAGTAGCGAT 59.167 41.667 0.00 0.00 34.50 4.58
2251 2475 1.260544 GCATGTTTCCTTCCAGGCTT 58.739 50.000 0.00 0.00 35.63 4.35
2270 2494 5.811100 GGCCTTAGTAGCTACTGTTAAGTTG 59.189 44.000 32.21 17.56 37.88 3.16
2271 2495 5.393896 CGGCCTTAGTAGCTACTGTTAAGTT 60.394 44.000 32.21 9.66 37.88 2.66
2294 2518 0.668706 GGATCATCGATGGACAGCCG 60.669 60.000 24.61 0.00 36.79 5.52
2326 2550 2.290367 GCATGTGTACAACTTGACTGCA 59.710 45.455 0.00 0.00 36.30 4.41
2396 2620 2.437359 CTGGGTGGCTGCTACTGC 60.437 66.667 15.83 0.03 40.20 4.40
2409 2633 0.804989 GGACTCATTTTGCGTCTGGG 59.195 55.000 0.00 0.00 33.01 4.45
2432 2656 0.466124 AGGGCTTAATCCGCTGAGTC 59.534 55.000 0.00 0.00 0.00 3.36
2441 2665 3.625764 TGTTACGAATGCAGGGCTTAATC 59.374 43.478 0.00 0.00 0.00 1.75
2442 2666 3.616219 TGTTACGAATGCAGGGCTTAAT 58.384 40.909 0.00 0.00 0.00 1.40
2443 2667 3.060736 TGTTACGAATGCAGGGCTTAA 57.939 42.857 0.00 0.00 0.00 1.85
2444 2668 2.772077 TGTTACGAATGCAGGGCTTA 57.228 45.000 0.00 0.00 0.00 3.09
2445 2669 2.128771 ATGTTACGAATGCAGGGCTT 57.871 45.000 0.00 0.00 0.00 4.35
2446 2670 2.170607 ACTATGTTACGAATGCAGGGCT 59.829 45.455 0.00 0.00 0.00 5.19
2447 2671 2.287915 CACTATGTTACGAATGCAGGGC 59.712 50.000 0.00 0.00 0.00 5.19
2448 2672 3.309682 CACACTATGTTACGAATGCAGGG 59.690 47.826 0.00 0.00 0.00 4.45
2449 2673 3.932710 ACACACTATGTTACGAATGCAGG 59.067 43.478 0.00 0.00 38.98 4.85
2450 2674 4.625311 TCACACACTATGTTACGAATGCAG 59.375 41.667 0.00 0.00 40.64 4.41
2452 2676 5.290885 TCATCACACACTATGTTACGAATGC 59.709 40.000 0.00 0.00 40.64 3.56
2453 2677 6.751888 TCTCATCACACACTATGTTACGAATG 59.248 38.462 0.00 0.00 40.64 2.67
2454 2678 6.863275 TCTCATCACACACTATGTTACGAAT 58.137 36.000 0.00 0.00 40.64 3.34
2455 2679 6.262193 TCTCATCACACACTATGTTACGAA 57.738 37.500 0.00 0.00 40.64 3.85
2456 2680 5.890424 TCTCATCACACACTATGTTACGA 57.110 39.130 0.00 0.00 40.64 3.43
2457 2681 6.183360 GGTTTCTCATCACACACTATGTTACG 60.183 42.308 0.00 0.00 40.64 3.18
2458 2682 6.649141 TGGTTTCTCATCACACACTATGTTAC 59.351 38.462 0.00 0.00 40.64 2.50
2459 2683 6.764379 TGGTTTCTCATCACACACTATGTTA 58.236 36.000 0.00 0.00 40.64 2.41
2461 2685 5.227569 TGGTTTCTCATCACACACTATGT 57.772 39.130 0.00 0.00 44.81 2.29
2462 2686 5.106555 GGTTGGTTTCTCATCACACACTATG 60.107 44.000 0.00 0.00 0.00 2.23
2463 2687 5.003804 GGTTGGTTTCTCATCACACACTAT 58.996 41.667 0.00 0.00 0.00 2.12
2464 2688 4.141597 TGGTTGGTTTCTCATCACACACTA 60.142 41.667 0.00 0.00 0.00 2.74
2467 2691 2.948979 GTGGTTGGTTTCTCATCACACA 59.051 45.455 0.00 0.00 0.00 3.72
2468 2692 2.948979 TGTGGTTGGTTTCTCATCACAC 59.051 45.455 0.00 0.00 31.41 3.82
2573 4458 1.861971 AGACCAAACGAACTTCCGTC 58.138 50.000 0.00 0.00 42.54 4.79
2576 4461 4.830826 AATCAAGACCAAACGAACTTCC 57.169 40.909 0.00 0.00 0.00 3.46
2593 4478 5.306419 CAGGTATCTGGAGATGAGGAAATCA 59.694 44.000 0.00 0.00 38.66 2.57
2601 4486 3.688049 TCCACAGGTATCTGGAGATGA 57.312 47.619 8.13 0.00 44.99 2.92
2618 4503 2.064434 TGACAATGTTGGTTGCTCCA 57.936 45.000 0.00 0.00 45.60 3.86
2619 4504 2.557924 TGATGACAATGTTGGTTGCTCC 59.442 45.455 0.00 0.00 32.32 4.70
2698 4583 6.600822 CCAGTTTTCATGATGGTGAAGATAGT 59.399 38.462 0.00 0.00 39.13 2.12
2699 4584 6.825213 TCCAGTTTTCATGATGGTGAAGATAG 59.175 38.462 11.86 0.00 39.13 2.08


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

AutoCloner maintained by Alex Coulton.